Document:

exv10w9

 

Exhibit 10.9

COLLABORATIVE RESEARCH AND LICENSE AGREEMENT

between

ARCHEMIX CORP.

and

MERCK KGaA

June 6, 2007

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

TABLE OF CONTENTS

	 	 	 	 	 
	 	 	Page
	1. DEFINITIONS
	 	 	1	 
	 
	 	 	 	 
	2. ADMINISTRATION OF THE COLLABORATION
	 	 	27	 
	 
	 	 	 	 
	2.1 Joint Steering Committee
	 	 	27	 
	2.2 Joint Project Team
	 	 	31	 
	2.3 Joint Development Committee
	 	 	34	 
	2.4 Alliance Management
	 	 	36	 
	 
	 	 	 	 
	3. RESEARCH PROGRAM
	 	 	36	 
	 
	 	 	 	 
	3.1 Implementation of the Research Program
	 	 	36	 
	3.2 Technology Transfer Activities 
	 	 	36	 
	3.3 Research Projects 
	 	 	37	 
	3.4 Annual Research Plans 
	 	 	37	 
	3.5 Conduct of Research Program
	 	 	38	 
	3.6 Records
	 	 	38	 
	3.7 Designation of Program Targets
	 	 	39	 
	3.8 Replacement of Program Targets; Target Exclusivity List; ARCHEMIX
Retained Rights
	 	 	41	 
	3.9 ARCHEMIX Internal Program Targets
	 	 	42	 
	3.10 Identification of Lead Compounds and Optimized Lead Compounds
	 	 	46	 
	3.11 Development Candidates 
	 	 	47	 
	3.12 MERCK Decision Not to Go Forward 
	 	 	47	 
	3.13 Supply of Proprietary Materials 
	 	 	47	 
	3.14 Research Program Term 
	 	 	48	 
	3.15 Conduct of Target Validation Activities 
	 	 	48	 
	 
	 	 	 	 
	4. DEVELOPMENT PROGRAM; COMMERCIALIZATION OF PRODUCTS
	 	 	48	 
	 
	 	 	 	 
	4.1 Objectives of the Development Program 
	 	 	48	 
	4.2 Responsibility for Development of Development Candidates and
Commercialization of Products 
	 	 	48	 
	4.3 Annual Development Plans
	 	 	49	 
	4.4 Product Commercialization Plans 
	 	 	50	 
	4.5 Manufacture and Supply of Products for Development and Commercialization
	 	 	50	 
	4.6 Development and Commercialization Diligence
	 	 	51	 
	4.7 Compliance 
	 	 	51	 
	4.8 Cooperation 
	 	 	52	 
	4.9 Exchange of Reports; Information; Updates
	 	 	52	 
	4.10 Development and Commercialization Rights and Restrictions
	 	 	53	 
	 
	 	 	 	 
	5. EQUITY PURCHASE RIGHT
	 	 	60	 
	 
	 	 	 	 
	5.1 Purchase of Equity
	 	 	60	 
	5.2 Equity Purchase Right
	 	 	61	 
	 
	 	 	 	 
	6. PAYMENTS
	 	 	63	 
	 
	 	 	 	 
	6.1 SELEX License Maintenance Fee
	 	 	63	 
	6.2 Research License Maintenance Fee
	 	 	63	 
	6.3 Compound Option Exercise Fees
	 	 	63	 
	6.4 R&D Funding
	 	 	64	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

i

 

	 	 	 	 	 
	 	 	Page
	6.5 Milestone Payments
	 	 	65	 
	6.6 Payment of Royalties; Royalty Rates; Accounting and Records
	 	 	67	 
	6.7 Net Income Payments
	 	 	72	 
	6.8 Payments
	 	 	73	 
	6.9 Taxes
	 	 	73	 
	6.10 US Partnership
	 	 	73	 
	6.11 Foreign Currency Exchange
	 	 	74	 
	 
	 	 	 	 
	7. TREATMENT OF CONFIDENTIAL INFORMATION; PUBLICITY; NON-SOLICITATION
	 	 	75	 
	 
	 	 	 	 
	7.1 Confidentiality
	 	 	 75	 
	7.2 Publicity
	 	 	 76	 
	7.3 Publications and Presentations
	 	 	 77	 
	7.4 Prohibition on Solicitation
	 	 	 77	 
	 
	 	 	 	 
	8. LICENSE GRANTS; EXCLUSIVITY
	 	 	78	 
	 
	 	 	 	 
	8.1 SELEX License; Research and Development Licenses
	 	 	 78	 
	8.2 Commercialization License
	 	 	 83	 
	8.3 Limitation on License Grants
	 	 	 84	 
	8.4 Right to Sublicense
	 	 	 84	 
	8.5 Right to Subcontract
	 	 	 84	 
	8.6 No Other Rights
	 	 	 85	 
	8.7 Exclusivity
	 	 	 85	 
	 
	 	 	 	 
	9. INTELLECTUAL PROPERTY RIGHTS
	 	 	85	 
	 
	 	 	 	 
	9.1 ARCHEMIX Intellectual Property Rights
	 	 	 85	 
	9.2 MERCK Intellectual Property Rights
	 	 	 85	 
	9.3 Joint Technology and Joint Co-Developed Program Technology Rights
	 	 	 85	 
	9.4 Patent Coordinators
	 	 	 86	 
	9.5 Inventorship
	 	 	 86	 
	9.6 Cooperation
	 	 	 86	 
	 
	 	 	 	 
	10. FILING, PROSECUTION AND MAINTENANCE OF PATENT RIGHTS
	 	 	86	 
	 
	 	 	 	 
	10.1 Patent Filing, Prosecution and Maintenance
	 	 	 86	 
	10.2 Legal Actions
	 	 	89	 
	10.3 Trademark and Copyright Prosecution, Defense and Enforcement
	 	 	 93	 
	10.4 Effect of Challenge
	 	 	 93	 
	 
	 	 	 	 
	11. TERM AND TERMINATION
	 	 	94	 
	 
	 	 	 	 
	11.1 Term
	 	 	 94	 
	11.2 Termination
	 	 	 94	 
	11.3 Consequences of Termination of Agreement
	 	 	 95	 
	11.4 Surviving Provisions
	 	 	 98	 
	 
	 	 	 	 
	12. REPRESENTATIONS AND WARRANTIES AND COVENANTS
	 	 	99	 
	 
	 	 	 	 
	12.1 Mutual Representations and Warranties
	 	 	 99	 
	12.2 ARCHEMIX’ Representations and Warranties
	 	 	 99	 
	12.3 Acknowledgment and Covenant of MERCK
	 	 	 100	 
	 
	 	 	 	 
	13. INDEMNIFICATION
	 	 	101	 
	 
	 	 	 	 
	13.1 Indemnification of MERCK by ARCHEMIX
	 	 	 101	 
	13.2 Indemnification of ARCHEMIX by MERCK
	 	 	 101	 
	13.3 Indemnification of Gilead and UTC by MERCK
	 	 	 101	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

ii

 

	 	 	 	 	 
	 	 	Page
	13.4 Conditions to Indemnification
	 	 	 102	 
	13.5 Warranty Disclaimer
	 	 	102	 
	13.6 No Warranty of Success
	 	 	102	 
	13.7 Limited Liability
	 	 	102	 
	 
	 	 	 	 
	14. MISCELLANEOUS
	 	 	103	 
	 
	 	 	 	 
	14.1 Arbitration
	 	 	103	 
	14.2 Change of Control
	 	 	104	 
	14.3 Notices
	 	 	106	 
	14.4 Governing Law
	 	 	107	 
	14.5 Binding Effect
	 	 	107	 
	14.6 Headings
	 	 	107	 
	14.7 Counterparts
	 	 	107	 
	14.8 Amendment; Waiver
	 	 	108	 
	14.9 No Third Party Beneficiaries
	 	 	108	 
	14.10 Purposes and Scope
	 	 	108	 
	14.11 Assignment and Successors
	 	 	108	 
	14.12 Force Majeure
	 	 	108	 
	14.13 Interpretation
	 	 	108	 
	14.14 Integration; Severability
	 	 	109	 
	14.15 Further Assurances
	 	 	109	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

iii

 

List of Exhibits

	 	 	 
	Exhibit A

	 	SELEX Technology Transfer Plan
	Exhibit B

	 	Form of Common Stock Purchase Agreement
	 
	 	 
	List of Schedules
	 
	 	 
	Schedule 1A

	 	Optimized Lead Compound Selection Criteria- MERCK Funded
Research Projects; MERCK Internal Research Projects
	 
	 	 
	Schedule 1B

	 	Optimized Lead Compound Selection Criteria — ARCHEMIX Internal
Research Projects
	 
	 	 
	Schedule 2A

	 	Target Exclusivity List
	 
	 	 
	Schedule 2B

	 	ARCHEMIX Internal Program Targets
	 
	 	 
	Schedule 3

	 	Licensed Patent Rights
	 
	 	 
	Schedule 4

	 	Excluded Aptamers
	 
	 	 
	Schedule 5A

	 	Development Candidate Selection Criteria — MERCK Funded
Research Projects; MERCK Internal Research Projects
	 
	 	 
	Schedule 5B

	 	Development Candidate Selection Criteria — ARCHEMIX Internal
Research Projects
	 
	 	 
	Schedule 6

	 	Form of Press Release
	 
	 	 
	Schedule 7

	 	Regional Offices or Countries in which Patent Applications are to be Nationalized or
Otherwise Prosecuted, Filed and Maintained
	 
	 	 
	Schedule 8

	 	Material Terms to be Included in Form of Co-Promotion Agreement
	 
	 	 
	Schedule 9

	 	MERCK’s Standard Exchange Rate Methodology Applied in Its External Reporting
	 
	 	 
	Schedule 10

	 	Program Chemistries
	 
	 	 
	Schedule 11

	 	Calculation of Net Income
	 
	 	 
	Schedule 12

	 	Form of Materials Transfer Agreement
	 
	 	 
	Schedule 13

	 	Co-Development Costs and Guidelines for their Allocation and Co-Development Regulatory Costs

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

iv

 

COLLABORATIVE RESEARCH AND LICENSE AGREEMENT

     This COLLABORATIVE RESEARCH AND LICENSE AGREEMENT (this “Agreement”) is entered into as of
June 6, 2007, by and between Archemix Corp., a Delaware corporation with offices at 300 Third
Street, Cambridge, MA 02142 (“ARCHEMIX”), and Merck KGaA, a company organized under the laws of
Germany with offices at Frankfurter Str. 250, 64293 Darmstadt, Germany (“MERCK”). Each of MERCK
and ARCHEMIX is sometimes referred to individually herein as a “Party” and collectively as the
“Parties.”

     WHEREAS, ARCHEMIX has developed and controls certain technology, patent rights and proprietary
materials related to (a) the identification and optimization of aptamers using its proprietary
SELEX process and SELEX technology, and (b) the use of such aptamers for treating, preventing or
delaying onset or progression of human diseases or conditions; and

     WHEREAS, MERCK is engaged in the research, development and commercialization of human
therapeutics; and

     WHEREAS, the Parties entered into the Collaborative Research and License Agreement dated as of
January 17, 2007 (the “Initial Collaboration Agreement”), pursuant to which the Parties agreed to
collaborate for the purposes of identifying aptamers against two identified targets (the “Initial
Targets”) and developing and commercializing products derived from such aptamers for the
prevention, treatment and delay of onset or progression of cancer; and

     WHEREAS, the Parties desire to enter into an additional agreement for the purpose of expanding
the scope of the collaboration by identifying additional targets for use in identifying aptamers,
and developing and commercializing products derived from such aptamers primarily for the
prevention, treatment, cure and delay of onset or progression of cancer, inflammatory and/or
autoimmune indications; and

     WHEREAS, the Parties agree that all Program Aptamer-Specific Technology (as hereinafter
defined) resulting from the collaboration under the terms of this Agreement shall become the sole
and exclusive property of MERCK; and

     WHEREAS, the Parties agree that all Technology (as hereinafter defined) relating to the SELEX
Technology (as hereinafter defined) or SELEX Process (as hereinafter defined) resulting from the
collaboration under the terms of this Agreement shall become the sole and exclusive property of
ARCHEMIX.

     NOW, THEREFORE, in consideration of the mutual covenants contained herein, and for other good
and valuable consideration, the Parties hereto, intending to be legally bound, hereby agree as
follows:

1. DEFINITIONS

     Whenever used in this Agreement with an initial capital letter, the terms defined in this
Section 1 and in Schedule 8, Schedule 11 and Schedule 13 attached hereto
shall have the meanings specified.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

     1.1 “Adverse Event” means any untoward, undesired or unplanned medical occurrence in a
human clinical trial subject or a patient, which occurrence has a temporal relationship to
administration of a Development Candidate or Product, whether or not considered related to the
Development Candidate or Product, including, without limitation, any undesirable sign (including
abnormal laboratory findings of clinical concern), symptom or disease associated with the use of
such Development Candidate or Product.

     1.2 “Affiliate” means, with respect to any Person, any other Person that, directly or
indirectly, through one or more affiliates, controls, or is controlled by, or is under common
control with, such Person. For purposes of this definition, “control” means (a) ownership of fifty
percent (50%) or more of the shares of stock entitled to vote for the election of directors in the
case of a corporation, or fifty percent (50%) or more of the equity interests in the case of any
other type of legal entity, (b) status as a general partner in any partnership, or (c) any other
arrangement whereby a Person controls or has the right to control the board of directors of a
corporation or equivalent governing body of an entity other than a corporation.

     1.3 “Annual Development Plan” means, with respect to each Optimized Lead Compound and
Development Candidate (including without limitation any Co-Developed Development Candidate) and
Contract Year, the written plan for the Development Program for such Optimized Lead Compound and
Development Candidate for such Contract Year (including a budget related thereto), as such written
plan may be amended, modified or updated, as further described in Section 4.3.

     1.4 “Annual Net Sales” means, with respect to any Calendar Year, the aggregate amount
of the Net Sales for such Calendar Year.

     1.5 “Annual Research Plan” means the written plan describing the research activities
to be carried out by each Party during each Contract Year of the Research Program Term in
conducting the Research Program pursuant to this Agreement as well as a budget therefore, as such
written plan may be amended, modified or updated, as further described in Section 3.4.

     1.6 “Applicable Laws” means Federal, state, local, national and supra-national laws,
statutes, rules and regulations, including any rules, regulations, guidance, guidelines or
requirements of Regulatory Authorities, national securities exchanges or securities listing
organizations, that are in effect from time to time during the Term and apply to a particular
activity hereunder.

     1.7 “Aptamer” means (a) any naturally or non-naturally occurring oligonucleotide
identified by ARCHEMIX through the SELEX Process or by MERCK through the SELEX Process in the
practice of the SELEX License, that binds with high specificity and affinity to a Target; and (b)
any oligonucleotide Derived from the oligonucleotide of (a) that has such high specifity and
affinity.

     1.8 “ARCHEMIX Background Technology” means any Technology that is used by ARCHEMIX, or
provided by ARCHEMIX for use, in the Research Program and/or the

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

2

 

Development Program that is (a) Controlled by ARCHEMIX as of the Effective Date or (b)
conceived or first reduced to practice by employees of, or consultants to, ARCHEMIX after the
Effective Date other than in the conduct of ARCHEMIX Research Activities or ARCHEMIX Development
Activities and without the use in any material respect of any MERCK Technology (other than
Collaboration Aptamers), MERCK Patent Rights or MERCK Materials. For purposes of clarity, ARCHEMIX
Background Technology (a) shall include the SELEX Process and SELEX Technology, other than MERCK
SELEX Improvements, and (b) shall not include Collaboration Aptamers, ARCHEMIX Program Technology
or ARCHEMIX’s interest in Joint Technology.

     1.9 “ARCHEMIX Co-Developed Program Patent Rights” means any Patent Rights Controlled
by ARCHEMIX that contain one or more claims that cover ARCHEMIX Co-Developed Program Technology.

     1.10 “ARCHEMIX Co-Developed Program Technology” means any Co-Developed Program
Technology that is conceived or first reduced to practice by employees of, or consultants to,
ARCHEMIX, alone or jointly with any Third Party, without the use in any material respect of any
MERCK Technology (other than Collaboration Aptamers), MERCK Patent Rights, MERCK Materials or Joint
Technology. For purposes of clarity, ARCHEMIX Co-Developed Program Technology does not include
ARCHEMIX Program Technology or Program Aptamer-Specific Technology.

     1.11 “ARCHEMIX Co-Development Participation Capacity” means, with respect to each
Co-Developed Development Candidate, the number of FTEs that ARCHEMIX reasonably determines in good
faith it has the capacity and capability to provide towards the Development of such Co-Developed
Development Candidate in each Calendar Year.

     1.12 “ARCHEMIX Co-Development Sharing Percentage” means, with respect to each
Co-Developed Product, a percentage equal to either [***] percent ([***]%) (the “ARCHEMIX [***]%
Co-Development Sharing Percentage”) or [***] percent ([***]%) (the “ARCHEMIX [***]% Co-Development
Sharing Percentage”), as designated by ARCHEMIX pursuant to Section 4.10.2(a).

     1.13 “ARCHEMIX Decision” means a decision with respect to the following issues: (a)
the conduct by ARCHEMIX of the [***] against [***]; (b) whether ARCHEMIX is to incur any [***]; (c)
whether ARCHEMIX is to be obligated to perform any [***] with respect to any [***] that is not a
[***]; (d) whether ARCHEMIX is to incur any [***] in the performance of [***] or [***]; (e) the
inclusion of any [***] MERCK on the [***]; (f) an increase in the number of FTEs used in any
Research Project above [***] FTEs per [***]; (g) the conduct of all research and development
activities with respect to an [***] prior to the receipt by ARCHEMIX of the applicable [***]; and
(h) the [***] applicable to any ARCHEMIX [***].

     1.14 “ARCHEMIX De Novo Research Activities” means, with respect to any ARCHEMIX
Internal Research Project and/or ARCHEMIX Internal Program Target, any research activities that (a)
are not ARCHEMIX Research Activities and (b) involve the use by

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

3

 

ARCHEMIX of the SELEX Process to identify Aptamers against ARCHEMIX Internal Program Targets.

     1.15 “ARCHEMIX Development Activities” means all Development activities (including
without limitation any Development activities with respect to Co-Developed Collaboration Aptamers)
specified to be conducted by ARCHEMIX in any Annual Development Plan (or amendment thereto) and
approved by ARCHEMIX’s representatives on the JPT, the JDC and the JSC (without resort to the
dispute resolution procedures set forth in Section 2.1.6).

     1.16 “ARCHEMIX Facility” means the facility of ARCHEMIX currently located at 300 Third
Street, Cambridge, MA 02142.

     1.17 “ARCHEMIX-Gilead License Agreement” means the License Agreement between Gilead
Sciences, Inc. and ARCHEMIX dated October 21, 2001, as amended.

     1.18 “ARCHEMIX Internal Program Targets” means the Program Targets identified on
Schedule 2B attached hereto.

     1.19 “ARCHEMIX Internal Research Projects” means the research projects being conducted
by ARCHEMIX for the ARCHEMIX Internal Program Targets.

     1.20 “ARCHEMIX Materials” means any Proprietary Materials that are Controlled by
ARCHEMIX and used by ARCHEMIX, or provided by ARCHEMIX for use, in the Research Program and/or the
Development Program. For purposes of clarity, ARCHEMIX Materials shall include all Aptamers
provided by ARCHEMIX for use in the Research Program.

     1.21 “ARCHEMIX Minimum Co-Development Participation Level” means with respect to each
Co-Developed Development Candidate, the lesser of (a) the ARCHEMIX Co-Development Participation
Capacity with respect to such Co-Developed Development Candidate and ; (b) with respect to the
ARCHEMIX [***]% Co-Development Sharing Percentage (i) for any Development activities conducted with
respect to a Co-Developed Development Candidate at any time during the period commencing on the
date of exercise by ARCHEMIX of the Co-Development and Co-Promotion Option with respect to such
Co-Developed Development Candidate and continuing until the Initiation of Phase I Clinical Trials
with respect to such Co-Developed Development Candidate, a number of ARCHEMIX FTEs equal to [***]
percent ([***]%) of the Estimated Aggregate FTEs; (ii) for any Development activities conducted
with respect to a Co-Developed Development Candidate at any time during the period commencing on
the Initiation of Phase I Clinical Trials with respect to such Co-Developed Development Candidate
and continuing until the Initiation of Phase II Clinical Trials with respect to such Co-Developed
Development Candidate, a number of ARCHEMIX FTEs equal to [***] percent ([***]%) of the Estimated
Aggregate FTEs; and (iii) for any Development activities conducted with respect to a Co-Developed
Development Candidate during the period commencing on the Initiation of Phase II Clinical Trials
with respect to such Co-Developed Development Candidate and continuing until the completion of
Phase III Clinical Trials with respect to such Co-Developed Development Candidate (the “Late Stage
Co-Development Activities”), a number of ARCHEMIX FTEs equal to [***] percent ([***]%) of the
Estimated Aggregate FTEs, or (c)

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

4

 

with respect to the ARCHEMIX [***]% Co-Development Percentage (i) for any Development
activities conducted with respect to a Co-Developed Development Candidate at any time during the
period commencing on the date of exercise by ARCHEMIX of the Co-Development and Co-Promotion Option
with respect to such Co-Developed Development Candidate and continuing until the Initiation of
Phase I Clinical Trials with respect to such Co-Developed Development Candidate, a number of
ARCHEMIX FTEs equal to [***] percent ([***]%) of the Estimated Aggregate FTEs; (ii) for any
Development activities conducted with respect to a Co-Developed Development Candidate at any time
during the period commencing on the Initiation of Phase I Clinical Trials with respect to such
Co-Developed Development Candidate and continuing until the Initiation of Phase II Clinical Trials
with respect to such Co-Developed Development Candidate, a number of ARCHEMIX FTEs equal to [***]
percent ([***]%) of the Estimated Aggregate FTEs; and (iii) for any Late Stage Co-Development
Activities, a number of ARCHEMIX FTEs equal to [***] percent ([***]%) of the Estimated Aggregate
FTEs. For purposes of clarity, the determination and application of the ARCHEMIX Minimum
Co-Development Participation Percentage shall not affect the determination or the application of
the ARCHEMIX Co-Development Sharing Percentage.

     1.22 “ARCHEMIX Patent Rights” means any Patent Rights Controlled by ARCHEMIX that
contain one or more claims that cover ARCHEMIX Technology.

     1.23 “ARCHEMIX Program Technology” means (a) any oligonucleotide of an Enriched Pool
that is not a Program Oligonucleotide; (b) any Program Technology that is conceived or first
reduced to practice by employees of, or consultants to, ARCHEMIX, alone or jointly with any Third
Party, without the use in any material respect of any MERCK Technology (other than Collaboration
Aptamers), MERCK Patent Rights, MERCK Materials or Joint Technology; and (c) any Program
Technology, regardless of whether conceived or first reduced to practice by employees of, or
consultants to, ARCHEMIX, MERCK, or both Parties, alone or jointly with any Third Party, that
relates to, or constitutes, the SELEX Process or SELEX Technology. For purposes of clarity,
ARCHEMIX Program Technology does not include Program Generic Technology, Program Aptamer-Specific
Technology and/or Development Program Technology.

     1.24 “ARCHEMIX Research Activities” means all activities specified to be conducted by
ARCHEMIX in any Annual Research Plan (or amendment thereto) that are (a) approved by the JPT and
the JSC and (b) to the extent involving matters that are ARCHEMIX Decisions, approved by ARCHEMIX
in accordance with Section 2.1.6.

     1.25 “ARCHEMIX Technology” means, collectively, ARCHEMIX Background Technology and
ARCHEMIX Program Technology.

     1.26 “Calendar Quarter” means each successive period of three (3) consecutive calendar
months commencing on January 1, April 1, July 1 or October 1, as the case may be, and ending on
March 31, June 30, September 30 or December 31, respectively; provided, that, the initial Calendar
Quarter shall commence on the Effective Date.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

5

 

     1.27 “Calendar Year” means each successive period of twelve (12) months commencing on
January 1 and ending on December 31.

     1.28 “Challenge” means any challenge to the validity or enforceability of any of the
Licensed Patent Rights in the absence of a material breach of this Agreement, including without
limitation by (a) filing a declaratory judgment action in which any of the Licensed Patent Rights
is alleged to be invalid or unenforceable; (b) citing prior art pursuant to 35 U.S.C. §301, filing
a request for re-examination of any of the Licensed Patent Rights pursuant to 35 U.S.C. §302 and/or
§311, or provoking or becoming party to an interference with an application for any of the Licensed
Patent Rights pursuant to 35 U.S.C. §135; or (c) filing or commencing any re-examination,
opposition, cancellation, nullity or similar proceedings against any of the Licensed Patent Rights
in any country.

     1.29 “Change of Control” means, with respect to a Party, (a) a merger, consolidation,
share exchange or other similar transaction involving such Party and any Third Party which results
in the holders of the outstanding voting securities of such Party immediately prior to such merger,
consolidation, share exchange or other similar transaction ceasing to hold more than fifty percent
(50%) of the combined voting power of the surviving, purchasing or continuing entity immediately
after such merger, consolidation, share exchange or other similar transaction, (b) any transaction
or series of related transactions (other than an investment transaction by an entity not engaged in
the pharmaceutical or biotechnology business, the purpose of which is to raise capital for a Party)
in which a Third Party, together with its Affiliates, becomes the beneficial owner of fifty percent
(50%) or more of the combined voting power of the outstanding securities of such Party, or (c) the
sale or other transfer to a Third Party of all or substantially all of such Party’s assets which
relate to this Agreement.

     1.30 “Clinical Trial” means, collectively, a Phase I Clinical Trial, Phase II Clinical
Trial, Phase III Clinical Trial, Phase IV Clinical Trial, or Marketing Support Clinical Trial, as
applicable.

     1.31 “Co-Developed Collaboration Aptamer” means, collectively, Co-Developed
Development Candidates and Co-Developed Products.

     1.32 “Co-Developed Development Candidate” means any Development Candidate as to which
ARCHEMIX has exercised a Co-Development and Co-Promotion Option as described in Section 4.10.2(a)
and has not exercised an Opt-Out Right with respect thereto.

     1.33 “Co-Developed Product” means any Product with respect to which ARCHEMIX has
exercised a Co-Development and Co-Promotion Option as described in Section 4.10.2(a) and has not
exercised an Opt-Out Right with respect thereto. For purposes of clarity, a Co-Promoted Product is
a Co-Developed Product.

     1.34 “Co-Developed Program Patent Rights” means, collectively, ARCHEMIX Co-Developed
Program Patent Rights, MERCK Co-Developed Program Patent Rights, and Joint Co-Developed Program
Patent Rights.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

6

 

     1.35 “Co-Developed Program Technology” means any Technology (including, without
limitation, any new and useful process, method of manufacture or composition of matter) or
Proprietary Materials that are conceived or first reduced to practice (actively or constructively)
in the conduct of the Development Program by employees of, or consultants to, MERCK and/or
employees of, or consultants to, ARCHEMIX in connection with the Development and/or
Commercialization of a Co-Developed Collaboration Aptamer. For purposes of clarity, any
Co-Developed Program Technology that relates to the SELEX Process or to the SELEX Technology shall
be considered ARCHEMIX Co-Developed Program Technology irrespective of which Party conceived or
reduced to practice such Technology.

     1.36 “Co-Development Costs” means the costs set forth in Schedule 13 hereto.

     1.37 “Co-Development and Co-Promotion Option Exercise Period” means, with respect to
each Development Candidate, the later of (a) [***] days after the acceptance by the JSC of such
Development Candidate in accordance with Section 3.11 and (b) [***] days after the submission by
MERCK to ARCHEMIX of an initial outline of the Development activities contemplated by MERCK for
such Development Candidate affecting the Co-Development Territory over a [***] year period
(including an estimated budget and the Estimated Aggregate FTEs for such activities).

     1.38 “Co-Development Regulatory Costs” means the cost components set forth in
Schedule 13 hereto.

     1.39 “Co-Development Territory” means the United States of America and its territories
and possessions.

     1.40 “Co-Promoted Product” means a Co-Developed Product with respect to which ARCHEMIX
has not exercised, and has no longer the right to exercise, an Opt-Out Right.

     1.41 “Collaboration” means the alliance of ARCHEMIX and MERCK established pursuant to
this Agreement for the purposes of identifying, researching and Developing Development Candidates
and Commercializing Products in the Field in the Territory.

     1.42 “Collaboration Aptamer” means, collectively, Program Oligonucleotides, Program
Aptamers, Lead Compounds, Optimized Lead Compounds, Development Candidates (including without
limitation Co-Developed Development Candidates) and/or Products (including without limitation
Co-Developed Products).

     1.43 “Combination Product” means a combination or bundled product that is sold
together in a single package or as a unit at a single price by a Party, its Affiliates or
sublicensees (or Sublicensees, as the case may be) and that includes: (a) a Royalty-Bearing
Product; and (b) a Supplemental Product that is not within the Licensed Patent Rights, where both
the Royalty-Bearing Product and the Supplemental Product are required to treat the intended
Indication and/or to achieve the intended use or effect.

     1.44 “Commercialization” or “Commercialize” means any and all activities
directed to the commercialization of a Product after Commercialization Regulatory Approval has been

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

7

 

obtained, including marketing, manufacturing for commercial sale, promoting, detailing,
distributing, offering to sell and selling a Product, importing a Product for sale, conducting
post-marketing human clinical studies and interacting with Regulatory Authorities regarding the
foregoing. When used as a verb, “to Commercialize” and “Commercializing” means to engage in
Commercialization and “Commercialized” has a corresponding meaning.

     1.45 “Commercially Reasonable Efforts” means (a) with respect to activities of
ARCHEMIX in the Research Program, or, with respect to the conduct of ARCHEMIX Development
Activities, if any, with respect to Co-Developed Collaboration Aptamers, or, with respect to
activities of ARCHEMIX in the Commercialization of any Co-Developed Collaboration Aptamers and/or
any Waived Compound which is the subject of a transition plan pursuant to Section 8.1.2(c), the
efforts and resources comparable to those undertaken by ARCHEMIX in pursuing the research,
discovery, development, commercialization and intellectual property protection of proprietary
materials and the development of product candidates, as applicable, that are not subject to the
Collaboration and that are at an equivalent stage of development or commercialization and have
similar market potential and are at a similar stage in their lifecycle; and (b) with respect to
activities of MERCK in the Research Program, the Development of a particular Development Candidate
or the Commercialization of a particular Product (including any Co-Developed Collaboration
Aptamer), the efforts and resources comparable to those undertaken by MERCK in pursuing
intellectual property protection and development of product candidates and commercialization of
products, as applicable, that are not subject to the Collaboration and that are at an equivalent
stage of development or commercialization and have similar market potential and are at a similar
stage in their lifecycle. For purposes of both (a) and (b) above, all relevant factors as measured
by the facts and circumstances at the time such efforts are due shall be taken into account,
including, as applicable and without limitation, mechanism of action; efficacy and safety; product
profile; actual or anticipated Regulatory Authority approved labeling; and the nature and extent of
market exclusivity (including patent coverage, proprietary position and regulatory exclusivity;
cost, time required for and likelihood of obtaining Commercialization Regulatory Approval;
competitiveness of alternative products and market conditions; actual or projected profitability
and availability of capacity to manufacture and supply for commercial sale).

     1.46 “Commercialization Regulatory Approval” means, with respect to any Product, the
Regulatory Approval required by Applicable Laws to sell such Product for use in the Field in a
country or region in the Territory. “Commercialization Regulatory Approval” shall include, without
limitation, the approval of any Drug Approval Application. For purposes of clarity,
“Commercialization Regulatory Approval” in the United States shall mean final approval of an NDA
for the first Indication or sNDA for an additional Indication permitting marketing of the
applicable Product in interstate commerce in the United States, “Commercialization Regulatory
Approval” in the European Union shall mean marketing authorization for the applicable Product
pursuant to Council Directive 2001/83/EC, as amended, or Council Regulation 2309/93/EEC, as amended
and “Commercialization Regulatory Approval” in Japan shall mean final approval of an application
submitted to the Ministry of Health, Labor and Welfare and the publication of a New Drug Approval
Information Package permitting marketing of the applicable Product in Japan, as any of the
foregoing may be supplemented or amended from time to time.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

8

 

     1.47 “Competitive Entity” means any Third Party (a) with worldwide annual sales of
pharmaceutical products in the most recently completed Calendar Year greater than USD [***] (US$
[***]), and (b) that is actively developing or commercializing pharmaceutical products in the
[***].

     1.48 “Competitive Program” means any research, development or commercialization
activity that involves an aptamer that targets a Program Target for use in the Field.

     1.49 “Compound Candidate” means, collectively, any Primary Compound Candidate and any
Backup Compound Candidate.

     1.50 “Compound Candidate Option” means, collectively, any Primary Compound Candidate
Option and any Backup Compound Candidate Option.

     1.51 “Confidential Information” means (a) with respect to ARCHEMIX, all tangible
embodiments of ARCHEMIX Technology, (b) with respect to MERCK, all tangible embodiments of MERCK
Technology and (c) with respect to each Party, (i) all tangible embodiments of Joint Technology and
(ii) all information, Technology and Proprietary Materials disclosed or provided by or on behalf of
such Party (the “disclosing Party”) to the other Party (the “receiving Party”) or to any of the
receiving Party’s employees, consultants, Affiliates or sublicensees (or Sublicensees, as the case
may be); provided, that, none of the foregoing shall be Confidential Information if: (A) as of the
date of disclosure, it is known to the receiving Party or its Affiliates as demonstrated by
contemporaneous credible written documentation, other than by virtue of a prior confidential
disclosure to such receiving Party; (B) as of the date of disclosure it is in the public domain, or
it subsequently enters the public domain through no fault of the receiving Party; (C) it is
obtained by the receiving Party from a Third Party having a lawful right to make such disclosure
free from any obligation of confidentiality to the disclosing Party; or (D) it is independently
developed by or for the receiving Party without reference to or use of any Confidential Information
of the disclosing Party as demonstrated by contemporaneous credible written documentation. For
purposes of clarity, unless excluded from Confidential Information pursuant to the proviso at the
end of the preceding sentence, any scientific, technical or financial information of a Party that
is disclosed at any meeting of the JSC, JPT, JDC or JCC or disclosed through an audit report shall
constitute Confidential Information of the disclosing Party. Notwithstanding anything herein to
the contrary, the terms of this Agreement shall constitute Confidential Information of each Party.

     1.52 “Contract Year” means (a) the period beginning on the Effective Date and ending
on the first anniversary of the Effective Date and (b) each succeeding twelve (12) month period
thereafter.

     1.53 “Control” or “Controlled” means (a) with respect to Technology or Patent
Rights, the possession by a Party of the right to grant a license or sublicense to such Technology
or Patent Rights as provided herein without the payment of additional consideration to, and without
violating the terms of any agreement or arrangement with, any Third Party and without violating any
Applicable Laws and (b) with respect to Proprietary Materials, the possession by a Party of the
right to supply such Proprietary Materials to the other Party as provided herein

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

9

 

without the payment of additional consideration to, and without violating the terms of, any
agreement or arrangement with any Third Party, and without violating any Applicable Laws.

     1.54 “Derived” means identified, obtained, developed, created, synthesized, generated,
designed or resulting from, based upon, containing or incorporating; conjugated to or complexed
with (whether directly or indirectly, or in whole or in part).

     1.55 “Detail” means, with respect to a Co-Promoted Product, an interactive, live,
face-to-face contact of a representative within the Co-Development Territory with a medical
professional with prescribing authority or other individuals or entities that have a significant
impact or influence on prescribing decisions, in an effort to increase physician prescribing
preferences of such Co-Promoted Product for its approved uses within the Co-Development Territory.
When used as a verb, “Detailing” means performing Details. When used as an adjective, “Detailing”
means of or related to performing Details.

     1.56 “Development” or “Develop” means, with respect to each Optimized Lead
Compound and Development Candidate (including without limitation any Co-Developed Development
Candidate), all non-clinical and clinical activities performed in order to obtain Regulatory
Approval of a Product (including without limitation any Co-Developed Product) Derived from such
Optimized Lead Compound or Development Candidate in accordance with this Agreement up to and
including the obtaining of Commercialization Regulatory Approval of such Product. For purposes of
clarity, these activities include, without limitation, in vivo animal efficacy testing, preclinical
safety testing, test method development and stability testing, regulatory toxicology studies,
formulation, process development, manufacturing, manufacturing scale-up, development-stage
manufacturing, quality assurance/quality control development, statistical analysis and report
writing, clinical trial design and operations, preparing and filing Drug Approval Applications, and
all regulatory affairs related to the foregoing. When used as a verb, “Developing” means to engage
in Development and “Developed” has a corresponding meaning.

     1.57 “Development Candidate” means (i) with respect to the MERCK Funded Research
Projects or MERCK Internal Research Projects, any Optimized Lead Compound that the JPT nominates
and the JSC accepts as a Development Candidate as set forth in Section 3.11 and for which MERCK has
paid the Development Candidate Milestone Payment in the time allotted for such payment in Section
6.5.1, provided, that, no Collaboration Aptamer shall, after [***], be nominated or accepted as a
Development Candidate, and (ii) with respect to the ARCHEMIX Internal Research Projects, any
Compound Candidate that MERCK designates as a Development Candidate in accordance with Section
3.9.1 or Section 3.9.2.

     1.58 “Development Candidate Milestone Payment” means the payment to be made to
ARCHEMIX upon occurrence of Milestone Event 2 pursuant to Section 6.5.1.

     1.59 “Development Candidate Selection Criteria” or “DCSC” means (i) with
respect to the DCSC for Development Candidates that arise from the MERCK Funded Research Projects
or MERCK Internal Research Projects, the guideline criteria for selecting Optimized Lead Compounds
that are sufficiently promising to warrant further Development as

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

10

 

Development Candidates as set forth in Schedule 5A attached hereto, as such
Schedule 5A shall be amended from time to time by the JSC in order to account for Target
specificities, which amendment shall occur before any activities with respect to such Development
Candidate are initiated, in any material respect, in the Development Program and (ii) with respect
to the DCSC for Development Candidates that arise from ARCHEMIX Internal Research Projects, the
guideline criteria for selecting Optimized Lead Compounds that are sufficiently promising to
warrant further Development as Development Candidates as set forth in Schedule 5B attached
hereto, as such Schedule 5B shall be amended from time to time by ARCHEMIX in order to
account for Target specificities.

     1.60 “Development Program” means the Development activities to be conducted during the
Term with respect to each Optimized Lead Compound and Development Candidate (including without
limitation Co-Developed Development Candidates) pursuant to the Annual Development Plan, with the
objective of developing such Optimized Lead Compound or Development Candidate into a Product.

     1.61 “Development Program Technology” means any Technology, other than Co-Developed
Program Technology, that is conceived or first reduced to practice within the Development Program,
including but not limited to any process for modifying, optimizing, using, formulating, delivering
and/or stabilizing a Collaboration Aptamer.

     1.62 “Diagnosis” means (a) the determination or monitoring of (i) the presence or
absence of a disease, (ii) the stage, progression or severity of a disease or (iii) the effect on a
disease of a particular treatment; and/or (b) the selection of patients for a particular treatment
with respect to a disease.

     1.63 “Diagnostic Product” means In Vitro Diagnostics, In Vivo Diagnostic Agents and
any product used for Diagnosis. For purposes of clarity, the term Diagnostic Product shall not
include a product used for the delay of onset or progression of, or the treatment, cure or
prevention of, an Indication.

     1.64 “Drug Approval Application” means, with respect to a Product in a particular
country or region, an application for Commercialization Regulatory Approval for such Product in
such country or region, including without limitation: (a) an NDA or sNDA; (b) a counterpart of an
NDA or sNDA in any country or region in the Territory; and (c) all supplements and amendments to
any of the foregoing.

     1.65 “Effective Date” means July 1, 2007. 

     1.66 “Enriched Pool” means a pool of oligonucleotides used to perform the SELEX
Process against a Program Target in the performance of the Research Program that (a) has undergone
[***] or more [***] of [***] and (b) wherein, using an [***] with [***] of [***] (i.e., [***]) and
[***] of the applicable Program Target, at least [***]% of the input pool of [***] is [***] in the
assay by the Program Target and the [***] fraction of the [***] pool is at least [***] relative to
the [***] fraction for [***] (i.e., [***]) pool of [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

11

 

     1.67 “Estimated Aggregate FTEs” means, with respect to each Co-Developed Development
Candidate, the total number of internal FTEs that MERCK reasonably determines in good faith are
required to Develop such Co-Developed Development Candidate in each Calendar Year.

     1.68 Excepted Decision” means any of the following decisions requiring the unanimous
approval of all members of the JSC: (a) any decision to approve the Annual Research Plan applicable
to the conduct by [***] of any [***] and/or [***]; (b) any decision as to whether a milestone has
been achieved under this Agreement for which a milestone payment is payable; (c) any decision as to
whether a proposed Target is a [***]; (d) the [***]; (e) whether ARCHEMIX is to be obligated to
perform any [***] in connection with the Development of any [***]; (f) the [***] of any
Co-Promotion Agreement; and (g) the determination that a [***] identified in the conduct of any
[***] meets the [***].

     1.69 “Excluded Aptamer” means any Aptamer listed on Schedule 4 attached
hereto.

     1.70 “Failed Compound” means any Collaboration Aptamer directed against a Failed
Target.

     1.71 “Failed Target” means (a) any [***] Program Target as to which the JPT concludes
and the JSC agrees that ARCHEMIX is unable or unlikely to identify [***] Program Target; (b) any
[***] Program Target for which ARCHEMIX fails to identify [***]; (c) any [***] Program Target for
which MERCK discontinues Development of an [***]; provided, that, at such time no other [***] for
such [***] Program Target are in Development; and (d) any [***] Program Target for which an [***]
meeting the applicable DCSC exists and, except for any [***] that results from an ARCHEMIX Internal
Research Project, for which MERCK has not paid the Development Candidate Milestone Payment in the
time allotted for such payment in Section 6.5.1. For purposes of clarity, a Failed Target shall
not be considered a Program Target.

     1.72 “FDA” means the United States Food and Drug Administration or any successor
agency or authority thereto.

     1.73 “FDCA” means the United States Federal Food, Drug, and Cosmetic Act, as amended.

     1.74 “Field” means the prevention, treatment, cure and/or delay of the onset or
progression of [***]. For purposes of clarity, the Field shall not include the research,
development, manufacture, use or sale of Diagnostic Products or Radio Therapeutics.

     1.75 “First Commercial Sale” means, with respect to a Product in a country in the
Territory, the first sale, transfer or disposition for value or for an end user of such Product in
such country. For purposes of clarity, the use of any Product in clinical trials, pre-clinical
studies or other research or development activities, or the disposal or transfer of Products for a
bona fide charitable purpose or a commercially reasonable sampling program, shall not be deemed to
be a sale, transfer or disposition for value or for an end user.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

12

 

     1.76 “Force Majeure” means any occurrence beyond the reasonable control of a Party
that (a) prevents or substantially interferes with the performance by such Party of any of its
obligations hereunder and (b) occurs by reason of any act of God, flood, fire, explosion,
earthquake, strike, lockout, labor dispute, casualty or accident, or war, revolution, civil
commotion, act of terrorism, blockage or embargo, or any injunction, law, order, proclamation,
regulation, ordinance, demand or requirement of any government or of any subdivision, authority or
representative of any such government.

     1.77 “FTE” shall mean [***] of work devoted to or in support of the ARCHEMIX Research
Activities or the ARCHEMIX Development Activities other than with respect to Co-Developed
Collaboration Aptamers that is carried out by one or more appropriately trained employees of
ARCHEMIX, measured in accordance with ARCHEMIX’s time allocation practices from time to time.

     1.78 “FTE Cost” means, for any period, the applicable FTE Rate multiplied by the
applicable number of FTEs in such period.

     1.79 “FTE Rate” means (a) with respect to the conduct by ARCHEMIX of any Technology
Transfer Activities, [***] Dollars (US $[***]); (b) with respect to the conduct by ARCHEMIX of
ARCHEMIX Research Activities in all MERCK Funded Research Projects, [***] Dollars (US $[***]); (c)
with respect to the conduct by ARCHEMIX of ARCHEMIX Research Activities in all ARCHEMIX Internal
Research Projects pursuant to MERCK’s Additional Research Request as described in Section 3.9.2 or
set forth in an Annual Research Plan approved by the JSC after MERCK’s payment of the applicable
Option Exercise Fee and/or the conduct by ARCHEMIX of ARCHEMIX Research Activities in all MERCK
Internal Research Projects pursuant to Section 3.7.2(c), [***] Dollars (US $[***]) and (d) with
respect to the conduct by ARCHEMIX of ARCHEMIX Development Activities other than with respect to a
Co-Developed Collaboration Aptamer, ARCHEMIX’s [***] FTE Rate; provided, that, for each Contract
Year on and after the first Contract Year, the applicable FTE Rate shall be adjusted by an amount
per Contract Year to be determined by multiplying the then-applicable FTE Rate by the cumulative
increase or decrease in the Consumer Price Index since the Effective Date ([***] for all items;
[***]; available at http://www.bls.gov/cpi/home.htm). The FTE Rate includes all salary, employee
benefits, materials and all other expenses including support staff and overhead for or associated
with the scientists of a Party performing activities but does not include Third Party Costs.

     1.80 “GAAP” means United States generally accepted accounting principles, consistently
applied.

     1.81 “Hatch-Waxman Act” means the Drug Price Competition and Patent Term Restoration
Act of 1984, as amended.

     1.82 “[***] Target” means the ARCHEMIX Internal Program Target identified on
Schedule B attached hereto as [***]. For purposes of clarity, the [***] Target includes
both or either of [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

13

 

     1.83 “ICC” means the International Chamber of Commerce in Paris, France.

     1.84 “IND” means: (a) an Investigational New Drug Application as defined in the FDCA
and regulations promulgated thereunder or any successor application or procedure required to
initiate clinical testing of a Development Candidate in humans in the United States; (b) a
counterpart of an Investigational New Drug Application that is required in any other country or
region in the Territory before beginning clinical testing of a Development Candidate in humans in
such country or region; and (c) all supplements and amendments to any of the foregoing.

     1.85 “Indication” means any human indication, disease or condition which can be
treated, prevented, cured or the progression of which can be delayed. For purposes of clarity,
distinctions between human indications, diseases or conditions with respect to a Product shall be
made by reference to the World Health Organization International Classification of Diseases,
version 10 (as revised and updated, “ICD10”).

     1.86 “Initiation” or “Initiate” means, with respect to a human clinical trial,
the first date that a subject or patient is dosed in such clinical trial.

     1.87 “In Vitro Diagnostics” means the use of the SELEX Process or aptamers
or photoaptamers identified through the use of the SELEX Process in the assay, testing
or determination, outside of a living organism, of a substance in a test material. In Vitro
Diagnostics shall include, among other things, the use of the SELEX Process or aptamers
or photoaptamers identified through the use of the SELEX Process in the assay, testing
or determination: (a) outside of a living organism, (i) of a human substance in a test material,
often to identify or follow the progression of a disease or disorder, or to select a patient for
treatment; (ii) of a plant substance, animal substance or other substance in a test material, often
to identify or follow the progression of a disease, process, or disorder in a human or non-human
organism; and (iii) of environmental substances (as in water quality testing); and (b) of a
substance on a test material such as cells (as in FACS analysis or other measurements of pathogens
within biological samples).

     1.88 “In Vivo Diagnostic Agent” means any product containing one or more aptamers that
is used for any human in vivo diagnostic purpose related to (inter alia) the identification,
quantification or monitoring of the propensity toward, or actual existence of, any disease state.

     1.89 “IPO Price” means the price per share paid by investors participating in the
Qualified IPO.

     1.90 “Joint Development Committee” or “JDC” means the committee composed of
ARCHEMIX and MERCK representatives established pursuant to Section 2.3.

     1.91 “Joint Patent Rights” means Patent Rights that contain one or more claims that
cover Joint Technology.

     1.92 “Joint Project Team” or “JPT” means the committee composed of ARCHEMIX
and MERCK representatives established pursuant to Section 2.2.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

14

 

     1.93 “Joint Steering Committee” or “JSC” means the committee composed of
ARCHEMIX and MERCK representatives established pursuant to Section 2.1.

     1.94 “Joint Co-Developed Program Patent Rights” means any Patent Rights that contain
one or more claims that cover Joint Co-Developed Program Technology.

     1.95 “Joint Co-Developed Program Technology” means any Co-Developed Program Technology
that is (a) jointly conceived or first reduced to practice (actively or constructively) by
employees of, or consultants to, MERCK and employees of, or consultants to, ARCHEMIX or (b)
conceived or reduced to practice solely by employees of, or consultants to, a Party with the use in
any material respect of any Technology, Patent Rights or Proprietary Materials of the other Party.
For purposes of clarity, Joint Co-Developed Program Technology shall not include Program
Aptamer-Specific Technology.

     1.96 “Joint Technology” means (a) all Program Generic Technology and (b) any Program
Technology (other than Program Aptamer-Specific Technology) that is (i) jointly conceived or
reduced to practice by employees of, or consultants to, MERCK and employees of or consultants to
ARCHEMIX or (ii) conceived or reduced to practice solely by employees of, or consultants to, a
Party with the use in any material respect of any Technology, Patent Rights or Proprietary
Materials of the other Party. For purposes of clarity, any Program Technology that relates to the
SELEX Process or to the SELEX Technology shall not be considered Joint Technology irrespective of
which Party conceived or reduced to practice such improvement. For purposes of clarity, Joint
Technology shall not include Program Aptamer-Specific Technology.

     1.97 “Knowledge” means, with respect to a Party, the actual knowledge of any employee
of such Party.

     1.98 “Lead Compound” means any Program Aptamer that [***] Program Target that is first
identified in the conduct of the Research Program or Development Program, or any Aptamer [***]
first identified in the conduct of the Research Program or Development Program that [***] Program
Target; provided, that, no Collaboration Aptamer shall, after [***], be nominated or designated as
a Lead Compound.

     1.99 “Licensed Patent Rights” means any ARCHEMIX Patent Rights and ARCHEMIX’s interest
in Joint Patent Rights that (a) contain one or more claims that cover any Collaboration Aptamer,
including its manufacture or its formulation or a method of its delivery or of its use, (b) contain
one or more claims that cover the SELEX Process or SELEX Technology or (c) are necessary for MERCK
to exercise the licenses granted to it pursuant to Sections 8.1.1 and 8.2. For purposes of
clarity, Licensed Patent Rights existing as of the Effective Date include those listed on
Schedule 3 attached hereto.

     1.100 “Licensed Technology” means any ARCHEMIX Technology and ARCHEMIX’s interest in
Joint Technology that (a) relates to any Collaboration Aptamer, including its manufacture or its
formulation or a method of its delivery or of its use; (b) relates to the SELEX Process or SELEX
Technology; and (c) is necessary for MERCK to exercise the licenses granted to it pursuant to
Sections 8.1.1 and 8.2.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

15

 

     1.101 “Major Market Country” means each of the [***] and [***].

     1.102 “Marketing Support Clinical Trial” means a clinical trial conducted in humans in
any country, the results of which are intended to be used to support the marketing of a drug within
its approved Indication in such country.

     1.103 “MERCK Background Technology” means any Technology that is used by MERCK, or
provided by MERCK for use, in the Research Program and/or Development Program that is (a)
Controlled by MERCK as of the Effective Date or (b) conceived or first reduced to practice by
employees of, or consultants to, MERCK after the Effective Date other than in the conduct of MERCK
Research Activities or MERCK Development Activities and without the use in any material respect of
any Collaboration Aptamers, ARCHEMIX Technology, ARCHEMIX Patent Rights, or ARCHEMIX Materials.
For purposes of clarity, MERCK Background Technology shall not include MERCK Program Technology or
MERCK’s interest in Joint Technology.

     1.104 “MERCK Co-Developed Program Patent Rights” means any Patent Rights Controlled by
MERCK that contain one or more claims that cover MERCK Co-Developed Program Technology.

     1.105 “MERCK Co-Developed Program Technology” means any Co-Developed Program
Technology that is conceived or first reduced to practice by employees of, or consultants to,
MERCK, alone or jointly with any Third Party, without the use in any material respect of any
ARCHEMIX Technology, ARCHEMIX Patent Rights, ARCHEMIX Materials or Joint Technology. For purposes
of clarity, MERCK Co-Developed Program Technology does not include MERCK Program Technology.

     1.106 “MERCK Co-Development Sharing Percentage” means, with respect to each
Co-Developed Collaboration Aptamer, a percentage equal to the [***] and the [***].

     1.107 “MERCK Development Activities” means all Development activities (including
without limitation all Development activities conducted with respect to Co-Developed Collaboration
Aptamers) specified to be conducted by MERCK in any Annual Development Plan (or amendment thereto).

     1.108 “MERCK Funded Program Targets” means up to five (5) Targets to be proposed by
MERCK and accepted by ARCHEMIX for inclusion in the MERCK Funded Research Projects pursuant to
Section 3.7.1. For purposes of clarity, at least three (3) of the MERCK Funded Program Targets
shall be for oncology Indications.

     1.109 “MERCK Funded Research Projects” means the Research Projects to be conducted by
ARCHEMIX at the ARCHEMIX Facility and funded by MERCK involving the identification and initial
testing of Aptamers against the MERCK Funded Program Targets. For purposes of clarity, each MERCK
Funded Research Project shall commence within [***] days of the date that the applicable MERCK
Internal Program Target is accepted by ARCHEMIX for inclusion on the Target Exclusivity List.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

16

 

     1.110 “MERCK Internal Program Targets” means up to five (5) Targets identified by
MERCK through its practice of the SELEX License to be proposed by MERCK and accepted by ARCHEMIX
for inclusion in the MERCK Internal Research Projects pursuant to Section 3.7.2. For purposes of
clarity, at least three (3) of the MERCK Internal Program Targets shall be for oncology
Indications.

     1.111 “MERCK Internal Research Projects” means the Research Projects to be conducted
by (i) MERCK through its practice of the SELEX License, and/or (ii) ARCHEMIX at the ARCHEMIX
Facility and funded by MERCK involving the identification and initial testing of Aptamers against
the MERCK Internal Program Targets. For purposes of clarity, each MERCK Internal Research Project
shall commence within [***] days of the date that the applicable MERCK Internal Program Target is
accepted by ARCHEMIX for inclusion on the Target Exclusivity List.

     1.112 “MERCK Materials” means any Proprietary Materials that are Controlled by MERCK
and used by MERCK, or provided by MERCK for use, in the Research Program and/or the Development
Program.

     1.113 “MERCK Non-SELEX Improvements” means any Technology Controlled by MERCK during
the Term of this Agreement that (a) is conceived or first reduced to practice (actively or
constructively) as a result of the practice by MERCK of the SELEX License and (b) is not a MERCK
SELEX Improvement.

     1.114 “MERCK Patent Rights” means any Patent Rights Controlled by MERCK that contain
one or more claims that cover MERCK Technology.

     1.115 “MERCK Program Technology” means (a) any Program Technology that (i) is not
ARCHEMIX Program Technology or Joint Technology and (ii) is conceived or first reduced to practice
by employees of, or consultants to, MERCK, alone or jointly with any Third Party, without the use
in any material respect of any ARCHEMIX Technology, ARCHEMIX Patent Rights, ARCHEMIX Materials or
Joint Technology; (b) any Program Aptamer-Specific Technology; and (c) any Development Program
Technology.

     1.116 “MERCK Research Activities” means all activities specified to be conducted by
MERCK in any Annual Research Plan (or amendment thereto) that are approved by the JPT and JSC.

     1.117 “MERCK SELEX Improvements” means any Technology that is conceived or first
reduced to practice by MERCK through the practice of the SELEX License that constitutes a
modification or improvement to the Licensed Technology or Licensed Patent Rights, including,
without limitation, the SELEX Process or the SELEX Technology.

     1.118 “MERCK Share Amount” means that number of shares of ARCHEMIX Common Stock equal
to the lesser of (a) [***] Dollars (US $[***]) divided by the IPO Price and (b) [***] percent
([***]%) of the total gross offering proceeds (prior to underwriter commissions

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

17

 

and expenses) raised by ARCHEMIX in the Qualified IPO and any concurrent private placement
divided by the IPO Price.

     1.119 “MERCK Technology” means, collectively, MERCK Background Technology and MERCK
Program Technology.

     1.120 “Minimum FTE Funding Commitment” means, with respect to each Research Project
conducted in any Contract Year during the Research Program Term (including [***] to the extent that
work is performed by [***] pursuant to MERCK’s Additional Research Request for the development of
an additional Compound Candidate as described in Section 3.9.2 or set forth in an Annual Research
Plan approved by the JSC after [***] of the [***]), the funding of at least [***] ARCHEMIX FTEs at
the applicable FTE Rate, but only to the extent that ARCHEMIX staffs each such Research Project
with [***] ARCHEMIX FTEs and employs, or is prepared to employ, each such FTE for the Research
Project in question.

     1.121 “NDA” means a New Drug Application, as defined in the FDCA and regulations
promulgated thereunder or any successor application or procedure required to sell a Product in the
United States.

     1.122 “Net Sales” means the gross amount billed or invoiced by MERCK or any of its
Affiliates or Sublicensees to Third Parties throughout the Territory for sales or other
dispositions or transfers for value of Products less (a) allowances for normal and customary trade,
quantity and cash discounts actually allowed and taken, (b) transportation, insurance and postage
charges, if prepaid by MERCK or any Affiliate or Sublicensee of MERCK and included on any such
party’s bill or invoice as a separate item, (c) credits, rebates, returns pursuant to agreements
(including, without limitation, the amounts written off by MERCK, or any of its Affiliates or
Sublicensees, by reason of uncollectible gross amounts billed or invoiced for sales of Product up
to a maximum of [***] percent ([***]%) of Net Sales per Calendar Year, managed care agreements) or
government regulations, to the extent actually allowed; and (d) sales, use and other consumption
taxes similarly incurred to the extent included on the bill or invoice as a separate item. In
addition, Net Sales are subject to the following:

          (i) If MERCK or any of its Affiliates or Sublicensees effects a sale, disposition or transfer
of a Product to a customer in a particular country other than on customary commercial terms or as
part of a package of products and services, the Net Sales of such Product to such customer shall be
deemed to be “the fair market value” of such Product. For purposes of this subsection, “fair
market value” shall mean the value that would have been derived had such Product been sold as a
separate product to another customer in the country concerned on customary commercial terms.

          (ii) In the case of pharmacy incentive programs, hospital performance incentive program
chargebacks, disease management programs, similar programs or discounts on “bundles” of products,
all discounts and the like shall be allocated among products on the basis on which such discounts
and the like were actually granted or, if such basis cannot be determined, in proportion to the
respective list prices of such products or such other reasonable allocation method as the Parties
shall agree.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

18

 

          (iii) For purposes of clarity, use of any Product in clinical trials, pre-clinical studies or
other research or development activities, or disposal or transfer of Products for a bona fide
charitable purpose or a commercially reasonable sampling program, shall not give rise to any Net
Sales.

     1.123 “Optimized Lead Compound” means (i) with respect to the MERCK Funded Research
Projects or MERCK Internal Research Projects, any [***] Compound that the JPT nominates and the JSC
accepts as meeting the OLSC for such Program Target; provided, that, no [***] shall, after becoming
a [***], be nominated or designated as an Optimized Lead Compound, and (ii) with respect to the
ARCHEMIX Internal Research Projects any Compound Candidate that MERCK designates as an Optimized
Lead Compound in accordance with Section 3.9.1 or Section 3.9.2.

     1.124 “Optimized Lead Compound Selection Criteria” or “OLSC” means (i) with
respect to the OLSC for Optimized Lead Compounds that arise from the MERCK Funded Research Projects
or MERCK Internal Research Projects, the guideline criteria for selecting Lead Compounds that are
sufficiently promising to warrant further research as an Optimized Lead Compound as set forth in
Schedule 1A attached hereto, as such Schedule 1A may be amended from time to time
by the JSC in order to account for Target specificities, which amendment shall occur before any
research activities are initiated with respect to such Optimized Lead Compound against the
applicable Program Target, and (ii) with respect to the OLSC for Optimized Lead Compounds that
arise from the ARCHEMIX Internal Research Projects, the guideline criteria for selecting Aptamers
that are sufficiently promising to warrant further research as an Optimized Lead Compound as set
forth in Schedule 1B attached hereto, as such Schedule 1B may be amended from time
to time by ARCHEMIX in order to account for Target specificities. Notwithstanding anything to the
contrary set forth in Schedule 1A, for purposes of determining whether a Lead Compound has
been designated as an Optimized Lead Compound for Milestone 1 in Section 6.5.1, [***] shall be
required to be performed with respect to such Lead Compound, whether or not included as part of the
OLSC.

     1.125 “Opt-Out Date” means, with respect to each Co-Developed Collaboration Aptamer,
[***] days from (a) the [***] by the [***] to [***] an [***] for [***] (the “[***] Opt-Out
Date”), (b) the [***] by ARCHEMIX of the[***] and any other [***]by MERCK to [***] the [***] by
the [***] into the [***] or[***] (the “[***] Opt-Out Date”), and/or (c) the [***] by
ARCHEMIX of the [***] and any other [***] by MERCK to [***] the [***]by the [***] to [***] the
[***] with respect to such [***] (the “[***] Opt-Out Date”).

     1.126 “Patent Rights” means the rights and interests in and to issued patents and
pending patent applications (which, for purposes of this Agreement, include certificates of
invention, applications for certificates of invention and priority rights) in any country or
region, including all provisional applications, substitutions, continuations,
continuations-in-part, divisions, renewals, all letters patent granted thereon, and all reissues,
re-examinations and extensions thereof, and all foreign counterparts of any of the foregoing.

     1.127 “Permitted Activities” means (a) [***] to any [***], any[***] ARCHEMIX [***] to
such [***] for [***]and/or for [***] for the [***] of [***] aptamers that [***] to a [***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

19

 

a [***] and (b) [***] ARCHEMIX [***] of [***] to [***] and/or [***] aptamers [***]of the [***]
but [***]; provided, that, ARCHEMIX [***] (y) [***] or otherwise [***] in the [***] of the [***]
are the [***] of any [***] of [***] and (z) [***] or [***] in the [***] and/or[***] of any [***] of
the [***].

     1.128 “Person” means an individual, sole proprietorship, partnership, limited
partnership, limited liability partnership, corporation, limited liability company, business trust,
joint stock company, trust, incorporated association, joint venture or similar entity or
organization, including a government or political subdivision, department or agency of a
government.

     1.129 “Phase I Clinical Trial” means a clinical trial conducted in healthy humans or
patients, which clinical trial is designed to establish the safety, drug-drug interactions and/or
pharmacokinetics of an investigational drug given its intended use, and to support continued
testing of such drug in Phase II Clinical Trials.

     1.130 “Phase II Clinical Trial” means a clinical trial conducted in patients with a
particular disease or condition, which clinical trial is designed to establish the safety,
appropriate dosage and pharmacological activity of an investigational drug given its intended use,
and to initially explore its efficacy for such disease or condition.

     1.131 “Phase III Clinical Trial” means a pivotal clinical trial conducted in patients
with a particular disease or condition, which clinical trial is designed to ascertain efficacy and
safety of an investigational drug for its intended use and to define warnings, precautions and
Adverse Events that are associated with an investigational drug in the dosage range intended to be
prescribed, with the purpose of preparing and submitting applications for Regulatory Approval or
label expansion to the pertinent Regulatory Authority in any country.

     1.132 “Product” means any pharmaceutical or medicinal item, substance or formulation
that contains, incorporates or comprises a Collaboration Aptamer or any Aptamer Derived therefrom
that binds a Program Target. Notwithstanding the above, if a first pharmaceutical or medicinal
item, substance or formulation is deemed to be a Product for purposes of this Agreement, any
subsequent pharmaceutical or medicinal item, substance or formulation will be considered to be an
additional Product for purposes of this Agreement only to the extent that it is a new chemical
entity (as defined by the FDCA) with respect to the existing Product(s). For purposes of clarity,
the term Product shall include, collectively, all Royalty-Bearing Products, all Co-Developed
Products and all Co-Promoted Products.

     1.133 “Product Commercialization Plan” means, with respect to each Product (including
without limitation any Co-Developed Product), the written plan for the Commercialization of such
Product in the Territory (including, without limitation, expected manufacturing scale-up,
manufacture, formulation and filling requirements for such Product and a detailed strategy, budget
and proposed timelines), as such plan may be amended or updated.

     1.134 “Product Trademark” means any trademark or trade name, whether or not
registered, or any trademark application or renewal, extension or modification thereof, in the

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

20

 

Territory, or any trade dress and packaging, in each case (a) that are applied to or used with
any Product by MERCK and (b) together with all goodwill associated therewith and promotional
materials relating thereto.

     1.135 “Program Aptamer” means any [***] that is an [***] that [***] and that is first
identified in the performance of the Research Program or during Development and/or any [***] that
[***] that is [***] from such [***] and that is first identified in the performance of the Research
Program or during Development.

     1.136 “Program Aptamer-Specific Patent Rights” means all Patent Rights on a
claim-by-claim basis that cover only Program Aptamer-Specific Technology.

     1.137 “Program Aptamer-Specific Technology” means any Program Technology that relates
specifically to (a) any Collaboration Aptamer or (b) the manufacture, formulation, delivery,
production or use of a Collaboration Aptamer. For purposes of clarity, all Co-Developed
Collaboration Aptamers shall be considered Program Aptamer-Specific Technology, irrespective of
which Party conceived or reduced to practice such Co-Developed Program Technology.

     1.138 “Program Generic Patent Rights” means Patent Rights on a claim-by-claim basis
that cover only Program Generic Technology.

     1.139 “Program Generic Technology” means any Program Technology that relates generally
to the manufacture, formulation, delivery, production or use of Aptamers.

     1.140 “Program Oligonucleotide” means the [***] and [***] obtained from an [***] and
[***] and [***] in the performance of the [***] against a [***] that is not a [***].

     1.141 “Program Target” means each Target listed on the Target Exclusivity List, as
amended from time to time in accordance with Section 3.8.2.

     1.142 “Program Technology” means any Technology (including, without limitation, any
new and useful process, method of manufacture or composition of matter) or Proprietary Materials
that are conceived or first reduced to practice (actively or constructively) by either Party in the
conduct of the Research Program.

     1.143 “Proprietary Materials” means tangible chemical, biological or physical
materials (a) that are furnished by or on behalf of one Party to the other Party in connection with
this Agreement, whether or not specifically designated as proprietary by the Transferring Party or
(b) that are otherwise conceived or reduced to practice in the conduct of the Research Program or
the Development Program.

     1.144 “Qualified IPO” means any firm commitment underwritten initial public offering
by ARCHEMIX on the New York Stock Exchange, the American Stock Exchange or the NASDAQ National
Market filed under the Securities Act of 1933, as amended, covering the offer and sale of shares of
Common Stock, $.001 par value per share, of ARCHEMIX, with total

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

21

 

gross offering proceeds to ARCHEMIX (prior to underwriter commissions and expenses) of at
least [***] dollars ($[***]).

     1.145 “Quarterly FTE Payment” means the amount payable by MERCK to ARCHEMIX for
ARCHEMIX’s FTE Costs for (i) all Research Projects to be conducted during each Calendar Quarter of
the Research Program Term, which shall equal ARCHEMIX’s estimated FTE Cost as set forth in the
Annual Research Plans for such Research Projects and Calendar Quarter and (ii) all Requested
ARCHEMIX Activities and/or ARCHEMIX De Novo Research Activities which shall equal ARCHEMIX’s
estimated FTE Cost for such activities and Calendar Quarter.

     1.146 “Radio Therapeutic” means any product for human therapeutic use that contains
one or more aptamers that targets specifically any diseased tissue, cells or disease-specific
molecules or any tissue or cells which are affected by a disease or located in the close
neighborhood of a disease process and is linked to or incorporates (a) radionucleotides or (b) any
structure or elements which develop therapeutic effects similar to the effect of linking or
incorporating radionucleotides after submission of any kind of radiation.

     1.147 “Regulatory Approval” means, with respect to any country or region in the
Territory, any approval, product and establishment license, registration or authorization of any
Regulatory Authority required for the manufacture, use, storage, importation, exportation,
distribution, transport or sale of a Product for use in the Field in such country or region.

     1.148 “Regulatory Authority” means the FDA, or any counterpart of the FDA outside the
United States, or any other national, supra-national, regional, state or local regulatory agency,
department, bureau, commission, council or other governmental entity with authority over the
distribution, importation, exportation, manufacture, production, use, storage, transport, clinical
testing or sale of a Product.

     1.149 “Regulatory Filings” means, collectively: (a) all INDs, establishment license
applications, drug master files, applications for designation as an “Orphan Product(s)” under the
Orphan Drug Act, for “Fast Track” status under Section 506 of the FDCA (21 U.S.C. § 356) or for a
Special Protocol Assessment under Section 505(b)(4)(B) and (C) of the FDCA (21 U.S.C. §
355(b)(4)(B)), NDAs and BLAs and all other similar filings (including, without limitation,
counterparts of any of the foregoing in any country or region in the Territory); (b) all
supplements and amendments to any of the foregoing; and (c) all data and other information
contained in, and correspondence relating to, any of the foregoing.

     1.150 “Research Program” means the research program to be conducted by the Parties for
each Research Project during the Research Program Term pursuant to the Annual Research Plan up to
and including the selection of Optimized Lead Compounds from Lead Compounds. For purposes of
clarity, the Research Program does not include any Development activities performed in the course
of the Development Program or any activities performed by MERCK under the SELEX License.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

22

 

     1.151 “Research Program Term” means the period beginning on the Effective Date and
ending on the last day of the fifth (5th) Contract Year; provided, that, if this
Agreement is terminated prior to the end of the Research Program Term, the effective date of such
early termination shall become the last day of the Research Program Term.

     1.152 “Research Projects” means, collectively, the MERCK Funded Research Projects, the
MERCK Internal Research Projects and any ARCHEMIX Internal Research Projects for which MERCK has
exercised its Compound Candidate Option.

     1.153 “Royalty-Bearing Product” means (a) any Product that is not a Co-Developed
Product and (b) any Co-Developed Product to the extent sold outside of the Co-Development
Territory.

     1.154 “Royalty Term” means, on a Royalty-Bearing Product-by-Royalty-Bearing Product
and country-by-country basis, the period beginning on the date of First Commercial Sale of a
Royalty-Bearing Product in a country and ending on the later to occur of (a) expiration of the last
to expire Valid Claim of the Licensed Patent Rights, Program Aptamer-Specific Patent Rights,
Co-Developed Program Patent Rights or Joint Patent Rights in such country that covers such
Royalty-Bearing Product or its identification, manufacture, use, import, offer for sale or sale or
(b) (i) with regard to the first Royalty-Bearing Product for each Program Target sold in such
country, fifteen (15) years from the date of the First Commercial Sale of such first Royalty-Bearing Product
in such country or (ii) with regard to each additional Royalty-Bearing Product for such Program
Target sold in such country, ten (10) years from the date of the First Commercial Sale of each such
additional Royalty-Bearing Product in such country.

     1.155 “SELEX License Term” means the period commencing on the Effective Date and
continuing until the [***] or [***] of the [***].

     1.156 “SELEX Portfolio” means those Patent Rights licensed by Gilead to ARCHEMIX
pursuant to the ARCHEMIX-Gilead License Agreement.

     1.157 “SELEX Process” means any means used for the identification or generation of a
nucleic acid that binds to a Target by means other than Watson-Crick base-pairing, including
without limitation any such process that (a) is covered by, or is described in, the SELEX
Portfolio, including without limitation U.S. Patent Nos[***] or [***], (b) is covered by, or
is described in, any other Patent Rights Controlled by ARCHEMIX, and (c) any continuations,
divisionals, and continuations-in-part, substitutions, renewals, reissues, re-examinations and
extensions of and improvements to the inventions covered by, or described in, the foregoing Patent
Rights.

     1.158 “SELEX Technology” means (a) generic aptamer compositions and (b) any process
for modifying, optimizing and/or stabilizing an aptamer wherein such modification, optimization or
stabilization includes, without limitation minimization, truncation, conjugation, pegylation,
complexation, substitution, deletion and/or incorporation of modified nucleotides.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

23

 

     1.159 “SELEX Technology Transfer Plan” means the written plan to be prepared by the
Parties and attached hereto as Exhibit A which describes the technology transfer and
training activities to be carried out by ARCHEMIX during the Technology Transfer Term pursuant to
Section 3.2 with respect to the use of the SELEX Process and the SELEX Technology, as such written
plan may be amended, modified or updated from time to time by the Parties.

     1.160 “Signing Date” means the date first written above.

     1.161 “sNDA” means a Supplemental New Drug Application, as defined in the FDCA and
applicable regulations promulgated thereunder.

     1.162 “Stock Purchase Agreement” means the Series C Convertible Preferred Stock
Purchase Agreement dated as of the Signing Date by and between the Parties.

     1.163 “Sublicense Agreement” means any agreement entered into by MERCK with a
Sublicensee.

     1.164 “Sublicensee” means any Third Party to which MERCK grants a sublicense under the
licenses granted to it under Section 8.1 or 8.2.

     1.165 “Supplemental Product” means a product having independent, supplementary or
enabling therapeutic effect (e.g., as a catalyst or adjuvant) or diagnostic utility.

     1.166 “Target” means a protein, cytokine, enzyme, receptor, transducer, transcription
factor, antigen or any other non-nucleic acid molecule.

     1.167 “Target Exclusivity List” means the list of Program Targets on Schedule
2A attached hereto, as amended pursuant to Section 3.8.2.

     1.168 “Target Selection Field” means the treatment, prevention, cure or delay of onset
or progression in humans of [***] Indications. For purposes of clarity, the Parties agree that the
treatment, prevention, cure or delay of onset or progression of [***] shall be included in the
Target Selection Field.

     1.169 “Target Validation Activities” means the use of Aptamers identified by MERCK
through the practice of the SELEX License to bind to a Target in [***] assays in order to activate,
inhibit or otherwise modulate the biological activity of such Target and thereby demonstrate that
such activation, inhibition or modulation may be useful for the development of Aptamers for use in
the Field.

     1.170 “Technology” means, collectively, inventions, discoveries, improvements, trade
secrets and proprietary methods, whether or not patentable, including without limitation: (a)
methods of production or use of, and structural and functional information pertaining to, chemical
compounds; and (b) compositions of matter, data, formulations, processes, techniques, know-how and
results (including, without limitation, any negative results).

 Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

24

 

     1.171 “Terminated Compounds” means (a) all Collaboration Aptamers upon any termination
of this Agreement by ARCHEMIX pursuant to Section 11.2.2 or 11.2.3 or by MERCK pursuant to Section
11.2.1; and (b) the relevant Collaboration Aptamers binding specifically to the Program Target for
which MERCK’s license is terminated by ARCHEMIX pursuant to Section 11.2.2 due to failure of MERCK
to meet its diligence obligations.

     1.172 “Territory” means all countries and territories of the world.

     1.173 “Third Party” means a Person other than MERCK and ARCHEMIX and their respective
Affiliates.

     1.174 “ULEHI” means University License Equity Holdings, Inc., formerly known as UTC.

     1.175 “URC License Agreement” means the Restated Assignment and License Agreement,
dated July 17, 1991, by and between University Research Corporation and Gilead as successor in
interest to NeXstar.

     1.176 “UTC” means University Technology Corporation, the successor to the University
Research Corporation.

     1.177 “Valid Claim” means any claim of a pending patent application or an issued
unexpired patent that (a) has not been finally cancelled, withdrawn, abandoned or rejected by any
administrative agency or other body of competent jurisdiction, (b) has not been permanently
revoked, held invalid, or declared unpatentable or unenforceable in a decision of a court or other
body of competent jurisdiction that is unappealable or unappealed within the time allowed for
appeal, (c) has not been rendered unenforceable through disclaimer or otherwise, and (d) is not
lost through an interference proceeding.

     1.178 “Waived Compound” means any Collaboration Aptamer directed against a Waived
Target.

     1.179 “Waived Target” means (a) any Program Target for which MERCK, in its sole
discretion, discontinues Development of a Development Candidate; provided, that, no other
Development Candidates for such Program Target are in Development at such time and (b) any Program
Target which MERCK designates as a Waived Target in writing to ARCHEMIX.

     Additional Definitions. In addition, each of the following definitions shall have the
respective meanings set forth in the section of this Agreement indicated below:

	 	 	 
	Definition	 	Section
	Annual Reconciliation Statement
	 	6.4.1(b)
	Additional Research Request
	 	3.9.2(a)
	ARCHEMIX Change of Control Notice
	 	13.2.1(a)
	ARCHEMIX Indemnitees
	 	12.2
	ARCHEMIX Internal Program Target Notice
	 	3.9.3

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

25

 

	 	 	 
	Definition	 	Section
	Backup Compound Candidate
	 	3.9.1(b)
	Backup Compound Candidate Evaluation Period
	 	3.9.1(b)
	Backup Compound Candidate Notice
	 	3.9.1(b)
	Backup Compound Candidate Option
	 	3.9.1(b)
	Claims
	 	12.1
	Co-Developed Development Candidate
	 	4.10.2(a)
	Co-Development and Co-Promotion Option
	 	4.10.2(a)
	Co-Development and Co-Promotion Option Notice
	 	4.10.2(a)
	Co-Development Option Exercise Period
	 	4.10.2(a)
	Collaboration Manager
	 	2.4
	Competing Aptamer Product
	 	7.10.1(d)
	Co-Promotion Agreement
	 	4.10.2(c)
	Co-Promotion Option Period
	 	4.11.1
	Designated Senior Officers
	 	2.1.6
	Designation Notice
	 	7.1.2(c)(i)
	Dispute
	 	13.1.1
	Disputed Matter
	 	2.1.6
	Evaluation Period
	 	3.9.1(a)
	Expert
	 	14.1.2(a)
	Filing Party
	 	10.1.4
	Generic Product
	 	6.6.1(e)
	Gilead Indemnitee
	 	13.3
	Indemnified Party
	 	13.4
	Indemnifying Party
	 	13.4
	Infringement
	 	10.2.1(a)
	Infringement Notice
	 	10.2.1(a)
	IPO Effective Date
	 	5.5.2(c)
	JCC
	 	Schedule 9
	JPT
	 	2.2.1
	JPT Term
	 	2.2.1
	JSC Term
	 	2.1.1
	Late Stage Development Activities
	 	4.10.6(b)
	Losses
	 	12.1
	MERCK Change of Control Notice
	 	13.2.2(a)
	MERCK Contribution
	 	6.4.1(b)
	MERCK Indemnitees
	 	13.1
	MERCK Internal Program Target Requests
	 	3.7.2(c)
	MERCK IPO Shares
	 	5.2.2(b)
	MERCK IPO Share Amount
	 	5.2.2(c)
	MERCK Private Placement Shares
	 	5.2.2(c))
	MERCK Private Placement Share Amount
	 	5.2.2(b)
	MTA
	 	3.9.1(a)
	Net Income Payments
	 	6.7.1
	Non-Filing Party
	 	10.1.4
	Opting-Out Party
	 	4.10.7(d)

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

26

 

	 	 	 
	Definition	 	Section
	Option Fee
	 	6.3
	Option Exercise Fee
	 	6.3
	Opt-Out Right
	 	4.10.6(d)
	Opt-Out Right Notice
	 	4.10.6(d)
	Opt-Out Right Notice Period
	 	4.10.6(d)
	Patent Coordinator
	 	8.4
	Primary Compound Candidate
	 	3.9.1(a)
	Primary Compound Candidate Notice
	 	3.9.1(a)
	Primary Compound Candidate Option
	 	3.9.1(a)
	Private Placement
	 	5.2.1
	Private Placement Closing
	 	5.2.2(d)
	Private Placement Closing Date
	 	5.2.2(d)
	Private Placement Purchase Price
	 	5.2.2(c)
	Purchase Notice
	 	5.2.2(c)
	Qualified IPO Notice
	 	5.2.2(a)
	Qualified IPO Purchase Price
	 	5.2.2(c)
	Requested ARCHEMIX Activities
	 	3.9.2(a)
	Requested Chemistry
	 	6.6.1(c)
	Recipient Party
	 	3.13
	Roll-Over Payment
	 	4.10.7(c)
	SELEX License
	 	7.1.1(a)(i)
	Separation Date
	 	4.10.6(d)
	Sole Developing Party
	 	4.10.6(d)
	Technology Transfer Activities
	 	3.2
	Technology Transfer Costs
	 	3.2
	Technology Transfer Term
	 	3.2
	Term
	 	11.1
	Third Party Chemistry Payments
	 	6.6.1(c)
	Third Party Costs
	 	7.5.3
	Third Party Payments
	 	6.6.1(c)
	Transferring Party
	 	3.13

2. ADMINISTRATION OF THE COLLABORATION

2.1 Joint Steering Committee.

          2.1.1 Establishment. Within [***] days from the Effective Date, ARCHEMIX and MERCK
shall establish the Joint Steering Committee. Unless otherwise agreed by the Parties, the term for
the JSC shall commence as of the Effective Date and continue until the last day of the Research
Program Term (“JSC Term”); provided, that, the JSC Term shall be extended in the event that, and
for so long as, the JPT Term is extended or the JDC and/or the JCC is in existence. The JSC shall
have and perform the responsibilities set forth in Section 2.1.4.

          2.1.2 Membership. Upon establishment of the JSC, each Party shall designate in
writing, in its sole discretion, [***] members to the JSC, which shall be members of its

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

27

 

management. Unless otherwise agreed by the Parties, one of MERCK’s designees shall be
designated by MERCK as the Chair. Each Party shall have the right at any time to substitute
individuals, on a permanent or temporary basis, for any of its previously designated
representatives to the JSC, by giving written notice to the other Party. Initial designees of the
Parties to the JSC shall be designated by each Party by written notice to the other Party as soon
as is reasonably practicable following the Effective Date.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

28

 

     2.1.3 Meetings.

          (a) Schedule of Meetings; Agenda. The JSC shall establish a schedule of times for
regular meetings, taking into account the planning needs of the Collaboration and its
responsibilities. In urgent cases, special meetings of the JSC may be convened by any member upon
[***] days (or, if such meeting is proposed to be conducted by teleconference, upon [***]) written
notice to the other members; provided, that, (i) notice of any such special meeting may be waived
at any time, either before or after such meeting, and such waiver shall be the equivalent to the
giving of a valid notice hereunder, and (ii) attendance of any member at a special meeting shall
constitute a valid waiver of notice from such member. In no event shall the JSC meet less
frequently than once in each Calendar Year. Regular and special meetings of the JSC may be held in
person or by teleconference or videoconference; provided, that, meetings held in person shall
alternate between the respective offices of the Parties. The Chair shall prepare and circulate to
each JSC member an agenda for each JSC meeting not later than one (1) week prior to such meeting.

          (b) Quorum; Voting; Decisions. At each JSC meeting (i) the presence in person of at
least [***] member designated by each Party shall constitute a quorum and (ii) all members
designated by each Party who are present shall have [***] on all matters before the JSC at such
meeting. All decisions of the JSC shall be made by unanimous vote Alternatively, the JSC may act
by written consent signed by at least [***] member designated by each Party subject to Section
2.1.6. Whenever any action by the JSC is called for hereunder during a time period in which the
JSC is not scheduled to meet, the Chair shall cause the JSC to take the action in the requested
time period by calling a special meeting or by circulating a written consent. Representatives of
each Party or of its Affiliates who are not members of the JSC may attend JSC meetings as
non-voting observers with the consent of the other Party, which shall not be unreasonably withheld,
conditioned or delayed.

          (c) Minutes. The JSC shall keep minutes of its meetings that record all decisions and
all actions recommended or taken in reasonable detail. Drafts of the minutes shall be prepared and
circulated to the members of the JSC within a reasonable time after the meeting, not to exceed
[***] business days. The Chair shall have responsibility for the preparation and circulation of
draft minutes. Each member of the JSC shall have the opportunity to provide comments on the draft
minutes. The minutes shall be approved, disapproved and revised as necessary at the next JSC
meeting or within [***] days of the meeting whichever occurs first. Upon approval, final minutes
of each meeting shall be circulated to the members of the JSC by the Chair.

     2.1.4 Responsibilities. The JSC shall be responsible for overseeing the conduct and
progress of the Research Program, the Development of Optimized Lead Compounds, the Development and
Commercialization of Co-Developed Collaboration Aptamers and the Development of other Aptamers for
which ARCHEMIX is performing Development activities. Without limiting the generality of the
foregoing, the JSC shall have the following responsibilities:

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

29

 

          (a) overseeing the JPT’s, JDC’s and JCC’s performance of its respective responsibilities;

          (b) reviewing and approving each Annual Research Plan and each Annual Development Plan under
which ARCHEMIX is responsible for performing ARCHEMIX Development Activities for a Collaboration
Aptamer, including, without limitation, a Co-Developed Development Candidate;

          (c) determining, in accordance with Section 4.10.6(b), the ARCHEMIX Co-Development
Participation Level with respect to a Co-Developed Development Candidate;

          (d) determining whether to file an IND and whether to Initiate any Clinical Trial, with
respect to a Collaboration Agreement;

          (e) reviewing and approving any amendment to each Annual Research Plan approved by the JPT and
submitted to it for its approval;

          (f) reviewing and approving any amendment to an Annual Development Plan that covers a
Co-Developed Development Candidate and/or under which ARCHEMIX is responsible for performing
Development activities approved by the JPT and submitted to it for its approval;

          (g) reviewing data, reports or other information submitted to it by the JPT from time to time;

          (h) resolving all JPT, JDC and JCC matters that are in dispute;

          (i) reviewing and either approving or rejecting any decision of the JPT to nominate any Lead
Compound as an Optimized Lead Compound or any decision of the JPT to nominate any Optimized Lead
Compound as a Development Candidate;

          (j) resolving any dispute as to whether a milestone event under this Agreement has occurred;
and

          (k) implementing a mutually acceptable mechanism for reporting Adverse Events between the
Parties for each Development Candidate and Product; and

          (l) making such other decisions as may be delegated to the JSC pursuant to this Agreement or
by mutual written agreement of the Parties after the Effective Date.

     2.1.5 Interests of the Parties. Notwithstanding any other provisions of this
Agreement, all decisions made and all actions taken by the JSC shall be made or taken in the best
interest of the Collaboration.

     2.1.6 Dispute Resolution. The JSC members shall use reasonable efforts to reach
agreement on any and all matters. Such reasonable efforts shall, if requested by any

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

30

 

member of the JSC, include the engagement of a mutually acceptable Person who is not
affiliated with either Party and has particular experience or expertise with respect to a
particular matter to advise the JSC, the expense of any such Person to be borne equally by the
Parties. In the event that, despite such reasonable efforts, agreement on a particular matter
cannot be reached by the JSC within thirty (30) days after the JSC first meets to consider such
matter (each such matter, a “Disputed Matter”), then, if the Disputed Matter does not involve an
Excepted Decision or an ARCHEMIX Decision, and except as set forth in the last sentence of this
section, MERCK shall have the right to make the final decision on such Disputed Matter, but shall
only exercise such right in good faith after full consideration of the positions of both Parties.
Notwithstanding the foregoing, (i) if the Disputed Matter involves an ARCHEMIX Decision, then
ARCHEMIX shall have the right to make the final decision on such Disputed Matter but shall only
exercise such right in good faith after full consideration of the positions of both Parties and
(ii) if the Disputed Matter involves an Excepted Decision, (A) the Chair of the JSC shall refer
such Disputed Matter to the President of ARCHEMIX and the head of pre-clinical R&D of MERCK (the
“Designated Senior Officers”), who shall promptly initiate discussions in good faith to resolve
such Disputed Matter and (B) if such Disputed Matter is not resolved by the Designated Senior
Officers within ten (10) days after the date the Designated Senior Officers first met to consider
such Disputed Matter or forty-five (45) days after the date the JSC first met to consider such
Disputed Matter, the Disputed Matter shall be resolved in accordance with Section 14.1. For
purposes of clarity, under no circumstances shall the determination of whether MERCK or ARCHEMIX
has used or is using Commercially Reasonable Efforts be submitted for resolution under this Section
2.1.6.

     2.2 Joint Project Team.

          2.2.1 Establishment. Within [***] days from the Effective Date, ARCHEMIX and MERCK
shall establish the Joint Project Team (the “JPT”). Unless otherwise agreed by the Parties, the
term for the JPT shall commence as of the Effective Date and continue until the last day of the
Research Program Term (“JPT Term”); provided, that, the JPT Term shall be extended in the event
that, and for so long as, ARCHEMIX has obligations to perform ARCHEMIX Development Activities other
than Development Activities with respect to Co-Developed Collaboration Aptamers. The JPT shall
have and perform the responsibilities set forth in Section 2.2.4.

          2.2.2 Membership. Upon establishment of the JPT, each Party shall designate in
writing, in its sole discretion, [***] members to the JPT (which members shall be employees of such
Party or its Affiliates). Unless otherwise agreed by the Parties, one of ARCHEMIX’s designees
shall be designated by ARCHEMIX as the Chair of the JPT; provided, that, to the extent the JPT Term
is extended as provided in Section 2.2.1 beyond the Research Program Term, MERCK shall have the
right to designate one of MERCK’s designees as the Chair of the JPT. Each Party shall have the
right at any time to substitute individuals, on a permanent or temporary basis, for any of its
previously designated representatives to the JPT, by giving written notice to the other Party.
Initial designees of the Parties to the JPT shall be designated by each Party by written notice to
the other Party as soon as is reasonably practicable following the Effective Date.

          2.2.3 Meetings.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

31

 

          (a) Schedule of Meetings; Agenda. The JPT shall establish a schedule of times for
regular meetings, in no event less frequently than once per [***] during the JPT Term taking into
account, without limitation, the planning needs of the Research Program and its responsibilities.
In urgent cases special meetings may be convened by any member upon [***] days (or, if such meeting
is proposed to be conducted by teleconference, upon [***] days) written notice to the other
members; provided, that, (i) notice of any such special meeting may be waived at any time, either
before or after such meeting, and such waiver shall be the equivalent to the giving of a valid
notice hereunder, and (ii) attendance of any member at a special meeting shall constitute a valid
waiver of notice from such member. Regular and special meetings of the JPT may be held in person
or by teleconference or videoconference; provided, that, meetings held in person shall alternate
between the respective offices of the Parties. The chair of the JPT shall prepare and circulate to
each JPT member an agenda for each JPT meeting no later than one (1) week prior to such meeting.

          (b) Quorum; Voting; Decisions. At each JPT meeting, (i) the presence in person of at
least [***] members designated by each Party shall constitute a quorum and (ii) all members
designated by each Party who are present shall have [***] on all matters before the JPT at such
meeting. All decisions of the JPT shall be made by unanimous vote. Alternatively, the JPT may act
by written consent signed by at least [***] members designated by each Party. Whenever any action
by the JPT is called for hereunder during a time period in which the JPT is not scheduled to meet,
the chair of the JPT shall cause the JPT to take the action in the requested time period by calling
a special meeting or by circulating a written consent. Representatives of each Party or of its
Affiliates who are not members of the JPT (including, without limitation, the Patent Coordinators)
may attend JPT meetings as non-voting observers without the consent of the other Party. In the
event that the JPT is unable to resolve any matter before it, such matter shall be referred to the
JSC for decision, and, in case the JSC is unable to resolve the matter, it shall be resolved in
accordance with Section 2.1.6.

          (c) Minutes. The JPT shall keep minutes of its meetings that record all decisions and
all actions recommended or taken in reasonable detail. Drafts of the minutes shall be prepared and
circulated to the members of the JPT within a reasonable time after the meeting, not to exceed
[***] business days. The chair of the JPT shall have responsibility for the preparation and
circulation of draft minutes. Each member of the JPT shall have the opportunity to provide
comments on the draft minutes. The minutes shall be approved, disapproved and revised as necessary
at the next JPT meeting. Upon approval, final minutes of each meeting shall be circulated to the
members of the JPT by the chair of the JPT.

     2.2.4 Responsibilities. The JPT shall be responsible for (a) overseeing the conduct
and progress of the Research Program, the recommendation of Optimized Lead Compounds and the
recommendation of Development Candidates for which ARCHEMIX is responsible for performing ARCHEMIX
Development Activities; provided, that, any ARCHEMIX Development Activities with respect to
Co-Developed Collaboration Aptamers shall fall in the scope of responsibility of the Joint
Development Committee described in Section 2.3 below; and (b) overseeing the Development of
Optimized Lead Compounds and Development Candidates for which, and the conduct and progress of each
Development Program under which, ARCHEMIX is responsible for performing ARCHEMIX Development
Activities,

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

32

 

provided, that, any ARCHEMIX Development Activities with respect to Co-Developed Collaboration
Aptamers shall fall in the scope of responsibility of the Joint Development Committee described in
Section 2.3 below. Without limiting the generality of the foregoing, the JPT shall have the
following responsibilities:

          (a) preparing or directing the preparation of, approving, and recommending to the JSC for its
approval all Annual Research Plans;

          (b) preparing or directing the preparation of and approving amendments to JSC-approved Annual
Research Plans as it deems appropriate in furtherance of the objectives of the Research Program as
set forth in the Research Plan and, if any member of the JPT asserts that any such JPT-approved
amendment would change the objectives of such Annual Research Plan, submitting such amendment to
the JSC for its consideration;

          (c) monitoring the progress of each Annual Research Plan and of each Party’s activities
thereunder;

          (d) providing a forum for consensual decision making with respect to the Research Program;

          (e) reviewing data, reports or other information submitted by either Party with respect to
work conducted in the Research Program;

          (f) preparing for the JSC on at least a semi-annual basis a progress report for the Research
Program in reasonable detail and providing to the JSC such additional information as it may
request;

          (g) recommending amendments to the OLSC and/or DCSC as it deems appropriate in furtherance of
the objectives of the Research Program or Development Program, as applicable, as set forth in the
Research Plan or Development Plan, as applicable;

          (h) nominating Lead Compounds as Optimized Lead Compounds for acceptance by the JSC;

          (i) nominating Optimized Lead Compounds for which ARCHEMIX is responsible for performing
ARCHEMIX Development Activities as Development Candidates for acceptance by the JSC;

          (j) preparing or directing the preparation of, approving, and recommending to the JSC for its
approval all Annual Development Plans under which ARCHEMIX is responsible for performing
Development activities;

          (k) preparing or directing the preparation of and approving amendments to JSC-approved Annual
Development Plans under which ARCHEMIX is responsible for performing ARCHEMIX Development
Activities, as it deems appropriate in furtherance of the Development of Development Candidates
and, if any member of the JPT asserts

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

33

 

           that any such JPT-approved amendment would change the objectives of that Annual Development
Plan, submitting such amendment to the JSC for its consideration;

          (l) monitoring the progress of the Development of each Development Candidate for which
ARCHEMIX is performing ARCHEMIX Development Activities, in accordance with, and of each Party’s
activities under, the applicable Annual Development Plan;

          (m) providing a forum for consensual decision making with respect to the Development Program
under which ARCHEMIX is responsible for performing ARCHEMIX Development Activities;

          (n) reviewing data, reports or other information submitted by either Party with respect to
work conducted in the Development Program under which ARCHEMIX is responsible for performing
ARCHEMIX Development Activities;

          (o) preparing for the JSC on at least a semi-annual basis a progress report for the
Development Program under which ARCHEMIX is responsible for performing ARCHEMIX Development
Activities, in reasonable detail and providing to the JSC such additional information as it may
request; and

          (p) making any other decisions as may be delegated to the JPT pursuant to this Agreement or by
mutual written agreement of the Parties after the Effective Date and performing such activities as
may be delegated to the JPT pursuant to this Agreement, or by mutual written agreement of the
Parties after the Effective Date.

          2.2.5 Interests of the Parties. Notwithstanding any other provisions of this
Agreement, all decisions made and all actions taken by the JPT shall be made or taken in the best
interest of the Collaboration.

     2.3 Joint Development Committee.

          2.3.1 Establishment. As soon as practicable following the exercise by ARCHEMIX of a
Co-Development and Co-Promotion Option with respect to a Co-Developed Development Candidate in
accordance with Section 4.10.2, ARCHEMIX and MERCK shall, at ARCHEMIX’s written request, establish
the Joint Development Committee (the “JDC”) which shall have and perform the responsibilities set
forth in Section 2.3.4.

          2.3.2 Membership. Each Party shall designate, in its sole discretion, [***] members
to the JDC which members shall be employees of such Party or its Affiliates. Unless otherwise
agreed by the Parties, one of MERCK’s designees shall serve as the Chair of the JDC. Each Party
shall have the right at any time to substitute individuals, on a permanent or temporary basis, for
any of its previously designated representatives to the JDC by giving written notice to the other
Party. Initial designees of the Parties to the JDC shall be designated by each Party by written
notice to the other Party as soon as reasonably practicable following the exercise of a
Co-Development and Co-Promotion Option.

          2.3.3 Meetings.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

34

 

          (a) Schedule of Meetings; Agenda. The JDC shall establish a schedule of times for
regular meetings, taking into account, without limitation, the planning needs for the Co-Developed
Development Candidates and its responsibilities. In urgent cases, special meetings may be convened
by any member of the JDC upon [***] days (or, if such meeting is proposed to be conducted by
teleconference, upon [***] days) written notice to the other members; provided that (i) notice of
any such special meeting may be waived at any time, either before or after such meeting, and such
waiver shall be the equivalent to the giving of a valid notice hereunder, and (ii) attendance of
any member at a special meeting shall constitute a valid waiver of notice from such member. If
formed, in no event shall the JDC meet less frequently than twice per Calendar Year. Regular and
special meetings of the JDC may be held in person or by teleconference or videoconference;
provided, that, meetings held in person shall alternate between the respective offices of the
Parties. The Chair shall prepare and circulate to each JDC member an agenda for each JDC meeting
not later than one (1) week prior to such meeting.

          (b) Quorum; Voting; Decisions. At each JDC meeting, (i) the presence in person of at
least [***] member designated by each Party shall constitute a quorum and (ii) all members
designated by each Party who are present shall have [***] on all matters before the JDC at such
meeting. All decisions of the JDC shall be made by unanimous vote. Alternatively, the JDC may act
by written consent signed by at least [***] members designated by each Party. Whenever any action
by the JDC is called for hereunder during a time period in which the JDC is not scheduled to meet,
the Chair of the JDC shall cause the JDC to take the action in the requested time period by calling
a special meeting or by circulating a written consent. Representatives of each Party or of its
Affiliates who are not members of the JDC may attend JDC meetings as non-voting observers. The JDC
shall use reasonable efforts to reach agreement on any and all matters. In the event that, despite
such reasonable efforts, agreement on a particular matter cannot be reached by the JDC within [***]
days after the JDC first meets to consider such matter, then (i) in the case of an ARCHEMIX [***]%
Co-Development Sharing Percentage, the matter shall be referred to the JSC for resolution pursuant
to Section 2.1.6, and (ii) in the case of an ARCHEMIX [***]% Co-Development Sharing Percentage,
MERCK shall have the right to make the final decision, but shall only exercise such right in good
faith after full consideration of the positions of both Parties.

     2.3.4 Responsibilities. The JDC shall be responsible for overseeing the Development
by the Parties of Co-Developed Development Candidates in the Co-Development Territory; provided,
that, any such Development is consistent with the global Development Plan for each such
Co-Developed Development Candidate, for which MERCK ultimately bears responsibility. Without
limiting the generality of the foregoing, the JDC shall have the following responsibilities:

          (a) preparing or directing the preparation and recommending to the JSC for its approval of an
Annual Development Plan for each Co-Developed Development Candidate in the Co-Development
Territory;

          (b) monitoring the activities of, and reconciling issues between, the Parties with respect to
the Parties’ respective share of Co-Development Costs and Co-Development Regulatory Costs incurred
with respect to Co-Developed Development Candidates;

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

35

 

                (c) preparing or directing the preparation of and approving amendments to JSC-approved Annual
Development Plans with respect to Co-Developed Development Candidates as it deems appropriate in
furtherance of the objectives of the Development Program as set forth in the Annual Development
Plan and, if any member of the JDC asserts that any such JDC-approved amendment would change the
objectives of such Annual Development Plan, submitting such amendment to the JSC for its
consideration;

               (d) monitoring the progress of each Annual Development Plan with respect to Co-Developed
Development Candidates and of each Party’s activities thereunder;

                (e) providing a forum for consensual decision making with respect to the Development of
Co-Developed Development Candidates;

                (f) reviewing data, reports or other information submitted by either Party with respect to
work conducted in the Development of Co-Developed Development Candidates affecting the Co-Developed
Territory;

                (g) preparing for the JSC on at least a semi-annual basis a progress report for the
Development of Co-Developed Development Candidates in reasonable detail and providing to the JSC
such additional information as it may request; and

                (h) performing such activities as may be delegated to the JDC pursuant to this Agreement, or
by mutual written agreement of the Parties after the Effective Date.

          2.3.5 Interests of the Parties. Notwithstanding any other provisions of this
Agreement, all decisions made and all actions taken by the JDC shall be made or taken in the best
interest of the Collaboration.

     2.4 Alliance Management. Within [***] days of the Effective Date, each Party shall
appoint a person who shall oversee contact between the Parties for all matters related to the
Collaboration between meetings of the JSC and JPT and shall have such other responsibilities as the
Parties may mutually agree in writing after the Effective Date (each, a “Collaboration Manager”).
Each Party may replace its Collaboration Manager at any time by notice in writing to the other
Party.

3. RESEARCH PROGRAM

     3.1 Implementation of the Research Program. The objectives of the Research Program
shall be the identification of Lead Compounds for nomination by the JPT to the JSC for approval as
Optimized Lead Compounds pursuant to this Agreement through the conduct by the Parties of separate
Research Projects. MERCK shall provide ARCHEMIX with access to MERCK Background Technology that
MERCK determines in good faith to be necessary or useful in the performance of the Research
Program.

     3.2 Technology Transfer Activities. During the period commencing [***] days from the
Effective Date, and, unless otherwise agreed by ARCHEMIX and MERCK, ending [***] months thereafter
(the “Technology Transfer Term”), ARCHEMIX shall provide MERCK with the training, documentation and
other information relating to the use of the SELEX Process

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to
to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

36

 

and the SELEX Technology set forth in the SELEX Technology Transfer Plan (the “Technology
Transfer Activities”) solely for the purpose of enabling MERCK to conduct Target Validation
Activities. Without limiting the generality of the foregoing, ARCHEMIX agrees to be available for
consultation and advice upon MERCK’s reasonable request after the initial training period at the
ARCHEMIX Facility set forth in the SELEX Technology Transfer Plan. MERCK shall pay ARCHEMIX the
FTE Cost of all FTEs used by ARCHEMIX in performing Technology Transfer Activities and reimburse
ARCHEMIX for the Third Party Costs incurred by ARCHEMIX in connection with its performance of the
Technology Transfer Activities (the “Technology Transfer Costs”) as set forth in Section 6.4.1(a)
and as described more fully in the SELEX Technology Transfer Plan.

     3.3 Research Projects. The Research Program shall be implemented through the conduct
of up to twelve (12) separate Research Projects, each of which will involve an individual Program
Target, as described in this Article 3, and each of which will be subject to a separate Annual
Research Plan, as described in Section 3.4.

     3.4 Annual Research Plans. The initial Annual Research Plans and budgets for the
MERCK Funded Research Projects and, if applicable, the MERCK Internal Research Projects shall be
developed by the JPT, and approved by the JSC and attached as exhibits to the minutes of the JSC
meeting at which such JSC approval is obtained as soon as practicable after the acceptance by
ARCHEMIX of the applicable Target proposed by MERCK for inclusion on the Target Exclusivity List as
provided in Sections 3.8.1 and 3.8.2. The JPT shall manage the preparation of the subsequent
Annual Research Plans in a manner designed to obtain JSC approval no later than [***] days prior to
the end of the then-current Contract Year. Each Annual Research Plan shall: (a) set forth (i) the
research objectives and activities to be performed for the Research Project and Contract Year
covered by the Annual Research Plan with reasonable specificity, (ii) the research plans and
protocols to be employed to complete each stage of the applicable Research Project, (iii) changes
to the OLSC and any other criteria that the JPT will utilize to evaluate the results of the
Research Project to nominate Optimized Lead Compounds, (iv) the Party that shall be responsible for
performing such activities, (v) a timeline and budget for such activities (including Third Party
Costs to be incurred for outsourced studies managed by ARCHEMIX or MERCK), and (vi) with respect to
ARCHEMIX Research Activities, the number of FTEs estimated to be required to perform such
activities; and (b) shall be consistent with the other terms of this Agreement. Without limiting
the generality of the foregoing, the objectives of each Annual Research Plan shall include, as
appropriate from time to time during the Research Program Term, conducting the necessary research
activities to identify Lead Compounds or to determine whether Lead Compounds should be nominated to
the JSC as Optimized Lead Compounds. Any Annual Research Plan may be amended from time to time by
the JPT pursuant to Section 2.2.4 or by the JSC pursuant to 2.1.4. Each amendment, modification
and update to the Annual Research Plan shall include the resulting changes to the budget, including
the number of FTEs to be utilized by ARCHEMIX, shall be set forth in a written document prepared
by, or at the direction of, the JPT and approved by the JSC, shall specifically state that it is an
amendment, modification or update to the Annual Research Plan and shall be attached to the minutes
of the meeting of the JSC at which such amendment, modification or update was approved by the JSC.
Without limiting the nature or frequency of any other amendments, modifications or updates to the
Annual Research Plan that may be approved by the JSC, the Annual Research Plan shall be updated at
least once prior to the end of

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

37

 

each Contract Year to describe the research activities to be carried out by each Party during
the applicable Contract Year during the Research Program Term in conducting the Research Program
pursuant to this Agreement. Notwithstanding anything to the contrary in this Agreement, ARCHEMIX
shall have sole responsibility for all research activities associated with ARCHEMIX Internal
Program Targets and neither MERCK nor the JSC shall have any right to prepare, review or approve
any research plans covering any Optimized Lead Compound researched and/or developed under an
ARCHEMIX Internal Research Project, until such time as MERCK pays the Option Exercise Fee
applicable to the designation of such Optimized Lead Compound as a Development Candidate pursuant
to Section 6.3, subject to MERCK’s right to provide an Additional Research Request pursuant to
Section 3.9.2.

     3.5 Conduct of Research Program.

          3.5.1 ARCHEMIX Responsibilities. During the Research Program Term, ARCHEMIX shall use
Commercially Reasonable Efforts to conduct the ARCHEMIX Research Activities using the number of
FTEs set forth in the Annual Research Plan.

          3.5.2 MERCK Responsibilities. During the Research Program Term, MERCK shall: (a) pay
ARCHEMIX (i) the applicable FTE Cost and the Technology Transfer Costs for all Technology Transfer
Activities and (ii) the applicable Quarterly FTE Payment for all Research Program Activities in
accordance with Section 6.4.1(b); (b) commit such resources as are reasonably necessary to conduct
the MERCK Research Activities set forth in the Annual Research Plan; and (c) use Commercially
Reasonable Efforts to conduct the MERCK Research Activities, if any, set forth in the Annual
Research Plan.

          3.5.3 Compliance and Funding. Each Party shall perform its obligations under each
Annual Research Plan in compliance in all material respects with all Applicable Laws. For purposes
of clarity, with respect to each activity performed under an Annual Research Plan that will or
would reasonably be expected to generate data to be submitted to a Regulatory Authority in support
of a Regulatory Filing or Drug Approval Application, the Party performing such activity shall
comply in all material respects with the regulations and guidance of the FDA that constitute Good
Laboratory Practice or Good Manufacturing Practice (or, if and as appropriate under the
circumstances, International Conference on Harmonization (ICH) guidance or other comparable
regulation and guidance of any Regulatory Authority in any country or region in the Territory).
Each Party shall be solely responsible for paying the salaries and benefits of its employees.

          3.5.4 Cooperation. Scientists at ARCHEMIX and MERCK shall cooperate in the
performance of the Research Program and, subject to the terms of this Agreement and any
confidentiality obligations to Third Parties, shall exchange such data, information and materials
as are reasonably necessary for the other Party to perform its obligations under any Annual
Research Plan.

     3.6 Records

          3.6.1 Record Keeping.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

38

 

               (a) Research Program Records. Each Party shall maintain complete and accurate records
of its activities in the Research Program in sufficient detail, in good scientific manner and
otherwise in a manner that reflects all work done and results achieved. Subject to Article 7, each
Party shall provide the other Party with access during normal business hours and upon reasonable
advance notice to review such records to the extent reasonably required for such other Party’s
performance of its obligations under this Agreement; provided, that, the non-reviewing Party may
redact information not relevant to the Research Program prior to such review. Notwithstanding the
foregoing, MERCK shall not have the right to review any records that relate to any Failed
Compounds, Waived Compounds or Terminated Compounds.

               (b) Record Keeping Policies. Without limiting the generality of Section 3.6.1(a),
each Party agrees to maintain a policy that requires its employees and consultants to record and
maintain all data and information developed during the Research Program.

          3.6.2 Reports. ARCHEMIX shall keep the JPT regularly informed of the progress of the
Research Program. Without limiting the generality of the foregoing, ARCHEMIX shall, at least once
each [***] during the Research Program Term, (a) provide reports to the JPT in reasonable detail
regarding the status of its activities under the Research Program, (b) advise the JPT of its
identification of Lead Compounds and provide the JPT with any supporting data applicable to such
Lead Compounds, (c) provide the JPT with the results of activities conducted in the Research
Program with respect to each Lead Compound so as to enable the JPT to determine whether such Lead
Compound meets the OLSC and should be proposed to the JSC as an Optimized Lead Compound, (d)
provide the JPT with the results of activities conducted in the Development Program, if any, with
respect to each Optimized Lead Compound so as to enable the JPT to determine whether such Optimized
Lead Compound meets the DCSC and should be proposed to the JSC as a Development Candidate, (e)
provide the JPT with such additional information that it has in its possession as may be reasonably
requested from time to time by the JPT, and (f) provide MERCK, on or before [***] days from the
termination or expiration of the Research Program Term, with a final report regarding all ARCHEMIX
Research Activities conducted by ARCHEMIX during the Research Program Term to the extent not
previously included in the reports described above. MERCK shall (i) provide the JPT, at least once
per [***], with reports in reasonable detail regarding the status of all MERCK Research Activities
and such additional information that it has in its possession as may be reasonably requested from
time to time by the JPT, (ii) provide the JPT with the results of activities conducted in the
Development Program under which ARCHEMIX is responsible for performing Development activities with
respect to each Optimized Lead Compound so as to enable the JPT to determine whether such Optimized
Lead Compound meets the DCSC and should be proposed to the JSC as a Development Candidate, and
(iii) provide ARCHEMIX, on or before [***] days from the termination or expiration of the Research
Program Term, with a final report regarding all MERCK Research Activities conducted by MERCK during
the Research Program Term to the extent not previously included in the reports described above.

     3.7  Designation of Program Targets.

          3.7.1 MERCK Funded Program Targets.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

39

 

               (a) MERCK Funded Target Proposals. Subject to Section 3.7.1(b) below, during the
Research Program Term, MERCK shall have the right, in its sole discretion, to propose [***] Targets
that have application within the Target Selection Field for inclusion on the Target Exclusivity
List as MERCK Funded Program Targets by providing written notice to the JSC and ARCHEMIX, which
shall include the data and information demonstrating that the Target has potential for development
within the Target Selection Field. ARCHEMIX shall accept or reject the proposed Target only as
specified under Section 3.8.2. To the extent ARCHEMIX accepts the proposed Target as a MERCK
Funded Program Target as specified under Section 3.8.2, the Parties shall (i) promptly update the
Target Exclusivity List to include such MERCK Funded Program Target (ii) direct the JPT to prepare
and submit to the JSC for its approval an Annual Research Plan with respect to such MERCK Funded
Program Target as soon as practicable thereafter and in any event prior to the initiation of any
ARCHEMIX Research Activities with respect to such MERCK Funded Program Target; (iii) direct the JPT
to review and, if necessary, revise the existing OLSC and DCSC for such MERCK Funded Program Target
as soon as practicable thereafter and in any event prior to the initiation of any ARCHEMIX Research
Activities with respect to such MERCK Funded Program Target; and (iv) commence the Research Project
with respect to such MERCK Funded Program Target in accordance with such Annual Research Plan.

               (b) Timing and Type of MERCK Funded Program Targets. Notwithstanding anything to the
contrary in Section 3.7.1(a), the Parties hereby agree that (i) the first [***] MERCK Funded
Program Targets will be added to the Target Exclusivity List no later than [***] months from the
Effective Date; (ii) the final [***] MERCK Funded Program Targets will be added to the Target
Exclusivity List no later than [***] months from the Effective Date; (iii) MERCK will request the
initiation of the first [***] MERCK Funded Research Projects within [***] months from [***]; (iv)
MERCK will request the initiation of the [***] MERCK Funded Research Project in the [***] Contract
Year and in any event no later than [***] months from [***]; (v) MERCK will request the initiation
of the [***] and [***] MERCK Funded Research Projects in the [***] Contract Year and in any event
no later than [***] months from [***] and (vi) not less than three (3) MERCK Funded Program Targets
shall be for oncology Indications. ARCHEMIX shall use Commercially Reasonable Efforts to initiate
each such Research Project as soon as is reasonably possible following its receipt of the
applicable initiation request by MERCK.

               (c) Minimum FTEs. Notwithstanding anything to the contrary in this Agreement, for
each Research Project commenced during the Research Program Term with respect to a MERCK Funded
Program Target in accordance with this Section 3.7.1, MERCK shall request and fund a number of
ARCHEMIX FTEs during the term of each such Research Project [***] to the Minimum FTE Funding
Commitment.

          3.7.2 MERCK Internal Program Targets.

               (a) MERCK Internal Target Proposals. Subject to Section 3.7.2(b) below, during the
Research Program Term, MERCK shall have the right, in its sole discretion, to propose up to five
(5)Targets that have application within the Target Selection Field for inclusion on the Target
Exclusivity List as MERCK Internal Program Targets by providing written notice to the JSC and
ARCHEMIX, which shall include the data and information demonstrating that the

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

40

 

Target has potential
for development within the Target Selection Field. ARCHEMIX shall accept or reject the proposed
Target only as specified under Section 3.8.2.

               (b) Timing and Type of MERCK Internal Program Targets. Notwithstanding anything to the
contrary in Section 3.7.2(a), the Parties hereby agree that (i) the first [***] MERCK Internal
Program Targets will be proposed by MERCK no later than [***] months from the [***] of the [***];
(ii) the final [***] MERCK Internal Program Targets will be proposed by MERCK no later than [***]
months from the [***] of the [***] and (iii) at least three (3) MERCK Internal Program Targets
shall be for oncology Indications.

               (c) Request for ARCHEMIX Research Activities. MERCK shall have the right, at any time
on or before the [***] of the [***] of the [***], to request that ARCHEMIX conduct ARCHEMIX
Research Activities with respect to each of the MERCK Internal Program Targets by providing written
notice to ARCHEMIX (the “MERCK Internal Program Target Request”). Following the receipt by
ARCHEMIX of each such MERCK Internal Program Target Request, the Parties shall (i) promptly update
the Target Exclusivity List to include such MERCK Internal Program Target (ii) direct the JPT to
prepare and submit to the JSC for its approval an Annual Research Plan with respect to such MERCK
Internal Program Target as soon as practicable thereafter and in any event prior to the initiation
of any ARCHEMIX Research Activities with respect to such MERCK Internal Program Target; (iii)
direct the JPT to review and, if necessary, revise the existing OLSC and DCSC for such MERCK
Internal Program Target as soon as practicable thereafter and in any event prior to the initiation
of any ARCHEMIX Research Activities with respect to such MERCK Internal Program Target; and (iv)
commence the Research Project with respect to such MERCK Internal Program Target in accordance with
such Annual Research Plan. ARCHEMIX shall use Commercially Reasonable Efforts to initiate any such
ARCHEMIX Research Activities as soon as is reasonably possible following its receipt of the
applicable request by MERCK.

               (d) Minimum FTEs. Notwithstanding anything to the contrary in this Agreement, for
each Research Project commenced during the Research Program Term with respect to a MERCK Internal
Program Target in accordance with this Section 3.7.2 (c), MERCK shall request and fund a number of
ARCHEMIX FTEs during the term of each such Research Project [***] to the Minimum FTE Funding
Commitment.

     3.8 Replacement of Program Targets; Target Exclusivity List; ARCHEMIX Retained Rights.

          3.8.1 Replacement of Program Targets. MERCK shall have the right (a) to replace up to
[***] [***] Program Target or [***] Program Target on the Target Exclusivity List per [***] at any
time during the first [***] Contract Years, for a total of [***] replacements, and (b) to replace
any [***] Program Target that is included on the Target Exclusivity List [***] during the Research
Program Term, solely to the extent that such [***] Program Target has been [***] as a [***]. For
purposes of clarity and notwithstanding the rights of MERCK to replace
Program Targets as provided in this Section 3.8.1, (a) under no circumstances shall ARCHEMIX
be obligated to [***] any Target for inclusion on the Target Exclusivity List and (b) unless and
until a Target is included as a Program Target on the Target Exclusivity List, ARCHEMIX shall be
free to research, develop and commercialize such Target for any and all purposes, alone or together
with any Third Party.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

41

 

          3.8.2 Target Exclusivity List. The Parties hereby acknowledge and agree that (a)
[***] Targets have been designated as Program Targets as of the Signing Date and (b) MERCK shall
have the right to have up to [***] MERCK Funded Program Targets and up to [***] MERCK Internal
Program Targets, for an aggregate of up to [***] such Targets, designated as Program Targets on the
Target Exclusivity List at any time during the Research Program Term. Subject to the foregoing, to
the extent MERCK proposes a Target for inclusion on the Target Exclusivity List as described in
Sections 3.7.1(a) or 3.7.2(a) or proposes that a [***] be replaced by a Target as described in
Section 3.8.1, MERCK shall provide written notice to ARCHEMIX. ARCHEMIX shall accept or reject the
proposed Target within [***] days after receipt of each such notice from MERCK. A Target proposed
by MERCK for inclusion on the Target Exclusivity List shall only be rejected by ARCHEMIX if prior
to MERCK’s notice: (A) ARCHEMIX is prohibited by an executed contract from licensing aptamers
against such proposed Target or its natural ligand(s), to MERCK, (B) ARCHEMIX is in active
negotiations, as demonstrated by written term sheets with a Third Party with respect to a license,
collaboration or similar agreement relating to aptamers against such Target or its natural
ligand(s), or (C) ARCHEMIX is researching or developing, for its own benefit, aptamers against such
Target or its natural ligand(s) under a bona fide internal research or development program against
such Target, as evidenced by the [***] and [***] by the applicable ARCHEMIX [***] of such Target
for inclusion in such internal research or development program. In addition to the reasons
specified in the foregoing clauses (A)-(C), ARCHEMIX may reject a Target proposed by MERCK for
inclusion on the Target Exclusivity List if such Target [***] the Target Selection Field; provided,
that, ARCHEMIX shall have not have the right to reject a Target for such reason if such Target was
[***] by the appropriate [***] MERCK for Indications within the Target Selection Field. ARCHEMIX
shall give MERCK prompt written notice during the Research Program Term if any of the restrictions
on any Target that is rejected by ARCHEMIX pursuant to the foregoing clause (A), (B) or (C) lapse,
or are otherwise terminated, such that the previously rejected Target becomes eligible for
inclusion on the Target Exclusivity List.

          3.8.3 ARCHEMIX Retained Rights. Notwithstanding anything to the contrary in this
Agreement, ARCHEMIX shall have the right, in its sole discretion, to conduct internal research
and/or development activities with respect to any Program Target until such time as a Research
Project is commenced with respect to such Program Target; provided, that, ARCHEMIX shall provide
MERCK with periodic updates as to the results of such activities as described in Section 3.6.2.

     3.9 ARCHEMIX Internal Program Targets.

          3.9.1 Compound Candidate Options.

               (a) Compound Candidate Notice; Evaluation Period. During the Research Program Term,
ARCHEMIX shall provide MERCK with written notice of its [***] identification of any Aptamer(s) in
the conduct of any ARCHEMIX Internal Research Project that ARCHEMIX believes qualifies as an
Optimized Lead Compound or Development Candidate for purposes of, and in accordance with, Sections
3.10.2 and 3.11 (each, a “Primary Compound Candidate”), which notice shall (i) identify the
applicable ARCHEMIX Internal Program Target and Primary Compound Candidate, and (ii) summarize
briefly the results of the

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

42

 

non-clinical studies and assessments on such Primary Compound Candidate
completed by or on behalf of ARCHEMIX under the applicable ARCHEMIX Internal Research Project (the
“Primary Compound Candidate Notice”). As soon as practicable following the issuance of each
Primary Compound Candidate Notice, but in no event later than [***] days from the issuance of each
Primary Compound Candidate Notice, the Parties shall execute a material transfer agreement in the
form attached hereto as Schedule 12 (each, an “MTA”) to allow MERCK to evaluate its
interest in the Primary Compound Candidate for a period of up to [***] months (each such period, a
“Primary Compound Candidate Evaluation Period”). Subject to the foregoing, during the Primary
Compound Candidate Evaluation Period applicable to each Primary Compound Candidate, (i) MERCK shall
have the option (each, a “Primary Compound Candidate Option”) to designate such Primary Compound
Candidate as an Optimized Lead Compound or Development Candidate, as the case may be, for purposes
of this Agreement as provided in Section 3.9.4 and (ii) ARCHEMIX shall use Commercially Reasonable
Efforts to conduct the ARCHEMIX Internal Research Project covering such Primary Compound Candidate.

               (b) Identification of Backup Compound Candidates. In the event that ARCHEMIX, in the
conduct of the ARCHEMIX Internal Research Project with respect to, and [***] the [***] applicable
to, a given Primary Compound Candidate, identifies any additional Aptamer(s) that ARCHEMIX believes
qualifies as an Optimized Lead Compound or Development Candidate for purposes of, and in accordance
with, Sections 3.10.2 and 3.11 (each a “Backup Compound Candidate”), then (i) ARCHEMIX shall
provide MERCK with written notice which notice shall (A) identify the applicable ARCHEMIX Internal
Program Target and Backup Compound Candidate, and (B) summarize briefly the results of the
non-clinical studies and assessments on such Backup Compound Candidate completed by or on behalf of
ARCHEMIX under the applicable ARCHEMIX Internal Research Project (the “Backup Compound Candidate
Notice”). As soon as practicable following the issuance of each Backup Compound Candidate Notice
but in no event later than [***] days from the issuance of each Backup Compound Candidate Notice,
the Parties shall execute an amendment to the MTA applicable to the Primary Compound Candidate to
allow MERCK to evaluate its interest in the Backup Compound Candidate for a period [***] (i) the
[***] term of the applicable Primary Compound Candidate Evaluation Period (to the extent the Backup
Compound Candidate is an Optimized Lead Compound) and (ii) up to [***] months (to the extent the
Backup Compound Candidate is a [***]) (the “Backup Compound Candidate Evaluation Period”). Subject
to the foregoing, during the applicable Backup Compound Candidate Evaluation Period, (i) MERCK
shall have the option (each, a “Backup Compound Candidate Option”) to designate such Backup
Compound Candidate as an Optimized Lead Compound or Development Candidate, as the case may be, for
purposes of this Agreement as provided in Section 3.9.4 and (ii) ARCHEMIX shall use Commercially
Reasonable Efforts to conduct the ARCHEMIX Internal Research Project
covering such Backup Compound Candidate. For purposes of clarity, with respect to the [***]
Target, Backup Compound Candidates include Aptamers directed against [***] (if any).

               (c) No Other Rights. For purposes of clarity, MERCK shall not have a Compound
Candidate Option for any Compound other than a Primary Compound Candidate or Backup Compound
Candidate that is identified by ARCHEMIX in a Primary Compound Candidate Notice or a Backup
Compound Candidate Notice pursuant to Sections 3.9.1(a) and (b).

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

43

 

               (d) Responsibility for Costs. Until such time as MERCK exercises a Compound Candidate
Option with respect to a Compound Candidate, (i) ARCHEMIX shall be [***] for [***] costs and
expenses incurred by it in conducting the applicable ARCHEMIX Internal Research Project and (ii)
MERCK shall be [***] for [***] costs and expenses incurred by it in evaluating such Compound
Candidate. Upon MERCK’s exercise of a Compound Candidate Option with respect to a Compound
Candidate that is a Development Candidate, MERCK shall be [***] for [***] costs and expenses
incurred by ARCHEMIX in conducting ARCHEMIX Research Activities with respect to such Compound
Candidate.

          3.9.2 Request for Additional Lead Compound Candidate. 

               (a) Additional Research Request. MERCK shall have the right, upon exercising a
Compound Candidate Option applicable to a Compound Candidate in accordance with Section 3.9.1(a) or
(b), to request that ARCHEMIX conduct ARCHEMIX research and/or development activities in order to
further develop such Compound Candidate (“Requested ARCHEMIX Activities”) and/or to request that
ARCHEMIX conduct ARCHEMIX De Novo Research Activities under the applicable ARCHEMIX Internal
Research Project (each, an “Additional Research Request”) by providing written notice to ARCHEMIX.
For purposes of clarity, with respect to the [***] Target, ARCHEMIX De Novo Research Activities
include any such activities wherein [***] is the Target.

               (b) Conduct of Additional Research Activities. Following the receipt by ARCHEMIX of
each such Additional Research Request, ARCHEMIX shall use Commercially Reasonable Efforts to
conduct the Requested ARCHEMIX Activities and/or ARCHEMIX De Novo Research Activities and MERCK
shall fund the conduct of such ARCHEMIX Research Activities and/or the ARCHEMIX De Novo Research
Activities in accordance with Section 6.4.1(b). Notwithstanding anything to the contrary in this
Section 3.9.2, if MERCK does not exercise a Compound Candidate Option applicable to a Compound
Candidate on or before the expiration of the applicable Evaluation Period, ARCHEMIX shall have the
right, in its sole discretion, to continue to conduct the ARCHEMIX Internal Research Project with
respect to such Compound Candidate.

               (c) De Novo Development Candidates. In the event that MERCK requests any ARCHEMIX De
Novo Research Activities, any Collaboration Aptamers resulting from such ARCHEMIX De Novo Research
Activities shall be treated hereunder in all respects as Collaboration Aptamers resulting from a
MERCK Funded Program Target; provided, however,
the [***] associated with [***], if applicable, shall be payable as set forth in Section
6.5.1(a) for any such Collaboration Aptamers.

               (d) Minimum Funding Obligation. Notwithstanding anything to the contrary in this
Agreement, for each Research Project commenced during the Research Program Term with respect to an
ARCHEMIX Internal Program Target in accordance with this Section 3.9.2, MERCK shall request and
fund a number of ARCHEMIX FTEs during the term of each such Research Project [***] the Minimum FTE
Funding Commitment.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

44

 

          3.9.3 ARCHEMIX De Novo Research Activities; Additional Funding Option. In that event
that, (a) on or before the expiration of the Evaluation Period applicable to any Compound Candidate
that is a Development Candidate, MERCK fails to exercise the Compound Candidate Option applicable
to such Compound Candidate; (b) ARCHEMIX ceases to conduct any development activities with respect
to any Aptamers identified on or before the expiration of the Evaluation Period or an Aptamer
Derived therefrom; and (c) ARCHEMIX initiates ARCHEMIX De Novo Research Activities during the
Research Program Term against the applicable ARCHEMIX Internal Program Target, ARCHEMIX shall
provide MERCK with written notice thereof (the “ARCHEMIX Internal Program Target Notice”). MERCK
shall have the right to [***] any such ARCHEMIX De Novo Research Activities by providing written
notice to ARCHEMIX within [***] days of its receipt of such ARCHEMIX Internal Program Target
Notice. In the event that ARCHEMIX determines, in its sole discretion, to initiate such ARCHEMIX
De Novo Research Activities with respect to the [***] Target and MERCK elects to [***] such
activities, then, to the extent an Optimized Lead Candidate or Development Candidate is identified
through the conduct of such ARCHEMIX De Novo Research Activities, (a) the [***] associated with
[***] shall be applicable to any such Development Candidate and (b) the [***] set forth in Section
[***] and the [***] set forth in Section [***] [***] from such [***]. For purposes of clarity,
with respect to the [***] Target, ARCHEMIX shall provide notice to MERCK upon the initiation of
ARCHEMIX De Novo Research Activities against [***] in accordance with this Section 3.9.3.

          3.9.4 Exercise of Compound Candidate Options. MERCK may exercise any Compound
Candidate Option by giving written notice of exercise to ARCHEMIX and paying the [***] and/or
[***], as applicable, as set forth in Section 6.3 at [***] [***] [***] to the [***] of the [***]
[***] applicable to such Compound Candidate Option; provided, that, (a) MERCK agrees that if it
determines not to exercise a Compound Candidate Option prior to expiration of the applicable
Evaluation Period, it shall in good faith provide written notice to ARCHEMIX promptly upon such
determination and (b) the date on which any such notice is given shall constitute the last
day of the applicable Evaluation Period. Upon the exercise by MERCK of each Compound Candidate
Option, (a) the Compound Candidate that is the subject of the Compound Candidate Option shall
become an Optimized Lead Compound or Development Candidate, as the case may be, for purposes of
this Agreement, (b) solely to the extent the Compound Candidate, is or thereafter becomes a
Development Candidate, (i) MERCK shall be granted the licenses set forth in Sections 8.1.1 and 8.2
with respect to such Development Candidate, and (ii) MERCK shall have an obligation to use
Commercially Reasonable Efforts to Develop such Development Candidate and to Commercialize a
Product Derived from such
Development Candidate in accordance with Section 4.6; and (c) the ARCHEMIX Internal Program
Target shall be included on the Target Exclusivity List.

          3.9.5 Termination of Rights For Failure to Exercise. If, on or before the expiration
of the applicable Evaluation Period with respect to a Compound Candidate identified in the conduct
of an ARCHEMIX Internal Research Project, MERCK fails to exercise the Compound Candidate Option
applicable to such Compound Candidate, then (i) MERCK shall have no further rights with respect to
the applicable ARCHEMIX Internal Program Target and any aptamers (including all Compound Candidates
and Back-Up Compound Candidates and any Aptamers Derived therefrom) that are the subject of such
ARCHEMIX Internal Research Project

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

45

 

and (ii) ARCHEMIX shall thereafter have the right, itself or
with, for the benefit of, or sponsored by, any Third Party, to research, develop and commercialize
such ARCHEMIX Internal Program Target and any aptamers (including all Compound Candidates and
Back-Up Compound Candidates and any Aptamers Derived therefrom) that are the subject of such
ARCHEMIX Internal Research Project for any and all purposes within or outside of the Field and/or
to grant a license or other rights to any Third Party to research, develop and commercialize such
ARCHEMIX Internal Program Target, and any aptamers (including all Compound Candidates and Back-Up
Compound Candidates and any Aptamers Derived therefrom) that are the subject of such ARCHEMIX
Internal Research Project for any and all purposes within or outside of the Field.

          3.9.6 Development Candidate Opt-In Requirement. Notwithstanding anything to the
contrary herein, upon ARCHEMIX’s [***] of a Development Candidate with respect to a Primary
Compound Candidate or a Back-Up Compound Candidate for a given ARCHEMIX Internal Program Target,
MERCK shall be required, within [***] days of MERCK’s receipt of such [***], or until the [***]
[***] the [***] applicable to such Primary Compound Candidate or Back-Up Compound Candidate,
whichever is later, to [***] the [***]. If MERCK fails to [***] the [***] as specified above, (i)
MERCK shall have no further rights to the applicable ARCHEMIX Internal Program Target, Primary
Compound Candidate and/or Backup Compound Candidate and any other aptamers directed against such
Target and (ii) ARCHEMIX shall thereafter have the right, itself or with, for the benefit of, or
sponsored by, any Third Party, to research, develop and commercialize such ARCHEMIX Internal
Program Target, Primary Compound Candidate and/or Backup Compound Candidate and any other aptamers
directed to such ARCHEMIX Internal Program Target for any and all purposes within or outside of the
Field and/or to grant a license or other rights to any Third Party to research, develop and
commercialize such ARCHEMIX Internal Program Target, Primary Compound Candidate and/or Backup
Compound Candidate and any other aptamers (including all Collaboration Aptamers and any Aptamers
Derived therefrom) directed to such ARCHEMIX Internal Program Target for any and all purposes
within or outside of the Field, subject only to Section 3.9.3.

          3.9.7 Replacement of the [***] ARCHEMIX Internal Program Target. In the event
ARCHEMIX is unable to identify any [***] it reasonably believes qualifies as an [***] for the [***]
ARCHEMIX Internal Program Target, (i) ARCHEMIX shall be required to initiate internal research
efforts during the Research Program Term against [***] Target having application against an [***]
Indication, (ii) within [***] days of initiation of such internal research efforts ARCHEMIX shall
provide written notice of such efforts and the identity of such
Target to MERCK, and (iii) such Target shall be deemed to replace [***] on Schedule 2B as an
ARCHEMIX Internal Program Target and shall be treated as such for all purposes under this Agreement
after the date of notice provided for in this Section 3.9.7.

     3.10 Identification of Lead Compounds and Optimized Lead Compounds.

          3.10.1 Lead Compounds. ARCHEMIX shall use Commercially Reasonable Efforts in good
faith to perform the SELEX Process to identify Lead Compounds for the MERCK Funded
Program Targets or, as applicable, the MERCK Internal Program Targets or

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

46

 

any ARCHEMIX Internal
Program Target for which MERCK has provided an Additional Research Request and paid the applicable
[***], in accordance with each Annual Research Plan, as amended.

          3.10.2 Optimized Lead Compounds. Within [***] days after its receipt of each report
from a Party pursuant to Section 3.6.2 identifying a Lead Compound for a MERCK Funded Program
Target or, as applicable, a MERCK Internal Program Target, or an ARCHEMIX Internal Program Target
for which MERCK has provided an Additional Research Request and paid the applicable Option Fee
and/or Option Exercise Fee, as meeting the applicable OLSC (or which either Party reasonably
believes should be an Optimized Lead Compound), the JPT shall review the data and information and
determine whether to nominate the Lead Compound to the JSC for designation as an Optimized Lead
Compound. If the JPT elects to nominate any such Lead Compound as an Optimized Lead Compound, the
JPT shall promptly furnish all available information to the JSC. The JSC shall consider such
nomination within [***] days, and if the JSC approves the nomination of the Lead Compound, such
Lead Compound shall be deemed to be an Optimized Lead Compound for purposes of this Agreement.

     3.11 Development Candidates. Within [***] days after either Party reasonably
concludes based upon available Research Project reports that an Optimized Lead Compound for a MERCK
Funded Program Target or, as applicable, a MERCK Internal Program Target or any ARCHEMIX Internal
Program Target for which MERCK has provided an Additional Research Request and paid the applicable
Option Fee and/or Option Exercise Fee, meets the applicable DCSC, the JPT shall review the data and
information and determine whether to nominate such Optimized Lead Compound for designation as a
Development Candidate. If the JPT elects to nominate any such Optimized Lead Compound as a
Development Candidate, the JPT shall promptly furnish all available information to the JSC. The
JSC shall consider such nomination within [***] days so as to enable MERCK to determine whether or
not to continue Development of such Optimized Lead Compound, and if the Optimized Lead Compound
meets the DCSC and MERCK accepts such Optimized Lead Compound for further Development, such
Optimized Lead Compound shall be deemed to be a Development Candidate for purposes of this
Agreement.

     3.12 MERCK Decision Not to Go Forward. MERCK has the right to determine [***] not to
continue the Development and Commercialization of a Development Candidate against a specific
Program Target.

     3.13 Supply of Proprietary Materials. From time to time during the Research Program
Term, either Party (the “Transferring Party”) may supply the other Party (the “Recipient Party”)
with Proprietary Materials of the Transferring Party for use in the Research Program. In
connection therewith, each Recipient Party hereby agrees that (a) it shall not use such Proprietary
Materials for any purpose other than exercising its rights or performing its obligations under this
Agreement; (b) it shall use such Proprietary Materials only in compliance with all Applicable Laws;
(c) it shall not transfer any such Proprietary Materials to any Third Party without the prior
written consent of the Transferring Party, except as expressly permitted by this Agreement; (d) the
Recipient Party shall not acquire any right, title or interest in or to such Proprietary Materials
as a result of such supply by the Transferring Party; and (e) upon the expiration or termination of

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

47

 

the Research Program Term, the Recipient Party shall, if and as instructed by the Transferring
Party, either destroy or return any such Proprietary Materials that are not the subject of the
grant of a continuing license hereunder.

     3.14 Research Program Term. The Research Program shall commence on the Effective Date
and shall continue until the last day of the Research Program Term.

     3.15 Conduct of Target Validation Activities. Notwithstanding anything to the
contrary herein, prior to performing any Target Validation Activities with respect to a Target
MERCK shall (a) provide ARCHEMIX’s outside counsel (“Counsel”) with a written notice (each, a
“Target Validation Notice”) identifying the Target(s) that would be the subject of such Target
Validation Activities and, simultaneously therewith, (b) provide ARCHEMIX with written notice that
it has provided a Target Validation Notice to Counsel. ARCHEMIX shall use commercially reasonable
efforts to ensure that Counsel provides MERCK with a written response (each, a “Target Validation
Response”) within [***] days of Counsel’s receipt of a Target Validation Notice identifying the
Targets identified in such Target Validation Notice for which MERCK is permitted to perform Target
Validation Activities under this Agreement. For purposes of clarity, (i) MERCK shall not have the
right to perform Target Validation Activities for any Target not identified in a Target Validation
Response, (ii) Counsel shall only have the right to reject a Target proposed by MERCK in a Target
Validation Notice if ARCHEMIX is prohibited by an [***] existing as of the [***] from [***] such
proposed Target [***] to MERCK, (iii) neither the inclusion by MERCK of a Target on a Target
Validation Notice nor the inclusion by Counsel of a Target on a Target Validation Response shall be
considered (A) a proposal by MERCK for inclusion of such Target on the Target Exclusivity List as a
MERCK Internal Program Target pursuant to Section 3.7.2 or (B) the acceptance by ARCHEMIX of such
Target on the Target Exclusivity List as a MERCK Internal Program Target pursuant to Section 3.7
and/or Section 3.8, and (iv) ARCHEMIX [***] have the [***] either a Target Validation Notice or a
Target Validation Response.

4. DEVELOPMENT PROGRAM; COMMERCIALIZATION OF PRODUCTS

     4.1 Objectives of the Development Program. The objectives of the Development Program
shall be the selection and Development of Development Candidates to enable the Commercialization of
Products in the Field in the Territory.

     4.2 Responsibility for Development of Development Candidates and Commercialization of
Products. Except for the ARCHEMIX Development Activities, MERCK shall have [***], for all
aspects of the Development of Optimized Lead Compounds and Development Candidates in accordance
with the applicable Annual Development Plan, and all aspects of the Commercialization of Products
in accordance with the applicable Product Commercialization Plan, in the Field in the Territory,
including, without limitation, the conduct of: (a) all IND-enabling non-clinical studies that are
outside of the Research Program; (b) all activities related to human clinical trials (including,
without limitation, Phase I Clinical Trials, Phase II Clinical Trials and Phase III Clinical
Trials); (c) all activities relating to the manufacture and supply of Development Candidates and
Products (including all required process

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

48

 

development and scale up work with respect thereto); and
(d) all pre-marketing, marketing, promotion, sales, distribution, import and export activities
(including securing reimbursement, conducting sales and marketing activities and any post-marketing
trials or post-marketing safety surveillance and maintaining databases). Without limiting the
generality of the foregoing, MERCK shall have [***], (i) to make all Regulatory Filings for
Development Candidates and Products and file all Drug Approval Applications and otherwise seek all
Regulatory Approvals for Products, as well as to conduct all correspondence and communications with
Regulatory Authorities regarding such matters, subject in each case to Section 4.10.2, and (ii) to
report all Adverse Events to Regulatory Authorities if and to the extent required by Applicable
Laws. All Regulatory Approvals for Products shall be owned by MERCK, subject to Section 11.3.
Notwithstanding anything to the contrary herein, MERCK shall have no rights or responsibilities
with respect to the Development of Optimized Lead Compounds and/or Development Candidates for
ARCHEMIX Internal Program Targets for which it has not exercised the applicable Compound Candidate
Option.

     4.3 Annual Development Plans.

          4.3.1 Optimized Lead Compounds. The initial Annual Development Plan for each
Optimized Lead Compound shall be prepared by MERCK and submitted to the JSC for its review within
[***] days of the date on which the JSC approves the selection of such Optimized Lead Compound and
in any event, on or prior to the initiation of Development activities with respect thereto, which
shall describe the Development activities to be conducted for the balance of the Contract Year.
Thereafter, subject to Section 4.10.5(a), for each Contract Year during the Term, an Annual
Development Plan for each Optimized Lead Compound shall be prepared by MERCK and provided to the
JSC for its review and MERCK shall consult with the JSC with respect to all significant Development
decisions to be made with respect to such Annual Development Plan.

          4.3.2 Development Candidates. The initial Annual Development Plan for each
Development Candidate shall be prepared by MERCK and submitted to the JSC for its review within
[***] days of the date on which the JSC approves the selection of such Development Candidate and in
any event, on or prior to the initiation of Development activities with respect thereto, which
shall describe the Development activities to be conducted for the balance of the Contract Year.
Thereafter, subject to Section 4.10.5(a), for each Contract Year during the Term, an Annual
Development Plan for each Development Candidate shall be prepared by MERCK
and provided to the JSC for its review and MERCK shall consult with the JSC with respect to
all significant Development decisions to be made with respect to such Annual Development Plan.

          4.3.3 Content of Annual Development Plans. Each Annual Development Plan shall: (a)
set forth (i) the Development objectives, activities, and timelines for the Contract Year covered
by the Annual Development Plan with reasonable specificity, (ii) which activities, if any, are
ARCHEMIX Development Activities; provided, that, ARCHEMIX has agreed to perform such activities,
(iii) with respect to such ARCHEMIX Development Activities, the number of FTEs estimated to be
required to perform such activities and the corresponding FTE Cost; (iv) with respect to each
Co-Developed Development Candidate, the Estimated Aggregate FTEs applicable thereto; and (v) the
expected Regulatory Filings and Drug Approval

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

49

 

Applications to be prepared and filed and the
expected timetable of completing such Development activities; and (b) be consistent with the other
terms of this Agreement. Any amendment to an Annual Development Plan shall be approved by the JSC.
Without limiting the nature or frequency of any other amendments, modifications or updates to the
Annual Development Plan, the Annual Development Plan shall be updated at least once prior to the
end of each Contract Year to describe the Development activities to be carried out by each Party
during the applicable Contract Year in conducting the Development Program pursuant to this
Agreement. Notwithstanding anything to the contrary in this Agreement, the Parties shall use
Commercially Reasonable Efforts to initially Develop Optimized Lead Compounds for Indications
within the Target Selection Field and within the Co-Development Territory and each Annual
Development Plan shall initially focus on such Development.

          4.3.4 ARCHEMIX Internal Program Targets. Notwithstanding anything to the contrary in
this Agreement, ARCHEMIX shall have sole responsibility for the development activities associated
with ARCHEMIX Internal Program Targets and neither MERCK nor the JSC shall have any right to
prepare, review or approve any development plan covering any Optimized Lead Compound researched
and/or developed under an ARCHEMIX Internal Research Project, until such time as MERCK pays the
Option Exercise Fee applicable to the designation of such Optimized Lead Compound as a Development
Candidate pursuant to Section 6.3.

     4.4 Product Commercialization Plans. Within [***] days after the Initiation of a
Phase III Clinical Trial with respect to each Development Candidate that is not being Co-Developed,
MERCK shall prepare and provide to the JSC for its review a Product Commercialization Plan for each
Product Derived from such Development Candidate, and shall inform the JSC with respect to all
significant Commercialization decisions to be made with respect to such Product.

     4.5 Manufacture and Supply of Products for Development and Commercialization.

          4.5.1 Co-Developed Development Candidates and Co-Developed Products. The Parties
shall discuss in good faith the manufacturing responsibilities (including all scale-up and process
development) for each Co-Developed Development Candidate and Co-Developed Product that is Developed
and Commercialized under this Agreement as set forth in this Section
4.5. It is the expectation of the Parties that such discussions will be conducted through the
JDC or such other committee as may be designated by the Parties. Unless otherwise agreed to by the
Parties, MERCK shall have the primary responsibility for all such manufacturing, either by itself,
its Affiliates or by a Third Party contract manufacturing organization provided, that, (a) MERCK
shall consult with ARCHEMIX with respect to the conduct of all such manufacturing activities; and
(b) in the event that MERCK indicates that it is unable or unwilling to manufacture and supply
Co-Developed Development Candidates and/or Co-Developed Products as required within the Territory,
the Parties shall identify in good faith one or more Third Parties to serve as alternate sources of
supply.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

50

 

          4.5.2 All Other Development Candidates and Products. Unless otherwise agreed to by
the Parties, and subject to Section 4.5.1, MERCK shall be responsible for manufacturing, either by
itself, its Affiliates or by a Third Party contract manufacturing organization, each Development
Candidate and Product that is Developed and Commercialized under this Agreement as MERCK considers
appropriate; provided, that MERCK shall keep the JSC informed as to its manufacturing strategies
and the progress made hereunder.

          4.5.3 MERCK Request for ARCHEMIX Support. MERCK may request in writing that ARCHEMIX
provide ARCHEMIX Development Activities involving the conduct of analytical, process development
and manufacturing support and management activities with respect to the manufacture of Co-Developed
Development Candidates and Co-Developed Products. To the extent MERCK requests ARCHEMIX to provide
such ARCHEMIX Development Activities, ARCHEMIX will provide MERCK with a prompt written response as
to whether ARCHEMIX agrees to provide such ARCHEMIX Development Activities, and, to the extent
ARCHEMIX so agrees, ARCHEMIX shall use Commercially Reasonable Efforts to provide such ARCHEMIX
Development Activities.

     4.6 Development and Commercialization Diligence.

          (a) MERCK Diligence Obligations.

               (i) MERCK Obligations. MERCK shall exercise Commercially Reasonable Efforts during
the Term to conduct the MERCK Development Activities, to Develop [***] Development Candidate
targeted at [***] Program Target and to Commercialize [***] Product targeted at [***] Program
Target in the Field in the Territory.

               (ii) Effect of Breach of Diligence Obligations. If ARCHEMIX at any time believes that
MERCK, on a country-by-country (or with respect to European countries, Europe) and
Product-by-Product basis, is not meeting its diligence obligations pursuant to subsection (i)
above, ARCHEMIX may give written notice to MERCK requesting written justification, in the form of
detailed reasons that would support the proposition that MERCK is meeting such diligence
obligation. In such event, MERCK shall provide such written justification to ARCHEMIX within [***]
days after such notice is given. In the event that ARCHEMIX does not receive such justification
within such [***] day period or does not agree with such justification, then ARCHEMIX shall have
the right to terminate MERCK’s rights in accordance with Section 11.2.2.

          (b) ARCHEMIX Diligence Obligations. ARCHEMIX shall exercise Commercially Reasonable
Efforts during the Term to conduct the ARCHEMIX Development Activities. With respect to (i)
ARCHEMIX Internal Research Projects, this Section 4.6(b) shall only apply to the extent MERCK has
paid the applicable Option Exercise Fee applicable to the designation of an Optimized Lead Compound
as a Development Candidate pursuant to 6.3, and (ii) ARCHEMIX De Novo Research Activities requested
by MERCK pursuant to Section 3.9.2.

     4.7 Compliance. Each Party shall perform its obligations under each Annual
Development Plan in good scientific manner and in compliance in all material respects with all

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

51

 

Applicable Laws. For purposes of clarity, with respect to each activity performed under an Annual
Development Plan that will or would reasonably be expected to generate data to be submitted to a
Regulatory Authority in support of a Regulatory Filing or Drug Approval Application, the Party
performing such activity shall comply in all material respects with, if and as applicable, the
regulations and guidance of the FDA that constitute Good Laboratory Practice, Good Manufacturing
Practice or Good Clinical Practices (or, if and as appropriate under the circumstances,
International Conference on Harmonization (ICH) guidance or other comparable regulation and
guidance of any Regulatory Authority in any country or region in the Territory). Each Party shall
be solely responsible for paying the salaries and benefits of its employees conducting its
activities under Annual Development Plans.

     4.8 Cooperation. Scientists at ARCHEMIX and MERCK shall cooperate in the performance
of each Development Program and, subject to the terms of this Agreement and any confidentiality
obligations to Third Parties, shall exchange such data, information and materials as are reasonably
necessary for the other Party to perform its obligations under any Annual Development Plan.

     4.9 Exchange of Reports; Information; Updates.

          4.9.1 Development Program Reports. Subject to 4.10.2, MERCK shall keep the JSC
regularly informed of the progress of its efforts to Develop Development Candidates in the Field in
the Territory. Without limiting the generality of the foregoing, MERCK shall, at least once each
[***], provide the JSC with reports in reasonable detail regarding the status of all preclinical
IND-enabling studies and activities (including toxicology and pharmacokinetic studies), clinical
trials and other activities conducted under the Development Program; provided, that, for so long as
ARCHEMIX is obligated to perform ARCHEMIX Development Activities or has in effect a Co-Development
Option with respect to a Product, (a) MERCK shall provide the JSC with the reports described above
at least once each [***] and (b) ARCHEMIX and MERCK shall, not less than once each [***], provide
the JSC with reports in reasonable detail regarding the status of all Development Activities and
such additional information that they have in their possession as may be reasonably requested from
time to time by the JSC.

          4.9.2 Commercialization Reports. Subject to Section 4.10.2, MERCK shall keep the JSC
and ARCHEMIX regularly informed of the progress of MERCK’s efforts to Commercialize Products in the
Field in the Territory through periodic updates. Without limiting the generality of the foregoing,
MERCK shall provide the JSC and ARCHEMIX with [***]
written updates to each Product Commercialization Plan, which shall (a) summarize MERCK’s
efforts to Commercialize Products, (b) identify the Regulatory Filings and Drug Approval
Applications with respect to such Product that MERCK or any of its Affiliates or Sublicensees have
filed, sought or obtained in the prior [***] month period or reasonably expect to make, seek or
attempt to obtain in the following [***] month period and (c) summarize all clinical and other data
generated by MERCK with respect to Products. In addition, MERCK shall provide such additional
information that it has in its possession as may be reasonably requested by ARCHEMIX regarding the
Commercialization of any Product, which request shall not be made more than once each Calendar
Year.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

52

 

          4.9.3 Adverse Event Reports; Review of Regulatory Filings and Correspondence.

               (a) Adverse Events. In addition to the updates described in Section 4.9.1 and 4.9.2,
MERCK shall provide ARCHEMIX with all Adverse Event information and product complaint information
relating to Development Candidates or Products as such information is compiled or prepared by MERCK
in the normal course of business in connection with the Development of any Development Candidates
or Commercialization of any Product and, in any event, within time frames consistent with reporting
obligations under Applicable Laws. MERCK shall provide such Adverse Event and product complaint
information hereunder to ARCHEMIX in accordance with Section 14.3. ARCHEMIX may provide all such
Adverse Event information to other licensees of ARCHEMIX who have the right to sell aptamers for
therapeutic purposes under a license from ARCHEMIX; provided, that, such other licensees agree to
maintain the confidentiality thereof. ARCHEMIX will provide to MERCK Adverse Event information
obtained from other licensees of ARCHEMIX who have the right to develop and sell aptamers for
therapeutic purposes under a license from ARCHEMIX; provided, that, such other licensees agree to
share such information and MERCK agrees to maintain the confidentiality thereof.

               (b) Preparation of Drug Approval Applications. Subject to Section 4.10.2, MERCK shall
(i) consult with ARCHEMIX in good faith in the preparation of all Drug Approval Applications for
Products in the United States, Japan and in the European Union and (ii) consider all timely
comments of ARCHEMIX in good faith, taking into account the best interests of the Collaboration and
of the Development of the applicable Development Candidate and Commercialization of the applicable
Product on a global basis.

               (c) Meeting Attendance and Information. MERCK shall use reasonable efforts to provide
ARCHEMIX with at least [***] days advance notice of any meeting with the FDA or other Regulatory
Authority regarding a Drug Approval Application relating to, or Regulatory Approval for, any
Development Candidate or Product, (i) prior to the acceptance of an IND with respect to each
Development Candidate or Product and (ii) after acceptance of an IND with respect to each
Development Candidate or Product if the subject matter of the meeting shall include any milestone
event applicable to such Development Candidate or Product. Upon written request ARCHEMIX may send
one person [***] to participate as an observer in such meeting [***]; provided, that, (A) MERCK
approves such ARCHEMIX request [***] to any Product that is not a Co-Developed Product for any such
meetings occurring after acceptance of the IND and (B) to the extent MERCK’s approval is required,
MERCK shall [***] any such
request of ARCHEMIX. With regard to any meeting with the FDA or other Regulatory Authority
regarding a Drug Approval Application relating to, or Regulatory Approval for, any Development
Candidate or Product, to which ARCHEMIX did not send a representative as provided in this Section
4.9.3(c), MERCK will provide ARCHEMIX with a written summary of information communicated and
received thereat.

               (d) Right to Review. Notwithstanding anything to the contrary in this Section 4.9.3,
ARCHEMIX shall have the right, upon written notice, to review all such Regulatory Filings and
correspondence at MERCK’s office at ARCHEMIX’s sole expense.

     4.10 Development and Commercialization Rights and Restrictions.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

53

 

          4.10.1 Development and Commercialization Rights in the Field. Except as provided in
Section 4.10.2, MERCK shall have the [***] during the Term to Develop Development Candidates and
Commercialize Products in the Territory for use in the Field.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

54

 

          4.10.2 Co-Development and Co-Promotion Option.

               (a) Exercise of Co-Development and Co-Promotion Option. ARCHEMIX shall have the
option (the “Co-Development and Co-Promotion Option”), but not the obligation, to co-develop any
Development Candidate, and subsequently co-promote the Product, by providing written notice to
MERCK which notice shall specify the applicable Development Candidate and the applicable ARCHEMIX
Co-Development Sharing Percentage (the “Co-Development and Co-Promotion Option Notice”) at any time
during the Co-Development and Co-Promotion Option Exercise Period. If ARCHEMIX exercises a
Co-Development and Co-Promotion Option for a Development Candidate as described in this Section
4.10.2, (i) that Development Candidate shall thereafter be deemed to be a “Co-Developed Development
Candidate” for purposes of this Agreement; (ii) ARCHEMIX shall be responsible for paying (A) with
respect to the ARCHEMIX [***]% Co-Development Sharing Percentage, (1) [***] percent ([***]%) of all
Co-Development Costs that are attributable to such Co-Developed Development Candidate in the
Territory and (2) [***] percent ([***]%) of Co-Development Regulatory Costs and Co-Development
Commercialization Costs incurred with respect to such Co-Developed Development Candidate in the
Co-Development Territory, and MERCK shall be responsible for [***] of the Co-Development Costs,
Co-Development Commercialization Costs and Co-Development Regulatory Costs attributable to that
Co-Developed Development Candidate, and (B) with respect to the ARCHEMIX [***]% Co-Development
Sharing Percentage, (1) [***] percent ([***]%) of all Co-Development Costs that are attributable to
such Co-Developed Development Candidate in the Territory and (2) [***] percent ([***]%) of
Co-Development Regulatory Costs and Co-Development Commercialization Costs incurred with respect to
such Co-Developed Development Candidate in the Co-Development Territory, and MERCK shall be
responsible for [***] of the Co-Development Costs, Co-Development Commercialization Costs and
Co-Development Regulatory Costs attributable to that Co-Developed Development Candidate; (ii)
ARCHEMIX shall receive the applicable ARCHEMIX Co-Development Sharing Percentage of all Net Income
derived from that Co-Developed Development Candidate/Co-Developed Product in the Co-Development
Territory in accordance with Section 6.7 below; (iii) with respect to the ARCHEMIX [***]%
Co-Development Sharing Percentage, ARCHEMIX shall [***] receive the United States [***] and [***]
[***] contemplated by Milestone Events [***], [***], [***] and [***] of Section 6.5.1(a) or any
[***] on Net Sales of such Co-Developed Development Candidate/Co-Developed Product in the
Co-Development Territory on and after the date of exercise of the applicable Co-Development and
Co-Promotion Option; and (iv) with respect to the ARCHEMIX [***]% Co-Development Sharing
Percentage, ARCHEMIX shall be entitled to receive [***] percent ([***]%) of the United States [***]
and [***] contemplated by Milestone Events [***], [***], [***] and [***] of Section 6.5.1(a)
achieved with respect to such Co-Developed Development Candidate/Co-Developed Product but ARCHEMIX
shall [***] any [***] on Net Sales of such Co-Developed Development Candidate in the Co-Development
Territory on and after the date of exercise of the applicable Co-Development and Co-Promotion
Option. In the event that MERCK initiates the [***] with respect to such Co-Developed Development
Candidate/Co-Developed Product, and ARCHEMIX has not exercised its Opt-Out Right in accordance with
the provisions of Section 4.10.6(d) below, the Parties shall (A) negotiate, within [***] days from
initiation of each Phase III Clinical Trial, a Co-Promotion Agreement for such Co-Developed
Development Candidate/Co-Developed Product in accordance with Section 4.10(c) below and (B) form at

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

55

 

ARCHEMIX’s request, as soon as practicable thereafter but in any event within [***] days, the
Joint Commercialization Committee in accordance with Schedule 8.

               (b) Cooperation; Additional Information. In connection with ARCHEMIX’s consideration
of the exercise of a Co-Development and Co-Promotion Option with respect to each Development
Candidate, MERCK shall provide ARCHEMIX (i) with an initial outline of the Development activities
contemplated by MERCK for such Development Candidate in the Co-Development Territory over a [***]
year period (including an estimated budget and the Estimated Aggregate FTEs for such activities)
and (ii) any information Controlled by MERCK that is necessary or useful to ARCHEMIX in determining
whether to exercise such Co-Development and Co-Promotion Option.

               (c) Negotiation of Co-Promotion Agreement. Within [***] days from the Initiation of
the first Phase III Clinical Trial with respect to each Co-Developed Product, the Parties shall
commence the preparation of a co-promotion agreement (the “Co-Promotion Agreement”) which shall
provide for the terms applicable to such Co-Promotion, which Co-Promotion Agreement will be
executed by ARCHEMIX and MERCK or an Affiliate of MERCK. The Co-Promotion Agreement shall conform
in all material respects with the terms and conditions set forth in Schedule 8 attached
hereto and such additional provisions [***] the respective Parties. For purposes of clarity, such
additional terms shall supplement and shall not materially expand, limit or change the terms set
forth on Schedule 8.

               (d) Dispute Resolution. In the event the Parties fail to execute and deliver the
Co-Promotion Agreement within [***] days, the Parties shall (i) use reasonable efforts to complete
such negotiations and to execute and deliver the Co-Promotion Agreement as soon as possible after
such [***] day period and (ii) without limiting the generality of the foregoing, after the
expiration of such [***] day period, each produce a list of issues on which they have failed to
reach agreement and submit its list to the JSC to be resolved in accordance with Section 2.1.6.

               (e) Use of Clinical Trial Data. Notwithstanding anything to the contrary in this
Section 4.10.2, MERCK shall have the right to use all data, results and information produced in the
conduct of any Clinical Trials conducted with respect to a Co-Developed Development
Candidate/Co-Developed Product in any Regulatory Filing made with respect to that Co-Developed
Development Candidate/Co-Developed Product outside of the Co-Development Territory.

          4.10.3 Product Recalls. Subject to the terms set forth in any Co-Promotion Agreement
applicable to Co-Promoted Products, in the event that any Regulatory Authority issues or requests a
recall or takes similar action in connection with a Product, or in the event a Party reasonably
believes that an event, incident or circumstance has occurred that may result in the need for a
recall, market withdrawal or other corrective action regarding a Product, such Party shall promptly
advise the other Party thereof by telephone or facsimile. Following such notification, MERCK shall
decide and have control of whether to conduct a recall or market withdrawal (except in the event of
a recall or market withdrawal mandated by a Regulatory Authority, in which case it shall be
required) or to take other corrective action in any country and the manner in which any such
recall, market withdrawal or corrective action shall be conducted; provided, that, MERCK shall keep
ARCHEMIX regularly informed regarding any such recall, market withdrawal or corrective action.
MERCK shall bear all expenses of any such recall,
Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

56

 

market withdrawal or corrective action (including, without limitation, expenses for
notification, destruction and return of the affected Product and any refund to customers of amounts
paid for such Product); provided, that, to the extent such recall is with respect to a Co-Developed
Product, such expenses shall be shared in accordance with the Co-Promotion Agreement.

          4.10.4 Failure to Exercise Co-Development Option. In the event ARCHEMIX fails to
exercise the Co-Development and Co-Promotion Option with respect to a Development Candidate on or
before the expiration of the applicable Co-Development and Co-Promotion Option Exercise Period, (i)
that Development Candidate shall be deemed to be a Royalty-Bearing Product for purposes of this
Agreement in all countries in the Territory (including, without limitation, the Co-Development
Territory) and (ii) ARCHEMIX shall be entitled to receive from MERCK, in lieu of receiving Net
Income Payments for what would have become a Co-Promoted Product, (A) the milestone payments
described in Section 6.5.1 of this Agreement for any milestones achieved with respect to such
Development Candidate or any Product Derived therefrom, and (B) the royalty payments described in
Section 6.6.1 on Net Sales of such Development Candidate or any Product Derived therefrom for sales
of such Product; and (iii) MERCK shall have the exclusive right to Develop and Commercialize that
Product in accordance with Section 4.10.1.

          4.10.5 Rights and Responsibilities with Respect to Co-Developed Development
Candidates. 

               (a) Annual Development Plans; Regulatory Filings. In the event ARCHEMIX exercises the
Co-Development and Co-Promotion Option applicable to a Development Candidate, (i) ARCHEMIX shall
have the right to actively participate in the preparation of all Annual Development Plans
(including all amendments thereto) for such Co-Developed Development Candidate and all Regulatory
Filings (including all amendments thereto) for such Co-Developed Development Candidate in the
Co-Development Territory; and (ii) MERCK shall work together in good faith with ARCHEMIX in
connection with the preparation of all such Annual Development Plans and all Regulatory Filings
(including all amendments thereto).

               (b) ARCHEMIX Co-Development Participation Rights. As soon as practicable following
the exercise by ARCHEMIX of a Co-Development and Co-Promotion Option with respect to a Co-Developed
Development Candidate, ARCHEMIX shall provide MERCK with written notice which shall set forth the
ARCHEMIX Co-Development Participation Capacity applicable to such Co-Developed Development
Candidate. Subject to the foregoing, MERCK shall, with respect to each Co-Developed Development
Candidate/Co-Developed Product (i) use [***] of ARCHEMIX FTEs in the Development of each such
Co-Developed Development Candidate/Co-Developed Product in each Calendar Year as shall [***] the
ARCHEMIX Minimum Co-Development Participation Level; provided, that, if the ARCHEMIX Co-Development
Participation Capacity is less than the applicable ARCHEMIX Minimum Co-Development Participation
Level, MERCK shall only be required to use [***] ARCHEMIX FTEs [***] the ARCHEMIX Co-Development
Participation Capacity. Notwithstanding the foregoing, (i) MERCK shall have no obligation to use
ARCHEMIX FTEs under this Section 4.10.5(b) for any [***]; provided, that, in the event that MERCK
determines

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

57

 

not to use ARCHEMIX FTEs to conduct any [***] and uses MERCK FTEs in the conduct of such [***]
then the FTE Cost applicable [***] of (1) the ARCHEMIX Minimum Co-Development Participation Level
for Late Stage Co-Development Activities and (2) the ARCHEMIX Minimum Co-Development Participation
Level, [***] as part of the Co-Development Costs pursuant to Schedule 13, and [***] to
ARCHEMIX pursuant to Section 4.10.6 and (ii) in the event that ARCHEMIX indicates that the ARCHEMIX
Co-Development Participation Capacity for a Co-Developed Development Candidate/Co-Developed Product
is [***] for a Calendar Year, MERCK shall [***] of such Co-Developed Development Candidate
/Co-Developed Product for that Calendar Year.

               (c) Participation in Regulatory Activities. MERCK shall provide ARCHEMIX with (i) at
least [***] days advance notice of any meeting with the FDA or other Regulatory Authority regarding
a Drug Approval Application relating to, or Regulatory Approval for, any Co-Developed Development
Candidate or Co-Developed Product and ARCHEMIX may elect to send at least [***] and, as may be
reasonably necessary, a number of additional persons (but in no event shall such number be [***])
to participate as observers in such meeting; (ii) drafts of each Regulatory Filing or other
document or correspondence pertaining to any Co-Developed Development Candidate or Co-Developed
Product prepared for submission to the FDA or other Regulatory Authority sufficiently in advance of
submission so that ARCHEMIX may review and comment on the substance of such Regulatory Filing or
other document or correspondence; and (iii) copies of any document or other correspondence received
from the FDA pertaining to any Co-Developed Development Candidate or Co-Developed Product. MERCK
shall consider all such comments of ARCHEMIX in good faith, taking into account the best interests
of the Collaboration and of the Development of the applicable Co-Developed Development Candidate or
Commercialization of the applicable Co-Developed Product. ARCHEMIX shall not interact with the FDA
or other Regulatory Authority without MERCK’s prior written consent, such consent not to be
unreasonably denied, withheld or conditioned, regarding a Drug Approval Application relating to, or
Regulatory Approval for, any Co-Developed Development Candidate or Co-Developed Product.

               (d) MERCK Technology. MERCK shall provide ARCHEMIX with access to MERCK Background
Technology that MERCK determines in good faith to be necessary or useful in Development.

          4.10.6 Reconciliation and Auditing of Co-Development Costs.

               (a) Reconciliation. Within [***] days following the end of each [***] following the
exercise of the Co-Development and Co-Promotion Option applicable to a Co-Developed Development
Candidate/Co-Developed Product, each of ARCHEMIX and MERCK shall submit to the JDC a written report
setting forth in reasonable detail all Co-Development Costs incurred by each such Party over such
[***] for the Co-Developed Development Candidate/Co-Developed Product. Within [***] days following
the JDC’s receipt of such written reports, the JDC shall prepare and submit to each Party a written
report setting forth in reasonable detail (a) the calculation of all such Co-Development Costs
incurred by both Parties over such Calendar Quarter and (b) the calculation of the net amount owed
by ARCHEMIX to MERCK or by MERCK to ARCHEMIX in order to ensure the appropriate sharing of such
Co-Development Costs in accordance with the ARCHEMIX Co-Development Sharing Percentage and the
MERCK

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

58

 

Co-Development Sharing Percentage. The net amount payable shall be paid by ARCHEMIX or MERCK
to the other, as applicable, within [***] days after the distribution by the JDC of such written
report.

               (b) Records; Audit Rights. Each Party shall keep and maintain for [***] years
complete and accurate records of Co-Development Costs incurred with respect to Co-Developed
Development Candidates/Co-Developed Products in sufficient detail to allow confirmation of same by
the JDC and the other Party. Each Party shall have the right for a period of [***] years after
such Co-Development Cost is reconciled in accordance with Section 4.10.6 to appoint at its expense
an independent certified public accountant reasonably acceptable to the other Party to audit the
relevant records of the other Party and its Affiliates to verify that the amount of such
Co-Development Costs was correctly determined. The Audited Party and its Affiliates shall each
make its records available for audit by such independent certified public accountant during regular
business hours at such place or places where such records are customarily kept, upon reasonable
notice from the Auditing Party, solely to verify that Co-Development Costs hereunder were correctly
determined. Such audit right shall not be exercised by the Auditing Party more than once in any
Calendar Year and no period may be audited more than once. All records made available for audit
shall be deemed to be Confidential Information of the Audited Party. The results of each audit, if
any, shall be binding on both Parties. In the event there was an error in the amount of
Co-Development Costs reported by the Audited Party hereunder, (i) if the amount of Co-Development
Costs was over reported, the Audited Party shall promptly (but in any event no later than [***]
days after the Audited Party’s receipt of the independent accountant’s report so concluding) make
payment to the Auditing Party of such amount as to ensure the appropriate sharing of such
Co-Development Costs in accordance with the ARCHEMIX Co-Development Sharing Percentage and the
MERCK Co-Development Sharing Percentage and (ii) if the amount of Co-Development Costs was
underreported, the Auditing Party shall promptly (but in any event no later than [***] days after
the Auditing Party’s receipt of the independent accountant’s report so concluding) make payment to
the Audited Party of such amount as to ensure the appropriate sharing of such Co-Development Costs
in accordance with the ARCHEMIX Co-Development Sharing Percentage and the MERCK Co-Development
Sharing Percentage. The Auditing Party shall bear the full cost of such audit unless such audit
discloses an over reporting by the Audited Party of more than [***] percent ([***]%) of the
aggregate amount of Co-Development Costs reportable in any Calendar Year, in which case the Audited
Party shall reimburse the Auditing Party for all costs incurred by the Auditing Party in connection
with such audit.

               (c) Roll-Over Payments. If, in any [***], the actual Co-Development Costs to be borne
by ARCHEMIX with respect to a Co-Developed Development Candidate/Co-Developed Product for that
Calendar Quarter exceeds by greater than [***] percent ([***]%) ARCHEMIX’s share of MERCK’s last
good faith estimate given at least [***] months before the start of the [***] of Co-Development
Costs for that Co-Developed Development Candidate for that [***], ARCHEMIX may, upon written notice
to MERCK, delay payment of its share of any such excess until the subsequent [***] (the “Roll-Over
Payment”). The Roll-Over Payment shall be paid by ARCHEMIX in [***] equal amounts over the [***]
of the subsequent [***].

               (d) Opt-Out Right. ARCHEMIX (the “Opting-Out Party”) shall have the right (the
“Opt-Out Right”) in its sole discretion, to cease further Development of any Co-

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

59

 

Developed Development Candidate/Co-Developed Product by providing MERCK (the “Sole Developing
Party”) with written notice (the “Opt-Out-Notice”) at any time within [***] days of each Opt-Out
Date applicable to the Co-Developed Development Candidate/Co-Developed Product which shall specify
the Co-Developed Development Candidate/Co-Developed Product with respect to which ARCHEMIX is
exercising its Opt-Out Right and shall indicate the date (the “Separation Date”) on which the
Opt-Out Right shall be effective, which shall under no circumstances be sooner than [***] days from
the date of the Opt-Out Notice (the “Opt-Out Notice Period”). During the Opt-Out Notice Period,
the Parties shall continue to jointly Develop the Co-Developed Development Candidate/Co-Developed
Product in accordance with the applicable Annual Development Plan for the Co-Developed Development
Candidate/Co-Developed Product that is the subject of the Opt-Out Notice; provided, that,
notwithstanding the foregoing, under no circumstances shall MERCK be obligated to continue to
Develop any Co-Developed Development Candidate/Co-Developed Product for which ARCHEMIX exercises
its Opt-Out Right. If ARCHEMIX exercises its Opt-Out Right as provided in this Section 4.10.6(d),
and MERCK determines to continue to Develop the Co-Developed Development Candidate/Co-Developed
Product that is the subject of the Opt-Out Right, then, as of the Separation Date (a) the
Co-Developed Development Candidate/Co-Developed Product that is the subject of the Opt-Out Right
shall be a Royalty-Bearing Product for purposes of this Agreement; (b) ARCHEMIX shall have no
further obligation to fund its Co-Development Percentage of the Co-Development Costs incurred for
such Co-Developed Development Candidate/Co-Developed Product; (c) ARCHEMIX will receive from MERCK,
in lieu of receiving Net Income Payments from Co-Promoting the Co-Developed Development
Candidate/Co-Developed Product that is the subject of the Opt-Out Notice, (i) the milestone
payments described in Section 6.5.1 for any milestones achieved with respect to such
Royalty-Bearing Product after the Separation Date, provided that ARCHEMIX shall not be entitled to
receive (A) the milestone payment for achievement of [***], in the event ARCHEMIX exercises its
Opt-Out Right at the [***] Opt-Out Date, (B) the milestone payment for achievement of [***] in
the event ARCHEMIX exercises its Opt-Out Right at the [***] Opt-Out Date, and (C) the milestone
payment for achievement of [***], in the event ARCHEMIX
exercises its Opt-Out Right at the [***] Opt-Out Date, and (ii) the royalty payments described in Section 6.6.1 on Net Sales of such
Royalty-Bearing Product for sales of such Royalty-Bearing Product that occur after the Separation
Date; and (d) MERCK shall have [***] right to Develop and Commercialize the Co-Developed
Development Candidate/Co-Developed Product for which ARCHEMIX exercised its Opt-Out Right in
accordance with Section 4.10.1.

5. EQUITY PURCHASE RIGHT

     5.1 Purchase of Equity. Concurrent with signature of this Agreement, MERCK shall
purchase from ARCHEMIX, and ARCHEMIX shall issue and sell to MERCK, on the Signing Date, ([***]) shares of Series C
Preferred Stock, $.001 par value per share, of ARCHEMIX for a purchase price of [***] Dollars (US
$[***]) per share or Twenty Nine Million Eight Hundred Forty Four Thousand Four Hundred Fourteen
Dollars (US $29,844,414) in the aggregate by wire transfer of immediately available funds according
to instructions that ARCHEMIX shall provide and pursuant to the terms and subject to the conditions
set forth in the Stock Purchase Agreement.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

60

 

     5.2 Equity Purchase Right.

          5.2.1 Right to Purchase. Contingent upon and subject to the execution and delivery
of, and compliance with the terms and conditions of this Agreement, ARCHEMIX shall have the option
to instruct its underwriters to a Qualified IPO that prices within [***] years of the Effective
Date to offer to MERCK the opportunity to purchase shares of ARCHEMIX Common Stock at the IPO Price
in an amount up to the lesser of (a) [***] percent ([***]%) of the total gross offering proceeds
(prior to underwriter commissions and expenses) raised by ARCHEMIX in the Qualified IPO or (b)
$[***]. Such option shall be exercised at ARCHEMIX’ sole discretion and shall be subject to (i)
the determination by ARCHEMIX or the underwriters, with the advice of counsel, that such offer does
not violate Applicable Laws (including any applicable state or federal securities laws or
regulations or any rule, policy or limit imposed by the U.S. Securities and Exchange Commission,
the National Association of Securities Dealers, any securities exchange or any other applicable
regulatory body) and (ii) the determination by the underwriters that an allotment of shares in such
manner would not be materially detrimental to the success of the Qualified IPO. MERCK in its sole
discretion, shall have the right to agree to the purchase of all or any portion of such shares as
an allotment in any such Qualified IPO consistent with the terms and conditions of this Section
5.2. The foregoing notwithstanding, in the event that ARCHEMIX or the underwriters, with the
advice of counsel, determine that such offer to participate in the Qualified IPO violates
Applicable Laws (including any applicable state or federal securities laws or regulations or any
rule, policy or limit imposed by the U.S. Securities and Exchange Commission, the National
Association of Securities Dealers, any securities exchange or any other applicable regulatory
body), then MERCK, in its sole, discretion shall have the option to agree to purchase all or any
portion of such shares by means of a private placement (the “Private Placement”) that closes
concurrently with any such Qualified IPO,; provided that the purchase of shares of ARCHEMIX Common
Stock in a Private Placement shall be subject to compliance with Applicable Laws, including but not
limited to compliance with the U.S. Securities and Exchange Commission’s integration doctrine. For
purposes of clarity, if the Qualified IPO occurs prior to the first anniversary of the Signing Date
then MERCK may only be offered the opportunity to consummate the stock purchase set forth in this
Section 5.2.1 as a Private Placement pursuant to Section 5.2.2 (d) below.

          5.2.2 Purchase Mechanics.

               (a) Notice of Qualified IPO. At least [***] days prior to the anticipated effective
date of the registration statement for the Qualified IPO, ARCHEMIX shall deliver to MERCK written
notice (the “Qualified IPO Notice”) specifying: (i) that ARCHEMIX has filed a registration
statement for a Qualified IPO; (ii) the anticipated effective date of the registration statement
for the Qualified IPO; (iii) the anticipated total gross offering proceeds (prior to underwriter
commissions and expenses) expected to be raised by ARCHEMIX in the Qualified IPO; (iv) the
anticipated range of the IPO Price; and (v) the anticipated number of shares of ARCHEMIX Common
Stock to be purchased and sold in the Qualified IPO (appropriately adjusted to reflect stock
splits, stock dividends, combinations of shares and the like).

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

61

 

               (b) MERCK Notice of Participation. MERCK shall inform ARCHEMIX in writing within
[***] days of the date of the Qualified IPO Notice whether MERCK wishes to purchase shares of
ARCHEMIX Common Stock in (x) the Qualified IPO and/or (y) the Private Placement and, if any, (ii)
the number of ARCHEMIX Common Shares MERCK wishes to purchase, specifying the maximum and minimum
prices within the range identified in the Qualified IPO Notice at which MERCK would be willing to
purchase such shares (x) as an allotment in any such Qualified IPO (the “MERCK IPO Shares”) and/or
(y) in the Private Placement (the “MERCK Private Placement Shares”).

               (c) Purchase Notice. To the extent MERCK wishes to purchase ARCHEMIX Common Stock in
the Qualified IPO and/or Private Placement, following the pricing of the Qualified IPO (the “IPO
Effective Date”), ARCHEMIX shall deliver to MERCK written notice within [***] (the “Purchase
Notice”) specifying: (i) that the registration statement for the Qualified IPO has been declared
effective; (ii) the total gross offering proceeds (prior to underwriter commissions and expenses)
to be raised by ARCHEMIX in the Qualified IPO; (iii) the IPO Price; (iv) the MERCK IPO Shares
allocated to MERCK in the Qualified IPO (the “MERCK IPO Share Amount”); (v) if applicable, details
for the purchase and settlement of the portion of the MERCK IPO Share Amount to be purchased by
MERCK in the Qualified IPO, as specified by the underwriter(s) to the Qualified IPO, and the
aggregate purchase price for such shares (the “Qualified IPO Purchase Price”); and (vi) if
applicable, the place and time at which the Private Placement Closing will occur, the portion of
the MERCK Private Placement Shares to be purchased by MERCK in the Private Placement (the “MERCK
Private Placement Share Amount”), the aggregate purchase price of such shares (the “Private
Placement Purchase Price”) and wire transfer instructions for the payment of the Private Placement
Purchase Price.

               (d) Private Placement Closing. The closing of the Private Placement, if applicable
(the “Private Placement Closing”), shall take place on the same day as the closing of the Qualified
IPO (the “Private Placement Closing Date”) at the place specified in the Purchase Notice; provided,
however, that: (i) if such purchase cannot be consummated on the Private Placement Closing Date by
reason of any applicable order, judgment, decree or other legal impediment, then MERCK and/or
ARCHEMIX may extend the Private Placement Closing Date to a date not more than [***] days after the
applicable order, judgment, decree or other legal impediment has been satisfied; and (ii) if prior
notification to or approval of any governmental body is required, or if any waiting period must
expire or be terminated, in connection with such purchase, then (A) the relevant Party shall
promptly cause to be filed the required notice or application for approval and shall cause such
notice or application to be processed as expeditiously as possible, (B) the other Party shall
cooperate with the filing Party in the filing of any such notice or application required to be
filed and in the obtaining of any such approval required to be obtained, and (C) the Private
Placement Closing Date shall be extended to a date not more than [***] days after the latest date
upon which any required notification has been made, any required approval has been obtained or any
required waiting period has expired or been terminated. The Private Placement Closing shall occur
as follows:

                    (i) On the Private Placement Closing Date, MERCK shall deliver to ARCHEMIX the Private
Placement Purchase Price by wire transfer, in immediately available funds, to the bank account
designated by ARCHEMIX in the Purchase Notice and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

62

 

ARCHEMX shall deliver to MERCK such number of ARCHEMIX Common Shares that is equal to the
MERCK Private Placement Share Amount.

                    (ii) At the Private Placement Closing, simultaneously with the delivery of the Private
Placement Purchase Price, ARCHEMIX and MERCK shall deliver to each other, executed counterparts of
the Common Stock Purchase Agreement set forth as Exhibit B.

               (e) Qualified IPO Closing. On the closing date of the Qualified IPO, MERCK shall
deliver to the underwriters the Qualified IPO Purchase Price in accordance with the purchase and
settlement instructions designated by the underwriters and ARCHEMIX shall instruct its transfer
agent to deliver to MERCK a certificate for such number of ARCHEMIX Common Shares that is equal to
the MERCK IPO Share Amount.

          5.2.3 Market Stand-Off Agreement. MERCK agrees that during the [***] day period
following the effective date of the registration statement for the Qualified IPO, or such other
period as requested of [***] ARCHEMIX by the underwriters in the Qualified IPO in order to comply
with Rule 2711 of the National Association of Securities Dealers or otherwise, MERCK shall not, to
the extent requested by ARCHEMIX and any underwriter to the Qualified IPO, sell, pledge, lend,
contract to sell, sell any option or contract to purchase, purchase any option or contract to sell,
grant any options, right or warrant to purchase, or otherwise transfer or dispose of (other than to
donees who agree to be similarly bound), or enter into any swap, hedging or similar transaction
with the same economic effect as a sale, any shares of Common Stock of ARCHEMIX; provided, however,
that all such executive officers, directors and significant shareholders of ARCHEMIX enter into
similar market stand-off agreements.

6. PAYMENTS

     6.1 SELEX License Maintenance Fee. In consideration of the grant by ARCHEMIX of the
SELEX License, MERCK shall pay ARCHEMIX a non-refundable license maintenance fee in the amount of
[***] Dollars (US $[***]) by wire transfer (i) within [***] days of the Effective Date and (ii) on
[***] the Effective Date during the SELEX License Term, according to instructions that ARCHEMIX
shall provide.

     6.2 Research License Maintenance Fee. In consideration of the grant by ARCHEMIX of
the licenses required to conduct the MERCK Funded Research Projects, MERCK shall pay ARCHEMIX a
non-refundable license maintenance fee in the amount of [***] Dollars (US $[***]) by wire transfer
(i) within [***] days of the Effective Date and (ii) on [***] the Effective Date during the
Research Program Term, according to instructions that ARCHEMIX shall provide.

     6.3 Compound Option Exercise Fees. For each Compound Candidate Option exercised by
MERCK pursuant to Section 3.9.2, MERCK shall pay ARCHEMIX (a) with respect to any Compound
Candidate Option that is exercised by MERCK that covers a [***] at the time of exercise, (i) an
option fee (the “Option Fee”) in the amount of [***] Dollars (US $[***]) within [***] days of the
exercise by MERCK of such Compound Candidate Option and (ii) an

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

63

 

option exercise fee (the “Option
Exercise Fee”) in the amount of [***] Dollars (US $[***]) within [***] days of such time as the
Compound Candidate is determined to meet the applicable [***] or is otherwise accepted as [***];
and (b) with respect to any Compound Candidate Option that is exercised by MERCK that covers a
Compound Candidate that meets the [***] at the time of exercise, an Option Exercise Fee in the
amount of [***] Dollars (US $[***]) within [***] days of the exercise by MERCK of such Compound
Candidate Option. For purposes of clarity, (a) only [***] Option Exercise [***] shall be paid for
a given ARCHEMIX Internal Research Program even if Compound Candidate Options covering [***]
Compound Candidate from such ARCHEMIX Internal Research Program are exercised by MERCK and (b) all
Option Exercise Fees shall be non-creditable and non-refundable.

     6.4  R&D Funding.

          6.4.1 Payment of R&D Funding.

               (a) Technology Transfer Activities. In consideration of the performance by ARCHEMIX
of the Technology Transfer Activities under the SELEX Technology Transfer Plan as described in
Section 3.2, during each Calendar Quarter of the Technology Transfer Term, MERCK will pay ARCHEMIX
the Technology Transfer Costs and the FTE Cost applicable to the Technology Transfer Activities
conducted during such Calendar Quarter within [***] days of MERCK’s receipt of an invoice
corresponding to such Calendar Quarter.

               (b) Research Program Activities. In consideration of the performance by ARCHEMIX of
its activities under the Research Projects as described in Section 3.3, during the Research Program
Term, MERCK will pay ARCHEMIX the applicable Quarterly FTE Payment on or prior to the first day of
each Calendar Quarter; provided, that, an invoice corresponding with such Calendar Quarter has been
received by MERCK. ARCHEMIX shall provide a report to the JPT within [***] days of the end of each
Calendar Quarter during the Research Program Term that specifies the actual number of FTEs expended
during the period covered therein. Within [***] days of the end of each Calendar Year during the
Research Program Term, ARCHEMIX shall provide MERCK with an annual reconciliation statement
(“Annual Reconciliation Statement”) that specifies the actual number of FTEs expended during the
previous [***] in the aggregate in the conduct of the Research Program. MERCK shall reimburse
ARCHEMIX in full for any FTEs expended by ARCHEMIX in excess of the cumulative FTE Costs owed by
MERCK for such Calendar Year (the “MERCK Contribution”) as indicated by any Annual Reconciliation
Statement if such excess was approved by the JSC. To the extent that any Annual Reconciliation
Statement indicates that ARCHEMIX expended FTEs in excess of the MERCK Contribution and such excess
was not approved by the JSC then, (a) MERCK shall reimburse ARCHEMIX for all FTE Costs in excess of
the MERCK Contribution equal to or less than [***] percent ([***]%) of the MERCK Contribution and
(b) all excess FTE Costs in excess of [***] percent ([***]%) of the MERCK Contribution shall be
borne by ARCHEMIX.

          6.4.2 R&D Funding Audit Rights. ARCHEMIX shall keep complete and accurate books and
financial records pertaining to the number of FTEs utilized in conducting the Technology Transfer
Activities, the ARCHEMIX Research Activities and the ARCHEMIX

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

64

 

Development Activities other than Development activities with respect to Co-Developed
Collaboration Aptamers, if any, which books and financial records shall be kept in accordance with
GAAP and shall be retained by ARCHEMIX until [***] years after the end of the Contract Year to
which they pertain. Upon [***] days written notice, MERCK shall have the right to appoint at its
expense an independent certified public accountant reasonably acceptable to ARCHEMIX to audit the
books and financial records of ARCHEMIX relating to the number of FTEs utilized in conducting the
Technology Transfer Activities, the ARCHEMIX Research Activities and the ARCHEMIX Development
Activities other than Development activities with respect to Co-Developed Collaboration Aptamers
during any Contract Year; provided, that, MERCK shall not have the right to audit any Contract Year
more than once or more than [***] years after the end of such Contract Year or to conduct more than
one such audit in any [***] period. All books and financial records made available for audit shall
be deemed to be Confidential Information of ARCHEMIX. The results of each audit, if any, shall be
reported in writing to both Parties promptly (but in no event later than [***] days) after the
audit and shall be binding on both Parties. In the event that there was an error relating to the
reported FTEs utilized in conducting the Technology Transfer Activities, the ARCHEMIX Research
Activities and/or the ARCHEMIX Development Activities other than Development activities with
respect to Co-Developed Collaboration Aptamers during such Contract Year, (a) if the effect of the
error resulted in an overpayment by MERCK, ARCHEMIX shall promptly (but in any event no later than
[***] days) after ARCHEMIX’ receipt of the report so concluding, make payment to MERCK of the
overpayment and (b) if the effect of the error resulted in an underpayment by MERCK, then MERCK
shall promptly (but in no event later than [***] days after MERCK’s receipt of the report so
concluding) make payment to ARCHEMIX of the underpayment amount. MERCK shall bear the full cost of
such audit unless such audit discloses an over reporting by ARCHEMIX of more than [***] percent
([***]%) of the aggregate amount of FTE Costs reportable in any Calendar Year in conducting the
Technology Transfer Activities, the ARCHEMIX Research Activities and the ARCHEMIX Development
Activities other than Development activities with respect to Co-Developed Collaboration Aptamers,
in which case ARCHEMIX shall reimburse MERCK for all reasonable costs incurred by MERCK in
connection with such audit.

          6.4.3 R&D External Costs. In addition to the funding obligations in Section 6.4.1
above, MERCK shall [***] for the payment of [***] Third Party research and Development activity
costs (“Third Party Costs”), including, without limitation, contract research organizations,
contract personnel and consultant costs, incurred by ARCHEMIX to the extent set forth in an Annual
Research Plan or Annual Development Plan or otherwise agreed to in writing by MERCK.

     6.5  Milestone Payments.

          6.5.1 Milestones.

               (a) Payment of Milestones. Within [***] days after the occurrence of the following
milestone events, MERCK shall make the corresponding non-refundable, non-creditable payments to
ARCHEMIX for each Program Target, regardless of the number of

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

65

 

Products that are Developed and Commercialized under this Agreement against such Program
Target except as expressly noted below for [***]:

	 	 	 
	Milestone Event	 	Milestone Payment
	1. [***]
	 	$[***]
	2. [***]
	 	$[***]
	3. [***]
	 	$[***]
	4. [***]
	 	$[***]
	5. [***]
	 	$[***]
	6. [***]
	 	$[***]
	7. [***]
	 	$[***]
	8. [***]
	 	$[***]
	9. [***]
	 	$[***]
	10. [***]
	 	$[***]
	11. [***]
	 	$[***]
	12. [***]
	 	$[***]
	13. [***]
	 	$[***]
	14. [***]
	 	$[***]
	15. [***]
	 	$[***]
	16. [***]
	 	$[***]

For purposes of clarity (a) [***] shall be paid for a given Product for up to [***] Indications;
and (b) if payment is made for any milestones with respect to any Product and any of the preceding
milestone payments have not been made with respect to such Product, then such earlier milestone
payments shall be made [***] (for example, if milestone 7 [***] is paid, but milestone 6 [***] has
not been paid, then [***]. Notwithstanding anything contained herein to the contrary, in no event
will MERCK be liable for milestone payments accrued for milestones 1 to 2 and 4 to 16 in excess of

(i) [***] US Dollars for the [***] program,

(ii) [***] US Dollars for the [***],

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

66

 

(iii) [***] US Dollars for [***].

               (b) Adjustments to Milestones. In the event that ARCHEMIX fails to exercise a
Co-Development and Co-Promotion Option applicable to a Development Candidate on or before the
expiration of the applicable Co-Development Option Period or exercises its Opt-Out Right with
respect to a Co-Developed Development Candidate in accordance with Section 4.10.6(d), MERCK shall
pay ARCHEMIX [***] with respect to any Product Derived from such Development Candidate, in
accordance with Section 6.5.1(a); provided, that, except as described in Section 3.9.3 with respect
to the [***] Target, to the extent that such Product was Developed from an ARCHEMIX Internal
Research Project, (i) [***] the [***] with respect to that Product set forth in Section 6.5.1(a)
shall be [***] by an additional [***] percent ([***]%) (e.g., milestone 7 shall be increased from
$[***] to $[***]) and (ii) to the extent ARCHEMIX exercises its Opt-Out Right as described above,
the milestone payments shall be adjusted as described in Section 4.10.6(d).

          6.5.2 Determination that Milestone Events have Occurred; Invoice for Milestone
Payments. MERCK shall provide ARCHEMIX with written notice within [***] days of each
occurrence of a milestone event set forth in Section 6.5.1(a). ARCHEMIX shall provide MERCK with
an invoice for the amount of the milestone payment that is due and payable as promptly as possible
after receipt of such notice. In the event that, notwithstanding the fact that MERCK has not given
such a notice, ARCHEMIX believes any such milestone event has occurred, it shall so notify MERCK in
writing and shall provide to MERCK data, documentation or other information that supports its
belief. Any dispute under this Section 6.5.2 that relates to whether or not a milestone event has
occurred shall be referred to the JSC to be resolved in accordance with Section 2.1.6.

     6.6  Payment of Royalties; Royalty Rates; Accounting and Records.

          6.6.1 Payment of Royalties.

               (a) Royalty Rates. MERCK shall pay ARCHEMIX a royalty based on Annual Net Sales of
each Royalty-Bearing Product in each Calendar Year (or partial Calendar Year) commencing with the
First Commercial Sale of such Royalty-Bearing Product in any country in the Territory and ending
upon the last day of the Royalty Term for such Royalty-Bearing Product, at the following rates:

	 	 	 
	Annual Net Sales	 	Royalty Rate (%)
	[***]
	 	[***]%
	[***]
	 	[***]%
	[***]
	 	[***]%
	[***]
	 	[***]%

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

67

 

     The following hypothetical example illustrates the calculation of royalties under Section
6.6.1(a): If, in any Calendar Year during the Term, Annual Net Sales of a Royalty-Bearing Product
are $[***], the applicable royalty would be $[***], [***]% of Net Sales for Net Sales up to $[***],
[***]% of Net Sales for Net Sales over $[***] and up to $[***] and [***]% of Net Sales for Net
Sales over $[***].

               (b) Royalty Rate Adjustments.

                    (i) Exercise of Co-Development and Co-Promotion Option. In the event that ARCHEMIX
exercises a Co-Development and Co-Promotion Option for a Development Candidate in accordance with
Section 4.10.2(a), the levels of Annual Net Sales for the royalty rates set forth in Section
6.6.1(a) that are applicable to a Product Derived from such Development Candidate in those
countries in which such Product is a Royalty-Bearing Product (i.e. outside the Co-Development
Territory) shall be [***] by [***] percent ([***]%), provided, that, only [***] shall be taken into
account.

                    (ii) Failure to Exercise Co-Development and Co-Promotion Option. In the event that
ARCHEMIX fails to exercise a Co-Development and Co-Promotion Option applicable to a Development
Candidate on or before the expiration of the applicable Co-Development Option Period, any Product
Derived from such Development Candidate shall be deemed to be a Royalty-Bearing Product and MERCK
shall pay ARCHEMIX a royalty based on Annual Net Sales of such Royalty-Bearing Product for purposes
of this Agreement at the rates set forth in Section 6.6.1(a); provided, that, to the extent that
such Royalty-Bearing Product was Developed from an ARCHEMIX Internal Research Project and was not
the result of ARCHEMIX De Novo Research Activities, the royalty rates applicable to the two top
tiers of Annual Net Sales set forth in Section 6.6.1(a) shall be [***] by [***] percentage points
(i.e., the [***]% rate shall be [***] to [***]% and the [***]% rate shall be [***] to [***]%).

                    (iii) Exercise of Opt-Out Right. To the extent that ARCHEMIX exercises its Opt-Out
Right with respect to a Co-Developed Development Candidate in accordance with Section 4.10.6(d),
any Product Derived from such Co-Developed Development Candidate shall be deemed to be a
Royalty-Bearing Product and MERCK shall pay ARCHEMIX a royalty based on Annual Net Sales of such
Royalty-Bearing Product for purposes of this Agreement at the rates set forth in Section 6.6.1(a);
provided, that, (A) except as set forth in Section 3.9.3 with respect to the [***] Target, to the
extent that such Royalty-Bearing Product was Developed from an ARCHEMIX Internal Research Project,
the royalty rates applicable to the two top tiers of Annual Net Sales set forth in Section 6.6.1(a)
shall be [***] by [***] percentage points (i.e., the [***]% rate shall be [***] to [***]% and the
[***]% rate shall be [***] to [***]%); and (B) the royalty rates applicable to sales of such
Royalty-Bearing Product in [***] shall be [***] (1) in the case of an ARCHEMIX 50% Co-Development
Percentage by (x) [***] percent ([***]%) if the Opt-Out Right is exercised on the [***] Opt-Out
Date (but not before) and (y) [***] percent ([***]%) if the Opt-Out Right is exercised after the
[***] Opt-Out Date but on or before the [***] Opt-Out Date, and (2) in the case of an ARCHEMIX
[***]% Co-Development Percentage by (y) [***] percent ([***]%) if the Opt-Out Right is
exercised on the [***] Opt-Out Date (but not before) and (z) [***] percent ([***]%) if the
Opt-Out Right is exercised after the [***] Opt-Out Date but on or before the [***] Opt-Out

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

68

 

Date. For purposes of clarity, the adjustment in the royalty rates described in this Section
6.6.1(b)(iii) shall be determined by first determining the adjustment pursuant to subsection (B)
above and then determining the increase pursuant to subsection (A) above. By way of example, if
ARCHEMIX exercises its Opt-Out Right with respect to a Co-Developed Development Candidate on the
[***] Opt-Out Date, the royalty rates applicable to the two highest tiers of Annual Net Sales
shall be [***] from [***]% and [***]% respectively, to [***]% and [***]%.

               (c) Royalty Offsets. In the event that MERCK, in order to practice the license
granted to it under Section 8.2 of this Agreement in any country in the Territory, is required to
and actually makes royalty, milestone or license fee payments to any Third Party (“Third Party
Payments”) in order (A) to obtain a license to an issued patent or patents in the absence of which
the Lead Compound portion of the Royalty-Bearing Product could not legally be manufactured,
imported, sold, exported, or otherwise exploited in such country and/or (B) to obtain a license to
an issued patent or patents, in the absence of which the Licensed Patent Rights cannot legally be
practiced in such country for making, using, importing, offering for sale, selling, exporting or
otherwise exploiting such Royalty-Bearing Product, then the royalties payable to ARCHEMIX for such
Product under Section 6.6.1(a) with respect to such country may be reduced by [***] percent
([***]%) of the amount of such Third Party Payments. Notwithstanding the foregoing, (i) such
reductions shall in no event reduce the royalty that would otherwise be payable for such
Royalty-Bearing Product under Section 6.6.1 with respect to such country by more than [***] percent
([***]%) of the amount otherwise payable with respect to Net Sales of such Product in such country,
(ii) MERCK shall be responsible for the payment of any royalty, milestone or license fee payments
to any Third Party relating to methods or processes for making or manufacturing the Royalty-Bearing
Product and the royalties payable to ARCHEMIX pursuant to Section 6.6.1(a) [***], and (iii) in the
event that MERCK requires that ARCHEMIX use in the Research Program molecules, methods and/or
processes not identified in Schedule 10 or MERCK requires that ARCHEMIX use in the Research
Program specific molecules, methods and/or processes where such molecules, methods and/or processes
are generically identified in Schedule 10 (“Requested Chemistry”), thereby giving rise to
the obligation to pay royalty, milestone or license fee payments to a Third Party (“Third Party
Chemistry Payments), MERCK [***] of such Third Party Chemistry Payments and the royalties payable
to ARCHEMIX pursuant to Section 6.6.1(a) [***] Third Party Chemistry Payments.

               (d) Competing Aptamer Products. In the event that a Third Party sells a Competing
Aptamer Product (as defined below) in a country in which a Royalty-Bearing Product is then being
sold and such Competing Aptamer Product is not covered by a Valid Claim under the Licensed Patent
Rights, Program Aptamer-Specific Patent Rights, or Joint Patent Rights in such country, then,
during the period in which sales of the Competing Aptamer Product by such Third Party are equal to
at least [***] percent ([***]%) of MERCK’s volume-based market share of the Royalty-Bearing Product
in such country (as measured by prescriptions or other similar information available in such
country) [***] in effect with respect to such Product in such country as specified in Section
6.6.1(a) shall be [***] by [***] percent ([***]%). Notwithstanding the foregoing, (i) MERCK’s
obligation to pay royalties at the full royalty rates shall be reinstated on the first day of the
Calendar Quarter immediately following the Calendar Quarter in which sales of such Competing
Aptamer Product account for less than [***] percent ([***]%) of MERCK’s volume-based market share
in such country and (ii) the provisions of this

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

69

 

Section 6.6.1(d) shall not apply for any country in which MERCK has not [***] for [***] for
the applicable Collaboration Aptamer(s) or has not otherwise used commercially reasonable efforts
to [***] for such Collaboration Aptamer(s). For purposes of this Section 6.6.1(d), a “Competing
Aptamer Product” means a pharmaceutical product that (i) contains an [***] and (ii) is marketed in
a country [***] as the [***].

               (e) Generic Products. In the event that a Third Party sells a Generic Product (as
defined below) in a country in which a Royalty-Bearing Product is then being sold and such Generic
Product is not covered by a Valid Claim under the Licensed Patent Rights, Program Aptamer-Specific
Patent Rights, or Joint Patent Rights in such country, then during the period in which sales of the
Generic Product by such Third Party are equal to at least [***] percent ([***]%) of MERCK’s
volume-based market share of the Royalty-Bearing Product in such country (as measured by
prescriptions or other similar information available in such country), MERCK shall pay [***]
percent ([***]%) of the full applicable royalties in effect with respect to such Royalty-Bearing
Product in such country as specified in Section 6.6.1(a). Notwithstanding the foregoing, (i)
MERCK’s obligation to pay royalties at the full royalty rates shall be reinstated on the first day
of the Calendar Quarter immediately following the Calendar Quarter in which sales of such Generic
Product account for less than [***] percent ([***]%), (ii) the provisions of this Section 6.6.1(e)
shall not apply for any country in which MERCK has not [***] for [***] for the applicable
Collaboration Aptamer(s) or has not otherwise used commercially reasonable efforts to [***] for
such Collaboration Aptamer(s). For purposes of this Section 6.6.1(e), a “Generic Product” means a
pharmaceutical product that contains the [***] and [***] to [***].

               (f) Maximum Adjustment of Royalty Rate. Notwithstanding anything to the contrary in
this Agreement, under no circumstances shall the royalty rates in Section 6.6.1(a) be cumulatively
reduced below [***] percent ([***]%) of the rates set forth therein.

               (g) Know-How Payments. The Parties hereby acknowledge and agree that any royalties
that are payable for a Product for which no Patent Rights exist shall be in consideration of (i)
ARCHEMIX’s expertise and know-how concerning the identification of aptamers in the Field, including
its development of the SELEX Process and its other aptamer-related development activities conducted
prior to the Effective Date; (ii) the performance by ARCHEMIX of the Research Program, (iii) the
disclosure by ARCHEMIX to MERCK of results obtained in the Research Program; (iv) the licenses
granted to MERCK hereunder with respect to Licensed Technology and Joint Technology that are not
within the claims of any Patent Rights Controlled by ARCHEMIX; (v) the restrictions on ARCHEMIX in
Section 8.7.1; and (vi) the “head start” afforded to MERCK by each of the foregoing.

               (h) Payment Dates and Reports. Royalty payments shall be made by MERCK within [***]
days after the end of each [***] commencing with the [***] in which the First Commercial Sale of a
Royalty-Bearing Product occurs. MERCK shall also provide, at the same time each such payment is
made, a report showing: (a) the Net Sales of each Royalty-Bearing Product by type of
Royalty-Bearing Product and country in the Territory; (b) the basis for any deductions from gross
amounts billed or invoiced to determine Net Sales; (c) the applicable royalty rates for such
Royalty-Bearing Product; (d) the exchange rates used in

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

70

 

calculating any of the foregoing; and (e) a calculation of the amount of royalty due to
ARCHEMIX.

               (i) Combination Products. The earned royalty due on a Combination Product shall be
determined pro rata on a Combination Product-by-Combination Product and country-by-country basis,
by multiplying Net Sales of the Combination Product by the fraction A/(A+B), where A is the invoice
price of the Royalty-Bearing Product when sold separately and B is the invoice price of the
Supplemental Product when sold separately by a Party, its Affiliate or its Sublicensee or, if not
sold by them, then the average invoice price when sold separately by Third Parties. If the
Supplemental Product in the Combination Product is not sold separately by any Person, Net Sales
shall be calculated by multiplying actual net revenues derived from sales of the Combination
Product by the fraction A/C, where A is as previously defined and C is the invoice price of the
Combination Product sold by a Party, its Affiliate or its Sublicensee. For purposes of clarity,
the average invoice price and the actual net revenues for any Supplemental Product shall be for a
quantity comparable to that contained in the Combination Product and shall be of the same class,
purity and potency as that contained in the Combination Product. If neither the Royalty-Bearing
Product nor the Supplemental Product included in the Combination Product are sold separately, Net
Sales shall be calculated based on the mutual written agreement of the Parties as to a reasonable
allocation between the Royalty-Bearing Product and the Supplemental Product, taking into account
total manufacturing costs, proprietary protection and relative contribution thereof. If the
Parties are unable to reach agreement on an appropriate method of determining royalties for a
Combination Product, the matter shall be submitted to the JSC for resolution under Section 2.1.6.

          6.6.2 Records; Audit Rights. MERCK and its Affiliates and Sublicensees shall keep and
maintain for [***] years from the date of each payment of royalties hereunder complete and accurate
records of gross sales and Net Sales by MERCK and its Affiliates and Sublicensees of each
Royalty-Bearing Product, in sufficient detail to allow royalties to be determined accurately.
ARCHEMIX shall have the right for a period of [***] years after receiving any such royalty payment
to appoint at its expense an independent certified public accountant reasonably acceptable to MERCK
to audit the relevant records of MERCK and its Affiliates and Sublicensees to verify that the
amount of such payment was correctly determined. MERCK and its Affiliates and Sublicensees shall
each make its records available for audit by such independent certified public accountant during
regular business hours at such place or places where such records are customarily kept, upon [***]
days written notice from ARCHEMIX, solely to verify that royalty payments hereunder were correctly
determined. Such audit right shall not be exercised by ARCHEMIX more than [***] in any [***] or
more than [***] with respect to sales of a particular Product in a [***]. All records made
available for audit shall be deemed to be Confidential Information of MERCK. The results of each
audit, if any, shall be binding on both Parties. In the event there was an underpayment by MERCK
hereunder, MERCK shall promptly (but in any event no later than [***] days after MERCK’s receipt of
the report so concluding) make payment to ARCHEMIX of any shortfall. ARCHEMIX shall bear the full
cost of such audit unless such audit discloses an underreporting by MERCK of more than [***]
percent ([***]%) of the aggregate amount of royalties payable in any Calendar Year, in which case
MERCK shall reimburse ARCHEMIX for all costs incurred by ARCHEMIX in connection with such audit.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

71

 

          6.6.3 Overdue Royalties and Milestones. All royalty payments not made within the time
period set forth in Section 6.6.1(h), including underpayments discovered during an audit, and all
milestone payments not made within the time period specified in Section 6.5.1, shall bear interest
at a rate of [***] percent ([***]%) per month from the due date until paid in full or, if less, the
maximum interest rate permitted by Applicable Laws. Any such overdue royalty or milestone payment
shall, when made, be accompanied by, and credited first to, all interest so accrued.

     6.7 Net Income Payments.

          6.7.1 Net Income Payments. ARCHEMIX shall receive from MERCK, in lieu of receiving
any royalty payments with respect to the Commercialization of each Co-Developed Product in the
Co-Development Territory, the ARCHEMIX Co-Development Sharing Percentage of all Annual Net Income
derived from sales of that Co-Developed Product in the Co-Development Territory as described herein
for as long as there are sales by MERCK, its Affiliates or Sublicensees of such Co-Developed
Product in the Co-Development Territory (such payments, the “Net Income Payments”). Within [***]
days following the end of each Calendar Quarter commencing on and after the date of First
Commercial Sale of each Co-Developed Product, (a) ARCHEMIX shall submit to the JDC all expenses
incurred by it that qualify as deductions from Net Sales with respect to such Co-Developed Product
in the Co-Development Territory as set forth in Schedule 11 in the definition of Net Income and (b)
MERCK shall submit to the JDC all expenses incurred by it that qualify as deductions from Net Sales
(again as set forth in Schedule 11 in the definition of Net Income) with respect to, as well as the
Net Sales and Cost of Goods of the Co-Developed Product applicable to, such Co-Developed Product.
Within [***] days following the end of the Calendar Quarter, the JDC shall submit to the Parties a
written report setting forth in reasonable detail (i) the calculation of Annual Net Income,
determined in accordance with Schedule 11 attached hereto and (ii) the calculation of the
amount of Annual Net Income payable to ARCHEMIX, or for which ARCHEMIX is responsible, as the case
may be, in accordance with its ARCHEMIX Co-Development Sharing Percentage for that Co-Developed
Product taking into account ARCHEMIX’s expenditures for the period. All Net Income Payments
payable by MERCK or ARCHEMIX, as the case may be, to the other Party shall be paid within [***]
days following issuance of such written report. For purposes of clarity, all references to the JDC
above shall be deemed to refer to MERCK if the Parties do not establish the JDC.

          6.7.2 Audit Rights. ARCHEMIX and MERCK shall each keep complete and accurate books
and financial records pertaining to its costs and expenses incurred in the Development and
Commercialization of Co-Developed Products and of Net Sales of such Co-Developed Products sold by
them, which books and financial records shall be retained by them until [***] years after the end
of the Calendar Year to which they pertain. Each Party shall have the right to appoint at its
expense an independent certified public accountant reasonably acceptable to the other Party to
audit the books and financial records of the other Party relating to the foregoing during any
Calendar Year; provided, that, the auditing Party shall not have the right to audit any Calendar
Year more than once or more than [***] years after the end of such Calendar Year or to conduct more
than one such audit in any [***] period. All books and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

72

 

           financial records made available for audit shall be deemed to be Confidential Information of
the audited Party.

     6.8 Payments. All payments made by MERCK hereunder shall be made by wire transfer in
US Dollars in accordance with instructions given in writing from time to time by ARCHEMIX and shall
be free and clear of any taxes, duties, levies, fees or charges including any withholding taxes.
If by law, regulations or fiscal policy of a particular country in the Territory, remittance of
royalties in United States Dollars is restricted or forbidden, written notice thereof shall
promptly be given to ARCHEMIX, and such payment shall be made by the deposit thereof in local
currency to the credit of ARCHEMIX in a recognized banking institution designated by ARCHEMIX by
written notice to MERCK. When in any country in the Territory the law or regulations prohibit both
the transmittal and the deposit of royalties, on sales in such country, such payments shall be
suspended for as long a such prohibition is in effect and as soon as such prohibition ceases to be
in effect, all royalties that MERCK would have been under an obligation to transmit or deposit but
for the prohibition shall forthwith be deposited or transmitted, to the extent allowable.

     6.9 Taxes. Any income taxes or other taxes which MERCK is required by law to pay or
withhold on behalf of ARCHEMIX with respect to milestones, royalties and any other monies or other
transfer for value payable or provided to ARCHEMIX under this Agreement shall be deducted from such
milestones, royalties, Net Income Payments and any other monies due to ARCHEMIX under this
Agreement. MERCK shall provide ARCHEMIX with documentation of such withholding in a manner that is
satisfactory for purposes of reporting to the U.S. Internal Revenue Service. Payments made by
either Party for goods and services provided by the other Party under this Agreement are exclusive
of Value Added Tax, sales tax or any other similar or substitute tax which will be additionally
payable by the Party receiving the goods or services in the event that Value Added Tax, sales tax
or any other similar or substitute tax applies to any of these payments; provided, that, the Party
providing the goods or services will issue to the other Party an appropriate invoice to support any
such charge. MERCK shall submit to ARCHEMIX reasonable proof of payment of the withholding taxes
contemplated by this Section 6.9, together with an accounting of the calculations of such taxes,
within [***] days after which such withholding taxes are remitted to the proper authority. The
Parties will cooperate reasonably in completing and filing documents required under the provisions
of any applicable tax laws or under any other Applicable Laws, in connection with the making of any
required tax payment or withholding payment, or in connection with any claim to a refund of or
credit for any such payment. The Parties will cooperate to minimize such taxes in accordance with
Applicable Laws.

     6.10 US Partnership. In the event that (i) ARCHEMIX exercises its Co-Development and
Co-Promotion Option as set forth in Section 4.10.2 above; and (ii) MERCK determines that such
collaboration in the Co-Development Territory should be characterized as a partnership for U.S.
income tax purposes (a “Partnership”), the Parties agree as follows:

(a) Only the activities of the Parties performed in the Co-Development Territory (the “U.S.
Activities”) after exercise by ARCHEMIX of a Co-Development and Co-Promotion Option will be
considered as Partnership activities, notwithstanding the allocation of global Development

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

73

 

expenses to the Partnership described below in Section 6.10(c); all prior and the remaining
activities under this Agreement will continue to be characterized as a licensing relationship
between MERCK and ARCHEMIX.

(b) In addition to the separate Co-Promotion Agreement the Parties will enter into a co-finance
agreement (the “Co-Finance Agreement”) that shall be structured as a partnership agreement with
respect to the US Activities. Such agreement shall contain provisions setting out in greater detail
the agreement of the Parties with respect to revenue and expense sharing, funding, risk of loss,
distributions and allocation of Net Income and separately stated items, as summarized in this
Section 6.10.

(c) For purposes of the Partnership, the Parties will treat [***]% of the Co-Development Costs as
attributable to the US Partnership. In addition, the Parties will treat [***]% of actual US related
Co-Development Regulatory Costs and Co-Development Commercialization Costs as attributable to the
US Partnership. The Parties agree that Net Income and Co-Development Commercialization Costs and
Co-Development Regulatory Costs attributable to the Partnership shall be shared either [***] or
[***], and that the Co-Development Costs shall be shared either [***] or [***], by MERCK and
ARCHEMIX, respectively, in accordance with which ever option is chosen by ARCHEMIX pursuant to
Section 4.10.2.(a). In any fiscal year, should actual Co-Development Costs associated with U.S.
Activities be less than [***]% of total Co-Development Costs, the difference between the actual
expenses performed in the U.S and [***]% of Co-Development Costs will be deemed to be non-US
incurred or foreign sourced, yet still allocable to the US Partnership. The remaining [***]% of the
Co-Development Costs will be considered development expenses related to activities outside the
Partnership, and thus to the MERCK license.

(d) The contribution or license of each Party’s intellectual property rights will be characterized
in a manner that maximizes both Parties` ability to claim R&D credits in the U.S. consistent with
I.R.C. Section 704(b) and the regulations thereunder.

(e) The Co-Finance Agreement shall include the provisions, terms and conditions necessary to
reflect the intent of the Parties that the tax credits, distributions, capital accounts and
liquidation values approximate the sharing percentages set forth in (c) above.

(f) That (i) all reasonable third party expenses incurred by both Parties to draft and execute a
Co-Finance Agreement, and to prepare any US Federal or state tax filings on behalf of the
Partnership, shall be borne (A) in the ARCHEMIX [***]% Co-Development Sharing Percentage, [***] by
MERCK (or an Affiliate of MERCK) and ARCHEMIX, respectively, and (B) in the ARCHEMIX [***]%
Co-Development Sharing Percentage [***]%/[***]% by MERCK (or an Affiliate of MERCK) and ARCHEMIX,
respectively, and (ii) EMD Serono Inc (or another US Affiliate of MERCK) shall be the tax matters
partner for administrative purposes.

     6.11 Foreign Currency Exchange. All royalties and Net Income Payments shall be
payable in full in the United States in United States Dollars, regardless of the countries in which
sales are made. With respect to amounts invoiced by MERCK (or its Affiliates or Sublicensees) for
Products, all such amounts shall be expressed in EURO and, if applicable, the currency in

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

74

 

which the amount was invoiced. Any conversion from a currency to EURO shall be calculated
using MERCK’s standard exchange rate methodology applied in its external reporting in effect as of
the Effective Date and set forth on Schedule 9 attached hereto. Such Net Sales shall be
converted into United States Dollars as follows:

          (A/B), where

                    A = “Net Sales” (as defined above) in such Calendar Quarter expressed in
EURO; and

                    B = foreign exchange conversion rate, expressed in EURO per United States
Dollar (using, the applicable EURO exchange rate, 

                    set forth on Schedule
9 attached hereto or any other mutually agreed upon source, for such
Calendar Quarter).

7. TREATMENT OF CONFIDENTIAL INFORMATION;

PUBLICITY; NON-SOLICITATION.

     7.1 Confidentiality.

          7.1.1 Confidentiality Obligations. ARCHEMIX and MERCK each recognizes that the other
Party’s Confidential Information and Proprietary Materials constitute highly valuable assets of
such other Party. ARCHEMIX and MERCK each agrees that, subject to Section 7.1.2, it will not
disclose, and will cause its Affiliates and sublicensees (or Sublicensees, as the case may be) not
to disclose, any Confidential Information or Proprietary Materials of the other Party and it will
not use, and will cause its Affiliates and sublicensees (or Sublicensees, as the case may be) not
to use, any Confidential Information or Proprietary Materials of the other Party except as
expressly permitted hereunder; provided, that, such obligations shall apply during the Term and for
an additional [***] years thereafter.

          7.1.2 Limited Disclosure. ARCHEMIX and MERCK each agrees that disclosure of its
Confidential Information or any transfer of its Proprietary Materials may be made by the other
Party to any employee, consultant or Affiliate of such other Party to enable such other Party to
exercise its rights or to carry out its responsibilities under this Agreement; provided, that, any
such disclosure or transfer shall only be made to Persons who are bound by written obligations as
described in Section 7.1.3. In addition, ARCHEMIX and MERCK each agrees that the other Party may
disclose its Confidential Information (a) on a need-to-know basis to such other Party’s legal and
financial advisors, (b) as reasonably necessary in connection with an actual or potential (i)
permitted sublicense of such other Party’s rights hereunder, (ii) Third Party collaborators,
subject to written obligations of confidentiality substantially similar to those of ARCHEMIX
hereunder, and provided that any Confidential Information so provided will in no event include
information identifying any Program Targets, (iii) debt or equity financing of such other Party or
(iv) Change of Control involving such other Party, (c) if such other Party is ARCHEMIX, to any
Third Party that is or may be engaged by ARCHEMIX to perform services in connection with the
Research Program, and (d) for any other purpose with the other Party’s written consent, not to be
unreasonably withheld, conditioned or delayed. In addition, each Party

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

75

 

agrees that the other Party may disclose such Party’s Confidential Information or Proprietary
Materials (A) as reasonably necessary to file, prosecute or maintain Patent Rights, or to file,
prosecute or defend litigation related to Patent Rights, in accordance with this Agreement; or (B)
as required by Applicable Laws; provided, that, in the case of any disclosure under this clause
(B), the disclosing Party shall (1) if practicable, provide the other Party with reasonable advance
notice of and an opportunity to comment on any such required disclosure and (2) if requested by the
other Party, cooperate in all reasonable respects with the other Party’s efforts to obtain
confidential treatment or a protective order with respect to any such disclosure, at the other
Party’s expense.

          7.1.3 Employees and Consultants. ARCHEMIX and MERCK each hereby represents that all
of its employees and consultants, and all of the employees and consultants of its Affiliates, who
participate in the activities of the Collaboration or have access to Confidential Information or
Proprietary Materials of the other Party are or will, prior to their participation or access, be
bound by written obligations to maintain such Confidential Information or Proprietary Materials in
confidence and not to use such information except as expressly permitted hereunder. Each Party
agrees to use, and to cause its Affiliates to use, reasonable efforts to enforce such obligations.

     7.2 Publicity. The Parties acknowledge that the terms of this Agreement constitute
Confidential Information of each Party and may not be disclosed except as permitted by Section
7.1.2 and this Section 7.2. Such terms may be disclosed by a Party to (i) investment bankers,
investors, and potential investors, lenders and potential lenders and other sources and other
potential sources of financing, acquirer or merger partners and potential acquirer or merger
partners but only to the extent reasonably necessary, (ii) Gilead but only to the extent required
pursuant to the ARCHEMIX-Gilead License Agreement and (iii) University License Equity Holdings,
Inc. but only to the extent required pursuant to the URC License Agreement. In addition, a copy of
this Agreement may be filed by either Party with the Securities and Exchange Commission if such
filing is required by law or regulation. In connection with any such filing, such Party shall
endeavor to obtain confidential treatment of economic and trade secret information, and shall
provide the other Party with the proposed confidential treatment request with reasonable time for
such other Party to provide comments, which comments shall be reasonably considered by the filing
Party; provided, that, in no event shall any of the Program Targets be disclosed. In addition,
ARCHEMIX shall only be permitted to disclose the identity of Program Targets to investment bankers,
investors and potential investors, lenders and potential lenders, and other sources and other
potential sources of financing, acquirer or merger partners and potential acquirer or merger
partners under confidentiality undertakings at least as stringent as the ones set forth herein.
Notwithstanding anything to the contrary in Section 7.1, the Parties, upon the execution of this
Agreement, shall agree to a press release with respect to this Agreement, in the form attached here
to as Schedule 6, and either Party may make subsequent public disclosure of the contents of
such press release without further approval of the other Party. After issuance of such press
release, except as required by Applicable Laws, neither Party shall issue a press or news release
or make any similar public announcement (it being understood that publication in scientific
journals, presentation at scientific conferences and meetings and the like are intended to be
covered by Section 7.3 and not subject to this Section 7.2) related to the Research Program or to
any Development Program without the prior written consent of the other

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

76

 

Party; provided, that, (a) notwithstanding the foregoing, ARCHEMIX shall be expressly
permitted to publicly announce the occurrence of any milestone event under Section 6.5.1 and any
other event that ARCHEMIX reasonably believes is material to ARCHEMIX; (b) MERCK (i) expressly
acknowledges that ARCHEMIX is an emerging company the success of which is substantially dependent
on its ability to attract and raise capital and that ARCHEMIX’s ability to attract and raise
capital is substantially dependent on its ability to announce publicly developments in its research
and development programs or product development pipeline and (ii) agrees that it shall not
unreasonably withhold, condition or delay its consent to any request by ARCHEMIX to announce
publicly developments in the Research Program or any Development Program; and (c) ARCHEMIX (i)
expressly acknowledges that MERCK’s Development and Commercialization is substantially dependent on
its ability to protect confidential information and (ii) agrees that it shall not unreasonably
request to announce developments in the Research Program or any Development Program that may reduce
a competitive advantage versus competing entities.

     7.3 Publications and Presentations. The Parties acknowledge that scientific
publications and presentations must be strictly monitored to prevent any adverse effect from
premature publication or dissemination of results of the activities hereunder. Each Party agrees
that, except as required by Applicable Laws, it shall not publish or present, or permit to be
published or presented, the results of the Research Program or any Development Program without the
prior review by and approval of the other Party. Each Party shall provide to the other Party the
opportunity to review each of the submitting Party’s proposed abstracts, manuscripts or
presentations (including, without limitation, information to be presented verbally) that relate to
the Research Program or any Development Program at least [***] days prior to its intended
presentation or submission for publication, and such submitting Party agrees, upon written request
from the other Party given within such [***] period, not to submit such abstract or manuscript for
publication or to make such presentation until the other Party is given up to [***] days from the
date of such written request to seek appropriate patent protection for any material in such
publication or presentation that it reasonably believes may be patentable. Once such abstracts,
manuscripts or presentations have been reviewed and approved by each Party, the same abstracts,
manuscripts or presentations do not have to be provided again to the other Party for review for a
later submission for publication. Each Party also shall have the right to require that any of its
Confidential Information that is disclosed in any such proposed publication or presentation be
deleted prior to such publication or presentation. In any permitted publication or presentation by
a Party, the other Party’s contribution shall be duly recognized, and co-authorship shall be
determined in accordance with customary standards. Each Party (i) expressly acknowledges that the
other Party’s business may be substantially dependent on its ability to publish results in
scientific journals, presentation at scientific conferences and meetings and (ii) agrees that it
shall not unreasonably withhold, condition or delay its consent to any request by the other Party
to publish results of the Research Program or any Development Program in accordance with its
internal publication guidelines.

     7.4 Prohibition on Solicitation. Without the written consent of the other Party,
neither Party nor its Affiliates shall, during the [***] or for [***] year thereafter, solicit
(directly or indirectly) any employee of the other Party or its Affiliates who participated in the
Research Program at any time during the Research Program Term. This provision shall not restrict
either

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

77

 

Party or its Affiliates from advertising employment opportunities in any manner that does not
directly target the other Party or its Affiliates.

8. LICENSE GRANTS; EXCLUSIVITY

     8.1 SELEX License; Research and Development Licenses.

          8.1.1 ARCHEMIX License Grants.

               (a) SELEX License.

                    (i) License Grant. Subject to the other terms of this Agreement, ARCHEMIX hereby
grants to MERCK and its Affiliates a non-exclusive, royalty-free, worldwide license during the
SELEX License Term, without the right to grant sublicenses, under the Licensed Technology and
Licensed Patent Rights, for the purpose of using the SELEX Process and the SELEX Technology solely
to conduct Target Validation Activities in accordance with Section 3.15 (the “SELEX License”).

                    (ii) Negative Covenants. Notwithstanding the foregoing but without limiting any of
the other terms, conditions and limitations contained in this Agreement, MERCK hereby acknowledges
and agrees that it shall not use the SELEX Process or the SELEX Technology or practice the SELEX
License for any purpose or use outside of the conduct of Target Validation Activities in accordance
with Section 3.15, including without limitation, (A) to perform any research or development on any
aptamer for any use outside of the Field and/or (B) to research, develop, make, use, sell, offer
for sale, import or export any Excluded Aptamers and/or (C) to perform Target Validation Activities
for any Target not identified in a Target Validation Response.

                    (iii) Reports Under SELEX License. MERCK shall provide ARCHEMIX with a written report
at least once each Calendar Year that describes any MERCK SELEX Improvements (including any patent
applications, if any, filed with respect to such MERCK SELEX Improvements) conceived or reduced to
practice over the [***] month period covered by such report. Each such report shall include, at a
minimum, information reasonably sufficient to enable ARCHEMIX to satisfy its reporting obligations
to Gilead under the Gilead-ARCHEMIX License Agreement with respect to this Agreement.

               (b) Research Program. Subject to the terms and conditions of this Agreement, ARCHEMIX
hereby grants to MERCK and its Affiliates a non-exclusive, royalty-free, worldwide license during
the Research Program Term, including the right to subcontract as provided in Section 8.5, under
Licensed Technology and Licensed Patent Rights, for the sole purpose of conducting MERCK Research
Activities in the Research Program.

               (c) Development Program. Subject to the terms and conditions of this Agreement,
ARCHEMIX hereby grants to MERCK and its Affiliates, an exclusive, royalty-free, worldwide license
during the Term, including the right to grant sublicenses as provided in Section 8.4 and the right
to subcontract as provided in Section 8.5, under Licensed Technology

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

78

 

and Licensed Patent Rights, for the sole purpose of Developing Optimized Lead Compounds and
Development Candidates in the Field and in the Territory.

          8.1.2 MERCK Grants.

               (a) Research Program. Subject to the terms and conditions of this Agreement, MERCK
hereby grants to ARCHEMIX and its Affiliates a non-exclusive, royalty-free, worldwide license
during the Research Program Term, including the right to subcontract as provided in Section 8.5,
under MERCK Technology and MERCK Patent Rights and MERCK’s interest in Joint Technology and Joint
Patent Rights, for the sole purpose of conducting the Research Program.

               (b) Development Program. Subject to the terms and conditions of this Agreement, MERCK
hereby grants to ARCHEMIX and its Affiliates a non-exclusive, royalty-free, worldwide license
during the Term, including the right to subcontract as provided in Section 8.5, under MERCK
Technology and MERCK Patent Rights and MERCK’s interest in Joint Technology and Joint Patent Rights
and under Licensed Technology and Licensed Patent Rights exclusively licensed to MERCK under
Section 8.1.1(c), for the sole purpose of conducting ARCHEMIX Development Activities in any
Development Program, to the extent such ARCHEMIX Development Activities are mutually agreed by the
Parties and of conducting the co-Development of Co-Developed Products.

               (c) Waived Targets.

                    (i) Designation Notice. Upon its designation of any Program Target as a Waived
Target, MERCK shall provide written notice (“Designation Notice”) to ARCHEMIX identifying each such
Program Target.

                    (ii) Assignment. MERCK hereby assigns to ARCHEMIX all right, title and interest in
and to all MERCK Program Technology relating to Waived Compounds or Waived Targets, Patent Rights
claiming MERCK Program Technology relating to Waived Compounds or Waived Targets, MERCK
Co-Developed Program Technology relating to Waived Compounds or Waived Targets, Patent Rights
claiming MERCK Co-Developed Program Technology relating to Waived Compounds or Waived Targets and
MERCK’s interest in Joint Technology relating to Waived Compounds or Waived Targets and Joint
Patent Rights relating to Waived Compounds or Waived Targets. ARCHEMIX may, at its option,
continue to Develop a Waived Compound, subject to the payment by ARCHEMIX to MERCK, for any Waived
Compound, and any Products Derived therefrom, that are Developed and Commercialized by ARCHEMIX,
its Affiliates or sublicensees, of (A) a [***] on the Milestone Payment Due Date (as defined below)
[***] the Applicable Milestone Payment (as defined below) and (B) royalty payments at rates [***]
the Applicable Percentage (as defined below) of the rates set forth in Sections 6.6.1, for the
remainder of the applicable Royalty Term.

                    (iii) Calculation of Royalties. In calculating the payments due to MERCK for the
assignments granted in this Section 8.1.2(c), the terms of Section 6.6 and all related obligations
(including the right to offset payments in accordance with Section 6.6.1(b)

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

79

 

through (e)) shall apply mutatis mutandis to each such Waived Compound and Product Derived
therefrom.

                    (iv) Transition Plan. ARCHEMIX shall have a period of up to [***] months commencing
on the date of receipt of the Designation Notice or a Program Target otherwise becomes a Waived
Target to notify MERCK that it intends to continue to Develop or Commercialize a Waived Compound.
Upon receipt of such notice, the Parties will agree on a transition plan pursuant to which MERCK
will, depending on the stage of development of such Waived Compound(s), obligate MERCK to timely
perform the activities in Sections 8.1.2(c)(iv)(A) through (J). In order for MERCK to agree to
each such transition plan, ARCHEMIX shall agree to use Commercially Reasonable Efforts to Develop
and Commercialize the Waived Compound(s) identified by ARCHEMIX and which are the subject of a
transition plan for continued Development and Commercialization. The transition plan shall
include, as applicable, an obligation by MERCK to:

                         (A) grant to ARCHEMIX an exclusive, worldwide, royalty-free, paid-up license under all Product
Trademarks applicable to such Waived Compound(s), if any;

                         (B) transfer to ARCHEMIX all of its right, title and interest in all Regulatory Filings, Drug
Approval Applications and Regulatory Approvals then in its name applicable to such Waived
Compound(s), if any;

                         (C) notify the applicable Regulatory Authorities and take any other action reasonably
necessary to effect such transfer;

                         (D) provide ARCHEMIX with copies of all correspondence between MERCK and such Regulatory
Authorities relating to such Regulatory Filings, Drug Approval Applications and Regulatory
Approvals;

                         (E) unless expressly prohibited by any Regulatory Authority, transfer control to ARCHEMIX of
all clinical trials of such Waived Compound(s) being conducted as of the time of designation by
MERCK of the Waived Compound and continue to conduct such trials at its expense for up to [***]
months commencing on the date of receipt of the Designation Notice or a Program Target otherwise
becomes a Waived Target to enable such transfer to be completed without interruption of any such
trial, unless ARCHEMIX demonstrates to MERCK to MERCK’s satisfaction that ARCHEMIX shall not be
able to assume such clinical trials within four months, in which case MERCK shall continue to
conduct such trials for up to [***] additional months;

                         (F) assign (or cause its Affiliates to assign) to ARCHEMIX all agreements with any Third Party
with respect to the conduct of clinical trials for such Waived Compound(s) including, without
limitation, agreements with contract research organizations, clinical sites and investigators,
unless expressly prohibited by any such agreement (in which case MERCK shall cooperate with
ARCHEMIX in all reasonable respects to secure the consent of such Third Party to such assignment);

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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                         (G) provide ARCHEMIX with all supplies of such Waived Compound(s) in the possession of MERCK
or any Affiliate or contractor of MERCK;

                         (H) provide ARCHEMIX with copies of all reports and data generated or obtained by MERCK or its
Affiliates pursuant to this Agreement that relate to such Waived Compound(s) that have not
previously been provided to ARCHEMIX;

                         (I) reimburse ARCHEMIX for all internal and out-of-pocket costs incurred by ARCHEMIX in
continuing the research and Development according to the pre-agreed Annual Development Plan of such
Waived Compound(s) for a period of [***] days; and

                         (J) if MERCK has manufactured, is manufacturing or having manufactured such Waived Compound(s)
or any intermediate thereof as of the date the applicable Program Target becomes a Waived Target:
(i) MERCK shall, if requested by ARCHEMIX, supply ARCHEMIX with its requirements for such Waived
Compound(s) and intermediates for up to [***] months following such date at a transfer price equal
to [***] for the supply of such Waived Compound(s) or intermediate, plus [***] percent ([***]%),
(ii) within [***] days after ARCHEMIX’s request, MERCK shall provide to ARCHEMIX or its designee
all information in its possession with respect to the manufacture of each such Waived Compound(s)
or intermediate.

                    (v) Definitions. For purposes of this Section 8.1.2(c), the following terms shall
have the following definitions:

“Applicable Milestone Payment” shall mean, with respect to each Waived Compound, an
aggregate amount equal to [***] by MERCK with respect to such Waived Compound for (a)
milestone events 2, 3 and 4 to the extent ARCHEMIX makes [***] of [***] applicable to such
Waived Compound; or (b) milestone events 2 and 3 to the extent ARCHEMIX makes [***] of [***]
and/or [***] applicable to such Waived Compound.

“Applicable Percentage” shall mean, with respect to each Waived Compound, (a) [***]
percent ([***]%), to the extent ARCHEMIX makes [***] of [***] in the development and
commercialization of such Waived Compound; (b) [***] percent ([***]%), to the extent
ARCHEMIX makes [***] of [***] and/or [***] in the development and commercialization of such
Waived Compound, (c) [***] percent ([***]%), if neither of the foregoing (a) nor (b) apply,
but ARCHEMIX is developing and commercializing a Waived Compound that was a [***], and (d)
[***] percent ([***]%) if ARCHEMIX is developing and commercializing an [***], other than a
[***] or an [***], against the Waived Target, provided that in such case ARCHEMIX shall not
make [***] of [***].

“Clinical Data” means all data, results and information produced in the conduct of a
Phase I Clinical Trial (“Phase I Clinical Data”), a Phase II Clinical Trial
(“Phase II Clinical Data”) or a Phase III Clinical Trial (“Phase III Clinical
Data”) conducted by MERCK with respect to a Waived Compound.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

81

 

“Material Use” means, with respect to Clinical Data, the inclusion of such Clinical
Data in a core report of an NDA filed by ARCHEMIX as evidenced by (i) the use of a bridging
study to utilize such Clinical Data, (ii) the elimination for the need to duplicate such
Clinical Data, or (iii) the ability to reduce the number of patients enrolled in a clinical
trial due to the use of such Clinical Data.

“Milestone Payment Due Date” means, with respect to a Waived Compound, (a) to the
extent a Program Target becomes a Waived Target prior to the Initiation of [***], the date
of the Initiation of [***] with respect to such Waived Compound; (b) to the extent a Program
Target becomes a Waived Target after [***] but prior to the Initiation of [***], the date of
the Initiation of [***] with respect to such Waived Compound; and (c) to the extent a
Program Target becomes a Waived Target after [***] but prior to filing for [***], the date
on which such filing for [***] occurs.

                    (vi) Further Assurances. Upon ARCHEMIX’s written request, MERCK shall execute and
deliver any documents of ownership, assignment or conveyance that are necessary or desirable to
convey the ownership rights granted pursuant to this Section 8.1.2(c).

               (d) Improvement Rights. Subject to the other terms of this Agreement, MERCK hereby
(i) grants to ARCHEMIX a royalty-free, paid-up, perpetual, irrevocable and exclusive license, with
the right to grant sublicenses, under MERCK’s interest in MERCK Non-SELEX Improvements, to
research, develop, make, use and sell for any and all purposes aptamers directed to any Targets
other than Program Targets and (ii) assigns to ARCHEMIX all of its right, title and interest in and
to MERCK’s interest in MERCK SELEX Improvements subject to Section 8.7.

               (e) Failed Target. Subject to the terms and conditions of this Agreement, MERCK
hereby grants to ARCHEMIX and its Affiliates an exclusive, worldwide, royalty-free license, with
the right to grant sublicenses under MERCK Program Technology, Patent Rights claiming MERCK Program
Technology, MERCK Co-Developed Program Technology, Patent Rights claiming MERCK Co-Developed
Program Technology and MERCK’s interest in Joint Technology and Joint Patent Rights to research,
develop, have developed, make, have made, use, distribute for sale, sell, offer for sale, import
and have imported aptamers and products Derived therefrom directed against any Failed Target for
all uses in or outside the Field. For purposes of clarity, Failed Targets for the purpose of this
Agreement shall not be construed as encompassing Waived Targets, and, ARCHEMIX shall have no
payment obligations to MERCK with regard to any Failed Target.

               (f) Terminated Compounds. Subject to the terms and conditions of this Agreement,
MERCK hereby grants to ARCHEMIX and its Affiliates an exclusive, worldwide, royalty-free license,
with the right to grant sublicenses, under MERCK Program Technology, Patent Rights claiming MERCK
Program Technology, MERCK Co-Developed Program Technology, Patent Rights claiming MERCK
Co-Developed Program Technology and MERCK’s interest in Joint Technology and Joint Patent Rights to
research, develop, have developed, make, have made, use, distribute for sale, sell, offer for sale,
import and have imported Terminated Compounds and products Derived therefrom in or outside of the
Field. For

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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purposes of clarity, an Aptamer directed against a Waived Target as set forth in sub-paragraph
(c) above shall in no event be considered a Terminated Compound.

                    (g) Non-Exclusive License to MERCK Program Technology For Aptamers Outside the
Collaboration. MERCK hereby grants to ARCHEMIX and its Affiliates a non-exclusive,
royalty-free, worldwide license, with the right to grant sublicenses, under MERCK Program
Technology and Patent Rights claiming MERCK Program Technology to the extent necessary to research,
develop, have developed, make, have made, use, distribute for sale, sell, offer for sale, import
and have imported aptamers and products Derived from aptamers other than those targeted to a
Program Target for any and all uses, except as otherwise provided herein.

                    (h) Exclusive License to MERCK Program Technology For Aptamers Outside the
Collaboration. To the extent requested in writing by ARCHEMIX, MERCK may grant to ARCHEMIX and
its Affiliates an exclusive, royalty-bearing, worldwide license, with the right to grant
sublicenses, under MERCK Program Technology, Patent Rights claiming MERCK Program Technology, MERCK
Co-Developed Program Technology, Patent Rights claiming MERCK Co-Developed Program Technology and
MERCK’s interest in Joint Technology and Joint Patent Rights to the extent necessary to research,
develop, have developed, make, have made, use, distribute for sale, sell, offer for sale, import
and have imported aptamers and products Derived from aptamers other than those targeted to a
Program Target for any and all uses, except as otherwise provided herein. The Parties agree to
negotiate in good faith the terms applicable to the foregoing license.

               8.1.3 Co-Developed Program Technology Grants. 

                    (a) ARCHEMIX Grants; ARCHEMIX Co-Developed Program Technology. Subject to the terms
and conditions of this Agreement, ARCHEMIX hereby grants to MERCK and its Affiliates, an exclusive,
royalty-free, worldwide license during the Term, including the right to subcontract as provided in
Section 8.5 and the right grant sublicenses as provided in Sections 8.4, under ARCHEMIX
Co-Developed Program Technology, for the sole purpose of Developing Optimized Lead Compounds and
Development Candidates and Commercializing Products in the Field and in the Territory.

                    (b) MERCK Grants; MERCK Co-Developed Program Technology. Subject to the terms and
conditions of this Agreement, MERCK hereby grants to ARCHEMIX and its Affiliates an exclusive,
royalty-free, worldwide license, with the right to grant sublicenses, under MERCK Co-Developed
Program Technology to research, develop, have developed, make, have made, use, distribute for sale,
sell, offer for sale, import and have imported aptamers and products Derived from aptamers other
than those targeted to a Program Target for any and all uses, except as otherwise provided herein.

          8.2 Commercialization License. Subject to the terms and conditions of this Agreement,
ARCHEMIX hereby grants to MERCK and its Affiliates an exclusive, royalty-bearing license during the
Term, including the right to grant sublicenses as provided in Section
8.4, under Licensed Technology and Licensed Patent Rights for the sole purpose of
Commercializing Products in the Field in the Territory.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the
Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

83

 

          8.3 Limitation on License Grants. For purposes of clarity and notwithstanding
anything to the contrary in this Agreement, under no circumstances shall the license granted by
ARCHEMIX to MERCK under Section 8.2 be deemed to extend to, and ARCHEMIX shall not be obligated to
extend such license to, the Commercialization of (any number of) Products directed to more than
eight (8) Targets.

          8.4 Right to Sublicense. MERCK shall have the right to grant sublicenses to
Sublicensees under the licenses granted to it under Section 8.1.1(c) with respect to any Optimized
Lead Compounds and Development Candidates (including, for greater certainty, Co-Developed
Development Candidates) and Section 8.2 with respect to any Product (including, for greater
certainty, Co-Developed Products); provided, that, (a) it shall be a condition of any such
sublicense that such Sublicensee agrees to be bound by all terms of this Agreement applicable to
the Development or Commercialization, as the case may be, of Products in the Field in the Territory
(including, without limitation, Article 7); (b) MERCK shall provide written notice to ARCHEMIX of
any such proposed sublicense at least [***] days prior to such execution and provide copies to
ARCHEMIX of each such sublicense in the form to be executed at least [***] business days prior to
such execution; (c) if MERCK grants a sublicense to a Sublicensee, MERCK shall be deemed to have
guaranteed that such Sublicensee will fulfill all of MERCK’s obligations under this Agreement
applicable to the subject matter of such sublicense; and (d) MERCK shall not be relieved of its
obligations pursuant to this Agreement as a result of such sublicense. Any sublicenses granted by
MERCK under Section 8.1.1(c) and/or Section 8.2 with respect to Co-Developed Development Candidates
and Co-Developed Products for which ARCHEMIX has exercised its Co-Development and Co-Promotion
Option and has not exercised its Opt-Out Right shall require ARCHEMIX’s consent, which consent
shall not be unreasonably withheld, delayed or conditioned; provided, that, any such sublicense
granted by MERCK with respect to a Co-Developed Product for Commercialization outside of the
Co-Development Territory shall not require ARCHEMIX’s consent.

          8.5 Right to Subcontract. Each Party shall have the right to subcontract portions,
but not all, of its responsibilities to be performed by it under the Annual Research Plan or Annual
Development Plan in the normal course of its business, and to grant sublicenses for such
activities, to any Third Party without the prior consent of the other Party; provided, that, (a)
such subcontracting shall not involve the transfer of Confidential Information of the other Party
to any Third Party unless the subcontracted party shall enter into a confidentiality agreement with
the subcontracting Party in accordance with Article 7; (b) the subcontracting Party shall provide
written notice to the other Party of any such proposed subcontract at least [***] days prior to
such execution; (c) if a Party enters into a subcontract as provided in this Section 8.5, such
Party shall be deemed to have guaranteed that such subcontractor will fulfill all of such Party’s
obligations under this Agreement applicable to the subject matter of such subcontract; (d) such
subcontracting Party shall not be relieved of its obligations pursuant to this Agreement as a
result of such subcontract, and (e) in the event ARCHEMIX is the subcontracting Party, MERCK shall
not be obligated to reimburse ARCHEMIX for any cost or expense related to such
subcontracting unless MERCK has approved such subcontracting, and the related cost and
expense, in the Annual Research Plan, the Annual Development Plan or otherwise in writing.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

84

 

          8.6 No Other Rights. MERCK shall have no rights to use or otherwise exploit ARCHEMIX
Technology, ARCHEMIX Patent Rights, or ARCHEMIX Proprietary Materials, and ARCHEMIX shall have no
rights to use or otherwise exploit MERCK Technology, MERCK Patent Rights or MERCK Proprietary
Materials, in each case, except as expressly set forth herein.

          8.7 Exclusivity.

               8.7.1 ARCHEMIX. During the Term, ARCHEMIX shall not, and shall cause each of its
Affiliates to not, conduct any activity, either on its own, or with, for the benefit of, or
sponsored by any Third Party, that is designed to research, develop or commercialize, or grant any
license or other rights to any Third Party to utilize, any Proprietary Materials, Technology or
Patent Rights Controlled in whole or in part by ARCHEMIX or any of its Affiliates for the purpose
of researching, developing or commercializing (a) any aptamer binding to a Program Target, or (b)
any Collaboration Aptamer or aptamer Derived therefrom, except for the conduct of Permitted
Activities and as otherwise provided under this Agreement.

               8.7.2 MERCK. During the Term, MERCK shall not, and shall cause each of its Affiliates
to not conduct any activity, either on its own, or with, for the benefit of, or sponsored by any
Third Party, that is designed to research, develop or commercialize, or grant any license or other
rights to any Third Party to utilize any Technology or Patent Rights Controlled by MERCK or any of
its Affiliates for the purpose of researching, developing or commercializing, any aptamer binding
to a Program Target or any aptamer Derived therefrom that binds specifically to the relevant
Program Target, except as provided under this Agreement.

9. INTELLECTUAL PROPERTY RIGHTS

          9.1 ARCHEMIX Intellectual Property Rights. ARCHEMIX shall have sole and exclusive
ownership of all right, title and interest on a worldwide basis in and to any and all ARCHEMIX
Technology, ARCHEMIX Patent Rights, ARCHEMIX Co-Developed Program Technology and ARCHEMIX
Co-Developed Program Patent Rights.

          9.2 MERCK Intellectual Property Rights. MERCK shall have sole and exclusive ownership
of all right, title and interest on a worldwide basis in and to any and all MERCK Technology, MERCK
Patent Rights, MERCK Co-Developed Program Technology, MERCK Co-Developed Program Patent Rights and
any and all Product Trademarks.

          9.3 Joint Technology and Joint Co-Developed Program Technology Rights. MERCK and
ARCHEMIX shall jointly own all Joint Technology, Joint Patent Rights, Joint Co-Developed Program
Technology and Joint Co-Developed Program Patent Rights. Notwithstanding anything to the contrary
contained in this Agreement or under Applicable Law, except to the extent exclusively licensed to
one Party under this Agreement, the Parties hereby agree that either Party may use or license or
sublicense to Affiliates or Third Parties all or any
portion of its interest in Joint Technology, Joint Patent Rights, Joint Co-Developed Program
Technology, Joint Co-Developed Program Patent Rights or jointly owned Confidential Information or
Proprietary Materials for any purposes without the prior written consent of the

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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other Party,
without restriction and without the obligation to provide compensation to the other Party, except
as otherwise provided under this Agreement.

          9.4 Patent Coordinators. ARCHEMIX and MERCK shall each appoint a patent coordinator
reasonably acceptable to the other Party (each, a “Patent Coordinator”) to serve as such Party’s
primary liaison with the other Party on matters relating to patent filing, prosecution, maintenance
and enforcement. Each Party may replace its Patent Coordinator at any time by notice in writing to
the other Party. The initial Patent Coordinators shall be:

               For ARCHEMIX: [***]

               For MERCK: [***]

          9.5 Inventorship. In case of a dispute between ARCHEMIX and MERCK over inventorship
and, as a result, whether any particular Technology is ARCHEMIX Technology, MERCK Technology, Joint
Technology, ARCHEMIX Co-Developed Program Technology, MERCK Co-Developed Program Technology or
Joint Co-Developed Program Technology such dispute shall be resolved by patent counsel who (and
whose firm) is not at the time of the dispute, and was not at any time during the [***] years prior
to such dispute, performing services for either of the Parties, such patent counsel to be selected
by the Patent Coordinators. Expenses of such patent counsel shall be shared equally by the
Parties.

          9.6 Cooperation. Each Party shall cooperate with the other Party to effect the intent
of this Article 9, including without limitation by executing documents and making its employees and
independent contractors available to execute documents as necessary to achieve the foregoing
allocation of ownership rights.

     10. FILING, PROSECUTION AND MAINTENANCE OF PATENT RIGHTS

          10.1  Patent Filing, Prosecution and Maintenance.

               10.1.1   MERCK’s Prosecution Rights.

                    (a) MERCK Program Technology; MERCK Co-Developed Program Technology. Subject to
Sections 10.1.4 and 10.1.5, MERCK, acting through patent counsel or agents of its choice, shall be
responsible for the preparation, filing, prosecution and maintenance in the countries listed on
Schedule 7, at its sole cost and expense, of Patent Rights covering MERCK Program
Technology and/or MERCK Co-Developed Program Patent Rights; provided, that, ARCHEMIX, acting
through patent counsel or agents of its choice, shall have the right but not the obligation, for
each Program Target, to prepare on MERCK’s behalf and with MERCK’s approval the first patent
application disclosing the corresponding Collaboration Aptamers. MERCK shall have no right or
responsibility with respect to the preparation, filing, prosecution and/or maintenance of any
claims within the Licensed Patent Rights that relate to any Failed Compound, Waived Compound or
Terminated Compound or their manufacture, formulation,
delivery, or use. MERCK shall nationalize such filings in the European Patent Office and the
other countries or regional offices listed on Schedule 7 and shall validate such filings in
the EPO contracting states as detailed in Schedule 7 hereto and the contracting states of
any other regional

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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offices identified on Schedule 7 and, at MERCK’s sole discretion, in any
other country. At MERCK’s request, ARCHEMIX shall cooperate with MERCK in all reasonable respects
in connection with such preparation, filing, prosecution and maintenance of such Patent Rights,
including but not limited to obtaining assignments to reflect chain of title consistent with the
terms of this Agreement, gaining United States patent term extensions, supplementary protection
certificates and any other extensions that are now or become available in the future wherever
applicable to Licensed Patent Rights. For purposes of clarity, notwithstanding anything to the
contrary herein, MERCK shall have no rights to prepare, file, prosecute and/or maintain any (1)
Licensed Patent Rights related to the SELEX Process or SELEX Technology, or
(2) Patent Rights included in the SELEX Portfolio.

                    (b) MERCK Background Technology. MERCK, at its sole expense and acting through patent
counsel or agents of its choice, shall be responsible for the preparation, filing, prosecution and
maintenance of all Patent Rights covering MERCK Background Technology.

               10.1.2 ARCHEMIX Prosecution Rights.

                    (a) ARCHEMIX Program Technology; ARCHEMIX Co-Developed Program Technology. ARCHEMIX,
at its sole expense and acting through patent counsel or agents of its choice, shall be responsible
for the preparation, filing, prosecution and maintenance of Patent Rights covering ARCHEMIX Program
Technology and/or ARCHEMIX Co-Developed Program Patent Rights. At ARCHEMIX’ request, MERCK shall
cooperate with and assist ARCHEMIX in all reasonable respects, at ARCHEMIX’ expense, in connection
with such preparation, filing, prosecution and maintenance of such Patent Rights, including but not
limited to obtaining assignments to reflect chain of title consistent with the terms of this
Agreement, gaining United States patent term extensions, supplementary protection certificates and
any other extensions that are now or become available in the future wherever applicable.

                    (b) ARCHEMIX Background Technology. ARCHEMIX, at its sole expense and acting through
patent counsel or agents of its choice, shall be responsible for the preparation, filing,
prosecution and maintenance of all Patent Rights covering ARCHEMIX Background Technology.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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               10.1.3 Joint Prosecution.

                    (a) Certain Program Technology. Notwithstanding anything to the contrary in Section
10.1.1(a) or 10.1.2(a), with respect to Patent Rights that contain one or more claims that cover
both Program Aptamer-Specific Technology and ARCHEMIX Program Technology, unless the Parties in
good faith otherwise agree, (a) the Parties, acting through patent counsel or agents of its choice,
shall separate such Patent Rights into separate patent applications seeking protection for Program
Aptamer-Specific Technology and ARCHEMIX Program Technology, respectively, and (b) the Parties
shall contemporaneously file the separate patent applications for such Patent Rights. Solely to the
extent the Parties mutually determine it is not feasible to prepare and file separate patent
applications covering such Technology: (i) the Parties shall be jointly responsible for the
preparation, filing and maintenance of such Patent Rights; (ii) MERCK shall be responsible for the
prosecution of any claims of such Patent Rights covering Program Aptamer-Specific Technology; (iii)
ARCHEMIX shall be responsible for the prosecution of any claims of such Patent Rights covering
ARCHEMIX Program Technology; and (iv) each Filing Party shall provide the Non-Filing Party and its
patent counsel with an opportunity to consult with the Filing Party and its patent counsel
regarding the filing and contents of any application, amendment, submission or response filed
pursuant to this Section 10.1.3(a); and (v) each Party shall be responsible for all expenses
incurred by it for the preparation, filing prosecution and maintenance of any Patent Rights for
which it has primary responsibility pursuant to this Section 10.1.3.

                    (b) Joint Patent Rights. In the case of Joint Patent Rights or Joint Co-Developed
Program Patent Rights, the Parties shall meet through the JSC and/or the Patent Coordinators to
discuss in good faith and agree upon the content and form of any application for a Joint Patent
Right or Joint Co-Developed Program Patent Rights and hereby agree that only the application in the
form as agreed between the Parties may be filed in respect of the Joint Patent Rights or Joint
Co-Developed Program Patent Rights. The Parties shall share the costs equally in respect of the
preparation of the application, filing, prosecution, grant and maintenance of any Joint Patent
Right or Joint Co-Developed Program Patent Right jointly filed; and jointly instruct an
appropriately qualified patent attorney to draft, file and prosecute the application and each Party
will have equal control over the prosecution of the filing such that the patent attorney will only
be able to act on unanimous instructions. In the event that one Party (i) is not interested, or
(ii) not willing to equally share the related cost and expense, with respect to any Joint Patent
Rights or Joint Co-Developed Program Patent Rights in a given country, then the other Party shall
have the right, at its own cost and expense, to file for and prosecute such Joint Patent Rights or
Joint Co-Developed Program Patent Rights in such country in both Parties’ names.

               10.1.4 Information and Cooperation. Each Party that has responsibility for filing and
prosecuting any Patent Rights under this Section 10.1.4 (a “Filing Party”) shall (a) regularly
provide the other Party (the “Non-Filing Party”) with copies of all patent applications filed
hereunder for Program Technology and Development Program Technology and other material submissions
and correspondence with the patent offices, in sufficient time to allow for review and comment by
the Non-Filing Party; and (b) provide the Non-Filing Party and its patent counsel with an
opportunity to consult with the Filing Party and its patent counsel regarding the filing and
contents of any such application, amendment, submission or response. The advice and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

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suggestions of the Non-Filing Party and its patent counsel shall be taken into consideration
in good faith by such Filing Party and its patent counsel in connection with such filing. Each
Filing Party shall pursue in good faith all reasonable claims and take such other reasonable
actions, as may be requested by the Non-Filing Party in the prosecution of any Patent Rights
covering any Program Technology or Development Program Technology under this Section 10.1;
provided, however, if the Filing Party incurs any additional expense as a result of any such
request, the Non-Filing Party shall be responsible for the cost and expenses of pursuing any such
additional claim or taking such other activities. In addition, MERCK (a) agrees that if ARCHEMIX
claims any action taken under Section 10.1.1(a) would be detrimental to Patent Rights covering
ARCHEMIX Background Technology (including without limitation the SELEX Portfolio), ARCHEMIX shall
provide written notice to MERCK and the Patent Coordinators shall, as promptly as possible
thereafter, meet to discuss and resolve such matter and, if they are unable to resolve such matter,
the Parties shall refer such matter to a mutually agreeable outside patent counsel for resolution.

               10.1.5 Abandonment. If a Filing Party decides to abandon or to allow to lapse any of
the Patent Rights covering any Program Technology or Development Program Technology for which it
has responsibility, it shall inform the Non-Filing Party of such decision promptly and, in any
event, so as to provide the Non-Filing Party a reasonable amount of time to meet any applicable
deadline to establish or preserve such Patent Rights in such country or region. The Non-Filing
Party shall have the right to assume responsibility for continuing the prosecution of such Patent
Rights in such country or region and paying any required fees to maintain such Patent Rights in
such country or region or defending such Patent Rights, through patent counsel or agents of its
choice, which shall be at the Non-Filing Party’s sole expense. The Non-Filing Party shall not
become an assignee of any such Patent Rights as a result of its assumption of any such
responsibility. Upon transfer of such responsibility under this Section 10.1.5, the Filing Party
shall promptly deliver to the Non-Filing Party copies of all necessary files related to the Patent
Rights with respect to which responsibility has been transferred and shall take all actions and
execute all documents reasonably necessary for the Non-Filing Party to assume such responsibility.

          10.2  Legal Actions. 

               10.2.1 Third Party Infringement.

                    (a) Notice. In the event either Party becomes aware of (i) any possible infringement
of any Licensed Patent Rights, MERCK Patent Rights, Joint Patent Rights or Co-Developed Program
Patent Rights through the Development or Commercialization of an aptamer covered by the Program
Aptamer-Specific Patent Rights, or (ii) the submission by any Third Party of an abbreviated new
drug application under the Hatch-Waxman Act for a product that includes an aptamer covered by the
Program Aptamer-Specific Patent Rights (each, an “Infringement”), that Party shall promptly notify
the other Party and provide it with all details of such Infringement of which it is aware (each, an
“Infringement Notice”).

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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                    (b) Royalty-Bearing Products.

                         (i) MERCK Right to Enforce.

                              (A) Enforcement of Section 10.1.1(b) Patent Rights. In the event that any
Infringement relates to any Patent Rights covering MERCK Background Technology, MERCK shall have
the sole right but not the obligation to enforce such claim.

                              (B) Enforcement of Sections 10.1.1(a) Patent Rights and Certain 10.1.3 (a) Patent
Rights. In the event that any Infringement relates to any Patent Right that MERCK is
responsible for prosecuting pursuant to Sections 10.1.1(a) and/or 10.1.3, then, subject to Section
10.2.1(c), MERCK shall have the first right (but not the obligation) to enforce such claim, which
may include the institution of legal proceedings or other action; provided, that, notwithstanding
the foregoing, MERCK shall not admit the invalidity or unenforceability of any Licensed Patent
Rights without ARCHEMIX’ prior written consent. MERCK shall keep ARCHEMIX reasonably informed on a
quarterly basis, in person or by telephone, prior to and during any such enforcement. ARCHEMIX
shall assist MERCK, upon request, in taking any action to enforce any such Patent Rights and shall
join in any such action if deemed to be a necessary party. MERCK shall incur no liability to
ARCHEMIX as a consequence of such litigation or any unfavorable decision resulting therefrom,
including any decision holding any such claim invalid, not infringed or unenforceable. All costs,
including without limitation attorneys’ fees, relating to such legal proceedings or other action
shall be borne by MERCK. If MERCK does not take commercially reasonable steps to
abate the Infringement of such Patent Rights within [***] days from any Infringement Notice (or [***] days in the case
of an Infringement resulting from the submission by any Third Party of an abbreviated new drug application under the Hatch-Waxman Act),
then ARCHEMIX shall have the right and option to do so at its expense.

                         (ii) ARCHEMIX Right to Enforce.

                              (A)  Enforcement of Section 10.1.2(b) Patent Rights. In the event that any Infringement
relates to any Patent Rights covering ARCHEMIX Background
Technology, ARCHEMIX shall have the sole
right but not the obligation to enforce such claim.

                              (B)  Enforcement of Section 10.1.2(a) Patent Rights and Certain 10.1.3(a) Patent Rights. In the event that any Infringement relates to any Patent Right that ARCHEMIX is responsible for prosecuting pursuant to
Sections 10.1.2(a) and/or 10.1.3, then, subject to Section 10.2.1(c), ARCHEMIX shall have the first right (but not the obligation) to enforce such claim, which may include the institution of legal proceedings or other action. ARCHEMIX shall keep MERCK reasonably informed on a quarterly basis, in person or by telephone, prior to and during any such enforcement. MERCK shall assist ARCHEMIX, upon request, in taking any action to enforce any such Patent Rights and shall join in any such
action if deemed to be a necessary party. ARCHEMIX shall incur no liability to MERCK as a consequence of such litigation or any unfavorable decision resulting therefrom, including any decision holding any
such claim invalid, not infringed or unenforceable. All costs, including without limitation attorneys’ fees, relating to such legal proceedings or other action shall be

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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borne by ARCHEMIX. If ARCHEMIX does not take commercially reasonable steps to abate the
Infringement of such Patent Rights within [***] days from any Infringement Notice (or [***] days
in the case of an Infringement resulting from the submission by any Third Party of an abbreviated
new drug application under the Hatch-Waxman Act), then MERCK shall have the right and option to do
so at its expense. For purposes of clarity, notwithstanding anything to the contrary herein, MERCK
shall have no rights to enforce any (1) ARCHEMIX Patents Rights covering the SELEX Process or SELEX Technology,
or (2) the SELEX Portfolio.

                         (iii) Joint Patent Rights. In the event of an Infringement of a Joint Patent Right,
then, subject to Section 10.2.1(c), the Parties shall enter into good faith discussions as to
whether and how to eliminate the Infringement. Subject to the foregoing, (i) ARCHEMIX shall have
the first right and option to eliminate such Infringement by reasonable steps, which may include
the institution of legal proceedings or other action and (ii) all costs, including without
limitation attorneys’ fees, relating to such legal proceedings or other action shall be borne by
ARCHEMIX. If ARCHEMIX does not take or initiate commercially reasonable steps to eliminate the
Infringement within [***] days from any Infringement Notice (or [***] days in the case of an
Infringement resulting from the submission by any Third Party of an abbreviated new drug
application under the Hatch-Waxman Act), then MERCK shall have the right and option to do so at its
expense.

                         (iv) Representation of Either Party. Each Party shall have the right to be
represented by counsel that it selects in any legal proceedings or other action instituted under
this Section 10.2.1 by the other Party.

                         (v) Cooperation by the Parties. In any action, suit or proceeding instituted under
this Section 10.2.1, the Parties shall cooperate with and assist each other in all reasonable
respects. Upon the reasonable request of the Party instituting such action, suit or proceeding,
the other Party shall join such action, suit or proceeding and shall be represented using counsel
of its own choice, at the requesting Party’s expense. If a Party with the right to initiate legal
proceedings under this Section 10.2.1 lacks standing to do so and the other Party has standing to
initiate such legal proceedings, then the Party with standing shall initiate such legal proceedings
at the request and expense of the other Party.

                         (vi) Allocation of Recoveries. Any amounts recovered by MERCK pursuant to actions
under Section 10.2.1(b)(ii), whether by settlement or judgment, shall be allocated in the following
order: (i) first, to reimburse MERCK and ARCHEMIX for their reasonable out-of-pocket expenses in
making such recovery (which amounts shall be allocated pro rata if insufficient to cover the
totality of such expenses); and (ii) second (A) with respect to actual damages, then, to MERCK and
ARCHEMIX [***] MERCK’s historic Net Sales of the Product or Products affected by the Infringement
bears to ARCHEMIX’ historic royalties hereunder in respect of such Net Sales, in each case as
determined in good faith, and (B) with respect to punitive, special or consequential damages, [***]
percent ([***]%) to MERCK. Any amounts recovered by ARCHEMIX pursuant to actions under Section
10.2.1(c)(ii) shall be allocated in the following order: (X) first, to reimburse ARCHEMIX and MERCK
for their reasonable out of pocket expenses in making such recovery (which amounts

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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shall be allocated pro rata if insufficient to cover the totality of such expenses); and (Y)
then, [***]% to ARCHEMIX.

                    (c) Co-Developed Products. Notwithstanding anything to the contrary set forth in this
Section 10.1, in the event of an Infringement of a Patent Right covering Co-Developed Products, the
Parties shall jointly decide as to whether and how to eliminate the Infringement and shall jointly
take actions to eliminate such Infringement by reasonable steps, which may include the institution
of legal proceedings or other action. All costs, including without limitation attorneys’ fees, and
all recoveries, relating to such legal proceedings or other action shall be borne equally by the
Parties.

               10.2.2 Defense of Claims.

                    (a) Notice. In the event that a Third Party alleges that the conduct of the Research
Program or the Development or Commercialization of an Optimized Lead Compound, Development
Candidate or Product infringes the Patent Rights of a Third Party, the Party becoming aware of such
allegation shall promptly notify the other Party hereof, in writing, reasonably detailing the
claim.

                    (b) Third Party Suit Relating Primarily to Program Targets or Requested Chemistry.

                         (i) In the event that any action, suit or proceeding is brought against either Party or any
Affiliate or sublicensee of either Party alleging the infringement of the Patent Rights of a Third
Party relating specifically to the Program Targets by reason of activities conducted pursuant to
this Agreement, (A) MERCK shall have the right and obligation to defend or otherwise resolve such
action, suit or proceeding (e.g., by way of entering into a settlement agreement or consent) at its
sole expense; (B) ARCHEMIX or any of its Affiliates or sublicensees shall have the right to
separate counsel at its own expense in any such action, suit or proceeding and, if such action,
suit or proceeding has been brought against ARCHEMIX or any of its Affiliates or sublicensees,
ARCHEMIX may elect to defend itself at its sole expense; and (C) the Parties shall cooperate with
each other in all reasonable respects in any such action, suit or proceeding. Settlement costs,
royalties paid in settlement of any such suit, and the payment of any damages to the Third Party
shall be borne solely by MERCK.

                         (ii) In the event that any action, suit or proceeding is brought against either Party or any
Affiliate or sublicensee of either Party alleging the infringement, by reason of activities
conducted pursuant to this Agreement, of the Technology or Patent Rights of a Third Party relating
specifically to the use of Requested Chemistry in (A) the Research Program or any Product
independent of any challenge to the right to practice the SELEX Process or SELEX
Technology or the SELEX Portfolio, (B) the Development of any Development
Candidate, or (C) the Commercialization, including without limitation the manufacture, use or sale,
of any Product, MERCK shall have the right and obligation to defend or otherwise resolve such
action, suit or proceeding (e.g., by way of entering into a settlement agreement or consent) at its
sole expense. Settlement costs, royalties paid in settlement of any such suit, and the payment of
any damages to the Third Party shall be borne solely by MERCK.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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                    (c) Third Party Suit Relating Primarily to the use of the SELEX Process
or the SELEX Technology. In the event that any action, suit or proceeding is brought against
either Party or any Affiliate or sublicensee of either Party alleging the infringement of the
Patent Rights of a Third Party by reason of the use of the SELEX Process or the use of the
SELEX Technology (excluding in either case any action, suit or proceeding based solely
on the use of Requested Chemistry) in the conduct of the Research Program (i) ARCHEMIX shall have
the right and obligation to defend or otherwise resolve such action, suit or proceeding (e.g., by
way of entering into a settlement agreement or consent) at its sole expense; and (ii) MERCK or any
of its Affiliates or Sublicensees shall have the right to separate counsel at its own expense in
any such action, suit or proceeding and, if such action, suit or proceeding has been brought
against MERCK or any of its Affiliates or Sublicensees, MERCK or its Affiliate or Sublicensee may
elect to defend itself at its sole expense. Settlement costs, royalties paid in settlement of any
such suit, and the payment of any damages to the Third Party shall be borne solely by ARCHEMIX.

                    (d) Cooperation in Defense. The Parties shall cooperate with each other in all
reasonable respects in any action, suit or proceeding under this Section 10.2.2. Each Party shall
provide the other Party with prompt written notice of the commencement of any such suit, action or
proceeding, or of any evidence or allegation of infringement of which such Party becomes aware, and
shall promptly furnish the other Party with a copy of each communication relating to the alleged
infringement that is received by such Party. The Party that is a party to the action, suit or
proceeding shall not admit the invalidity of any patent within the Licensed Patent Rights, Joint
Patent Rights or MERCK Patent Rights, nor settle such action, suit or proceeding in a manner that
adversely affects the other Party’s rights under this Agreement, without the written consent of the
other Party, which consent shall not be unreasonably withheld, delayed or conditioned.

               10.3 Trademark and Copyright Prosecution, Defense and Enforcement. MERCK shall be
responsible for the filing, prosecution, maintenance, defense and enforcement of all Product
Trademarks and copyrights created during the Research Program, Development and/or Commercialization
at MERCK’s expense.

               10.4 Effect of Challenge. In further consideration of ARCHEMIX’s grant of the
licenses hereunder and except to the extent the following is unenforceable under the Applicable
Laws of a particular jurisdiction where a patent application within the Licensed Patent Rights is
pending or a patent within the Licensed Patent Rights issued, in the event that MERCK, its
Affiliates and/or Sublicensees (a) determines to initiate a Challenge or MERCK, its Affiliates
and/or Sublicensees determines to assist a Third Party in initiating a Challenge, (i) MERCK will
provide written notice to ARCHEMIX at least ninety (90) days prior thereto, which notice will
include an identification of all prior art it believes invalidates any claim of the Licensed Patent
Rights; (ii) the Designated Senior Officers shall promptly initiate discussing in good faith to
resolve the issue for a period of up [***] (which discussions may include the engagement of a
mutually acceptable independent patent counsel to advise the Designated Senior Officers on such
issue, the expense of which shall be borne equally by the Parties; and (b) initiates a Challenge or
assists a Third Party in initiating a Challenge, (i) the exclusive licenses granted by ARCHEMIX to
MERCK hereunder shall, at the option of the ARCHEMIX and upon written notice to

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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MERCK, be converted into non-exclusive as of the date of such notice, (ii) should the outcome
of such Challenge determine that any claim that is the subject of the Challenge is valid or
enforceable or is infringed by any Products, the royalty rates set forth in Section 8.7.1 shall be
increased by an additional [***] percentage points and (iii) should the outcome of any Challenge
determine no claim of Licensed Patent Rights Challenged by MERCK, its Affiliates and/or
Sublicensees is valid or enforceable or infringed by a Product, MERCK, its Affiliates and/or
Sublicensees shall continue to pay royalties based on Annual Net Sales of Products sold in the
Territory at the rate of [***] percent ([***]%) until the last day of the Royalty Term for such
Product notwithstanding such determination.

11. TERM AND TERMINATION

          11.1 Term. The term (“Term”) of this Agreement shall commence on the Effective Date
and shall continue in full force and effect until the end of the Research Program Term and, if
MERCK is Developing a Development Candidate or Commercializing a Product as of the end of the
Research Program Term (including any Co-Developed Product), thereafter until (a) such time as MERCK
is no longer Developing at least one (1) Development Candidate or (b) if, as of the time MERCK is
no longer Developing at least one (1) Development Candidate, MERCK is Commercializing a Product
(including a Co-Developed Product), such time as all Royalty Terms for all Royalty-Bearing Products
have ended or sales of Co-Developed Products have ceased (whether any such sales are made by or on
behalf of MERCK alone or jointly with ARCHEMIX), whichever is later, unless earlier terminated in
accordance with the provisions of this Article 11. After expiration of the applicable Royalty
Term, MERCK’s rights and licenses contained herein with respect to each such Royalty-Bearing
Product shall revert to a non-exclusive, worldwide, fully paid up and perpetual license to
Commercialize such Royalty-Bearing Product.

          11.2 Termination. This Agreement may be terminated at any time by either Party as
follows:

               11.2.1 Unilateral Right to Terminate. MERCK may terminate this Agreement, effective
upon not less than [***] days written notice to ARCHEMIX, at any time on or after expiration of the
Research Program Term.

               11.2.2 Termination for Breach. Either Party may terminate this Agreement, effective
immediately upon written notice to the other Party, for a material breach by the other Party of any
term of this Agreement that remains uncured for [***] days ([***] days in the event that the breach
is a failure of either Party to make any payment required hereunder) after the non-breaching Party
first gives written notice to the other Party of such breach and its intent to terminate this
Agreement if such breach is not cured; provided, that, (a) in the event MERCK is in breach of its
diligence obligations with respect to a given Program Target, and/or any Collaboration Aptamer
against such Program Target, ARCHEMIX shall only have the right, on a country-by-country (or with
respect to European countries, Europe) and Collaboration Aptamer-by-Collaboration Aptamer and/or
Product-by-Product basis, to (i) terminate MERCK’s rights with respect to such Program Target
and/or such Collaboration Aptamer and/or Product (but leaving unaffected MERCK’s rights under this
Agreement to any other Program Target,

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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Collaboration Aptamer(s) or Product(s)) or (ii) upon [***] days written notice to MERCK, to
convert the exclusive license granted to MERCK for each such Program Target, Collaboration Aptamer
and/or Product to a non-exclusive license, in which case the provisions of Section 8.7.1 will not
apply to such Program Target, Collaboration Aptamer and/or Product and (b) in the event ARCHEMIX is
in breach of its diligence obligations solely with respect to ARCHEMIX’s Co-Development Activities,
MERCK shall only have the right, on a Collaboration Aptamer-by-Collaboration Aptamer basis and/or
Product-by-Product basis, to terminate the right of ARCHEMIX to Co-Develop such Collaboration
Aptamer and/or Product. For purposes of clarity, a breach by MERCK of any of Sections 4.10.6(a)
through 4.10.6(c) shall constitute a material breach.

               11.2.3 Termination for Insolvency. In the event that either Party files for
protection under bankruptcy laws, makes a general assignment for the benefit of creditors, appoints
or suffers appointment of a receiver or trustee over its business, files a petition under any
bankruptcy or insolvency act or has any such petition filed against it which is not dismissed or
stayed within [***] days of the filing thereof, the other Party may terminate this Agreement
effective immediately upon written notice to such Party. In connection therewith, all rights and
licenses granted under this Agreement are, and shall be deemed to be, for purposes of Section
365(n) of the United States Bankruptcy Code, licenses of rights to “intellectual property” as
defined under Section 101(35A) of the United States Bankruptcy Code.

          11.3 Consequences of Termination of Agreement. In the event of the termination of
this Agreement pursuant to Section 11.2, the following provisions shall apply, as applicable.

               11.3.1 Termination Pursuant to Section 11.2.1. If this Agreement is terminated by
MERCK pursuant to Section 11.2.1:

                    (a) all licenses granted to MERCK under Article 8 to any Collaboration Aptamers as of the
effective date of termination, if any, shall immediately terminate and all such Lead Compounds,
Optimized Lead Compounds, Development Candidates and Products shall be Terminated Compounds, and
ARCHEMIX shall have no further obligations under Section 8.7.1;

                    (b) each Party shall promptly return all Confidential Information and Proprietary Materials of
the other Party that are not subject to a continuing license hereunder; provided, that, each Party
may retain one copy of the Confidential Information of the other Party in its archives solely for
the purpose of establishing the contents thereof and ensuring compliance with its obligations
hereunder;

                    (c) upon request of ARCHEMIX, MERCK and ARCHEMIX shall agree on a transition plan pursuant to
which MERCK will transfer to ARCHEMIX all of its right, title and interest in Terminated Compounds
to ARCHEMIX which transition plan shall, depending on the stage of development of the Terminated
Compounds, obligate MERCK to:

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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                         (i) grant to ARCHEMIX an exclusive, worldwide, royalty-free, paid-up license under all Product
Trademarks applicable to the Terminated Compounds, if any;

                         (ii) transfer to ARCHEMIX all of its right, title and interest in all Regulatory Filings, Drug
Approval Applications and Regulatory Approvals then in its name applicable to the Terminated
Compounds, if any;

                         (iii) notify the applicable Regulatory Authorities and take any other action reasonably
necessary to effect such transfer;

                         (iv) provide ARCHEMIX with copies of all correspondence between MERCK and such Regulatory
Authorities relating to such Regulatory Filings, Drug Approval Applications and Regulatory
Approvals;

                         (v) unless expressly prohibited by any Regulatory Authority, transfer control to ARCHEMIX of
all clinical trials of the Terminated Compounds being conducted as of the effective date of
termination and continue to conduct such trials at its expense for up to [***] months to enable
such transfer to be completed without interruption of any such trial, unless ARCHEMIX demonstrates
to MERCK to MERCK’s satisfaction that ARCHEMIX shall not be able to assume such clinical trials
within [***] months, in which case MERCK shall continue to conduct such trials for up to [***]
additional months;

                         (vi) assign (or cause its Affiliates to assign) to ARCHEMIX all agreements with any Third
Party with respect to the conduct of clinical trials for the Terminated Compounds including,
without limitation, agreements with contract research organizations, clinical sites and
investigators, unless expressly prohibited by any such agreement (in which case MERCK shall
cooperate with ARCHEMIX in all reasonable respects to secure the consent of such Third Party to
such assignment);

                         (vii) provide ARCHEMIX with all supplies of the Terminated Compounds in the possession of
MERCK or any Affiliate or contractor of MERCK;

                         (viii) provide ARCHEMIX with copies of all reports and data generated or obtained by MERCK or
its Affiliates pursuant to this Agreement that relate to any Terminated Compounds that have not
previously been provided to ARCHEMIX;

                         (ix) reimburse ARCHEMIX for all internal and out-of-pocket costs incurred by ARCHEMIX in
continuing the research and Development according to the pre-agreed Annual Development Plan of all
the Terminated Compounds for a period of [***] days; and

                         (x) if MERCK has manufactured, is manufacturing or having manufactured any Terminated
Compounds or any intermediate thereof: (i) MERCK shall, if requested by ARCHEMIX, supply ARCHEMIX
with its requirements for all Terminated Compounds and intermediates for up to [***] months
following such termination at a transfer price equal to [***] for the supply of such Terminated
Compounds or intermediates, plus [***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

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percent ([***]%), (ii) within [***] days after ARCHEMIX’s request, MERCK shall provide to
ARCHEMIX or its designee all information in its possession with respect to the manufacture of each
such Terminated Compound or intermediate.

               11.3.2 Termination by MERCK Pursuant to Section 11.2.2. If this Agreement is
terminated by MERCK pursuant to Section 11.2.2, the license granted by ARCHEMIX to MERCK pursuant
to Section 8.1.1(c) shall survive solely as applied to Development Candidates being Developed by
MERCK as of the effective date of termination, if any, and the license granted by ARCHEMIX to MERCK
pursuant to Section 8.2 shall survive solely as applied to Products being Commercialized by MERCK
as of the effective date of termination or Derived from Development Candidates being Developed by
MERCK as of the effective date of termination, if any, in each case subject to MERCK’s continued
payment of [***] milestone, royalty, and other payments under and in accordance with this Agreement
with respect thereto; provided, that, (a) to the extent the breach that gave rise to MERCK’s right
to terminate under Section 11.2.2 is with regard to ARCHEMIX’s obligations under Section 8.7.1
then, solely with respect to the Aptamer or Collaboration Aptamer and Products Developed therefrom,
that is the subject of such breach, the license granted by ARCHEMIX to MERCK under this Section
11.3.2 with respect to such Product shall survive as a fully paid-up, royalty-free license; (b) to
the extent that the breach that gave rise to MERCK’s right to terminate under Section 11.2.2 is
with regard to ARCHEMIX’s diligence obligations solely with respect to ARCHEMIX’s Co-Development
Activities, the applicable Co-Developed Development Candidate or Product shall be deemed a
Royalty-Bearing Product; and (c) to the extent the breach that gave rise to MERCK’s right to
terminate under Section 11.2.2 is with respect to any other obligation of ARCHEMIX under this
Agreement, all milestone, Net Income Payments (in the case of a Co-Developed Product) royalty and
other payments applicable to such Products under this Agreement shall be [***] by [***] percent
([***]%).

               11.3.3 Termination by MERCK Pursuant to Section 11.2.3. If this Agreement is
terminated by MERCK pursuant to Section 11.2.3, unless prohibited by Applicable Laws:

                    (a) the license set forth in Section 8.1.1(b) shall survive solely as applied to Development
Candidates being Developed by MERCK as of the effective date of termination, if any, and the
license set forth in Section 8.2 shall survive solely as applied to Products being Commercialized
by MERCK as of the effective date of termination or Derived from Development Candidates being
Developed by MERCK as of the effective date of termination, if any, subject to MERCK’s continued
payment of [***] milestone, royalty, and other payments under and in accordance with this Agreement
with respect thereto; and

                    (b) each Party shall promptly return all Confidential Information and Proprietary Materials of
the other Party that are not subject to a continuing license hereunder; provided, that, each Party
may retain one copy of the Confidential Information of the other Party in its archives solely for
the purpose of establishing the contents thereof and ensuring compliance with its obligations
hereunder.

               11.3.4 Termination by ARCHEMIX Pursuant to Section 11.2.2.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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                    (a) Diligence Obligations. If MERCK’s rights to a Target and all Development
Candidates, Products and any other Collaboration Aptamers directed against such Target are
terminated by ARCHEMIX pursuant to Section 11.2.2 for breach by MERCK of its diligence obligations
under Section 4.6, the provisions of Section 11.3.1 shall apply but only to the Target and
Collaboration Aptamers for which MERCK’s rights were terminated. If MERCK’s rights to one or more
but not all Development Candidates, Products and any other Collaboration Aptamers directed against
a Program Target are terminated by ARCHEMIX pursuant to Section 11.2.2 for breach by MERCK of its
diligence obligations under Section 4.6, (i) the provisions of Section 11.3.1 shall apply but only
to the Collaboration Aptamers and/or Product for which MERCK’s rights were terminated and (ii) the
exclusive license(s) granted to MERCK for each such terminated Collaboration Aptamer and/or
terminated Product and the Program Target to which they bind shall convert to a non-exclusive
license(s) and the provisions of Section 8.7.1 shall not apply to such Program Target, terminated
Collaboration Aptamers and/or terminated Products.

                    (b) Other Obligations. If this Agreement is terminated by ARCHEMIX pursuant to
Section 11.2.2 for breach by MERCK of its obligations under this Agreement other than its
diligence obligations under Section 4.6:

                         (i) the provisions of Section 11.3.1 shall apply; and

                         (ii) if such termination is effective prior to the end of the Research Program Term, (x) MERCK
shall, for a period of [***] days from the effective date of termination, pay ARCHEMIX the Minimum
FTE Funding Commitment and (y) the Research Program shall terminate without any further obligation
of ARCHEMIX.

               11.3.5 Termination by ARCHEMIX Pursuant to Section 11.2.3. If this Agreement is
terminated by ARCHEMIX pursuant to Section 11.2.3, unless prohibited by Applicable Laws, the
provisions of Section 11.3.1 shall apply, except that MERCK shall have no obligation to continue to
conduct any clinical trial.

     11.4 Surviving Provisions. Termination or expiration of this Agreement for any reason
shall be without prejudice to:

                    (a) the rights and obligations of the Parties provided in Section 3.6.1 (Record Keeping),
Section 4.10.6(b) (Records and Audit Rights in the event of Co-Development), Section 6.4.2 (R&D
Funding Audit Rights), Section 6.6.2 (Records; Audit Rights), Section 6.7.2 (Net Income Audit
Rights), Section 11.3 (Consequences of Termination of Agreement), Section 11.4 (Surviving
Provisions), Section 14.1 (Arbitration), Section 14.4 (Governing Law), Section 14.9 (No Third Party
Beneficiaries), Section 14.15 (Further Assurances), Article 7 (Confidentiality), Article 9
(Intellectual Property Rights), Sections 10.1.3(b) and 10.2.1(b)(iii) (Joint Patent Rights),
Article 13 (Indemnification) and all other Sections or Articles referenced in any such Section or
Article including Article 1, all of which shall survive such termination;

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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                    (b) unless otherwise provided for in this Agreement, ARCHEMIX’s rights to receive royalties
and milestone payments for the duration of all applicable Royalty Terms, if any; and

                    (c) any other rights or remedies provided at law or equity which either Party may otherwise
have.

12. REPRESENTATIONS AND WARRANTIES AND COVENANTS

     12.1 Mutual Representations and Warranties. ARCHEMIX and MERCK each represents and
warrants to the other, as of the Effective Date, as follows:

               12.1.1 Organization. It is a corporation duly organized, validly existing and in good
standing under the laws of the jurisdiction of its organization, and has all requisite power and
authority, corporate or otherwise, to execute, deliver and perform this Agreement.

               12.1.2 Authorization. The execution and delivery of this Agreement and the
performance by it of the transactions contemplated hereby have been duly authorized by all
necessary corporate action and will not violate (a) such Party’s certificate of incorporation or
bylaws, (b) any agreement, instrument or contractual obligation to which such Party is bound in any
material respect, (c) any requirement of any Applicable Laws, or (d) any order, writ, judgment,
injunction, decree, determination or award of any court or governmental agency presently in effect
applicable to such Party.

               12.1.3 Binding Agreement. This Agreement is a legal, valid and binding obligation of
such Party enforceable against it in accordance with its terms and conditions.

               12.1.4 No Inconsistent Obligation. It is not under any obligation, contractual or
otherwise, to any Person that conflicts with or is inconsistent in any respect with the terms of
this Agreement or that would impede the diligent and complete fulfillment of its obligations
hereunder.

     12.2 ARCHEMIX’ Representations and Warranties. ARCHEMIX represents and warrants to
MERCK as follows:

               12.2.1 All Licensed Technology existing as of the Effective Date is Controlled by ARCHEMIX.

               12.2.2 All Licensed Patent Rights listed on Schedule 3 are Controlled by ARCHEMIX.

               12.2.3 To the Knowledge of ARCHEMIX, as of the Effective Date, except as previously disclosed
to MERCK, no Third Party has initiated, or threatened in writing to initiate, any litigation
against ARCHEMIX or its Affiliates, including, without limitation, by initiating any declaratory
judgment lawsuit, or by sending a cease-and-desist letter, alleging that the Licensed Patent Rights
are invalid or unenforceable or that the use of the Licensed Patent Rights

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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or Licensed Technology as contemplated by this Agreement infringes the Patent Rights of such
Third Party.

               12.2.4 To the Knowledge of ARCHEMIX, as of the Effective Date, except as previously disclosed
to MERCK, neither ARCHEMIX nor its Affiliates has received written notice from Gilead or URC or any
other Third Party alleging that (a) either the ARCHEMIX-Gilead License Agreement or the URC License
Agreement is not in full force and effect, (b) either the ARCHEMIX-Gilead License Agreement or the
URC License Agreement is subject to any dispute, either in court or otherwise, and (c) ARCHEMIX or
its Affiliates is in breach of the ARCHEMIX-Gilead License Agreement or the URC License Agreement,
respectively.

     12.3 Acknowledgment and Covenant of MERCK. MERCK acknowledges that the licenses
granted to MERCK hereunder are subject to certain limitations and restrictions set forth in the
ARCHEMIX-Gilead License Agreement and the URC License Agreement and agrees that MERCK shall comply
with the terms of the ARCHEMIX-Gilead License Agreement and the URC License Agreement that ARCHEMIX
is subject to thereunder. MERCK hereby acknowledges and agrees and covenants that (a) it may and
will not use the SELEX Process or the SELEX Technology as described in the
SELEX Portfolio (i) to research, make, use, sell, offer for sale, import or export any
aptamers for In Vitro Diagnostics, In Vivo Diagnostic Agents, or Radio Therapeutics or (ii)
develop, modify, manufacture, have manufactured, export, import, use, sell or offer to sell (A) any
aptamer other than a Collaboration Aptamer, or (B) any Excluded Aptamer and/or any product
containing an Excluded Aptamer; (b) under the ARCHEMIX-Gilead License Agreement and under the URC
License Agreement, ARCHEMIX’ rights in the SELEX Process or the SELEX
Technology as described in the SELEX Portfolio may revert to Gilead if ARCHEMIX,
its Affiliates and all assignees and sublicensees cease reasonable efforts to develop the
commercial applications of products and services utilizing the SELEX Process or the
SELEX Technology; (c) in the event of any termination of the URC License Agreement, the
licenses granted to MERCK hereunder shall remain in full force and effect in accordance with
Section 3.4 of the URC License Agreement; provided, that, MERCK is not then in breach of this
Agreement and MERCK agrees to be bound to UTC as the licensor under the terms and conditions of the
URC License Agreement as described in the SELEX Portfolio; and (d) in the event of any
termination of the ARCHEMIX-Gilead License Agreement, the licenses granted to MERCK hereunder shall
remain in full force and effect in accordance with Section 2.3 of the ARCHEMIX-Gilead License
Agreement; provided, that, MERCK agrees to be bound to Gilead as the licensor under the terms and
conditions of the ARCHEMIX-Gilead License Agreement; and, provided, that, if the termination of the
ARCHEMIX-Gilead License Agreement arises out of the action or inaction of MERCK, Gilead, at its
option, may terminate such license.

     12.4 Covenant of ARCHEMIX. ARCHEMIX hereby covenants that to the extent it enters
into an agreement with a Third Party that grants a license to such Third Party to research,
develop, and/or commercialize aptamers that bind to a Program Target in accordance with Section
8.7.1 it will include in any such license a covenant which prohibits such Third Party and any
sublicensee of such Third Party from asserting any patent rights relating to the Program Targets
arising under any such license (or any sublicense granted thereunder) against ARCHEMIX or any
licensee or sublicensee of ARCHEMIX (including, for clarity, MERCK and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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its Affiliates) to which ARCHEMIX has granted a license or sublicense to aptamers that bind to
a Program Target for the treatment, prevention, cure or delay of progression of an indication,
disease or disorder for ARCHEMIX’s or its licensee’s or sublicensee’s research, development or
commercialization of aptamers that bind to a Program Targets for the treatment, prevention, cure or
delay of progression of an indication, disease or disorder.

13. INDEMNIFICATION

     13.1 Indemnification of MERCK by ARCHEMIX. ARCHEMIX shall indemnify, defend and hold
harmless MERCK, its Affiliates, their respective directors, officers, employees and agents, and
their respective successors, heirs and assigns (collectively, the “MERCK Indemnitees”), against all
liabilities, damages, losses and expenses (including, without limitation, reasonable attorneys’
fees and expenses of litigation) (collectively, “Losses”) incurred by or imposed upon the MERCK
Indemnitees, or any one of them, as a direct result of claims, suits, actions, demands or judgments
of Third Parties, including without limitation personal injury and product liability claims
(collectively, “Claims”), arising out of (i) ARCHEMIX’s research and development activities under
this Agreement, (ii) the Development or Commercialization of any Co-Developed Product by ARCHEMIX
and (iii) the development, manufacture, use or sale of any Failed Compound, Waived Compound or
Terminated Compound by ARCHEMIX or any of its Affiliates, sublicensees, distributors or agents,
except with respect to any Claim or Losses that result from a breach of this Agreement by, or the
gross negligence or willful misconduct of, MERCK; provided, that, with respect to any Claim for
which ARCHEMIX has an obligation to any MERCK Indemnitee pursuant to this Section 13.1 and MERCK
has an obligation to any ARCHEMIX Indemnitee pursuant to Section 13.2, each Party shall indemnify
each of the other Party’s Indemnitees for its Losses to the extent of its responsibility, relative
to the other Party, for the facts underlying the Claim.

     13.2 Indemnification of ARCHEMIX by MERCK. MERCK shall indemnify, defend and hold
harmless ARCHEMIX, its Affiliates, their respective directors, officers, employees and agents, and
their respective successors, heirs and assigns (the “ARCHEMIX Indemnitees”), against any Losses
incurred by or imposed upon the ARCHEMIX Indemnitees, or any one of them, as a direct result of
Claims arising out of (i) the Development of any Development Candidate or the Commercialization
(including, without limitation, the production, manufacture, promotion, import, sale or use by any
Person) of any Product by MERCK or any of its Affiliates, Sublicensees, distributors or agents and
(ii) the Development or Commercialization of any Co-Developed Product by MERCK or any of its
Affiliates, Sublicensees, distributors or agents, except with respect to any Claim that results
from a breach of this Agreement by, or the gross negligence or willful misconduct of, ARCHEMIX;
provided, that, with respect to any Claim for which ARCHEMIX has an obligation to any MERCK
Indemnitee pursuant to Section 13.1 and MERCK has an obligation to any ARCHEMIX Indemnitee pursuant
to this Section 13.2, each Party shall indemnify each of the other Party’s Indemnitees for its
Losses to the extent of its responsibility, relative to the other Party, for the facts underlying
the Claim.

     13.3 Indemnification of Gilead and UTC by MERCK. If, and solely to the extent,
legally required by the ARCHEMIX-Gilead License Agreement, MERCK shall indemnify, defend and hold
harmless Gilead, its Affiliates and UTC and any of their respective directors,

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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officers, employees and agents (each, a “Gilead Indemnitee”), from and against any Losses that
are incurred by a Gilead Indemnitee as a result of any Claims, to the extent such Claims arise out
of the possession, research, development, manufacture, use, offer for sale, sale or other
commercialization, distribution, administration, storage or transport, by MERCK or its Affiliates
or Sublicensees of (a) any Aptamers or Licensed Products, or (b) any other products, services and
activities developed by MERCK relating to the Covered Intellectual Property, including any Licensed
Products, Aptamers or Documentation (as such terms are defined in the ARCHEMIX-Gilead License
Agreement), except with respect to any Claim or Losses that result from the activities of ARCHEMIX
under the ARCHEMIX-Gilead License Agreement.

     13.4 Conditions to Indemnification. A Person seeking recovery under this Article 12
(the “Indemnified Party”) in respect of a Claim shall give prompt notice of such Claim to the Party
from which recovery is sought (the “Indemnifying Party”) and, provided that the Indemnifying Party
is not contesting its obligation under this Article 13, shall permit the Indemnifying Party to
control any litigation relating to such Claim and the disposition of such Claim; provided, that,
the Indemnifying Party shall (a) act reasonably and in good faith with respect to all matters
relating to the settlement or disposition of such Claim as the settlement or disposition relates to
such Indemnified Party and (b) not settle or otherwise resolve such claim without the prior written
consent of such Indemnified Party (which consent shall not be unreasonably withheld, conditioned or
delayed). Each Indemnified Party shall cooperate with the Indemnifying Party in its defense of any
such Claim in all reasonable respects and shall have the right to be present in person or through
counsel at all legal proceedings with respect to such Claim.

     13.5 Warranty Disclaimer. EXCEPT AS OTHERWISE EXPRESSLY PROVIDED IN THIS AGREEMENT,
NEITHER PARTY MAKES ANY WARRANTY WITH RESPECT TO ANY TECHNOLOGY, GOODS, SERVICES, RIGHTS OR OTHER
SUBJECT MATTER OF THIS AGREEMENT AND EACH PARTY HEREBY DISCLAIMS ALL WARRANTIES, EXPRESS OR
IMPLIED, INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE, VALIDITY AND NONINFRINGEMENT.

     13.6 No Warranty of Success. Nothing contained in this Agreement shall be construed
as a warranty on the part of either Party that (a) the Research Program will yield any Lead
Compound, Optimized Lead Compound or Development Candidate or otherwise be successful, (b) any
Development Program will yield a Product or otherwise be successful or (c) the outcome of the
Research Program or any Development Program will be commercially exploitable in any respect.

     13.7 Limited Liability. NOTWITHSTANDING ANYTHING TO THE CONTRARY IN THIS AGREEMENT,
NEITHER PARTY SHALL BE LIABLE TO THE OTHER PARTY OR ANY OF ITS AFFILIATES FOR (I) ANY SPECIAL,
PUNITIVE, INDIRECT, INCIDENTAL OR CONSEQUENTIAL DAMAGES, INCLUDING WITHOUT LIMITATION LOST PROFITS
OR LOST REVENUES, OR (II) COST OF PROCUREMENT OF SUBSTITUTE GOODS, TECHNOLOGY OR SERVICES, WHETHER
UNDER ANY

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

102

 

CONTRACT, WARRANTY, NEGLIGENCE, STRICT LIABILITY OR OTHER LEGAL OR EQUITABLE THEORY.

14. MISCELLANEOUS

14.1 Arbitration.

               14.1.1 Full Arbitration. Any dispute, controversy or claim arising between the
Parties with respect to this Agreement, including any dispute, controversy or claim relating to any
Excepted Decision (each, a “Dispute”), shall be resolved by binding arbitration before a panel of
three (3) arbitrators in accordance with the rules of the ICC in effect at the time the proceeding
is initiated; provided, that, any Dispute as to an Excepted Decision shall be resolved pursuant to
Section 14.1.2. In any such arbitration, the following procedures shall apply:

                    (a) The panel will be comprised of one arbitrator chosen by MERCK, one by ARCHEMIX and the
third by the two so chosen. If either, or both, of MERCK or ARCHEMIX fails to choose an arbitrator
or arbitrators within thirty (30) days after receiving notice of commencement of arbitration or if
the two arbitrators fail to choose a third arbitrator within thirty (30) days after their
appointment, then either or both Parties shall immediately request that the ICC select the
remaining number of arbitrators to be selected, which arbitrator(s) shall have the requisite
scientific background, experience and expertise. The place of arbitration shall be New York, New
York.

                    (b) Either Party may apply to the arbitrators for interim injunctive relief until the
arbitration decision is rendered or the Dispute is otherwise resolved. Either Party also may,
without waiving any right or remedy under this Agreement, seek from any court having jurisdiction
any injunctive or provisional relief necessary to protect the rights or property of that Party
pending resolution of the Dispute pursuant to this Section 14.1.1. The arbitrators shall have no
authority to award punitive or any other type of damages not measured by a Party’s compensatory
damages. Each Party shall bear its own costs and expenses and attorneys’ fees in connection with
any such arbitration; provided, that, the non-prevailing Party shall pay the costs and expenses
incurred by the prevailing Party in connection with any such arbitration, including reasonable
attorneys’ fees and costs. The Parties acknowledge that while Section 14.4 shall apply to any such
Dispute, it is the intention of the Parties not to use the discovery rules of the State of New York
in connection with any such Dispute.

                    (c) Except to the extent necessary to confirm an award or decision or as may be required by
Applicable Laws, neither Party nor any arbitrator may disclose the existence or results of any
arbitration without the prior written consent of both Parties. In no event shall any arbitration be
initiated after the date when commencement of a legal or equitable proceeding based on the Dispute
would be barred by the applicable New York statute of limitations.

                    (d) In the event of a Dispute involving the alleged breach of this Agreement (including,
without limitation, whether a Party has satisfied its diligence obligations hereunder), (i) neither
Party may terminate this Agreement under Section 11.2.2 until resolution

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

103

 

of the Dispute pursuant to this Section 14.1.1 and (ii) if the arbitrators render a decision
that a breach of this Agreement has occurred, the arbitrators shall have no authority to modify the
right of the non-breaching Party to terminate this Agreement in accordance with Section 11.2.2.

                    (e) Any disputed performance or suspended performance pending the resolution of a Dispute that
the arbitrators determine to be required to be performed by a Party shall be completed within a
reasonable time period following the final decision of the arbitrators.

                    (f) The decision of the arbitrators shall be the sole, exclusive and binding remedy between
the Parties regarding the determination of all Disputes presented. Any monetary payment to be made
by a Party pursuant to a decision of the arbitrators shall be made in United States dollars, free
of any tax or other deduction.

               14.1.2 Accelerated Arbitration. To the extent a Dispute submitted to arbitration by a
Party under Section 14.1.1 is claimed, by either Party, to involve an Excepted Decision, the
following procedures shall apply:

                    (a) The Parties shall mutually select a single independent, conflict-free arbitrator (the
“Expert”), who shall have sufficient scientific background and experience to resolve the Dispute.
If the Parties are unable to reach agreement on the selection of an Expert within fifteen (15)
business days after submission to arbitration, then either or both Parties shall immediately
request that the ICC select an arbitrator with the requisite scientific background, experience and
expertise. The place of arbitration shall be New York, New York.

                    (b) Each Party shall prepare and submit a written summary of such Party’s position and any
relevant evidence in support thereof to the Expert within thirty (30) days of the selection of the
Expert. Upon receipt of such summaries from each Party, the Expert shall provide copies of the
same to the other Party. Within thirty (30) days of the delivery of such summaries by the Expert,
each Party shall submit a written rebuttal of the other Party’s summary and may also amend and
re-submit its original summary. Oral presentations shall not be permitted unless otherwise
requested by the Expert. The Expert shall make a final decision with respect to the Dispute within
thirty (30) days following receipt of the last of such rebuttal statements submitted by the
Parties. Each Party shall bear its own costs and expenses and attorneys’ fees, and the Party that
does not prevail in the arbitration proceeding shall pay the Expert’s fees and any administrative
fees of arbitration.

     14.2 Change of Control.

               14.2.1 ARCHEMIX Change of Control.

                    (a) Notice. ARCHEMIX shall notify MERCK in writing in the event it receives an
indication of interest from a Third Party (or any other form of binding or non-binding offer) that
might result in a Change of Control for ARCHEMIX unless ARCHEMIX in good faith and acting
reasonably determines that any such notice would violate the terms of a confidentiality undertaking
with such Third Party. Notwithstanding the foregoing, in the event ARCHEMIX enters into an
agreement that results or, if the transaction contemplated thereby is

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

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completed, would result in a Change of Control, ARCHEMIX shall provide MERCK with prompt
written notice describing such Change of Control in reasonable detail (the “ARCHEMIX Change of
Control Notice”). The ARCHEMIX Change of Control Notice shall be provided by ARCHEMIX prior to
execution of such agreement, if permitted under Applicable Laws and not prohibited by the terms of
any agreement between ARCHEMIX and any Third Party, and otherwise as soon as practicable thereafter
and, in any event, not later than promptly following the consummation of the transaction
contemplated by such agreement.

                    (b) Change of Control Involving Competitive Entity. If the Change of Control that is
described in the ARCHEMIX Change of Control Notice results or, if completed, would result in a
Competitive Entity becoming an Affiliate of ARCHEMIX, then, within [***] days after such ARCHEMIX
Change of Control Notice is provided by ARCHEMIX, MERCK shall have the right to provide written
notice to ARCHEMIX, in its sole discretion, (i) if the ARCHEMIX Change of Control Notice is
provided prior to expiration of the Research Program Term, [***] the Research Program; (ii) if the
ARCHEMIX Change of Control Notice is received at any time during the Term, (A) [***] ARCHEMIX’s
[***] in any [***] pursuant to Article 4 (including ARCHEMIX’s right to [***] in the [***] and
[***]); (B) to the extent not exercised as of the date of the ARCHEMIX Change of Control Notice is
given, [***] ARCHEMIX’s right to [***] any [***] and [***] pursuant to Sections 4.10.2; (C) [***]
ARCHEMIX’s [***] activities pursuant to this Agreement, provided, that, MERCK shall [***] to
ARCHEMIX as if the Co-Promoted Product was a Royalty Bearing Product; (D) [***] ARCHEMIX’s
Co-Promotion activities, provided, that MERCK shall [***] to ARCHEMIX as if the Co-Promoted Product
was a Royalty Bearing Product; and (E) to the extent MERCK is prosecuting Program Aptamer-Specific
Patent Rights in accordance with Section 11.1.1(a), [***] MERCK’s obligation to [***] pursuant to
Section 11.1.4 with respect to such Program Aptamer-Specific Patent Rights. In all other aspects,
this Agreement shall remain unchanged. If MERCK should fail to give such notice to ARCHEMIX within
such [***] day period, MERCK shall have no further rights under this Section 14.2.1 as a result of
the Change of Control described in the ARCHEMIX Change of Control Notice.

                    (c) Change of Control Involving Competitive Program. If the Change of Control that is
described in the ARCHEMIX Change of Control Notice involves a Third Party that has a Competitive
Program, then, notwithstanding any provision hereof, the existence and continuation of such
Competitive Program in any respect following the Change of Control shall not be deemed to be a
breach of this Agreement.

               14.2.2 MERCK Change of Control.

                    (a) Notice. If MERCK enters into an agreement that results or, if the transaction
contemplated thereby is completed, would result in a Change of Control, MERCK shall provide
ARCHEMIX with prompt written notice describing such Change of Control in reasonable detail (the
“MERCK Change of Control Notice”). The MERCK Change of Control Notice shall be provided by MERCK
prior to execution of such agreement, if permitted under Applicable Laws and not prohibited by the
terms of any agreement between MERCK and any Third Party, and otherwise as soon as practicable
thereafter and, in any event, not later than promptly following the consummation of the transaction
contemplated by such agreement.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

105

 

                    (b) Change of Control Involving Competitive Program. If the Change of Control that is
described in the MERCK Change of Control Notice involves a Third Party that has a Competitive
Program, then, notwithstanding any provision hereof, the existence and continuation of such
Competitive Program in any respect following such Change of Control shall not be deemed to be a
breach of this Agreement; provided, that, each chemical compound or product that is part of the
Competitive Program shall be deemed to be an Optimized Lead Compound, Development Candidate or
Product in the event such chemical compound or product meets standards or criteria hereunder for
Optimized Lead Compounds, Development Candidates or Products, and shall be subject to royalty
payments as set forth in this Agreement (but not milestone payments) applicable to Optimized Lead
Compounds, Development Candidates and Products.

     14.3 Notices. All notices and communications shall be in writing and delivered
personally or by courier or mailed via certified mail, return receipt requested, addressed as
follows, or to such other address as may be designated from time to time:

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

106

 

	 	 	 	 	 
	 

	 	If to MERCK:
	 	If to ARCHEMIX:
	 

	 	Merck KGaA
	 	Archemix Corp.
	 

	 	Legal Department
	 	300 Third Street
	 

	 	Frankfurter Str. 250
	 	Cambridge, MA 02142
	 

	 	64293 Darmstadt
	 	Tel: (617) 621-7700
	 

	 	Germany
	 	Fax: (617) 621-9300
	 

	 	Tel: +49 6151 72 0
	 	Attention: Chief Executive Officer
	 

	 	Fax: +49 6151 72 [***]
	 	Attention: General Counsel
	 
	 	 	 	 
	 

	 	 	 	With a copy to:
	 
	 	 	 	 
	 

	 	 	 	Mintz, Levin, Cohn, Ferris, Glovsky
	 

	 	 	 	     and Popeo, P.C.
	 

	 	 	 	One Financial Center
	 

	 	 	 	Boston, Massachusetts 02111
	 

	 	 	 	Attention: John J. Cheney, Esq.
	 

	 	 	 	Tel: (617) 542-6000
	 

	 	 	 	Fax: (617) 542-2241

     In addition, all notices to the JPT or JSC shall be sent to each Party’s designees at such
Party’s address stated above or to such other address as such Party may designate by written notice
given in accordance with this Section 14.3.

     Except as otherwise expressly provided in this Agreement or mutually agreed in writing, any
notice, communication or document (excluding payment) required to be given or made shall be deemed
given or made and effective upon actual receipt or, if earlier, (a) three (3) business days after
deposit with an internationally-recognized overnight express courier with charges prepaid, or (b)
five (5) business days after mailed by certified, registered or regular mail, postage prepaid, in
each case addressed to a Parties at its address stated above or to such other address as such Party
may designate by written notice given in accordance with this Section 14.3.

     14.4 Governing Law. This Agreement shall be governed by and construed in accordance
with the laws of the State of New York, without regard to the application of principles of
conflicts of law.

     14.5 Binding Effect. This Agreement shall be binding upon and inure to the benefit of
the Parties and their respective legal representatives, successors and permitted assigns.

     14.6 Headings. Section and subsection headings are inserted for convenience of
reference only and do not form a part of this Agreement.

     14.7 Counterparts. This Agreement may be executed simultaneously in two or more
counterparts, each of which shall be deemed an original and both of which, together, shall
constitute a single agreement.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

107

 

     14.8 Amendment; Waiver. This Agreement may be amended, modified, superseded or
canceled, and any of the terms of this Agreement may be waived, only by a written instrument
executed by each Party or, in the case of waiver, by the Party or Parties waiving compliance. The
delay or failure of either Party at any time or times to require performance of any provisions
shall in no manner affect the rights at a later time to enforce the same. No waiver by either
Party of any condition or of the breach of any term contained in this Agreement, whether by
conduct, or otherwise, in any one or more instances, shall be deemed to be, or considered as, a
further or continuing waiver of any such condition or of the breach of such term or any other term
of this Agreement.

     14.9 No Third Party Beneficiaries. Except as set forth in Sections 13.1, 13.2 and
13.3, no Third Party (including, without limitation, employees of either Party) shall have or
acquire any rights by reason of this Agreement.

     14.10 Purposes and Scope. The Parties hereto understand and agree that this
Collaboration is limited to the activities, rights and obligations as set forth in this Agreement.
Nothing in this Agreement shall be construed (a) to create or imply a general partnership between
the Parties, (b) to make either Party the agent of the other for any purpose, (c) to alter, amend,
supersede or vitiate any other arrangements between the Parties with respect to any subject matters
not covered hereunder, (d) to give either Party the right to bind the other, (e) to create any
duties or obligations between the Parties except as expressly set forth herein, or (f) to grant any
direct or implied licenses or any other right other than as expressly set forth herein.

     14.11 Assignment and Successors. Neither this Agreement nor any obligation of a Party
hereunder may be assigned by either Party without the consent of the other which shall not be
unreasonably withheld, except that each Party may assign this Agreement and the rights, obligations
and interests of such Party, in whole or in part, to any of its Affiliates, to any purchaser of all
or substantially all of its assets or all or substantially all of its assets to which this
Agreement relates or to any successor corporation resulting from any merger, consolidation, share
exchange or other similar transaction.

     14.12 Force Majeure. Neither MERCK nor ARCHEMIX shall be liable for failure of or
delay in performing obligations set forth in this Agreement, and neither shall be deemed in breach
of its obligations, if such failure or delay is due to a Force Majeure. In event of such Force
Majeure, the Party affected shall use reasonable efforts to cure or overcome the same and resume
performance of its obligations hereunder.

     14.13 Interpretation. The Parties hereto acknowledge and agree that: (a) each Party
and its counsel reviewed and negotiated the terms and provisions of this Agreement and have
contributed to its revision; (b) the rule of construction to the effect that any ambiguities are
resolved against the drafting Party shall not be employed in the interpretation of this Agreement;
and (c) the terms and provisions of this Agreement shall be construed fairly as to each Party and
not in a favor of or against either Party, regardless of which Party was generally responsible for
the preparation of this Agreement.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

108

 

     14.14 Integration; Severability. This Agreement is the entire agreement with respect
to the subject matter hereof and supersedes all other agreements and understandings between the
Parties with respect to such subject matter. Notwithstanding the foregoing, this Agreement shall
not supersede the Initial Collaboration Agreement between ARCHEMIX and MERCK, which shall continue
to be in full force and effect in accordance with its terms and conditions. If any provision of
this Agreement is or becomes invalid or is ruled invalid by any court of competent jurisdiction or
is deemed unenforceable, it is the intention of the Parties that the remainder of the Agreement
shall not be affected.

     14.15 Further Assurances. Each of ARCHEMIX and MERCK agrees to duly execute and
deliver, or cause to be duly executed and delivered, such further instruments and do and cause to
be done such further acts and things, including, without limitation, the filing of such additional
assignments, agreements, documents and instruments, as the other Party may at any time and from
time to time reasonably request in connection with this Agreement or to carry out more effectively
the provisions and purposes of, or to better assure and confer unto such other Party its rights and
remedies under, this Agreement.

[Remainder of page intentionally left blank.]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

109

 

     IN WITNESS WHEREOF, the Parties have caused this Agreement to be executed by their duly
authorized representatives.

	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 	 	MERCK KGaA	 	 
	 
	 	 	 	 	 	 
	 	 	ppa.      i.V.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Dr. B. Kirschbaum      J. Eckhardt
	 	 
	 

	 	Title:
	 	Senior Executive         Legal Counsel 

Vice President
	 	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

110

 

EXHIBIT A

SELEX TECHNOLOGY TRANSFER PLAN

Plan Components

	 	 	 	 	 	 	 	 	 	 	 	 	 
	Location	 	Archemix, Cambridge MA	 	 	 	 
	 
	Staffing	 	•	 	Merck: [***], [***] (or [***])	 	 	 	 
	Requirements	 	•	 	Archemix: [***] , [***]	 	 	 	 
	 	 	 	 	 
	 	 	 	 	 	 	 	 
	Duration	 	•	 	[***] at Archemix	 	 	 	 
	 	 	 	 	o	 	May be acceptable for [***] to spend [***], [***] to stay [***]
	 	 	•	 	Archemix may provide subsequent consultation on an as needed basis
via phone, e-mail, e-room, or in person.
	 	 	 	 	 
	 	 	 	 	 	 	 	 
	Components of
classroom training	 	•	 	Archemix scientists to provide [***] covering:	 	 	 	 
	 	 	 	 	o	 	[***]: what is it?	 	 	 	 
	 	 	 	 	o	 	[***]	 	 	 	 
	 	 	 	 	o	 	[***]	 	 	 	 
	 	 	 	 	o	 	[***]	 	 	 	 
	 	 	 	 	 	 	§	 	 What [***] of [***] are used	 	 
	 	 	 	 	 	 	§	 	 What [***] choice	 	 
	 	 	 	 	o	 	[***] for [***]	 	 	 	 
	 	 	 	 	 	 	§	 	 [***] for [***]	 	 
	 	 	 	 	 	 	§	 	 [***] for [***]	 	 
	 	 	 	 	o	 	[***] for [***] the [***] of a [***]	 	 	 	 
	 	 	 	 	o	 	[***]	 	 	 	 
	 	 	 	 	o	 	[***]	 	 	 	 
	 	 	 	 	o	 	Concepts to [***] when [***]	 	 	 	 
	 
	Components of
laboratory training
	 	•
	 	[***]
	 	 	 	 	 	 	 	 
	 
	 	•
	 	[***]
	 	 	 	 	 	 	 	 
	 	 	•	 	[***] and [***] for [***]
	 	 	•	 	[***]
	 
	Materials to be provided to Merck	 	•	 	[***] materials from [***]
	KGaA	 	•	 	[***] for all [***] of [***] from [***] [***] through [***]
	 	 	•	 	[***] and [***] for [***]
	 
	Required equipment	 	•	 	[***]	 	 	 	 	 	 	 	 
	(Merck site)	 	•	 	[***]
	 	 	•	 	[***]
	 	 	•	 	[***] with [***] for [***], [***]
	 	 	•	 	[***] and [***]
	 	 	•	 	[***]
	 	 	•	 	[***] with [***]
	 	 	•	 	Other standard laboratory equipment (e.g., [***], [***], etc.)

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

EXHIBIT B

FORM OF COMMON STOCK PURCHASE AGREEMENT

COMMON STOCK PURCHASE AND REGISTRATION RIGHTS AGREEMENT

by and between

ARCHEMIX CORP.

and

MERCK KGaA

Dated as of [___]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

 

 

Table Of Contents

	 	 	 	 	 
	 	 	Page
	SECTION 1 DEFINITIONS
	 	 	1	 
	 
	 	 	 	 
	SECTION 2 AUTHORIZATION, PURCHASE AND SALE OF THE SHARES
	 	 	3	 
	 
	 	 	 	 
	2.1 Purchase and Sale of the Shares
	 	 	3	 
	2.2 Closing
	 	 	3	 
	 
	 	 	 	 
	SECTION 3 REPRESENTATIONS AND WARRANTIES AND CERTAIN COVENANTS OF THE COMPANY
	 	 	4	 
	 
	 	 	 	 
	3.1 Organization, Qualifications and Corporate Power
	 	 	4	 
	3.2 Authorization of Agreements, Etc
	 	 	4	 
	3.3 Validity
	 	 	5	 
	3.4 Consents
	 	 	5	 
	3.5 Subsidiaries
	 	 	5	 
	3.6 Capitalization
	 	 	5	 
	3.7 Litigation
	 	 	5	 
	3.8 Financial Statements
	 	 	5	 
	3.9 Taxes
	 	 	5	 
	3.10 Intellectual Property
	 	 	6	 
	3.11 Brokers
	 	 	6	 
	3.12 Insurance
	 	 	6	 
	 
	 	 	 	 
	SECTION 4 REPRESENTATIONS AND WARRANTIES OF PURCHASER
	 	 	6	 
	 
	 	 	 	 
	4.1 Experience
	 	 	6	 
	4.2 Investment
	 	 	6	 
	4.3 Rule 144
	 	 	6	 
	4.4 Access to Data
	 	 	7	 
	4.5 Brokers
	 	 	7	 
	4.6 Authorization
	 	 	7	 
	 
	 	 	 	 
	SECTION 5
	 	 	7	 
	 
	 	 	 	 
	5.1 “Piggyback” Registration
	 	 	7	 
	5.2 Furnish Information
	 	 	8	 
	5.3 Sale or Transfer of Shares; Legend
	 	 	8	 
	5.4 Indemnification
	 	 	10	 
	5.5 Assignment of Registration Rights
	 	 	12	 
	5.6 “Market Stand-Off” Agreement
	 	 	12	 
	5.7 Termination of Registration Rights
	 	 	13	 
	 
	 	 	 	 
	SECTION 6 PURCHASER’S CONDITIONS TO CLOSING
	 	 	13	 
	 
	 	 	 	 
	6.1 Representations and Warranties
	 	 	13	 
	6.2 Performance
	 	 	13	 
	6.3 Legal Investment
	 	 	13	 
	6.4 Proceedings and Documents
	 	 	13	 
	6.5 Qualifications
	 	 	13	 
	 
	 	 	 	 
	SECTION 7 COMPANY’S CONDITIONS TO CLOSING
	 	 	14	 
	 
	 	 	 	 
	7.1 Representations and Warranties
	 	 	14	 
	7.2 Performance
	 	 	14	 
	7.3 Legal Investment
	 	 	14	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

(i)

 

	 	 	 	 	 
	 	 	Page
	7.4 Payment of Purchase Price
	 	 	14	 
	 
	 	 	 	 
	SECTION 8 MISCELLANEOUS
	 	 	14	 
	 
	 	 	 	 
	8.1 Governing Law
	 	 	14	 
	8.2 Survival
	 	 	14	 
	8.3 Successors and Assigns
	 	 	14	 
	8.4 Entire Agreement; Amendment and Waiver
	 	 	14	 
	8.5 Notices
	 	 	15	 
	8.6 Transferability of Shares
	 	 	15	 
	8.7 Delays or Omissions
	 	 	16	 
	8.8 Severability
	 	 	16	 
	8.9 Interpretation
	 	 	16	 
	8.10 Information Confidential
	 	 	16	 
	8.11 Further Assurances
	 	 	16	 
	8.12 Headings
	 	 	17	 
	8.13 Counterparts
	 	 	17	 

Schedules

Disclosure Schedule

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

(ii)

 

ARCHEMIX CORP.

COMMON STOCK PURCHASE AND REGISTRATION RIGHTS AGREEMENT

     THIS COMMON STOCK PURCHASE AND REGISTRATION RIGHTS AGREEMENT dated as of [___] (the
“Agreement”) is made by and between Archemix Corp., a Delaware corporation (the “Company”), and
Merck KGaA, a company organized under the laws of Germany (the “Purchaser”).

     WHEREAS, the Company desires to issue and sell to the Purchaser, and the Purchaser desires to
purchase, shares of the Company’s common stock, par value $.001 per share (“Common Stock”), as
provided in Section 5.1 of that certain Collaborative Research and License Agreement between the
Company and the Purchaser dated June 6, 2007.

     NOW, THEREFORE, in consideration of the premises and mutual agreements set forth herein and
for other good and valuable consideration, the receipt and sufficiency of which are hereby mutually
acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows:

Definitions

     1.1 For purposes of this Agreement, the following terms shall have the meanings set forth
below:

          14.15.1 “Act” shall mean the Securities Act of 1933, as amended, or any similar federal
statute and the rules, regulations and policies of the Commission thereunder, all as the same
shall be in effect at the time.

          14.15.2 “1934 Act” means the Securities Exchange Act of 1934, as amended, or any similar
federal statute and the rules, regulations and policies of the Commission thereunder, all as the
same shall be in effect at the time.

          14.15.3 “Affiliate” shall mean an individual, trust, business trust, joint venture,
partnership, corporation, limited liability company, association or any other entity which
(directly or indirectly) is controlled by, controls or is under common control with the Purchaser.
For the purposes of this definition, the term “control” (including, with correlative meanings,
the term “controlled by” and “under common control with”) as used with respect to the Purchaser,
means the possession of the power to direct or cause the direction of the management and policies
of an entity, through the ownership of the outstanding voting securities or by contract or
otherwise.

          14.15.4 “By-laws” shall mean the Amended and Restated By-Laws of the Company, as amended from
time to time.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-1

 

          14.15.5 “Certificate of Incorporation” shall mean the Company’s Restated Certificate of
Incorporation on file with the Secretary of State of the State of Delaware, as amended from time
to time.

          14.15.6 “Closing” and “Closing Date” shall have the meanings specified in Section 2.2 hereof.

          14.15.7 “Commission” shall mean the Securities and Exchange Commission or any other federal
agency at the time administering the Act.

          14.15.8 “Common Stock” shall have the meaning specified in the recitals.

          14.15.9 “Competitor of the Company” shall mean a person or entity that poses a competitive
threat to the Company’s business or is engaged in the same or a substantially similar business as
the Company, as determined by the Company’s board of directors.

          14.15.10 “Holder” means the Purchaser (so long as the Purchaser holds Registerable
Securities) and any person owning or having the right to acquire Registrable Securities or any
assignee thereof in accordance with Section 5.5 hereof.

          14.15.11 “Purchase Price” shall have the meaning specified in Section 2.1 hereof.

          14.15.12 “Prospectus” shall mean the prospectus contained in the Registration Statement.

          14.15.13 “Qualified Public Offering” means the Company’s firm commitment underwritten initial
public offering filed under the Act covering the offer and sale of the Company’s Common Stock,
with gross offering proceeds to the Company of not less than $30,000,000 exclusive of any amount
issued to the Purchaser pursuant to the this Agreement.

          14.15.14 “Registrable Securities” means (i) any shares of Common Stock issued to the
Purchaser pursuant to this Agreement, (ii) any Common Stock of the Company issued as (or issuable
upon the conversion or exercise of any warrant, right or other security which is issued as) a
dividend or other distribution with respect to, or in exchange for or in replacement of the shares
referenced in (i) above, excluding in all cases, however, any Registrable Securities sold by a
person in a transaction in which the rights under this Agreement are not assigned;
provided, however, that shares of Common Stock which are Registrable Securities
shall cease to be Registrable Securities upon any sale pursuant to a registration statement,
Section 4(1) of the Act or Rule 144 under the Act, any sale in any manner to a person or entity
which, by virtue of Section

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-2

 

5.5 of this Agreement, is not entitled to the rights provided by this Agreement or upon the
eligibility for sale of such shares under Rule 144(k) under the Act.

          14.15.15 “Registration Statement” shall mean the Registration Statement on Form S-1 (File No.
333-[___]) filed with the Commission relating to the Company’s initial public offering of
its Common Stock.

          14.15.16 “Shares” shall have the meaning specified in Section 2.1 hereof.

     1.2 Certain other words and phrases are defined or described elsewhere in this Agreement and
the Exhibits and Schedules hereto.

     1.3 Wherever used in this Agreement:

          the words “include” or “including” shall be construed as also incorporating “but not limited
to” and “without limitation”;

          14.15.17 the word “day” means a calendar day unless specified otherwise; and

          14.15.18 the word “law” (or “laws”) means any statute, ordinance, regulation or code.

     1.4 Unless specified to the contrary, references to Articles, Sections, Schedules and/or
Exhibits mean the particular Article, Section, Schedule or Exhibit in or to this Agreement.

     1.5 References to this Agreement shall include this Agreement as varied or modified from time
to time by the parties.

     1.6 Unless the context requires otherwise, words in the singular number include the plural and
vice versa.

     1.7 All Schedules and Exhibits hereto are hereby incorporated herein and made a part hereof.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-3

 

Authorization, Purchase and Sale of the Shares

     14.16 Purchase and Sale of the Shares. At the Closing (as defined in Section 2.2
hereof), and subject to the terms and conditions hereof and in reliance upon the representations,
warranties and agreements contained herein, the Company shall issue and sell to the Purchaser and
the Purchaser shall purchase from the Company [___] shares of Common Stock (the “Shares”)
at a purchase price of $[___] per share for a total purchase price of $[___] (the
"Purchase Price”).

     14.17 Closing. The purchase and sale of the Shares being purchased by the Purchaser
shall take place at the offices of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., One
Financial Center, Boston, MA 02111, at 10:00 a.m., local time, on [___], or at such
other location, date and time as may be agreed upon among the Purchaser and the Company (such
closing being called the “Closing” and such date and time being called the “Closing Date”). At the
Closing, the Company shall issue and deliver to the Purchaser a certificate in definitive form,
registered in the name of the Purchaser, representing the Shares being purchased by the Purchaser
at the Closing. As payment in full for the Shares being purchased by it under this Agreement, and
against delivery of the certificate therefor as aforesaid, on the Closing Date, the Purchaser (a)
shall deliver to the Company a check payable to the order of the Company in the amount of the
Purchase Price, (b) shall transfer such amount to the account of the Company by wire transfer, or
(c) shall deliver a combination of (a) and (b) above.

Representations and Warranties and Certain Covenants of the Company

     Except as set forth in any disclosure schedules delivered herewith (which shall be
numbered to correspond with the sections of this Section 3), the Company hereby represents and
warrants to and covenants to the Purchaser as follows:

     14.18 Organization, Qualifications and Corporate Power. The Company is a corporation
duly incorporated, validly existing and in good standing under the laws of the State of Delaware
and the Company is duly licensed or qualified to transact business as a foreign corporation and is
in good standing in each jurisdiction in which the nature of the business transacted by it or the
character of the properties owned or leased by it requires such licensing or qualification, except
where failure to qualify would not have a material adverse effect on the business or financial
condition of the Company. The Company has the corporate power and authority to own and hold its
properties and to carry on its business as now conducted or as planned to be conducted in the
foreseeable future, to execute, deliver and perform this Agreement and any other agreements,
documents or instruments contemplated hereby to which it is a party, to issue, sell and deliver the
Shares.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-4

 

14.19 Authorization of Agreements, Etc. 

          14.19.1 The execution and delivery by the Company of this Agreement, the performance by the
Company of its obligations hereunder and thereunder, and the issuance, sale and delivery of the
Shares have been duly authorized by all requisite corporate action and will not violate any
provision of law, any order of any court or other agency of government specifically naming the
Company, the Certificate of Incorporation, or the By-laws or any material provision of any
indenture, agreement or other instrument which is filed as an exhibit to the Registration
Statement, or conflict with, result in a breach of or constitute (with due notice or lapse of time
or both) a default under any such indenture, agreement or other instrument, which violation,
conflict or default could have a material adverse effect on the Company, or result in the creation
or imposition of any material lien, charge, restriction, claim or encumbrance upon any of the
properties or assets of the Company.

          14.19.2 The Shares have been duly authorized and the Shares, when issued in accordance with
this Agreement, will be validly issued, fully paid and nonassessable and free of all liens,
charges, restrictions, claims and encumbrances imposed by or through the Company. None of the
issuance, sale or delivery of the Shares is subject to any preemptive right of stockholders of the
Company or to any right of first refusal or other right in favor of any person which has not been
waived.

     14.20 Validity. This Agreement has been duly executed and delivered by the Company.
This Agreement constitutes the legal, valid and binding obligations of the Company, enforceable in
accordance with its respective terms subject to bankruptcy, insolvency, reorganization, moratorium
and other similar laws affecting the rights of creditors and to general principles of equity.

     14.21 Consents. All consents, approvals, orders, or authorizations of, or
registrations, qualifications, designations, declarations, or filings with any federal or state
governmental authority, any party to a contract to which the Company is bound or any other third
party on the part of the Company required in connection with the consummation of the transactions
contemplated by this Agreement shall have been obtained prior to, and be effective as of, the
Closing (other than such filings under the “blue sky” law of any state governmental authority and
any federal securities law filings that may be made after the Closing, which such filings shall be
timely made).

     14.22 Subsidiaries. The Company has no subsidiaries other than as listed in an
Exhibit to the Registration Statement.

     14.23 Capitalization. The authorized and outstanding shares of capital stock and
options, warrants and other rights to purchase capital stock of the Company is as set forth in the
Prospectus.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-5

 

     14.24 Litigation. Except as set forth in the Prospectus and required to be disclosed
therein, there is no (i) action, suit, claim, proceeding or investigation pending or, to the best
of the Company’s knowledge, threatened against the Company, at law or in equity, or before or by
any federal, state, municipal or other governmental department, commission, board, bureau, agency
or instrumentality, domestic or foreign, (ii) arbitration proceeding relating to the Company
pending under collective bargaining agreements or otherwise or (iii) governmental inquiry pending
or, to the best of the Company’s knowledge, threatened against the Company (including without
limitation any inquiry as to the qualification of the Company to hold or receive any license or
permit), and to the best of the Company’s knowledge there is no basis for any of the foregoing.

     14.25 Financial Statements. The financial statements of the Company contained in the
Prospectus (i) are true and correct in all material respects, (ii) are in accordance with the books
and records of the Company, (iii) present fairly in all material respects the financial position of
the Company on as of the dates thereof and (iv) were prepared in accordance with United States
generally-accepted accounting principles (except, with respect to any interim financial statements,
for all of the required footnotes and year end adjustments).

     14.26 Taxes. The Company has accurately prepared in all material respects and timely
filed all federal, state, county and local tax returns required to be filed by it, and the Company
has paid all taxes required to be paid by it pursuant to such returns as well as all other taxes,
assessments and governmental charges which have become due or payable, including, without
limitation all taxes which the Company is obligated to withhold from amounts owing to employees,
creditors and third parties. All such taxes with respect to which the Company has become obligated
pursuant to elections made by the Company in accordance with generally accepted practice have been
paid and adequate reserves have been established for all taxes accrued but not payable.

     14.27 Intellectual Property. The Company owns or possesses adequate licenses or other
rights to use all patents, patent applications, trademarks, trademark applications, service marks,
service mark applications, trade names, copyrights, manufacturing processes, formulae, trade
secrets, customer lists and know how (collectively, “Intellectual Property”) necessary to the
conduct of its business as conducted consistent with the description of the Company’s business as
set forth in the Prospectus. The Company has not been informed that the licenses granted by or to
the Company and listed in Section 3.10 of Schedule II are not valid and enforceable. To
the knowledge of the Company, all right, title and interest in any Intellectual Property which has
been developed by key employees or founders of the Company in their capacity as either employees or
consultants to the Company which is necessary for the conduct of the Company’s business as
conducted has been unconditionally assigned to the Company.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-6

 

     14.28 Brokers. The Company has no contract, arrangement or understanding with any
broker, finder or similar agent with respect to the transactions contemplated by this Agreement.

     14.29 Insurance. The Company will use its commercially reasonable efforts to maintain
insurance with financially sound and reputable insurance companies or associations, in such amounts
and covering such risks as are adequate and customary for the type and scope of its properties and
business as currently conducted and as planned to be conducted in the foreseeable future.

Representations and Warranties of Purchaser

     The Purchaser represents and warrants to the Company as follows:

     14.30 Experience. The Purchaser: (a) is an accredited investor within the definition
of Regulation D promulgated under the Act; (b) is experienced in evaluating and in investing in
developing biotechnology companies such as the Company and can afford a loss of its entire
investment; and/or (c) has a pre-existing personal or business relationship with the Company and/or
certain of its officers, directors or controlling persons of a nature and duration that enable it
to be aware of the character, business acumen and financial circumstance of such persons.

     14.31 Investment. The Purchaser is acquiring the Shares for investment for its own
account and not with the view to, or for resale in connection with, any distribution thereof. It
understands that the Shares have not been registered under the Act by reason of specified
exemptions form the registration provisions of the Act.

     14.32 Rule 144. The Purchaser acknowledges that the Shares must be held indefinitely
unless they are subsequently registered under the Act or an exemption from such registration is
available. It has been advised or is aware of the provisions of Rule 144 promulgated under the Act,
which permit limited release of shares purchased in a private placement subject to the satisfaction
of certain conditions, and is aware that such Rule may not become available for resale of the
Shares.

     14.33 Access to Data. The Purchaser has had an opportunity to discuss the Company’s
business, management and financial affairs with the Company’s management and has had the
opportunity to review the Company’s facilities.

     14.34 Brokers. The Purchaser has no contract, arrangement or understanding with any
broker, finder or similar agent with respect to the transactions contemplated by this Agreement.

     14.35 Authorization. The Purchaser has full power and authority to enter into and to
perform this Agreement in accordance with its terms. All action (corporate or

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-7

 

otherwise) on the part of the Purchaser necessary for the authorization, execution, delivery
and performance by the Purchaser of this Agreement and the consummation of the transactions
contemplated herein has been taken. This Agreement is valid and binding obligation of the
Purchaser, enforceable in accordance with its terms, subject to bankruptcy, insolvency,
reorganization, moratorium and other similar laws affecting the rights of creditors and to general
principles of equity.

Registration Rights

     14.36 “Piggyback” Registration.

          14.36.1 Registration Statement. Following the consummation of a Qualified Public
Offering, if (but without any obligation to do so) the Company shall determine to register
(including for this purpose a registration effected by the Company for stockholders other than the
Holders) any of its stock or other securities under the Act in connection with the public offering
of such securities solely for cash (other than a registration or Form S-4 or S-8 or relating
solely to the sale of securities to participants in a stock plan or a registration relating solely
to a Rule 145 transaction or a registration on any form which does not include substantially the
same information as would be required to be included in a registration statement covering the sale
of the Registrable Securities), the Company shall, at such time, promptly give each Holder written
notice of such registration. Upon the written request of each Holder given within fifteen (15)
days after receipt of such notice by the Holder in accordance with Section 8.5, the Company shall,
subject to the provisions of this Section.5.1, use its reasonable best efforts to include in such
registration all of the Registrable Securities that each such Holder has requested to be
registered.

          14.36.2 Company Deferral. If the Company shall furnish to the Holders a certificate
signed by the President of the Company stating that in the good faith judgment of the Board, it
would be seriously detrimental to the Company and its stockholders for such Holder’s shares to be
included in the registration statement to be filed and it is therefore essential to defer the
inclusion of all or some of the Holders’ Registrable Securities in such registration statement,
the Company shall have the right to exclude such number of shares as the Company deems, in its
good faith judgment, are necessary.

          14.36.3 Underwriting Requirements. In connection with any offering involving an
underwriting of shares of the Company’s capital stock, the Company shall not be required under
this Section 5.1 to include any of the Holders’ Registrable Securities in such underwriting unless
such Holders accept the terms of the underwriting as agreed upon between the Company and the
underwriters selected by the Company (or by other persons entitled to select the underwriters and
then only in such quantity as the underwriters determine in their sole reasonable discretion will
not

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-8

 

jeopardize the successes of their offering by the Company or such other persons). If the
total amount of securities, including Registrable Securities, requested by stockholders to be
included in an offering exceeds the amount that the underwriters determine, in their sole
reasonable discretion, is compatible with the success of the offering, then the Company shall be
required to include in the offering only that number of such securities, including Registrable
Securities, which the underwriters determine in their sole reasonable discretion will not
jeopardize the success of the offering. If the number of Registrable Securities to be included in
the underwriting in accordance with the foregoing is less than the total number of shares which
the Holders of Registrable Securities have requested to be included, then the other holders of all
other shares of capital stock with registration rights who have requested to be included in the
registration statement shall participate in the underwriting prior to the Holders of Registrable
Securities who have requested registration.

          14.36.4 Withdrawal. Notwithstanding the foregoing provisions, the Company may
withdraw any registration statement referred to in this Section 5.1 for any reason without thereby
incurring any liability to the holders of Registrable Securities.

     14.37 Furnish Information. It shall be a condition precedent to the obligations of
the Company to take any action pursuant to this Section 5 with respect to the Registrable
Securities of any selling Holder that such Holder shall furnish to the Company such information
regarding itself, the Registrable Securities held by it, and the intended method of disposition of
such securities as shall be required to effect the registration of such Holder’s Registrable
Securities.

     14.38 Sale or Transfer of Shares; Legend.

          14.38.1 The Registrable Securities shall not be sold or transferred unless either (i) such
            shares first shall have been registered under the Act, or (ii) the transfer complies with Rule
144, Rule 144A or an exemption from registration under the Act, provided that, if requested by the
Company, the Company shall have been first furnished with an opinion of legal counsel, to the
effect that such sale or transfer is exempt from the registration requirements of the Act.

          14.38.2 Each certificate representing the Registrable Securities shall bear a legend
substantially in the following form:

“THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933 OR ANY STATE SECURITIES LAW AND THEY MAY NOT BE OFFERED,
SOLD, TRANSFERRED, HYPOTHECATED OR OTHERWISE ASSIGNED BY ANY PERSON, INCLUDING A
PLEDGEE, UNLESS (1) EITHER (a) SUCH SHARES FIRST SHALL HAVE BEEN REGISTERED UNDER
THE SECURITIES ACT OF

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-9

 

1933, AS AMENDED, OR (b) THE TRANSFER COMPLIES WITH RULE 144, RULE 144A OR AN
EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND, IF
REQUESTED BY THE COMPANY, THE COMPANY SHALL HAVE RECEIVED AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT AN EXEMPTION FROM REGISTRATION UNDER SUCH ACTS IS
THEN AVAILABLE, AND (2) THERE SHALL HAVE BEEN COMPLIANCE WITH ALL APPLICABLE STATE
SECURITIES LAWS.

THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO A COMMON STOCK PURCHASE
AND REGISTRATION RIGHTS AGREEMENT, AS AMENDED FROM TIME TO TIME (COPIES OF WHICH
MAY BE OBTAINED FROM THE COMPANY), AND BY ACCEPTING ANY INTEREST IN SUCH SHARES
THE PERSON ACCEPTING SUCH INTEREST SHALL BE DEEMED TO AGREE TO AND SHALL BECOME
BOUND BY ALL THE PROVISIONS OF SUCH REGISTRATION RIGHTS AGREEMENT. THE SALE,
TRANSFER, HYPOTHECATION OR OTHER DISPOSITION OF SUCH SHARES IS SUBJECT TO THE
TERMS OF SUCH AGREEMENT AND SUCH SHARES ARE TRANSFERABLE ONLY UPON PROOF OF
COMPLIANCE THEREWITH.”

The foregoing legend shall be removed from the certificates representing any Registrable
Securities, at the request of the holder thereof, at such time as they become eligible for resale
pursuant to Rule 144(k) under the Act.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-10

 

     14.39 Indemnification. In the event any Registrable Securities are included in a
registration statement under this Section 5:

          14.39.1 To the extent permitted by law, the Company will indemnify, defend and hold harmless
each Holder, its officers, directors, employees, agents and representatives, any underwriter (as
defined in the Act) for such Holder and each person, if any, who controls such Holder or
underwriter within the meaning of the Act or the 1934 Act (each, a “Company Indemnified Person”),
against any losses, claims, damages, or liabilities (joint or several) to which they may become
subject under the Act, the 1934 Act or other federal or state law, insofar as such losses, claims,
damages, or liabilities (or actions in respect thereof) (the “Company Indemnified Amount”) arise
out of or are based upon any of the following (collectively, a “Violation”): (i) any untrue
statement of a material fact contained in such registration statement, including any preliminary
prospectus or final prospectus contained therein or any amendments or supplements thereto, (ii)
the omission to state therein a material fact required to be stated therein, or necessary to make
the statements therein not misleading, or (iii) any violation by the Company of the Act, the 1934
Act, any state securities law or any rule or regulation promulgated under the Act, the 1934 Act or
any state securities or Blue Sky laws or any rule or regulation thereunder in connection with such
registration; and the Company will pay to each such Company Indemnified Person, as incurred, any
legal or other expenses reasonably incurred by them in connection with investigating or defending
any Company Indemnified Amount; provided, however, that the indemnity agreement
contained in this subsection 5.4(a) shall not apply to amounts paid in settlement of any such
loss, claim, damage, liability, or action if such settlement is effected without the consent of
the Company (which consent shall not be unreasonably withheld), nor shall the Company be liable in
any such case for any such Company Indemnified Amount as to any Company Indemnified Person to the
extent such liability arises out of or is based upon a Violation (i) which occurs in reliance upon
and in conformity with written information relating to such Company Indemnified Person and
furnished expressly for use in connection with such registration by such Company Indemnified
Person or (ii) contained in a preliminary prospectus and corrected in a final or amended
prospectus if such seller, underwriter or controlling person received notice of such final or
amended prospectus prior to the effective date of the registration statement but failed to deliver
a copy of the final or amended prospectus at or prior to the confirmation of the sale of the
Registrable Securities to the person asserting any such loss, claim, damage or liability resulting
from a Violation contained in such preliminary prospectus, in any case where such delivery is
required by the Act.

          14.39.2 To the extent permitted by law, each selling Holder will indemnify and hold harmless
the Company, each of its directors, each of its officers who has signed the registration
statement, each person, if any, who controls the Company within the meaning of the Act, any
underwriter, any other Holder selling securities in such registration statement and any
controlling person of any such underwriter or other Holder, against any losses, claims, damages,
or liabilities (joint or several) to which any

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-11

 

of the foregoing persons may become subject, under the Act, the 1934 Act or other federal or
state law, insofar as such losses, claims, damages, or liabilities (or actions in respect thereto)
(the “Holder Indemnified Amount”) arise out of or are based upon any Violation, in each case to
the extent (and only to the extent) that such Violation occurs in reliance upon and in conformity
with written information relating to such Holder and furnished by such Holder expressly for use in
connection with such registration; and each such Holder will pay, as incurred, any legal or other
expenses reasonably incurred by any person intended to be indemnified pursuant to this subsection
5.4(b), in connection with investigating or defending any Holder Indemnified Amount;
provided, however, that the indemnity agreement contained in this subsection
5.4(b) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability or
action if such settlement is effected without the consent of the Holder, which consent shall not
be unreasonably withheld; and provided, that, in no event shall any indemnity
under this subsection 5.4(b) exceed the net proceeds from the offering received by such Holder.

          14.39.3 Promptly after receipt by an indemnified party under this Section 5.4 of notice of
the commencement of any action (including any governmental action), such indemnified party will,
if a claim in respect thereof is to be made against any indemnifying party under this Section 5.4,
deliver to the indemnifying party a written notice of the commencement thereof and the
indemnifying party shall have the right to participate in, and, to the extent the indemnifying
party so desires, jointly with any other indemnifying party similarly noticed, to assume the
defense thereof with counsel mutually satisfactory to the parties; provided,
however, that an indemnified party (together with all other indemnified parties which may
be represented without conflict by one counsel) shall have the right to retain one separate
counsel, with the fees and expenses to be paid by the indemnifying party, if representation of
such indemnified party by the counsel retained by the indemnifying party would be inappropriate
due to actual or potential differing interests between such indemnified party and any other party
represented by such counsel in such proceeding. The failure to deliver written notice to the
indemnifying party within a reasonable time of the commencement of any such action, if prejudicial
to its ability to defend such action, shall relieve such indemnifying party of any liability to
the indemnified party under this Section 5.4, but the omission so to deliver written notice to the
indemnifying party will not relieve it of any liability that it may have to any indemnified party
otherwise than under this Section 5.4.

          14.39.4 If the indemnification provided for in this Section 5.4 is held by a court of
competent jurisdiction to be unavailable to an indemnified party with respect to any loss,
liability, claim, damage, or expense referred to herein, then the indemnifying party, in lieu of
indemnifying such indemnified party hereunder, shall contribute to the amount paid or payable by
such indemnified party as a result of such loss, liability, claim, damage, or expense in such
proportion as is appropriate to reflect the relative fault of the indemnifying party on the one
hand and of the indemnified party on the other in connection with the Violation that resulted in
such loss, liability, claim,

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-12

 

damage, or expense as well as any other relevant equitable considerations. The relative
fault of the indemnifying party and of the indemnified party shall be determined by reference to,
among other things, whether the untrue or alleged untrue statement of a material fact or the
omission to state a material fact relates to information supplied by the indemnifying party or by
the indemnified party and the parties’ relative intent, knowledge, access to information, and
opportunity to correct or prevent such statement or omission; and provided, that, in no
event shall any contribution under this subsection 5.4d) exceed the net proceeds from the offering
received by such Holder.

          14.39.5 Notwithstanding the foregoing, to the extent that the provisions on indemnification
and contribution contained in the underwriting agreement entered into in connection with the
underwritten public offering are in conflict with the foregoing provisions, the provisions in the
underwriting agreement shall control.

          14.39.6 The obligations of the Company and Holders under this Section 5.4 shall survive the
completion of any offering of Registrable Securities in a registration statement under this
Section 5, and otherwise.

     14.40 Assignment of Registration Rights. Subject to Section 8.6, the rights to cause
the Company to register Registrable Securities pursuant to this Section 5 may be assigned (but only
with all related obligations) by a Holder to a Permitted Assignee (as defined below),
provided that: (a) the Company is, within a reasonable time after such transfer, furnished
with written notice of the name and address of such transferee or assignee and the securities with
respect to which such registration rights are being assigned; (b) such transferee or assignee
agrees in writing to be bound by and subject to the terms and conditions of this Agreement; (c)
such assignment shall be effective only if immediately following such transfer the further
disposition of such securities by the transferee or assignee is restricted under the Act; and (d)
such transferee or assignee is not a Competitor of the Company. For purposes of this Section 5.5 a
“Permitted Assignee” shall mean an entity that acquires all or substantially all of the ownership
interests of a Holder.

     14.41 “Market Stand-Off” Agreement. The Purchaser hereby agrees that, during the one
hundred eighty (180) day period following the effective date of the registration statement for the
Qualified Public Offering or such other period as requested of all Company executive officers
required to file Forms 3 and 4 and directors of the Company by the underwriters in the Qualified
Public Offering in order to comply with Rule 2711 of the National Association of Securities Dealers
or otherwise, the Purchaser shall not, to the extent requested by the Company and such underwriter,
directly or indirectly sell, offer to sell, contract to sell (including, without limitation, any
short sale), grant any option to purchase or otherwise transfer or dispose of (other than to donees
who agree to be similarly bound) any securities of the Company held by it at any time during such
period except Common Stock included in such registration; provided, however, that
all executive officers and directors of the Company enter into similar agreements. In

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-13

 

addition to the obligations under this Section, the Purchaser agrees to execute a separate
agreement on form satisfactory to such underwriter containing such covenant and obligation.

     In order to enforce the foregoing covenant, the Company may impose stop-transfer instructions
with respect to the Registrable Securities of the Purchaser (and the shares or securities of every
other person subject to the foregoing restriction) until the end of such period.

     Notwithstanding the foregoing, the obligations described in this Section 5.6 shall not apply
to a registration relating solely to employee benefit plans on Form S-1 or Form S-8 or similar
forms which may be promulgated in the future, or a registration relating solely to SEC Rule 145, or
a transaction on Form S-4 or similar forms which may be promulgated in the future.

     14.42 Termination of Registration Rights.

          The right of any Holder to request registration or inclusion in any registration pursuant to
Section 5 shall terminate once the securities held by such Holder cease to be Registrable
Securities, and this Agreement, other than Sections 5.3, 5.6 and Sections 8.1-8.13, shall terminate
once all of the securities covered hereby cease to be Registrable Securities.

Purchaser’s Conditions to Closing

     The Purchaser’s obligation to purchase Shares at the Closing is subject to the
fulfillment to its satisfaction on or prior to the Closing Date of each of the following
conditions:

     14.43 Representations and Warranties. The representations and warranties contained in
Section 3 shall be true, complete and correct on and as of the Closing Date with the same effect as
though such representations and warranties had been made on and as of such date.

     14.44 Performance. The Company shall have performed and complied with all covenants,
agreements and conditions contained herein required to be performed or complied with by it prior to
or at the Closing Date.

     14.45 Legal Investment. At the time of the Closing, the purchase of the Shares shall
be legally permitted by all laws and regulations to which the Purchaser and the Company are
subject.

     14.46 Proceedings and Documents. All corporate and other proceedings in connection
with the transactions contemplated hereby and all documents and instruments

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-14

 

incident to such transactions shall be reasonably satisfactory in form and substance to the
Purchaser and its counsel. Prior to the Closing, the Company shall have obtained all consents or
waivers, if any, necessary to execute and deliver this Agreement, issue the Shares and to carry out
the transactions contemplated hereby and thereby, and all such consents and waivers shall be in
full force and effect.

     14.47 Qualifications. All other authorizations, approvals or permits if any, of any
governmental authority or regulatory body of the United States or any state that are required prior
to and in connection with the lawful issuance and sale of the Shares pursuant to this Agreement
shall be effective on and as of the Closing Date.

Company’s Conditions to Closing

     The Company’s obligation to sell the Shares at the Closing is subject to the fulfillment
on or prior to the Closing Date of each of the following conditions:

     14.48 Representations and Warranties. The representations and warranties made by the
Purchaser pursuant to Section 4 hereof shall be true and correct when made and shall be true and
correct on the Closing Date.

     14.49 Performance. The Purchaser shall have performed and complied with all
covenants, agreements and conditions contained herein required to be performed or complied with by
it prior to or at the Closing Date.

     14.50 Legal Investment. At the time of the Closing, the purchase of the Shares shall
be legally permitted by all laws and regulations to which the Purchaser and the Company are
subject.

     14.51 Payment of Purchase Price. The Purchaser shall have delivered to the Company a
check or a transfer of funds to the account of the Company in the full amount of the Purchase
Price.

Miscellaneous

     14.52 Governing Law. This Agreement shall be governed in all respects by the laws
of the State of Delaware without giving effect to principles of conflicts of law thereunder.

     14.53 Survival. All covenants, agreements, representations and warranties made
herein, or in any certificate or instrument delivered to the Purchaser pursuant to or in connection
with this Agreement shall not survive the execution and delivery of this Agreement.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-15

 

     14.54 Successors and Assigns. Except as otherwise expressly provided herein, the
provisions hereof shall inure to the benefit of, and be binding upon, the successors, assigns,
heirs, executors and administrators of the parties hereto. Nothing in this Agreement, express or
implied, is intended to confer upon any party other than the parties hereto or their respective
successors and assigns any rights, remedies, obligations, or liabilities under or by reason of this
Agreement, except as expressly provided in this Agreement. Subject to the terms of this Agreement,
no party hereby may assign its rights or obligations hereunder (whether by operation of law or
otherwise, including by merger, asset sale, sale of stock or otherwise) without the prior written
consent of the other parties hereto.

     14.55 Entire Agreement; Amendment and Waiver. This Agreement (including the Schedules
and Exhibits hereto) and the other documents delivered pursuant hereto constitute the full and
entire understanding and agreement between the parties with regard to the subjects hereof and
thereof. Neither this Agreement nor any term hereof may be amended, modified, waived or terminated,
except by a written instrument signed by the Company and the Purchaser.

     14.56 Notices. Unless otherwise provided, all notices, requests, consents and other
communications hereunder shall be in writing, shall be addressed to the receiving party’s address
set forth below or to such other address as a party may designate by notice hereunder, and shall be
either (i) delivered by hand, (ii) made by telecopy or facsimile transmission, (iii) sent by
overnight courier, or (iv) sent by registered or certified mail, return receipt requested, postage
prepaid.

	 	 	 
	If to the Company:

	 	Archemix Corp.
	 

	 	300 Third Street
	 

	 	Cambridge, MA
	 

	 	Attn: Chief Executive Officer
	 

	 	Attn: General Counsel
	 

	 	Facsimile: (617) 686-7679
	 
	 	 
	With a copy to:

	 	Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
	 

	 	One Financial Center
	 

	 	Boston, MA 02111
	 

	 	Attn: Jeffrey M. Wiesen, Esquire
	 

	 	Facsimile: (617) 542-2241
	 
	 	 
	If to the Purchaser:

	 	Merck KGaA
	 

	 	Legal Department
	 

	 	Frankfurter Str. 250
	 

	 	64293 Darmstadt
	 

	 	Germany
	 

	 	Facsimile: +49 6151 72 [***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-16

 

or, in any such case, at such other address or addresses as shall have been furnished in
writing by such party to the others.

     All notices, requests, consents and other communications hereunder shall be deemed to have
been given either (i) if by hand, at the time of the delivery thereof to the receiving party at the
address of such party set forth above, (ii) if made by telecopy or facsimile transmission, at the
time that receipt thereof has been acknowledged by electronic confirmation or otherwise, (iii) if
sent by overnight courier, on the next business day following the day such notice is delivered to
the courier service, or (iv) if sent by registered or certified mail, on the fifth business day
following the day such mailing is made.

     14.57 Transferability of Shares. The Purchaser or any transferee or assignee of
Registrable Securities hereby agrees not to sell, transfer, assign, exchange, pledge, hypothecate
or otherwise dispose of the Registerable Securities, or any right or interest therein, whether
voluntary, by operation of law or otherwise, (including by merger, asset sale, sale of stock or
otherwise), except to a Permitted Assignee in accordance with Section 5.5 or with the express
written consent of the Company.

     14.58 Delays or Omissions. No delay or omission to exercise any right, power or
remedy accruing to any holder of any shares upon any breach or default of the Company under this
Agreement shall impair any such right, power or remedy of such holder nor shall it be construed to
be a waiver of any such breach or default, or an acquiescence therein, or in any similar breach or
default occurring thereafter; nor shall any waiver of any single breach or default be deemed a
waiver of any other breach or default theretofore or thereafter occurring. Any waiver, permit,
consent or approval of any kind or character on the part of any holder or any breach or default
under this Agreement, or any waiver on the part of any holder of any provisions or conditions of
this Agreement must be made in writing and shall be effective only to the extent specifically set
forth in such writing. All remedies, either under this Agreement or by law or otherwise afforded to
any holder, shall be cumulative and not alternative.

     14.59 Severability. If one or more provisions of this Agreement are held to be
unenforceable under applicable law, such provision shall be excluded from this Agreement and the
balance of the Agreement shall be interpreted as if such provision were so excluded and shall be
enforceable in accordance with its terms.

     14.60 Interpretation. The parties hereby acknowledge and agree that: (i) each party
and its counsel reviewed and negotiated the terms and provisions of this Agreement and have
contributed to its revision; (ii) the rule of construction to the effect that any

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-17

 

ambiguities are resolved against the drafting party shall not be employed in the
interpretation of this Agreement; and (iii) the terms and provisions of this Agreement shall be
construed fairly as to all parties hereto and not in a favor of or against any party, regardless of
which party was generally responsible for the preparation of this Agreement.

     14.61 Information Confidential. The Purchaser agrees that it shall keep confidential
and shall not use any confidential, proprietary or secret information received by it with respect
to the Company which has been marked or otherwise designated as confidential, including, without
limitation, information regarding the nature of the Company’s business, financial, business
development, product and marketing strategies, financial statements and reports, or reproduce,
disclose or disseminate such information to any other person (other than to its employees, agents,
attorneys having a need to know the contents of such information or an Affiliate that is not a
Competitor of the Company), except in connection with this Agreement, unless (a) the Company has
made such information available to the public generally; (b) such Purchaser is required to disclose
such information by a governmental body; or (c) the Purchaser received such information in a lawful
disclosure from a third party after the date of this Agreement.

     14.62 Further Assurances. From and after the date of this Agreement, the Company and
the Purchaser shall execute and deliver such instruments, documents or other writings as may be
reasonably necessary or desirable to confirm and carry out and to effectuate fully the intent and
purposes of this Agreement.

     14.63 Headings. The headings and subheadings used in this Agreement are used for
convenience only and are not to be considered in construing or interpreting this Agreement.

     14.64 Counterparts. This Agreement may be executed in two or more counterparts, each
of which shall be deemed an original, but all of which together shall constitute one and the same
instrument. One or more counterparts of this Agreement may be delivered via telecopier with the
intention that they shall each have the same effect as an original counterpart hereof.

[Remainder of Page Intentionally Left Blank]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-18

 

     IN WITNESS WHEREOF, the parties have duly executed this Agreement as of the date first above
written.

	 	 	 	 	 	 	 
	 	 	COMPANY:	 	 
	 
	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	Name:	 	 	 	 
	 

	 	Title:	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	PURCHASER:	 	 
	 
	 	 	 	 	 	 
	 	 	Merck KGaA	 	 
	 	 	ppa. i.V.	 	 
	 
	 	 	 
	 	 
	 

	 	[***]	 	 	 	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Exhibit B-19

 

SCHEDULE 1A

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA

MERCK Funded Research Projects; MERCK Internal Research Projects

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA

Lead Compound is ready for [***] including, at a minimum, [***] but shall not include [***].

     Optimized Lead Selection Criteria

	 	•	 	[***] for [***] is [***] or [***] to [***]
	 
	 	•	 	[***] in [***] with an [***] and an [***].
	 
	 	•	 	[***] for the [***] (e.g., no [***] to [[***]]).*
	 
	 	•	 	[***] to [***] (e.g., to [***] of [***] with an [***], [***]% of [***] in [***] and
[***]% of [***]).
	 
	 	•	 	[***] (e.g., [***] on [***]).
	 
	 	•	 	[***] as [***] by [***] of [***], a [***] of the [***], or [***] of [***].*
	 
	 	•	 	[***] can be [***] using [***] with [***].
	 
	 	•	 	[***] can be [***] for [***] at [***] and [***] of [***] and with [***] and [***].
	 
	 	•	 	[***] for [***] use as [***] using [***] that [***] (e.g., [***]).
	 
	 	•	 	[***] does not [***] an [***] in the [***] of [***] to [***] other [***]).

*Specific criteria would be [***] on a [***], reflecting [***] for each program and
[***] of [***], and approved by the JSC:

	 	•	 	[***]
	 
	 	•	 	[***] of the [***] for its [***] (e.g. [***])
	 
	 	•	 	[***] and [***] for [***]
	 
	 	•	 	[***]

Comments

	 	•	 	[***] include [***] but not [***]. [***] with [***] provides a [***] for [***]
from [***].
	 
	 	•	 	The [***] of [***] is [***] by [***] the [***] of [***]. No efforts at [***] are
envisioned [***] to [***].
	 
	 	•	 	[***] for [***], etc.) have yet to be established. We have [***] any [***] for
[***] in these [***] up to [***] of [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 1A-1

 

SCHEDULE 1B

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA

ARCHEMIX Internal Research Projects

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA — [***]

[***] is ready for [***] including, at a minimum, [***] but shall not include [***].

     Optimized Lead Selection Criteria

	 	•	 	[***] for [***] is [***] or [***].
	 
	 	•	 	[***] with an [***].
	 
	 	•	 	[***] to [***] on [***] with an [***].
	 
	 	•	 	[***] to [***] on [***].
	 
	 	•	 	[***].
	 
	 	•	 	[***] shows [***] over [***].
	 
	 	•	 	[***] is [***] so it can be [***] using [***] with [***], and [***] has been
demonstrated without [***] that would [***] risk.
	 
	 	•	 	[***] of [***]% of [***] remaining following [***] in [***] and [***]% of [***]
remaining following [***] in [***].
	 
	 	•	 	[***] of [***]% of [***] remaining following [***] in [***] and [***]% of [***]
remaining following [***] in [***].
	 
	 	•	 	[***] to [***] and [***] of the [***].
	 
	 	•	 	[***] at [***] in [***].
	 
	 	•	 	[***] has been [***] for [***] at [***] e.g. [***] and [***] (e.g. [***]) [***]
without [***] of [***] and with [***] and [***].
	 
	 	•	 	[***] of [***] at least [***] for [***] when [***].
	 
	 	•	 	[***] as [***] by [***] of [***], a [***] of the [***], or [***] of [***].
	 
	 	•	 	[***] for [***] as [***] using [***] that [***] (e.g., [***]).
	 
	 	•	 	[***] does not [***] an [***] in the [***] of [***] to [***] other [***] and/or
[***]).

Comments

	 	•	 	[***] include [***] but not [***]. [***] with [***] provides a [***] for [***]
from [***].
	 
	 	•	 	The [***] of [***] is [***] by [***] the [***] of [***]. No efforts at [***] are
envisioned [***] to [***].
	 
	 	•	 	[***] for [***], etc.) have yet to be established. We have [***] any [***] for
[***] in these [***] up to [***] of [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 1B-1

 

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA — [***]

[***] is [***] for [***] in [***] including, at a minimum, [***] but shall not include [***] or
[***] of [***].

     Optimized Lead Selection Criteria

	 	•	 	[***] for [***] is [***] or [***] to [***].
	 
	 	•	 	[***] with an [***].
	 
	 	•	 	[***] of [***] with an [***].
	 
	 	•	 	[***] and [***] with an [***].
	 
	 	•	 	[***] is [***] so it can be [***] using [***] with [***], and [***] has been
demonstrated without [***] that would [***].
	 
	 	•	 	[***]) of [***]% of [***] remaining following [***] in [***] and/or [***] and
[***]% of [***] remaining following [***] in [***].
	 
	 	•	 	[***] to [***] of the [***].
	 
	 	•	 	[***] at [***] in [***].
	 
	 	•	 	[***] has been [***] for [***] at [***] e.g. [***] and [***] (e.g. [***]) [***]
without [***] of [***] and with [***] and [***].
	 
	 	•	 	[***] at [***] for [***] when [***] and/or [***].
	 
	 	•	 	[***] for the [***] (e.g., no [***] to [[***]]).
	 
	 	•	 	[***] as [***] by [***], a [***] of the [***], or [***] of [***].
	 
	 	•	 	[***] for [***] as [***] using [***] that [***] (e.g., [***]).
	 
	 	•	 	[***] does not [***] an [***] in the [***] of [***] to [***] other [***] (typically
restricted to [***] and/or [***]).

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 1B-2

 

Comments

	 	•	 	[***] include [***] but not [***]. [***] with [***] provides a [***] for [***]
from [***].
	 
	 	•	 	The [***] of [***] is [***] by [***] the [***] of [***]. No efforts at [***] are
envisioned [***].
	 
	 	•	 	[***] for [***], etc.) have yet to be established. We have [***] any [***] for
[***] in these [***] up to [***] of [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 1B-3

 

SCHEDULE 2A

TARGET EXCLUSIVITY LIST

[Left Intentionally Blank]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 2A-1

 

SCHEDULE 2B

ARCHEMIX INTERNAL PROGRAM TARGETS

	•	 	[***]
	 
	•	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 2B-1

 

SCHEDULE 3

LICENSED PATENT RIGHTS

[see following pages]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-1

 

	 	 	 	 	 	 	 	 	 	 	 
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Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-2

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
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	 	[***]
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	[***]
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	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-3

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	 	 	[***]
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	[***]
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	 	[***]
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	 	[***]
	[***]
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	 	[***]
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	[***]
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	[***]
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	 	[***]
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	[***]
	 	[***]
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	 	[***]
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	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
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	 	[***]
	 	 	 	[***]
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	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-4

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
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	 	 	 	[***]
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	[***]
	 	[***]
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	 	[***]
	[***]
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	 	[***]
	 	[***]
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	[***]
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	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-5

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	 	 	[***]
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	[***]
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	[***]
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	[***]
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	 	 	 	[***]
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	[***]
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	[***]
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	[***]
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	 	 	 	[***]
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	[***]
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	 	[***]
	 	 	 	[***]
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	[***]
	 	[***]
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	 	[***]
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	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-6

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
	[***]
	 	[***]
	 	[***]
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	 	[***]
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	 	 	 	[***]
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	 	[***]
	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-7

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	 	 	[***]
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	[***]
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	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-8

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	 	 	[***]
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	[***]
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	[***]
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	[***]
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	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-9

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	[***]
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	[***]
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	 	 	 	[***]
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	 	 	 	[***]
	 	[***]
	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-10

 

	 	 	 	 	 	 	 	 	 	 	 
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	 	 	 	[***]
	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-11

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-12

 

	 	 	 	 	 	 	 	 	 	 	 
	[***]	 	[***]	[***]	[***]	 	[***]	 	[***]
	 
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Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting
confidential treatment under Rule 406 of the Securities Act.

Sched. 3-13

 

SCHEDULE 4

EXCLUDED APTAMERS

	•	 	[***]
	 
	•	 	[***]
	 
	•	 	[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 4-1

 

SCHEDULE 5A

DEVELOPMENT CANDIDATE SELECTION CRITERIA

MERCK Funded Research Projects; MERCK Internal Research Projects

DEVELOPMENT CANDIDATE SELECTION CRITERIA

     Development Candidate Selection Criteria

	 	•	 	[***] from [***] and [***] of [***] and [***] in [***] (e.g., [***] (or [***]) by a
[***]).
	 
	 	•	 	[***] of [***] with [***] or [***] of [***] with [***] to [***] of [***] in [***]
and [***] with the [***].
	 
	 	•	 	[***] in [***] appears [***] for the [***].
	 
	 	•	 	[***] and [***].
	 
	 	•	 	[***] (incl. [***])
	 
	 	•	 	[***] with [***], as defined [***] the [***] (thus [***])

([***] requires [***] of [***])

	 	o	 	[***] remain [***] than a [***] (as measured by [***]) [***]
the [***] (e.g., after [***]).

	 	•	 	(If [***] requires [***])

	 	o	 	[***] after [***] in [***], with [***] to [***].
	 
	 	o	 	With [***] in [***], no [***] of [***] in [***] of [***] the
[***] (e.g., after [***]) which would result in a [***] in the [***] to [***]
of [***].

	 	•	 	(If [***] requires [***])

	 	o	 	[***] of [***] in [***].
	 
	 	o	 	[***] and [***] must permit a [***] that can [***] be [***]
though a [***] or [***].
	 
	 	o	 	[***] at [***] in [***] at [***] and [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 5A-1

 

SCHEDULE 5B

DEVELOPMENT CANDIDATE SELECTION CRITERIA

ARCHEMIX Internal Research Projects.

DEVELOPMENT CANDIDATE SELECTION CRITERIA

Development Candidate Selection Criteria

	•	 	[***] from [***] and [***] of [***] and [***] in [***] (e.g., [***] (or [***]) by a
[***]).
	 
	•	 	[***] of [***] with [***] or [***] of [***] with [***] to [***] of [***] in [***]
and [***] with the [***].
	 
	•	 	[***] in [***] appears [***] for the [***].
	 
	•	 	[***] and [***].
	 
	•	 	[***]
	 
	•	 	[***] with [***], as defined [***] the [***] (thus no [***])

(If [***] requires [***] of [***])

	 	o	 	[***] remain [***] than a [***] (as measured by [***]) [***]
the [***] (e.g., after [***]).

	•	 	(If [***] requires [***])

	 	o	 	[***] after [***] in [***], with [***] to [***].
	 
	 	o	 	With [***] in [***], no [***] of [***] in [***] of [***] the
[***] (e.g., after [***]) which would result in a [***] in the [***] to [***]
of [***].

	•	 	(If [***])

	 	o	 	[***] of [***]
	 
	 	o	 	[***] and [***] must permit a [***] that can [***] be [***]
though a [***] or [***].
	 
	 	o	 	[***] at [***] in [***] at [***] and [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 5B-1

 

SCHEDULE 6

FORM OF PRESS RELEASE

[see following pages]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 6-1

 

MEDIA CONTACTS

For Archemix:

Kathryn Morris

Yates and Associates

Tel: 914-204-6412

INVESTOR CONTACTS

Lilian Stern

Stern Investor Relations

Tel: 212-362-1200

Archemix and Merck KGaA Sign Strategic Alliance

Collaboration to Focus Primarily on Cancer Therapeutics Using Novel Aptamer Technology

CAMBRIDGE, Mass. — June 11, 2007 — Archemix Corp. and Merck Serono, a division of Merck KGaA,
Darmstadt, Germany, announced today that they have formed a multi-year strategic alliance to
discover, develop and commercialize first-in-class aptamer therapeutics with a primary focus on the
treatment of cancer. The alliance combines Archemix’ proprietary SELEX technology to discover and
generate aptamer candidates with Merck’s demonstrated oncology drug development and
commercialization capabilities.

The collaboration gives Merck Serono the option to obtain product licenses to certain of Archemix’s
lead stage aptamer programs in oncology and the right to select and develop aptamers against six
additional targets in oncology and other indications, including autoimmune and inflammation
disorders. In addition, Merck Serono is granted a license to use Archemix’s SELEX®
technology for internal target validation. Archemix has the option to exercise a co-development
and co-promote option on any of the products being developed on a 50:50 cost and profit-sharing
basis in the United States. This is the second research agreement this year between the two
companies.

Under the terms of the agreement, Archemix will receive a $29.8 million equity investment from
Merck KGaA. Merck KGaA also retains an option, under certain circumstances, to acquire additional
Archemix common stock upon an initial public offering. Other financial terms were not disclosed.

“The collaboration with Merck Serono represents a key strategic initiative for Archemix and
the development of our pipeline, especially in the area of cancer,” said Errol De Souza, Ph.D.,
President and CEO, Archemix. “We will be working with a recognized leader in drug development to
discover, develop and commercialize first-in-class aptamer-based therapeutics. With our
co-development and co-promote options we can participate in the development and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 6-2

 

commercialization of certain of the products that come out of the collaboration while
simultaneously generating cash flows to fund our proprietary aptamer pipeline.”

“Aptamers have the potential to play a key role in the next generation of drugs in our core
therapeutic areas,” said Dr. Bernhard Kirschbaum, Executive Senior Vice President and Director of
Research, Merck Serono. “Archemix is the leader in the discovery of aptamer therapeutics and we
believe that, as a class, aptamers can create a new paradigm of treatment.”

About Aptamers

Aptamers are single-stranded nucleic acids that form well-defined three dimensional shapes,
allowing them to bind target molecules in a manner that is conceptually similar to antibodies.
Aptamers combine the optimal characteristics of small molecules and antibodies, including high
specificity and affinity, chemical stability, low immunogenicity and the ability to target
protein-protein interactions. In contrast to monoclonal antibodies, aptamers are chemically
synthesized rather than biologically expressed.

About Archemix

Archemix Corp. is a privately-held biopharmaceutical company developing aptamers as a class of
directed therapeutics for the prevention and treatment of human disease. The company is leveraging
its proprietary drug discovery technology to fuel the growth of its development portfolio, which is
primarily focused on acute cardiovascular and hematology diseases and cancer. Archemix’s broad
product pipeline, being developed both by the company as well as its licensees, includes multiple
investigational compounds at various stages of development, several of which are moving into
advanced clinical trials. Archemix’s lead proprietary product, ARC1779, a selective platelet
inhibitor, is anticipated to start Phase IIa clinical trials before the end of 2007. Archemix’
leadership position in intellectual property, technology and expertise relating to aptamers has
enabled it to form numerous collaborations with biotechnology and pharmaceutical collaborators,
including Merck Serono, Pfizer Inc., Elan Pharma, Nuvelo, Inc., Antisoma plc., and Regado
Biosciences. For more information, please visit www.archemix.com.

About Merck

Merck is a global pharmaceutical and chemical company with sales of EUR 6.3 billion in 2006, a
history that began in 1668, and a future shaped by 35,091 employees in 62 countries. Its success is
characterized by innovations from entrepreneurial employees. Merck’s operating activities come
under the umbrella of Merck KGaA, in which the Merck family holds an approximately 70% interest and
free shareholders own the remaining approximately 30%. In 1917 the U.S. subsidiary Merck & Co. was
expropriated and has been an independent company ever since.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 6-3

 

	 	 	 
	 

	 	Your Contact
	 
	News Release

	 	Phyllis Carter
	 

	 	Phone +49 6151-72 7144

June 11, 2007

Merck KGaA Signs Strategic Alliance With Archemix

Darmstadt, June 11, 2007 — Merck KGaA announced today that it has formed a multi-year
strategic alliance between its Merck Serono division and Archemix Corp. of Cambridge,
Massachusetts, to discover, develop and commercialize first-in-class aptamer therapeutics with a
primary focus on the treatment of cancer. Additional areas of the collaboration include autoimmune
and inflammatory disorders. The alliance combines Archemix’ proprietary SELEX®
technology to discover and generate aptamer candidates with Merck Serono’s drug development and
commercialization capabilities. In addition, Merck Serono is granted a license to use Archemix’s
SELEX® technology for internal target validation.

The collaboration gives Merck Serono the option to obtain product licenses to certain of Archemix’s
lead-stage aptamer programs and the right to select and develop aptamers against six targets in
oncology and other indications. Archemix has the option to exercise a co-development and co-promote
option on any of the products being developed on a 50:50 cost and profit-sharing basis in the
United States. This is the second research agreement this year between the two companies.

Additionally, Merck KGaA will make a $29.8 million equity investment in Archemix. Merck KGaA also
retains an option, under certain circumstances, to acquire additional Archemix common stock upon an
initial public offering. Other financial terms were not disclosed.

“Aptamers have the potential to play a key role in the next generation of drugs in our core
therapeutic areas.” said Dr. Bernhard Kirschbaum, Executive Senior Vice President and Director of
Research, Merck Serono. “Archemix is the leader in the discovery of aptamer therapeutics and we
believe that, as a class, aptamers can create a new paradigm of treatment.”

“The collaboration with Merck Serono represents a key strategic initiative for Archemix and the
development of our pipeline, especially in the area of oncology,” said Errol De Souza, Ph.D.,
President and CEO, Archemix. “We will be working with a recognized leader in drug development to
discover, develop and commercialize first-in-class aptamer-based therapeutics. With our
co-development and co-promote options we can participate in the development and commercialization
of certain of the products that come out of the collaboration while simultaneously generating
significant cash flows to fund our proprietary aptamer pipeline.”

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 6-4

 

About Aptamers

Aptamers are single-stranded nucleic acids that form well-defined three dimensional shapes,
allowing them to bind target molecules in a manner that is conceptually similar to antibodies.
Aptamers combine the optimal characteristics of small molecules and antibodies, including high
specificity and affinity, chemical stability, low immunogenicity and the ability to target
protein-protein interactions. In contrast to monoclonal antibodies, aptamers are chemically
synthesized rather than biologically expressed.

About Archemix

Archemix Corp. is a privately-held biopharmaceutical company developing aptamers as a class of
directed therapeutics for the prevention and treatment of human disease. The company is leveraging
its proprietary drug discovery technology to fuel the growth of its development portfolio, which is
primarily focused on acute cardiovascular and hematology diseases and cancer. Archemix’s broad
product pipeline, being developed both by the company as well as its licensees, includes multiple
investigational compounds at various stages of development several of which are moving into
advanced clinical trials. Archemix’s lead proprietary product, ARC1779, a selective platelet
inhibitor, is anticipated to start Phase IIa clinical trials before the end of 2007. Archemix’
leadership position in intellectual property, technology and expertise relating to aptamers has
enabled it to form numerous collaborations with biotechnology and pharmaceutical collaborators,
including Merck Serono, Pfizer Inc., Elan Pharma, Nuvelo, Inc., Antisoma plc., and Regado
Biosciences. For more information, please visit www.archemix.com.

All Merck Press Releases are distributed by e-mail at the same time they become available on the
Merck Website. Please go to http://www.subscribe.merck.de to register online, change your
selection or discontinue this service.

Merck is a global pharmaceutical and chemical company with sales of EUR 6.3 billion in 2006, a
history that began in 1668, and a future shaped by 35,091 employees in 62 countries. Its success is
characterized by innovations from entrepreneurial employees. Merck’s operating activities come
under the umbrella of Merck KGaA, in which the Merck family holds an approximately 70% interest and
free shareholders own the remaining approximately 30%. In 1917 the U.S. subsidiary Merck & Co. was
expropriated and has been an independent company ever since.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 6-5

 

SCHEDULE 7

REGIONAL OFFICES OR COUNTRIES IN WHICH

PATENT APPLICATIONS ARE TO BE NATIONALIZED

OR OTHERWISE PROSECUTED, FILED AND MAINTAINED

[***] (PCT)

[***]* (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (national)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (PCT)

[***] (national via extension)

 

* [***]

In addition, any country not listed above in which MERCK customarily pursues patent protection for
a commercial product, taking into account all relevant factors (including, as applicable and
without limitation, stage of development, mechanism of action, efficacy and safety relative to
competitive products in the marketplace, actual or anticipated Regulatory Authority approved
labeling, the nature and extent of market exclusivity (including patent coverage and regulatory
exclusivity), cost and likelihood of obtaining Commercialization Regulatory Approval, actual or
projected profitability and availability of capacity to manufacture and supply for commercial
sale).

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 7-1

 

SCHEDULE 8

TERMS TO BE INCLUDED IN

FORM OF CO-PROMOTION AGREEMENT

          The Co-Promotion Agreement to be negotiated by the Parties in accordance with Section 4.10.2
shall contain the following terms. Capitalized terms used in this Schedule 8 and not otherwise
defined have the meanings given to them in the Agreement. For purposes of this Schedule 8,
references to MERCK shall be deemed to refer to any Affiliate of MERCK executing the Co-Promotion
Agreement.

	 	•	 	ARCHEMIX and MERCK shall [***], at ARCHEMIX’s [***]ARCHEMIX and MERCK [***] MERCK, which
shall be[***] of the [***] shall be [***] as set forth in the [***]. In the [***] on a
[***] by the [***], then [***] of an ARCHEMIX [***], and [***]ARCHEMIX [***], the [***]
shall be [***] to the [***], but if the [***]MERCK shall [***], but shall only [***] of the
[***].
	 
	 	•	 	A [***] shall be [***] by MERCK for [***] [***] for the [***] for [***] by the [***]
which shall [***], but not be [***] of such [***] in the [***] to be [***] of any[***] of
the [***] of such [***] at least [***] and [***] for such [***]in the [***] for such
[***]in the [***].
	 
	 	•	 	[***] of both MERCK and ARCHEMIX. For the ARCHEMIX [***] on the [***]. For the [***]
of the [***], provided that the [***] of MERCK [***].
	 
	 	•	 	Each [***] that ARCHEMIX [***] of the [***] of the [***] for the [***] in the [***] of
the [***] in the [***]. The [***] shall be [***]shall be [***].
	 
	 	•	 	Each [***] under each [***] and to [***] with the other [***]. The [***] that the [***]
the [***] (which [***], and a [***] that shall be [***] for purposes of the [***].
	 
	 	•	 	Each [***] for a [***]. Each [***] shall have the r[***] of the [***].
	 
	 	•	 	MERCK shall [***] and for [***] as may be [***] and other [***], but shall, in [***].
	 
	 	•	 	MERCK shall [***] for the [***].
	 
	 	•	 	MERCK shall [***].
	 
	 	•	 	MERCK shall [***] for the [***].
	 
	 	•	 	MERCK shall [***] under which [***]. The [***] in the [***] under such [***].
	 
	 	•	 	[***]MERCK.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 8-1

 

	 	•	 	[***] shall be [***] with the [***].
	 
	 	•	 	The [***]with [***]. With regard to any [***] by a [***] to the [***] and to [***] that,
to the [***] of the [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 8-2

 

SCHEDULE 9

MERCK’S STANDARD EXCHANGE RATE METHODOLOGY

APPLIED IN ITS EXTERNAL REPORTING

MERCK’s
standard exchange rate methodology uses the applicable [***] foreign exchange
rate as published by the [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 9-1

 

SCHEDULE 10

PROGRAM CHEMISTRIES

	 	 	[***]: [***] containing [***], or [***] of [***].
	 
	 	 	[***]:

[***]

[***]

[***]

[***]

[***]

[***]

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 10-1

 

SCHEDULE 11

CALCULATION OF NET INCOME

“Advertising” means the [***] of the [***] in the [***] through [***] and [***] for [***], and
[***] and [***] and [***]; provided, however, that [***]. With regard to [***] and [***] of such
[***] and [***] for the [***] of this [***] “Annual Net Income” means the [***].

     “Co-Development Commercialization Costs” means the [***] and [***] and [***], and/or MERCK
[***]; and [***] or [***] to be a [***].

     “Cost of Goods” means the [***] to the [***] of a [***] for [***] with [***] with the [***]and
[***] and [***] , or other such [***] to the [***] and [***] with a [***].

     “Detail” has the meaning [***].

     “General Public Relations” means [***] which [***] the [***] or [***] in a [***] that such
[***] or its [***] of the [***] of the [***] to this [***] are not [***]and [***].

     “License Fees” means [***] to the [***] of a [***] in the [***]. If the [***] other than
[***] in the [***], then only an [***] by the [***].

     “Marketing Expense” means [***] and all [***] for those [***] to the [***] by the [***] to the
[***] for the [***] in the [***] on such [***]and for [***] shall not [***] or any other [***] as a
[***].

     “Net Income” means, [***] in the [***] of such [***] to the [***] in the [***] to the [***]
with or [***] in each [***] for that [***] of a [***] and not for the [***].

     “Net Sales” has the meaning [***].

     “Personnel Costs” means the [***] by or under [***], but not [***].

     “Product Trademark” has the meaning [***].

     “Promotion Expense” means [***]by MERCK or ARCHEMIX and [***] to the [***] of a [***] in the
[***] to the [***], but not [***] and [***] for the [***]. [***]:

1. There shall be [***] has been [***] it shall [***].

2. To the extent an [***] or a [***] and shall [***].

[***], and all [***]MERCK and ARCHEMIX in [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 11-1

 

SCHEDULE 12

FORM OF MATERIALS TRANSFER AGREEMENT

MATERIAL TRANSFER AGREEMENT FOR RESEARCH

     This Agreement, effective this ___day of                     , is by and between Merck KGaA, a company
organized under the laws of Germany with offices at Frankfurter Str. 250, 64293 Darmstadt, Germany
(“Merck”), and Archemix Corp., a company organized under the laws of the State of Delaware having a
place of business at 300 Third Street, Cambridge, Massachusetts 02142 (“Archemix”).

     WHEREAS, Archemix has provided a Primary Compound Candidate Notice or Backup Compound
Candidate Notice pursuant to Section 3.9.1(a) or (b), respectively, of the Collaborative Research
and License Agreement (“License Agreement”) executed by the parties on June ___, 2007.

     NOW THEREFORE, in consideration of the mutual covenants and conditions contained herein, the
parties agree as follows:

     1. Supply of Materials. Archemix shall supply Merck with ___mg of the applicable
Primary Compound Candidate or Backup Compound Candidate (“Materials”). Materials shipped to Merck
shall be delivered by special courier to the attention of [INSERT NAME AND ADDRESS].

     2. Use of Materials. The Materials provided to Merck by Archemix under the terms of
this Agreement may only be used by Merck to conduct experiments during the Term (the “Research”)
for purposes of determining whether to exercise a Compound Candidate Option pursuant to Section
3.9.4 of the License Agreement (the “Evaluation”). The Materials (i) may not be used other than in
the Research for purposes of conducting the Evaluation, (ii) may not be altered in any way, whether
by an addition to, or a disassembly of, the Material, (iii) may only be used by employees of Merck
or any of its Affiliates for the Research, and (iv) may not be provided, transferred, or sold by
Merck to any third party without the prior written consent of Archemix.

     3. Return of Materials. Upon the earlier of completion of the Research or expiration
of the Agreement, Merck shall return to Archemix all unused Materials.

     4. No Implied Licenses. The transfer of the Materials by Archemix under this
Agreement does not grant to Merck any rights or licenses to any intellectual or other proprietary
property owned or controlled by Archemix.

     5. Research Results.

     5.1 Merck shall keep complete, accurate, and authentic accounts, notes, technical

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 12-1

 

reports, data, information, records and results of the Research performed under this Agreement
(“Research Results”) and shall provide Archemix with a monthly report thereof during the Term.

     5.2 Subject to Merck’s exercise of a Primary Compound Candidate Option or Backup Compound
Candidate Option, as applicable, pursuant to Section 3.9.4 of the License Agreement, the Research
Results shall be held in strict confidence by Merck. The Research Results shall not be used by
Merck for any purpose other than for performing the Evaluation without Archemix’s prior written
consent.

     6. Inventions. Subject to Merck’s exercise of a Primary Compound Candidate Option or
Backup Compound Candidate Option, as applicable, pursuant to Section 3.9.4 of the License
Agreement, (i) all data, improvements, discoveries, inventions or know-how, whether patentable or
not (“Inventions”), arising out of the Research including Inventions pertaining to the Materials
and/or therapeutic or diagnostic uses of the Materials shall be the sole property of Archemix and
(ii) Merck hereby assigns to Archemix its entire right, title and interest in and to any Inventions
developed pursuant to this Agreement and agrees to execute such documents and to take such actions
as may be necessary to give effect to this provision.

     7. Confidentiality. Subject to Merck’s exercise of a Primary Compound Candidate
Option or Backup Compound Candidate Option, as applicable, pursuant to Section 3.9.4 of the License
Agreement and Section 5.2.2 of this Agreement, during the Term of this Agreement and for a period
of ten (10) years thereafter, Merck shall maintain in confidence all know-how, data, processes,
techniques, formulas, test data and other information and all tangible and intangible embodiments
thereof of any kind whatsoever (“Confidential Information”) disclosed by Archemix in connection
with the Research. This obligation of confidentiality shall not apply to the extent that it can be
established by Merck that the Confidential information:

	 	(a)	 	was already known to Merck at the time of disclosure as evidenced by competent
business records of Merck;
	 
	 	(b)	 	was generally available to the public or otherwise part of the public domain at
the time of its disclosure;
	 
	 	(c)	 	became generally available to the public or otherwise part of the public domain
after its disclosure to Merck through no act or omission of Merck;
	 
	 	(d)	 	was disclosed to Merck by a third party who had no obligation to Archemix not
to disclose such information;
	 
	 	(e)	 	was independently developed by Merck without the use of the Archemix’s
Confidential Information as evidenced by competent business records of Merck.

     8. Term and Termination. This Agreement shall remain in force for six (6) months or
until the Research has been completed, whichever occurs first (the “Term”). Subject to Merck’s
exercise of a Primary Compound Candidate Option or Backup Compound Candidate Option,

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 12-2

 

upon expiration of this Agreement, Merck shall cease all Research and Archemix shall have no
further obligation to supply Merck with Materials and may request the return of all unused
Materials in Merck’s possession. Any rights or obligations set forth herein which by their nature
are intended to extend beyond the Term of the Agreement shall survive the expiration or termination
of the Agreement, including, but not limited to the obligations set forth in paragraphs 2, 3, 6, 7,
8 and 9.

     9. Authorization; Compliance with Laws. Merck warrants that: (i) it is permitted to
enter into this Agreement, (ii) the terms of this Agreement are not inconsistent with other
contractual obligations (express or implied) it has or may have, and (iii) all research conducted
by Merck will comply with all applicable government laws, regulations and guidelines, including,
but not limited to, those relating to animal testing, to biotechnological research and to the
handling and containment of hazardous and biohazardous materials.

     10. No Warranties. THE MATERIALS BEING SUPPLIED TO MERCK ARE SUPPLIED BY ARCHEMIX
WITH NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE. ARCHEMIX MAKES NO REPRESENTATIONS THAT THE USE OF THE MATERIALS WILL NOT
INFRINGE ANY PATENT OR PROPRIETARY RIGHTS OF THIRD PARTIES.

     11. Indemnification. Merck agrees to indemnify, defend and hold harmless Archemix,
its directors, officers, agents and employees from and against any and all costs, expenses or
liabilities arising as a result of or in connection with Merck’s use of Materials provided under
the terms of this Agreement or any violation of the terms and conditions herein.

     12. Parties Independent. In making and performing under this Agreement, the parties
shall act as independent contractors without the authority to bind one another or act as agent for
one another.

     13. Amendment. This Agreement may only be amended by an instrument in writing signed
by a duly authorized officer of each of the parties.

     14. Assignment. This Agreement shall not be assignable by either party to this
Agreement to a third party without the prior written consent of the other party to this Agreement,
except that either party may assign this Agreement to a third party without the prior written
consent of the other party in the event of a merger of the party with, or sale of substantially all
of the party’s assets to, the third party.

     15. Governing Law. This Agreement shall be governed by the laws of the State of New
York, without regard to its choice of law principles.

     16. No Conflict. Merck represents that any existing or future obligations to any
third party shall neither conflict with nor compromise the Research to be performed pursuant to
this Agreement. Further, Merck represents that the execution of this Agreement and performance of

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 12-3

 

the Research hereunder does not and will not breach any other agreement, arrangement,
understanding, or obligation of confidentiality to which the Merck is a party or by which Merck is
bound, and during the term of this Agreement Merck will not enter into any agreement, either
written or oral, in conflict herewith.

     17. Integration. This Agreement and the License Agreement constitutes the entire
agreement of the Parties with respect to the Research and Materials and supersedes all previous
oral and written agreements, if any, among the Parties regarding the Research and Materials.

     IN WITNESS WHEREOF, this Agreement shall be effective on the date it has been signed below by
both parties.

	 	 	 	 	 
	ARCHEMIX CORP.	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Name:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Title:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Date:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	MERCK KGaA	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Name:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Title:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Date:
	 	 	 	 
	 

	 	 	 	 

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 12-4

 

SCHEDULE 13

CO-DEVELOPMENT COSTS

(AND [***] FOR THEIR [***])

AND CO-DEVELOPMENT REGULATORY COSTS

	1	 	Definitions.
	 
	Words and phrases used in this Schedule shall have the meanings defined elsewhere in the Agreement.
In addition, the following words and phrases shall have the following stated or referenced
meanings in this Schedule:
	 
	[***]1.2 “Co-Development Costs” means [***] to [***] for a [***] in the [***] for a [***]
shall [***]and [***], of the [***]:

	 	(a)	 	[***] and other [***] ;
	 
	 	(b)	 	[***] and [***];
	 
	 	(c)	 	[***] and [***] for use in [***];
	 
	 	(d)	 	[***] and [***], and other [***] with the [***];
	 
	 	(e)	 	[***]; and
	 
	 	(f)	 	[***] to [***] in the [***].

	“Co-Development FTE” shall mean [***] of [***] to or in [***] with respect to a [***] that
are [***], with [***] in effect at the [***]“ARCHEMIX Co-Development FTE Rate(s)” means, [***] to a
[***] at the [***] for such [***]for [***] at such [***], that, on [***]of each [***] for such
[***], the [***] shall be [***] in the [***]. For [***] of this [***] of this [***] is as [***]
to[***] and/or [***].
	 
	“MERCK Co-Development FTE Rate(s)” means, [***] to a [***] at the [***] provided, that, on [***] of
each [***] of its [***], the [***] shall be [***]in the [***]. For purposes of this [***] of this
[***].
	 
	“Co-Development FTE Rate(s)” means, [***]. For [***] to the [***].
	 
	“Co-Development FTE Cost” means, [***] in such [***] to be [***] by the [***], at
the [***].
	 
	1.3	 	“External Co-Development Costs” means the [***] by a [***] or to be [***].
	 
	1.4	 	“Internal Co-Development Costs” means the [***] by [***]. For purposes of [***].
	 
	1.5	 	“Co-Development Regulatory Costs” means [***] that are [***]with the [***] to the
[***], and the [***], for any [***] for a [***] shall [***], of the [***]:

	 	(a)	 	[***] for the [***];
	 
	 	(b)	 	[***] or other [***]; and

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 13-1

 

(c) [***] with a [***] with a [***] with respect to [***].

1.6 “External Co-Development Regulatory Costs” means the [***] by a [***] or to be [***].

“Internal Co-Development Regulatory Costs” means the [***]. For purposes of [***]2 [***]
shall be [***]:

2.1 [***] in the [***] of the [***], to the [***] of the [***].

At the [***] of an [***] of a [***] from the [***] of the [***].

2.2 Consistent with [***] of the [***], to the extent that the [***] with such [***] of such [***],
shall be [***].

2.3 Consistent with [***], and the [***] from or in [***] with such [***] to be [***] shall be
[***], and none of such [***] for a [***] with any[***] of the [***] shall not be [***] provided,
that, [***] in the [***] shall be [***].

2.4 If a [***] of the [***], and the [***] from or in [***] outside the [***] with respect to [***]
shall be [***]. To the extent [***] which is [***] of the [***] outside the [***] shall be [***]
MERCK, and [***]shall be [***].

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the
Commission pursuant to the Company’s application requesting confidential treatment under Rule 406
of the Securities Act.

Sched. 13-2exv10w10

 

Exhibit 10.10

Execution Copy

LICENSE AGREEMENT

BETWEEN

GILEAD SCIENCES, INC.

AND

ARCHEMIX CORP.

October 23, 2001

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

LICENSE AGREEMENT

     This License Agreement (“Agreement”), is entered into as of October 23, 2001
(the “Effective Date”), by and between Gilead Sciences, Inc., a Delaware corporation with
its principal offices located at 333 Lakeside Drive, Foster City, CA 94404 (“Gilead”), and
Archemix Corp., a Delaware corporation with its principal offices located at One Hampshire
Street, Cambridge, MA 02139 (“Company”).

Recitals

     A. Gilead owns, or possesses licenses under certain patents, patent applications, and
know-how related to the SELEX Process (as defined in Section 1.29 below).

     B. Gilead is a party, either in its own right or as a successor in interest, to
certain Preexisting Agreements (as defined in Section 1.26 below) with third parties pursuant to
which such third parties have obtained certain rights and licenses to the SELEX Process and
Aptamers (as defined in Section 1.2 below).

     C. Gilead wishes to grant to Company a license under such patents, patent applications and
know-how for all uses other than those exclusively granted to third parties as set forth in the
Preexisting Agreements (as defined herein), and Company wishes to receive such license, subject to
the terms and conditions set forth in this Agreement.

     D. Gilead also wishes to assign and transfer to Company, and Company wishes to
acquire from Gilead, a certain agreements relating to the SELEX Process and/or Aptamers.

     Now, Therefore, in consideration of the foregoing, of the mutual covenants and
undertakings contained in this Agreement and of other good and valuable consideration, the receipt
and sufficiency of which are hereby acknowledged, the Parties, intending to be legally bound,
hereby agree as follows:

1. Definitions.

     In addition to the other terms defined elsewhere in this Agreement, the following terms shall
have the following meanings when used herein (any term defined in the singular shall have the same
meaning when used in the plural and vice versa, unless stated otherwise):

     1.1 “Affiliate” means any Person that, directly or indirectly, through one or more
intermediaries, Owns, is Owned by or is under common Ownership with, a Party, where “Own” or
“Ownership” means (a) direct or indirect possession of at least fifty percent (50%) of the
outstanding voting securities of a corporation or a comparable ownership in any other type of
Person or (b) that a Person or group of Persons otherwise has the unilateral ability to control and
direct the management of the entity, whether by contract or otherwise.

     1.2 “Aptamers” means oligonucleotides, including any structural variations and modifications,
derivatives, homologs, analogs and/or mimetics thereof, identified through the SELEX Process.

Portions of this Exhibit were omitted and have been filed separately with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

1

 

     1.3 “Assumed Liabilities” is defined in Section 2.6 below.

     1.4 “[***] Agreement” means the Collaborative Research Agreement and License Agreement, dated
May 5, 1993 and Termination Agreement, dated February 27, 1998, between NeXagen, Inc. and [***].

     1.5 “Company Improvements” means any inventions, patentable or not, information and/or data
Controlled by the Company after the Effective Date and during the term of this Agreement, that were
derived from the practice of the Covered Intellectual Property, and that relate to: (a)
improvements in the SELEX Process and (b) improvements made to the Covered Intellectual Property.

     1.6 “Consent Date” means, with respect to a Transferred Asset, the date on which all Third
Parties to such Transferred Asset have given their written consent to assignment thereof to Company
pursuant to Section 2.5.

     1.7 “Control”, “Controls”, and “Controlled” means, with respect to a particular item of
information or intellectual property right, that the applicable Party owns or has a license to such
item or right and has the ability to grant to the other Party access to and a license or sublicense
(as applicable) under such item or rights as provided for in this Agreement without violating the
terms of any agreement or other arrangement with any Third Party.

     1.8 “Covered Intellectual Property” means the Licensed Patents and Licensed Know-How.

     1.9 “Damages” means any and all costs, losses, claims, liabilities, fines, penalties, damages
and expenses, court costs, and reasonable fees and disbursements of counsel, consultants and expert
witnesses incurred by a Party hereto (including any interest payments which may be imposed in
connection therewith).

     1.10 “Documentation” means the documents, information, data, and other written materials
described in Exhibit A.

     1.11 “Excluded Aptamers” means (a) Radio Therapeutics, (b) In Vivo Diagnostic Agents, (c) the
compound identified as [***] as more fully described in the [***] Agreement listed in Exhibit B
attached to this Agreement, (d) any Aptamer directed to [***], (e) the Aptamers identified as the
[***] in the [***] Agreement listed in Exhibit B, and (f) the [***] identified in the [***]
Agreement listed in Exhibit B. In addition, “Excluded Aptamers” shall until September 1, 2003,
include any Aptamer directed to the [***], as defined in the [***] Agreement identified in Exhibit
B, which Aptamer is subject to [***] granted to [***] pursuant to the [***] Agreement, and after
September 1, 2003, shall include any such Aptamer for which [***] exercises such [***] in
accordance with the terms and conditions set forth in the [***] Agreement.

     1.12 “Excluded Liabilities” is defined in Section 2.6 below.

     1.13 “Gilead Key Personnel” means [***].

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

2

 

     1.14 “[***] Agreement” means the SELEX Research Agreement, dated May 27, 1998, by and among
Gilead (as successor in interest to NeXstar Pharmaceuticals, Inc. (“NeXstar”)), [***] and [***]

     1.15 “[***] Agreement” means the Collaborative Research Agreement, dated as of February 26,
1998, by and between Gilead (as successor to NeXstar) and [***], as amended by letter agreement
dated January 6, 2000.

     1.16 “In Vitro Diagnostics” shall have the meaning provided in the [***] Agreement listed in
Exhibit B, as such Agreement is in effect on the Effective Date.

     1.17 “In Vivo Diagnostic Agent” shall have the meaning provided in the [***] Agreement listed
in Exhibit B, as such Agreement is in effect on the Effective Date; provided that, (a) in the event
Third Parties shall no longer have any rights to In Vivo Diagnostic Agents pursuant to the [***]
Agreement, all references to “In Vivo Diagnostic Agent” in this Agreement shall be automatically
deleted, without further action by the Parties, and (b) in the event that the field rights embodied
in the definition of “In Vivo Diagnostic Agent” contained in the [***] Agreement shall at any time
be modified or amended to reduce the scope thereof, the definition of “In Vivo Diagnostic Agent”
contained in this Agreement shall be automatically reduced in scope to the same extent, without
further action by the Parties, provided that nothing in this Section 1.17 shall give Company any
rights to or interest in any products developed by or licensed to Third Parties pursuant to the
[***] Agreement that are in clinical development, submitted for regulatory approval or being
commercialized.

     1.18 “Licensed Field” means use of the Licensed Processes and Methods, including without
limitation, the SELEX Process, the Licensed Know-How, the inventions claimed in the Licensed
Patents, any Aptamers and any Licensed Products, as applicable, for any and all purposes for which
exclusive rights have not been granted to Third Parties under the Preexisting Agreements, including
without limitation (a) the [***], (b) any [***], and (c) Target Validation and other drug
development and research purposes, including [***], but specifically excluding (x) use in any In
Vitro Diagnostics application, (y) use of any Excluded Aptamers, or (z) any purpose for which
exclusive rights have been granted to Third Parties under the Preexisting Agreements; provided
however, that in the event that Third Parties to no longer have rights pursuant to a Preexisting
Agreement in any field, or the scope of the licenses granted therein is reduced, then the Licensed
Field shall be automatically extended, without further action by the Parties, to include the uses
or fields in which Third Parties no longer have rights, or the uses or fields removed from the
Preexisting Agreement as a result of the reduction of the scope of the licenses granted therein,
provided that (i) nothing in this Section 1.18 shall give Company any rights to or interest in any
products developed by or licensed to any Third Party to any Preexisting Agreement that are in
clinical development, submitted for regulatory approval or being commercialized and (ii) nothing in
this Section 1.18 shall give Company any rights to or interest in any Aptamer directed to [***].

     1.19 “Licensed Know-How” means trade secrets, know-how and unpatentable and/or unpatented
inventions and discoveries Controlled by Gilead as of the Effective Date and necessary or
reasonably useful in the practice of the Licensed Patents or the performance of the Licensed
Processes or Methods.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

3

 

     1.20 “Licensed Patents” means the patents and patent applications set forth in Exhibit C, and
all divisional, continuations, continuations-in-part, and any foreign counterparts thereof and all
patents issuing on any of the foregoing and any foreign counterparts thereof, together with all
registrations, reissues, re-examinations, supplemental protection certificates, or extensions
thereof, and any foreign counterparts thereof.

     1.21 “Licensed Processes and Methods” means any and all processes and methods claimed by the
Licensed Patents or consisting, in whole or in part, of Licensed Know-How.

     1.22 “Licensed Product” means (a) any product that contains one or more Aptamers (b) any
product covered by the Licensed Patents or the use of which is covered by the Licensed Patents, and
(c) any product made through the use of the Licensed Know-How, but in no case any of the Excluded
Aptamers, within the Licensed Field.

     1.23 “NeXstar Merger Date” means July 29, 1999.

     1.24 “Party” means Company or Gilead and “Parties” means Company and Gilead.

     1.25 “Person” means a natural person, a corporation, a partnership, a limited liability
company, a trust, a joint venture, any governmental authority or any other entity or organization.

     1.26 “Preexisting Agreements” means (a) the agreements identified in Exhibit B and (b) any
other agreements entered into by Gilead or its predecessors prior to the NeXstar Merger Date
relating to the SELEX Process or to any Aptamers.

     1.27 “Proprietary Information” means, subject to the limitations set forth in Section 8.1
hereof, any confidential information of a Party disclosed by such Party to the other Party in the
course of negotiating or performing under this Agreement that is identified as confidential by the
disclosing party at the time of its disclosure. The Licensed Patents, the Licensed Processes and
Methods, the Licensed Know-How, the due diligence materials identified in Exhibit F attached to
this Agreement, and the terms and provisions of the Preexisting Agreements attached at Exhibit G
are deemed to be Gilead’s Proprietary Information whether or not marked or identified as
confidential or proprietary. The terms and provisions of this Agreement and any information that
is “Confidential Information” as defined in the Confidential Disclosure Agreement, dated June 6,
2001, between Company and Gilead are deemed to be the Proprietary Information of both Parties
whether or not marked or identified as confidential or proprietary.

     1.28 “Radio Therapeutics” shall have the meaning provided in the [***] Agreement listed in
Exhibit B, as such Agreement is in effect on the Effective Date; provided that, (a) in the event
that Third Parties no longer have rights to Radio Therapeutics pursuant to the [***] Agreement, all
references to “Radio Therapeutics” in this Agreement shall be automatically deleted, without
further action by the Parties, and (b) in the event that the field rights embodied in the
definition of “Radio Therapeutics” contained in the [***] Agreement shall at any time be modified
or amended to reduce the scope thereof, the definition of “Radio Therapeutics” contained in this
Agreement shall be automatically reduced in scope to the same extent, without further action by the
Parties, provided that nothing in this Section 1.28 shall give Company any rights to or interest in
any products developed by or licensed to a Third Party pursuant to the

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

4

 

[***] Agreement in clinical development, submitted for regulatory approval or being
commercialized.

     1.29 “SELEX Process” means any process for identification or use of a nucleic acid, which
process is disclosed in or falls within the claimed scope of U.S. Patent Nos. [***] or [***].

     1.30 “Target Validation” means the use of the SELEX Process to create Aptamers that bind to a
target and the use of such Aptamers, through testing in [***] studies and other assay and studies,
to provide information as to a target’s biological utility through the [***] of the target or some
[***] on the target.

     1.31 “Territory” means the world.

     1.32 “Third Party” means any Person other than the Parties or their respective Affiliates.

     1.33 “Transferred Assets” shall have the meaning given such term in Section 2.5.

     1.34 “URC License Agreement” means the Restated Assignment and License Agreement, dated July
17, 1991, by and between University Research Corporation and Gilead as successor in interest to
NeXstar.

     1.35 “UTC” means University Technology Corporation, the successor to the University Research
Corporation.

     1.36 “Valid Claim” means a claim of an issued and unexpired patent that has not been held
permanently revoked, unenforceable or invalid by a decision of a court or governmental agency of
competent jurisdiction over such claim, which decision is unappealable or unappealed within the
time allowed for appeal.

     1.37 “[***] Agreement” means that certain License Agreement between [***] and Gilead (as
successor-in-interest to Nexagen, Inc.) dated September 15, 1992.

2. License.

     2.1 License Grants and Certain Restrictions.

          (a) Subject to the terms and conditions of this Agreement, during the term of this Agreement,
Gilead hereby grants to Company, and Company hereby accepts, an exclusive (subject to the
restrictions and limitations specified in Sections 2.1(b), 2.1(c), and 2.2 below, and except that
such license shall be non-exclusive for portions of the Licensed Field as to which one or more
Third Parties has such non-exclusive rights pursuant to a Preexisting Agreement) license and
sublicense, as applicable, under the Covered Intellectual Property (a) to exploit, use and practice
the Licensed Processes and Methods, including without limitation, the SELEX Process, within the
Licensed Field throughout the Territory, (b) to develop, make, have made, use, sell, offer to sell
and import Licensed Products within the Licensed Field throughout the Territory and

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

5

 

(c) to utilize the Licensed Know-How and the inventions claimed in the Licensed Patents for
any purpose within the Licensed Field throughout the Territory.

          (b) Company acknowledges that the Covered Intellectual Property remains subject to the
licenses granted to certain Third Parties pursuant to the [***] Agreement. In addition, Company
acknowledges that, pursuant to the [***] Agreement, certain covenants and restrictions shall apply
to Company’s use and sublicensing of the Covered Intellectual Property, including restrictions on
Company’s further sublicensing of rights in the field of Target Validation and certain Aptamers
specified in Paragraph 8.3 of the [***] Agreement.

          (c) If at any time during the term of this Agreement, Company develops any products, pursuant
to the exercise of its rights granted under this Agreement, that incorporate [***] as defined in
the [***] Collaboration Agreement listed in Exhibit B and attached in Exhibit G, including without
limitation Aptamers directed at [***] or [***], to the extent any obligations to pay to [***]
royalties upon such products arise pursuant to Section 3.2 of the [***] License Agreement listed in
Exhibit B and attached in Exhibit G, Company shall be responsible for such obligations.

          (d) If at any time during the term of this Agreement, any Third Party develops, identifies,
generates, or commercializes any products pursuant to the exercise of the rights granted to it
under a Preexisting Agreement, and such Preexisting Agreement is terminated, amended or modified in
such a way as to cause an enlargement of the Licensed Field hereunder, such termination, amendment
or modification shall not create a claim for Company to any right, title or interest in any such
products developed by such Third Parties or the commercialization of any such products.

     2.2 Negative Covenant of Company. Company shall not use or practice the Covered Intellectual
Property (a) outside the Licensed Field, (b) for any other purpose except activities that it
conducts in compliance with this Agreement, (c) to make, use, sell, offer for sale, import or
export any products containing any Excluded Aptamers, (d) to make, use, sell, offer for sale,
import or export any Excluded Aptamers, or (e) to make, use, sell, offer for sale, import or export
any Aptamers for In Vitro Diagnostics.

     2.3 Sublicensing Rights. Company shall have the right to sublicense the rights granted to it
by Gilead under this Agreement without the consent of Gilead; provided that: (a) prompt notice of
such sublicense shall be given by Company to Gilead pursuant to Section 10.5 of this Agreement; (b)
a true, correct and complete copy of such sublicense shall be provided by Company to Gilead
promptly after the date the parties enter into such sublicense agreements, provided that Company
may redact any financial and other information to the extent not required to enable Gilead to
fulfill its reporting obligations under the URC License Agreement or to monitor compliance with
this Agreement; and (c) Company shall remain at all times fully liable for performance of its
obligations under this Agreement without regard to whether it has sublicensed its rights or whether
Company’s sublicensee is obligated to perform such obligations. Any such sublicense granted by
Company shall contain provisions providing for the assignment to Gilead of Company’s interest
therein upon termination of this Agreement, subject to the last sentence of this Section 2.3,
unless the termination of this Agreement arises out of the action or inaction of such sublicensee,
in which case Gilead, at its option, may

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

6

 

terminate such sublicense, and shall further contain provisions which obligate such
sublicensee to comply with such terms, conditions, agreements and obligations that are consistent
with the terms, conditions, agreements and obligations to which Company is subject under this
Agreement including, without limitation, the provisions of Sections 2.1(b), 2.1(c), 2.2, Section 4,
Section 5, Section 6.4, Section 7.1(b), Section 8 and Section 9.3. Gilead hereby agrees to accept
such assignment and that such sublicense, as assigned, will remain in full force and effect,
provided that Gilead shall have no obligation thereunder except to maintain the continued
effectiveness of the sublicense.

     2.4 Grant Back To Gilead. As of the Effective Date, and subject to the terms and conditions
hereof, Company hereby grants back to Gilead, and Gilead hereby accepts the following worldwide,
royalty-free, paid-up, perpetual, irrevocable and nonexclusive licenses: (a) (i) under the rights
licensed to Company under Section 2.1 above, and (ii) under Company’s intellectual property rights
to such of the Company Improvements as constitute improvements to the SELEX Process, in both cases
solely to conduct internal research and (b) under Company’s intellectual property rights in the
Company Improvements to use and practice any Company Improvements developed by Company under the
licenses granted pursuant to Section 2.1 above as may be necessary for Gilead to fulfill its
obligations, including, without limitation, sublicensing obligations, under the Preexisting
Agreements (the “Grant-Back License”).

     2.5 Assignment of Agreement and Delivery of Documentation. Gilead shall use diligent,
reasonable, good faith efforts to obtain from each Third Party to the [***] Agreement, the [***]
Agreement, the [***] Agreement, and the [***] Agreement (collectively, the “Transferred Assets”) a
written consent to the assignment of the respective Transferred Asset to Company as promptly as
reasonably practicable after the Effective Date, and Company shall provide reasonable assistance in
such efforts as requested by Gilead (e.g., by agreeing to assume Gilead’s rights and obligations
thereunder). Effective as of the respective Consent Dates therefor, Gilead hereby assigns to
Company all of Gilead’s right, title and interest in and to the Transferred Assets (subject to the
reversion rights specified in Section 9.3 below), and Company hereby accepts such assignment and
agrees to assume Gilead’s rights and obligations thereunder (subject to Gilead remaining liable for
certain Excluded Liabilities). On the date of receipt by Gilead of the first Payment due from
Company pursuant to Section 3.1 below, Gilead shall ship a single copy of the Documentation to
Company FCA to Company’s designated facilities (Incoterms 2000). The Documentation shall be
provided to Company in computer-readable format, where available, and otherwise in printed format.
Gilead shall be under no obligation to convert to electronic format any portion of the
Documentation that currently is available only in printed format. Gilead shall have no further
obligation to Company to provide any other documentation or transfer additional copies of the
Documentation after the delivery to Company pursuant to this Section 2.5. Gilead hereby grants to
Company a non-exclusive and royalty-free right to use and reproduce the Documentation as required
to exercise Company’s rights to the Covered Intellectual Property granted under Section 2.1 above.
Gilead retains ownership of all intellectual property rights in and to the Documentation, subject
only to this license and the Documentation shall be deemed to be Gilead’s Proprietary Information
subject to the provisions of Section 8 below.

     2.6 Assumed Liabilities. Except as otherwise provided in this Agreement, Company hereby
assumes and agrees to bear and be responsible for and to perform and satisfy [***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

7

 

responsibilities, duties (including, without limitation, compliance with all applicable laws
and regulations), obligations (including payment obligations, such as payments for filing,
prosecution and maintenance of Licensed Patents), claims, Damages, liabilities, burdens and
problems of any nature whatsoever (collectively, the “Obligations”) arising out of (a) Company’s
licensing and/or practice of the Covered Intellectual Property from and after the Effective Date,
(b) such Obligations relating to payments that may be due to the UTC under the URC License
Agreement resulting from actions or in-action of Company, its Affiliates or its sublicensees, and
(c) any such Obligations under any and all of the Transferred Assets arising on or after the
respective Consent Dates and prior to a reversion of any of those Transferred Assets pursuant to
Section 9.3(c) of this Agreement or after such a reversion if caused by a breach by Company of the
Transferred Assets, except for the hereinafter defined Excluded Liabilities, which items shall
remain the responsibility of Gilead as set forth in this Agreement (collectively, the “Assumed
Liabilities”). For purposes of this Agreement, the “Excluded Liabilities” means (1) those Damages
with respect to which Gilead is providing indemnification pursuant to the provisions of Section
7.1(a)(i) of this Agreement, (2) any Obligations that have accrued under the Transferred Assets
prior to the respective Consent Dates or after a reversion of any such Transferred Assets pursuant
to Section 9.3(c) of this Agreement (except to the extent caused by a breach by Company of the
Transferred Assets), and (3) any Obligations under the Preexisting Agreements listed in Exhibit B,
except for any Obligations arising from or related to Company’s breach of any Obligations or duties
specified in this Agreement or any conduct described in Section 7.1(b)(i) through (vii) of this
Agreement.

     2.7 Modification of URC License Agreement. Gilead shall not enter into any amendment,
modification or supplement of or to the URC License Agreement, or exercise any right or option to
terminate the URC License Agreement in whole or in part, without the express prior written consent
of Company in each instance, which shall not be unreasonably withheld.

3. Financial Terms.

     3.1 Consideration. Company shall pay to Gilead a nonrefundable fee which shall consist of the
sum of seventeen million five hundred thousand dollars ($17,500,000) payable in three nonrefundable
installments of [***] dollars ($[***]), [***] dollars ($[***]) and [***] dollars ($[***]) (the
“Payments”), plus a warrant to purchase up to [***] shares of Company Common Stock in the form
attached hereto as Exhibit I (the “Warrant”). The first Payment shall be due and payable one (1)
day after the Effective Date, the second Payment shall be due and payable on or before December 31,
2001 and the third Payment shall be due and payable on or before June 30, 2002. The Warrant shall
be issued to Gilead on the Effective Date. Failure to make any Payment when due shall give rise to
an immediate right of termination by Gilead as set forth in Section 9.2(a) below. Company has
furnished to Gilead a copy of the Put Agreement pursuant to which it has the right to call on
certain investors in Company to purchase equity to provide funds for the Payments in this Section
3.1. Company covenants and agrees to exercise such right if needed to provide such funds and to
utilize such funds to pay Gilead any amounts payable under this Section 3.1, to the extent Company
does not use other funds to make such Payments, and the Parties acknowledge and agree that Gilead
shall have the right to specifically enforce the preceding covenants in this sentence.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

8

 

     3.2 Payment Procedure. The Payments shall be paid to Gilead in U.S. Dollars by Federal
Reserve wire transfer in accordance with the wire transfer instructions specified in Exhibit H
attached to this Agreement.

     3.3 Third Party Payments. If royalties, fees or other amounts become due and payable to any
Third Party, including any such payments that become due and payable under the Preexisting
Agreements listed in Exhibit B, solely on account of Company’s exercise of its rights under the
licenses granted by Gilead in Section 2.1 above, Company shall be liable for, and promises to make,
such payments to such Third Parties except to the extent that such Third Party payments are caused
by circumstances that also result in a breach by Gilead of its representations, covenants and/or
warranties as set forth in Section 6 below. Notwithstanding the foregoing, as between the Parties,
Gilead shall be solely responsible for making all payments under the Preexisting Agreements,
including without limitation the URC License Agreement, on account of its receipt, or right to
receive, payments from Company hereunder.

     3.4 Taxes. The Payments are exclusive of and Company will remain fully liable for any sales,
transfer or other tax assessments, or duty payable based on the transactions described in this
Agreement except for taxes based on the net income or net worth of Gilead.

4. Patent Prosecution, Maintenance and Enforcement.

4.1 Prosecution and Maintenance.

          (a) Company Obligations. Company shall prosecute and maintain the Licensed Patents in
the Territory (excluding the patents set forth on Exhibit D) in Gilead’s name using reasonably
diligent efforts, at Company’s expense, except as otherwise provided in Section 4.1(c) below.
Company shall promptly provide Gilead with notice of its intention not to file a response to any
office actions or other requests from the United States Patent and Trademark Office or the
equivalent authority in a foreign jurisdiction, to abandon filings, or to make material limitations
to claims for the Licensed Patents and, at Gilead’s request, shall promptly provide Gilead, or
Third Parties to Preexisting Agreements designated by Gilead who have a right to such information
under the applicable Preexisting Agreement and who have requested such information, with copies of
correspondence and proposed or actual filings relating to Company’s prosecution and maintenance of
the Licensed Patents, with any proposed filings to be provided at least [***] days prior to the
date of filing. Company shall direct all such correspondence and filings provided to Gilead to
Gilead’s Vice President of Intellectual Property at the address listed below.

Gilead Sciences, Inc.

333 Lakeside Drive

Foster City, California 94404

Telephone: (650) 522-5878

Telefax: (650) 522-5575

Attention: Vice President of Intellectual Property

Company agrees to give good faith consideration to any reasonable comments with respect to such
filings that are provided by Gilead or by any Third Parties to Preexisting Agreements

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

9

 

designated by Gilead but Company shall have final authority on all decisions concerning such
filings. Company shall control the conduct of any inter partes patent proceeding, including
without limitation oppositions, interferences or contested re-examinations. Company shall bear the
expense of all such proceedings. Company shall honor the consultation rights of [***] under
Section 6.4 of the [***] Collaboration Agreement (as defined on Exhibit B) and the rights of [***]
under Section 5.1(b) of the [***] Agreement (as defined on Exhibit B), including fulfillment of
Gilead’s obligations thereunder, in each case as applicable to any Licensed Patents. If any
conflict arises concerning the representation of the Parties with respect to the Licensed Patents
by the firm of [***] hereby agrees to waive any such conflict and any objection it may have to
[***] representation of Gilead with respect to the Licensed Patents.

          (b) Assistance. Gilead shall assist Company in obtaining patent extensions and
supplementary protection certificates, and provide such other assistance as reasonably requested by
Company in connection with the prosecution and maintenance of the Licensed Patents in any part of
the Territory at Company’s sole expense, including without limitation, by making reasonable efforts
on behalf of Company to obtain the assistance in such efforts of any individual who is obligated to
provide such assistance at the direction or request of Gilead.

          (c) Reversion of Rights. Company shall promptly notify Gilead in writing if Company
determines that it has no material or commercially useful application for a Licensed Patent.
Gilead or any party to a Preexisting Agreement, as determined by Gilead (the “Assuming Party”),
shall have the right to prosecute and maintain such Licensed Patents or file for such patent term
extension therefor at the Assuming Party’s sole discretion and expense. In this event all rights
in and to such Licensed Patents shall revert to the Assuming Party and shall be removed from the
list of patents or patent applications included within the definition of Licensed Patents under
this Agreement. Company shall assist the Assuming Party in obtaining patent extensions and
supplementary protection certificates, and provide such other assistance as reasonably requested by
the Assuming Party in connection with the prosecution and maintenance of such Licensed Patents in
any part of the Territory at the Assuming Party’s sole expense.

     4.2 Enforcement.

          (a) Notice. Each Party shall promptly notify the other in writing its knowledge of
any actual or potential infringement or misappropriation of any Licensed Patent or Licensed
Know-How by Third Parties within the Territory and provide any information available to that Party
relating to such actual or potential infringement or misappropriation. Company shall have no
rights with respect to any infringement of Licensed Patents or infringement or misappropriation of
Licensed Know-How that occurs outside of the Licensed Field and/or outside the Territory except the
right to receive notice pursuant to this Section 4.2(a); provided however, that, to the extent
within the control of Gilead, Gilead shall not enter into any settlement, consent judgment or other
voluntary final disposition with respect to any such infringement or misappropriation if it would
have a material adverse effect on any Licensed Patent or Licensed Know-How within the Licensed
Field without the prior consent of Company, which consent shall not be unreasonably withheld.

          (b) Enforcement of Licensed Patents. With respect to any infringement of Licensed
Patents within the Licensed Field or with respect to any Licensed Products within the

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

10

 

Licensed Field, Company shall have the primary right, but not the obligation, to initiate,
prosecute and control any action with respect to such infringement, by counsel of its own choice,
to secure the cessation of the infringement or to enter suit against the infringer. Gilead shall
have the right to participate in any such action and to be represented by counsel of its own choice
and at its own expense. If Company fails to exercise its right to bring an action or proceeding to
so enforce a Licensed Patent within a period of [***] days after receipt of written notice of
infringement of such Licensed Patent, then Gilead shall have the right to bring and control any
such action by counsel of its own choice and at its own expense. Gilead shall have the right to
extend the right to participate in and control, as applicable, any such action to its Affiliates
and sublicensees, as Gilead in its sole discretion deems necessary to satisfy its obligations under
the Preexisting Agreements. If a Party brings any such action or proceeding hereunder, the other
Party agrees to be joined as a party plaintiff and to give the first Party reasonable assistance
and authority to control, file and prosecute the suit as necessary, at the first Party’s sole
expense. The costs and expenses of the Party bringing suit under this Section 4.2(b) (including
the internal costs and expenses specifically attributable to such suit) shall be reimbursed first
out of any damages or other monetary awards recovered in favor of the Parties, and any remaining
damages shall be paid to the Party that controlled such action. No settlement or consent judgment
or other voluntary final disposition of a suit under this Section 4.2(b) relating to a Licensed
Patent may be entered into without the consent of the Party not controlling such action, such
consent not to be unreasonably withheld, delayed or conditioned.

     4.3 Infringement of Third Party Rights.

          (a) Notice of Claim. If the practice of the Licensed Patents by Company, its
Affiliates or sublicensees, in accordance with the licenses granted under Section 2.1 above,
results in a claim of patent infringement against Company, its Affiliates or sublicensees, the
Party to this Agreement first having notice of that claim shall promptly notify the other Party in
writing. The notice shall set forth the facts of the claim in reasonable detail.

          (b) Resolution of Claims. If a Third Party asserts that a patent or other right owned
by or licensed to it is infringed within a country by the practice of the Licensed Patents by
Company, its Affiliates or sublicensees, in accordance with the licenses granted under Section 2.1
above, Company may attempt to resolve the asserted infringement; provided, however that Gilead
shall have the right, at its sole discretion, to participate in any such resolution and to be
represented by counsel of its own choice and at its own expense. Company shall control the process
to resolve any such infringement. The matter shall be deemed resolved if Company obtains: (i) a
license permitting Company to manufacture, use, import, offer for sale and sell Licensed Products
in that country on a royalty-free basis (ii) a legally binding statement or representation from the
Third Party that: (A) no action will be taken against Company, its Affiliates or its sublicensees,
or (B) that the patent or other right is not infringed the practice of the Licensed Patents by
Company, its Affiliates or its sublicensees in such country; or (iii) a final judgment by a court
of competent jurisdiction from which no appeal has or can be taken that the Third Party’s patent(s)
alleged to be infringed is invalid, or the Third Party’s patent(s) or other right(s) are
unenforceable or not infringed by the practice of the Licensed Patents by Company, its Affiliates
or sublicensees. Company shall have the primary right to defend any such claim. Gilead shall have
the right, but not the obligation, to participate in any such suit at its sole option and at its
own expense. Each Party shall reasonably cooperate with the Party conducting the

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

11

 

defense of the claim. Neither Party shall enter into any settlement that affects the other
Party’s rights or interests without such other Party’s prior written consent, not to be
unreasonably withheld, delayed or conditioned.

     4.4 Reimbursement under Preexisting Agreements. Gilead covenants that it will make reasonable
efforts to collect all amounts owing from Third Parties under Preexisting Agreements in connection
with the prosecution, maintenance and enforcement of the Licensed Patents as and when such amounts
become due and payable and that Gilead will forward all such amounts to Company as and when they
are collected by Gilead.

5. Progress Report and Commercial Application.

     5.1 Progress Report. On or before [***] and [***] of each year, commencing as of [***] and
ending on [***] of the calendar year following the calendar year in which Company, its Affiliates
or sublicensees first begins to market any product or service utilizing the Covered Intellectual
Property, Company shall provide a [***] progress report to Gilead, each report covering the [***]
month period preceding the due date of the report. Thereafter, Company shall provide such reports
on an annual basis covering the [***] month period preceding the due date of the report. Each
report shall describe any Company Improvements (including any modifications and the updates to the
Documentation), notice of any patents filed by Company in connection with any Company Improvements
and the progress made by Company, its Affiliates or sublicensees toward the commercial development
of any products or services utilizing the Covered Intellectual Property. Such report shall include
at a minimum, information reasonably sufficient to enable Gilead to satisfy its reporting
obligations to the UTC under the URC License Agreement with respect to this Agreement, including
any reporting obligations of the U.S. Government, and to assess the progress made by Company toward
meeting the diligence requirements of Section 5.2 below. Company shall also provide to Gilead on
or before the February 28 reporting date set forth in this Section 5.1 an updated version, if any,
to the SELEX Manual (in an electronic, organized and printable format) provided to Company as part
of the Documentation listed on Exhibit A.

     5.2 Commercial Application. Company, either directly or with and through the efforts of its
Affiliates and sublicensees, shall at all times use commercially reasonable efforts to proceed with
the development, manufacture and sale of products and services utilizing the Covered Intellectual
Property, including, without limitation, maintaining sufficient facilities, resources and personnel
to fulfill its obligations under this Agreement. In the event that Company, its Affiliates,
assignees and sublicensees cease reasonable efforts to develop the commercial applications of the
products and services utilizing the Covered Intellectual Property for a period of at least [***]
months Gilead will have the option, at its sole discretion, to terminate this Agreement pursuant to
Section 9.2(a) below; provided that Gilead may exercise such option only if Gilead shall have
received written notice from UTC of a default under the URC License Agreement by reason of the
failure by Company to use reasonable efforts to develop the commercial application of the Covered
Intellectual Property, and UTC has sent to Gilead written notice of termination of the URC License
Agreement as a consequence thereof. In such event, Gilead may exercise its option; provided that
(a) Gilead delivers advance written notice of its decision to exercise such option to force a
reversion of the technology to Gilead, and (b) for a period of [***] months following Company’s
receipt of such notice, Company, its

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

12

 

Affiliates, and all assignees and sublicensees, shall have the right and opportunity to cure
the alleged cessation of such reasonable commercial development. Company acknowledges and agrees
that under the URC License Agreement, Company’s rights in the Covered Intellectual Property may
revert to the UTC if Company, its Affiliates and all assignees and sublicensees cease reasonable
efforts to develop the commercial applications of the products and services utilizing the Covered
Intellectual Property. Company and Gilead further acknowledge and agree that, in the event of any
termination of the URC License Agreement, the sublicenses granted to Company hereunder shall remain
in full force and effect in accordance with Section 3.4 of the URC License Agreement, provided that
Company is not then in breach of this Agreement and agrees to be bound to UTC as a licensor under
the terms and conditions of this Agreement.

6. Representations, Covenants and Warranties.

     6.1 Corporate Existence and Power. As of the Effective Date, each Party represents and
warrants to the other that it (a) is a corporation duly organized, validly existing and in good
standing under the laws of the state in which it is incorporated, and (b) has full corporate power
and authority and the legal right to own and operate its property and assets and to carry on its
business as it is now being conducted and as contemplated in this Agreement, including, without
limitation, the right to grant the licenses granted hereunder, other than what has been disclosed
by Gilead to Company pursuant to a letter that shall be delivered by Gilead to Company on the
Effective Date.

     6.2 Authority and Binding Agreement. As of the Effective Date, each Party represents and
warrants to the other that it (a) has the corporate power and authority and the legal right to
enter into this Agreement and perform its obligations hereunder, other than what has been disclosed
by Gilead to Company pursuant to a letter that shall be delivered by Gilead to Company on the
Effective Date, (b) has taken all necessary corporate action on its part required to authorize the
execution and delivery of the Agreement and the performance of its obligations hereunder, and (c)
the Agreement has been duly executed and delivered on behalf of such Party, and constitutes a
legal, valid and binding obligation of such Party and is enforceable against it in accordance with
its terms.

     6.3 Additional Representations, Covenants and Warranties of Gilead. Gilead covenants to
Company that Gilead shall not enter into any agreements, written or otherwise, including without
limitation, any amendment, modification or supplement to any of the Preexisting Agreements or the
Transferred Assets, which would conflict with, restrict, limit or impair any of the rights, powers
and benefits conferred on Company hereunder or Company’s ability to exercise and enjoy such rights,
powers and benefits to the full extent permitted herein. Gilead further represents and warrants to
Company that:

          (a) In Exhibit C, Gilead has in good faith supplied a complete list of the Licensed Patents.
If Gilead or Company reasonably determine that there is a patent or patent application that was
Controlled by Gilead as of the Effective Date and that dominates or is dominated by the claims of
one or more Licensed Patents but that is not listed on Exhibit C, then there shall be no breach of
Gilead’s representations and warranties in this Section 6.3(a), but such Party shall give notice
promptly to the other Party of such determination. The Parties shall negotiate in good faith
towards the addition of any such patent or patent application to Exhibit C

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

13

 

without any additional financial obligation. If the Parties are unable to reach agreement on
the addition of such patent, the Parties shall submit the matter of whether such patent or patent
application that was Controlled by Gilead as of the Effective Date dominates or is dominated by the
claims of one or more Licensed Patents to binding arbitration pursuant to Section 10.3 below. If
it is determined pursuant to such arbitration that such patent or patent application dominates or
is dominated by the claims of one or more Licensed Patents, it shall be deemed to be included in
Exhibit C and to be a Licensed Patent. In the event the patent application or patent in dispute is
not added to Exhibit C as a result of the arbitration, then Gilead agrees not to assert its rights
under such patent or patent application, directly or indirectly, to prevent or restrict Company’s
practice of the Covered Intellectual Property in accordance with this Agreement. The foregoing
shall not obligate Gilead to license to Company any patents or patent applications Controlled by
Gilead that are not listed in Exhibit C where such patent or patent application describes a
particular chemical compound, whether or not such compound is a Licensed Product or an Aptamer
under the terms of this Agreement.

          (b) After the NeXstar Merger Date, Gilead has not granted to any Third Party any license or
right to practice any of the Licensed Patents or Licensed Know-How within the Licensed Field or to
make, use or sell any Licensed Products in the Licensed Field, except for those rights granted to
Third Parties pursuant to the Transferred Assets or the Preexisting Agreements listed on Exhibit B
and other than what has been disclosed by Gilead to Company pursuant to a letter that shall be
delivered by Gilead to Company on the Effective Date. To the actual knowledge of the Gilead Key
Personnel as of the Effective Date, prior to the NeXstar Merger Date, Gilead has not granted any
such license or right, except for those rights granted to Third Parties pursuant to Transferred
Assets, or any such Preexisting Agreement listed on Exhibit B.

          (c) For the purposes of this Section 6.3(c), capitalized terms that are not otherwise defined
herein shall be ascribed the meaning given to them under the [***] Agreement. Gilead has provided
to Company a complete and correct copy of the [***] Agreement and any Third Party agreements
entered into by [***] thereunder known to Gilead. Gilead has not entered into any Development
License(s) with [***]. Gilead has not received any Development Notice(s) from [***].

          (d) Gilead has supplied complete and correct copies of the URC License Agreement and the
Transferred Assets to Company and redacted copies of the other Preexisting Agreements that, except
for such redactions, are otherwise complete and correct.

          (e) No party to the URC License Agreement or the Transferred Assets has committed a material
default or breach under any of those agreements and the execution and delivery of this Agreement
does not, and will not with the passage of time alone, constitute a material default or breach
under any of the Preexisting Agreements, the URC License Agreement or the Transferred Assets, other
than what has been disclosed by Gilead to Company pursuant to a letter that shall be delivered by
Gilead to Company prior to the Effective Date.

          (f) Gilead will use commercially reasonable efforts to keep the URC License in full force and
effect. In the event that UTC or any of its affiliates or successors provides a notice of default
under the URC License Agreement to Gilead, Gilead covenants that it shall

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

14

 

promptly provide a copy of such notice to Company and shall thereafter keep Company reasonably
advised as to the status of any such alleged or actual default and how it may or may not affect
Company’s rights under this Agreement. In addition, if the alleged default is based on an action or
inaction by Company, Gilead shall allow Company to take action to cure such alleged default, or
otherwise to settle such dispute, on behalf of Gilead, at Company’s sole discretion within a
reasonable time but subject to Gilead’s termination rights pursuant to Sections 5.2 and 9.2.

     6.4 Additional Representations and Warranties of Company.

          (a) Company acknowledges and agrees that a redacted copy of each of the Preexisting Agreements
listed in Exhibit B (including without limitation, the URC License Agreement) is attached hereto as
Exhibit G and that Company has been provided with a copy of the Transferred Assets. Company
represents and warrants that it understands the terms of such agreements, acknowledges that its
rights are subject to such agreements and, furthermore, Company, its Affiliates and sublicensees
shall take no action that would give rise to a breach by Gilead under the Preexisting Agreements,
(including without limitation, the URC License Agreement) or the Transferred Assets. As required
under Section 3.3 of the URC License Agreement, Company hereby acknowledges Gilead’s obligations
under the following sections of the URC License Agreement: (i) the quarterly royalty payments and
reports under Section 6; (ii) the warranties and disclaimers set forth in Section 7; (iii) the
indemnity obligations under Section 8; and (iv) the restrictions on promotional association under
Section 10, and Company agrees to assume all such obligations to the extent they relate to
Company’s rights and obligations under this Agreement and expressly acknowledges that Company’s
failure to perform its obligations under this Agreement may result in a breach of Gilead’s
obligations under the URC License Agreement.

          (b) The execution and delivery by the Company of this Agreement, the Warrant and the Put
Agreement, the performance by the Company of its obligations thereunder, and the issuance, sale and
delivery of any shares of Company capital stock to be issued, sold or delivered pursuant to the
Warrant and the Put Agreement, have been duly authorized by all requisite corporate action and will
not violate any provision of law, any order of any court or other agency of government, the
Certificate of Incorporation of the Company, as amended (the “Charter”) or the By-laws of the
Company, as amended, or any provision of any indenture, agreement or other instrument to which the
Company, any of its subsidiaries or any of their respective properties or assets is bound, or
conflict with, result in a breach of or constitute (with due notice or lapse of time or both) a
default under any such indenture, agreement or other instrument, or result in the creation or
imposition of any lien, charge, restriction, claim or encumbrance of any nature whatsoever upon any
of the properties or assets of the Company.

          (c) The issuance, sale and delivery of all shares of Company capital stock to be issued, sold
or delivered pursuant to the Put Agreement (the “Put Shares”) have been duly authorized and, when
issued in accordance with the Put Agreement, will be validly issued, fully paid and nonassessable
shares of Series A Convertible Preferred Stock of the Company and will be free and clear of all
liens, charges, restrictions, claims and encumbrances imposed by or through the Company except as
set forth in the Put Agreement. Except as set forth in the Put Agreement, neither the issuance,
sale or delivery of the Put Shares is subject to any preemptive

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

15

 

right of stockholders of the Company or to any right of first refusal or other right in favor
of any person.

     6.5 Absence of Litigation. As of the Effective Date, other than what has been disclosed by
Gilead to Company pursuant to a letter that shall be delivered by Gilead to Company on the
Effective Date, (a) each Party represents and warrants to the other that as of the Effective Date
there is no pending litigation against it and that it has not received written notice that overtly
threatens litigation, which litigation alleges that such Party’s activities related to this
Agreement have infringed or misappropriated, or that by conducting the activities as contemplated
in this Agreement such Party would infringe or misappropriate, any of the intellectual property
rights of any other Person, and (b) Gilead further represents that prior to the NeXstar Merger
Date, to the knowledge of Gilead Key Personnel, Gilead has not received, and after the NeXstar
Merger Date Gilead has not received, any written communication asserting that Gilead’s activities
relating to this Agreement or its conduct of activities relating to this Agreement infringe or
misappropriate the intellectual property rights of any other person.

     6.6 Survival of Warranties. Each of Gilead’s representations and warranties made in this
Section 6 shall survive only for a period of [***] years after the Effective Date and shall
thereafter be of no force or effect provided, however, that Gilead’s representations and warranties
made in Section 6.3(a) shall survive indefinitely.

     6.7 Disclaimer of Warranties. Company acknowledges that it accepts the Documentation “as
is” and without warranty of any kind. Except as expressly provided in this Section 6, neither
party makes any representation or warranty as to the Covered Intellectual Property, express or
implied, either in fact or by operation of law, by statute or otherwise, including without
limitation any implied warranty of merchantability, fitness for a particular purpose,
non-infringement of third party rights, or warranty against infringement, or otherwise, and each
party specifically disclaims any and all implied or statutory warranties. Gilead makes no
warranties as to the validity or enforceability of any Covered Intellectual Property. Without
limiting the foregoing, each party acknowledges that it has not and is not relying upon any implied
warranty of merchantability, fitness for a particular purpose, non-infringement of third party
rights, or warranty against infringement, or otherwise, or upon any representation or warranty
whatsoever as to the prospects (financial, regulatory or otherwise), or the validity or likelihood
of success, of any products or services based on the Covered Intellectual Property or any Company
intellectual property after the Effective Date.

7. Indemnification.

     7.1 Indemnity.

          (a) By Gilead. Gilead shall indemnify, defend and hold harmless Company, and its
respective directors, officers, employees and agents (each, a “Company Indemnitee”), from and
against any Damages that are incurred by a Company Indemnitee as a result of Third Party claims,
demands, actions or proceedings (collectively, the “Company Claims”) to the extent such Company
Claims arise out of:

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

16

 

                    (i) the breach or alleged breach of any representation or warranty by Gilead in Sections 6.1,
6.2, 6.3 and 6.5 provided that notice of a Company Claim based upon any such breach is received by
Gilead prior to expiration of such representation and warranty pursuant to Section 6.6 above;

                    (ii) the breach or alleged breach by Gilead of any Preexisting Agreement, excluding any
disclosed in the letter referenced in Sections 6.1(b), 6.2(a), 6.3(b), 6.3(e) and 6.5; or

                    (iii) any of the Excluded Liabilities;

except to the extent Company has an obligation to indemnify Gilead under Section 7.1(b).

          (b) By Company. Company shall indemnify, defend and hold harmless Gilead, its
Affiliates and UTC and any of their respective directors, officers, employees and agents (each, a
“Gilead Indemnitee”), from and against any Damages that are incurred by a Gilead Indemnitee as a
result of Third Party claims, demands, actions or proceedings (collectively, the “Gilead Claims”)
to the extent such Gilead Claims arise out of:

                    (i) the breach or alleged breach of any representation or warranty by Company hereunder;

                    (ii) failure to perform duly and punctually any of Company’s covenants or undertakings under
this Agreement, including, without limitation Company’s covenants in Section 5.2 above;

                    (iii) any of the Assumed Liabilities;

                    (iv) the possession, research, development, manufacture, use, offer for sale, sale or other
commercialization, distribution, administration, storage or transport, by Company or its Affiliates
or sublicensees (other than Gilead) of (A) any Aptamers or Licensed Products or (B) any other
products, services and activities developed by Company relating to the Covered Intellectual
Property, including any Licensed Products, Aptamers or Documentation;

                    (v) the failure or delay on the part of Company to make payments required pursuant to Section
3.3 above;

                    (vi) the failure on the part of Company to make payments required pursuant to Section 3.4
above; or

                    (vii) a suit by [***] to the extent [***] alleges in such suit that the granting of the rights
and licenses hereunder to Company was wrongful conduct on the part of Gilead due to: (A) the
alleged infringement of [***] intellectual property rights by Company prior to the Effective Date,
(B) other wrongful conduct by Company prior to the Effective Date, provided that Company’s costs of
providing a defense for such suit shall be promptly reimbursed to Company by Gilead in the event
Gilead is found liable to [***] in such a suit for wrongful conduct by Gilead other than as set
forth in (A) or (B) above, or Gilead pays an amount to [***] in connection with the settlement of
such a suit without the prior written consent of Company,

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

17

 

except to the extent such Gilead has an obligation to indemnify Company under Section 7.1(a).

     7.2 Procedure. Any Gilead Indemnitee or Company Indemnitee shall notify Company or Gilead
(the “Indemnifying Party”), as the case may be, promptly in writing of an indemnifiable claim or
cause of action under Section 7.1 above upon receiving notice or being informed of the existence
thereof. The Indemnifying Party shall assume, at its cost and expense, the sole defense of such
claim or cause of action through counsel selected by the Indemnifying Party and reasonably
acceptable to the other Party, such acceptance not to be unreasonably withheld, delayed or
conditioned. The Indemnifying Party shall maintain control of such defense, including any decision
as to settlement; provided that, if the Indemnifying Party has failed to conduct such defense on a
timely basis, then, without prejudice to any other rights and remedies available to other Party
under this Agreement, the other Party may give written notice of such failure to the Indemnifying
Party and, if the Indemnifying Party has not cured such failure within sixty (60) days after
receipt of such notice, the other Party may take over such defense with counsel of its choosing, at
the Indemnifying Party’s cost and expense. The other Party may, at its option and expense,
participate in the Indemnifying Party’s defense at the other Party’s sole expense, and if the other
Party so participates, the Parties shall cooperate with one another in such defense. Gilead shall
have the right to extend the right to participate in and control, as applicable, any such defense
to its Affiliates and UTC, as Gilead in its sole discretion deems necessary to satisfy its
obligations under the URC License Agreement. The Indemnifying Party shall bear the total costs of
any court award or settlement of such claim or cause of action and all other costs, fees and
expenses related to the resolution thereof (including reasonable attorneys’ fees except for
attorneys’ fees for which the other Party is responsible if the other Party participates in the
Indemnifying Party’s defense of such claim or cause of action). In the event that the Parties
cannot agree as to the application of Sections 7.1(a) and (b) to any Gilead Claim or Company Claim,
as the case may be, the Parties may conduct separate defenses of such claim. In such case, each
Party further reserves the right to claim indemnity from the other in accordance with Sections
7.1(a) and (b) upon resolution of such underlying claim.

     7.3 Insurance Coverage. Each Party represents and warrants that it is covered and will
continue to be covered by a comprehensive general liability insurance program which covers all of
each Party’s activities and obligations hereunder in accordance with reasonable pharmaceutical
industry standards. Each Party will provide the other Party with a certificate of insurance and
other reasonable evidence of such insurance program upon the written request of the other Party.
Each Party will provide the other Party with written notice at least [***] days prior to any
cancellation or material change in such insurance program. Each Party will maintain such insurance
program, or other program with comparable coverage, beyond the expiration or termination of this
Agreement during the period in which any product or service is being commercially distributed or
sold, and for a commercially reasonable period thereafter.

     7.4 Indemnification Payment. Upon the final determination of liability and the amount of the
indemnification payment under this Section 7, the appropriate Party shall pay to the other in
immediately available funds, within thirty (30) business days after such determination, the amount
of any claim for indemnification made hereunder.

     7.5 Survival. The provisions of this Section 7 shall survive any termination of this
Agreement with respect to actions of the Parties during the term of the Agreement or the term of

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

18

 

any license to Company, whichever occurs later, except for Gilead’s indemnity obligation under
Section 7.1(a)(i), which shall survive only for the period set forth therein. Each Indemnified
Party’s rights under this Section 7 shall not be deemed to have been waived or otherwise affected
by such Indemnified Party’s waiver of the breach of any representation, warranty, agreement or
covenant contained in or made pursuant to this Agreement, unless such waiver expressly and in
writing also waives any or all of the Indemnified Party’s right under Section 7.

8. Confidentiality and Publicity.

     8.1 Proprietary Information; Exceptions. Each Party will maintain all Proprietary Information
of the other Party received by it under this Agreement in trust and confidence and will not
disclose any such Proprietary Information of the other Party to any Third Party or use any such
Proprietary Information of the other Party for any purposes other than those necessary or permitted
for performance under this Agreement without the express prior written permission of the other
Party. In particular, Company shall not use any Licensed Know-How for any purpose other than those
expressly licensed under Section 2.1 above. Each Party may use Proprietary Information of the
other Party only to the extent required to accomplish the purposes of this Agreement. Neither
Party shall use Proprietary Information of the other Party for any purpose or in any manner that
would constitute a violation of any laws or regulations, including without limitation the export
control laws of the United States. Neither Party shall use Proprietary Information of the other
Party in any form except as required to accomplish the intent of this Agreement. Neither Party
shall disclose Proprietary Information of the other Party to any employee, agent, consultant,
Affiliate, or sublicensee who does not have a need for such information. To the extent that
disclosure is authorized by this Agreement, the disclosing Party will obtain prior agreement, from
its employees, directors, agents, consultants, Affiliates, sublicensees or clinical investigators
to whom disclosure is permitted to be made, to obligations to hold in confidence and not make use
of such Proprietary Information of the other Party for any purpose other than those permitted by
this Agreement, that are at least as restrictive as those of this Section 8.1. Each Party will use
at least the same standard of care as it uses to protect its own Proprietary Information of a
similar nature to ensure that such employees, agents, consultants and clinical investigators do not
disclose or make any unauthorized use of Proprietary Information of the other Party, but no less
than reasonable care. Each Party will notify the other Party promptly upon discovery of any
unauthorized use or disclosure of the Proprietary Information of the other Party. For purposes of
this Agreement, Proprietary Information concerning the Covered Intellectual Property is deemed to
be the Proprietary Information of both Parties.

     Proprietary Information shall not include any information that the receiving Party can
demonstrate by competent written evidence:

          (a) is now, or hereafter becomes, through no act or failure to act on the part of the
receiving Party, its employees or contractors in breach hereof, generally known or available;

          (b) is known by the receiving Party at the time of receiving such information, as evidenced by
its contemporaneous written records;

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

19

 

          (c) is hereafter furnished to the receiving Party by a Third Party, as a matter of right and
without restriction on disclosure; or

          (d) is independently developed by the receiving Party without any breach of this Agreement, as
shown by independent, contemporaneous, written records.

     8.2 Authorized Disclosure. Notwithstanding any other provision of this Agreement, each Party
may disclose Proprietary Information if such disclosure:

          (a) is in response to a valid order of a court or other governmental body of the United States
or a foreign country, or any political subdivision thereof; provided, however, that the receiving
Party shall first have given notice to the other Party hereto to allow the other Party the
opportunity to obtain a protective order, with the reasonable cooperation of the receiving Party as
necessary, requiring that the Proprietary Information so disclosed be used only for the purposes
for which the order was issued;

          (b) is otherwise required by governmental law, rule or regulation, including without
limitation rules or regulations of the U.S. Securities and Exchange Commission, or by rules of the
National Association of Securities Dealers; provided, however, that the receiving Party shall first
have given notice to the other Party hereto in order to allow such Party the opportunity to seek
confidential treatment of the Proprietary Information; or

          (c) is otherwise necessary to prosecute or defend litigation or comply with applicable
governmental regulations or otherwise enforce obligations under this Agreement, but only to the
extent that any such disclosure is necessary for such enforcement.

     In addition, either Party may disclose Proprietary Information: (i) as required under any
Preexisting Agreement, (ii) to any bona fide potential or actual sublicensee of rights granted
under this Agreement, (iii) to any potential or actual corporate sponsor, (iv) to any Third Party
with which such Party has a bona fide potential or actual bona fide strategic alliance, joint
venture or other business relationship, (v) to any bona fide potential or actual source of funding,
(vi) to any bona fide potential or actual acquiror of the business of such Party, or (vii) as may
be reasonably necessary for such Party to exercise its rights and perform its obligations
hereunder, so long as in each case the recipient is subject to obligations of confidentiality at
least as protective as this Section 8.

     8.3 Return of Proprietary Information. In the event that any of the licenses granted to
Company pursuant to above 2.1 terminates or expires, Company shall, at Gilead’s election, promptly
return or destroy all Proprietary Information received by it from Gilead and shall certify in
writing to Gilead the completion thereof.

     8.4 Publicity. Company shall make no public announcement of this Agreement or the
relationship between the Parties without Gilead’s prior written consent. The Parties shall issue a
mutually agreed upon press release within [***] days after the Effective Date, such press release
to be substantially in the form set forth in Exhibit E attached to this Agreement.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

20

 

9. Term and Termination.

     9.1 Term. This Agreement and the licenses granted in Section 2.1 shall continue in full force
and effect, unless terminated sooner in their entirety in accordance with Section 9.2 below, or
until their expiration, on a country-by-country basis, upon the later of:

          (a) The expiration date of the last Valid Claim of the Licensed Patents in the country; or

          (b) Seven (7) years after the date of the first commercial sale of the last Licensed Product
to be introduced into the commercial marketplace.

     Upon expiration of this Agreement pursuant to this Section 9.1, Company shall have a fully
paid-up license hereunder.

     9.2 Termination Rights.

          (a) Termination for failure to make Payments. Gilead shall have the right to
terminate the license granted to Company hereunder in the event of the failure of Company to make
any payment specified in this Agreement when due in its entirety, which failure has continued for
[***] days after written notice of the failure is provided to Company, except that Gilead shall
have an immediate right of termination for failure to make the first Payment under Section 3.1 when
due and payable or for failure to issue the Warrant as set forth in Section 3.1. Such termination
shall be immediately effective upon the receipt by Company of written notice of termination from
Gilead.

          (b) Termination for Breach. Subject to Section 9.2(a), each Party shall have the
right to terminate this Agreement and its obligations hereunder for material breach by the other
Party, which breach remains uncured for [***] days after written notice of the breach is provided
to the breaching Party; provided, however, that any right of Gilead to terminate this Agreement in
the event Company, its Affiliates, assignees and sublicensees cease reasonable efforts towards
commercialization as set forth in Section 5.2 above, shall be governed by such Section 5.2.

          (c) Termination by Company. After receipt by Gilead of all of the Payments set forth
in Section 3.1 above, Company shall have the right to terminate this Agreement at any time for any
reason (or for no reason), with or without cause, by giving at least thirty (30) days’ prior
written notice thereof to Gilead.

     9.3 Rights Upon Termination. In the event of termination of this Agreement under Section 9.2
above (a) the licenses granted by Gilead to Company shall immediately terminate, (b) the license
granted by Company to Gilead to Company Improvements shall immediately terminate, and (c) all of
Company’s right, title and interest under the Transferred Assets shall immediately be reassigned to
and assumed by Gilead (provided, however, that Company will cooperate as reasonably necessary to
enable Gilead to comply with its obligations thereunder), in each case, with no further action or
notice required by either Party. Company hereby appoints Gilead as its attorney-in-fact to execute
such documents on its behalf if Gilead cannot obtain Company’s assistance with such execution after
using reasonable efforts. In the event of such

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

21

 

termination and if Gilead so requests, Company shall provide reasonable assistance to Gilead
for a period of [***] days following the date of notice of termination.

     9.4 Survival. All rights granted to and obligations undertaken by the Parties hereunder shall
terminate immediately upon the expiration or termination of this Agreement except for the accrued
rights and obligations of the Parties, which shall survive, and the following, which shall survive
according to their terms:

          (a) The indemnification obligations of Section 7;

          (b) The confidentiality and nondisclosure obligations of Section 8;

          (c) The obligations of the Parties under this Section 9; and

          (d) The provisions of Section 10, other than Section 10.4.

     In addition, termination of this Agreement shall not affect the remedies of the Parties
otherwise available at law or in equity in relation to any rights accrued under this Agreement
prior to this Agreement’s termination.

10. Miscellaneous.

     10.1 Independence of Parties. Nothing in this Agreement is intended or shall be deemed to
constitute a partnership, agency, joint venture or affiliate relationship between the Parties
hereto. This Agreement shall not constitute any Party the legal representative or agent of
another, nor shall any Party have the right or authority to assume, create, or incur any Third
Party liability or obligation of any kind, express or implied, against or in the name of or on
behalf of another except as expressly set forth in this Agreement.

     10.2 Applicable Law. This Agreement shall be governed and construed in accordance with the
laws of the State of California, excluding its choice of law rules.

10.3 Dispute Resolution.

          (a) The Parties recognize that disputes as to certain matters may from time to time arise
during the term of this Agreement which relate to either Party’s rights and/or obligations
hereunder or thereunder. It is the objective of the Parties to establish procedures to facilitate
the resolution of disputes arising under this Agreement in an expedient manner by mutual
cooperation and without resort to litigation. To accomplish this objective, the Parties agree to
follow the procedures set forth in this Section 10.3 if and when a dispute arises under this
Agreement. In the event of disputes between the Parties, a Party seeking to resolve such dispute
will, by written notice to the other Party, have such dispute referred to their respective
executive officers designated below or their successors, for attempted resolution by good faith
negotiations within [***] days after such notice is received. Said designated officers are as
follows:

For Company: [***]

For Gilead: [***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

22

 

     In the event the designated executive officers are not able to resolve such dispute, either
party may at any time after the [***] day period invoke the provisions of Section 10.3(b)
hereinafter.

          (b) Following settlement efforts pursuant to Section 10.3(a), any dispute, controversy or
claim arising out of or relating to the validity, construction, enforceability or performance of
this Agreement, including disputes relating to alleged breach or to termination of this Agreement
under Section 9, other than disputes which are expressly prohibited herein from being resolved by
this mechanism, shall be settled by binding Alternative Dispute Resolution (“ADR”) in the manner
described below:

                    (i) If a party intends to begin an ADR to resolve a dispute, such party shall provide written
notice (the “ADR Request”) to counsel for the other party informing such other party of such
intention and the issues to be resolved. From the date of the ADR Request and until such time as
any matter has been finally settled by ADR, the running of the time periods contained in Section
9.2 as to which party must cure a breach of this Agreement shall be suspended as to the subject
matter of the dispute.

                    (ii) Within [***] business days after the receipt of the ADR Request, the other party may, by
written notice to the counsel for the party initiating ADR, add additional issues to be resolved.

                    (iii) Disputes regarding the scope, validity and enforceability of Patents shall not be
subject to this Section 10.3, except for Section 10.3(a), and shall be submitted to a court of
competent jurisdiction.

          (c) The ADR shall be conducted pursuant to JAMS Comprehensive Arbitration Rules and Procedures
then in effect, except that notwithstanding those rules, the following provisions shall apply to
the ADR hereunder:

                    (i) The arbitration shall be conducted by a panel of three arbitrators (the “Panel”). The
Panel shall be selected from a pool of retired independent federal judges (and others who have
relevant experience in the pharmaceutical industry) to be presented to the Parties by JAMS. At
least one arbitrator on the Panel shall have relevant experience in the pharmaceutical industry.

                    (ii) The time periods set forth in the JAMS rules shall be followed, unless a party can
demonstrate to the Panel that the complexity of the issues or other reasons warrant the extension
of one or more of the time tables. In such case, the Panel may extend such time tables, but in no
event shall the time tables being extended so that the ADR proceeding extends more than [***]
months from its beginning to the Award. In regard to such time tables, the Parties (A) acknowledge
that the issues that may arise in any dispute involving this Agreement may involve a number of
complex matters and (B) confirm their intention that each party will have the opportunity to
conduct complete discovery with respect to all material issues involved in a dispute within the
framework provided above. Within such time frames, each party shall have the right to conduct
discovery in accordance with the Federal Rules of Civil

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

23

 

Procedure. The Panel shall not award punitive damages to either party and the Parties shall
be deemed to have waived any right to such damages. The Panel shall, in rendering its decision,
apply the substantive law of the State of California, without regard to its conflict of laws
provisions, except that the interpretation of and enforcement of this Section 10.3(c)(ii) shall be
governed by the Federal Arbitration Act. The Panel shall apply the Federal Rules of Evidence to
the hearing. Any proceeding initiated hereunder shall take place in Cook County, Illinois. The
fees of the Panels and JAMS shall be paid by the losing Party which shall be designated by the
Panel. If the Panel is unable to designate a losing party, it shall so state and the fees shall be
split equally between the Parties.

                    (iii) The Panel is empowered to award any remedy allowed by law, including money damages,
multiple damages, prejudgment interest and attorneys’ fee, and to grant final, complete, interim,
or interlocutory relief, including injunctive relief but excluding punitive damages.

                    (iv) Except as set forth in Section 10.3(c)(ii), above, each party shall bear its own legal
fees. The Panel shall assess its costs, fees and expenses against the party losing the ADR unless
it believes that neither party is the clear loser, in which case the Panel shall divide such fees,
costs and expenses according to the Panel’s sole discretion.

                    (v) The ADR proceeding shall be confidential and the Panel shall issue appropriate protective
orders to safeguard each Party’s Proprietary Information. Except as required by law, no party
shall make (or instruct the Panel to make) any public announcement with respect to the proceedings
or decision of the Panel without prior written consent of each other party. The existence of any
dispute submitted to ADR, and the award, shall be kept in confidence by the Parties and the Panel,
except as required in connection with the enforcement of such award or as otherwise required by
applicable law.

     The Parties agree that judgment on any arbitral award issued pursuant to this Section 10.3
shall be entered in any United States District Court of competent jurisdiction, and each Party
agrees to the co-exclusive personal jurisdiction of such courts for the purpose of entry of such a
judgment.

     10.4 Counterparts. This Agreement may be executed in any number of counterparts and may be
executed by facsimile. Each counterpart shall be deemed to be an original instrument, but all
counterparts shall collectively constitute one and the same Agreement.

     10.5 Notices. In any case where any notice or other communication is required or permitted to
be given hereunder, such notice of communication shall be in writing and sent by overnight express
or registered or certified mail (with return receipt requested) and shall be sent to the following
address (or such other address as any Party may designate from time to time in writing):

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

24

 

If to Company:

Archemix Corp.

One Hampshire Street

Cambridge, MA 02139

Telephone: (617) 621-7700

Telefax: (617) 621-9300

Attention: Marty Stanton, President

Copy to:

Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, PC

One Financial Place

Boston, MA 02111

Telephone: (617) 542-6000

Telefax: (617) 542-2241

Attention: Jeffrey M. Wiesen, Esq.

If to Gilead (except as provided in Section 4.1(a) above):

Gilead Sciences, Inc.

333 Lakeside Drive

Foster City, California 94404

Telephone: (650) 522-5756

Telefax: (650) 522-5488

Attention: Vice President, Corporate Development

Copy to:

Gilead Sciences, Inc.

333 Lakeside Drive

Foster City, California 94404

Telephone: (650) 522-5783

Telefax: (650) 522-5537

Attention: Vice President and General Counsel

     10.6 Force Majeure. Each of the Parties hereto shall be excused from the performance of its
obligations hereunder (except the payment of money) in the event such performance is prevented by
force majeure, provided that the non-performing Party promptly provides notice of the prevention to
the other Party. Such excuse shall be continued so long as the condition constituting force majeure
continues and the non-performing Party makes and continues to make reasonable efforts to remove or
overcome the condition. For the purposes of this Agreement, force majeure shall mean any act of
God, fire, casualty, flood, war, earthquake, strike, failure of public utilities, any act,
exercise, assertion or requirement of governmental authority, accident, epidemic, destruction of
facilities, or such other similar occurrences beyond the control of the Party whose performance is
affected.

     10.7 Limitation of Liability.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

25

 

          (a) Except for each Party’s Indemnity obligations set forth in Section 7 above and
excluding any measure of Damages available for enforcement of a Party’s intellectual property
rights, in no event shall either Party or its Affiliates be liable for any indirect, special,
exemplary, consequential or punitive damages, whether in contract, warranty, tort, strict liability
or otherwise, arising out of such Party’s performance or nonperformance under this Agreement, even
if it has been advised of the possibility of such damages.

          (b) Gilead’s cumulative liability for any and all claims, Damages or causes of action
relating to this Agreement in the aggregate, but excluding Damages payable pursuant to its
indemnity obligation set forth in Section 7.1(a) above, shall not exceed the amount of the
Payment received by Gilead from Company pursuant to Section 3.1 above. Company’s cumulative
liability for any and all claims, Damages or causes of action relating to this Agreement in the
aggregate, but excluding Damages paid or payable pursuant to its indemnity obligation set forth in
Section 7.1(b) above shall not exceed amounts payable by Company pursuant to Section
3.1. The existence of multiple claims will not enlarge these limits.

     10.8 Binding Effect: Assignment. This Agreement shall not be assigned, in whole or in part,
by either Party without the prior written consent of the other Party, which shall not be
unreasonably withheld, provided, however, that either Party may assign this Agreement in connection
with any merger, reorganization or sale of all or substantially all of its assets or capital stock
without the prior consent of the other Party, if: (a) the proposed assignor has provided prior
written notice of such assignment to the other Party, (b) the proposed assignee expressly agrees in
writing to assume all of the assignor’s rights and obligations under this Agreement, and (c) in the
event the assignor is Company, Company has paid all Payments under Section 3.1 above to Gilead
prior to such assignment. Any attempted assignment or transfer not in compliance with this Section
10.8 shall be null and void. This Agreement shall inure to the benefit of and be binding upon each
of the Parties hereto and their respective successors and permitted assigns.

     10.9 Entire Agreement. The terms and conditions herein contained and the Put Agreement and
the Warrant constitute the entire agreement between the Parties relating to the subject matter of
this Agreement and shall supersede all previous communications and agreements between the Parties
with respect to the subject matter of this Agreement, including without limitation the Confidential
Disclosure Agreement referred to in Section 1.24. Neither Party has entered into this Agreement in
reliance upon any representation, warranty, covenant or undertaking of the other Party that is not
set out or referred to in this Agreement.

     10.10 Attachments. All Exhibits and other attachments to this Agreement are by this reference
incorporated herein and made a part of this Agreement.

     10.11 Amendment. This Agreement may be varied, amended or extended only by the written
agreement of the Parties through their duly authorized officers or representatives, specifically
referring to this Agreement.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

26

 

     10.12 Severability. If any provision of this Agreement is found or declared to be invalid or
unenforceable by any court or other competent authority having jurisdiction, such finding or
declaration shall not invalidate any other provision hereof, and this Agreement shall thereafter
continue in full force and effect. In the event any such provision is so declared invalid or
unenforceable, the Parties shall negotiate an alternative provision that closely approximates the
Parties’ intent, to the extent allowable under law.

     10.13 Headings. All section titles or captions contained in this Agreement, in any Exhibit
referred to herein and the table of contents, if any, to this Agreement are for convenience only,
shall not be deemed a part of this Agreement and shall not affect the meaning or interpretation of
this Agreement.

     10.14 No Waiver of Rights. No failure or delay on the part of either Party in the exercise of
any power or right hereunder shall operate as a waiver thereof. No single or partial exercise of
any right or power hereunder shall operate as a waiver of such right or of any other right or
power. The waiver by either Party of a breach of any provision of this Agreement shall not operate
or be construed as a waiver of any other or subsequent breach hereunder.

     10.15 Remedies Cumulative: Specific Performance. All rights and remedies granted to either
Party under this Agreement are cumulative and in addition to, and not in lieu of, any other rights
or remedies otherwise available to such Party at law or in equity. The Parties agree that any
breach by either Party of, or failure of either Party to perform, any obligation under Section 8 of
this Agreement shall constitute immediate and irreparable damage to the other Party which cannot be
fully and adequately compensated in money damages and that, in the event of such breach or failure,
the other Party shall be entitled to injunctive relief and specific performance in addition to any
other remedies to which it may be entitled at law or in equity.

[Remainder of Page Intentionally Left Blank]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

27

 

     In Witness Whereof, the Parties hereto have caused this Agreement to be executed by
their duly authorized officers as of the date first written above.

	 	 	 	 	 
	Archemix Corp.	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 

	 	 

	 	 
	Name:
	 	 	 	 
	 

	 	 

	 	 
	Title:
	 	 	 	 
	 

	 	 

	 	 
	Date:
	 	 	 	 
	 

	 	 

	 	 
	 
	 	 	 	 
	Gilead Sciences, Inc.	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 

	 	 

	 	 
	Name:
	 	 	 	 
	 

	 	 

	 	 
	Title:
	 	 	 	 
	 

	 	 

	 	 
	Date:
	 	 	 	 
	 

	 	 

	 	 

License Agreement

Signature Page

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

Exhibit A

DOCUMENTATION

Binders

SELEX NON-PUBLIC PATENT APPLICATIONS

[***]       [***]

[***]       [***]

[***]       [***]

[***]       [***]

SELEX ARTICLES 1 (Contains one each of the articles from 1990 through 1996, listed on the file,
“SELEX Articles 1990-2001” found on the SELEX Package CDROM.)

SELEX ARTICLES 2 (Contains one each of the articles from 1997 through 2001, including the Draft
articles, listed on the file, “SELEX Articles 1990-2001” found on the SELEX Package CDROM.)

MISCELLANEOUS [***] I

[***]

Description:

[***] [***]

[***]

US Patent No. [***]

[***]

[***]

US Patent No. [***] (dated August 11, 1998)

US Patent No. [***] (dated November 14, 1995)

US Patent No. [***]dated November 11, 1997)

US Patent No. [***] (dated February 8, 2000)

[***]

US Patent No[***] is available on the Patents Referenced in Misc. [***] CDROM

[***]

Description:

[***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

1

 

           [***]

[***]

                [***]

[***]

                 [***]

[***]

[***]

                 [***]

US Patents [***]; [***]; [***] and [***] are available on the
Patents Referenced in Misc. [***] CDROM

[***]

US Patents [***]; [***] [***]; [***] and [***] are available on the
Patents Referenced in Misc. [***] CDROM
[***] [***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

Description:

[***]

                 [***]

[***]

                 [***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

[***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

A-2

 

[***]

[***]

European Patent No. [***] in both German and English

(Application dated September 14, 1993)

[***]

[***] (EP Patent Application No. [***] is available on the Patents Referenced
in Misc. [***] CDROM

[***]

     [***]

MISCELLANEOUS IP ISSUES 2

[***]

Description

Third New Divisional Application

[***]

[***]

[***]

[***]

[***]

[***]

AUDIT LETTERS

Description:

January 22, 2001

March 27, 2000

January 26, 2000

March 9, 1999

January 19, 1999

February 18, 1998

October 2, 1997

September 12, 1997

July 28, 1997

July 17, 1997

February 19, 1997

February 9, 1996

February 8, 1996

January 26, 1996

EMPLOYEE INVENTOR LIST FOR SELEX

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

3

 

Description:

[***]

COPY OF THE SELEX PROCESS CONFIDENTIAL BINDER (This document may also be found as “SELEX –
Confidential Description” on the SELEX Package CDROM.)

Booklets

COPY OF THE SELEX PROCESS NON-CONFIDENTIAL BOOKLET (This document may also be found as “The SELEX
Process – Non-Confidential” on the SELEX Package CDROM.)

Manuals

SELEX PROTOCOL MANUAL 1

SELEX PROTOCOL MANUAL 2

CDROMs

PATENTS REFERENCED IN MISCELLANEOUS [***]

SELEX PROTOCOL MANUAL

SELEX PACKAGE

EXHIBIT F

NEX [***]

NEX [***]

NEX [***]

NEX [***]

SELEX ARTICLES 1990 – 2001 (BIBLIOGRAPHY)

SELEX – CONFIDENTIAL DESCRIPTION

SELEX ARTICLE REPRINT – BOXES 1 – 16 (BIBLIOGRAPHY)

SELEX PROTOCOL MANUAL VOL. 1

SELEX PROTOCOL MANUAL VOL. 2

THE SELEX PROCESS – NON-CONFIDENTIAL

Boxes

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

A-4

 

     Sixteen (16) boxes containing one or more reprints of each article from the SELEX Articles binders.
(The contents of each box are listed on the file, “SELEX Article Reprint – Boxes 1-16.”)

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

A-5

 

Exhibit B

PREEXISTING AGREEMENTS

	1.	 	Restated Assignment and License Agreement, dated July 17, 1991, by and between University
Research Corporation and Gilead as successor in interest to NeXstar.
	 
	2.	 	[***] Agreement and [***] Agreement (including [***]), dated [***], between NeXagen, Inc. and
[***] (respectively, the “[***] Agreement” and the “[***] Agreement” and, collectively the
“[***]”).
	 
	3.	 	[***] Agreement, dated [***], between NeXstar and [***] (the “[***] Agreement”).
	 
	4.	 	[***] Agreement, dated [***], between NeXstar and [***] [***] (the “[***] Agreement”).
	 
	5.	 	[***] Agreement, dated [***], among Gilead, [***] and University Technology Corporation (the
“[***] Agreement”)
	 
	6.	 	Agreement, dated [***], between Gilead and [***].
	 
	7.	 	[***] Agreement, dated [***], among Gilead, NeXstar and [***] (including a [***] Amendment,
dated [***]) (the “[***] Agreement”).

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

B-1

 

Exhibit C

LICENSED PATENTS

[***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

C-1

 

Exhibit D

PATENTS EXCLUDED FROM SECTION 4.1

[***]

[***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

D-1

 

Exhibit E

PRESS RELEASE

	 	 	 
	ARCHEMIX CONTACT:

	 	GILEAD CONTACTS:
	Investors and Media

	 	Investors
	Martin Stanton

	 	Susan Hubbard
	(617) 621-7700

	 	(650) 522-5715
	 
	 

	 	Media
	 

	 	Amy Flood
(650) 522-5643

For Immediate Release

GILEAD LICENSES RIGHTS UNDER ITS SELEX AND

APTAMER PATENT ESTATE TO ARCHEMIX

Foster City, CA; and Cambridge, MA; October 23, 2001 – Gilead Sciences, Inc. (Nasdaq: GILD)
announced today that it has out-licensed its previously unlicensed intellectual property rights
under the SELEXTM (Systemic Evolution of Ligands through Exponential
Enrichment) process patent estate to Cambridge, MA-based Archemix Corporation.

Gilead will receive $17.5 million in cash, $9.0 million in 2001 and $8.5 million in 2002.
Additionally, Gilead will receive warrants in Archemix.

The agreement with Archemix provides exclusive rights to the SELEX process, including therapeutic
and other commercial applications to the extent not already licensed under pre-existing agreements.
Aptamers are three-dimensional oligonucleotides made through the SELEX process that bind to
molecular targets in a manner conceptually similar to antibodies. Aptamers, like antibodies, have
potential in a broad range of applications including therapeutic drug discovery and target
validation.

“The very broad SELEX patent estate significantly expands the scope of our discovery platform,”
said Martin Stanton, Ph.D., Archemix Founder and President. “Archemix is now positioned to use the
complete array of selection technologies to accelerate all steps in the drug discovery process. We
recognize that other companies have an interest in the SELEX technology and are looking forward to
establishing productive partnerships to enable applications outside our core business.”

Gilead Sciences will retain a non-exclusive right to utilize this technology for internal research
purposes.

“This deal is another important step for Gilead as we continue to focus solidly on our core
competencies,” said John Martin, Ph.D., President and Chief Executive Officer of Gilead

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

E-1

 

Sciences. “Because of their expertise in the field of oligonucleotides, Archemix is poised to
maximize the potential of this technology.”

About Archemix

Archemix Corporation (www.archemix.com), a privately held company located in Cambridge,
Massachusetts, is developing the RiboReporterTM platform to integrate all steps in drug
discovery. RiboReporters are molecular sensors created through the process of in vitro evolution
and can be used to build unique molecular profiling arrays that enable proteomic and metabolomic
analysis. RiboReporter-based cellular assays make it possible to follow proteins, metabolites, and
drugs in real time in live cells.

About Gilead Sciences

Gilead Sciences, Inc., headquartered in Foster City, CA, is an independent biopharmaceutical
company that seeks to provide accelerated solutions for patients and the people who care for them.
Gilead discovers, develops, manufactures and commercializes proprietary therapeutics for
challenging infectious diseases (viral, fungal and bacterial infections) and cancer. Gilead
maintains research, development or manufacturing facilities in the United States, Europe and
Australia. For more information on Gilead Sciences, please visit the company’s Web site at
www.gilead.com or call the Gilead Corporate Communications Department at 1-800-GILEAD-5
(1-800-445-3235).

# # #

SELEX is a trademark of Gilead Sciences, Inc.

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

E-2

 

Exhibit F

PROPRIETARY DUE DILIGENCE MATERIALS

Binders

	 	 	 	 	 
	REDACTED SELEX AGREEMENTS 1
	 	 	 	 
	 
	 	 	 	 
	University of Colorado
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4[***]5[***]6[***]7[***]8[***]9[***]10[***]11[***]12[***]13[***]14
	 	 	 	 
	 
	 	 	 	 
	Becton, Dickinson & Company
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4[***]5
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4[***]5[***]6
	 	 	 	 
	 
	 	 	 	 
	REDACTED SELEX AGREEMENTS 2
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4[***]5[***]6
	 	 	 	 
	 
	 	 	 	 
	Roche Molecular Systems
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]3[***]4[***]5
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	 
	 	 	 	 
	Description
	 	Tab
	[***]1[***]2[***]
	 	3

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

F-1

 

	 	 	 	 	 
	SELEX NON-PUBLIC PATENT APPLICATIONS
	 	 	 	 
	 
	 	 	 	 
	[***]               [***]
	 	 	 	 
	[***]               [***]
	 	 	 	 
	[***]     [***]
	 	 	 	 
	[***]     [***]
	 	 	 	 

SELEX ARTICLES 1 (Contains one each of the articles from 1990 through 1996,
listed on the file, “SELEX Articles 1990-2001” found on the SELEX Package CDROM.)

SELEX ARTICLES 2 (Contains one each of the articles from 1997 through 2001,
including the draft articles, listed on the file, “SELEX Articles 1990-2001” found on the
SELEX Package CDROM.)

	 	 	 	 	 
	MISCELLANEOUS [***] I
	 	 	 	 
	[***]
	 	 	 	 
	Description
	 	Tab
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	US Patent No. [***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	US Patent No. [***] (dated August 11, 1998)
	 	 	 	 
	US Patent No. [***] (dated November 14, 1995)
	 	 	 	 
	US Patent No. [***] (dated November 11, 1997)
	 	 	 	 
	US Patent No. [***] (dated February 8, 2000)
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	US Patent No. [***] is available on the Patents Referenced in Misc. [***] CDROM
	 	 	 	 
	 
	 	 	 	 
	ICT
	 	 	 	 
	Description
	 	Tab
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	US Patents [***] and [***] are available on the
Patents Referenced in Misc. [***] CDROM
	 	 	 	 
	 
	 	 	 	 
	[***]
	 	 	 	 
	US Patents [***] and [***] are available on the
Patents Referenced in Misc. [***] CDROM
	 	 	 	 
	[***] [***]
	 	 	 	 

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

F-2

 

	 	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	Description
	 	Tab
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	European Patent [***] in both German and English
(Application dated September 14, 1993)
	 	 	 	 
	[***]
	 	 	 	 
	[***] is available on the Patents Referenced
in Misc. [***] CDROM
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	MISCELLANEOUS [***] 2
	 	 	 	 
	[***]
	 	 	 	 
	Description
	 	Tab
	Third New Divisional Application
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	[***]
	 	 	 	 
	Audit Letters
	 	 	 	 
	Description
	 	Tab

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

F-3

 

	 	 	 	 	 
	January 22, 2001
	 	 	 	 
	March 27, 2000
	 	 	 	 
	January 26, 2000
	 	 	 	 
	March 9, 1999
	 	 	 	 
	January 19, 1999
	 	 	 	 
	February 18, 1998
	 	 	 	 
	October 2, 1997
	 	 	 	 
	September 12, 1997
	 	 	 	 
	July 28, 1997
	 	 	 	 
	July 17, 1997
	 	 	 	 
	February 19, 1997
	 	 	 	 
	February 9, 1996
	 	 	 	 
	February 8, 1996
	 	 	 	 
	January 26, 1996
	 	 	 	 

COPY OF THE SELEX PROCESS CONFIDENTIAL BINDER (This document may also be
found as “SELEX – Confidential Description” on the SELEX Package CDROM.)

Booklets

COPY OF THE SELEX PROCESS NON-CONFIDENTIAL BOOKLET (This document may also be
found as “The SELEX Process – Non-Confidential” on the SELEX Package CDROM.)

Manuals

SELEX PROTOCOL MANUAL 1

SELEX PROTOCOL MANUAL 2

CDROMs

PATENTS REFERENCED IN MISCELLANEOUS [***]

SELEX PROTOCOL MANUAL

SELEX PACKAGE

     Exhibit F

     NEX [***]

     NEX [***]

     NEX [***]

     NEX [***]

     SELEX Articles 1990 – 2001 (Bibliography)

     SELEX – Confidential Description

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

F-4

 

     SELEX Article Reprint – Boxes 1 – 16 (Bibliography)

     SELEX Protocol Manual Vol. 1

     SELEX Protocol Manual Vol. 2

     The SELEX Process – Non-confidential

Boxes

Sixteen (16) boxes containing one or more reprints of each article from the SELEX
Articles binders. (The contents of each box are listed on the file, “SELEX Article Reprint
– Boxes 1-16.”)

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

F-5

 

Exhibit G

REDACTED COPIES OF PREEXISTING AGREEMENTS

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

G-2

 

Exhibit H

WIRE TRANSFER INSTRUCTIONS

Wells Fargo Bank

San Francisco, CA

ABA:       [***]

Account:      Gilead Sciences, Inc.

Number:      [***]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

H-1

 

Exhibit I

FORM OF WARRANT

[Expired]

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

I-2

 

Table of Contents

	 	 	 	 	 
	 	 	PAGE
	Recitals
	 	 	 1	 
	1. Definitions
	 	 	 1	 
	2. License
	 	 	 5	 
	2.1 License Grants and Certain Restrictions
	 	 	5	 
	2.2 Negative Covenant of Company
	 	 	6	 
	2.3 Sublicensing Rights
	 	 	6	 
	2.4 Grant Back To Gilead
	 	 	7	 
	2.5 Assignment of Agreement and Delivery of Documentation
	 	 	7	 
	2.6 Assumed Liabilities
	 	 	8	 
	2.7 Modification of URC License Agreement.
	 	 	8	 
	3. Financial Terms
	 	 	 8	 
	3.1 Consideration
	 	 	8	 
	3.2 Payment Procedure
	 	 	9	 
	3.3 Third Party Payments
	 	 	9	 
	3.4 Taxes
	 	 	9	 
	4. Patent Prosecution, Maintenance and Enforcement
	 	 	 9	 
	4.1 Prosecution and Maintenance
	 	 	9	 
	4.2 Enforcement
	 	 	10	 
	4.3 Infringement of Third Party Rights
	 	 	11	 
	4.4 Reimbursement under Preexisting Agreements
	 	 	12	 
	5. Progress Report and Commercial Application
	 	 	12	 
	5.1 Progress Report
	 	 	12	 
	5.2 Commercial Application
	 	 	12	 
	6. Representations, Covenants and Warranties
	 	 	13	 
	6.1 Corporate Existence and Power
	 	 	13	 
	6.2 Authority and Binding Agreement
	 	 	13	 
	6.3 Additional Representations, Covenants and Warranties of Gilead
	 	 	13	 
	6.4 Additional Representations and Warranties of Company
	 	 	15	 
	6.5 Absence of Litigation
	 	 	16	 
	6.6 Survival of Warranties
	 	 	16	 

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

 

 

Table of Contents
(Continued)

	 	 	 	 	 
	 	 	PAGE
	6.7 Disclaimer of Warranties
	 	 	16	 
	7. Indemnification
	 	 	17	 
	7.1 Indemnity
	 	 	17	 
	7.2 Procedure
	 	 	18	 
	7.3 Insurance Coverage
	 	 	18	 
	7.4 Indemnification Payment
	 	 	19	 
	7.5 Survival
	 	 	19	 
	8. Confidentiality and Publicity
	 	 	19	 
	8.1 Proprietary Information; Exceptions
	 	 	19	 
	8.2 Authorized Disclosure
	 	 	20	 
	8.3 Return of Proprietary Information
	 	 	21	 
	8.4 Publicity
	 	 	21	 
	9. Term and Termination
	 	 	21	 
	9.1 Term
	 	 	21	 
	9.2 Termination Rights
	 	 	21	 
	9.3 Rights Upon Termination
	 	 	22	 
	9.4 Survival
	 	 	22	 
	10. Miscellaneous
	 	 	22	 
	10.1 Independence of Parties
	 	 	22	 
	10.2 Applicable Law
	 	 	22	 
	10.3 Dispute Resolution
	 	 	22	 
	10.4 Counterparts
	 	 	24	 
	10.5 Notices
	 	 	24	 
	10.6 Force Majeure
	 	 	25	 
	10.7 Limitation of Liability
	 	 	26	 
	10.8 Binding Effect: Assignment
	 	 	26	 
	10.9 Entire Agreement
	 	 	26	 
	10.10 Attachments
	 	 	26	 
	10.11 Amendment
	 	 	27	 
	10.12 Severability
	 	 	27	 

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

ii.

 

Table of Contents
(Continued)

	 	 	 	 	 
	 	 	PAGE
	10.13 Headings
	 	 	27	 
	10.14 No Waiver of Rights
	 	 	27	 
	10.15 Remedies Cumulative: Specific Performance
	 	 	27	 

Portions of this Exhibit were omitted and have been filed separatelyly with the Secretary of the Commission pursuant to the Company’s application requesting confidential treatment under Rule 406 of the Securities Act.

iii.

 

An extra section break has been inserted above this paragraph. Do not delete this section break if
you plan to add text after the Table of Contents/Authorities. Deleting this break will cause Table
of Contents/Authorities headers and footers to appear on any pages following the Table of
Contents/Authorities.

 

Portions
of this Exhibit were omitted and have been filed separately with the
Secretary of the Commission pursuant to the Company’s
application requesting confidential treatment under Rule 406 of
the Securities Act.

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