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defined in the Original Agreement), ARC 183, has been withdrawn from Development; and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.