Document:

exv10w33

Exhibit 10.33

AMENDED AND RESTATED

COLLABORATION AND LICENSE AGREEMENT

     This Amended and Restated Collaboration and License Agreement (the “Agreement”)
is entered into and made effective as of July ___, 2006 (the “Effective Date”), by and between
Nuvelo, Inc., a Delaware corporation having its principal place of business at 201
Industrial Road, Suite 310, San Carlos, CA 94070 (“Nuvelo”), and Archemix Corp.,
a Delaware corporation having its principal place of business at 300 Third Street, Cambridge, MA
02142 (“Archemix”). Nuvelo and Archemix are sometimes referred to herein individually as a “Party”
and collectively as the “Parties.”

Recitals

     Whereas, the Parties entered into a Collaboration Agreement as of January 12, 2004
(the “Original Agreement”), for the purpose of identifying aptamers with anti-thrombin activity
(the terms and conditions contained therein, the “Original Terms”); and

     Whereas, the particular aptamer that was the original Development Compound (as
defined in the Original Agreement), ARC 183, has been withdrawn from Development; and

     Whereas, on March 4, 2006, Archemix initiated arbitration proceedings with Judicial
Arbitration and Mediation Services, Inc., New York (“JAMS”), Case No. 1425000626 (the
“Arbitration”), and Nuvelo submitted counterclaims on May 17, 2006; and

     Whereas, the Parties wish to revise their collaboration so that Archemix will be
responsible for the discovery of short-acting aptamers which bind to specifically defined protein
targets causing an anti-coagulation effect, and Nuvelo will have the exclusive right to develop and
commercialize aptamers so identified by Archemix; and

     Whereas, the Parties have by mutual agreement, agreed to supersede the terms of the
Original Agreement, with those set forth in this Agreement as of the Effective Date.

     Now, Therefore, the Parties agree as follows:

	1.	 	Definitions

     The following terms and those set forth in Exhibit A have the meanings set forth below or in
Exhibit A, as the case may be, as used in this Agreement:

     1.1 “Affiliate” means a person, corporation, partnership, or other entity that controls, is
controlled by or is under common control with a Party. For the purposes of this Section 1.1, the
word “control” (including, with correlative meaning, the terms “controlled by” or “under the common
control with”) means the actual power, either directly or indirectly through one or more
intermediaries, to direct the management and policies of such entity, whether by the ownership of
at least fifty percent (50%) of the voting stock of such entity, or by contract or otherwise.

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.

 

 

     1.2 “Allowable Commercialization Expenses” means those expenses incurred during the term of
this Agreement which are specifically attributable to the actual or contemplated Commercialization
of a specific Licensed Product(s), and shall consist of: (a) Costs of Goods; (b) Marketing, Sales
and Distribution Costs; (c) out of pocket costs to identify potential partners and to negotiate
Partnering Agreements; (d) all patent prosecution, maintenance and litigation expenses incurred
under Article 9 of this Agreement; (e) Post Launch Research and Development Expenses; (f) Allocated
Administrative Expenses; (g) the costs of engaging Third Parties to assist with Commercialization;
and (h) Currency Gains or Losses. “Allowable Commercialization Expenses” shall exclude Development
Costs.

     1.3 “Aptamer” means any oligonucleotide that binds to a target through means other than
Watson-Crick base-pairing.

     1.4 “ARC 2172” means the Aptamer having the nucleotide sequence set forth in Exhibit D.

     1.5 “Archemix Background Technology” means any Technology used by Archemix, or provided by
Archemix for use hereunder and/or which is otherwise necessary or useful for the Research,
Development, Commercialization, manufacture, importation or use of any Candidate Compound,
Development Compound or Licensed Product and that is (a) Controlled by Archemix as of the Effective
Date, (b) conceived or first reduced to practice by employees of, or consultants to, Archemix after
the Effective Date other than in the conduct of Research, Development or Commercialization, (c)
conceived or first reduced to practice in the conduct of Research, Development or Commercialization
and that constitutes SELEX Inventions or SELEX Technology, or (d) Archemix’s interest in all
Program Technology to the extent it is not Compound Technology.

     1.6 “Archemix Patent Rights” means Patent Rights Controlled by Archemix claiming or disclosing
Archemix Technology. For clarity, Archemix Patent Rights include all Licensed Patent Rights.

     1.7 “Archemix Product” has the meaning assigned in Section 12.2(a)(ii).

     1.8 “Archemix Program Technology” means any Program Technology that is conceived or first
reduced to practice by or through employees of, or consultants to, Archemix, alone or with any
Third Party, in the conduct of the Research, Development or Commercialization of Candidate
Compounds, Development Compounds or Licensed Products.

     1.9 “Archemix Technology” means, collectively, Archemix Background Technology, Archemix’s
interest in all Joint Technology, and Archemix Program Technology. “Archemix Technology” includes
the Compound Technology.

     1.10 “Bankrupt Party” has the meaning assigned in Section 16.2(a).

     1.11 “Candidate Compound” means an Aptamer that is a Short Acting Coagulation Cascade Aptamer
that is identified by Archemix in the course of its Research under this Agreement pursuant to an
approved Research Plan.

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.

 

 

     1.12 “Coagulation Cascade Protein” means a protein that is included on the list set forth in
Exhibit B.

     1.13 “Collaboration” means all activities performed by or on behalf of Nuvelo or Archemix in
the course of performing the activities described in, or fulfilling of their obligations pursuant
to, this Agreement.

     1.14 “Commercialization” or “Commercialized” means all activities that are undertaken prior
to, during or after completion of an NDA filing for a particular Licensed Product and that relate
to the commercial manufacture, marketing and sale of such Licensed Product including but not
limited to pre-commercialization, advertising, education, planning, marketing, promotion,
distribution, market and product support studies, and Phase 4 Trials.

     1.15 “Compound Patent Rights” means Patent Rights to the extent claiming (a) Compound
Technology or (b) ARC 2172.

     1.16 “Compound Technology” means any Program Technology developed solely by Archemix or which
is Joint Technology and in either case to the extent specifically disclosing the composition of
matter, formulation or use in the Field of a Short Acting Coagulation Cascade Aptamer that is or
was discovered or made by Archemix under this Agreement or the Original Agreement, including any
Candidate Compound, Development Compound or Licensed Product.

     1.17 “Confidential Information” has the meaning assigned to it in Section 10.1.

     1.18
“Contract Year” means (a) the period beginning on the Effective Date and ending on the
first anniversary of the last day of the calendar month in which the Effective Date falls and (b)
each succeeding twelve (12) month period thereafter.

     1.19 “Control” means, with respect to an item of Technology, a molecule or an intellectual
property right, that a Party owns or has a license to such item, to a Patent Right claiming such
molecule, or to such right and has the ability to disclose and grant a license or sublicense as
provided for in this Agreement under such item, Patent Right, or right without the payment of
additional consideration to, and without violating the terms of any agreement or other arrangement
with, any Third Party.

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

     1.21 “Develop” or “Development” means all activities with respect to a Development Compound or
Licensed Product relating to: (a) the preparation for and conducting of Phase 1 Trials, Phase 2
Trials, and Phase 3 Trials; (b) the filing and obtaining of Regulatory Approval for a Licensed
Product; and (c) all activities relating to developing the ability to manufacture Development
Compounds or Licensed Products. This includes, but is not limited to: (i) preclinical testing,
toxicology, formulation development, clinical studies, regulatory affairs and outside counsel
regulatory legal services; and (ii) manufacturing process development and scale up for bulk and
final forms of Development Compounds and Licensed Products, validation

3.

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.

 

 

documentation, all documentation generated in connection with the manufacturing or processing
activities and manufacturing and quality assurance technical support activities for such
Development Compounds or Licensed Products prior to first commercial sale.

     1.22 “Development Compound:”

          (a) means any Candidate Compound that is discovered or made by Archemix under the Original
Agreement or this Agreement and selected by Nuvelo for IND-enabling studies and designated by
Nuvelo as a Development Compound pursuant to Section 2.2 and 2.3 of this Agreement;

          (b) any compound Derived from a Development Compound, as defined in subsection (a) above,
under the Original Agreement or this Agreement that is a Short Acting Coagulation Cascade
Aptamer(for clarity, any such compound defined in this subsection (b) shall be designated as a
separate Development Compound under this Agreement); and

          (c) ARC 2172.

     1.23 “Development Costs:”

          (a) means the expenses incurred by Nuvelo or Archemix or for its account after the Effective
Date, and which are specifically attributable to the Development of Development Compounds and
Licensed Products, including, without limitation:

               (i) costs of preclinical design and evaluation of Candidate Compounds, Development Compounds
and Licensed Products, and costs of studies on the toxicological, pharmacokinetic, metabolic or
clinical aspects of Candidate Compounds, Development Compounds and Licensed Products (such costs
include the costs of any consultants or other Third Parties engaged by Nuvelo to conduct such
design or evaluation);

               (ii) costs of pre-IND studies including the manufacturing cost of preclinical supplies of
Candidate Compounds, Development Compounds and Licensed Products, including GMP materials;

               (iii) costs of conducting clinical trials on Development Compounds and Licensed Products
including the manufacturing cost of clinical supplies of the Development Compounds and Licensed
Products;

               (iv) costs of preparing, submitting, reviewing or developing data or information for the
purpose of submission to a Regulatory Authority to obtain approval to Commence Phase 1 Trials or to
obtain Regulatory Approval for Development Compounds and Licensed Products;

               (v) fees, including FDA user fees, associated with U.S. and foreign regulatory filings or
other U.S. and foreign governmental requirements related to Development Compounds and Licensed
Products;

4.

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.

 

 

               (vi) costs of Third Party licenses under Patents or other intellectual property rights
reasonably necessary to develop Development Compounds or Licensed Products or to commercialize
Licensed Products;

               (vii) external and internal costs of process development, manufacturing, quality assurance,
release testing, and clinical materials relating to Development Compounds or Licensed Products; and

               (viii) such other costs directly incurred in Development of Development Compounds or Licensed
Products.

          (b) Development Costs excludes Nuvelo’s and Archemix’s overhead expenses and FTE expenses, and
any FTE payments to Archemix hereunder, notwithstanding anything else in this Section 1.23.

          (c) Development Costs will be calculated on an accrual basis consistent with GAAP except for
the expenses incurred by Nuvelo in manufacturing clinical supplies of each Development Compound or
Licensed Compound, which will be calculated on a cash basis prior to the Commercialization of the
Development Compound or Licensed Compound.

     1.24 “Diligent Efforts” means the carrying out of obligations or tasks in a reasonable, good
faith, and diligent manner consistent with efforts and resources as commonly used in the
research-based biotechnology industry for a company of a similar size and a similar market
capitalization, for a therapeutic product at a similar stage of research, development or
commercialization, and having similar market potential, taking into account issues of safety,
efficacy, product profile, the costs to develop, the competitiveness of alternative products that
are or are expected to be in the relevant marketplace, the proprietary position of the product, the
regulatory structure and the likelihood of regulatory approval and product reimbursement, the
profitability of the product, and all other relevant commercial factors.

     1.25 “Drug Approval Application” means an application for Regulatory Approval required before
commercial sale or use of a Licensed Product as a drug in a regulatory jurisdiction.

     1.26 “EMEA” means the European Medicines Agency, or any successor thereof.

     1.27 “EMEA and Pricing Approval” means approval by the EMEA to sell a Licensed Product
together with pricing approval in at least one of France, Germany, Italy, Spain or United Kingdom.

     1.28 “FDA” means the United States Food and Drug Administration, or any successor federal
agency thereto.

     1.29 “Field” means the use of Short Acting Coagulation Cascade Aptamers to Modulate blood
clotting times in acute therapeutic applications, including but not limited to coronary artery
bypass graft surgery and percutaneous coronary intervention. “Field” [***]: (a) the
[***] of [***]; (b) [***] Aptamer [***] a [***]; (c) [***] Aptamers, [***], but not [***] to,

5.

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.

 

 

[***] and/or [***] of an Aptamer [***] of an Aptamer [***] as a [***]; or (d) [***] of a [***]
in [***] with a [***], where the[***] is [***] to [***] or [***] the [***] of the [***] [***] For
clarity, if any Short Acting Coagulation Cascade Aptamers Developed under this Agreement for use in
the “Field”, as described in the previous sentences, have additional therapeutic uses, those
additional therapeutic uses will also be considered part of the “Field.”

     1.30 “FTE” means the equivalent of one person working full time for one 12-month period in a
Research, Development, Commercialization, regulatory or other relevant capacity, for [***] hours
per year. For clarity, a single individual who works more than [***] hours in a single year shall
be treated as one FTE regardless of the number of hours worked.

     1.31 “FTE Reimbursement Rate” means the rate at which Nuvelo shall reimburse Archemix for
costs related to FTEs under this Agreement. Such costs shall cover all salary and benefits, and
facilities and infrastructure costs, travel expenses, laboratory supplies and materials used
internally by Archemix in fulfilling its obligations under this Agreement and all overhead charges
which are allocable to company departments based on space occupied or headcount or another
activity-based costing method and related to FTE obligations necessary for performance under this
Agreement. Such FTE Reimbursement Rate shall be $[***] per FTE. For clarity, each Party shall be
responsible, at its sole cost and expense, for paying the salaries and benefits of its employees.

     1.32 “Generic IP” has the meaning assigned in Section 5.7.

     1.33 “Gilead” means Gilead Sciences, Inc., a Delaware corporation with its principal offices
located at 333 Lakeside Drive, Foster City, California 94404.

     1.34 “Gilead-Archemix Agreement” means the License Agreement entered into by and between
Gilead and Archemix dated October 23, 2001, as amended September 4, 2003.

     1.35 “IND” means: (a) an Investigational New Drug Application as defined in the Federal Food,
Drug and Cosmetic Act (“FDCA”) and regulations promulgated thereunder or any successor application
or procedure required to initiate clinical testing of a Development Compound and/or Licensed
Product 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 Compound and/or Licensed Product in humans in such country or
region; and (c) all supplements and amendments to any of the foregoing.

     1.36 “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 [***] other [***], the
[***] of the [***] or Aptamers or[***] through the [***] of the [***] in the [***] or [***]: (a)
[***] of a [***], (i) of a [***] in a [***], often to [***] or [***] of a [***], or to [***] for
[***](ii) of a [***] or other [***] in a [***], often to [***]or [***] the [***] of a [***], or
[***] in a [***] or [***]and (iii) of [***] (as in [***]; (b) of a [***] on a [***] such as [***]
(as in [***] or other [***] of [***] within [***]; and (c) any [***] in vitro diagnostic [***] of
the [***] or Aptamers or [***] through the [***] of the [***] in

6.

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.

 

 

[***]
for example, [***] and [***], and the [***] of [***] of Aptamer [***]: (i) to [***],
through [***] in [***] or [***] of [***], and to [***] are [***] for the [***] of [***]; (ii) to
[***] of [***] in a [***] of [***] in [***](iii) to [***] or [***] in[***] to [***] during [***]
(e.g., as [***] of [***] or [***]; and (iv) to [***] or [***] in [***] to [***] (e.g., as [***] of
[***] or [***]

     1.37 “Indemnitees” has the meaning assigned in Section 14.1.

     1.38 “Internal FTE” means an FTE performing activities related to the Collaboration by
Archemix or its Affiliate(s).

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

     1.40 “Joint Management Committee” or “JMC” means the committee described in Section 3.2.

     1.41 “Joint Patent Rights” means Patent Rights claiming Joint Technology.

     1.42 “Joint Technology” means any Program Technology jointly conceived or reduced to practice
by employees of or consultants to Nuvelo and employees of or consultants to Archemix under this
Agreement. For clarity, any jointly developed Technology that is SELEX Technology or SELEX
Inventions shall not be considered Joint Technology regardless of which Party conceived or reduced
to practice such Technology or Inventions.

     1.43 “Licensed Patent Rights” means any Archemix Patent Rights (a) to the extent claiming any
Compound Technology, Candidate Compound, Development Compound or Licensed Product or the
manufacture thereof or the use thereof in the Field, or (b) that are necessary or useful for Nuvelo
to exercise the relevant licenses granted to it pursuant to Article 5. For clarity, the Licensed
Patent Rights shall exclude any Patent Rights that relate to the SELEX Inventions or the SELEX
Technology and shall include, without limitation, the following United States Patents and their
counterparts throughout the world to the extent not SELEX Inventions or SELEX Technology: 6,334,318
B1; 5,476,766; 5,543,293; 5,582,981; 5,688,291; 5,817,785; 5,840,867; and 6,331,398 B1.

     1.44 “Licensed Product” means a product that comprises, consists of, or which incorporates a
Development Compound regardless of its formulation or mode of administration; provided, that, any
Aptamer contained therein is a Short Acting Coagulation Cascade Aptamer, and provided, further,
that such Short Acting Coagulation Cascade Aptamer is not formulated, modified or administered such
that the Short Acting Coagulation Cascade Aptamer or the Licensed Product does not demonstrate the
short acting characteristics set forth in Exhibit C. For clarity, and without limitation, a
Licensed Product shall not include any pegylated Aptamer.

     1.45 “Licensed Technology” means any Archemix Technology that (a) specifically relates to any
Candidate Compound, Development Compound or Licensed Product relevant to the license grant, or (b)
is necessary or useful for Nuvelo to exercise the relevant licenses granted to it pursuant to
Article 5.

7.

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.

 

 

     1.46 “Licensing Revenue” means any and all forms of consideration that Nuvelo or any Nuvelo
Affiliate receives directly or indirectly from a Third Party Partner in connection with a
Partnering Agreement, which may include upfront license fees, annual license or maintenance
payments, milestone payments, royalties, imputed income on interest-free loans received from such
Third Party Partner, the portion of an equity investment in Nuvelo or a Nuvelo Affiliate that is
greater than the fair market value of Nuvelo’s or its Affiliate’s stock sold in such investment at
the time of sale and other similar payments; but Licensing Revenue shall exclude any of the
following amounts received by Nuvelo or its Affiliates under a Partnering Agreement: (a) an equity
investment by such Third Party (but solely to the extent that such investment is at a price equal
to or less than the fair market value of Nuvelo’s or its Affiliate’s stock sold in such investment
at the time of sale); (b) a loan at reasonable interest rates for work required to be performed by
Nuvelo and directed to the Development or Commercialization of Licensed Products subject to the
Agreement; (c) research and development support (at a reasonable FTE value); (d) reimbursement of
patent prosecution, maintenance, enforcement or defense expenses; or (e) payments directly
attributable to supplying goods (at no more than one hundred twenty-five percent (125%) of actual
manufacturing cost) or services to such Third Party Partner to enable the commercialization of the
Licensed Product that is subject to the Partnering Agreement.

     1.47 “Losses” has the meaning assigned in Section 14.1.

     1.48 “MHLW” means the Ministry of Health, Labor and Welfare, otherwise referred to as
“Korosho” or any successor thereto, which governs the scientific review of human pharmaceutical
products in Japan.

     1.49 “Minimum FTE Funding Requirement” has the meaning assigned to it in Section 2.4.

     1.50 “Modulate” or “Modulation” means the inhibition or activation of a Coagulation Cascade
Protein using a Short Acting Coagulation Cascade Aptamer. As used in this definition, “inhibition”
means either (a) inhibition at a therapeutically useful level of a Short Acting Coagulation Cascade
Aptamer by binding of a Short Acting Coagulation Cascade Aptamer to a pre-selected Coagulation
Cascade Protein or (b) inhibition at a therapeutically useful level of a Short Acting Coagulation
Cascade Aptamer of a second pre-selected Coagulation Cascade Protein by binding at a
therapeutically useful level of a Short Acting Coagulation Cascade Aptamer to a first pre-selected
Coagulation Cascade Protein. As used in this definition, “activation” means either (a) activation
at a therapeutically useful level of a Short Acting Coagulation Cascade Aptamer by binding of a
Short Acting Coagulation Cascade Aptamer to a pre-selected Coagulation Cascade Protein or (b)
activation at a therapeutically useful level of a Short Acting Coagulation Cascade Aptamer of a
second pre-selected Coagulation Cascade Protein by binding at a therapeutically useful level of a
Short Acting Coagulation Cascade Aptamer to a first pre-selected Coagulation Cascade Protein.

     1.51 “NDA” means a New Drug Application submitted and filed with the FDA or the equivalent
application or filing filed with any equivalent agency or government authority outside of the
United States (including any supra-national agency such as in the European Union) necessary for
approval of a drug in such jurisdiction.

8.

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.

 

 

     1.52 “Net Sales:”

          (a) means the gross amount invoiced by Nuvelo or its Affiliate or a licensee or sublicensee
(at any level, including a sublicensee of a sublicensee) for sales of Licensed Products to a Third
Party (other than a Third Party Partner or a licensee or sublicensee) less, to the extent included
within the gross amount invoiced to and paid by the customer, deductions for: (i) transportation,
and customs clearance, duty charges and insurance relating to such transportation; (ii) sales and
excise taxes, customs and any other governmental charges, all to the extent imposed upon the sale
of the Licensed Products and paid by the selling party; (iii) distributors fees, rebates or
allowances actually granted or allowed, including government and managed care rebates; (iv)
quantity discounts, cash discounts or chargebacks actually granted, allowed or incurred in the
ordinary course of business in connection with the sale of the Licensed Products; and (v)
allowances or credits to customers, not in excess of the selling price of the Licensed Products, on
account of governmental requirements, rejection, recalls or return of the Licensed Products.

          (b) Solely for the purpose of calculating Net Sales of Licensed Products, if a Party or its
Affiliate, or a licensee or sublicensee, sells such Licensed Products in the form of a combination
product containing any such Licensed Product and one or more active ingredients or a delivery
device (whether combined in a single formulation or package, as applicable, or formulated or
packaged separately but sold together for a single price) (a “Combination Product”), Net Sales of
such Combination Product for the purpose of determining the royalty due to the other Party pursuant
to Sections 7.4(b)(i) and/or 12.2(b) will be calculated by multiplying actual Net Sales of such
Combination Product as determined in subsection (a) above by the fraction A/(A+B) where A is the
invoice price of such Licensed Product if sold separately, and B is the total invoice price of the
other active ingredient(s) or the delivery device in the combination if sold separately. If, on a
country-by-country basis, such other active ingredient or ingredients or delivery device in the
Combination Product are not sold separately in such country, but the Licensed Product component of
the Combination Product is sold separately in such country, Net Sales for the purpose of
determining royalties due to the other Party pursuant to Sections 7.4(b)(i) and/or 12.2(b) for the
Combination Product shall be calculated by multiplying actual Net Sales of such Combination Product
as determined in subsection (a) above by the fraction A/C where A is the invoice price of such
Licensed Product component if sold separately, and C is the invoice price of the Combination
Product. If, on a country-by-country basis, such Licensed Product component is not sold separately
in such country, Net Sales for the purposes of determining royalties due to the other Party
pursuant to Sections 7.4(b)(i) and/or 12.2(b) for the Combination Product shall be D/(D+E) where D
is the fair market value of the portion of the Combination Products that contains the Licensed
Product and E is the fair market value of the portion of the Combination Products containing the
other active ingredient(s) or delivery device included in such Combination Product as such fair
market values are determined by mutual agreement of the Parties.

     1.53 “Nuvelo Background Technology” means any Technology that is (a) Controlled by Nuvelo as
of the Effective Date or (b) conceived or first reduced to practice by Nuvelo after the Effective
Date other than in the conduct of Research, Development or Commercialization, and in either case is
necessary or useful for the Research, Development, Commercialization, manufacture, importation, use
or sale of Candidate Compounds, Development Compounds or

9.

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.

 

 

Licensed Products under this Agreement. Nuvelo Background Technology does not include Nuvelo
Program Technology or Nuvelo’s interest in Joint Technology. For clarity, any Program Technology
that is SELEX Technology or SELEX Inventions shall not be considered Nuvelo Background Technology
regardless of which Party conceived or reduced to practice such Technology or Inventions.

     1.54 “Nuvelo IPO Share Amount” means that number of shares of Archemix Common Stock equal to
the lesser of (a) Ten Million Dollars ($10,000,000) divided by the IPO Price or (b) fifteen percent
(15%) of the total gross offering proceeds (prior to underwriter commissions and expenses) raised
by Archemix in the Qualified IPO divided by the IPO Price.

     1.55 “Nuvelo Patent Rights” means Patent Rights Controlled by Nuvelo claiming or disclosing
Nuvelo Technology.

     1.56 “Nuvelo Product” has the meaning assigned to it in Section 12.2(a)(i).

     1.57 “Nuvelo Program Technology” means any Program Technology that is conceived or first
reduced to practice by or through employees of, or consultants to, Nuvelo, alone or with any Third
Party, in the conduct of the Research, Development or Commercialization of Candidate Compounds,
Development Compounds or Licensed Products. For clarity, any Program Technology that is SELEX
Technology or SELEX Inventions shall not be considered Nuvelo Program Technology regardless of
which Party conceived or reduced to practice such Technology or Inventions.

     1.58 “Nuvelo Technology” means, collectively, Nuvelo Background Technology, Nuvelo Program
Technology, and Nuvelo’s interest in all Joint Technology.

     1.59 “Partnered Product” means a Licensed Product that is the subject of a Partnering
Agreement.

     1.60 “Partnering Agreement” means an executed and in-force written agreement between Nuvelo
and a Third Party or between a Third Party Partner and another Third Party, wherein such Third
Party is granted the right to Develop or Commercialize, alone or in collaboration with Nuvelo or
another Third Party Partner, a Licensed Product.

     1.61 “Patent Rights” means the rights and interests in and to (a) a pending application for a
patent anywhere in the world, including without limitation any provisional, converted provisional,
continued prosecution application, substitution, continuation, divisional or continuation-in-part
thereof; (b) any patent issuing on any of the foregoing, including any inventor’s certificate, that
has not expired or been declared invalid by a court from which no appeal can be or has been taken;
or (c) any extension, renewal, reissue or reexamination of any of the foregoing.

     1.62 “Phase 1 Trial” means that portion of the clinical development program that generally
provides for the first introduction into humans of a product with the primary purpose of
determining safety, metabolism and pharmacokinetic properties and clinical pharmacology of the

10.

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.

 

 

product, and that is consistent with 21 CFR §312.21(a) or the applicable rules and regulations of
the jurisdiction in which the clinical trial is conducted.

     1.63 “Phase 2 Trial” means that portion of the clinical development program that provides for
a clinical trial of a product on patients, which may include pharmacokinetic studies, the principal
purpose of which is to make a preliminary determination that such product is safe for its intended
use, to determine potential doses and to obtain sufficient information about such product’s
efficacy to permit the design of further clinical trials, and that is consistent with 21 CFR
§312.21(b) or the applicable rules and regulations of the jurisdiction in which the clinical trial
is conducted.

     1.64 “Phase 3 Trial” means that portion of the clinical development program that provides for
a pivotal human clinical trial of a product, which trial is designed to: (a) establish that a
product is safe and efficacious for its intended use; (b) define warnings, precautions and adverse
reactions that are associated with the product in the dosage range to be prescribed; and (c)
support Regulatory Approval of such product; and which trial is consistent with 21 CFR §312.21(c)
or the applicable rules and regulations of the jurisdiction in which the clinical trial is
conducted.

     1.65 “Phase 4 Costs” means all expenses incurred by either Party or for its account, and
specifically attributable to: (a) direct support of the performance of a Phase 4 Trial for a
Licensed Product; or (b) process development for a Licensed Product in a Phase 4 Trial. All Phase
4 Costs shall be treated as Post Launch R&D Expenses in accordance with Exhibit A.

     1.66 “Phase 4 Trial” means a clinical trial of a Licensed Product commenced in a particular
country after receipt of Regulatory Approval in such country in order to support commercialization
of the Licensed Product.

     1.67 “Product Profit and Loss” means the profits or losses resulting from the
Commercialization of Licensed Products and is equal to Net Sales plus Licensing Revenue less
Allowable Commercialization Expenses.

     1.68 “Program Target” means a Coagulation Cascade Protein identified in Exhibit B that is the
subject of an approved Research Plan.

     1.69 “Program Technology” means any Technology that is generated, conceived or first reduced
to practice (actively or constructively) by either Party or both Parties in the conduct of the
Research, Development or Commercialization of Candidate Compounds, Development Compounds or
Licensed Products.

     1.70 “Qualified IPO” means Archemix’s firm commitment underwritten initial public offering 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
Archemix Common Stock, with total gross offering proceeds to Archemix (prior to underwriter
commissions and expenses) of at least thirty million dollars
($30,000,000) exclusive of the dollar value
represented by the Nuvelo IPO Share Amount.

11.

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.

 

 

     1.71 “Radio Therapeutic Aptamer” 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.

     1.72 THIS SECTION LEFT INTENTIONALLY BLANK.

     1.73 “Regulatory Approval” means any and all approvals (including supplements, amendments,
pre- and post-approvals, pricing and reimbursement approvals), licenses, registrations or
authorizations of any national, supra-national (e.g., the European Commission or the Council of the
European Union), regional, state or local regulatory agency, department, bureau, commission,
council or other governmental entity, that are necessary for the manufacture, distribution, use or
sale of a Licensed Product in a regulatory jurisdiction.

     1.74 “Regulatory Authority” means the FDA or any counterpart of the FDA outside the United
States, or 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 or clinical testing or
sale of a Licensed Product.

     1.75 “Regulatory Documentation” means, with respect to a Licensed Product, all regulatory
filings and supporting documents created, submitted to the FDA or any equivalent agency or
government authority outside of the United States (including any supra-national agency such as in
the European Union) relating to such product, and all data contained therein, including, without
limitation, any IND(s), NDA(s), Biologics License Application(s) (“BLA(s)”), Investigator’s
Brochures, Drug Master File(s) , correspondence to and from the FDA or any equivalent agency or
governmental authority outside of the United States, minutes from teleconferences with Regulatory
Authorities, registrations and licenses, regulatory drug lists, advertising and promotion documents
shared with Regulatory Authorities, adverse event files, complaint files and manufacturing records.

     1.76 “Regulatory Filing” means the NDA, BLA, IND, or any foreign counterparts thereof and any
other filings required by Regulatory Authorities relating to the study, manufacture or
commercialization of any Licensed Product.

     1.77 “Research” means: (a) the discovery and identification of Candidate Compounds for use
within the Field; (b) the biological characterization (including, without limitation, preclinical
activities such as in vivo analysis) of such Candidate Compounds; and (c) any other activities
related to the Field specified in an approved Research Plan, in each case which are to be conducted
pursuant to this Agreement.

     1.78 “Research Plan” means the written plan describing the Research and any other activities
to be carried out by the Parties during each Contract Year during the Term of this Agreement as
such written plan may be amended, modified or updated in accordance with the

12.

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.

 

 

terms of this Agreement. Each Research Plan shall include a budget and shall specify the
number of FTEs to be utilized by Archemix.

     1.79 “Research Program Term” means the period during which Archemix shall be obligated to
conduct Research on Nuvelo’s behalf hereunder. The Research Program Term shall begin on the
Effective Date and end on the last day of the third Contract Year or such later date as the Parties
may mutually agree in writing; provided, that, if this Agreement is terminated prior to the end of
the Research Program Term, the effective date of termination shall be the last day of the Research
Program Term.

     1.80 “Royalty Period” has the meaning assigned to it in Section 7.4(b)(iii).

     1.81 “SELEX Inventions” means any and all inventions, including any improvements, made solely
by employees or independent contractors of one Party, or jointly by employees or independent
contractors of each Party, in the course of the Party’s or Parties’ performance under this
Agreement, specifically relating to the SELEX Technology.

     1.82 “SELEX Portfolio” means those Patent Rights licensed by Gilead to Archemix pursuant to
the Gilead-Archemix Agreement.

     1.83 “SELEX Technology” means any Technology or process for identifying, modifying, optimizing
and/or stabilizing an Aptamer, whether (i) existing as of the Effective Date or invented
thereafter. For clarity for the purposes of this Section 1.83: (i) the process of “identifying”
includes, without limitation, any process which is disclosed in or falls within the claimed scope
of U.S. Patent Nos. 5,270,163 or 5,843,653 “); and (ii) the processes of “modifying”, “optimizing”
and “stabilizing” include, without limitation, minimization, truncation, conjugation, pegylation,
complexation, substitution, and deletion and/or incorporation of modified nucleotides. “SELEX
Technology” and “SELEX Inventions” does not include any Compound Technology.

     1.84 “Short Acting Coagulation Cascade Aptamer” means ARC 2172 and any other Aptamer that: (a)
binds to a pre-selected Coagulation Cascade Protein identified on Exhibit B; (b) Modulates the
blood coagulant function of any Coagulation Cascade Protein identified on Exhibit B; and (c)
demonstrates the short-acting characteristics and limitations that are set forth in Exhibit C. For
clarity, Short Acting Coagulation Cascade Aptamers do not include [***] Nothing in this Section
1.84 will be interpreted to exclude an Aptamer from the definition of “Short Acting Coagulation
Cascade Aptamer” if it Modulates functions other than the blood coagulant function of a Coagulation
Cascade Protein; provided, that, it Modulates the blood coagulant function of a Coagulation Cascade
Protein.

     1.85 “SomaLogic Agreements” means the [***] by and between [***] and [***], the [***] between
[***] and [***], and the [***]

     1.86 “Technology” means, collectively, inventions, discoveries, improvements, trade secrets,
proprietary materials 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; (b) compositions of matter, data, formulations, processes,

13.

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.

 

 

techniques, know-how and results (including any negative results); and (c) any proprietary
data, instructions, processes, methods, formulae, materials, expert opinions and information
including, without limitation, biological, chemical, pharmacological, toxicological,
pharmaceutical, physical and analytical, clinical, safety, manufacturing and quality control data
and information in the Control of a Party either prior to or during this Agreement that relates in
any way to Research or Development activities.

     1.87 “Term” has the meaning assigned to it in Section 11.

     1.88 “Third Party” means any entity other than: (a) Nuvelo; (b) Archemix; or (c) an Affiliate
of either of them.

     1.89 “Third Party Partner” means a Third Party that has entered into a Partnering Agreement.

     1.90 “Third Party Royalty” has the meaning assigned to it in Section 7.4(b)(ii).

     1.91 “Title 11” has the meaning assigned to it in Section 16.2(a).

     1.92 “ULEHI Agreement” means the [***] and [***] by and between [***] and [***] to the [***]

     1.93 “URC License Agreement” means the [***] and [***], by and between [***] and [***]

     1.94 “UTC” means [***], the [***] to the[***]

     1.95 “Valid Claim” means (a) any claim of a pending patent application which has been pending
for a period of less than five (5) years from the date of issuance of a first patent office
communication during examination of the first application related thereto, and shall not have been
earlier cancelled, withdrawn or abandoned on a country-by-country basis, or (b) an issued unexpired
patent that (i) has not been finally cancelled, withdrawn, abandoned or rejected by any
administration agency or other body of competent jurisdiction, (ii) 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, (iii) has not been rendered unenforceable through disclaimer or otherwise, and (iv) is not
lost through an interference proceeding.

	2.	 	Research

     2.1 Research Overview. Archemix will conduct Research in the Field in accordance with an
approved Research Plan to generate Candidate Compounds during the Research Program Term. The
Parties will prepare a Research Plan for Nuvelo’s approval for the initial twelve (12) months of
the Research Program Term within sixty (60) days of the Effective Date. For the second and third
years of the Research Program Term the Parties shall prepare an updated Research Plan for
discussion by the JMC and approval by Nuvelo at least ninety (90) days prior to the first and
second anniversaries of the Effective Date. Each Research Plan will include, without limitation,
(a) a prioritized list of the Coagulation Cascade Protein targets for which

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.

 

 

Archemix will generate Aptamers; (b) a target product profile for Short Acting Coagulation Cascade
Aptamers to meet for each Coagulation Cascade Protein pursued so that such Aptamers can be
considered as Candidate Compounds; and (c) a proposed work plan and resource allocation plan.

     2.2 Diligence. The Parties will use Diligent Efforts to conduct their respective tasks
throughout the Term, and will conduct all Research, Development and Commercialization activities in
good scientific manner, and in compliance in all material respects with the requirements of
applicable laws, rules and regulations, to attempt to achieve their objectives efficiently and
expeditiously. Without limiting the generality of the foregoing:

          (a) Nuvelo will: (i) determine whether any Candidate Compounds should be designated as
Development Compounds, and (ii) use Diligent Efforts to Develop, manufacture and Commercialize at
least one (1) Development Compound and related Licensed Product for use in the Field.

          (b) Archemix will use Diligent Efforts to conduct Research and Nuvelo will use Diligent
Efforts to evaluate in good faith and decide in a timely manner whether to designate Candidate
Compounds as Development Compounds following receipt of all data requested by Nuvelo with regard to
Candidate Compounds and to Develop and Commercialize any Development Compound or Licensed Product.

     2.3 Designation of Candidate Compounds and Development Compounds. Nuvelo will have the sole
right to designate a Candidate Compound as a Development Compound based on whether the Candidate
Compound meets the relevant target product profile established by Nuvelo and set forth in the
Research Plan or as subsequently modified by Nuvelo in good faith and communicated in writing to
Archemix.

     2.4 FTE Funding. Nuvelo shall pay Archemix a minimum of One Million Seven Hundred Fifty
Thousand Dollars ($1,750,000) per Contract Year (the “Minimum FTE Funding Requirement”) for
Archemix Internal FTEs dedicated to conducting Research or any Development activities in accordance
with Research Plans approved by Nuvelo, and any other activities conducted in accordance with an
approved Research Plan or in conducting Development activities approved in writing by Nuvelo. For
clarity, the Minimum FTE Funding shall be paid to Archemix regardless of whether or not (a) a
Research Plan has been approved by Nuvelo or (b) the number of FTEs contemplated by the Minimum FTE
Funding Requirement are utilized in any Contract Year; provided, that, to the extent that Nuvelo
provides Archemix with a Research Plan that calls for Archemix Internal FTEs up to the Minimum FTE
Funding Requirement for the purpose of conducting Research or Development in the Field, Archemix
shall be required to provide the services of such FTEs as a condition to its entitlement to the
Minimum FTE Funding Requirement. To the extent that Nuvelo requires Archemix Internal FTEs above
the amount contemplated by the Minimum FTE Funding Requirement such obligation to provide these
additional FTE’s shall come only with (i) Archemix’s prior written consent and (ii) as part of an
approved Research Plan. Unless otherwise stated herein, Nuvelo will have no other obligation to
reimburse Archemix for any expenses Archemix incurs in connection with Archemix’s performance of
Research under this Agreement. Notwithstanding any other provision hereof: (y) Archemix will have
no obligation to engage any Third Party in

15.

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.

 

 

its performance of the Research hereunder, and Nuvelo will have no obligation to reimburse Archemix
for any such Third Party engagement, unless Nuvelo agrees in writing to reimburse Archemix for the
costs associated with such Third Party contracts, and (z) Archemix shall have no obligation to
perform any activities not identified in an agreed Research Plan, and Nuvelo will have no
obligation to reimburse Archemix for any such activities. Nuvelo will have no on-going obligation
to fund any Research by Archemix after the expiration of the Research Program Term.

	3.	 	Management of the Collaboration

     3.1 Overall Management Structure. The Joint Management Committee (“JMC”) will be established
as set forth below and will be responsible for reviewing the Research Plan, and all amendments
thereto, under this Agreement as further described below. If Archemix exercises its Profit Share
Option (as defined below), then the responsibility of the JMC will expand to include Nuvelo’s
sharing of information relating to its Commercialization activities with respect to a particular
Development Compound, and the Licensed Products relating thereto, pursuant to Section 6.2.

     3.2 Joint Management Committee.

          (a) Membership. The JMC shall be composed of six (6) members, with an equal number of members
appointed by each Party. Immediately following the Effective Date, each Party shall appoint its
initial representatives to the JMC. Each Party may replace its JMC representatives at any time
upon written notice to the other Party. Nuvelo will designate one of its representatives as the
Chairperson of the JMC. The Chairperson shall be responsible for scheduling meetings, preparing
and circulating an agenda in advance of each meeting, and preparing and issuing minutes of each
meeting within thirty (30) days thereafter. Minutes of a JMC meeting shall be final only when
approved by the JMC.

          (b) Power and Responsibilities. During the Research Program Term of this Agreement, the JMC
shall meet a minimum two (2) times per year as provided in Section 3.3. The JMC is responsible
for: (i) reviewing the annual Research Plan; and (ii) receiving updates on Nuvelo’s Development
activities hereunder with regard to any Development Compounds or Licensed Products then under
Development. If Archemix exercises its Profit Share Option, then the responsibility of the JMC will
expand to include receiving updates on Nuvelo’s Commercialization activities with respect to
Licensed Products. The JMC shall have no power to amend this Agreement. Any amendments that alter
the terms of this Agreement shall be implemented pursuant to Section 16.1 below.

     3.3 Meetings. The Parties shall endeavor to schedule meetings of the JMC at least thirty (30)
days in advance. Committee meetings held in person will alternate between sites designated by each
Party, unless otherwise agreed by the Parties. With the consent, not to be unreasonably withheld,
of the representatives of each Party serving on the JMC, other representatives of each Party may
attend meetings of the JMC as nonvoting observers. A meeting of the JMC may be held by audio or
video teleconference. Each Party shall be responsible for all of its own expenses of participating
in the meetings of the JMC, and such

16.

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.

 

 

expenses shall not be included in the Development Costs or Allowable Commercialization
Expenses if Archemix exercises its Profit Share Option pursuant to Article 6.

     3.4 Decision Making. If the JMC is unable to reach a unanimous agreement on any matter that
the JMC is responsible for, then Nuvelo shall have the final decision; provided, however, that, to
the extent that a Research Plan contemplates Archemix Research or Development activities in excess
of the minimum commitment described in Section 2.4, Archemix shall not be required to perform any
Research or Development activities as part of a Research Plan without its prior written consent.
Nuvelo will have the sole right to designate a Candidate Compound as a Development Compound based
on whether the Candidate Compound meets a target product profile acceptable to Nuvelo and set forth
in an approved Research Plan or subsequently modified by Nuvelo in good faith and communicated in
writing to Archemix.

     3.5 Access to Information. Archemix shall provide Nuvelo and its authorized representatives
with reasonable access during regular business hours to records, documents, and other information
relating to the Candidate Compounds that Nuvelo may reasonably require in order to evaluate their
potential as Development Compounds or, following their designation as Development Compounds, to
Develop such Development Compounds pursuant to the exclusive licenses granted hereunder.

     3.6 Research Expenses. Nuvelo will reimburse Archemix for the Minimum FTE Funding Requirement
per year during each Contract Year during the Research Program Term of this Agreement. Nuvelo
shall pay twenty five percent (25%) of the annual Minimum FTE Funding Requirement for each Contract
Year quarterly in advance; provided that, in the event that an approved Research Plan sets forth a
number of FTE’s higher than those indicated in the Minimum FTE Funding Requirement, then Nuvelo
shall pay quarterly in advance twenty five percent (25%) of the annual FTE funding requirement
based on the number of FTEs set forth in the Research Plan.

     3.7 Independence. Subject to the terms of this Agreement, each Party shall manage its own
activities and resources, acting independently and in its individual capacity. The relationship
between Nuvelo and Archemix is that of independent contractors and neither Party shall have the
power to bind or obligate the other Party in any manner, other than as is expressly set forth in
this Agreement.

	4.	 	Development, Manufacture and Commercialization

     4.1 Designation of ARC 2172. Nuvelo hereby designates ARC 2172 as a Development Compound.

     4.2 Development and Commercialization. Nuvelo has sole and full control, authority and
responsibility for conducting, funding (subject to Sections 6.1 and 7.5) and pursuing all aspects
of the designation, Development and Commercialization of Development Compounds and Licensed
Products throughout the world, so long as Nuvelo uses Diligent Efforts with respect thereto.
Nuvelo may, at its discretion, contract with or grant sublicenses to Third Parties in connection
with the exercise of its rights with regard to the Development and Commercialization of Development
Compounds and Licensed Products.

17.

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.

 

 

     4.3 Abandonment of Development Compounds. Any time after a Candidate Compound has been
designated as a Development Compound, Nuvelo may determine that Development of such Development
Compound should be abandoned. If Nuvelo decides to abandon Development of a particular Development
Compound, and is not pursuing another Candidate Compound or Development Compound for the same
therapeutic indication for which the first Development Compound was in Development, or against the
same Target to which such abandoned Development Compound binds, then Archemix will have the right
to continue such Development within the Field either by itself or with a Third Party only with
Nuvelo’s prior, written consent and upon the terms and conditions, if any, on which the Parties may
agree in writing based on good faith negotiations. In addition, Archemix shall have the right to
continue Development within the Field either by itself or with a Third Party of ARC 183 (as defined
in the Original Agreement), whose joint Development the Parties have previously agreed to abandon,
with Nuvelo’s prior, written consent and on terms and conditions, if any, on which the Parties may
agree in writing based on good faith negotiations.

     4.4 Regulatory Affairs. With respect to each Development Compound, at its discretion Nuvelo
will prepare, file and own all right, title and interest in Regulatory Filings and Regulatory
Approvals relating to each such Development Compound.

     4.5 Manufacturing. Nuvelo will be responsible for manufacturing and supplying Development
Compounds and Licensed Products for Development and Commercialization and for making all decisions
with respect thereto in its sole discretion including, without limitation, decisions relating to
process development work to support quality assurance, improving manufacturing/cost efficiency and
commercial scale-up manufacturing. For clarity, Nuvelo shall have final decision making authority
to fulfill its regulatory responsibilities over all steps of the manufacturing process (including
bulk, finish and fill, labeling and packaging, lot release and management of contractors and
subcontractors). The Parties recognize that Nuvelo may use Third Parties to conduct some or all of
Nuvelo’s manufacturing responsibilities hereunder, and Nuvelo will have sole decision making
authority for contracting with any such Third Parties.

	5.	 	LICENSES AND RELATED RIGHTS

     5.1 Research Licenses.

          (a) Subject to the other terms of this Agreement, Archemix hereby grants to Nuvelo a
worldwide, non-exclusive license, without the right to grant sublicenses, under the Licensed
Technology and Licensed Patent Rights, for the sole purpose of conducting Research on Short Acting
Coagulation Cascade Aptamers identified by Archemix in the course of performance of Research.

          (b) Subject to the other terms of this Agreement, Nuvelo hereby grants to Archemix a
worldwide, non-exclusive license during the Research Program Term, without the right to grant
sublicenses, under Nuvelo Technology and Nuvelo Patent Rights, for the sole purpose of conducting
Research or Development.

     5.2 Commercialization License. Archemix hereby grants to Nuvelo an exclusive (even as to
Archemix), worldwide, sublicensable license under the Licensed Technology and

18.

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.

 

 

Licensed Patent Rights, to Develop, Commercialize, make, have made, use, have used, sell, have
sold, lease, offer for sale or lease, import and export Development Compounds and Licensed Products
within the Field.

     5.3 License Grant upon Termination of the Collaboration. Upon termination the license grants
between the Parties of this Agreement shall be governed under Section 12.2 of this Agreement.

     5.4 License Limitations. Notwithstanding any provision hereof to the contrary, (a) Archemix
does not grant to Nuvelo a license to the SELEX Technology or SELEX Inventions and Nuvelo hereby
covenants that it will not practice any SELEX Technology or SELEX Inventions Controlled by Archemix
and (b) Nuvelo hereby covenants that it will not practice any of the rights granted hereunder to
any of the Licensed Patent Rights or Licensed Technology or use, make, have made, import, sell,
have sold, or offer for sale any Short Acting Coagulation Cascade Aptamer, Development Compound or
Licensed Product for a purpose other than that expressly permitted in Sections 5.1 and 5.2 hereof.

     5.5 Exclusivity. During the Term of this Agreement, and for a period of one (1) year
thereafter, unless otherwise provided in Section 4.3 or Section 12.2, neither Party nor its
Affiliates shall, except with respect to the Parties’ activities under this Agreement: (a) [***]
any [***] the [***] to [***]or [***] any [***] for [***] within the [***]; (b) [***] or with a
[***] to [***]and [***] any [***] for [***] within the [***] or (c) license or otherwise enable any
Third Party to perform any of the activities set forth in subsections (a) through (c) above. For
clarity, nothing herein shall be deemed to prohibit Archemix from identifying, discovering,
researching, developing, making, using or selling Aptamers that are not Short Acting Coagulation
Cascade Aptamers, so long as such actions are consistent with Sections 5.1, 5.2 and Article 10
hereof. In addition, neither Party may independently or with a Third Party [***] or [***] any
[***] for [***] in the [***] or [***] any [***] so that [***] the [***] in a [***] or other [***]
the [***] from the [***] so that [***] the [***] in Exhibit C or that [***] the [***] from the
[***]

     5.6 Sharing of Data.

          (a) During the Term of this Agreement, Nuvelo will have reasonable access to all Program
Technology (including, without limitation, all raw data) as it is generated.

          (b) The Parties’ access to Program Technology and Nuvelo Technology after the termination of
the Agreement shall be governed by Section 12.2(a) and Section 9.1.

     5.7 Grantback. Notwithstanding anything in this Agreement to the contrary, Nuvelo hereby
grants to Archemix a non-exclusive, paid-up, royalty-free license to any Nuvelo Technology and
Nuvelo Patent Rights that generically relates to and covers the manufacturing, formulation, methods
of use and/or processing of Aptamers (such Patent Rights hereinafter referred to as “Generic
IP”). Archemix shall have the right to practice the Generic IP and to grant sublicenses to the
Generic IP to Third Parties who have a license from Archemix to Archemix technology and/or
intellectual property solely in order to permit Archemix or such Third Party to research, discover,
make, have made, keep, use, sell and/or have sold, import or export Aptamers which are not subject
to Nuvelo’s exclusive rights hereunder, and to the extent

19.

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.

 

 

such actions are consistent with Section 5.5 hereof and for no other purpose. For clarity, the
rights granted to Archemix by Nuvelo under this Section 5.7 are limited to the claims to Generic IP
and no rights are granted under other claims in any patent or patent application of Nuvelo that
contains the claim(s) which is (are) Generic IP.

     5.8 Sublicenses. Nuvelo has the right to subcontract its Development and Commercialization
responsibilities under this Agreement (and grant any necessary sublicenses in connection therewith)
without obtaining the written consent of Archemix; provided, that, Nuvelo shall at all times remain
primarily responsible and liable for all such activities.

          With respect to each sublicense granted hereunder: (a) such sublicense shall be subject to all
the material terms and conditions of the Agreement as applicable; (b) the scope of such sublicense
shall be limited to performing Development or Commercialization activities hereunder; (c) Nuvelo
shall be liable to Archemix as if Nuvelo is exercising such sublicensed rights itself under this
Agreement; and (d) Nuvelo shall provide, upon written request by Archemix, reasonable assurance
that its sublicensees are bound by confidentiality, indemnity, reporting, audit rights, access to
data, and information and inventions assignment obligations substantially the same as those set
forth in this Agreement. Nuvelo shall promptly provide notice to Archemix of any sublicense
granted pursuant to this Section 5.8.

     5.9 No Other Rights. No licenses other than as expressly provided herein are granted by
either Party to such Party’s Technology or Patent Rights.

	6.	 	Option 

     6.1 Option Exercise.

          (a) With respect to each Development Compound, Archemix shall have the right, but not
obligation, to elect to share in the expenses incurred and profits obtained in connection with the
Development and Commercialization of such Development Compound and all Licensed Products comprising
such Development Compound (the “Profit Share Option”) by providing Nuvelo a written notification
of such election within forty-five (45) days after receipt from Nuvelo of written notification of
the dosing of the first patient in the first Phase 3 Trial for a Licensed Product comprising,
consisting of or incorporating such Development Compound. For clarity, such Profit Share Option
with respect to a particular Development Compound shall expire after such forty-five (45) day
period.

          (b) Within thirty (30) days after Nuvelo receives notice that Archemix elects to exercise its
Profit Share Option pursuant to (a) above, Nuvelo shall provide Archemix with an invoice for a
payment that equals the sum of: twenty-five percent (25%) of (i) the sum of all costs incurred by
Nuvelo in the Research and all Development Costs incurred by Nuvelo, both as of the date of
invoice, with respect to such Development Compound and Licensed Product; and (ii) the total for all
milestone payments paid by Nuvelo to Archemix as of the date of the invoice to Archemix with
respect so such Development Compound and Licensed Product. Archemix shall pay such invoice within
ten (10) days after its receipt in order to effect its exercise of such Profit Share Option.

20.

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.

 

 

     6.2 Consequence of Option Exercise.

          (a) Upon Archemix exercising its Profit Share Option with respect to a particular Development
Compound, Archemix shall be responsible for twenty-five percent (25%) of all subsequent Development
and Commercialization Costs with respect to such Development Compound and all of its related
Licensed Products, and Archemix shall share in the Product Profit and Loss with respect to such
Licensed Products pursuant to Section 7.5 below. Nuvelo shall have no payment obligations to
Archemix for milestone events pursuant to Section 7.4 which are not yet due as of the date of
exercise of the Profit Share Option with respect to such Development Compounds or Licensed
Products.

          (b) Upon Archemix exercising its Profit Share Option with respect to a particular Development
Compound and its related Licensed Products, Nuvelo will share all Nuvelo Information reasonably
requested by Archemix regarding its Commercialization activities of any such Licensed Products in
connection with the JMC meetings.

     6.3 Option Exercise and Third Party License. Archemix’s rights to its Profit Share Option
hereunder shall survive and remain in full force and effect relative to any Development Compound
that becomes subject to a Partnering Agreement for so long as such Partnering Agreement remains in
effect. Further, Archemix shall be entitled to twenty-five percent (25%) of all Licensing Revenue
associated with such Partnering Agreement regardless of whether such Licensing Revenue is received
before or after Archemix’s exercise of its Profit Share Option.

	7.	 	Compensation

     7.1 Obligations Prior to the Effective Date. Within sixty (60) days of the Effective Date,
each Party will fulfill any and all of its payment obligations accrued and due under the Original
Agreement.

     7.2 Upfront Payment. Nuvelo shall pay to Archemix Four Million Dollars ($4,000,000) within
ten (10) days of the Effective Date by wire transfer of immediately available funds.

     7.3 Stock Purchase and Sale.

          (a) Stock Purchase. Contingent upon and subject to the execution and delivery of, and
compliance with the terms and conditions of, this Agreement and the agreements contemplated herein,
and provided that this Agreement is still in effect, Archemix shall instruct its underwriters to
the Qualified IPO to offer to Nuvelo, subject to the determination by Archemix or the underwriters,
with the advice of counsel, that such offer does not violate 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 (together, the “Applicable Regulations”), the opportunity to purchase
the Nuvelo IPO Share Amount as an allotment in any Qualified IPO that closes within five (5) years
of the Effective Date at the IPO Price; provided, however, that if the underwriters determine in
good faith that an allotment of shares in such manner would be materially detrimental to the
success of the Qualified IPO, then the

21.

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.

 

 

underwriters may limit all or a portion of the Nuvelo IPO Share Amount. Should Nuvelo not be
offered or elect not to accept the opportunity to purchase the full Nuvelo IPO Share Amount as an
allotment in any such Qualified IPO, then Nuvelo shall instead purchase from Archemix, and Archemix
shall sell to Nuvelo in a private placement (the “Private Placement”), concurrently with a
Qualified IPO that closes within five (5) years of the Effective Date, the portion of the Nuvelo
IPO Share Amount that is not included in the Qualified IPO at the IPO Price. The purchase of
shares of Archemix Common Stock in the Private Placement shall be subject to compliance with
Applicable Regulations, including but not limited to compliance with the U.S. Securities and
Exchange Commission’s integration doctrine. For clarity, if the Qualified IPO occurs prior to the
first anniversary of this Agreement then Nuvelo shall consummate the stock purchase set forth in
this Section 7.3 as a Private Placement pursuant to Section 7.3(c) below.

          (b) Purchase Mechanics.

               (i) Notice of Qualified IPO. At least ten (10) days prior to the anticipated effective date
of the registration statement for the Qualified IPO, Archemix shall deliver to Nuvelo written
notice (the “Qualified IPO Notice”) specifying:

                    (1) that Archemix has filed a registration statement for a Qualified IPO;

                    (2) the anticipated effective date of the registration statement for the Qualified IPO;

                    (3) the anticipated total gross offering proceeds (prior to underwriter commissions and
expenses) expected to be raised by Archemix in the Qualified IPO;

                    (4) the anticipated range of the IPO Price; and

                    (5) 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).

               (ii) Nuvelo Notice of Participation. Nuvelo shall inform Archemix in writing within eight (8)
days of the date of the Qualified IPO Notice whether Nuvelo wishes to purchase shares of Archemix
Common Stock in the Qualified IPO and the portion of the Nuvelo IPO Share Amount it wishes to
purchase.

               (iii) Purchase Notice. Following the pricing of the Qualified IPO (the “IPO Effective Date”),
Archemix shall deliver to Nuvelo written notice within one (1) business day (the “Purchase Notice”)
specifying:

                    (1) that the registration statement for the Qualified IPO has been declared effective;

                    (2) the total gross offering proceeds (prior to underwriter commissions and expenses) to be
raised by Archemix in the Qualified IPO;

22.

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.

 

 

                    (3) the IPO Price;

                    (4) the number of shares of Archemix Common Stock comprising the Nuvelo IPO Share Amount;

                    (5) if applicable, details for the purchase and settlement of the portion of the Nuvelo IPO
Share Amount to be purchased by Nuvelo 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”);

                    (6) if applicable, the place and time at which the Private Placement Closing will occur, the
portion of the Nuvelo IPO Share Amount to be purchased by Nuvelo in the Private Placement, 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.

          (c) 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: (A) 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 Nuvelo and/or
Archemix may extend the Private Placement Closing Date to a date not more than ten (10) days after
the applicable order, judgment, decree or other legal impediment has been satisfied; and (B) 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 (1) 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, (2) 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 (3) the Private
Placement Closing Date shall be extended to a date not more than ten (10) 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, Nuvelo 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.

               (ii) At the Private Placement Closing, simultaneously with the delivery of the Private
Placement Purchase Price, Archemix and Nuvelo shall deliver to each other, executed counterparts of
the Stock Purchase Agreement set forth as Exhibit F and the Registration Rights Agreement set forth
as Exhibit G.

          (d) Qualified IPO Closing. On the closing date of the Qualified IPO, Nuvelo shall deliver to
the underwriters the Qualified IPO Purchase Price in accordance with the purchase and settlement
instructions designated by the underwriters.

23.

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.

 

 

          (e)
“Market Stand-Off” Agreement. Nuvelo agrees that during
the one hundred eighty (180) day period following
the effective date of the registration statement for the Qualified IPO, or such other period as
requested of all Archemix executive officers required to file Forms 3 and 4 and directors 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, Nuvelo shall not, to the extent requested by the
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 or any securities convertible into or
exercisable or exchangeable for Common Stock held by Nuvelo at any time during such period;
provided, however, that all executive officers and directors of Archemix enter into similar market
stand-off agreements.

     7.4 Payments for Development Compounds and Licensed Products for which Archemix has not
Exercised its Profit Share Option.

          (a) Milestone Payments. With respect to each Development Compound, Nuvelo shall pay to
Archemix the milestone payments as set forth below, which shall be due and payable within ten (10)
business days of the occurrence of the event for the Development Compound for which the payment is
due. For clarity, each milestone payment is due only once for each Development Compound, regardless
of the number of Licensed Products Developed or Commercialized under this Agreement which comprise,
consist of or incorporate such Development Compound. Each milestone payment is due only for
Development Compounds for which Archemix has not exercised its Profit Share Option.

	 	 	 	 	 	 	 
	 	 	 	 	 
	 	 	Milestone Event	 	Payment Amount
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 [***]

	 	[***]
	 	 	[***]	 
	 

	 	Total
	 	$	35,000,000	 

          (b) Royalties.

               (i) Nuvelo shall pay Archemix royalties on Net Sales of Licensed Products for which Archemix
has not exercised its Profit Share Option at the royalty rates set forth below:

24.

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.

 

 

	 	 	 
	Portion of Net Sales of Each Licensed Product during Each	 	 
	Calendar Year	 	Royalty Rate
	Up to $[***]

	 	[***]%
	 
	 	 
	The portion of Net Sales that is greater than $[***] and less
than or equal to $[***]

	 	[***]%
	 
	 	 
	The portion of Net Sales that is greater than $[***] and less
than or equal to $[***]

	 	[***]%
	 
	 	 
	The portion of Net Sales that is greater than $[***] and less
than or equal to $[***]

	 	[***]%
	 
	 	 
	The portion of Net Sales that is greater than $[***]

	 	[***]%

               (ii) Third Party Royalties. Nuvelo shall be responsible for any and all royalties due to a
Third Party in connection with the Development of any Development Compound and/or Commercialization
of any Licensed Product (the “Third Party Royalty”), except that Archemix shall be responsible for
all royalties due to ULEHI for payments made by Nuvelo to Archemix with respect to all Licensed
Products. Archemix hereby warrants that the only Third Party Royalty obligation of which Archemix
is aware that exists as of the Effective Date of this Agreement is set forth in the ULEHI
Agreement.

               (iii) Royalty Adjustment and Term. The royalty amounts set forth above shall be due on a
Licensed Product-by-Licensed Product and country-by-country basis for so long as a Valid Claim of
(a) Licensed Patent Rights cover the manufacture, use or sale of such Licensed Product in such
country or (b) Nuvelo Patent Rights that cover Nuvelo Program Technology cover the manufacture, use
or sale of such Licensed Product in such country. In the event that no such Valid Claim exits, the
royalty amounts set forth above, which shall be due on a country-by-country basis, shall be reduced
by fifty percent (50%) on a Licensed Product-by-Licensed Product and country-by-country basis until
the tenth (10th) anniversary of the first commercial sale of such Licensed Product in
such country if such anniversary has not yet occurred.

               (iv) Royalty Report and Payment. Commencing with the first commercial sale of a Licensed
Product by Nuvelo or its licensees or sublicensees, Nuvelo or its licensees or sublicensees making
such sales shall make quarterly written reports to Archemix within sixty (60) days after the end of
each calendar quarter (the “Royalty Period”), stating in each such report, by Licensed Products and
by country, the number, description and aggregate Net Sales in U.S. dollars of such Licensed
Products sold during such Royalty Period by Nuvelo and its licensees or sublicensees, respectively. The report shall also show: (A) the
calculation of Net Sales made by Nuvelo and the royalty payments due to Archemix on such Net Sales
for such Royalty Period; (B) the calculation of Net Sales made by Nuvelo’s licensees or
sublicensees, the amount of sublicense revenue and royalty received from such licensees or
sublicensees and the royalty payments due to Archemix on such sublicensee Net Sales for such
royalty period; (C) the amount of taxes, if any, withheld to comply with applicable law; and (D)
the exchange rates used

25.

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.

 

 

in calculating the payments due to the other Party, which exchange rates
shall comply with Section 7.4(b)(vi) below. Simultaneously with the delivery of each such report,
Nuvelo or its licensee or sublicensee making such sales shall pay to Archemix the total royalties,
if any, due to Archemix for such Royalty Period. If no royalties are due, Nuvelo or its licensee
or sublicensee making such sales shall so report.

               (v) Blocked Currency. In each country where the local currency is blocked and cannot be
removed from the country, royalties arising from sales made in that country shall be paid in the
country in local currency by deposit in a local bank designated by Archemix, unless the Parties
otherwise agree.

               (vi) Foreign Exchange. Conversion of sales recorded in local currencies to U.S. dollars will
be performed using an exchange rate for conversion of the foreign currency into U.S. dollars, at
the average rate of exchange for the calendar quarter to which such payments relate, quoted for
current transactions for buying U.S. dollars, as reported in The Wall Street Journal for the last
business day of the week before such payment is due, except as provided in Section 7.4(b)(v).

     7.5 Payments for Development Compounds and Licensed Products for which Archemix Exercises its
Profit Share Option.

          (a) Overview. For Licensed Products for which Archemix has exercised its Profit Share Option,
the Parties shall share all Product Profit and Loss with respect to such Licensed Product so that
Nuvelo shall be entitled to seventy-five percent (75%) of such Product Profit and Loss and Archemix
shall be entitled to twenty-five percent (25%) of such Product Profit and Loss.

          (b) Reporting and Reconciliation.

               (i) Within sixty (60) days after the end of each calendar quarter following the first receipt
of revenues under this Agreement (which may be either from Net Sales or Licensing Revenue), Nuvelo
shall prepare and submit to Archemix a statement of quarterly Product Profit and Loss, prepared on
an accrual basis in accordance with GAAP in substantially the form attached as Exhibit H, which
shall include a calculation of the equalization payment which is necessary to cause the ratio of
the participation of Nuvelo and Archemix in the Product Profit and Loss for such quarter on an
accrual basis to be seventy-five percent/twenty-five percent (75%/25%), respectively (the
“Financial Statement”). The reports and equalization payments for the fourth quarter of the fiscal
year may include reconciliations and year-end adjustments with respect to previous quarters. All
payments required by this Section 7.5 shall be made concurrently with the submittal of the
Financial Statement or, if a payment is due from Archemix to Nuvelo, within ten (10) days after
receipt thereof by Archemix. Nuvelo will provide to Archemix such supporting information for the Financial Statement as Archemix may
reasonably request. Archemix may audit, in accordance with the procedures set forth in Article 8,
the accuracy of Nuvelo’s submissions pursuant to this Section 7.5(b)(i).

               (ii) By way of example, on an accrual basis, if during a particular quarter Nuvelo realized
revenues from Licensed Products for which Archemix has exercised its

26.

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.

 

 

Profit Share Option of One Hundred Million Dollars ($100,000,000) and incurred Allowable Commercialization Expenses of Thirty
Million Dollars ($30,000,000), then the Equalization Payment for such quarter would be a payment by
Nuvelo to Archemix in the amount of Seventeen Million Five Hundred Thousand Dollars ($17,500,000).
For clarity, the example set forth in this Section 7.5(b)(ii) is calculated on an accrual basis of
accounting.

     7.6 Payment Method. All payments due under this Agreement shall be made by bank wire transfer
in immediately available funds to an account designated by the receiving Party. All payments
hereunder shall be made in U.S. dollars from the United States.

     7.7 Taxes. Each Party shall pay any and all taxes levied on account of all payments it
receives under this Agreement. If laws or regulations require that taxes be withheld, the paying
Party will: (a) deduct those taxes from the remittable payment; (b) pay the taxes to the proper
taxing authority; and (c) send evidence of the obligation together with proof of tax payment to the
receiving Party within thirty (30) days following that tax payment.

	8.	 	Records; Audits

Both Parties shall keep complete, true and accurate books of accounts and records for the purpose
of determining the payments to be made under this Agreement. Such books and records shall be kept
for at least three (3) years following the end of the calendar quarter to which they pertain. Such
records will be open for inspection during such three (3) year period by independent accountants,
solely for the purpose of verifying payment statements hereunder. Such inspections shall be made
no more than once each calendar year, at reasonable time and on reasonable notice. If any errors
that favor the inspected Party are discovered in the course of such inspection, then within thirty
(30) days after its receipt of the inspection report, the inspected Party shall pay the inspecting
Party those amounts (plus interest equal to the Prime Lending Rate as published in the Wall Street
Journal on the day preceding the inspection plus two hundred (200) basis points; provided, however,
that in no event shall such rate exceed the maximum annual interest rate permitted under applicable
law) that the inspecting Party would have received in the absence of such errors. If any errors
that favor the inspecting Party are discovered in the course of such inspection, then within thirty
(30) days after its receipt of the inspection report, the inspecting Party shall pay the inspected
Party those amounts. Inspections conducted under this Article 8 shall be at the expense of the
inspecting Party, unless a variation or error that favors the inspected Party exceeding five
percent (5%) of the amount stated for any year covered by the inspection is established in the
course of such inspection, whereupon all costs relating to the inspection for such period will be
paid promptly by the inspected Party.

	9.	 	INFORMATION, INVENTIONS AND INTELLECTUAL PROPERTY

     9.1 Ownership.

          (a) Patent Rights and Technology. Subject to Section 9.1(b), all Patent Rights will be the
property of the inventing Party, provided that all Joint Patent Rights will be jointly owned by the
Parties with each Party having full rights to use and license same subject only to the licenses
expressly granted and the terms set forth herein. In all cases, inventorship shall be determined
according to United States Patent law.

27.

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.

 

 

          (b) SELEX Inventions and SELEX Technology. Notwithstanding anything to the contrary herein,
the SELEX Inventions and SELEX Technology shall be the property of Archemix. Nuvelo shall and
hereby does assign to Archemix all of Nuvelo’s right, title and interest in and to all SELEX
Inventions and SELEX Technology.

          (c) Technology. Subject to Section 9.1(b), ownership of all unpatented Technology is and will
be the property of the Party who created it.

          (d) Further Acts. Each Party shall perform such additional actions necessary to affect the
intent of this Section 9.1, and shall reasonably cooperate with the other Party in doing so.

     9.2 Patent Prosecution and Maintenance.

          (a) ARC 2172 and Compound Patent Rights. Archemix will transfer all responsibility for the
prosecution and maintenance of the ARC 2172 Patents to Nuvelo promptly after the Effective Date.
In addition, if Archemix discovers any Short Acting Coagulation Cascade Aptamer for use within the
Field or makes any new invention relating to any Short Acting Coagulation Cascade Aptamer for use
within the Field in the course of its Research under this Agreement, Archemix will transfer all
responsibility for the filing, prosecution and maintenance of the relevant Compound Patent Rights
to Nuvelo and will provide Nuvelo with all necessary documents and information to effect the
transfer of responsibility. For so long as Nuvelo has an exclusive license hereunder to ARC 2172
or such Development Compound, Nuvelo has the right to pursue worldwide filing, prosecution and
maintenance of such ARC 2172 Patents or Compound Patent Rights using mutually acceptable outside
counsel. Unless Archemix exercises its Profit Share Option, in which event Section 7.5 shall
apply, Nuvelo will be solely responsible for all costs incurred in this Section 9.2(a). Nuvelo
will keep Archemix apprised of all prosecution matters, and will provide a copy of all official
correspondence to Archemix, and Nuvelo will consider any comments in good faith from Archemix and
incorporate them to the extent possible. Nuvelo shall file, prosecute and maintain the ARC 2172
Patents and Compound Patent Rights in Archemix’ name using reasonably diligent efforts including
filing, prosecuting and maintaining the ARC 2172 Patents and Compound Patent Rights, at a minimum,
in the countries listed on Exhibit E. If Nuvelo decides to not pursue prosecution or maintenance
of any such Patent Rights, control of such Patent Rights shall be transferred to Archemix at no
cost. For purposes of this Agreement, “ARC 2172 Patents” means the following United States Patent
Applications and their counterparts throughout the world to the extent not SELEX Inventions or
SELEX Technology: U.S. Patent Application Serial No. 60/711,768 and Serial No. 60/808,590.

          (b) SELEX Technology and SELEX Inventions. Archemix shall have the sole right but not the
obligation to file, prosecute and maintain Patent Rights on SELEX Technology or SELEX Inventions,
at its own expense.

          (c) Archemix Technology. Except as set forth in Section 9.2(a), Archemix shall have the sole
right but not the obligation to file, prosecute and maintain Patent Rights on Archemix Background
Technology and Archemix Program Technology, at its own expense, including without limitation all
Patent Rights in and to the SELEX Portfolio.

28.

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.

 

 

          (d) Nuvelo Background Technology. Nuvelo shall have the sole right but not the obligation to
file, prosecute and maintain Patent Rights claiming Nuvelo Background Technology, at its own
expense.

          (e) Nuvelo Program Technology. Nuvelo shall have the first right but not the obligation to
file, prosecute and maintain Patent Rights claiming Nuvelo Program Technology at its own expense.
If, at any time, Nuvelo elects not to pursue patent protection for, or maintenance of, any Nuvelo
Program Technology, Archemix shall have the right to pursue patent protection for such Technology
at Archemix’s sole expense.

          (f) Joint Patent Rights. Archemix has the first right, but not the obligation, to pursue
worldwide patent protection of all Joint Technology not covered by Section 9.2(a) above. The
Parties will be jointly (on a fifty/fifty (50/50) basis) responsible for all costs incurred
pursuant to this Section 9.2(f). If Archemix elects to pursue such patent protection, it will use
outside counsel mutually acceptable to the Parties. Archemix will keep Nuvelo apprised of all
prosecution matters, and will provide a copy of all official correspondence to Nuvelo. Archemix
will consider in good faith any comments from Nuvelo and incorporate them to the extent possible.
If, at any time, Archemix elects to not pursue patent protection for, or maintenance of, any such
Joint Patent Rights, control of such Joint Patent Rights shall be transferred to Nuvelo at no cost.
For clarity, Patent Rights claiming any SELEX Technology or SELEX Invention are governed by
Section 9.2(b) and not this Section 9.2(f).

          (g) Information and Cooperation. Each Party that has responsibility for filing and
prosecuting any Patent Rights under this Section 9.2 (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 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) to the
extent practicable, 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, and the advice and 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 under this Section 9.2; 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, Nuvelo (a) agrees that if Archemix claims any action
taken under Section 9.2 would be detrimental to Patent Rights
covering Archemix Background Technology (including without limitation the SELEX Portfolio),
Archemix shall provide written notice to Nuvelo and the Parties 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.

29.

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.

 

 

     9.3 Enforcement of Patent Rights.

          (a) Notice. If a Third Party is apparently infringing any Patent Right to which exclusive
licenses are granted under this Agreement, the Party first obtaining knowledge of such a claim
shall immediately provide the other Party notice of such claim and the related facts in reasonable
detail.

          (b) Enforcement Responsibility. Nuvelo, as exclusive commercial licensee, has the first
right, but not the obligation, to solely enforce all Compound Patent Rights against any actual or
suspected Third Party infringer in the Field. Such enforcement will be in Nuvelo’s own name and
entirely under its own direction and control, and Nuvelo may settle any such action, proceeding or
dispute by license, subject to the remainder of this Section 9.3(b). Unless Archemix exercises its
Profit Share Option, in which event Section 7.5 shall apply, or unless otherwise provided below,
Nuvelo will be solely responsible for all costs incurred in this Section 9.3(b).

               (i) Enforcement by Nuvelo. Archemix will, upon Nuvelo’s request, reasonably assist
Nuvelo in any action or proceeding being prosecuted by Nuvelo under this Section 9.3(b) if so
requested, and shall lend its name to such actions or proceedings if reasonably requested by Nuvelo
or required by applicable law. Nuvelo shall reimburse Archemix for the documented external costs
Archemix reasonably incurs in providing such assistance as specifically requested in writing by
Nuvelo. Archemix shall have the right to participate and be represented in any such suit by its
own counsel at its own expense; provided, that, Nuvelo shall retain overall responsibility for the
prosecution of such suit or proceedings in such event. No settlement of any such action or
proceeding which restricts the scope, or adversely affects the enforceability, of an Archemix
Patent Right, or which could be reasonably expected to have a material adverse financial impact on
Archemix, may be entered into by Nuvelo without the prior written consent of Archemix, which
consent shall not be unreasonably withheld, delayed or conditioned.

               (ii) Enforcement by Archemix. If Nuvelo elects not to settle or bring any action for
infringement described in this Section 9.3(b) and so notifies Archemix, including following any
request by Archemix to do so, then Archemix may settle or bring such action at its own expense, in
its own name; provided, however, that Archemix agrees not to so settle or bring such action for
infringement upon Nuvelo’s request based on Nuvelo’s good faith reasonable determination that it is
not in the best interest of the Parties to so settle or bring such action for infringement. In the
case where Archemix proceeds to settle or bring an action for such infringement, the following
shall apply. Nuvelo shall reasonably assist Archemix in any action or proceeding being prosecuted
if so requested, and shall lend its name to such actions or proceedings if requested by Archemix or
required by applicable law. Archemix shall reimburse Nuvelo for the documented external costs
Nuvelo reasonably incurs in providing such assistance as specifically requested in writing by
Archemix. Nuvelo shall have the right to participate and
be represented in any such suit by its own counsel at its own expense; provided, that, Archemix
shall retain overall responsibility for the prosecution of such suit or proceedings in such event.
No settlement of any such action or proceeding which restricts the scope, or adversely affects the
enforceability, of a Licensed Patent Right hereunder, or which could be reasonably expected to have
a material adverse financial impact on Nuvelo, may be entered into by Archemix without

30.

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.

 

 

the prior
written consent of Nuvelo, which consent shall not be unreasonably withheld, delayed or
conditioned.

               (iii) Withdrawal. If either Party brings an action or proceeding under this Section
9.3(b) and subsequently ceases to pursue or withdraws from such action or proceeding, it shall
promptly notify the other Party and the other Party may substitute itself for the withdrawing Party
under the terms of this Section 9.3(b).

               (iv) Damages. In the event that either Party exercises the rights conferred in this
Section 9.3(b) and recovers any damages or other sums in such action, suit or proceeding or in
settlement thereof, such damages or other sums recovered shall first be applied to all
out-of-pocket costs and expenses incurred by the Parties in connection therewith, including,
without limitation, attorneys fees. Except as otherwise provided in this Section 9.3(b), each
Party will bear its own expenses with respect to any suit or other proceeding against an infringer.
If such recovery is insufficient to cover all such costs and expenses of both Parties, it shall be
shared in proportion to the total of such costs and expenses incurred by each Party. If after such
reimbursement any funds shall remain from such damages or other sums recovered, such funds shall be
divided as follows: (i) as to ordinary damages based on lost sales or profit, Nuvelo shall retain
such funds and Archemix shall receive payment equivalent to payments that would have been due to
Archemix under this Agreement had the infringing sales that Nuvelo lost to the infringer been made
by Nuvelo; and (ii) as to special or punitive damages, the Party that brought the enforcement
action at its expense shall be entitled to receive eighty percent (80%) of the amount of such
special or punitive damages and the other Party shall receive twenty percent (20%) of the amount of
such special or punitive damages.

          (c) Archemix Background Technology and SELEX Technology and SELEX Inventions. Archemix shall
have the sole right but not the obligation to enforce Patent Rights on SELEX Technology and SELEX
Inventions and, subject to Section 9.3(b), on Archemix Background Technology.

          (d) Nuvelo Patent Rights. Nuvelo shall have the sole right but not the obligation to enforce
Nuvelo Patent Rights.

     9.4 Defense of Third Party Claims.

          (a) Nuvelo will have the first right to defend any claims by a Third Party alleging
infringement of any Third Party Patents or misappropriation of any Third Party trade secrets in
connection with the Development, manufacture or Commercialization of any Development Compound or
Licensed Product by Nuvelo, its Affiliates, sublicensees, contractors or consultants. Nuvelo may,
at its sole option, settle any such claim; provided, that, such settlement does not, or will not
have any material adverse effect on Archemix.

          (b) Archemix will be solely responsible, at its sole expense, for defending any claims against
it by a Third Party alleging infringement of any Third Party Patents or misappropriation of any
Third Party trade secrets by Archemix in connection with its Research activities under this
Agreement. Archemix may, at its sole option, settle any such claim; provided, that, such
settlement does not, or will not, have any material adverse effect on Nuvelo.

31.

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.

 

 

	10.	 	Confidentiality

     10.1 Nondisclosure of Confidential Information. All Technology and other information
disclosed by one Party to the other Party pursuant to this Agreement that it is marked or otherwise
identified as “confidential” or “proprietary” shall be “Confidential Information” of the disclosing
Party. Confidential Information also includes all Technology and other information developed by
either Party in carrying out this Agreement and disclosed to the other Party, or disclosed by
either Party under the Original Agreement, which agreement is superseded by this Agreement. The
Parties agree that during the Term, and for a period of five (5) years thereafter, a Party
receiving Confidential Information of the other Party will: (a) maintain in confidence such
Confidential Information to the same extent such Party maintains its own proprietary industrial
information of similar kind and value; (b) not disclose such Confidential Information to any Third
Party without prior written consent of the disclosing Party, except as otherwise permitted in this
Article 10; and (c) not use such Confidential Information for any purpose except those permitted by
this Agreement.

     10.2 Exceptions. The obligations in Section 10.1 shall not apply to information that the
receiving Party can show by competent written proof:

          (a) Is publicly disclosed by the disclosing Party, either before or after the Confidential
Information is disclosed to the receiving Party hereunder;

          (b) Was known to the receiving Party, without obligation to keep it confidential, before
disclosure of the Confidential Information by the disclosing Party;

          (c) Is subsequently disclosed to the receiving Party by a Third Party lawfully in possession
thereof and without obligation to keep it confidential;

          (d) Has been published by a Third Party; or

          (e) Has been independently developed by the receiving Party without the aid, application or
use of the Confidential Information.

     10.3 Authorized Disclosure.

          (a) A Party may disclose the Confidential Information belonging to the other Party to the
extent such disclosure is reasonably necessary in the following instances, in each case, to the
extent consistent with the terms of this Agreement:

               (i) Filing or prosecuting Patent Rights;

               (ii) Making Regulatory Filings;

               (iii) Prosecuting or defending litigation;

               (iv) Complying with applicable governmental regulations;

32.

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.

 

 

               (v) Conducting business discussions with Third Parties who potentially or actually enter into
a Partnering Agreement with Nuvelo and who have signed confidentiality agreements consistent with
this Article 10; and

               (vi) Making disclosures, in connection with the performance of this Agreement, to Affiliates
and actual or prospective licensees, sublicensees, contractors, research collaborators, employees,
consultants, or agents, each of whom before disclosure must be bound by similar obligations of
confidentiality and non-use at least equivalent in scope to those set forth in this Article 10.
Nuvelo and its sublicensees may also publicly disclose clinical data for use in connection with the
marketing of Licensed Products in accordance with the customary practice of the pharmaceutical
industry.

          (b) The Parties acknowledge that the terms of this Agreement shall be treated as Confidential
Information of both Parties. Such terms may be disclosed by a Party to investment bankers,
investors, and potential investors, lenders and potential lenders and other sources and other
potential sources of financing, licensees and potential licensees, acquirer or merger partners and
potential acquirer or merger partners and Gilead and University License Equity Holdings, Inc. 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.

     10.4 Publicity. The Parties agree that the public announcement of the execution of this
Agreement shall be made pursuant to a press release approved by the Parties. Any other
publication, news release or other public announcement relating to this Agreement or to the
performance hereunder, shall also be reviewed and approved by both Parties; provided, however, that
any disclosure which is required by law as advised by the disclosing Party’s counsel may be made
without the prior consent of the other Party, although the other Party shall be given prompt notice
of any such legally required disclosure and to the extent practicable shall provide the other Party
an opportunity to comment on the proposed disclosure.

     10.5 Publications. During the Research Term, neither Party shall publish or present the
results of studies carried out on ARC 2172, Short Acting Coagulation Cascade Aptamers, or Candidate
Compounds under this Agreement without the opportunity for prior review by the other Party.
Subject to Section 10.3, each Party agrees to provide the other Party the opportunity to review any
proposed abstracts, manuscripts or presentations (including verbal presentations) which relate to
ARC 2172, Short Acting Coagulation Cascade Aptamers, or Candidate Compounds at least thirty (30)
days before its intended submission for publication and agrees, upon request, not to submit any
such abstract or manuscript for publication until the other Party is given a reasonable period of
time to secure patent protection for any material in such publication as appropriate and as
governed by Article 9. Both Parties understand that a
reasonable commercial strategy may require delay of publication of information or filing of
patent applications. The Parties agree to review and consider delay of publication and filing of
patent applications under certain circumstances. The JMC will review such requests and recommend
subsequent action. Neither Party shall have the right to publish or present

33.

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.

 

 

Confidential
Information of the other Party, which is subject to Section 10.1, without the other Party’s written
consent. Nothing contained in this Section 10.5 shall prohibit the inclusion of information
necessary for a patent application, so long as the Non-Filing Party is given a reasonable
opportunity to review and comment on the information to be included before submission of such
patent application. Any disputes between the Parties regarding delaying a publication or
presentation or advertising or promotional materials used during commercialization in order to
permit the filing of a patent application shall be referred to the JMC for resolution. Following
termination of the Agreement, a Party that continues to develop or commercialize a Licensed Product
as an Archemix Product or Nuvelo Product, as the case may be, may publish results of studies of
such Licensed Product without prior consultation with the other Party.

	11.	 	Term 

Subject to Article 11, the term during which this Agreement is in effect (the “Term”) commences on
the Effective Date and expires at such time as all obligations of the Parties to make payments
pursuant to Article 7 for all Licensed Products have ended, unless earlier terminated in accordance
with the provisions of Article 12 below.

	12.	 	Termination

     12.1 Termination of Agreement.

          (a) Termination for Material Breach. Either Party may terminate this Agreement, on a Licensed
Product by Licensed Product basis (along with the relevant Development Compound), if the other
Party has materially breached or defaulted in the performance of any relevant obligations under
this Agreement or failed to use Diligent Efforts in the performance of any relevant obligations
under this Agreement, and the non-breaching Party has provided written notice to the other Party
specifying the basis for the termination. For a failure to make a payment set forth in Section 2.4
or Article 7, the allegedly breaching Party shall have ten (10) days to cure such breach. For all
breaches other than a failure to make a payment set forth in Section 2.4 or Article 7, the
allegedly breaching Party shall have sixty (60) days to either cure such breach or, if cure cannot
be reasonably effected within such sixty (60) day period, to deliver to the other Party a plan for
curing such breach that is reasonably sufficient to effect a cure within ninety (90) days from
receipt of the notice of breach. If the breaching Party does not cure the breach before the
expiration of ten (10), sixty (60) or ninety (90) days, as applicable, after receipt of the written
notice specifying the basis for termination, the Agreement shall terminate upon the expiration of
the ten (10), sixty (60) or ninety (90) day period, as applicable. If the Parties cannot agree as
to whether a breach exists, the dispute shall be resolved pursuant to Article 15, and no
termination shall be effective until the matter is so resolved. In the event that either Party
files for protection under bankruptcy laws, makes an assignment for the benefit of creditors,
appoints or suffers appointment of a receiver or trustee over its property, files a petition under
any bankruptcy or insolvency act or has any such petition filed against it
which is not discharged within sixty (60) days of the filing thereof, then the other Party may
terminate this Agreement effective immediately upon written notice to such Party.

34.

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.

 

 

          (b) Voluntary Termination Other Than for Material Breach. For reasons other than Archemix’s
material breach of its obligations under this Agreement pursuant to Section 12.1(a) Nuvelo may
terminate this Agreement, on a Development Compound by Development Compound or Licensed Product by
Licensed Product basis, or terminate the Agreement in its entirety, in its discretion upon sixty
(60) days prior written notice to Archemix. In the event that Nuvelo elects to voluntarily
terminate this Agreement pursuant to this Section 12.1(b), Nuvelo shall pay Archemix the amount of
the Minimum FTE Funding for the ninety (90) days following the effective date of such termination.

     12.2 Effects of Termination.

          (a) Development of Products.

               (i) Nuvelo Product. If this Agreement is terminated by Nuvelo, in whole or in part, for
Archemix’s material breach under this Agreement pursuant to Section 12.1(a), upon the effective
date of such termination, any Licensed Product then under Development or being Commercialized shall
cease to be a Licensed Product and will automatically become a “Nuvelo Product.” Promptly after the
effective date of such termination: (A) Archemix shall assign to Nuvelo all of Archemix’s right,
title and interest in and to all Compound Technology and all Regulatory Documentation, Regulatory
Filings and Regulatory Approvals, to the extent relevant to the Development and/or
Commercialization of such Nuvelo Product in the Field and any trademarks for such product; (B)
Archemix shall provide Nuvelo with at least two (2) accurate and legible copies (including both
paper and electronic copies, where available) of all such Technology as defined in Section 1.86(c)
related the Development and/or Commercialization of such Nuvelo Product; (C) upon Nuvelo’s written
request and to the extent Archemix has the right to do so, Archemix shall assign to Nuvelo all
agreements with Third Parties that are specific for the Development and/or Commercialization of
such Nuvelo Product; and (D) Archemix shall no longer have access to future Nuvelo Technology that
is related to such Nuvelo Product. Nuvelo shall be free to develop and commercialize such Nuvelo
Product and to collaborate with any Third Parties on such endeavors, notwithstanding any Patent
Rights of Archemix which would prevent such actions and subject only to Section 12.2(b)(1).

               (ii) Archemix Product. If this Agreement is terminated by Archemix, in whole or in part,
pursuant to Section 12.1(a) for Nuvelo’s material breach under this Agreement, or by Nuvelo
pursuant to Section 12.1(b) (voluntary termination), upon the effective date of such termination,
any Licensed Product then under Development or being Commercialized shall cease to be a Licensed
Product and will automatically become an “Archemix Product.” Promptly after the effective date of
such termination: (A) Nuvelo shall assign to Archemix all of Nuvelo’s right, title and interest in
and to the Nuvelo Technology, Regulatory Documentation, Regulatory Filings and Regulatory
Approvals, to the extent relevant to the Development and/or Commercialization of such Archemix
Product in the Field and any trademarks for such product; (B) Nuvelo shall provide Archemix with at
least two (2) accurate and legible copies (including both paper and electronic copies, where
available) of all Nuvelo
Technology as defined in Section 1.86(c) related to the Development and/ or Commercialization
of such Archemix Product; (C) upon Archemix’s written request and to the extent Nuvelo has the
right to do so, Nuvelo shall assign to Archemix all agreements with Third Parties that are

35.

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.

 

 

specific
for the Development or Commercialization of such Archemix Product; and (D) Nuvelo shall no longer
have access to future Program Technology that is related to such Archemix Product. Archemix shall
be free to develop and commercialize such Archemix Product and to collaborate with any Third
Parties on such endeavors, notwithstanding any patent rights of Nuvelo which would prevent such
actions and subject only to Section 12.2(b)(2).

          (b) Royalties and Payments on Nuvelo Products and Archemix Products.

               (i) Royalty Rate and Payments Upon Termination. If this Agreement is terminated with respect
to any Nuvelo Product or Archemix Product pursuant to Section 12.1(a) or (b) after the achievement
of the Phase 2 Milestone, then the Parties shall pay to each other royalties as set forth below,
and the procedures set forth in Sections 7.4(b)(iii) through (vi) shall apply to both Parties (in
the case when Archemix is the royalty paying Party, such provisions shall apply to Archemix
correlatively). Otherwise no royalty shall be due to a Party hereto with respect to Archemix
Products or Nuvelo Products.

                    (1) With respect to Nuvelo Products, Nuvelo (a) shall pay to Archemix a royalty equal to [***]
percent [***] of the Net Sales of such Nuvelo Products and (b) shall be solely responsible for any
Third Party Royalty; and

                    (2) With respect to Archemix Products, Archemix (a) shall pay to Nuvelo a royalty equal to
[***] percent [***] of the Net Sales of such Archemix Products and (b) shall be solely responsible
for any Third Party Royalty.

          (c) Manufacturing.

               (i) If this Agreement is terminated by Nuvelo, Nuvelo shall, or shall make the Third Party
manufacturer, as necessary, immediately provide to Archemix all process and manufacturing
technology, material and data and either transfer or provide access to regulatory filings
sufficient to enable Archemix or its Third Party designee to produce and supply Archemix’s
requirements of Development Compound or Licensed Product. Nuvelo shall cooperate with Archemix
with respect to such transfer so as to permit Archemix to begin manufacturing and supplying its own
requirements as soon as possible, including without limitation assigning any Third Party
manufacturing agreement to Archemix and providing technical advice (including reasonable advice
provided at the site of the new manufacturer). In addition, Nuvelo shall provide, or take such
action as necessary to make the then current Third Party manufacturer provide, a right of reference
and access to Archemix to all of Nuvelo’s or the Third Party manufacturer’s appropriate regulatory
filings for the manufacture of such Licensed Product.

               (ii) Transition Period. In an event Nuvelo terminates the Agreement pursuant to Section
12.1(b) and Archemix desires to carry on the Development and Commercialization of any Licensed
Product or Development Compound involved in such termination, Nuvelo shall remain obligated to its
responsibilities under the Development Plan,
and the Commercialization Plan, at the cost of Archemix, until it transitions to Archemix such
responsibilities, but in any event such period shall last no longer than ninety (90) days.
Promptly

36.

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.

 

 

following such termination, the Parties shall agree upon and implement a plan for
effecting such transition.

          (d) Other Effect of Termination; Completion of Clinical Trials. In any event, termination of
this Agreement shall not relieve the Parties of any liability which accrued hereunder before the
effective date of such termination nor preclude either Party from pursuing all rights and remedies
it may have hereunder or at law or in equity with respect to any breach of this Agreement nor
prejudice either Party’s right to obtain performance of any obligation.

          (e) Partnering Agreement. If Archemix terminates this Agreement under Section 12.1(a) and
Nuvelo has a Partnering Agreement in effect as of the effective date of such termination, the
Partnering Agreement will automatically be assigned to Archemix, and pursuant to the Partnering
Agreement the Third Party will be entitled to take an assignment of any and all rights of Nuvelo
under any manufacturing agreement with a third party supplier of the Licensed Product(s) that
is(are) the subject of the Partnering Agreement.

     12.3 Survival. In the event of expiration or termination of this Agreement, the following
provisions of this Agreement shall survive for the period of time set forth in the applicable
Section or Article, or if no period is specified, in perpetuity or the maximum amount of time
permitted under applicable law: Sections [***]

	13.	 	Representations and Covenants 

     13.1 Mutual Authority.

          (a) Nuvelo represents and warrants to Archemix that: (i) it has the authority and right to
enter into and perform this Agreement; and (ii) to the best of its knowledge the execution,
delivery and performance of this Agreement by Nuvelo will not conflict in any material fashion with
the terms of any other agreement to which it is or becomes a Party or by which it is or becomes
bound.

          (b) Archemix represents and warrants to Nuvelo that: (i) it has the authority and right to
enter into and perform this Agreement; and (ii) to the best of its knowledge the execution,
delivery and performance of this Agreement will not conflict in any material fashion with the terms
of any other agreement to which it is or becomes a Party or by which it is or becomes bound,
specifically including, without limitation, the Gilead-Archemix Agreement, the URC License
Agreement, the ULEHI Agreement, and the SomaLogic Agreements.

     13.2 Performance by Affiliates. The Parties recognize that each Party may perform some or all
of its obligations under this Agreement through Affiliates. Each Party shall remain responsible
and be guarantor of the performance by its Affiliates of any of the obligations under this
Agreement and shall cause its Affiliates to comply with the provisions of this Agreement in
connection with such performance. In particular, if any Affiliate of a Party participates in
Research or Development under this Agreement: (a) the restrictions of this Agreement which apply to
the activities of a Party with respect to Development Compounds shall apply equally to
the activities of such Affiliate; (b) the Party affiliated with such Affiliate shall assure,
and hereby guarantees, that any intellectual property developed by such Affiliate shall be governed
by the

37.

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.

 

 

provisions of this Agreement (and subject to the licenses set forth in Articles 8) as if
such intellectual property had been developed by the Party; and (c) the Party affiliated with such
Affiliate shall assure, and hereby guarantees, that such Affiliate shall abide by the
confidentiality obligations set forth in Article 10 as if such Affiliate were such Party.

     13.3 Receipt, Review and Understanding of Relevant Licenses.

          (a) As required under Section [***] of the URC License Agreement, the Parties to this
Agreement each hereby acknowledge and reference Gilead’s obligations under Articles [***] of the
URC License Agreement for the benefit of URC. In addition, the Parties to this Agreement
understand that, in accordance with Section [***] of the URC License Agreement, [***] with the
[***] to and[***] to the [***] of the [***], except as [***]

          (b) Nuvelo represents and warrants that prior to the execution of this Agreement, Nuvelo
received and reviewed the URC License Agreement and the Gilead-Archemix Agreement. Nuvelo further
represents and warrants that after receipt and review of the URC License Agreement and the
Gilead-Archemix Agreement, Nuvelo acknowledges and believes that the URC License Agreement and the
Gilead-Archemix Agreement state that: (i) Archemix’s rights in the Archemix Patents may revert to
Gilead or the UTC if Archemix, its Affiliates and all assignees and sublicensees cease reasonable
efforts to Develop and Commercialize Development Compounds and Licensed Products utilizing the
Archemix Patents; (ii) in the event of any termination of the URC License Agreement, the
sublicenses granted to Nuvelo hereunder shall remain in full force and effect in accordance with
Section 3.4 of the URC License Agreement so long as Nuvelo 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; and
(iii) in the event of any termination of the Gilead-Archemix Agreement, the sublicenses granted to
Nuvelo hereunder shall remain in full force and effect in accordance with Section 2.3 of the
Gilead-Archemix Agreement so long as Nuvelo agrees to be bound to Gilead as a licensor under the
terms and conditions of this Agreement and provided, that, if the termination of the
Gilead-Archemix Agreement arises out of the action or inaction of Nuvelo, Gilead, at its option,
may terminate such sublicense. In accordance with the representations and warranties made in
accordance with this Section 13.3, Nuvelo hereby agrees to conform to the obligations and
restrictions imposed upon it as a sublicensee under the Gilead-Archemix Agreement.

          (c) Archemix represents and warrants that it acknowledges and believes that the URC License
Agreement and the Gilead-Archemix Agreement state that: (i) in [***] of any [***] of the [***], the
[***] to [***] in [***] and [***] in accordance with [***] so long [***] in [***] of this [***] and
[***] to be [***] to[***] the [***] and [***] of this [***]; and (ii) in [***] of any [***] of the
[***] to [***] in this [***] in [***] in accordance with [***] so long [***] to be [***] to [***]
as a [***] the[***] and [***] of this [***] and [***], that, if the [***] of the [***] of the [***]
or [***] of [***], at its [***] such [***]. In accordance with the [***] and [***] this Section
13.3, [***] to the [***] as a [***] under the [***] under the [***] and as a [***] to the [***]

     13.4 Disclosure. Archemix represents and warrants that, to the best of its knowledge as of
the Effective Date, except as disclosed by Archemix to Nuvelo prior to the Effective Date, the
practice by Nuvelo of its rights under this Agreement with regard to the Research,

38.

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.

 

 

Development and
Commercialization of ARC2172 only does not infringe any Valid Claim of any issued patent owned or
Controlled by any Third Party. If Archemix becomes aware of any Valid Claim owned or controlled
by a Third Party that may be infringed by the manufacture, use or sale of any Short Acting
Coagulation Cascade Aptamer in the Field during the Term, Archemix will notify Nuvelo.

	14.	 	Indemnification and Limitation of Liability 

     14.1 Indemnification.

          (a) Archemix shall indemnify, defend and hold harmless Nuvelo, its Affiliates, their
respective directors, officers, employees and agents, and their respective successors, heirs and
assigns (collectively, the “Nuvelo 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 Nuvelo 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”), (i) arising in
the course of performance of the Research by Archemix during the Research Program Term or in the
exercise by Archemix of rights pursuant to Section 12.2 hereof, or (ii) arising out of Archemix’s
breach of a material obligation under, or representation or warranty contained in, this Agreement
or Archemix’s gross negligence or willful misconduct with respect to the performance of its
responsibilities hereunder, in all cases except to the extent arising from a breach of this
Agreement by, or the gross negligence or willful misconduct of, Nuvelo, its Affiliates, licensees
or sublicensees.

          (b) Nuvelo hereby agrees to defend and hold harmless Archemix and its directors, officers,
agents and employees (the “Archemix Indemnitees”) from and against any and all Losses resulting
from any Claims brought by a Third Party against the Archemix Indemnitees: (i) based on any breach
by Nuvelo of a material obligation under, or a representation or warranty contained in, this
Agreement; (ii) based on the possession, Research, Development, manufacture, use, offer for sale,
sale or other Commercialization, distribution, administration, storage or transport of any
Candidate Compound, Development Compound, Licensed Product or Nuvelo Product by Nuvelo, its
Affiliates, licensees or sublicensees, or (iii) based on the gross negligence or willful misconduct
of Archemix, its Affiliates, licensees or sublicensees, in the performance of this Agreement.

          (c) In the event that an Archemix Indemnitee or a Nuvelo Indemnitee, as the case may be, is
seeking indemnification under Section 14.1, it shall inform the indemnifying Party of a claim as
soon as reasonably practicable after it receives notice of the claim, shall permit the indemnifying
Party to assume direction and control of the defense of the claim (including the right to settle
the claim solely for monetary consideration), and shall cooperate as requested by the indemnifying
Party (at the expense of the indemnifying Party) in the defense of the claim.

     14.2 Limitation of Liability. EXCEPT AS EXPRESSLY PROVIDED IN SECTION 14.1, IN NO EVENT SHALL
EITHER PARTY, ITS DIRECTORS, OFFICERS, EMPLOYEES, AGENTS OR AFFILIATES BE LIABLE TO THE OTHER PARTY
FOR ANY INDIRECT,

39.

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.

 

 

INCIDENTAL, SPECIAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES, WHETHER BASED UPON A
CLAIM OR ACTION OF CONTRACT, WARRANTY, NEGLIGENCE, STRICT LIABILITY OR OTHER TORT, OR OTHERWISE,
ARISING OUT OF THIS AGREEMENT.

     14.3 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, INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR
OF FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT OF THIRD PARTY RIGHTS. IN ADDITION,
ARCHEMIX MAKES NO WARRANTIES AS TO THE VALIDITY OR ENFORCEABILITY OF THE LICENSED PATENT RIGHTS.

     14.4 Third Party Beneficiaries. To the [***] that [***] and/or [***] by the [***] and [***]
of this [***] to any [***] or [***] by a [***], the [***] and [***] as [***] Section 14.1 [***] to
[***] and [***]

	15.	 	Dispute Resolution 

     15.1 Disputes. The Parties recognize that disputes as to certain matters may from time to
time arise during the term of this Agreement that relate to either Party’s rights or obligations
hereunder. 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 Article 15 if and when a dispute arises under this Agreement. Either Party may
formally request resolution of a dispute by providing written notice to the other Party. The
Parties will refer any such dispute to the Chief Executive Officers of the Parties for attempted
resolution by good faith negotiations within thirty (30) days. In the event the Chief Executive
Officers are not able to resolve the dispute within such period, either Party may then invoke the
provisions of Sections 15.2 through 15.13.

     15.2 Arbitration for Disputes. Any dispute not resolved pursuant to Section 15.1 may be
submitted by either Party for final and binding arbitration in accordance with the terms of this
Agreement by JAMS. The arbitration will be conducted in New York, New York under the rules then in
effect for JAMS, except as provided herein, and the Parties consent to the personal jurisdiction of
the United States federal courts, for any case arising out of or otherwise related to this
arbitration, its conduct and its enforcement. Any situation not expressly covered by this
Agreement shall be decided in accordance with such rules of JAMS.

     15.3 Arbitrator for Dispute Resolution.

          (a) Subject to Section 15.3(b), the arbitrator shall be one (1) neutral, independent and
impartial arbitrator selected from a pool of retired federal judges to be presented
to the Parties by JAMS. Failing the agreement of the Parties as to the selection of the
arbitrator within thirty (30) days, the arbitrator shall be appointed by JAMS within the subsequent
30 days.

40.

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.

 

 

          (b) Upon the written request of either Party before the commencement of the arbitrator’s
duties pursuant to this Article 15, there shall be three (3) arbitrators rather than one (1). If
such request is made before the selection of an arbitrator pursuant to Section 15.3(a), then within
thirty (30) days after such request each Party shall select one (1) neutral, independent and
impartial arbitrator from the pool of retired federal judges presented to the Parties by JAMS and
within thirty (30) days thereafter those two (2) arbitrators shall select the third
(3rd) arbitrator from such pool. If such request is made after the selection of an
arbitrator pursuant to Section 15.3(a), then within thirty (30) days after such request each Party
shall select one (1) additional arbitrator from the pool from which the first arbitrator was
selected.

     15.4 Governing Law for Dispute Resolution. Resolution of all disputes and any remedies
relating thereto, shall be governed by and construed under the substantive laws of the State of New
York, without regard to conflicts of law rules that would provide for application of the law of a
jurisdiction outside New York.

     15.5 Rules of Procedure. The Parties shall be entitled to discovery as provided in the
Federal Rules of Civil Procedure and the local rules of the Federal District Court in the Southern
District of New York, provided, however, that all discovery shall be conducted expeditiously within
the time limit set by the arbitrators selected pursuant to Section 15.3. At the hearing, the
Parties may present testimony (either by live witness or deposition) and documentary evidence.
Each Party shall have the right to be represented by counsel.

     15.6 Rules of Evidence. The Federal Rules of Evidence shall apply to any and all matters
submitted to final and binding arbitration under this Agreement.

     15.7 Decision. The power of the arbitrator to fashion procedures and remedies within the
scope of this Agreement is recognized by the Parties as essential to the success of the arbitration
process. The arbitrator shall not have the authority to fashion remedies which would not be
available to a federal judge hearing the same dispute. The arbitrator is encouraged to operate on
this premise in an effort to reach a fair and just decision but shall fashion such rules and
procedures to best approximate Federal rules and procedures except with respect to procedural time
limits and delays (which shall be set by the arbitrator pursuant to Section 15.5). Reasons for the
arbitrator’s decisions should be complete and explicit. A full transcript and record of the
proceedings as well as written decisions including all determinations of law and fact shall be
provided for the appellate process. The written reasons should also include the basis for any
damages awarded and a statement of how the damages were calculated. Such a written decision shall
be rendered by the arbitrator following a full comprehensive hearing no later than twelve (12)
months following the selection of the arbitrator as provided for in Section 15.3.

     15.8 Award.

          (a) The award shall be paid in U.S. dollars free of any tax, deduction or offset; and any
costs, fees or taxes incident to enforcing the award shall, to the maximum extent permitted by law,
be charged against the Party resisting enforcement.

          (b) If as to any issue the arbitrator should determine under the applicable law that the
position taken by a Party is frivolous or otherwise irresponsible or that any wrongdoing

41.

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.

 

 

they find is in callous disregard of law and equity or the rights of the other Party, the
arbitrator shall also award an appropriate allocation of the adversary’s reasonable attorney fees,
costs and expenses to be paid by the offending Party, the precise sums to be determined after a
bill of attorney fees, expenses and costs consistent with such award has been presented following
the award on the merits.

          (c) Each Party agrees to abide by the award rendered in any arbitration conducted pursuant to
this Article 15, and agrees that a judgment of any Federal District Court having jurisdiction may
be entered upon the final award and that other courts may award full faith and credit to such
judgment in order to enforce such award.

          (d) The award shall include interest from the date of any damages incurred for breach of the
Agreement, and from the date of the award until paid in full, at a rate fixed by the arbitrator.

          (e) With respect to money damages, nothing contained herein shall be construed to permit the
arbitrator(s) or any court or any other forum to award punitive, consequential or exemplary
damages. By entering into this agreement to arbitrate, the Parties expressly waive any claim for
punitive or exemplary damages. The only damages recoverable under this Agreement are compensatory
damages. For clarity, the foregoing shall not be interpreted to limit or to expand the express
rights specifically granted in this Agreement.

     15.9 Costs. Except as set forth in Section 15.8, each Party shall bear its own legal fees.
The arbitrator shall assess his or her costs, fees and expenses against the Party losing the
arbitration unless he or she believes that neither Party is the clear loser, in which case the
arbitrator shall divide his or her fees, costs and expenses according to his or her sole
discretion.

     15.10 Injunctive Relief. Provided a Party has made a sufficient showing under the rules and
standards set forth in the Federal Rules of Civil Procedure and applicable case law, the arbitrator
shall have the freedom to invoke, and the Parties agree to abide by, injunctive measures after
either Party submits in writing for arbitration claims requiring immediate relief.

     15.11 Confidentiality for Dispute Resolution. The arbitration proceeding shall be confidential
and the arbitrator shall issue appropriate protective orders to safeguard each Party’s Confidential
Information. Except as required by law, no Party shall make (or instruct the arbitrator to make)
any public announcement with respect to the proceedings or decision of the arbitrator without prior
written consent of each other Party. The existence of any dispute submitted to arbitration, and
the award, shall be kept in confidence by the Parties and the arbitrator, except as required in
connection with the enforcement of such award or as otherwise required by applicable law.

     15.12 Survivability. Any duty to arbitrate under this Agreement shall remain in effect and be
enforceable after termination of the contract for any reason.

     15.13 Jurisdiction. For the purposes of this Article 15, the Parties acknowledge their
diversity (Nuvelo having its principal place of business in California and Archemix having its
principal place of business in Massachusetts).

42.

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.

 

 

     15.14 Patents and Trademarks. Any dispute, controversy or claim relating to the scope,
validity, enforceability or infringement of any Compound Patent Rights covering the manufacture,
use, importation, offer for sale or sale of any Licensed Product or of any Nuvelo trademarks,
Archemix trademarks, or trademark rights related to any Licensed Product shall be submitted to a
court of competent jurisdiction in the country in which such Patent or trademark rights were
granted or arose.

     15.15 Termination of Pending Arbitration.

          (a) No later than five (5) business days after the Effective Date, the Parties will
submit a written agreement to JAMS, consenting to terminate the Arbitration, with prejudice.

          (b) With respect to the dismissal with prejudice of the Arbitration, each Party will
bear its own fees and costs.

16. Miscellaneous 

     16.1 Entire Agreement; Amendment. This Agreement, including the Exhibits attached hereto and
the expressly referenced provisions of the other agreements referenced herein, sets forth the
complete, final and exclusive agreement between the Parties, and this Agreement sets forth all the
covenants, promises, agreements, warranties, representations, conditions and understandings between
the Parties hereto and supersedes all prior agreements and understandings between the Parties,
including without limitation the Original Agreement. There are no covenants, promises, agreements,
warranties, representations, conditions or understandings, either oral or written, between the
Parties other than as are set forth in this Agreement. No subsequent alteration, amendment, change
or addition to this Agreement shall be binding upon the Parties unless reduced to writing and
signed by an authorized officer of each Party.

     16.2 Bankruptcy.

          (a) All rights and licenses granted under or pursuant to this Agreement, including amendments
hereto, by each Party to the other Party are, for all purposes of Section 365(n) of Title 11 of the
U.S. Code (“Title 11”), licenses of rights to intellectual property as defined in Title 11. Each
Party agrees during the term of this Agreement to create and maintain current copies or, if not
amenable to copying, detailed descriptions or other appropriate embodiments, to the extent
feasible, of all such intellectual property. If a case is commenced by or against either Party
(the “Bankrupt Party”) under Title 11, then, unless and until this Agreement is rejected as
provided in Title 11, the Bankrupt Party (in any capacity, including debtor-in-possession) and its
successors and assigns (including, without limitation, a Title 11 Trustee) shall, at the election
of the Bankrupt Party made within sixty (60) days after the commencement of the case (or, if no
such election is made, immediately upon the request of the non-Bankrupt Party) either: (i) perform
all of the obligations provided in this Agreement to be performed by the Bankrupt Party including,
where applicable and without limitation, providing to the non-Bankrupt Party portions of such
intellectual property (including embodiments thereof) held by the Bankrupt Party and such
successors and assigns or otherwise available to them; or (ii) provide to the non-Bankrupt Party
all such intellectual property (including all embodiments

43.

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.

 

 

thereof) held by the Bankrupt Party and such successors and assigns or otherwise available to
them.

          (b) If a Title 11 case is commenced by or against the Bankrupt Party and this Agreement is
rejected as provided in Title 11 and the non-Bankrupt Party elects to retain its rights hereunder
as provided in Title 11, then the Bankrupt Party (in any capacity, including debtor-in-possession)
and its successors and assigns (including, without limitations, a Title 11 Trustee) shall provide
to the non-Bankrupt Party all such intellectual property (including all embodiments thereof) held
by the Bankrupt Party and such successors and assigns or otherwise available to them immediately
upon the non-Bankrupt Party’s written request therefore. Whenever the Bankrupt Party or any of its
successors or assigns provides to the non-Bankrupt Party any of the intellectual property licensed
hereunder (or any embodiment thereof) pursuant to this Section 16.2, the non-Bankrupt Party shall
have the right to perform the obligations of the Bankrupt Party hereunder with respect to such
intellectual property, but neither such provision nor such performance by the non-Bankrupt Party
shall release the Bankrupt Party from any such obligation or liability for failing to perform it.

          (c) All rights, powers and remedies of the non-Bankrupt Party provided herein are in addition
to and not in substitution for any and all other rights, powers and remedies now or hereafter
existing at law or in equity (including, without limitation, Title 11) in the event of the
commencement of a Title 11 case by or against the Bankrupt Party. The non-Bankrupt Party, in
addition to the rights, power and remedies expressly provided herein, shall be entitled to exercise
all other such rights and powers and resort to all other such remedies as may now or hereafter
exist at law or in equity (including, without limitation, under Title 11) in such event. The
Parties agree that they intend the foregoing non-Bankrupt Party rights to extend to the maximum
extent permitted by law and any provisions of applicable contracts with Third Parties, including
without limitation for purposes of Title 11: (i) the right of access to any intellectual property
(including all embodiments thereof) of the Bankrupt Party or any Third Party with whom the Bankrupt
Party contracts to perform an obligation of the Bankrupt Party under this Agreement, and, in the
case of the Third Party, which is necessary for the development, registration and manufacture of
licensed products; and (ii) the right to contract directly with any Third Party described in
subsection (i) above to complete the contracted work. Any intellectual property provided pursuant
to the provisions of this Section 16.2 shall be subject to the licenses set forth elsewhere in this
Agreement and the payment obligations of this Agreement, which shall be deemed to be royalties for
purposes of Title 11.

     16.3 Force Majeure. Both Parties shall be excused from the performance of their obligations
under this Agreement to the extent that such performance is prevented by force majeure and 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 takes reasonable efforts to remove the condition. For purposes of this
Agreement, force majeure shall include conditions beyond the control of the Parties, including,
without limitation, an act of God, voluntary or involuntary compliance with any regulation, law or
order of any government, war, civil commotion, labor strike or lock-out, epidemic, failure or
default of public utilities or common carriers, destruction of production facilities or materials
by fire, earthquake, storm or like catastrophe; provided, however, the payment of invoices due and
owing hereunder shall not be delayed by the payer because of a

44.

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.

 

 

force majeure affecting the payer, unless such force majeure specifically precludes the
payment process.

     16.4 Notices. Any notice required or permitted to be given under this Agreement shall be in
writing, shall specifically refer to this Agreement and shall be deemed to have been sufficiently
given for all purposes if (a) mailed by first class certified or registered mail, return receipt
requested, postage prepaid, (b) express delivery service providing evidence of receipt or (c)
personally delivered. Unless otherwise specified in writing, the mailing addresses of the Parties
shall be as described below.

	 	 	 	 	 	 	 
	 

	 	For Nuvelo:
	 	Nuvelo, Inc.

201 Industrial Road, Suite 310

San Carlos, CA 94070

Fax: (650) 517-8058

Attention: CEO

Copy: Legal Department
	 	 
	 
	 	 	 	 	 	 
	 

	 	For Archemix:
	 	Archemix Corp.

300 Third Street

Cambridge, MA 02142

Fax: (617) 621-9300

Attention: Legal Department	 	 

     16.5 Consents Not Unreasonably Withheld or Delayed. Except as expressly stated to the
contrary, whenever provision is made in this Agreement for either Party to secure the consent or
approval of the other Party, that consent or approval shall not unreasonably be withheld or
delayed, and whenever in this Agreement provisions are made for one Party to object to or
disapprove a matter, such objection or disapproval shall not unreasonably be exercised.

     16.6 Maintenance of Records. Each Party shall keep and maintain all records required by law
or regulation with respect to Products and shall make copies of such records available to the other
Party upon reasonable request.

     16.7 United States Dollars. References in this Agreement to “Dollars” or “$” shall mean the
legal tender of the United States of America.

     16.8 No Strict Construction. This Agreement has been prepared jointly and shall not be
strictly construed against either Party.

     16.9 Assignment. Except as otherwise specifically provided to the contrary in this Agreement,
neither Party may assign or transfer this Agreement or any rights or obligations hereunder without
the prior written consent of the other; provided, that, a Party may make such an assignment without
the other Party’s consent to an Affiliate or in conjunction with a merger, acquisition, or sale of
all or substantially all of the assets of such Party to which this Agreement pertains. Any
assignment or attempted assignment by either Party in violation of the terms of this Section 16.9
shall be null and void and of no legal effect.

45.

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.

 

 

     16.10 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.

     16.11 Further Actions. Each Party agrees to execute, acknowledge and deliver such further
instruments, and to do all such other acts, as may be necessary or appropriate in order to carry
out the purposes and intent of this Agreement.

     16.12 Severability. If any one or more of the provisions of this Agreement is held to be
invalid or unenforceable by any court of competent jurisdiction from which no appeal can be or is
taken, the provision shall be considered severed from this Agreement and shall not serve to
invalidate any remaining provisions hereof. The Parties shall make a good faith effort to replace
any invalid or unenforceable provision with a valid and enforceable one such that the objectives
contemplated by the Parties when entering this Agreement may be realized.

     16.13 Ambiguities. Ambiguities, if any, in this Agreement shall not be construed against any
Party, irrespective of which Party may be deemed to have authored the ambiguous provision.

     16.14 Headings. The headings for each Article and Section in this Agreement, and in the
Exhibits, have been inserted for convenience of reference only and are not intended to limit or
expand on the meaning of the language contained in the particular Article or Section.

     16.15 No Waiver. Any delay in enforcing a Party’s rights under this Agreement or any waiver
as to a particular default or other matter shall not constitute a waiver of such Party’s rights to
the future enforcement of its rights under this Agreement, excepting only as to an express written
and signed waiver as to a particular matter for a particular period of time.

     16.16 Tax Treatment and Tax Structure Disclosure. Notwithstanding anything herein to the
contrary, any Party to this Agreement (and any employee, representative, or other agent of any
Party to this Agreement) may disclose to any and all persons, without limitation of any kind, the
tax treatment and tax structure of the transactions contemplated by this Agreement and all
materials of any kind (including opinions or other tax analyses) that are provided to it relating
to such tax treatment and tax structure; provided, however, that such disclosure may not be made to
the extent a lack of disclosure is reasonably necessary to comply with any applicable federal or
state securities laws. For the purposes of the foregoing sentence: (a) the “tax treatment” of a
transaction means the purported or claimed federal income tax treatment of the transaction; and (b)
the “tax structure” of a transaction means any fact that may be relevant to understanding the
purported or claimed federal income tax treatment of the transaction.

46.

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.

 

 

In Witness Whereof, the Parties have executed this Agreement in duplicate originals by
their proper officers as of the date and year first above written.

	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Nuvelo, Inc.	 	Archemix Corp.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
	 	/s/ Ted W. Love 	 	 	By:	 	/s/ Errol De Souza 
	 
	 	 	 	 	 	 	 	 	 
	 	 	Name:
	 	Ted W. Love, M.D.	 	 	 	 	Name:	 	Errol De Souza	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Title:
	 	Chairman and Chief Executive
Officer	 	 	 	 	Title:	 	President and CEO	 	 
	 

	 	 	 	 
	 	 	 	 	 	 	 	 	 

47.

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 A

DETERMINATION OF CERTAIN ACCOUNTING TERMS

Except where the context requires otherwise, capitalized terms used but not defined below shall
have the meanings assigned to them in the Agreement to which this Exhibit A is attached.

1. “Product Profit and Loss” has the meaning assigned to it in Section 1.67 of the Agreement and
shall be determined in the manner specified below. All amounts shall be determined in accordance
with generally accepted accounting principles (“GAAP”), consistently applied.

2. “Cost of Goods” means the actual cost of Licensed Products shipped in either bulk or final
therapeutic form as appropriately invoiced to the Parties by the then current Third Party
manufacturer of the applicable Licensed Products. The cost of Licensed Product manufactured by
Third Parties shall equal Nuvelo’s actual costs therefore. For purposes of calculating Product
Profit and Loss in any calendar quarter, the actual cost of Licensed Products shipped shall be
calculated on an accrual basis.

3. Marketing, Sales and Distribution Costs

     3.1. “Marketing, Sales and Distribution Costs” shall be the sum of Selling Expenses, Marketing
Management, Market and Consumer Research, Advertising, Trade Promotion, Consumer Promotion,
Education, and Distribution Expenses, each of which is specified below, and all other costs which
are generally consistent with the Commercialization Plan, and attributable to the sale, promotion
or marketing of Licensed Products.

     3.2. “Selling Expenses” means all costs and expenses directly associated with the efforts of
field sales representatives with respect to Licensed Products, including field sales force
(including field sales managers); field sales offices; home offices staffs directly involved in the
management of and the performance of the selling functions; and payments to Third Parties under
co-promotion agreements. Field samples shall normally be charged to Trade Promotion, but if sales
management has direct decision-making authority for the distribution of field sales samples, it may
be appropriate to charge these costs to Selling Expenses. In cases where the same sales force is
detailing Licensed Products and other products that are not Licensed Products, the costs of
detailing sales calls shall be allocated on a pro rata basis based upon net sales of each
respective product during the most recent quarter.

     3.3. “Marketing Management” shall include product management and sales promotion management
compensation and departmental expenses, including product related public relations, relationships
with opinion leaders and professional societies, health care economics studies, contract pricing
and administration, market information systems, governmental affairs activities for reimbursement,
formulary acceptance and other activities directly related to the Licensed Products, management and
administration of managed care and national accounts and other activities associated with
developing overall sales and marketing strategies and planning for Licensed Products. In addition,
payments to Third Parties in connection with trademark selection, filing, prosecution and
enforcement shall be included 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.

 

 

this category. In the event that Nuvelo is concurrently selling additional products that are
not Licensed Products, such costs may be allocated on a pro rata basis based upon net sales of each
respective product during the most recent quarter.

     3.4. “Market and Consumer Research” shall include compensation and departmental expenses for
market and consumer research personnel and payments to Third Parties related to conducting and
monitoring professional and consumer appraisals of existing, new or proposed Licensed Products such
as market share services (e.g., IMS data), special research testing and focus groups. In the event
that Nuvelo is concurrently selling additional other products, expenditures not directly related to
a Licensed Product may be allocated on a pro rata basis based upon net sales of each respective
product during the most recent quarter on a percent of sales or other basis consistently applied
which is no less favorable to the Licensed Products than the internal allocation for Nuvelo’s other
products.

     3.5. “Advertising” means all costs incurred for the advertising and promotion of Licensed
Products through any means, including, without limitation: (a) television and radio advertisements;
(b) advertisements appearing in journals, newspapers, magazines or other media; (c) seminars and
conventions; (d) packaging design; (e) professional education programs; (f) samples, visual aids
and other selling materials; (g) hospital formulary committee presentations; (h) presentations to
state and other governmental formulary committees; and (i) all media costs associated with Licensed
Product advertising as follows: production expense/artwork including set up; design and art work
for an advertisement; the cost of securing print space, air time, and the like in newspapers,
magazines, trade journals, television, radio, billboards, and the like.

     3.6. “Trade Promotion” shall include the allowances given to retailers, brokers, distributors,
hospital buying groups, and the like for purchasing, promoting, and distribution of Licensed
Products. This shall include purchasing, advertising, new distribution, and display allowances as
well as free goods, wholesale allowances and field sales samples. To the extent multiple products
are involved and some of such products are not Licensed Products, then such allowances shall be
allocated on a pro rata basis based upon net sales of each respective product during the most
recent quarter.

     3.7. “Consumer Promotion” shall include the expenses associated with programs to promote
Licensed Products directly to the end user. This category shall include expenses associated with
promoting products directly to the professional community such as professional samples,
professional literature, promotional material costs, patient aids and detailing aids. To the
extent multiple products are involved and some of such products are not Licensed Products, then
such allowances shall be allocated on a pro rata basis based upon net sales of each respective
product during the most recent quarter.

     3.8. “Education” shall include expenses associated with professional education with respect to
Licensed Products through any means not covered above, including articles appearing in journals,
newspapers, magazines or other media; seminars, scientific exhibits, and conventions; and symposia,
advisory boards and opinion leader development activities.

     3.9. “Distribution Expenses” means an amount equal to a percentage of Net Sales to be
determined after the characteristics and anticipated price of the Licensed Products have been

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.

 

 

determined. Such percentage shall be agreed upon by the Parties in good faith, and shall be
designed to approximate Nuvelo’s cost of distributing such Licensed Products.

4. Post-Launch Product R&D Expenses

     4.1. “Post-Launch Product R&D Expenses” shall include certain research and development costs
incurred by a Party in relation to a Licensed Product after the first commercial launch and shall
exclude administrative expenses and costs that are included within Costs of Goods or Development
Costs. Such post-launch research and development costs shall include the following expenses only
if such expenses are directly attributable to a Licensed Product:

          (a) Phase 4 Clinical Trials;

          (b) Ongoing product support;

          (c) Ongoing medical affairs;

          (d) Preclinical research;

          (e) Contract research and development costs performed by others for a particular project that
have no alternative future uses in other research and development projects or otherwise; and

          (f) Fees and expenses of outside counsel in respect of regulatory affairs unrelated to
obtaining Regulatory Approvals.

5. Allocated Administration Expenses

     5.1. The costs eligible for allocation as “Allocated Administration Expenses” shall include
the following: The direct costs of finance, management information services, human resources,
payroll, information system, accounting and employees engaged in general management functions for
the operating units in question, including direct costs of employees performing administration
functions, the costs of supporting such individuals in the performance of their job (e.g.,
occupancy costs, travel, computers, and telephones), and outside services (e.g., consulting and
audit services). Such costs shall be calculated in accordance with Nuvelo’s customary accounting
methodology, consistently applied throughout such organization. Such costs shall be allocated
based on the percentage such costs are of Nuvelo’s total net sales during the relevant quarter.
Cost categories included within Allocated Administration Expenses shall not be included in any
other cost recoverable under this Agreement.

     5.2. The Parties shall attempt to agree upon a fixed percentage of Net Sales to cover the
expected Allocated Administration Expenses.

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.

 

 

6. Currency Gains or Losses 

     6.1. “Currency Gains or Losses” shall include the following:

          (a) Unhedged Transactions. Transaction gains or losses are those which result from a change
in exchange rates between the functional currency and the currency in which the transaction is
denominated. The transaction gain or loss is determined by measuring the increase or decrease in
the functional currency cash flow due to the changes in the exchange rate from the date of the
transaction to the settlement date. The difference between the functional currency amount
calculated using the current exchange rate at the transaction date and the amount calculated using
the currency exchange rate at the settlement date is the transaction gain or loss. Transaction
gains or losses on unsettled foreign currency transactions are also reported in this manner. When
there is a balance sheet date between the transaction date and settlement date, the gain or loss on
the unsettled balance shall be measured using the current exchange rate at the balance sheet date.

          (b) Hedged Transactions. For purposes of this collaboration, Nuvelo will not buy or sell
forward, directly or indirectly, foreign currencies in amounts greater than those which can
reasonably be expected to be received or paid, as the case may be, over the relevant time period.
If Nuvelo enters into a hedged transaction, the gain or loss realized from the hedge, net of
hedging transaction costs, must be included in the underlying transaction. If the currency
transaction gain or loss has been included in Net Sales, inventories, Costs of Goods, or any other
category defined herein, it shall not be included in this category.

7. Calculation of the cost of capital. The Parties shall attempt to agree upon a fixed
percentage of Net Sales to cover the expected cost of capital committed to the Collaboration.

8. Allocation of Costs. The following guidelines shall be used to allocate costs to the
Licensed Products:

          (a) If the expense is specifically and exclusively used for the Commercialization of a
Licensed Product, one hundred percent (100%) of such expense shall be an Allowable
Commercialization Expense.

          (b) If the expense is not specifically and exclusively used for the Commercialization of a
Licensed Product (i.e., also for other products of Lead Marketing Party), it shall be allocated
based on objective means (such as man-hours or amounts consumed) or, if such method cannot
reasonably be used, based on Net Sales of each such product.

          (c) No item of cost shall be duplicated in any of the categories comprising Allowable
Commercialization Expenses.

          (d) As more fully set forth above, for purposes of calculating Product Profit and Loss in any
calendar quarter, the expense shall be the accrued costs.

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

Coagulation Cascade Proteins

[***] Thrombin [***]

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 C

Criteria for Short Acting Characteristics of Aptamers

For purposes of this Agreement, an Aptamer is a “Short Acting Coagulation Cascade Aptamer” if the
Aptamer has [***]

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 D

ARC 2172 Sequence

[***]

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 E

REGIONAL OFFICES OR COUNTRIES IN WHICH

PATENT APPLICATIONS ARE TO BE NATIONALIZED

OR OTHERWISE PROSECUTED, FILED AND MAINTAINED

[***]

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 F

Stock Purchase Agreement

STOCK PURCHASE AGREEMENT

by and between

ARCHEMIX CORP.

and

NUVELO, INC.

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	 	 	 	3
	 

	 	 	3.1	 	 	Organization, Qualifications and Corporate Power
	 	 	 	3
	 

	 	 	3.2	 	 	Authorization of Agreements, Etc.
	 	 	 	3
	 

	 	 	3.3	 	 	Validity
	 	 	 	4
	 

	 	 	3.4	 	 	Consents
	 	 	 	4
	 

	 	 	3.5	 	 	Subsidiaries
	 	 	 	4
	 

	 	 	3.6	 	 	Capitalization
	 	 	 	4
	 

	 	 	3.7	 	 	Litigation
	 	 	 	5
	 

	 	 	3.8	 	 	Financial Statements
	 	 	 	5
	 

	 	 	3.9	 	 	Taxes
	 	 	 	5
	 

	 	 	3.10	 	 	Intellectual Property
	 	 	 	5
	 

	 	 	3.11	 	 	Brokers
	 	 	 	5
	 

	 	 	3.12	 	 	Insurance
	 	 	 	5
	 

	 	 	3.13	 	 	Prospectus
	 	 	 	6
	 

	 	 	3.14	 	 	Offering Valid
	 	 	 	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
	 	 	 	6
	 

	 	 	4.5	 	 	Brokers
	 	 	 	6
	 

	 	 	4.6	 	 	Authorization
	 	 	 	6
	 
	 	 	 	 	 	 	 	 	 	 
	SECTION 5 Purchaser’s Conditions to Closing	 	 	 	7
	 

	 	 	5.1	 	 	Representations and Warranties
	 	 	 	7
	 

	 	 	5.2	 	 	Performance
	 	 	 	7
	 

	 	 	5.3	 	 	Legal Investment
	 	 	 	7

(i)

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.

 

 

	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	5.4	 	 	Rights Agreement
	 	 	 	7
	 

	 	 	5.5	 	 	Proceedings and Documents
	 	 	 	7
	 

	 	 	5.6	 	 	Qualifications
	 	 	 	7
	 

	 	 	5.7	 	 	Qualified IPO
	 	 	 	7
	 

	 	 	5.8	 	 	Legal Opinion
	 	 	 	7
	 
	 	 	 	 	 	 	 	 	 	 
	SECTION 6 Company’s Conditions to Closing	 	 	 	8
	 

	 	 	6.1	 	 	Representations and Warranties
	 	 	 	8
	 

	 	 	6.2	 	 	Performance
	 	 	 	8
	 

	 	 	6.3	 	 	Legal Investment
	 	 	 	8
	 

	 	 	6.4	 	 	Rights Agreement
	 	 	 	8
	 

	 	 	6.5	 	 	Payment of Purchase Price
	 	 	 	8
	 
	 	 	 	 	 	 	 	 	 	 
	SECTION 7 Miscellaneous	 	 	 	8
	 

	 	 	7.1	 	 	Governing Law
	 	 	 	8
	 

	 	 	7.2	 	 	Survival
	 	 	 	8
	 

	 	 	7.3	 	 	Successors and Assigns
	 	 	 	8
	 

	 	 	7.4	 	 	Entire Agreement; Amendment and Waiver
	 	 	 	9
	 

	 	 	7.5	 	 	Notices
	 	 	 	9
	 

	 	 	7.6	 	 	Delays or Omissions
	 	 	 	10
	 

	 	 	7.7	 	 	Severability
	 	 	 	10
	 

	 	 	7.8	 	 	Interpretation
	 	 	 	10
	 

	 	 	7.9	 	 	Further Assurances
	 	 	 	10
	 

	 	 	7.10	 	 	Headings
	 	 	 	10
	 

	 	 	7.11	 	 	Counterparts
	 	 	 	10

Exhibits

Exhibit A — Registration Rights Agreement

Schedules

[Disclosure Schedule]

(ii)

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.

 

 

ARCHEMIX CORP.

STOCK PURCHASE AGREEMENT

     THIS STOCK PURCHASE AGREEMENT dated as of [                    ] (the “Agreement”) is made by and between
Archemix Corp., a Delaware corporation (the “Company”), and Nuvelo, Inc., a Delaware corporation
(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 7.3 of that certain Amended and Restated Collaboration and License Agreement
between the Company and the Purchaser dated July [          ], 2006;

     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:

          “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.

          “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.

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

          “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.

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

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

 

 

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

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

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

          “Qualified IPO” means the Company’s firm commitment underwritten initial public offering on
the New York Stock Exchange, the American Stock Exchange or the NASDAQ Global Market filed under
the Securities Act of 1933, as amended, covering the offer and sale of Company Common Stock, with
total gross offering proceeds to Company (prior to underwriter commissions and expenses) of at
least thirty million dollars ($30,000,000) exclusive of the Purchase Price.

          “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.

          “Rights Agreement” shall mean the Registration Rights Agreement dated as of the date hereof
by and between the Company and the Purchaser in the form attached hereto as Exhibit A.

          “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”;

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

          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.

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.

 

 

Authorization, Purchase and Sale of the Shares

     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”).

     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:

     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, the Rights Agreement and any other
agreements, documents or instruments contemplated hereby to which it is a party, to issue, sell and
deliver the Shares.

     Authorization of Agreements, Etc. 

The execution and delivery by the Company of this Agreement and the Rights 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

3.

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.

 

 

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 to which the
Company is a party or by which it or its assets are 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, 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.

          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 except as set forth in the
Rights Agreement. 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.

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

     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 or its assets are 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, or such filings required by the Rights Agreement). The sale of the Shares is not
subject to any preemptive rights or rights of first refusal that have not been properly waived or
complied with.

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

     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. All issued and outstanding shares of the Company’s capital stock have been duly
authorized and validly issued, are fully paid and nonassessable, and were issued in compliance with
all applicable state and federal laws concerning the issuance of securities.

     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

4.

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.

 

 

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.

     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, for all of
the required footnotes and year end adjustments, which are not expected to be material).

     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.

     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. Without diminishing the representation set forth in the preceding
sentence, the Company further represents that it has taken commercially reasonable steps to ensure
that 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.

     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.

     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.

     Prospectus. The Prospectus does not contain any untrue statement of a material fact
or omit to state any material fact required to be stated therein or necessary to make the
statements therein not misleading in light of the circumstances under which they were made.

5.

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.

 

 

     Offering Valid. Assuming the accuracy of the representations and warranties of
Purchaser contained in Section 4 hereof, the offer, sale and issuance of the Shares will be exempt
from the registration requirements of the Act, and will have been registered or qualified (or are
exempt from registration and qualification) under the registration, permit or qualification
requirements of all applicable state securities laws.

Representations and Warranties of Purchaser

     The Purchaser represents and warrants to the Company as follows:

     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.

     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.

     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.

     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.

     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.

     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 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.

Purchaser’s Conditions to Closing

6.

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.

 

 

     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:

     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.

     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.

     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.

     Rights Agreement. The Company and the Purchaser shall have executed and delivered the
Rights Agreement.

     Proceedings and Documents. All corporate and other proceedings in connection with the
transactions contemplated hereby and all documents and instruments 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 and the Rights 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.

     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.

     Qualified IPO. The Qualified IPO shall have been completed and the proceeds therefrom
shall have been received by the Company.

     Legal Opinion. The Purchaser shall have received from legal counsel to the Company an
opinion addressed to the Purchaser, dated as of the Closing Date, in form customarily delivered in
connection with the private placement of shares of common stock of a publicly traded company and
acceptable to the Purchaser, acting reasonably.

7.

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.

 

 

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:

     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.

     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.

     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.

     Rights Agreement. The Company and the Purchaser shall have executed and delivered the
Rights Agreement.

     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

     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.

     Survival. The representations, warranties, covenants and agreements made herein shall
survive the closing of the transactions contemplated hereby. All statements as to factual matters
contained in any certificate or other instrument delivered by or on behalf of the Company pursuant
hereto in connection with the transactions contemplated hereby shall be deemed to be
representations and warranties by the Company hereunder solely as of the date of such certificate
or instrument.

     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.

     Entire Agreement; Amendment and Waiver. This Agreement (including the Schedules and
Exhibits hereto) and the other documents delivered pursuant hereto constitute the full and

8.

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.

 

 

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.

     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: Legal Department
	 

	 	Facsimile: (617) 621-9300
	 
	 	 
	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:

	 	Nuvelo, Inc.
	 

	 	201 Industrial Road, Suite 310
	 

	 	San Carlos, CA 94070
	 

	 	Attn: Chief Executive Officer
	 

	 	Facsimile: (650) 517-8058
	 
	 	 
	With a copy to:

	 	Cooley Godward LLP
	 

	 	Five Palo Alto Square
	 

	 	3000 El Camino Real
	 

	 	Palo Alto, CA 94306-2155
	 

	 	Attn: John Geschke, Esquire
	 

	 	Facsimile: (650) 849-7400

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.

9.

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.

 

 

     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.

     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.

     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 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.

     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.

     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.

     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]

10.

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.

 

 

     IN WITNESS WHEREOF, the parties have duly executed this Stock Purchase Agreement as of the
date first above written.

	 	 	 	 	 
	 	COMPANY:

ARCHEMIX CORP.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 
	 	PURCHASER:

NUVELO, INC.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

 11.

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 G

Registration Rights Agreement

ARCHEMIX CORP.

REGISTRATION RIGHTS AGREEMENT

     This REGISTRATION RIGHTS AGREEMENT dated as of [___] (the “Agreement”) is made by and
between Archemix Corp., a Delaware corporation (the “Company”), and Nuvelo, Inc., a Delaware
corporation (the “Investor”).

     WHEREAS, the Company proposes to issue and sell to the Investor certain shares of its common
stock, par value $.001 per share (“Common Stock”) pursuant to the Stock Purchase Agreement by and
between the Company and Investor of even date herewith (the “Stock Purchase Agreement”) as provided
in Section 7.3 of that certain Amended and Restated Collaboration and License Agreement between the
Company and the Purchaser dated July [  ], 2006 (the “Collaboration Agreement”);

     WHEREAS, as a condition to entering into the Stock Purchase Agreement, the Investor has
requested that the Company grant to it registration rights and certain other rights and covenants
set forth herein;

     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:

     Registration Rights. The Company and the Investor, as applicable, covenant and agree as
follows:

          Definitions. For purposes of this Agreement:

               The term “Act” means 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.

               The term “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.

               The term “Common Stock” shall have the meaning set forth in the recitals.

               The term “Form S-1” means a registration statement on Form S-1 or such other form under the
Act as in effect on the date hereof, or any registration form under the Act subsequently adopted by
the SEC, which permits the registration of securities under the Act for which no other form is
authorized or prescribed.

12.

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.

 

 

               The term “Form S-3” means a registration statement on Form S-3 or such other form under the
Act as in effect on the date hereof or any registration form under the Act subsequently adopted by
the SEC, which permits inclusion or incorporation of substantial information by reference to other
documents filed by the Company with the SEC or relates to secondary offerings.

               The term “Holder” means the Investor (so long as the Investor holds Registrable Securities)
and any person owning or having the right to acquire Registrable Securities or any assignee thereof
in accordance with Section 1.10 hereof.

               The term “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 Investor pursuant to the Collaboration Agreement.

               The terms “register”, “registered,” and “registration” refer to a registration effected by
preparing and filing a registration statement, other than a registration statement on Form S-4 on
Form S-8 or successor or comparable forms thereto, or similar document in compliance with the Act
and the declaration or ordering of effectiveness of such registration statement or document.

               The term “Registrable Securities” means (i) any shares of Common Stock issued to the Investor
pursuant to the Stock Purchase 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 Section 1 are not assigned;
provided, however, that shares of Common Stock which are Registrable Securities
shall cease to be Registrable Securities upon sale of such shares pursuant to a registration
statement or Rule 144 under the Act or upon the eligibility for immediate sale of all Registrable
Securities under Rule 144(k) under the Act.

               The term “SEC” means the Securities and Exchange Commission.

               The term “Special Registration Statement” means (i) a registration statement relating to any
employee benefit plan or (ii) with respect to any corporate reorganization or transaction under
Rule 145 of the Act, any registration statements related to the issuance or resale of securities
issued in such a transaction or (iii) a registration related to stock issued upon conversion of
debt securities.

          Sale or Transfer of Shares; Legend.

               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, in the event of a sale
pursuant to an exemption under the Act, if requested by the Company, the Company shall

13.

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.

 

 

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, provided further,
however, that an opinion of counsel shall not be required for sales under Rule 144 under
the Act.

               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 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, PROVIDED, HOWEVER, THAT AN
OPINION OF COUNSEL SHALL NOT BE REQUIRED FOR SALES MADE UNDER RULE 144 AND (2) THERE
SHALL HAVE BEEN COMPLIANCE WITH ALL APPLICABLE STATE SECURITIES LAWS.

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.

          “Piggyback” Registration.

               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 2.5, the Company shall, subject to
the provisions of this Section 1.3, use its reasonable best efforts to include in such registration
all of the Registrable Securities that each such Holder has requested to be registered.

               Company Deferral. In connection with any offering not involving an underwriting of
shares of the Company’s capital stock, if the Company shall furnish to the

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.

 

 

Holders a certificate signed by the Chairman of the Company stating that in the good faith
judgment of the Board of Directors, it would be seriously detrimental to the Company and its
stockholders for all of the Holders’ 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 reduce
such number of shares as the Board of Directors determines, in its good faith judgment, are
necessary, provided, however, that if the number of Registrable Securities to be
included in the registration statement 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 number of shares that may be included in the registration statement shall be allocated, first,
to the Company; second, to holders of shares of capital stock (other than a Holder) with
registration rights under that certain Second Amended and Restated Registration Rights Agreement
dated as of March 31, 2004 by and among the Company and the Purchasers named therein, as amended
from time to time (the “Existing Registration Rights Agreement”); and third to the Holders on a pro
rata basis based on the total number of Registrable Securities held by each Holder.

               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 1.3
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. 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 good faith, 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 good faith 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 number of shares that may be included in the
underwriting shall be allocated, first, to the Company; second, to holders of shares of capital
stock (other than a Holder) with registration rights under the Existing Registration Rights
Agreement; and third to the Holders on a pro rata basis based on the total number of Registrable
Securities held by each Holder.

               Withdrawal. Notwithstanding the foregoing provisions, the Company may withdraw any
registration statement referred to in this Section 1.3 for any reason without thereby incurring any
liability to the holders of Registrable Securities.

          Demand Registration. In case the Company shall, at any time following the one year
anniversary of the closing of a Qualified Public Offering, receive from any Holder or Holders of
Registrable Securities a written request or requests that the Company effect a registration on Form
S-3 (or any successor to Form S-3) or any similar short-form registration statement, or, if such
short-form registration statement is not available for use by the Company, on Form S-1 (or any
successor to Form S-1) and any related qualification or compliance with respect to all or a part of
the Registrable Securities owned by such Holder or Holders, the Company will:

               promptly give written notice of the proposed registration, and any related

15.

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.

 

 

qualification or compliance, to all other Holders of Registrable Securities; and

                    as soon as practicable, but in any event within thirty (30) days of receipt of such request,
file such registration statement and all such qualifications and compliances as may be so requested
and as would permit or facilitate the sale and distribution of all or such portion of such Holder’s
or Holders’ Registrable Securities as are specified in such request, together with all or such
portion of the Registrable Securities of any other Holder or Holders joining in such request as are
specified in a written request given within fifteen (15) days after receipt of such written notice
from the Company; provided, however, that the Company shall not be obligated to
effect any such registration, qualification or compliance pursuant to this Section 1.4:

          (i) if the Holders, together with the holders of any other securities of the Company
entitled to inclusion in such registration, propose to sell Registrable Securities and such
other securities (if any) at an aggregate price to the public of less than one million
dollars ($1,000,000);

          (ii) if the Company shall furnish to the Holders a certificate signed by the Chairman
of the Board of Directors of the Company stating either (A) that in the good faith judgment
of the Board of Directors of the Company, it would be seriously detrimental to the Company
and its stockholders for such registration to be effected at such time, or (B) that the
Company intends to make a public offering within one hundred five (105) days of the receipt
of the request of such Holder or Holders, the Company shall have the right to defer the
filing of the registration statement for a period of not more than one hundred five (105)
days after receipt of the request of the Holder or Holders under this Section 1.4;
provided that such right to delay a request shall be exercised by the Company not
more than once in any twelve (12) month period;

          (iii) if the Company has already effected a registration for the Holders pursuant to
this Section 1.4, and such registration statement remains effective; or

          (iv) in any particular jurisdiction in which the Company would be required to qualify
to do business or to execute a general consent to service of process in effecting such
registration, qualification or compliance.

          Obligations of the Company. Whenever required under this Section 1 to effect the
registration of any Registrable Securities, the Company shall, as expeditiously as reasonably
possible (and subject to the foregoing):

                    Prepare and file with the SEC a registration statement with respect to such Registrable
Securities and use its reasonable best efforts to cause such registration statement to become
effective as soon as possible, and keep such registration statement effective until all shares
registered thereunder cease to be Registrable Securities; provided, however, that
at any time upon written notice to the participating Holders and for a period not to exceed ninety
(90) days thereafter (exclusive of any deferral under Section 1.4) (the “Suspension Period”), the
Company may suspend the use or effectiveness of any registration statement (and the participating
Holders hereby agree not to offer or sell any Registrable Securities pursuant to such registration
statement during the Suspension Period) if the Company reasonably concludes that

16.

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.

 

 

there is or may be in existence material nonpublic information or events involving the
Company, the failure of which to be disclosed in the prospectus included in the registration
statement could result in a Violation (as defined below), or the Company intends to complete a
public offering within ninety (90) days, other than pursuant to a Special Registration Statement.
In no event shall any Suspension Period, when taken together with all prior Suspension Periods,
exceed ninety (90) days in the aggregate in any twelve (12) month period. If so directed by the
Company, all Holders registering shares under such registration statement shall (i) not offer to
sell any Registrable Securities pursuant to the registration statement during the period in which
the delay or suspension is in effect after receiving notice of such delay or suspension; and (ii)
use their best efforts to deliver to the Company (at the Company’s expense) all copies, other than
permanent file copies then in such Holders’ possession, of the prospectus relating to such
Registrable Securities current at the time of receipt of such notice.

               Prepare and file with the SEC such amendments and supplements to such registration statement
and the prospectus used in connection with such registration statement as may be necessary to
comply with the provisions of the Act with respect to the disposition of all securities covered by
such registration statement;

               Furnish to the Holders such numbers of copies of a prospectus, including a preliminary
prospectus, in conformity with the requirements of the Act, and such other documents as they may
reasonably request in order to facilitate the disposition of Registrable Securities owned by them;

               Use its reasonable best efforts to register and qualify the securities covered by such
registration statement under such other securities or Blue Sky laws of such jurisdictions as shall
be reasonably requested by the Holders; provided that the Company shall not be required in
connection therewith or as a condition thereto to qualify to do business or to file a general
consent to service of process in any such states or jurisdictions, unless the Company is already
subject to service in such jurisdiction and except as may be required by the Act;

               In the event of any underwritten public offering, enter into and perform its obligations under
an underwriting agreement, in usual and customary form, with the managing underwriter of such
offering. Each Holder participating in such underwriting shall also enter into and perform its
obligations under such an agreement, and such agreement shall specify that, and the Company shall
cause, the same opinions of counsel of the Company and “comfort letters” of the auditors of the
Company as are delivered to the managing underwriter of such offering to also be addressed and
delivered to each Holder;

               Promptly notify each Holder of Registrable Securities covered by such registration statement
at any time when a prospectus relating thereto is required to be delivered under the Act as a
result of the happening of any event as a result of which the prospectus included in such
registration statement, as then in effect, includes an untrue statement of a material fact or omits
to state a material fact required to be stated therein or necessary to make the statements therein
not misleading in the light of the circumstances then existing and promptly prepare and distribute
any amendment, prospectus or supplement necessary to render the registration statement not
deficient or misleading;

17.

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.

 

 

               Cause all such Registrable Securities registered hereunder to be listed on each securities
exchange on which similar securities issued by the Company are then listed (or the Nasdaq Global
Market, if applicable);

               Provide a transfer agent and registrar for all Registrable Securities registered hereunder and
a CUSIP number for all such Registrable Securities, in each case not later than the effective date
of such registration;

               Otherwise use its best efforts to comply with the securities laws of the United States and
other applicable jurisdictions and all applicable rules and regulations of the SEC and comparable
governmental agencies in other applicable jurisdictions and make generally available to its
holders, in each case as soon as practicable, an earnings statement of the Company which will
satisfy the provisions of Section 11(a) of the Act; and

               Otherwise cooperate with the underwriter or underwriters, the SEC and other regulatory
agencies and take all actions and execute and deliver or cause to be executed and delivered all
documents necessary to effect the registration of any Registrable Securities hereunder.

          Furnish Information. It shall be a condition precedent to the obligations of the
Company to take any action pursuant to this Section 1 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.

          Expenses of Registration. The Company shall bear and pay all expenses incurred in
connection with any registration, filing or qualification of Registrable Securities with respect to
the registrations pursuant to this Section 1 for each Holder, including (without limitation) all
registration, filing, and qualification fees, printers and accounting fees relating or
apportionable thereto and the fees and disbursements of one counsel for the Holders registering
their shares thereunder, but excluding underwriting discounts and commissions relating to the
Registrable Securities.

18.

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.

 

 

          Indemnification. In the event any Registrable Securities are included in a
registration statement under this Section 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 or alleged 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 1.8(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.

               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 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

19.

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.

 

 

Holder will pay, as incurred, any legal or other expenses reasonably incurred by any person
intended to be indemnified pursuant to this subsection 1.8(b), in connection with investigating or
defending any Holder Indemnified Amount; provided, however, that the indemnity
agreement contained in this subsection 1.8(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 1.8(b) exceed the net proceeds from the
offering received by such Holder.

               Promptly after receipt by an indemnified party under this Section 1.8 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 1.8,
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 1.8, 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 1.8.

               If the indemnification provided for in this Section 1.8 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, 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 1.8(d) exceed the net proceeds from the offering
received by such Holder.

               Notwithstanding the foregoing, to the extent that the provisions on indemnification and
contribution contained in the underwriting agreement entered into in

20.

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.

 

 

connection with the underwritten public offering are in conflict with the foregoing
provisions, the provisions in the underwriting agreement shall control.

               The obligations of the Company and Holders under this Section 1.8 shall survive the completion
of any offering of Registrable Securities in a registration statement under this Section 1, and
otherwise.

          Reports Under 1934 Act. With a view to making available to the Holders the benefits
of Rule 144 promulgated under the Act and any other rule or regulation of the SEC that may at any
time permit a Holder to sell securities of the Company to the public without registration or
pursuant to a registration on Form S-3, the Company agrees to use its reasonable best efforts to:

               make and keep public information available, as those terms are understood and defined in SEC
Rule 144, at all times after ninety (90) days after the effective date of the first registration
statement filed by the Company for the offering of its securities to the general public;

               take such action, including the voluntary registration of its Common Stock under Section 12 of
the 1934 Act, as is necessary to enable the Holders to utilize Form S-3 for the sale of their
Registrable Securities, such action to be taken as soon as practicable after the end of the fiscal
year in which the first registration statement filed by the Company for the offering of its
securities to the general public is declared effective;

               file with the SEC in a timely manner all reports and other documents required of the Company
under the Act and the 1934 Act; and

               furnish to any Holder, so long as the Holder owns any Registrable Securities, forthwith upon
request (i) a written statement by the Company that it has complied with the reporting requirements
of SEC Rule 144 (at any time after ninety (90) days after the effective date of the first
registration statement filed by the Company), the Act and the 1934 Act (at any time after it has
become subject to such reporting requirements), or that it qualifies as a registrant whose
securities may be resold pursuant to Form S-3 (at any time after it so qualifies), (ii) a copy of
the most recent annual or quarterly report of the Company and such other reports and documents so
filed by the Company, and (iii) such other information as may be reasonably requested in availing
any Holder of any rule or regulation of the SEC which permits the selling of any such securities
without registration or pursuant to such form.

          Assignment of Registration Rights. The rights to cause the Company to register
Registrable Securities pursuant to this Section 1 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; and (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. For purposes of this Section

21.

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.

 

 

1.10 a “Permitted Assignee” shall mean an entity that acquires all or substantially all of the
ownership interests of a Holder.

          “Market Stand-Off” Agreement. The Investor 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 Investor 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 addition to
the obligations under this Section, the Investor 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 Investor (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 1.11 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.

          Termination of Registration Rights.

          The right of any Holder to request registration or inclusion in any registration pursuant to
Section 1 shall terminate once all Company securities held by such Holder cease to be Registrable
Securities, and this Agreement shall terminate once all of the securities covered hereby cease to
be Registrable Securities.

     Miscellaneous.

          Successors and Assigns. Except as otherwise provided herein, the terms and conditions
of this Agreement shall inure to the benefit of and be binding upon the respective successors and
permitted assigns of the parties (including transferees of any shares of Registrable Securities).
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.

          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.

22.

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.

 

 

          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.

          Titles and Subtitles. The titles and subtitles used in this Agreement are used for
convenience only and are not to be considered in construing or interpreting this Agreement.

          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 02142
	 

	 	Attn: Legal Department
	 

	 	Facsimile: (617) 621-9300
	 
	 	 
	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 Investor:

	 	Nuvelo, Inc.
	 

	 	201 Industrial Road, Suite 310
	 

	 	San Carlos, CA 94070
	 

	 	Attn: Chief Executive Officer
	 

	 	Facsimile: (650) 517-8058
	 
	 	 
	With a copy to:

	 	Cooley Godward LLP
	 

	 	Five Palo Alto Square
	 

	 	3000 El Camino Real
	 

	 	Palo Alto, CA 94306-2155
	 

	 	Attn: John Geschke, Esquire
	 

	 	Facsimile: (650) 849-7400

     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.

23.

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.

 

 

          Expenses. If any action at law or in equity is necessary to enforce or interpret the
terms of this Agreement, the prevailing party shall be entitled to reasonable attorneys’ fees,
costs and necessary disbursements in addition to any other relief to which such party may be
entitled.

          Entire Agreement; Amendments and Waivers. This Agreement constitutes the full and
complete agreement of the parties hereto, and supersedes all prior agreements, whether written or
oral, with respect to the subject matter hereof. Any term of this Agreement may be amended and the
observance of any term of this Agreement may be waived (either generally or in a particular
instance and either retroactively or prospectively), only with the written consent (i) of the
Company, (ii) the Investor (so long as the Investor holds Registrable Securities) and (iii) any
transferee or assignee of Registrable Securities pursuant to Section 1.10 of this Agreement who
holds not less than 250,000 shares of Registrable Securities. Any amendment or waiver effected in
accordance with this paragraph shall be binding upon each holder of any Registrable Securities then
outstanding, each future holder of all such Registrable Securities, and the Company.

          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.

          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 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.

          Remedies. It is specifically understood and agreed that any breach of the provisions
of this Agreement by any person subject hereto will result in irreparable injury to the other
parties hereto, that the remedy at law alone will be an inadequate remedy for such breach, and
that, in addition to any other remedies which they may have, such other parties may enforce their
respective rights by actions for specific performance (to the extent permitted by law).

[THE REMAINDER OF THE PAGE IS LEFT INTENTIONALLY BLANK]

24.

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.

 

 

     IN WITNESS WHEREOF, the parties hereto have executed this Registration Rights Agreement or
caused this Agreement to be executed by their duly authorized representatives, as of the date first
written above.

	 	 	 	 	 
	 	COMPANY:

ARCHEMIX CORP.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 
	 	INVESTOR:

NUVELO, INC.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

25.

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 H

FINANCIAL STATEMENT FORMAT

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	 	 	 	Total Product	 	 	 	 	 	 
	 	 	 	 	Line P(L)	 	 	 	% Net Sales	 	 
	 	 	 	 	 	 	 	 	 
	 	Gross Sales
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Less:
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Transportation Charges
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Credits & Allowances
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Taxes & Duties
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Net Sales
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Cost of Goods:
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Gross Profit
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Commercialization Costs:
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Selling Expenses (including
provisions for
uncollectible accounts)
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Marketing Management
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Market & Consumer Research
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Advertising
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Trade Promotion
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Consumer Promotion
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Education
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Total Distribution Expenses
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Other
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Total Commercialization Costs
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Post-Launch Product R&D Expenses:
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Phase 4 Clinical Trials
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Product Support
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Medical Affairs
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Preclinical Research
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Other Contract R&D
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Total Post-Launch Product R&D Expenses
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Allocated Administration Expenses:
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Patent Expenses
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Currency Gains (Losses):
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Unhedged Transactions
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Hedged Transactions
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Total Currency Gains (Losses)
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 

26.

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.

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	 	 	 	Total Product	 	 	 	 	 	 
	 	 	 	 	Line P(L)	 	 	 	% Net Sales	 	 
	 	 	 	 	 	 	 	 	 
	 	Net Sublicense Revenues
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Product Profits (Losses)
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Equalization Receipt (Payment)
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 
	 	Balance After Equalization
 
	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 

27.

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.exv10w34

Exhibit
10.34

COLLABORATIVE RESEARCH AND LICENSE AGREEMENT

between

ARCHEMIX CORP.

and

MERCK, KGaA

January 17, 2007

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	 
	1. DEFINITIONS
	 	 	1	 
	 
	 	 	 	 
	2. ADMINISTRATION OF THE COLLABORATION
	 	 	19	 
	 
	 	 	 	 
	2.1 Joint Steering Committee
	 	 	19	 
	2.2 Joint Project Team
	 	 	21	 
	 
	 	 	 	 
	3. RESEARCH PROGRAM
	 	 	24	 
	 
	 	 	 	 
	3.1 Implementation of the Research Program
	 	 	24	 
	3.2 Annual Research Plans
	 	 	25	 
	3.3 Conduct of Research Program
	 	 	25	 
	3.4 Records
	 	 	26	 
	3.5 Selection of Program Targets
	 	 	27	 
	3.6 Identification of Lead Compounds and Optimized Lead Compounds
	 	 	29	 
	3.7 Development Candidates
	 	 	29	 
	3.8 MERCK Decision Not to Go Forward
	 	 	29	 
	3.9 Supply of Proprietary Materials
	 	 	30	 
	3.10 Research Program Term
	 	 	30	 
	 
	 	 	 	 
	4. DEVELOPMENT PROGRAM; COMMERCIALIZATION OF PRODUCTS
	 	 	30	 
	 
	 	 	 	 
	4.1 Objectives of the Development Program
	 	 	30	 
	4.2 Responsibility for Development of Development Candidates and Commercialization
of Products
	 	 	30	 
	4.3 Annual Development Plans
	 	 	31	 
	4.4 Product Commercialization Plans
	 	 	31	 
	4.5 Development and Commercialization Diligence
	 	 	31	 
	4.6 Compliance
	 	 	32	 
	4.7 Cooperation
	 	 	32	 
	4.8 Exchange of Reports; Information; Updates
	 	 	32	 
	4.9 Development and Commercialization Rights and Restrictions
	 	 	34	 
	4.10 Product Recalls
	 	 	35	 
	 
	 	 	 	 
	5. PAYMENTS
	 	 	35	 
	 
	 	 	 	 
	5.1 Technology Access and License Fee
	 	 	35	 
	5.2 License Maintenance Fee
	 	 	35	 
	5.3 R&D Funding
	 	 	35	 
	5.4 Milestone Payments
	 	 	36	 
	5.5 Payment of Royalties; Royalty Rates; Accounting and Records
	 	 	38	 

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	 
	6. TREATMENT OF CONFIDENTIAL INFORMATION; PUBLICITY; NON-SOLICITATION
	 	 	42	 
	 
	 	 	 	 
	6.1 Confidentiality
	 	 	42	 
	6.2 Publicity
	 	 	44	 
	6.3 Publications and Presentations
	 	 	44	 
	6.4 Prohibition on Solicitation
	 	 	45	 
	 
	 	 	 	 
	7. LICENSE GRANTS; EXCLUSIVITY
	 	 	45	 
	 
	 	 	 	 
	7.1 Research and Development Licenses
	 	 	45	 
	7.2 Commercialization License
	 	 	50	 
	7.3 Right to Sublicense
	 	 	50	 
	7.4 Right to Subcontract
	 	 	50	 
	7.5 No Other Rights
	 	 	50	 
	7.6 Exclusivity
	 	 	51	 
	 
	 	 	 	 
	8. INTELLECTUAL PROPERTY RIGHTS
	 	 	51	 
	 
	 	 	 	 
	8.1 ARCHEMIX Intellectual Property Rights
	 	 	51	 
	8.2 MERCK Intellectual Property Rights
	 	 	51	 
	8.3 Joint Technology Rights
	 	 	51	 
	8.4 Patent Coordinators
	 	 	51	 
	8.5 Inventorship
	 	 	52	 
	8.6 Cooperation
	 	 	52	 
	 
	 	 	 	 
	9. FILING, PROSECUTION AND MAINTENANCE OF PATENT RIGHTS
	 	 	52	 
	 
	 	 	 	 
	9.1 Patent Filing, Prosecution and Maintenance
	 	 	52	 
	9.2 Legal Actions
	 	 	55	 
	9.3 Trademark and Copyright Ownership Prosecution, Defense and Enforcement
	 	 	58	 
	 
	 	 	 	 
	10. TERM AND TERMINATION
	 	 	58	 
	 
	 	 	 	 
	10.1 Term
	 	 	58	 
	10.2 Termination
	 	 	59	 
	10.3 Consequences of Termination of Agreement
	 	 	59	 
	10.4 Rights and Duties of the Parties following Breach by MERCK of Diligence
Obligations
	 	 	62	 
	10.5 Surviving Provisions
	 	 	62	 
	 
	 	 	 	 
	11. REPRESENTATIONS AND WARRANTIES
	 	 	63	 
	 
	 	 	 	 
	11.1 Mutual Representations and Warranties
	 	 	63	 
	11.2 ARCHEMIX’ Representations and Warranties
	 	 	63	 
	11.3 Acknowledgment of MERCK
	 	 	64	 

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

 

	 	 	 	 	 
	 	 	Page	 
	12. INDEMNIFICATION
	 	 	64	 
	 
	 	 	 	 
	12.1 Indemnification of MERCK by ARCHEMIX
	 	 	64	 
	12.2 Indemnification of ARCHEMIX by MERCK
	 	 	65	 
	12.3 Indemnification of Gilead and UTC by MERCK
	 	 	65	 
	12.4 Conditions to Indemnification
	 	 	65	 
	12.5 Warranty Disclaimer
	 	 	66	 
	12.6 No Warranty of Success
	 	 	66	 
	12.7 Limited Liability
	 	 	66	 
	 
	 	 	 	 
	13. MISCELLANEOUS
	 	 	66	 
	 
	 	 	 	 
	13.1 Arbitration
	 	 	66	 
	13.2 Change of Control
	 	 	68	 
	13.3 Notices
	 	 	69	 
	13.4 Governing Law
	 	 	70	 
	13.5 Binding Effect
	 	 	70	 
	13.6 Headings
	 	 	70	 
	13.7 Counterparts
	 	 	70	 
	13.8 Amendment; Waiver
	 	 	70	 
	13.9 No Third Party Beneficiaries
	 	 	71	 
	13.10 Purposes and Scope
	 	 	71	 
	13.11 Assignment and Successors
	 	 	71	 
	13.12 Force Majeure
	 	 	71	 
	13.13 Interpretation
	 	 	71	 
	13.14 Integration; Severability
	 	 	71	 
	13.15 Further Assurances
	 	 	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.

iii

 

	 	 	 
	List of Schedules	 	 
	 
	Schedule 1

	 	Optimized Lead Compound Selection Criteria
	Schedule 2A

	 	Program Targets
	Schedule 2B

	 	Target Replacement List
	Schedule 3

	 	Licensed Patent Rights
	Schedule 4

	 	Excluded Aptamers
	Schedule 5

	 	Excluded Targets
	Schedule 6

	 	Development Candidate Selection Criteria
	Schedule 7

	 	Form of Press Release
	Schedule 8

	 	Regional Offices or Countries in which Patent Applications are to be Nationalized or
Otherwise Prosecuted, Filed and Maintained
	Schedule 9

	 	Material Terms to be Included in Form of Co-Promotion Agreement
	Schedule 10

	 	Merck’s Standard Exchange Rate Methodology Applied In Its External Reporting
	Schedule 11

	 	Program Chemistries

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.

iv

 

COLLABORATIVE RESEARCH AND LICENSE AGREEMENT

     This COLLABORATIVE RESEARCH AND LICENSE AGREEMENT (this “Agreement”) is entered into as of
January 17, 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
SELEXTM process and SELEXTM 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 desire to enter into a collaboration for the purposes of identifying
aptamers against certain identified targets, and developing and commercializing products derived
from such aptamers for the prevention, treatment and delay of onset or progression of cancer.

     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 9 attached hereto shall have the meanings specified.

     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 and Contract Year, the written plan for the 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.

 

Program for such Optimized Lead Compound and Development Candidate for such Contract Year, 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 3.2.

     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 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 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 and (b) shall not include Collaboration
Aptamers, ARCHEMIX Program Technology or ARCHEMIX’s interest in Joint Technology.

     1.9 “ARCHEMIX Decision” means a decision with respect to the following issues: (a)
the conduct of the [***] against [***]; (b) whether ARCHEMIX is to incur any [***]; (c) whether
ARCHEMIX is to be obligated to perform any [***]; (d) whether ARCHEMIX is to incur any [***] in the
performance of [***] or [***]; (e) the expansion, at MERCK’s request, of the number of FTEs to be
provided by ARCHEMIX under the Research Program beyond [***] in any [***]; and (f) the inclusion of
any [***] MERCK as [***] Program Target.

     1.10 “ARCHEMIX Development Activities” means all Development activities specified to
be conducted by ARCHEMIX in any Annual Development Plan (or amendment thereto) and approved by
ARCHEMIX’s representatives on the JPT and JSC (without resort to the dispute resolution procedures
set forth in Section 2.1.6).

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.

2

 

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

     1.12 “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.

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

     1.14 “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.

     1.15 “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.

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

     1.17 “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 and end on March 31, 2007.

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

     1.19 “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

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.

3

 

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.

     1.20 “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.

     1.21 “Collaboration Aptamer” means, collectively, Program Oligonucleotides, Program
Aptamers, Lead Compounds, Optimized Lead Compounds, Development Candidates and/or Products.

     1.22 “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 Product; and (b) a
Supplemental Product that is not within the Licensed Patent Rights, where both the Product and the
Supplemental Product are required to treat the intended Indication and/or to achieve the intended
use or effect.

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

     1.24 “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, or, with respect to activities of ARCHEMIX in the Commercialization of a Waived
Compound which is the subject of a transition plan pursuant to Section 7.1.2(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, 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

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.

4

 

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).

     1.25 “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 amended from time to time.

     1.26 “Competitive Entity” means any Third Party in the top [***] companies ranked by
[***] in the most recently completed Calendar Year for which such ranking is readily available from
an unaffiliated Third Party.

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

     1.28 “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 or JMC or disclosed

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.

5

 

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.

     1.29 “Contract Year” means (a) the period beginning on the Effective Date and ending
on the first anniversary of the last day of the calendar month in which the Effective Date falls
and (b) each succeeding twelve (12) month period thereafter.

     1.30 “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 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.

     1.31 “CTN” means the notification submitted to the Japanese Ministry of Health, Labor
and Welfare prior to the Initiation of a clinical trial in Japan.

     1.32 “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).

     1.33 “Detail” means, with respect to a Co-Promoted Product, an interactive, live,
face-to-face contact of a Representative within the Co-Promotion 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-Promotion Territory.
When used as a verb, “Detailing” means performing Details. When used as an adjective, “Detailing”
means of or related to performing Details.

     1.34 “Development” or “Develop” means, with respect to each Optimized Lead
Compound and Development Candidate, all non-clinical and clinical activities performed in order to
obtain Regulatory Approval of a 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.

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.

6

 

     1.35 “Development Candidate” means any Optimized Lead Compound that the JPT nominates
and the JSC accepts as a Development Candidate as set forth in Section 3.7 and for which MERCK has
paid the Development Candidate Milestone Payment in the time allotted for such payment in Section
5.4.1; provided, that, no Collaboration Aptamer shall, after [***], be nominated or accepted as a
Development Candidate.

     1.36 “Development Candidate Milestone Payment” means the payment to be made to
ARCHEMIX upon occurrence of Milestone 2 pursuant to Section 5.4.1.

     1.37 “Development Candidate Selection Criteria” or “DCSC” means the guideline
criteria for selecting Optimized Lead Compounds that are sufficiently promising to warrant further
Development as Development Candidates as set forth in Schedule 6 attached hereto, as such
Schedule 6 shall be amended from time to time by the JSC, which amendment shall occur
before any activities with respect to such Development Candidate are initiated, in any material
respect, in the Development Program.

     1.38 “Development Program” means the Development activities to be conducted during the
Term with respect to each Optimized Lead Compound and Development Candidate pursuant to the Annual
Development Plan, with the objective of developing such Optimized Lead Compound or Development
Candidate into a Product.

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

     1.40 “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.

     1.41 “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 the onset or progression of, or the treatment or prevention
of, an Indication.

     1.42 “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 (including, without limitation, a CTN); and
(c) all supplements and amendments to any of the foregoing.

     1.43 “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

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.

7

 

[***] 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 [***].

     1.44 “Effective Date” means the date first set forth above.

     1.45 “Excepted Decision” means any of the following decisions requiring the unanimous
approval of all members of the JSC: (a) any decision as to whether a milestone has been achieved
under this Agreement for which a milestone payment is payable; and (b) any decision as to whether a
proposed Target is a [***].

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

     1.47 “Excluded Target” means any Target listed on Schedule 5 attached hereto.

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

     1.49 “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 [***], provided, that, at such time no other [***] for such Program
Target are in Development, and (d) any Program Target for which [***] meeting the applicable [***]
exists and for which MERCK has not [***] the [***] in the time allotted for such [***] in Section
5.4.1. For purposes of clarity, a Failed Target shall not be considered a Program Target.

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

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

     1.52 “Field” means [***]. For purposes of clarity, the Field shall not include the
research, development, manufacture, use or sale of Diagnostic Products or Radio Therapeutics.

     1.53 “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.

     1.54 “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.

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.

8

 

     1.55 “FTE” shall mean [***] hours of work devoted to or in support of the ARCHEMIX
Research Activities or the ARCHEMIX Development Activities 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.

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

     1.57 “FTE Rate” means (a) for the [***] Contract Year, [***] Dollars (US $[***]); (b)
for the [***] Contract Year, [***] Dollars (US $[***]); (c) for the [***] Contract Year, [***]
Dollars (US $[***]); (d) for each FTE or portion thereof greater than [***] in [***] Contract Year
during the Research Program Term, [***] Dollars (US $[***]); and (e) for [***] Contract Year on and
after the expiration of the Research Program Term, an amount per Contract Year to be determined by
multiplying [***] Dollars (US $[***]) by the [***] in the Consumer Price Index since the Effective
Date ([***] for all items; [***]; available at [***] and adding or subtracting the product of such
multiplication to or from [***] Dollars (US $[***]). The FTE rate includes all salary, employee
benefits, materials and all other expenses including support staff and overhead for or associated
with ARCHEMIX scientists performing activities but does not include Third Party Costs as set forth
in Section 5.3.3.

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

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

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

     1.61 “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.

     1.62 “Indication” means any human indication, disease or condition in the Field, 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”).

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

     1.64 “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

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.

9

 

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).

     1.65 “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.

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

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

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

     1.69 “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 the avoidance of doubt, 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.

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

     1.71 “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.

     1.72 “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

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.

10

 

or of its use, or (b) are necessary for MERCK to exercise the licenses granted to it pursuant
to Sections 7.1 and 7.2. For purposes of clarity, Licensed Patent Rights existing as of the
Effective Date include those listed on Schedule 3 attached hereto.

     1.73 “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, and (b) is necessary for MERCK to exercise
the licenses granted to it pursuant to Sections 7.1 and 7.2.

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

     1.75 “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.

     1.76 “MERCK Development Activities” means all Development activities specified to be
conducted by MERCK in any Annual Development Plan (or amendment thereto).

     1.77 “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.

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

     1.79 “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.

     1.80 “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.

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

11

 

     1.82 “Minimum FTE Funding Commitment” means the funding of at least [***] ARCHEMIX
FTEs at the applicable FTE Rate for each Contract Year during the Research Program Term.

     1.83 “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.

     1.84 “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, 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:

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.

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.

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.

     1.85 “Optimized Lead Compound” means 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.

     1.86 “Optimized Lead Compound Selection Criteria” or “OLSC” means 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 1 attached hereto, as such
Schedule 1 may be amended from time to time by the JSC, which amendment shall occur before

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.

12

 

any research activities are initiated with respect to such Optimized Lead Compound against the
applicable Program Target. Notwithstanding anything to the contrary set forth in Schedule
1, for purposes of determining whether a Lead Compound has been designated as an Optimized Lead
Compound for Milestone 1 in Section 5.4.1, [***] shall be required to be performed with respect to
such Lead Compound, whether or not included as part of the OLSC.

     1.87 “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.

     1.88 “Permitted Screening Activities” means, [***] to any [***], any [***] ARCHEMIX
[***] to such [***] for [***] and/or for [***] for the [***] of [***] Aptamers [***] bind to a
[***] a [***].

     1.89 “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.

     1.90 “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.

     1.91 “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.

     1.92 “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 the Development Candidate 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.

     1.93 “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

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.

13

 

to the extent that it is a new chemical entity (as defined by the FDCA) with respect to the
existing Product(s).

     1.94 “Product Commercialization Plan” means, with respect to each 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.

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

     1.96 “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.

     1.97 “Program Aptamer-Specific Patent Rights” means all Patent Rights that cover only
Program Aptamer-Specific Technology.

     1.98 “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.

     1.99 “Program Generic Patent Rights” means Patent Rights that cover only Program
Generic Technology.

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

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

     1.102 “Program Target” means the Targets listed on Schedule 2A attached
hereto, as amended from time to time in accordance with Section 3.5.

     1.103 “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.

     1.104 “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

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.

14

 

or (b) that are otherwise conceived or reduced to practice in the conduct of the Research
Program or the Development Program.

     1.105 “Quarterly FTE Payment” means the minimum amount payable by MERCK to ARCHEMIX
for FTEs during each Calendar Quarter of the Research Program Term pursuant to Section 5.3, which
shall equal the greater of: (a) $[***] per Calendar Quarter in the [***] Contract Year, $[***] per
Calendar Quarter in the [***] Contract Year, and $[***] per Calendar Quarter in the [***] Contract
Year; or (b) the estimated FTE Cost as set forth in the Annual Research Plan for such Calendar
Quarter.

     1.106 “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.

     1.107 “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.

     1.108 “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.

     1.109 “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.

     1.110 “Representative” means an individual (including a medical service liaison, sales
representative or other representative) employed and trained by either Party or employed by a Third
Party or self-employed and trained by or on behalf of a Party, in any case, to Detail a Co-Promoted
Product.

     1.111 “Research Program” means the research program to be conducted by the Parties
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

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.

15

 

Research Program does not include any Development activities performed in the course of the
Development Program.

     1.112 “Research Program Term” means the period beginning on the Effective Date and
ending on the last day of the third 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.

     1.113 “Royalty Term” means, on a Product-by-Product and country-by-country basis, the
period beginning on the date of First Commercial Sale of a 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 or Joint Patent Rights in such country that covers such
Product or its identification, manufacture, use, import, offer for sale or sale or (b) (i) with
regard to the first Product for each Program Target sold in such country, fifteen (15) years from
the date of the First Commercial Sale of such first Product in such country or (ii) with regard to
each additional Product for such Program Target sold in such country, ten (10) years from the date
of the First Commercial Sale of each such additional Product in such country.

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

     1.115 “SELEX® Process” means any process 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.

     1.116 “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.

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

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

     1.119 “Sublicensee” means any Third Party to which MERCK grants a sublicense under the
licenses granted to it under Section 7.1 or 7.2.

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

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.

16

 

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

     1.122 “Target Replacement List” means the list of Targets on Schedule 2B
attached hereto, as amended pursuant to Section 3.5.1.

     1.123 “Target Selection Field” means the treatment or prevention in humans of cancer.

     1.124 “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).

     1.125 “Terminated Compounds” means (a) all Collaboration Aptamers upon any termination
of this Agreement by ARCHEMIX pursuant to Section 10.2.3 or Section 10.2.2 or by MERCK pursuant to
Section 10.2.1; and (b) the relevant Collaboration Aptamers binding specifically to the Program
Target for which MERCK’s license is terminated by ARCHEMIX pursuant to Section 10.2.2 due to
failure of MERCK to meet its diligence obligations, as provided in Section 10.4.

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

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

     1.128 “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.

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

     1.130 “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.

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

     1.132 “Waived Target” means (a) any Program Target for which MERCK, in its sole
discretion, discontinues Development of a Development Candidate; provided, that, no 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.

17

 

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
	 	 	5.3.1	 
	ARCHEMIX Change of Control Notice
	 	 	13.2.1(a)	 
	ARCHEMIX Indemnitees
	 	 	12.2	 
	Claims
	 	 	12.1	 
	Collaboration Manager
	 	 	2.2.6	 
	Co-Promote
	 	 	4.9.2(a)	 
	Co Promoted Product
	 	 	4.9.2(a)	 
	Co-Promotion
	 	 	4.9.2(a)	 
	Co-Promotion Agreement
	 	 	4.9.2(a)	 
	Designated Senior Officers
	 	 	2.1.6	 
	Dispute
	 	 	13.1.1	 
	Disputed Matter
	 	 	2.1.6	 
	Expert
	 	 	13.1.2(a)	 
	Filing Party
	 	 	9.1.4	 
	Gilead Indemnitee
	 	 	12.3	 
	Indemnified Party
	 	 	12.4	 
	Indemnifying Party
	 	 	12.4	 
	Infringement
	 	 	9.2.1(a)	 
	Infringement Notice
	 	 	9.2.1(a)	 
	JPT Term
	 	 	2.2.1	 
	JSC Term
	 	 	2.1.1	 
	Losses
	 	 	12.1	 
	MERCK Change of Control Notice
	 	 	13.2.2(a)	 
	MERCK Contribution
	 	 	5.3.1	 
	MERCK Indemnitees
	 	 	12.1	 
	Non-Filing Party
	 	 	9.1.4	 
	Patent Coordinator
	 	 	8.4	 
	Requested Chemistry
	 	 	5.5.1(b)	 
	Recipient Party
	 	 	3.8	 
	Term
	 	 	10.1	 
	Third Party Chemistry Payments
	 	 	5.5.1(b)	 
	Third Party Costs
	 	 	5.3.3	 
	Third Party Payments
	 	 	5.5.1(b)	 
	Transferring Party
	 	 	3.8	 

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.

18

 

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 any Co-Promoted Products are being Commercialized. 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
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.

          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 [***] 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. 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 [***] [***] 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 [***] [***] 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

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.

19

 

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 and the Development of Optimized Lead Compounds and Development
Candidates for which ARCHEMIX is performing Development activities. Without limiting the
generality of the foregoing, the JSC shall have the following responsibilities:

               (a) overseeing the JPT’s performance of its responsibilities;

               (b) reviewing and approving each Annual Research Plan and each Annual Development Plan under
which ARCHEMIX is responsible for performing Development activities;

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

               (d) reviewing and approving any amendment to an Annual Development Plan under which ARCHEMIX
is responsible for performing Development activities approved by the JPT and submitted to it for
its approval;

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

               (f) resolving all JPT matters that are in dispute;

               (g) 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;

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

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

20

 

               (j) 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 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 13.1. 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. 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. 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). 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  

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.

21

 

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.

               (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.

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.

22

 

          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
Development activities; 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 Development activities. 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
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;

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.

23

 

               (k) preparing or directing the preparation of and approving amendments to JSC-approved Annual
Development Plans under which ARCHEMIX is responsible for performing Development activities, as it
deems appropriate in furtherance of the Development of Development Candidates and, if any member of
the JPT asserts 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 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 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
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 Development activities, in
reasonable detail and providing to the JSC such additional information as it may request;

               (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.

          2.2.6 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. Except for the MERCK Research Activities, if
any, which shall be conducted by MERCK at its sole expense, ARCHEMIX shall have the primary right
and responsibility to conduct the Research Program.

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.

24

 

     3.2 Annual Research Plans.

          3.2.1 Research Plan. The initial Annual Research Plan and budget, which describes the
research activities to be carried out by each Party during the first Contract Year of the Research
Program Term, shall be prepared by the JPT and submitted to, and approved by, the JSC within [***]
days of the Effective Date. For each Contract Year during the Research Program Term commencing
with the second Contract Year, an Annual Research Plan and budget shall be prepared by or at the
direction of the JPT and submitted to the JSC for its approval. The JPT shall manage the
preparation of each Annual Research Plan 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 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 Research Program, (iii) changes to the OLSC
and any other criteria that the JPT will utilize to evaluate the results of the Research Program 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 expenses to be
incurred for outsourced studies managed by ARCHEMIX), 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
Research Plan that may be approved by the JSC, the Annual Research Plan shall be updated at least
once prior to the end of 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.

          3.2.2 Minimum FTEs. MERCK shall request and fund a minimum of [***] FTEs per Contract
Year during the three (3) year Research Program Term. MERCK shall have
the right to increase the number of FTEs to be provided by ARCHEMIX for any Contract Year;
provided, that, (a) any increase above [***] FTEs for any Contract Year shall be subject to MERCK’s
notice obligation under Section 3.3.2(c) and (b) any increase, at MERCK’s request, above [***] FTEs
for any Contract Year shall be an ARCHEMIX Decision.

     3.3 Conduct of Research Program.

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.

25

 

          3.3.1 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.

          3.3.2 MERCK Responsibilities. During the Research Program Term, MERCK shall: (a) pay
ARCHEMIX the Minimum Quarterly FTE Payment in accordance with Section 5.3; (b) pay ARCHEMIX the
applicable FTE Rate per FTE per Contract Year for FTEs greater than [***] in accordance with
Section 5.3.1; (c) give ARCHEMIX not less than [***] days’ written notice in the event that MERCK
requires a number of FTEs above [***] FTEs in any Contract Year; (d) commit such resources as are
reasonably necessary to conduct the MERCK Research Activities set forth in the Annual Research
Plan; and (e) use Commercially Reasonable Efforts to conduct the MERCK Research Activities, if any,
set forth in the Annual Research Plan.

          3.3.3 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.

          3.3.4 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.

     3.4 Records.

          3.4.1 Record Keeping.

               (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 6, 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.

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.

26

 

               (b) Record Keeping Policies. Without limiting the generality of Section 3.4.1(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.

          3.4.2 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.

     3.5 Selection of Program Targets.

          3.5.1 Selection of Program Targets.

               (a) Initial Program Targets. The Parties hereby acknowledge and agree that one (1)
Program Target, as set forth on Schedule 2A, has been so designated by the
Parties as of the Effective Date. MERCK shall provide written notice of a second Program
Target to ARCHEMIX within [***] weeks of the Effective Date. ARCHEMIX shall accept or reject the
proposed Target as specified under 3.5.1.d) for the inclusion of a Target into the Research
Program.

               (b) Target Replacement List. The Parties hereby acknowledge and agree that two (2)
Targets, as set forth on the Target Replacement List on Schedule 2B, have

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.

27

 

been designated
by the Parties as replacement Targets as of the Effective Date. MERCK shall have the right to
request that a Target on the Target Replacement List be replaced (a) [***] and (b) [***]. During
the first [***] Contract Years of the Research Program Term, ARCHEMIX will inform MERCK in writing,
if it intends to commence negotiations with a Third Party with respect to a license, collaboration
or similar agreement relating to Aptamers against a Target on the Target Replacement List.

               (c) Replacement of Program Targets. If at any time during the first [***] Contract
Years of the Research Program Term, the JSC agrees that a Program Target is unlikely to produce an
[***] or [***], then (i) all activities under the Research Program with respect to such Program
Target shall cease; (ii) such Program Target shall thereafter be deemed to be a Failed Target; and
(iii) MERCK shall have the right to replace such Failed Target with a Target from the Target
Replacement List in accordance with Section 3.5.1(d). In addition, MERCK shall have the right at
any time during the first [***] Contract Years of the Research Program Term to replace a Program
Target with a Target from the Target Replacement List in accordance with Section 3.5.1(d) if: (i)
MERCK reasonably believes based on published literature or proprietary data first available after
the designation of a Target as a Program Target that such Program Target is [***] for use in the
Target Selection Field; or (ii) MERCK reasonably determines that it is legally necessary to obtain
a license or other right, title or interest in and to an issued patent that had not issued and/or
had not been published as a pending application at the time a Target was designated as a Program
Target in order to successfully research, Develop and Commercialize a Product that binds such
Program Target. Notwithstanding anything to the contrary herein, any Program Target replaced in
accordance with the preceding sentence of this Section 3.5.1(c) shall be deemed a Failed Target. A
Target proposed by MERCK for inclusion in the Research Program which is not on the Target
Replacement List may be rejected by ARCHEMIX for any reason, in its sole discretion.

               (d) Replacement of Targets. To the extent MERCK has the right to propose that a
Target be added to the Target Replacement List as described in Section 3.5.1(b) or that a Failed
Target be replaced by a Target from the Target Replacement List as described in Section 3.5.1(c),
MERCK shall provide written notice to ARCHEMIX. ARCHEMIX shall accept or reject the proposed
Target within [***] days after receipt of such notice from MERCK. A Target proposed by MERCK for
inclusion on the Target Replacement List or in the Research Program shall only be rejected by
ARCHEMIX if prior to MERCK’s notice: (A) it is an [***], (B) ARCHEMIX is prohibited by an executed
contract from licensing Aptamers against such proposed Target or its natural ligand(s), to MERCK,
(C) ARCHEMIX is in active negotiations, as [***] by [***] 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 (D) ARCHEMIX is developing, for its own benefit, Aptamers against such Target or its
natural ligand(s) under a
bona fide internal development program against such Target, has adopted a research plan for
such Target or its natural ligand, or has formally designated such Target or its natural ligand(s)
for research. In addition to the reasons specified in the foregoing clauses (A)-(D), ARCHEMIX also
may reject a Target proposed by MERCK for inclusion on the Target Replacement List if such Target
does not fall 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), (C) or (D) lapse, or are

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.

28

 

otherwise terminated,
such that the previously rejected Target becomes eligible for inclusion as a Program Target or for
inclusion on the Target Replacement List.

               (e) Obligations of JPT. As promptly as practicable after designation of a new Program
Target in accordance with Section 3.5.1(d), the JPT shall (i) develop and submit to the JSC for its
approval the OLSC and DCSC for such new Program Target and (ii) prepare an update to the Annual
Research Plan to include the ARCHEMIX Research Activities to be conducted to identify Lead
Compounds against such new Program Target for potential nomination as an Optimized Lead Compound.

          3.5.2 Termination of Replacement Right. Notwithstanding anything to the contrary in
this Agreement, MERCK’s right to add Targets to the Target Replacement List pursuant to Section
3.5.1(b) and/or replace Program Targets pursuant to Section 3.5.1(c) shall terminate on the [***]
of the [***] Contract Year.

3.6 Identification of Lead Compounds and Optimized Lead Compounds.

          3.6.1 Lead Compounds. ARCHEMIX shall use Commercially Reasonable Efforts in good
faith to perform the SELEX® Process to identify Lead Compounds in accordance with each
Annual Research Plan, as amended.

          3.6.2 Optimized Lead Compounds. Within [***] days after its receipt of each report
from ARCHEMIX pursuant to Section 3.4.2 identifying a Lead Compound 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.

     3.7 Development Candidates. Within [***] days after either Party reasonably concludes
based upon available project reports that an Optimized Lead Compound meets the applicable DCSC, the
JPT shall review the data and information and determine whether to nominate the 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 continue Development of such 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.

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

29

 

     3.9 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
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.

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

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, if any, 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 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), subject in each case to
Section 4.9.2. 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 4.9.2, 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 10.3.

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.

30

 

     4.3 Annual Development Plans. The initial Annual Development Plan 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 an 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, for each Contract
Year during the Term, an Annual Development Plan for each Optimized Lead Compound and 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. 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 and (iv) the expected Regulatory Filings and Drug Approval 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 Annual Development Plan may be
amended from time to time by MERCK. 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 the above, the preparation and
management of the Annual Development Plan by the JPT and JSC approval is only required for any
Annual Development Plan or amendment thereto under which ARCHEMIX is responsible for performing any
Development activities.

     4.4 Product Commercialization Plans. Within [***] days after the Initiation of a
Phase III Clinical Trial with respect to each Development Candidate, 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 Development and Commercialization Diligence.

               (a) Diligence 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.

               (b) Effect of Breach of Diligence Obligations. If ARCHEMIX at any time believes that
MERCK, on a country-by-country and Product-by-Product basis, is not meeting its diligence
obligations pursuant to subsection (a) 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

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.

31

 

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, in its sole discretion, on a country-by-country
and Product-by-Product basis, to terminate MERCK’s rights with respect to such Target, Development
Candidate or Product, and the Collaboration Aptamers against such Target pursuant to Section 10.4
(but leaving unaffected MERCK’s rights under this Agreement to any other Target and Collaboration
Aptamer directed against such Target).

     4.6 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
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.

     4.7 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.

     4.8 Exchange of Reports; Information; Updates.

          4.8.1 Development Program Reports. 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, (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.

          4.8.2 Commercialization Reports. 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

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.

32

 

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.

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

               (a) Adverse Events. In addition to the updates described in Section 4.8.1 and 4.8.2,
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 13.3. 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. 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 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 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.

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.

33

 

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 4.8.3(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 4.8.3,
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.

     4.9 Development and Commercialization Rights and Restrictions.

          4.9.1 Development and Commercialization Rights in the Field. Except as provided in
this Section 4.9, MERCK shall have the [***] during the Term to Develop Development Candidates and
Commercialize Products in the Territory for use in the Field.

          4.9.2 Co-Promotion.

               (a) Negotiation of a Potential Co-Promotion Agreement. Within thirty (30) days from
filing the NDA for a Product, ARCHEMIX shall provide MERCK with (i) a written notice indicating
ARCHEMIX’ interest in the promotion and Detailing of such Product in the United States of America
and its territories and possessions jointly with MERCK using a coordinated sales force consisting
of Representatives of both Parties (“Co-Promote” or “Co-Promotion”) and (ii) a business plan so as
to document how such proposed Co-Promotion for such Product is in the best interest of both
Parties. Upon receipt of such written notice, MERCK shall enter into good faith negotiations with
ARCHEMIX with the aim of determining whether or not to enter into a separate Co-Promotion agreement
(“Co-Promotion Agreement”) between the Parties. In the event MERCK, in its sole discretion, agrees
to enter into such Co-Promotion Agreement with ARCHEMIX, then the terms applicable to such
Co-Promotion of the Product identified therein (each, a “Co-Promoted Product”) shall conform in all
material respects with the terms, conditions and provisions set forth in Schedule 9
attached hereto and such additional provisions as are usual and customary for inclusion in a
co-promotion agreement between companies in the pharmaceutical industry of comparable sizes to 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 9. The Parties shall
negotiate the Co-Promotion Agreement in good faith and with sufficient diligence as is required to
execute and deliver the Co-Promotion Agreement
within [***] days after ARCHEMIX provides its written indication of interest pursuant to the
first sentence of this paragraph.

               (b) Failure to Agree. To the extent that MERCK enters into and conducts negotiations
with respect to the Co-Promotion Agreement for a Product in good faith and the Parties fail to
execute and deliver the Co-Promotion Agreement within [***] day period described in Section
4.9.2(a) above, then (i) MERCK shall continue to have the exclusive right and responsibility during
the Term to Commercialize such Product in the Territory (including the United States of America and
its territories and possessions) for use in the Field and (ii) the fact

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.

34

 

that the Parties were
unable to agree on a Co-Promotion Agreement shall not entitle ARCHEMIX to claim damages or any
other sort of compensation whatsoever.

     4.10 Product Recalls. 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, 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).

5. PAYMENTS

     5.1 Technology Access and License Fee. MERCK shall pay ARCHEMIX a non-refundable
technology access and license fee in the amount of Three Million Dollars (US $3,000,000) by wire
transfer within thirty (30) days of the Effective Date, according to instructions that ARCHEMIX
shall provide.

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

     5.3 R&D Funding.

          5.3.1 Payment of R&D Funding. In consideration of the performance by ARCHEMIX of its
activities under the Annual Research Plan(s) as described in Section 3.2, 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. Notwithstanding the
above, in view of the activities to be performed by ARCHEMIX during the initial Calendar
Quarter, MERCK will pay ARCHEMIX [***] Dollars (US $[***]) on the Effective Date; provided, that,
an invoice corresponding with the initial 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 [***] Calendar
Quarters in the aggregate. MERCK shall

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.

35

 

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 amounts in excess of the MERCK Contribution, not to exceed
[***] percent ([***]%) of the MERCK Contribution and (b) all FTE Costs in excess of [***] percent
([***]%) of the MERCK Contribution shall be borne by ARCHEMIX.

          5.3.2 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 Research Program and
the ARCHEMIX Development Activities, 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 Research Program and the ARCHEMIX Development Activities 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 Research Program and/or the ARCHEMIX Development Activities 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 which case ARCHEMIX shall reimburse MERCK for all reasonable costs incurred by
MERCK in connection with such audit.

          5.3.3 R&D External Costs. In addition to the funding obligations in Section 5.3.1
above, and without limiting the generality of the provisions of Section 4.2 hereof, 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.

     5.4 Milestone Payments.

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.

36

 

          5.4.1 Milestones. Within [***] days after the occurrence of the following milestone
events, MERCK shall make the corresponding non-refundable, non-creditable (except as provided in
Section 5.4.2) payments to ARCHEMIX for each Program Target, regardless of the number of Products
that are Developed and Commercialized under this Agreement against such Program Target:

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

     For purposes of clarity (a) milestone 1 shall be paid for the first [***] Project Targets to yield
an Optimized Lead Compounds; (b) [***] shall be paid for a given Product for up to [***] different
Indications; and (c) if payment is made for any of [***] 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 concurrently therewith (for example, if milestone 5 [***] is paid,
but milestone 4[***] has not been paid, then milestone payments 5 and 4 shall [***] on the basis of
[***]). Notwithstanding anything contained herein to the contrary, in no event will MERCK be liable
for milestone payments accrued for achievement of any of milestones 1-14 in excess of milestone
payments made by MERCK of [***] Dollars ($[***]) in the aggregate for each 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.

37

 

          5.4.2 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 5.4.1. 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 5.4.2 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.

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

          5.5.1 Payment of Royalties.

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

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

	 	[***]%
	[***]

	 	[***]%
	[***]

	 	[***]%
	[***]

	 	[***]%

     The following hypothetical example illustrates the calculation of royalties under Section
5.5.1(a): If, in any Calendar Year during the Term, Annual Net Sales of a 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 Offsets. In the event that MERCK, in order to practice the license
granted to it under Section 7.2 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 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 Product, then the royalties payable to ARCHEMIX for such Product under
Section 5.5.1(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

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

 

shall in
no event reduce the royalty that would otherwise be payable for such Product under Section 5.5.1
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 Product and the royalties payable to ARCHEMIX pursuant to
Section 5.5.1(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 11 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 11
(“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 5.5.1(a) [***] Third
Party Chemistry Payments.

               (c) Competing Aptamer Products. In the event that a Third Party sells a Competing
Aptamer Product (as defined below) in a country in which a 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 Product in such country (as measured
by prescriptions or other similar information available in such country) all applicable royalties
in effect with respect to such Product in such country as specified in Section 5.5.1(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 Section 5.5.1(c) 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
5.5.1(c), a “Competing Aptamer Product” means a pharmaceutical product that (i) contains an [***]
and (ii) is marketed in such country for the same [***] as the [***].

               (d) Generic Products. In the event that a Third Party sells a Generic Product (as
defined below) in a country in which a 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: (i) at least [***] percent
([***]%) of MERCK’s volume-based market share of the 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 Product in such
country as specified in Section 5.5.1(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 5.5.1(d) shall not apply
for any country in which MERCK has not [***] for [***] for the applicable Collaboration

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

 

Aptamer(s)
or has not otherwise used commercially reasonable efforts to [***] for such Collaboration
Aptamer(s). For purposes of this Section 5.5.1(d), a “Generic Product” means a pharmaceutical
product that contains the [***] and [***] to such [***].

               (e) Maximum Adjustment of Royalty Rate. Notwithstanding anything to the contrary in
this Agreement, under no circumstances shall the royalty rates in Section 5.5.1(a) be cumulatively
reduced below [***] percent ([***]%) of the rates set forth therein.

               (f) 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 7.6.1; and (vi) the “head start” afforded to MERCK by each of
the foregoing.

               (g) 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
Product occurs. MERCK shall also provide, at the same time each such payment is made, a report
showing: (a) the Net Sales of each Product by type of 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 Product; (d) the exchange rates used in calculating any of the
foregoing; and (e) a calculation of the amount of royalty due to ARCHEMIX.

               (h) 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 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
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 Product and the Supplemental Product, taking into account total
manufacturing costs, proprietary protection and relative contribution thereof. If the Parties

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

 

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.

          5.5.2 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 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.

          5.5.3 Overdue Royalties and Milestones. All royalty payments not made within the time
period set forth in Section 5.5.1(g), including underpayments discovered during an audit, and all
milestone payments not made within the time period specified in Section 5.4.1, 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.

          5.5.4 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

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

 

obligation to
transmit or deposit but for the prohibition shall forthwith be deposited or transmitted, to the
extent allowable.

          5.5.5 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 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, 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 Law, 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 Law.

          5.5.6 Foreign Currency Exchange. All royalties 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 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 10 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
10 attached hereto or any other mutually agreed upon source, for such
Calendar Quarter).

6. TREATMENT OF CONFIDENTIAL INFORMATION;

PUBLICITY; NON-SOLICITATION.

     6.1 Confidentiality.

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

 

          6.1.1 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 6.1.2, 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.

          6.1.2 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 6.1.3. 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 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.

          6.1.3 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.

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

 

     6.2 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
6.1.2 and this Section 6.2. Such terms may be disclosed by a Party 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 and Gilead and University License Equity Holdings, Inc. 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.
Notwithstanding anything to the contrary in Section 6.1, 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 7, 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 6.3 and not subject to this Section 6.2) related to the Research Program or to
any Development Program without the prior written consent of the other Party; provided, that, (a)
notwithstanding the foregoing, ARCHEMIX shall be expressly permitted to publicly announce the
occurrence of any milestone event under Section 5.4 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.

     6.3 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 [***]

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

 

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.

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

7. LICENSE GRANTS; EXCLUSIVITY

     7.1 Research and Development Licenses.

          7.1.1 ARCHEMIX License Grants.

               (a) 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 grant sublicenses as provided in Sections 7.3 and
7.4, under Licensed Technology and Licensed Patent Rights, for the sole purpose of conducting MERCK
Research Activities in the Research Program.

               (b) Development Programs. 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 Sections 7.3 and 7.4, under Licensed Technology and Licensed Patent Rights, for the sole purpose
of Developing Optimized Lead Compounds and Development Candidates in the Field and in the
Territory.

          7.1.2 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-

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

 

free, worldwide license during the Research Program Term, including the right to grant
sublicenses as provided in Sections 7.3 and 7.4, 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, without the right to grant sublicenses, 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 7.1.1(b), 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.

               (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, Patent Rights claiming MERCK Program Technology and MERCK’s
interest in Joint Technology 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 5.5.1, for the remainder of the applicable Royalty Term.

                    (iii) Calculation of Royalties. In calculating the payments due to MERCK for the
licenses granted in this Section 7.1.2(c), the terms of Sections 5.5 and all related obligations
(including the right to offset payments in accordance with Section 5.5.1(b) 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 7.1.2(c)(iv)(1) through (10). 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

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

 

of a transition plan for continued Development and Commercialization. The transition plan
shall include, as applicable, an obligation by MERCK to:

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

                         (2) 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;

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

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

                         (5) 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;

                         (6) 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);

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

                         (8) 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;

                         (9) 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

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

 

                    (10) 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 7.1.2(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 [***] previously made 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.

“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

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

 

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 7.1.2(c).

               (d) 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 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.

               (e) 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 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 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.

               (f) Non-Exclusive License 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.

               (g) Exclusive License 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 and Patent Rights claiming MERCK 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 with
respect to the foregoing license.

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

 

          7.2 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 7.3, under Licensed
Technology and Licensed Patent Rights for the sole purpose of Commercializing Products in the Field
in the Territory.

          7.3 Right to Sublicense. MERCK shall have the right to grant sublicenses to
Sublicensees under the licenses granted to it under Section 7.1.1(b) with respect to any Optimized
Lead Compounds and Development Candidates and Section 7.2 with respect to any Product; 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 6); (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.

          7.4 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 6; (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 7.4, 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.

          7.5 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. Without limiting the generality of
the foregoing or Section 11.3, MERCK shall have no right to practice the SELEX® Process
or to use the SELEX® Technology for any reason or to research, develop, make, have made,
use, offer for sale, distribute for sale, sell, import and have imported Diagnostic Products.

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

 

          7.6 Exclusivity.

               7.6.1 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
Screening Activities and as otherwise provided under this Agreement.

               7.6.2 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 [***] to [***] or [***], or [***]or other [***] to any [***] to [***]MERCK
[***] for the purpose of [***] to a [***] or any [***] that [***] to the [***], except as provided
under this Agreement.

8. INTELLECTUAL PROPERTY RIGHTS

          8.1 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 and ARCHEMIX Patent Rights.

          8.2 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 and
MERCK Patent Rights.

          8.3 Joint Technology Rights. MERCK and ARCHEMIX shall jointly own all Joint
Technology and Joint 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 or jointly owned Confidential Information or Proprietary Materials for any purposes without
the prior written consent of the other Party, without restriction and without the obligation to
provide compensation to the other Party, except as otherwise provided under this Agreement.

          8.4 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:
	 	[***]

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

 

          8.5 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 or
Joint 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.

          8.6 Cooperation. Each Party shall cooperate with the other Party to effect the intent
of this Article 8, 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.

     9. FILING, PROSECUTION AND MAINTENANCE OF PATENT RIGHTS

          9.1 Patent Filing, Prosecution and Maintenance

               9.1.1 MERCK’s Prosecution Rights.

                    (a) Program Technology. Subject to Sections 9.1.4 and 9.1.5, 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 8, at its sole cost and
expense, of Patent Rights covering MERCK Program Technology; 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 8 and shall validate such filings in the EPO contracting states as detailed in
Schedule 8 hereto and the contracting states of any other regional offices identified on
Schedule 8 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.

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

 

               9.1.2 ARCHEMIX Prosecution Rights.

                    (a) 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. 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.

               9.1.3 Joint Prosecution.

                    (a) Certain Program Technology. Notwithstanding anything to the contrary in Section
9.1.1(a) or 9.1.2(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 9.1.3(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 9.1.3.

                    (b) Joint Patent Rights. In the case of Joint 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 and hereby agree that only the application in
the form as agreed between the Parties may be filed in respect of the Joint

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

 

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 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 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 in such
country in both Parties’ names.

               9.1.4 Information and Cooperation. Each Party that has responsibility for filing and
prosecuting any Patent Rights under this Section 9.1 (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 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 9.1; 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
9.1.1(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.

               9.1.5 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 9.1.5, 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

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

 

take all actions and execute all documents reasonably necessary for the Non-Filing Party to assume such responsibility.

          9.2 Legal Actions.

               9.2.1 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 or Joint 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”).

                    (b) MERCK Right to Enforce.

                         (i) Enforcement of Section 9.1.1(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.

                         (ii) Enforcement of Sections 9.1.1(a) Patent Rights and Certain 9.1.3 (a) Patent
Rights. In the event that any Infringement relates to any Patent Right that MERCK is
responsible for prosecuting pursuant to Sections 9.1.1(a) and/or 9.1.3, 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.

                    (c) ARCHEMIX Right to Enforce.

                         (i) Enforcement of Section 9.1.2(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.

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

 

                         (ii) Enforcement of Section 9.1.2(a) Patent Rights and Certain 9.1.3(a) Patent Rights.
In the event that any Infringement relates to any Patent Right that ARCHEMIX is responsible for
prosecuting pursuant to Sections 9.1.2(a) and/or 9.1.3, 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 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.

                    (d) Joint Patent Rights. In the event of an Infringement of a Joint Patent Right, 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.

                    (e) 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
9.2.1 by the other Party.

                    (f) Cooperation by the Parties. In any action, suit or proceeding instituted under
this Section 9.2.1, 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 9.2.1 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.

                    (g) Allocation of Recoveries. Any amounts recovered by MERCK pursuant to actions
under Section 9.2.1(b)(ii), whether by settlement or judgment, 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.

56

 

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

               9.2.2 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

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

 

or otherwise resolve such action, suit or proceeding (e.g., by way of entering into a settlement agreement or consent) at its
sole expense.

                    (c) Third Party Suit Relating Primarily to the use of the SELEX®
Process or the SELEXTM 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 SELEXTM 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 9.2.2. 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.

          9.3 Trademark and Copyright Ownership Prosecution, Defense and Enforcement. MERCK
shall own and 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. TERM AND TERMINATION

          10.1 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, 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, such time as all Royalty Terms for all
Products have ended, unless earlier terminated in accordance with the provisions of this Article
10. Thereafter MERCK’s rights and licenses contained herein shall

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

 

revert to a non-exclusive, worldwide, fully paid up and perpetual license to Commercialize a Product.

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

               10.2.1 Unilateral Right to Terminate. MERCK may terminate this Agreement, effective
upon not less than [***] days written notice to ARCHEMIX, (a) at any time on or after expiration of
the Research Program Term, or (b) on and after the [***] anniversary of the
Effective Date in the event that both [***] listed on Schedule 2A on the Effective
Date have been designated as [***] and the Parties cannot [***] on any Targets to [***] such [***].

               10.2.2 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 MERCK 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.

               10.2.3 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.

          10.3 Consequences of Termination of Agreement. In the event of the termination of
this Agreement pursuant to Section 10.2, the following provisions shall apply, as applicable.

               10.3.1 Termination Pursuant to Section 10.2.1. If this Agreement is terminated by
MERCK pursuant to Section 10.2.1:

                    (a) MERCK shall make a [***] payment to ARCHEMIX no later than the effective date of
termination equal to the difference between (i) the greater of the Minimum FTE Funding Commitment
and the actual FTE Costs incurred by ARCHEMIX through the effective date of termination and (ii)
the aggregate amount of all payments made by MERCK to ARCHEMIX for FTE Costs incurred in accordance
with Section 5.3 through the effective date of termination and all accrued and agreed Third Party
Costs;

                    (b) all licenses granted to MERCK under Article 7 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

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

 

and Products shall be Terminated Compounds, and ARCHEMIX shall have no further obligations under Section 7.6.1

                    (c) 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;

                    (d) 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:

                         (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;

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

 

                         (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 [***]
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.

               10.3.2 Termination by MERCK Pursuant to Section 10.2.2. If this Agreement is
terminated by MERCK pursuant to Section 10.2.2, the license granted by ARCHEMIX to MERCK pursuant
to Section 7.1.1(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 granted by ARCHEMIX to MERCK
pursuant to Section 7.2 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 all 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 10.2.2 is with regard to ARCHEMIX’s obligations under Section 7.6.1
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
10.3.2(a) with respect to such Product shall survive as a fully paid-up, royalty-free license; and
(b) to the extent the breach that gave rise to MERCK’s right to terminate under Section 10.2.2 is
with respect to any other obligation of ARCHEMIX under this Agreement, all milestone, royalty and
other payments applicable to such Products under this Agreement shall be [***] by [***] percent
([***]%).

               10.3.3 Termination by MERCK Pursuant to Section 10.2.3. If this Agreement is
terminated by MERCK pursuant to Section 10.2.3, unless prohibited by Applicable Laws:

                    (a) the license set forth in Section 7.1.1(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 7.2 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

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) 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.

               10.3.4 Termination by ARCHEMIX Pursuant to Section 10.2.2. If this Agreement is
terminated by ARCHEMIX pursuant to Section 10.2.2 (including, without limitation, for breach by
MERCK of its diligence obligations under Section 4.5):

                    (a) the provisions of Section 10.3.1 shall apply; and

                    (b) if such termination is effective prior to the end of the Research Program Term, (i) MERCK
shall, on the effective date of termination, pay ARCHEMIX the balance of the Minimum FTE Funding
Commitment that remains unpaid as of that date and (ii) the Research Program shall terminate
without any further obligation of ARCHEMIX.

               10.3.5 Termination by ARCHEMIX Pursuant to Section 10.2.3. If this Agreement is
terminated by ARCHEMIX pursuant to Section 10.2.3, unless prohibited by Applicable Laws, the
provisions of Section 10.3.1 shall apply, except that MERCK shall have no obligation to continue to
conduct any clinical trial.

          10.4 Rights and Duties of the Parties following Breach by MERCK of Diligence
Obligations. If MERCK breaches its diligence obligations pursuant to Section 4.5 with respect
to a given Program Target or Product, as the case may be, then in lieu of termination of this
Agreement pursuant to Section 10.2.2, ARCHEMIX shall have the right, in its sole discretion, upon
ten (10) days written notice to MERCK, to (i) convert the exclusive license granted to MERCK for
each such Program Target to a non-exclusive license, in which case the provisions of Section 7.6.1
will not apply to such Program Target, or (ii) exercise its rights pursuant to Section 10.2.2 only
on a Program Target-by-Program Target, Product-by-Product and country-by-country basis.

          10.5 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 3.4.1 (Record Keeping),
Section 5.5.2 (Records; Audit Rights), Section 10.3 (Consequences of Termination of Agreement),
Section 10.5 (Surviving Provisions), Section 13.1 (Arbitration), Section 13.4 (Governing Law),
Section 13.9 (No Third Party Beneficiaries), Section 13.15 (Further Assurances), Article 6
(Confidentiality), Article 8 (Intellectual Property Rights), Sections 9.1.3(b) and 9.2.1(d) (Joint
Patent Rights), Article 12 (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.

62

 

                    (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.

11. REPRESENTATIONS AND WARRANTIES

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

               11.1.1 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.

               11.1.2 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 Law, or (d) any order, writ, judgment,
injunction, decree, determination or award of any court or governmental agency presently in effect
applicable to such Party.

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

               11.1.4 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.

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

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

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

               11.2.3 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

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

 

are invalid or unenforceable or that the use of the Licensed Patent Rights or Licensed Technology
as contemplated by this Agreement infringes the Patent Rights of such Third Party.

               11.2.4 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.

          11.3 Acknowledgment 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 for any reason, including without
limitation (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. INDEMNIFICATION

          12.1 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

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

 

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, and (ii) 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 12.1 and
MERCK has an obligation to any ARCHEMIX Indemnitee pursuant to Section 12.2, 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.

          12.2 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 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,
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 12.1 and MERCK has an
obligation to any ARCHEMIX Indemnitee pursuant to this Section 12.2, 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.

          12.3 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, 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.

          12.4 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

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

 

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 12, 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.

          12.5 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.

          12.6 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.

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

13. MISCELLANEOUS

          13.1 Arbitration.

               13.1.1 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 13.1.2. 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

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

 

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 13.1.1. 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 13.4 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 10.2.2 until resolution of the Dispute pursuant to
this Section 13.1.1 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 10.2.2.

                    (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.

               13.1.2 Accelerated Arbitration. To the extent a Dispute submitted to arbitration by a
Party under Section 13.1.1 is claimed, by either Party, to involve an Excepted Decision, the
following procedures shall apply:

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

 

                    (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.

          13.2 Change of Control.

               13.2.1  ARCHEMIX Change of Control.

                    (a) Notice. If ARCHEMIX enters into an agreement that results or, if the transaction
contemplated thereby is 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 (subject to
MERCK’s obligation to [***] ARCHEMIX the [***] of the [***] that remains [***] as of on the
effective date of termination pursuant to Section 5.3); (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 mutually agreed as of the date of the ARCHEMIX Change of Control Notice is given, [***]
ARCHEMIX’s right to [***] a [***] pursuant to Section 4.9.2; and (C) to the extent MERCK is
prosecuting Program

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

 

Aptamer-Specific Patent Rights in accordance with Section 9.1.1(a), [***]
MERCK’s obligation to [***] pursuant to Section 9.1.4 with respect to such Program Aptamer-Specific
Patent Rights. In all other aspects, this Agreement remains unchanged. If MERCK should fail to
give such notice to ARCHEMIX within such [***] day period, MERCK shall have no further rights under
this Section 13.2.1 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.

               13.2.2 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.

                    (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.

          13.3 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:

	 	 	 	 	 
	 

	 	If to MERCK:
	 	If to ARCHEMIX:
	 
	 

	 	MERCK KGaA	 	 
	 

	 	Legal Department
	 	Archemix Corp.
	 

	 	Frankfurter Str. 250
	 	300 Third Street
	 

	 	64293 Darmstadt
	 	Cambridge, MA 02142

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

 

	 	 	 	 	 
	 

	 	Germany
	 	Tel: (617) 621-7700
	 

	 	Tel: +49 6151 72 0
	 	Fax: (617) 621-9300
	 

	 	Fax: +49 6151 72 [***]
	 	Attention: Chief Executive Officer
	 

	 	 	 	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 13.3.

          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 13.3.

          13.4 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.

          13.5 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.

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

          13.7 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.

          13.8 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,

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

 

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.

          13.9 No Third Party Beneficiaries. Except as set forth in Sections 12.1, 12.2 and
12.3, no Third Party (including, without limitation, employees of either Party) shall have or
acquire any rights by reason of this Agreement.

          13.10 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.

          13.11 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.

          13.12 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.

          13.13 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.

          13.14 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. 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.

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

 

          13.15 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.

72

 

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

	 	 	 	 	 	 	 
	 	 	ARCHEMIX CORP.	 	 
	 
	 	 	 	 	 	 
	 
	 	By:	 	/s/ John Harre 	 	 
	 
	 	 	 	 
	 	 
	 
	 	Name:	 	John A. Harre 	 	 
	 
	 	 	 	 
	 	 
	 
	 	Title:	 	V.P. Intellectual Property 	 	 
	 
	 	 	 	 
	 	 
	 
	 	 	 	 	 	 
	 	 	MERCK KGaA	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	ppa.            i.V.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ [*]	 	 
	 
	 	[***]	 	 
	 	 
	 
	 	 	 	/s/ [*]
	 	 
	 
	 	 	 	[***]	 	 

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

 

SCHEDULE 1

OPTIMIZED LEAD COMPOUND SELECTION CRITERIA

[Lead Compound is ready for efficacy testing in animal models including, at a minimum, binding
affinity, specificity, activity, size, and rodent PK criteria but shall not include animal
efficacy, animal toxicology, process development or cost of goods criteria.]

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. 1-1

 

 

SCHEDULE 2A

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. 2A-1

 

 

SCHEDULE 2B

REPLACEMENT 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

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
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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. 3-1

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
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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. 3-2

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
	 	[***]
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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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	 	[***]
	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
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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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	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
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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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	[***]

	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
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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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	 	[***]
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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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	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
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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. 3-8

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
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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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	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
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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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	 	[***]
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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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	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 
	IMATTERNO	 	COUNTRYID	 	SERIALNO	 	PATENTNO	 	TITLE	 	STATUS
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	 	 	[***]
	 	[***]
	[***]

	 	[***]
	 	[***]
	 	[***]
	 	[***]
	 	[***]
	[***]

	 	[***]
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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. 3-11

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
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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

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
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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. 3-14

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
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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. 3-15

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
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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. 3-16

 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	[***]

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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. 3-17

 

 

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 5

EXCLUDED 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. 5-1

 

 

SCHEDULE 6

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. 6-1

 

 

SCHEDULE 7

FORM OF PRESS RELEASE

Merck KGaA and Archemix to Collaborate on Aptamer-Based Cancer Therapeutics

Darmstadt, January xx, 2007 – Merck KGaA announced today that it has signed a multi-year,
multi-target agreement with Archemix Corp. of Cambridge, Massachusetts, that focuses on the
discovery, development, and commercialization of first-in-class aptamer-based therapeutics to treat
cancer.

Under terms of the agreement, Archemix will receive an upfront payment and committed research
funding of as much as $10 million. Archemix also could receive milestones and royalty payments for
products successfully commercialized under the collaboration. In addition, Archemix may participate
in the co-promotion of products that result from the collaboration. Other financial terms were not
disclosed.

“Archemix is the leader in the field of aptamers, a new class of drugs that has tremendous
potential in the battle against cancer,” said Dr. Bernhard Kirschbaum, Executive Senior Vice
President and Director of Research for Merck Serono. “We hope this collaboration will further our
efforts to provide physicians and oncology patients with innovative, targeted cancer treatments.”

Dr. Errol De Souza, President and Chief Executive Officer of Archemix, commented: “Merck is a
recognized global leader in oncology drug development and marketing and we are excited to be
working with them to apply our scientific expertise in developing novel aptamer therapeutics for
cancer. This alliance is the fourth major partnership we have formed over the past 6 months and is
consistent with our strategy to enable partners to leverage aptamers as drugs on a target by target
basis.”

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

 

 

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, offering a significant cost advantage.

About Archemix Corp.

Archemix Corp. is a privately-held biopharmaceutical company based in Cambridge, Massachusetts. The
company’s mission is to develop aptamers as a class of directed therapeutics for the prevention and
treatment of human disease. Because of their unique properties and proven efficacy, aptamers offer
an alternative to biologics and small molecules in numerous applications and offer the potential to
be a major class of drugs for the treatment of unmet medical needs.

Archemix’s aptamer expertise is complemented by a robust patent estate comprised of over 220 issued
and 230 pending patents covering the identification, composition, and use of therapeutic aptamers.
In addition to the company’s core aptamer generation technology, Archemix possesses strong
expertise in both pre-clinical and clinical drug development. Further information on Archemix can
be found at 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 5.9 billion in 2005, a
history that began in 1668, and a future shaped about 35,000 employees in 56 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 a 73% interest and free
shareholders own the remaining 27%. 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. 7-2

 

 

Archemix and Merck KGaA to Collaborate on Aptamer-Based Cancer Therapeutics

CAMBRIDGE, MA – January XX, 2007 – Archemix Corp. announced today that it has signed a
multi-year, multi-target agreement with Merck KGaA of Darmstadt, Germany, that focuses on the
discovery, development, and commercialization of first-in-class aptamer-based therapeutics to treat
cancer.

Under terms of the agreement, Archemix will receive an upfront payment and committed research
funding of as much as $10 million. Archemix also could receive milestones and royalty payments for
products successfully commercialized under the collaboration. In addition, Archemix may participate
in the co-promotion of products that result from the collaboration. Other financial terms were not
disclosed.

Dr. Errol De Souza, President and Chief Executive Officer of Archemix, commented: “Merck is a
recognized global leader in oncology drug development and marketing and we are excited to be
working with them to apply our scientific expertise in developing novel aptamer therapeutics for
cancer. This alliance is the fourth major partnership we have formed over the past six months and
is consistent with our strategy to enable partners to leverage aptamers as drugs on a target by
target basis.”

“Archemix is the leader in the field of aptamers, a new class of drugs that has tremendous
potential in the battle against cancer,” said Dr. Bernhard Kirschbaum, Executive Senior Vice
President and Director of Research for Merck Serono. “We hope this collaboration will further our
efforts to provide physicians and oncology patients with innovative, targeted cancer treatments.”

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, offering a significant cost advantage.

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. 7-3

 

 

About Archemix Corp.

Archemix Corp. is a privately-held biopharmaceutical company based in Cambridge, Massachusetts. The
company’s mission is to develop aptamers as a class of directed therapeutics for the prevention and
treatment of human disease. Because of their unique properties and proven efficacy, aptamers offer
an alternative to biologics and small molecules in numerous applications and offer the potential to
be a major class of drugs for the treatment of unmet medical needs.

Archemix’s aptamer expertise is complemented by a robust patent estate comprised of over 220 issued
and 230 pending patents covering the identification, composition, and use of therapeutic aptamers.
In addition to the company’s core aptamer generation technology, Archemix possesses strong
expertise in both pre-clinical and clinical drug development. Further information on Archemix can
be found at www.archemix.com.

     About Merck

Merck is a global pharmaceutical and chemical company with sales of EUR 5.9 billion in 2005, a
history that began in 1668, and a future shaped by about 35,000 employees in 56 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 a 73% interest
and free shareholders own the remaining 27%. 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. 7-4

 

 

SCHEDULE 8

REGIONAL OFFICES OR COUNTRIES IN WHICH

PATENT APPLICATIONS ARE TO BE NATIONALIZED

OR OTHERWISE PROSECUTED, FILED AND MAINTAINED

	 	 	 
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]

	 	[***]
	[***]
	 	 

 

			
	*	 	[***]

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. 8-1

 

 

SCHEDULE 9

MATERIAL TERMS TO BE INCLUDED IN

FORM OF CO-PROMOTION AGREEMENT

     The Co-Promotion Agreement is to be negotiated by the Parties in accordance with Section 4.9.2
and shall contain the following material terms. Capitalized terms used in this Schedule 9
and not otherwise defined have the meanings given to them in the Agreement.

     1. Joint Marketing Committee.

          (a) Establishment. [***] of the [***] but in [***], ARCHEMIX and MERCK shall [***]
ARCHEMIX and MERCK [***], which shall have and [***].

          (b) Membership. Each of ARCHEMIX and MERCK shall [***] to the [***] by the[***], one
of [***], on a [***] to the [***].

          (c) Meetings.

                         (i) Schedule of Meetings; Agenda. [***], without [***] for the [***] and its [***]by
any [***] (or, if such [***] to be [***] to the [***]; provided, that, [***], either before or
after such [***] of any [***], unless such [***] for the [***] to its [***]; provided, that, [***]
for each [***].

                         (ii) Quorum; Voting; Decisions. [***] of the [***]; provided, that, [***] from the
[***]. Whenever [***] by the [***] in which the [***]of the [***] or by [***] of the [***], which
shall not [***].

          (d) Responsibilities. [***] shall be [***] in the [***] shall have the [***]:

                         (i) the [***] for the [***] of each [***];

                         (ii) [***] of a [***] for each [***] in the [***];

                         (iii) [***] and [***] for [***];

                         (iv) [***] and the [***] of all [***] in the [***], but [***];

                         (v) [***] of [***] in the [***];

                         (vi) [***] and any [***] in the [***];

                         (vii) [***] to [***];

                         (viii) [***] to be [***] to [***] to [***];[***] to the [***] to[***]; 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. 9-1

 

 

                         (ix) [***] as may be [***], or by [***] of the [***].

          (e) Dispute Resolution. The [***]. In the event that, [***] on a [***] after the
[***], then the [***].

     2. Co-Promotion Plan. The [***] for the [***], but not be [***] in the [***] and
[***] for such [***] for such [***] for such [***] shall be [***] ARCHEMIX’S [***] and shall be
[***] and [***] MERCK’s and ARCHEMIX’s [***]r.

     3. Labeling. [***] MERCK and ARCHEMIX. The [***] and [***] in the [***] and [***] or
in the [***].

     4. Co-Promotion Rights.

          (a) ARCHEMIX and MERCK [***] is to [***] of the [***] for [***] that the [***] to the [***]
but [***]; provided, that, the [***] of the [***] and the [***] in such [***] as the [***] for the
[***] of such [***] with the [***] from which each [***] and [***] of [***] that it may be
[***]shall be [***] to be [***].

          (b) The [***] to the [***] with a [***]. It is [***] to the [***]. With respect to each
[***] as the [***] to be [***].

          (c) MERCK s[***] ARCHEMIX a [***]MERCK [***] the MERCK [***] and MERCK [***].

          (d) ARCHEMIX and MERCK [***] if that [***] that is [***] that is [***] shall be [***] that its
[***] and/or the [***] of the [***] with an [***] for the [***] for its [***] in the [***].

     5. Commercialization Efforts. [***] with the [***], and to [***] with each [***] out
such [***].

     6. Co-Promotion Marketing and Sales Plan and Budget.

          (a) Preparation of Plan and Budget. MERCK, [***]ARCHEMIX, [***] for each [***] for
the [***], and each such [***] shall be [***] by the [***]; provided, that each such [***] with
ARCHEMIX’s [***] but not be[***] and [***] for the [***] in the [***] and [***] for the [***] for
each [***] for the [***]. Each [***] of the [***] shall be [***] to the [***] by a [***], but no
[***].

          (b) Changes to Plans/Budgets. [***] in a [***] of the [***] to the [***], MERCK
[***]to the [***] with such [***] by MERCK [***].

          (c) Detail Audit Rights. [***] MERCK and ARCHEMIX [***] for a [***] from the [***]
shall have the [***] of the [***] to the [***] at such [***] shall not be [***] in [***] in the
course of [***], shall be [***] of the [***]. The [***] of such [***] in the [***] in the [***] by
such [***].

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. 9-2

 

 

     7. Control Over Advertising and Detailing.

          (a) [***] in any [***] or other [***] (to be [***] with a [***] in the [***] and [***] by the
[***].

          (b) [***] on the [***], but all [***] ARCHEMIX or MERCK and [***] shall be [***].

          (c) [***] shall be [***] with a [***] of the [***].

          (d) [***] with the [***] of the [***] of the [***] of the [***].

          (e) MERCK [***] and for [***] as may be [***]; and [***] but shall, in [***] with, and [***].

          (f) MERCK [***] for the [***].

          (g) [***] in any [***] or other [***] with a [***] unless the [***] by the [***] by the [***],
but all [***] ARCHEMIX or MERCK [***] which is not [***] shall be [***]. Without the [***] of the
[***] of the [***].

     8. Sales Efforts in the Co-Promotion Territory. As [***] for the [***] of the [***]
for the [***] and [***] in the [***], of the [***] to be [***] with the [***] that ARCHEMIX [***]
of the [***] to the [***] in an [***] with the [***] to each [***] in the [***] of such [***] of
the [***] that it may be [***] in the [***], and, [***] in the [***] as it [***] to be [***].

     9. Training Program. [***] for the [***] of all [***] to be [***] in the [***] that
is [***] that for the [***] and the [***] of such [***] as a [***] under this [***].

     10. Trademarks. MERCK [***], and MERCK [***]ARCHEMIX [***]MERCK [***] in the [***]
all such [***] in the [***] for all [***] be the [***] of the [***] in the [***].

     11. Product Recalls. In the [***], or in the [***] that an [***] in the [***] and
have [***] in the [***] by a [***] or to [***] in which [***], the [***] shall be [***] that
ARCHEMIX [***], ARCHEMIX [***] MERCK. MERCK [***] or [***] of the [***] for such [***].

     12. Co-Promotion Mechanism.

          (a) Sales. [***] in the [***] MERCK. If, during the [***], ARCHEMIX [***] for a
[***] MERCK.

          (b) Processing of Orders for Co-Promoted Products.

                         (i) [***] by MERCK [***] by MERCK in a [***] with the [***] by it 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. 9-3

 

 

                         (ii) MERCK [***] by it for a [***], that MERCK [***] on an [***], but only with [***] with the
[***] by it with [***].

                         (iii) MERCK [***] with [***].

     13. Termination of Co-Promotion Participation. I[***], at the [***], ARCHEMIX [***]
to MERCK, to [***] of any [***], provided that ARCHEMIX [***] from ARCHEMIX’ [***].

     14. Cost of Detailing. [***], in no event shall [***] to an [***] of the [***], such
as [***] MERCK [***] 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.

Sched. 9-4

 

 

SCHEDULE 10

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. 10-1

 

 

SCHEDULE 11

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. 11-1

 

 

AMENDMENT TO COLLABORATIVE RESEARCH AND LICENSE AGREEMENT

BETWEEN ARCHEMIX CORP. AND MERCK KGaA DATED JANUARY 17, 2007

     This AMENDMENT TO 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, MERCK and ARCHEMIX entered into a Collaborative Research and License Agreement (the
“First License Agreement”) on January 17, 2007; and

     WHEREAS, concurrent with the signature of this Agreement MERCK and ARCHEMIX shall enter into a
second Collaborative Research and License Agreement (the “Second License Agreement”); and

     WHEREAS, MERCK and ARCHEMIX now wish to amend certain provisions of the First License
Agreement to make them consistent with the provisions of the Second License Agreement.

     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.	 	Effective as of the date first written above, Section 1.64 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	“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).

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

 

	2.	 	Effective as of the date first written above, Section 1.65 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	“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.
	 
	3.	 	Effective as of the date first written above, Section 1.88 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	“Permitted Activities” means (a) with respect to any Program Target, any screening
activities conducted by ARCHEMIX with respect to such Program Target for itself and/or for
any Third Party for the purpose of identifying aptamers that bind to a Target other [***]
select or otherwise participate in the identification of the targets that are the subject of
any such grant of rights and (z) fund or participate in the discovery, development and/or
commercialization of any such aptamers outside of the Field.
	 
	4.	 	Effective as of the date first written above, Section 1.106 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	“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.
	 
	5.	 	Effective as of the date first written above, Section 4.8.3(a) of the First License Agreement
is hereby amended to read as follows:
	 
	 	 	Adverse Events. In addition to the updates described in Section 4.8.1 and 4.8.2,
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 13.3. 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

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.

2

 

	 	 	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.
	 
	6.	 	Effective as of the date first written above, Section 5.4.1 of the First License Agreement is
hereby amended to read as follows:

	 	 	 	 	 
	 	 	Milestone Event	 	Milestone Payment
	1.

	 	[***]
	 	$[***]
	2.

	 	[***]
	 	$[***]
	3.

	 	[***]
	 	$[***]
	4.

	 	[***]
	 	$[***]
	5.

	 	[***]
	 	$[***]
	6.

	 	[***]
	 	$[***]
	7.

	 	[***]
	 	$[***]
	8.

	 	[***]
	 	$[***]
	9.

	 	[***]
	 	$[***]
	10.

	 	[***]
	 	$[***]
	11.

	 	[***]
	 	$[***]
	12.

	 	[***]
	 	$[***]
	13.

	 	[***]
	 	$[***]
	14.

	 	[***]
	 	$[***]

	7.	 	Effective as of the date first written above, Section 5.5.1(f) of the First License Agreement
is hereby amended to read as follows:

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.

3

 

	 	 	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 7.6.1; and (vi)
the “head start” afforded to MERCK by each of the foregoing.
	 
	8.	 	Effective as of the date first written above, Section 7.1.2(f) of the First License Agreement
is hereby amended to read as follows:
	 
	 	 	Non-Exclusive License 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.
	 
	9.	 	Effective as of the date first written above, Section 7.1.2(g) of the First License Agreement
is hereby amended to read as follows:
	 
	 	 	Exclusive License 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 and Patent Rights claiming MERCK 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 with respect to the foregoing license.
	 
	10.	 	Effective as of the date first written above, Section 7.6.1 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	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

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.

4

 

	 	 	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.
	 
	11.	 	Effective as of the date first written above, Section 9.2.1(a) of the First License Agreement
is hereby amended to read as follows:
	 
	 	 	Notice. In the event either Party becomes aware of (i) any possible infringement of
any Licensed Patent Rights, MERCK Patent Rights or Joint 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”).
	 
	12.	 	Effective as of the date first written above, Section 11.3 of the First License Agreement is
hereby amended to read as follows:
	 
	 	 	Acknowledgment 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 for any reason, including
without limitation (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

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.

5

 

	 	 	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.
	 
	13.	 	Effective as of the date first written above, a new paragraph shall be inserted into the
First License Agreement as Section 11.4 which new Section 11.4 shall read as follows:
	 
	 	 	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 7.6.1
(as amended herein) 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 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.
	 
	14.	 	Except to the extent amended herein, the First License Agreement shall remain unchanged and
in full force and effect.

[REMAINDER OF PAGE 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.

6

 

	 	 	 	 	 	 	 
	 	 	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
	 
	 	 	 	 	 	 
	 

	 	 	 	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.

7

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