Document:

Securities Purchase Agreement

 Exhibit 10.1 

SECURITIES PURCHASE AGREEMENT 

This Securities Purchase Agreement (this “Agreement”) is dated as of August 18, 2010 by and among
Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and the several purchasers identified in the attached Exhibit A (each a “Purchaser” and, collectively, the
“Purchasers”). 
 WHEREAS, the Company desires to issue and sell to the Purchasers an aggregate
of (i) 19,775,101 shares (the “Shares”) of the authorized but unissued shares of common stock, par value $0.001 per share, of the Company (the “Common Stock”) and (ii) warrants in the form attached hereto
as Exhibit B to purchase an aggregate of 6,291,285 shares of Common Stock (each, a “Common Warrant” and collectively, the “Common Warrants”); and 

WHEREAS, the Purchasers, severally and not jointly, wish to purchase the Shares and the Common Warrants on the terms and
subject to the conditions set forth in this Agreement. 
 NOW, THEREFORE, IN CONSIDERATION of the mutual
covenants contained in this Agreement, and for other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the Company and the Purchasers agree as follows: 

ARTICLE I 

DEFINITIONS 

1.1 Definitions. In addition to the terms defined elsewhere in this Agreement, the following terms have the
meanings indicated in this Section 1.1: 
 “Action” shall have the meaning ascribed to
such term in Section 3.1(j). 
 “Affiliate” means any Person that, directly or indirectly
through one or more intermediaries, controls or is controlled by or is under common control with a Person, as such terms are used in and construed under Rule 144 under the Securities Act. With respect to a Purchaser, any investment fund or managed
account that is managed on a discretionary basis by the same investment manager as such Purchaser will be deemed to be an Affiliate of such Purchaser. 

“Board of Directors” means the Company’s board of directors, as constituted from time to time.

 “Closing” means the closing of the purchase and sale of the Closing Securities pursuant to
Section 2.1. 
 “Closing Date” means the Trading Day when all of the Transaction Documents
have been executed and delivered by the applicable parties thereto, and all conditions precedent to (i) the Purchasers’ obligations to pay the Subscription Amount and (ii) the Company’s obligations to deliver the Closing
Securities have been satisfied or waived. 
 “Closing Securities” means the Shares and the
Common Warrants. 

 “Commission” means the Securities and Exchange Commission.

 “Common Stock” shall have the meaning ascribed to such term in the recitals to this
Agreement. 
 “Common Stock Equivalents” means any securities of the Company that would entitle
the holder thereof to acquire at any time Common Stock, including, without limitation, any debt, preferred stock, rights, options, warrants or other instrument that is at any time convertible into or exercisable or exchangeable for, or otherwise
entitles the holder thereof to receive, Common Stock. 
 “Common Warrants” shall have the
meaning ascribed to such term in the recitals to this Agreement. 
 “Common Warrant Shares”
means the shares of Common Stock issuable upon exercise of the Common Warrants. 
 “Company
Counsel” means Wilmer Cutler Pickering Hale & Dorr LLP. 
 “Company Intellectual
Property Rights” shall have the meaning ascribed to such term in Section 3.1(p). 

“Disclosure Schedules” shall have the meaning ascribed to such term in Section 3.1. 

“Effective Date” means the date that a Registration Statement filed by the Company pursuant to the
Registration Rights Agreement is first declared effective by the Commission. 
 “Environmental
Laws” shall have the meaning ascribed to such term in Section 3.1(ii). 
 “Exchange
Act” means the Securities Exchange Act of 1934, as amended, and the rules and regulations promulgated thereunder. 

“FDA” shall have the meaning ascribed to such term in Section 3.1(n)(i). 

“GAAP” shall have the meaning ascribed to such term in Section 3.1(h). 

“knowledge” means, with respect to any Person, what such Person actually knows or reasonably should
know, and, in the case of a corporation or other entity, what its executive officers and directors actually know or reasonably should know. 

“Liens” means a lien, charge, with respect to any asset, any mortgage, lien, pledge, charge, security
interest, or encumbrance of any kind in respect of such asset, whether or not filed, recorded or otherwise perfected under applicable law (including conditional sale or other retention agreement, any lease in the nature thereof, any option or other
agreement to sell or give a security interest in and any filing of or agreement to give any financing statement under the Uniform Commercial Code (or equivalent statutes) of any jurisdiction). 

 

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 “Legend Removal Date” shall have the meaning ascribed to
such term in Section 4.1(c). 
 “Majority Purchasers” means (i) prior to the Closing,
Purchasers that agreed to purchase an aggregate of greater than fifty percent (50%) of the Shares to be issued and sold pursuant to this Agreement and (ii) following the Closing, Purchasers which, at any given time, hold greater than fifty
percent (50%) of the outstanding Shares issued and sold pursuant to this Agreement that have not been resold pursuant to an effective Registration Statement or Rule 144. 

“Material Adverse Effect” shall have the meaning ascribed to such term in Section 3.1(b).

 “Non Disclosure Agreements” means the non-disclosure agreements entered into by the Company
with the Purchasers in connection with the transactions contemplated by this Agreement. 

“Person” means an individual or corporation, partnership, trust, incorporated or unincorporated
association, joint venture, limited liability company, joint stock company, government (or an agency or sub-division thereof) or other entity of any kind. 

“Purchaser Party” shall have the meaning ascribed to such term in Section 4.7. 

“Registration Rights Agreement” means the Registration Rights Agreement, dated the date hereof, among
the Company and the Purchasers, in the form of Exhibit C attached hereto. 
 “Registration
Statement” means a registration statement meeting the requirements set forth in Section 2(a) of the Registration Rights Agreement, including without limitation, covering the resale of the Shares and/or the Underlying Shares, as
applicable, by the Purchasers as provided for in the Registration Rights Agreement. 
 “Required
Approvals” shall have the meaning ascribed to such term in Section 3.1(e). 
 “Required
Minimum” means, as of any date, the maximum aggregate number of shares of Common Stock then issued or potentially issuable in the future pursuant to the Transaction Documents, including any Underlying Shares issuable upon exercise in full
of all Common Warrants, ignoring any exercise limits set forth therein. 
 “Rule 144” means
Rule 144 promulgated by the Commission pursuant to the Securities Act, as such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule.

 “SEC Reports” shall have the meaning ascribed to such term in Section 3.1(h).

  

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 “Securities” means the Shares, the Common Warrants and the
Common Warrant Shares. 
 “Securities Act” means the Securities Act of 1933, as amended.

 “Shares” shall have the meaning ascribed to such term in the recitals to this Agreement.

 “Short Sales” shall include all “short sales” as defined in Rule 200 of Regulation
SHO under the Exchange Act (but shall not be deemed to include the location and/or reservation of borrowable shares of Common Stock). 

“Subscription Amount” means, as to a Purchaser, the aggregate amount to be paid for the Closing
Securities purchased hereunder as specified opposite such Purchaser’s name on Exhibit A attached hereto, under the column entitled “Aggregate Purchase Price of Closing Securities,” in United States Dollars and in immediately
available funds. 
 “Trading Affiliate” shall have the meaning ascribed to such term in
Section 3.2(f). 
 “Trading Day” means a day on which the Common Stock is traded on a
Trading Market. 
 “Trading Market” means the following markets or exchanges on which the
Common Stock is listed or quoted for trading on the date in question: the Nasdaq Capital Market, the Nasdaq Global Market or the New York Stock Exchange. 

“Transaction Documents” means this Agreement, the Common Warrants and the Registration Rights Agreement.

 “Underlying Shares” means the Common Warrant Shares. 

ARTICLE II 

PURCHASE AND SALE 

2.1 Closing. On the Closing Date, upon the terms and subject to the conditions set forth herein, the Company will
issue and sell, and the Purchasers will purchase, severally and not jointly, (i) the number of Shares set forth opposite the name of such Purchaser under the heading “Number of Shares to be Purchased” on Exhibit A attached
hereto at a price per Share equal to $2.49 and (ii) Common Warrants to purchase 0.35 of a share of Common Stock for every one Share purchased at Closing at a price per Common Warrant equal to $0.125. Each Purchaser shall deliver to the Company
via wire transfer of immediately available funds pursuant to wire instructions sent by the Company to each Purchaser on or prior to the Closing Date, an amount equal to the Subscription Amount. The Closing shall take place as soon as practicable
upon satisfaction or waiver of the conditions set forth in Section 2.3, but in any event no later than 5:00 pm (Eastern Time) on August 27, 2010, remotely via exchange of documents and signatures. 

 

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 2.2 Deliveries. 

(a) On the Closing Date, the Company shall deliver or cause to be delivered to each Purchaser the following: 

(i) Shares registered in the names of the Purchaser, in an amount equal to number of Shares set forth opposite the name
of such Purchaser under the heading “Number of Shares to be Purchased” on Exhibit A attached hereto; and 

(ii) a Common Warrant, substantially in the form of Exhibit B attached hereto, registered in the name of such
Purchaser, to purchase up to the number of Common Warrant Shares set forth opposite the name of such Purchaser under the heading “Number of Common Warrant Shares Underlying Common Warrants Purchased” on Exhibit A attached hereto.

 (b) On the Closing Date, each Purchaser shall deliver or cause to be delivered to the Company the
Subscription Amount via wire transfer of immediately available funds pursuant to the wire instructions delivered to such Purchaser by the Company on or prior to the Closing Date. 

2.3 Closing Conditions. 

(a) The obligations of the Company hereunder in connection with the Closing are subject to the following conditions being
met, any or all of which may be waived by the Company in writing: 
 (i) the accuracy in all material respects
on the Closing Date of the representations and warranties of the Purchasers contained herein; 
 (ii) all
obligations, covenants and agreements of the Purchasers required to be performed at or prior to the Closing Date shall have been performed; and 

(iii) the delivery by the Purchasers of the Registration Rights Agreement duly executed by such Purchaser. 

(b) The obligations of each Purchaser hereunder in connection with the Closing are subject to the following conditions
being met, any or all of which may be waived by the Majority Purchasers in writing: 
 (i) the accuracy in all
material respects on the Closing Date of the representations and warranties of the Company contained herein; 

(ii) all obligations, covenants and agreements of the Company required to be performed at or prior to the Closing Date
shall have been performed; 
  

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 (iii) the delivery by the Company to such Purchaser of the following items:

 (A) a legal opinion of Company Counsel, substantially in the form of Exhibit D attached hereto;

 (B) a certificate, dated the Closing Date, duly executed by an officer of the Company to the effect that the
conditions specified in Sections 2.3(b)(i) and 2.3(b)(ii) have been satisfied; and 
 (C) the Registration
Rights Agreement duly executed by the Company; 
 (iv) the entry into Amendment No. 1 to the Third Amended
and Restated Investor Rights Agreement, dated as of August 11, 2008, by and among the Company and the Holders (as defined therein); 

(v) there shall have been no Material Adverse Effect with respect to the Company since the date hereof; 

(vi) from the date hereof to the Closing Date, trading in the Common Stock shall not have been suspended by the
Commission or the Company’s principal Trading Market and, at any time prior to the Closing Date, trading in securities generally as reported by Bloomberg Financial Markets shall not have been suspended or limited, or minimum prices shall not
have been established on securities whose trades are reported by such service, or on any Trading Market, nor shall a banking moratorium have been declared either by the United States or New York State authorities, nor shall there have occurred any
material adverse change in the financial markets which, in each case, makes it impracticable or inadvisable to purchase the Closing Securities at the Closing; and 

(vii) there shall have been no change in facts or circumstances that could reasonably lead to the discontinuation of
further development of, or failure of the Company to be able to market, the Company’s ACH-1625 program from the date hereof to the Closing Date. 

ARTICLE III 

REPRESENTATIONS AND WARRANTIES 

3.1 Representations and Warranties of the Company. Except as set forth under the corresponding section of the
disclosure schedules delivered to each Purchaser concurrently herewith (the “Disclosure Schedules”), which Disclosure Schedules shall be deemed a part hereof, and except as otherwise described in the SEC Reports, which qualify the
following representations and warranties in their entirety, the Company hereby makes the representations and warranties set forth below to each Purchaser. 

(a) Subsidiaries. The Company does not own or control, directly or indirectly, any interest in any other Person.
The Company is not a participant in any joint venture, partnership or similar arrangement. 
  

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 (b) Organization and Qualification. Except as described in Schedule
3.1(b), the Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of Delaware, with the requisite corporate power and authority to own and use its properties and assets and to carry on its
business as currently conducted. The Company is not in violation or default of any of the provisions of its certificate of incorporation, bylaws or other organizational or charter documents. The Company is duly qualified to conduct business and is
in good standing as a foreign corporation or other entity in each jurisdiction in which the nature of the business conducted or property owned by it makes such qualification necessary, except where the failure to be so qualified or in good standing,
as the case may be, could not have or reasonably be expected to result in (i) a material adverse effect on the legality, validity or enforceability of any Transaction Document, (ii) a material adverse effect on the results of operations,
assets, business, condition (financial or otherwise) or prospects of the Company or (iii) a material adverse effect on the Company’s ability to perform in any material respect on a timely basis its obligations under any Transaction
Document (any of (i), (ii) or (iii), a “Material Adverse Effect”) and no Proceeding has been instituted in any such jurisdiction revoking, limiting or curtailing or seeking to revoke, limit or curtail such power and authority
or qualification. 
 (c) Authorization; Enforcement. The Company has the requisite corporate power and
authority to enter into and to consummate the transactions contemplated by each of the Transaction Documents and otherwise to carry out its obligations hereunder and thereunder. The execution and delivery of each of the Transaction Documents by the
Company and the consummation by it of the transactions contemplated hereby and thereby have been duly authorized by all necessary corporate action on the part of the Company and no further action is required by the Company, its board of directors or
its stockholders in connection therewith other than in connection with the Required Approvals. Each Transaction Document has been (or upon delivery will have been) duly executed by the Company and, when delivered in accordance with the terms hereof
and thereof, will constitute the valid and binding obligation of the Company enforceable against the Company in accordance with its terms except (i) as limited by applicable bankruptcy, insolvency, reorganization, moratorium and other laws of
general application affecting enforcement of creditors’ rights generally and (ii) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies. 

(d) No Conflicts. The execution, delivery and performance of the Transaction Documents by the Company and the
consummation by the Company of the other transactions contemplated hereby and thereby do not and will not: (i) conflict with or violate any provision of the Company’s certificate of incorporation, bylaws or other organizational or charter
documents, or (ii) subject to the Required Approvals and assuming the accuracy of the representations and warranties in Section 3.2, conflict with or result in a violation of any law, rule, regulation, order, judgment, injunction, decree
or other restriction of any court or governmental authority to which the Company is subject (including federal and state securities laws and regulations), or by which any property or asset of the Company is bound or affected, or (iii) conflict
with, or constitute a default (or an event that with notice or lapse of time or both would become a default) under, result in the creation of any Lien upon any of the properties or assets of the Company, or give to others any rights of termination,
amendment, acceleration or cancellation (with or without notice, lapse of time or both) of, any agreement, credit facility, debt or other instrument (evidencing a Company debt or otherwise) or other agreement or understanding to which the Company is
a party or by which any property or asset of the Company is bound or affected; except in the case of clauses (ii) and (iii), such as could not have a Material Adverse Effect. 

 

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 (e) Filings, Consents and Approvals. The Company is not required to
obtain any consent, waiver, authorization or order of, give any notice to, or make any filing or registration with, any court or other federal, state, local or other governmental authority or other Person in connection with the execution, delivery
and performance by the Company of the Transaction Documents, other than (i) filings required pursuant to Section 4.5, (ii) the filing with the Commission of any Registration Statements and any other filings required pursuant to the
Registration Rights Agreement, (iii) the notice and/or application(s) to each applicable Trading Market for the issuance and sale of the Closing Securities and the listing of the Shares and the Underlying Shares for trading thereon in the time
and manner required thereby and (iv) the filing of a Form D with the Commission and such filings as are required to be made under applicable state securities laws (collectively, the “Required Approvals”). 

(f) Issuance of the Securities. The Closing Securities have been duly authorized for issuance and sale to the
Purchasers pursuant to this Agreement and, when issued and delivered by the Company against payment therefor in accordance with the terms of this Agreement, will be duly and validly issued and fully paid and nonassessable, and will be sold free and
clear of all Liens. The Common Warrant Shares have been duly and validly authorized and reserved for issuance and, upon exercise of the Common Warrants in accordance with their terms, including the payment of any exercise price therefor, will be
validly issued, fully paid and nonassessable and will be sold free and clear of any Liens. The Company has reserved from its duly authorized capital stock a number of shares of Common Stock for issuance of the Shares and the Underlying Shares at
least equal to the Required Minimum on the date hereof. The Company has not, and to the knowledge of the Company, no Affiliate of the Company has sold, offered for sale or solicited offers to buy or otherwise negotiated in respect of any security
(as defined in Section 2 of the Securities Act) that would be integrated with the offer or sale of any of the Securities in a manner that would require the registration under the Securities Act of the sale of any of the Securities to the
Purchasers, or that would be integrated with the offer or sale of any of the Securities for purposes of the rules and regulations of any Trading Market. 

(g) Capitalization. Schedule 3.1(g) sets forth the number of authorized and outstanding shares of the
Company’s capital stock and outstanding Common Stock Equivalents. The Company has not issued any capital stock since its most recently filed periodic report under the Exchange Act, other than pursuant to the exercise of employee stock options
under the Company’s stock option plans, the issuance of shares of Common Stock to employees pursuant to the Company’s employee stock purchase plan and pursuant to the conversion or exercise of Common Stock Equivalents outstanding as of the
date of the most recently filed periodic report under the Exchange Act. No Person has any right of first refusal, preemptive right, right of participation, or any similar right to participate in the transactions contemplated by the Transaction
Documents. Except as a result of the purchase and sale of the Securities, there are no outstanding options, warrants, script rights to subscribe to, calls or commitments of any character whatsoever relating to, or securities, rights or obligations
convertible into or exercisable or exchangeable for, or giving any Person any right to subscribe for or acquire, any shares of Common Stock, or contracts, commitments, understandings or arrangements by which the Company is or may become bound to
issue additional shares of Common Stock or Common 
  

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Stock Equivalents. The issuance and sale of the Securities will not obligate the Company to issue shares of Common Stock or other securities to any Person (other than the Purchasers) and will not
result in a right of any holder of Company securities to adjust the exercise, conversion, exchange or reset price under such securities. All of the outstanding shares of capital stock of the Company are validly issued, fully paid and nonassessable,
have been issued in compliance with all federal and state securities laws, and none of such outstanding shares was issued in violation of any preemptive rights or similar rights to subscribe for or purchase securities. No further approval or
authorization of any stockholder, the Board of Directors or others is required for the issuance and sale of the Securities. There are no stockholders agreements, voting agreements or other similar agreements with respect to the Company’s
capital stock to which the Company is a party or, to the knowledge of the Company, between or among any of the Company’s stockholders. 

(h) SEC Reports; Financial Statements. The Company has complied with requirements to file all reports, schedules,
forms, statements and other documents required to be filed by it under the Securities Act and the Exchange Act, including pursuant to Section 13(a) or 15(d) thereof, for the two years preceding the date hereof (or such shorter period as the
Company was required by law to file such material) (the foregoing materials, including the exhibits thereto and documents incorporated by reference therein, being collectively referred to herein as the “SEC Reports”) on a timely
basis or has received a valid extension of such time of filing and has filed any such SEC Reports prior to the expiration of any such extension. As of their respective dates, the SEC Reports complied in all material respects with the requirements of
the Securities Act and the Exchange Act and the rules and regulations of the Commission promulgated thereunder, and none of the SEC Reports, when filed, contained any untrue statement of a material fact or omitted to state a material fact required
to be stated therein or necessary in order to make the statements therein, in the light of the circumstances under which they were made, not misleading. The financial statements of the Company included in the SEC Reports comply in all material
respects with applicable accounting requirements and the rules and regulations of the Commission with respect thereto as in effect at the time of rules and regulations of the Commission with respect thereto as in effect at the time of filing. Such
financial statements have been prepared in accordance with United States generally accepted accounting principles applied on a consistent basis during the periods involved (“GAAP”), except as may be otherwise specified in such
financial statements or the notes thereto and except that unaudited financial statements may not contain all footnotes required by GAAP, and fairly present in all material respects the financial position of the Company as of and for the dates
thereof and the results of operations and cash flows for the periods then ended, subject, in the case of unaudited statements, to normal, immaterial, year-end audit adjustments. The Company has not provided to the Purchasers any material non-public
information or other information which, according to applicable law, rule or regulation, was required to have been disclosed publicly by the Company but which has not been so disclosed, other than with respect to the transactions contemplated by
this Agreement and which is covered by the Non-Disclosure Agreements. 
 (i) Material Changes. Since the
date of the latest audited financial statements included within the SEC Reports (i) there has been no event, occurrence or development that could have a Material Adverse Effect, (ii) the Company has not incurred any liabilities (contingent
or otherwise) other than (A) trade payables and accrued expenses incurred in the ordinary course of business consistent with past practice and (B) liabilities not required to be 

 

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reflected in the Company’s financial statements pursuant to GAAP or required to be disclosed in filings made with the Commission, (iii) the Company has not materially altered its method
of accounting, (iv) the Company has not declared or made any dividend or distribution of cash or other property to its stockholders or purchased, redeemed or made any agreements to purchase or redeem any shares of its capital stock and
(v) the Company has not issued any equity securities to any officer, director or Affiliate, except pursuant to existing Company stock option plans. Except for the issuance of the Securities contemplated by this Agreement, no event, liability or
development has occurred or exists with respect to the Company or its business, properties, operations or financial condition, that would be required to be disclosed by the Company under applicable federal securities laws at the time this
representation is made that has not been publicly disclosed. 
 (j) Litigation. There is no action, suit,
inquiry, notice of violation, proceeding or investigation pending or, to the knowledge of the Company, threatened against the Company or any of its properties or intellectual property rights before or by any court, arbitrator, governmental or
administrative agency or regulatory authority (federal, state, county, local or foreign) (collectively, an “Action”) which (i) adversely affects or challenges the legality, validity or enforceability of any of the Transaction
Documents or the Securities or (ii) could reasonably be expected to have a Material Adverse Effect. Neither the Company nor any director or executive officer thereof, is or has been the subject of any Action involving a claim of violation of or
liability under federal or state securities laws or a claim of breach of fiduciary duty. There has not been, and to the knowledge of the Company, there is not pending or contemplated, any investigation by the Commission involving the Company or any
current or former director or executive officer of the Company. The Commission has not issued any stop order or other order suspending the effectiveness of any outstanding registration statement filed by the Company under the Exchange Act or the
Securities Act. 
 (k) Employee Benefit Plans; Employee Matters. The consummation of the transactions
contemplated by this Agreement will not (i) entitle any current or former employee or other service provider of the Company to severance benefits or any other payment, compensation or benefit (including forgiveness of indebtedness), except as
expressly provided by this Agreement, or (ii) accelerate the time of payment or vesting, or increase the amount of compensation or benefit due any such employee or service provider, alone or in conjunction with any other possible event
(including termination of employment). Except as set forth on Schedule 3.1(k), the Company does not have any employment agreements, or any other similar agreements that contain any severance or termination pay liabilities or obligations, that are
not filed as exhibits to the SEC Documents and that have annual cash compensation in excess of $100,000 or that have potential severance or termination liabilities in excess of $50,000 per person. The Company is in compliance in all material
respects with all U.S. federal, state, local and foreign laws and regulations respecting employment, discrimination in employment, terms and conditions of employment, wages, hours and occupational safety and health and employment practices, and is
not engaged in any unfair labor practice. To the Company’s knowledge, no employees of the Company are in violation of any term of any material employment contract, patent disclosure agreement, noncompetition agreement, or any restrictive
covenant to a former employer relating to the right of any such employee to be employed by the Company because of the nature of the business conducted or presently proposed to be conducted by the Company or to the use of trade secrets or proprietary
information of others. No key employee of the Company has given written notice to the Company, and the Company is not otherwise aware, that any such key employee intends to terminate his or her employment with the Company. 

 

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 (l) Labor Relations. No material labor dispute exists or, to the
knowledge of the Company, is imminent with respect to any of the employees of the Company which could reasonably be expected to result in a Material Adverse Effect. None of the Company’s employees is a member of a union that relates to such
employee’s relationship with the Company, and the Company is not a party to a collective bargaining agreement. No executive officer or key employee is, or, to the knowledge of the Company, is expected to be, in violation of any material term of
any employment contract, confidentiality, disclosure or proprietary information and inventions agreement or non-competition agreement, or any other contract or agreement or any restrictive covenant, and the continued employment of such executive
officer or key employee does not subject the Company to any liability with respect to any of the foregoing matters. 

(m) Compliance. The Company (i) is not in violation of any order of any court, arbitrator or governmental
body, (ii) is not or has not been in violation of any statute, rule or regulation of any governmental authority, including without limitation all foreign, federal, state and local laws applicable to its business, employees, wages and all such
laws that affect the environment, or (iii) is not in default under or in violation of (and no event has occurred that, with notice or lapse of time or both, would result in a default by the Company under), nor has the Company received notice of
a claim that it is in default under or that it is in violation of, any indenture, loan or credit agreement or any other agreement or instrument to which it is a party or by which it or any of its properties is bound (whether or not such default or
violation has been waived); except in the case of clauses (ii) and (iii), such as could not reasonably be expected to have a Material Adverse Effect. 

(n) Regulatory Compliance. 

(i) The Company possesses all certificates, authorizations and permits issued by the appropriate federal, state, local or
foreign regulatory authorities necessary to conduct its business as described in the SEC Reports, including without limitation, and as applicable, all such certificates, authorizations and permits required by the United States Food and Drug
Administration (the “FDA”) or any other federal, state or foreign agencies or bodies engaged in the regulation of pharmaceuticals or biohazardous materials, except where the failure to possess could not reasonably be expected to
have a Material Adverse Effect. The Company has not received any notice of proceedings relating to the revocation or modification of any such certificate, authorization or permit. 

(ii) The Company has not received any written notices or statements from the FDA or any other governmental agency that
(i) any new drug application or marketing authorization application for any product or potential product of the Company is or has been rejected or determined to be non-approvable in a final determination by any such regulatory authority;
(ii) any license, approval, permit or authorization to conduct any clinical trial of or market any product or potential product of the Company has been, will be or may be suspended, revoked, modified or limited. 

 

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 (iii) To the Company’s knowledge, and to the extent submitted by the
Company in an application to support regulatory approval, the preclinical and clinical testing, application for marketing approval of, manufacture, distribution, promotion and sale of the products and potential products of the Company is in
compliance, in all material respects, with all laws, rules and regulations applicable to such activities, including without limitation applicable good laboratory practices, good clinical practices and good manufacturing practices. The descriptions
of the results of such tests and trials contained in the SEC Reports are accurate in all material respects. The Company has not received any written notice of adverse finding, warning letter or clinical hold notice from the FDA or any non-U.S.
counterpart of any of the foregoing, or any untitled letter or other correspondence or notice from the FDA or any other governmental authority or agency or any institutional or ethical review board alleging or asserting noncompliance with any law,
rule or regulation applicable in any jurisdiction. The Company has not, either voluntarily or involuntarily, initiated, conducted or issued, or caused to be initiated, conducted or issued, any recall, field correction, market withdrawal or
replacement, safety alert, warning, “dear doctor” letter, or other notice or action relating to an alleged or potential lack of safety or efficacy of any product or potential product of the Company, any alleged product defect of any
product or potential product of the Company, or any violation of any material applicable law, rule, regulation or any clinical trial or marketing license, approval, permit or authorization for any product or potential product of the Company, and the
Company has no knowledge of any facts that would reasonably cause it to initiate any such notice or action and has no knowledge or reason to believe that the FDA or any other governmental agency or authority or any institutional or ethical review
board or other non-governmental authority intends to impose, require, request or suggest such notice or action. 

(o) Title to Assets. The Company has good and marketable title in fee simple to all real property owned by it and
good and marketable title in all personal property owned by it, in each case free and clear of all Liens, except as disclosed on Schedule 3.1(o). Any real property and facilities held under lease by the Company are held by it under valid, subsisting
and enforceable leases of which the Company is in compliance. 
 (p) Intellectual Property. The Company
solely owns, or has sufficient rights to use and otherwise exercise, exploit and license all patents, patent applications, trademarks, trademark applications, service marks, trade names, trade secrets, inventions, copyrights, licenses, domain names,
and similar rights necessary or material for use in connection with its business, as currently conducted (collectively, the “Company Intellectual Property Rights”). There are no outstanding options, licenses, agreements, claims,
encumbrances or shared ownership of interests of any kind relating to material Company Intellectual Property Rights, nor is the Company bound by or a party to any material options, licenses or agreements of any kind with respect to the patents,
trademarks, service marks, trade names, domain names, copyrights, trade secrets, licenses, information, proprietary rights and/or processes of any other person or entity. The Company has not received notice that the Intellectual Property Rights used
by the Company violates or infringes upon the rights of any Person, and Company does not have any reason to believe any such notice may be forthcoming. To the Company’s knowledge, all such Company Intellectual Property Rights are enforceable
and there is no existing infringement by another Person of any of the Company Intellectual Property Rights. The Company has taken reasonable security measures to protect the secrecy, confidentiality and value of all of its intellectual properties.
Each present and former employee and officer of the Company has 
  

 12 

 
executed a proprietary information and inventions agreement, and each consultant to the Company has executed a consulting agreement. The Company is not aware that any of its present and former
employees, officers or consultants are in violation thereof, and the Company will use its commercially reasonable efforts to prevent any such violation. All persons who have had access to Company trade secrets or confidential information have signed
a customary non-disclosure and non-use agreement. 
 (q) Insurance. The Company is insured by insurers of
recognized financial responsibility against such losses and risks and in such amounts as are prudent and customary in the business in which the Company is engaged, including, but not limited to, directors and officers insurance coverage. The Company
has no reason to believe that it will not be able to renew its existing insurance coverage as and when such coverage expires or to obtain similar coverage from similar insurers as may be necessary to continue its business. 

(r) Transactions With Affiliates and Employees. None of the executive officers or directors of the Company and, to
the knowledge of the Company, none of the employees of the Company is presently a party to any transaction with the Company (other than for services as employees, executive officers and directors), including any contract, agreement or other
arrangement providing for the furnishing of services to or by, providing for rental of real or personal property to or from, or otherwise requiring payments to or from any executive officer, director or such employee or any entity in which any
executive officer, director, or any such employee has a substantial interest or is an executive officer, director, trustee or partner other than (i) for payment of salary or consulting fees for services rendered, (ii) reimbursement for
expenses incurred on behalf of the Company and (iii) for other employee benefits, including stock option agreements under any stock option plan of the Company. 

(s) Sarbanes-Oxley. The Company is in compliance in all material respects with all provisions of the
Sarbanes-Oxley Act of 2002 (“Sarbanes-Oxley”) and all applicable rules and regulations promulgated by the Commission thereunder, which are applicable to it as of the Closing Date. The Company maintains a system of internal controls,
including, but not limited to, disclosure controls and procedures, internal controls over accounting matters and financial reporting (collectively, “Internal Controls”) that comply with the Securities Act, the Exchange Act,
Sarbanes-Oxley, and the rules and regulations of the Nasdaq Global Market. The Internal Controls are overseen by the Audit Committee of the Board of Directors in accordance with the rules and regulations of the Nasdaq Global Market. The Company has
not publicly disclosed or reported to the Audit Committee or the Board of Directors, a significant deficiency, material weakness, change in Internal Controls, any violation of, or failure to comply with, applicable securities laws, or any matter
which, if determined adversely, would reasonably be expected to have a Material Adverse Effect. 
 (t)
Certain Fees. No brokerage or finder’s fees or commissions are or will be payable by the Company to any broker, financial advisor or consultant, finder, placement agent, investment banker, bank or other Person with respect to the
transactions contemplated by the Transaction Documents. None of the Purchasers shall have any obligation with respect to any fees or with respect to any claims made by or on behalf of other Persons for fees of a type contemplated in this Section
that may be due in connection with the transactions contemplated by the Transaction Documents. 
  

 13 

 (u) Private Placement. Assuming the accuracy of the Purchasers’
representations and warranties set forth in Section 3.2, no registration under the Securities Act is required for the offer and sale of the Securities by the Company to the Purchasers as contemplated hereby. The issuance and sale of the
Securities hereunder does not contravene the rules and regulations of the Trading Market. 
 (v) Investment
Company. The Company is not, and is not an Affiliate of, and immediately after receipt of payment for the Securities, will not be or be an Affiliate of, an “investment company” within the meaning of the Investment Company Act of 1940,
as amended. The Company shall conduct its business in a manner so that it will not become subject to the Investment Company Act. 

(w) Registration Rights. Other than the Purchasers, no Person has any right to cause the Company to effect the
registration under the Securities Act of any securities of the Company. The granting and performance of the registration rights under the Transaction Documents will not violate or conflict with, or result in a breach of any provision of, or
constitute a default under, any agreement, indenture or instrument to which the Company is a party. 
 (x)
Listing and Maintenance Requirements. The Company has not, in the 12 months preceding the date hereof, received notice from any Trading Market on which the Common Stock is or has been listed or quoted to the effect that the Company is not in
compliance with the listing or maintenance requirements of such Trading Market. The Company is, and has no reason to believe that it will not in the foreseeable future continue to be, in compliance with all such listing and maintenance requirements.

 (y) Disclosure. The Company understands and confirms that the Purchasers are relying on the
representations and covenants in this Section 3.1 in effecting transactions in the Securities. All disclosure provided to such Purchaser regarding the Company, its business and the transactions contemplated hereby, including the Disclosure
Schedules to this Agreement, furnished by or on behalf of the Company with respect to the representations and warranties made herein are true and correct with respect to such representations and warranties and do not contain any untrue statement of
a material fact or omit to state any material fact necessary in order to make the statements made therein, in light of the circumstances under which they were made, not misleading. The Company acknowledges and agrees that no Purchaser makes or has
made any representations or warranties with respect to the transactions contemplated hereby other than those specifically set forth in the Transaction Documents. 

(z) Tax Status. The Company has filed all necessary federal, state and foreign income and franchise tax returns
and has paid or accrued all taxes owed thereunder, and the Company has no knowledge of a tax deficiency or other tax liability which has been asserted or threatened against the Company or upon any of its properties or assets. The Company has
complied with all applicable legal requirements relating to the payment and withholding of taxes and, within the time and in the manner prescribed by law, has withheld from wages, fees and other payments and paid over to the proper governmental or
regulatory authorities all amounts required. 
  

 14 

 (aa) No General Solicitation. Neither the Company nor any person
acting on behalf of the Company has offered or sold any of the Securities by any form of general solicitation or general advertising. The Company has offered the Securities for sale only to the Purchasers. 

(bb) Foreign Corrupt Practices. Neither the Company, nor to the knowledge of the Company, any agent or other
person acting on behalf of the Company, has (i) directly or indirectly, used any funds for unlawful contributions, gifts, entertainment or other unlawful expenses related to foreign or domestic political activity, (ii) made any direct or
indirect unlawful payment to foreign or domestic government officials or employees or to any foreign or domestic political parties or campaigns from corporate funds, (iii) failed to disclose fully any contribution made by the Company (or made
by any person acting on its behalf of which the Company is aware) which is in violation of law, (iv) violated, or is in violation of, in any material respect any provision of the Foreign Corrupt Practices Act of 1977, as amended, or
(v) made or received any unlawful bribe, rebate, payoff, influence payment, kickback or other unlawful payment to or from any domestic or foreign government official or employee. 

(cc) Acknowledgment Regarding Purchasers’ Purchase of Securities. The Company acknowledges and agrees that
each of the Purchasers is acting solely in the capacity of an arm’s length purchaser with respect to the Transaction Documents and the transactions contemplated hereby. The Company further acknowledges that none of the Purchasers is acting as a
financial advisor or fiduciary of the Company (or in any similar capacity) with respect to this Agreement and the transactions contemplated hereby and any advice given by any Purchaser or any of their respective representatives or agents in
connection with this Agreement and the transactions contemplated hereby is merely incidental to such Purchaser’s purchase of the Securities. 

(dd) Acknowledgement Regarding Purchasers’ Trading Activity. Anything in this Agreement or elsewhere herein
to the contrary notwithstanding (except for Section 4.9 hereof), it is understood and agreed by the Company (i) that such Purchaser has not been asked to agree, nor has such Purchaser agreed, to desist from purchasing or selling, long
and/or short, securities of the Company, or “derivative” securities based on securities issued by the Company or to hold the Securities for any specified term; (ii) that past or future open market or other transactions by such
Purchaser, including, without limitation, Short Sales or “derivative” transactions, before or after the closing of this or future private placement transactions, may negatively impact the market price of the Company’s publicly-traded
securities; (iii) that such Purchaser, and counter parties in “derivative” transactions to which such Purchaser is a party, directly or indirectly, presently may have a “short” position in the Common Stock, and
(iv) that such Purchaser shall not be deemed to have any affiliation with or control over any arm’s length counter-party in any “derivative” transaction. The Company further understands and acknowledges that (a) such
Purchaser may engage in hedging activities at various times during the period that the Securities are outstanding and (b) such hedging activities (if any) could reduce the value of the existing stockholders’ equity interests in the Company
at and after the time that the hedging activities are being conducted. The Company acknowledges that such aforementioned hedging activities, if conducted in compliance with applicable law (including federal securities laws), do not constitute a
breach of any of the Transaction Documents. 
  

 15 

 (ee) Manipulation of Price. The Company has not, and to its knowledge
no one acting on its behalf has, (i) taken, nor will take, directly or indirectly, any action designed to cause or to result in the stabilization or manipulation of the price of any security of the Company to facilitate the sale or resale of
any of the Securities, (ii) sold, bid for, purchased, or, paid any compensation for soliciting purchases of, any of the Securities (other than for the placement agent’s placement of the Securities), or (iii) paid or agreed to pay to
any person any compensation for soliciting another to purchase any other securities of the Company. 
 (ff)
Form S-3 Eligibility. The Company is eligible to utilize the registration statement on Form S-3 in connection with fulfilling its obligations to the Purchasers under the Registration Rights Agreement and, to the Company’s knowledge, no
facts or circumstances currently exist or are pending or threatened which could reasonably be expected to prevent the Company from remaining eligible to use Form S-3 to register the Shares and Underlying Shares pursuant to said Registration Rights
Agreement. 
 (gg) Books and Records. The minute books of the Company for the Company’s fiscal years
2008, 2009 and year-to-date 2010 contain accurate and complete records of all meetings held of, and corporate action taken by, the stockholders, the Board of Directors and committees of the Board of Directors during such period, and no meeting of
any such stockholders, the Board of Directors or such committees has been held for which minutes have not been prepared and are not contained in such minute books. 

(hh) Accountants. PricewaterhouseCoopers LLP, whose report on the financial statements of the Company was included
in the Company’s Annual Report on Form 10-K for the year ended December 31, 2009, are independent registered public accountants as required by the Securities Act and the rules and regulations of the Commission. Except as preapproved in
accordance with the requirements set forth in Section 10A of the Exchange Act, to the Company’s knowledge, PricewaterhouseCoopers LLP has not engaged in any “prohibited activities” (as defined in Section 10A of the Exchange
Act) on behalf of the Company. 
 (ii) Environmental. The Company is in material compliance with all
rules, laws and regulations relating to the use, treatment, storage and disposal of toxic substances and protection of health or the environment (“Environmental Laws”) which are applicable to its business. The Company has not
received any notice from any governmental authority or third party of an asserted claim under Environmental Laws, which claim is required to be disclosed in the SEC Reports. The Company is not currently required to make future material capital
expenditures to comply with Environmental Laws. No property that is owned, leased or occupied by the Company has been designated a Superfund site pursuant to the Comprehensive Response, Compensation and Liability Act of 1980, as amended (42 U.S.C.
Section 9601, et seq.), or otherwise designated as a contaminated site under applicable state or local law. 

(jj) No Stockholder Approval. Based in part upon the representation letter of Clarus Ventures, LLC attached hereto
as Exhibit E, the consummation of the transactions contemplated hereby will not require the approval of the Company’s stockholders pursuant to Nasdaq Listing Rule 5635. 

 

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 3.2 Representations and Warranties of the Purchasers. Each Purchaser
hereby, for itself, severally and not jointly, represents and warrants as of the date hereof and as of the Closing Date to the Company as follows: 

(a) Organization; Authority. Such Purchaser is an entity duly organized, validly existing and in good standing
under the laws of the jurisdiction of its organization with full right, corporate or partnership power and authority to enter into and to consummate the transactions contemplated by the Transaction Documents and otherwise to carry out its
obligations hereunder and thereunder. The execution, delivery and performance by such Purchaser of the transactions contemplated by this Agreement have been duly authorized by all necessary corporate or similar action on the part of such Purchaser.
Each Transaction Document to which it is a party has been duly executed by such Purchaser, and when delivered by such Purchaser in accordance with the terms hereof and thereof, will constitute the valid and legally binding obligation of such
Purchaser, enforceable against it in accordance with its terms, except (i) as limited by general equitable principles and applicable bankruptcy, insolvency, reorganization, moratorium and other laws of general application affecting enforcement
of creditors’ rights generally, (ii) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies and (iii) insofar as indemnification and contribution provisions may be
limited by applicable law. 
 (b) Own Account. Such Purchaser understands that (i) the Securities
are “restricted securities” and that the offer and sale of the Securities have not been registered under the Securities Act or any applicable state securities law and (ii) the Securities must be held indefinitely unless a subsequent
disposition thereof is registered under the Securities Act or is exempt from such registration. Such Purchaser is acquiring the Securities as principal for its own account and not with a view to or for distributing or reselling such Securities or
any part thereof in violation of the Securities Act or any applicable state securities law, has no present intention of distributing any of such Securities in violation of the Securities Act or any applicable state securities law and has no direct
or indirect arrangement or understanding with any other Persons regarding the distribution of such Securities (this representation and warranty not limiting such Purchaser’s right to sell the Securities pursuant to a Registration Statement or
otherwise in compliance with applicable federal and state securities laws) in violation of the Securities Act or any applicable state securities law. Such Purchaser is acquiring the Securities hereunder in the ordinary course of its business.

 (c) Purchaser Status. At the time such Purchaser was offered the Securities, it was, and at the date
hereof it is, and on each date on which it exercises any Common Warrants it will be either: (i) an “accredited investor” as defined in Rule 501(a)(1), (a)(2), (a)(3), (a)(7) or (a)(8) under the Securities Act or (ii) a
“qualified institutional buyer” as defined in Rule 144A(a) under the Securities Act. Such Purchaser is not required to be registered as a broker-dealer under Section 15 of the Exchange Act. 

(d) Experience of Such Purchaser. Such Purchaser, either alone or together with its representatives, has such
knowledge, sophistication and experience in business and financial matters so as to be capable of evaluating the merits and risks of the prospective investment in the Securities, and has so evaluated the merits and risks of such investment. Such
Purchaser is able to bear the economic risk of an investment in the Securities and, at the present 
  

 17 

 
time, is able to afford a complete loss of such investment. Such Purchaser understands that nothing in the Agreement or any other materials presented to the Purchaser in connection with the
purchase and sale of the Securities constitutes legal, tax or investment advice. Such Purchaser acknowledges that it must rely on legal, tax and investment advisors of its own choosing in connection with its purchase of the Securities. 

(e) General Solicitation. Such Purchaser is not purchasing the Securities as a result of any advertisement,
article, notice or other communication regarding the Securities published in any newspaper, magazine or similar media or broadcast over television or radio or presented at any seminar or any other general solicitation or general advertisement.

 (f) Certain Trading Activities. Other than with respect to the transactions contemplated herein, since
the earlier to occur of (1) the time that such Purchaser was first contacted by the Company or any other Person regarding this investment in the Company and (2) the tenth (10th) day prior to the date of this Agreement, neither such
Purchaser nor any Affiliate of such Purchaser which (x) had knowledge of the transactions contemplated hereby, (y) has or shares discretion relating to such Purchaser’s investments or trading or information concerning such
Purchaser’s investments, including in respect of the Securities, and (z) is subject to such Purchaser’s review or input concerning such Affiliate’s investments or trading (collectively, “Trading Affiliates”) has
directly or indirectly, nor has any Person acting on behalf of or pursuant to any understanding with such Purchaser or Trading Affiliate, effected or agreed to effect any transactions in the securities of the Company (including, without limitation,
any Short Sales involving the Company’s securities). Notwithstanding the foregoing, no Purchaser makes any representation, warranty or covenant hereby that it will not engage in Short Sales in the securities of the Company after the time that
the transactions contemplated by this Agreement are first publicly announced, other than as provided in Section 4.9 and provided such Short Sales are conducted in compliance with applicable law (including federal securities laws). 

(g) Independent Investigation. Such Purchaser, in acquiring the Securities, has relied solely upon an independent
investigation made by such Purchaser and his or her representatives, if any. Prior to the date hereof, such Purchaser has been given the opportunity to ask questions of, and receive answers from, representatives of the Company regarding the
Company’s management, finances, and business. Such Purchaser also has received and carefully reviewed the SEC Reports and is knowledgeable about the affairs of the Company. Neither such inquiries nor any other diligence investigation conducted
by such Purchaser or any of its advisors or representatives shall modify, amend or effect such Purchaser’s right to rely upon the Company’s representations and warranties and covenants contained herein or in the Transaction Documents.

 (h) No Government Recommendation or Approval. Such Purchaser understands that no United States federal
or state agency, or similar agency of any other country, has reviewed, approved, passed upon, or made any recommendation or endorsement of the Company or the purchase of the Securities. 

(i) No Intent to Effect a Change of Control. Such Purchaser has no present intent to effect a “change of
control” of the Company as such term is understood under the rules promulgated pursuant to Section 13(d) of the Exchange Act. The Company acknowledges and agrees that such Purchaser does not make or has not made any representations or
warranties with respect to the transactions contemplated hereby other than those specifically set forth in this Section 3.2. 
  

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 ARTICLE IV 

OTHER AGREEMENTS OF THE PARTIES 

4.1 Transfer Restrictions. 

(a) The Securities may only be disposed of in compliance with state and federal securities laws. In connection with any
transfer of Securities other than pursuant to an effective registration statement, to the Company or to an affiliate of a Purchaser in accordance with Section 4.1(e)(iii), the Company may require the transferor thereof to provide to the Company
an opinion of counsel, the form and substance of which opinion shall be reasonably satisfactory to the Company, to the effect that such transfer does not require registration of such transferred Securities under the Securities Act. As a condition of
transfer, any such transferee shall agree in writing to be bound by the terms of this Agreement and shall have the rights of a Purchaser under this Agreement and the Registration Rights Agreement. 

(b) Each Purchaser agrees to the imprinting, so long as is required by this Section 4.1(b), of a legend on any of
the Securities in the following form: 
 NEITHER THIS SECURITY NOR ANY SECURITIES INTO WHICH THIS SECURITY IS
EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”),
AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO AN AVAILABLE EXEMPTION FROM, OR IN A TRANSACTION NOT SUBJECT TO, THE REGISTRATION REQUIREMENTS OF THE
SECURITIES ACT AND IN ACCORDANCE WITH APPLICABLE STATE SECURITIES LAWS AS EVIDENCED BY A LEGAL OPINION OF COUNSEL TO THE TRANSFEROR TO SUCH EFFECT, THE SUBSTANCE OF WHICH SHALL BE REASONABLY ACCEPTABLE TO THE COMPANY. 

(c) Certificates evidencing the Securities shall not contain any legend (including, without limitation, the legend set
forth in Section 4.1(b) hereof): (i) while a registration statement (including, without limitation, a Registration Statement) covering the resale of such security is effective under the Securities Act, provided such security is not
beneficially owned by an Affiliate, (ii) following any sale of such Securities pursuant to Rule 144, (iii) if such Securities are eligible for sale under Rule 144(b)(1), or (iv) if such legend is not required under applicable
requirements of the Securities Act (including, without limitation, judicial interpretations and pronouncements issued by the staff of the Commission). If all or any 

 

 19 

 
portion of a Common Warrant is exercised at a time when there is an effective registration statement (including, without limitation, a Registration Statement) to cover the resale of the Common
Warrant Shares at a time when such legend is not otherwise required under applicable requirements of the Securities Act (including, without limitation, judicial interpretations thereof), then such securities shall be issued free of all legends. The
Company agrees that following the Effective Date or at such time as such legend is no longer required under this Section 4.1(c), it will use its reasonable best efforts to, no longer than three Trading Days following the delivery by a Purchaser
to the Company or the Company’s transfer agent of (i) a certificate representing Securities issued with a restrictive legend and (ii) a letter acknowledging that sales of such securities shall be made in a manner consistent with the
plan of distribution set forth in the Registration Statement (such third Trading Day, the “Legend Removal Date”), deliver or cause to be delivered to such Purchaser a certificate representing such Securities that is free from all
restrictive and other legends. The Company may not make any notation on its records or give instructions to any transfer agent of the Company that enlarge the restrictions on transfer set forth in this Section. Certificates for Securities subject to
legend removal hereunder shall be transmitted by the transfer agent of the Company to the Purchaser by crediting the account of the Purchaser’s prime broker with the Depository Trust Company System. The failure to timely deliver certificates
without restrictive legends by the Legend Removal Date shall not be a breach of the foregoing covenant if such delay is solely due to the action or inaction of the Company’s transfer agent and if the Company has taken all reasonable steps
necessary to facilitate the removal of such legends. 
 (d) Each Purchaser agrees that the removal of the
restrictive legend from certificates representing Securities as set forth in this Section 4.1 is predicated upon the Company’s reliance that such Purchaser will sell any Securities pursuant to either the registration requirements of the
Securities Act, including any applicable prospectus delivery requirements, or an exemption therefrom. 
 (e)
Notwithstanding anything herein to the contrary, no registration statement or opinion of counsel shall be necessary for a transfer (i) by a Purchaser that is a partnership to a partner (limited or general) of such partnership or a retired
partner of such partnership who retires after the date hereof, or to the estate of any such partner or retired partner or the transfer by gift, will or intestate succession of any partner to his or her spouse or to the siblings, lineal descendants
or ancestors of such partner or his or her spouse, (ii) by a Purchaser that is a limited liability company to a member of such limited liability company or a retired member of such limited liability company who retires after the date hereof, or
to the estate of any such member or retired member or the transfer by gift, will or intestate succession of any member to his or her spouse or to the siblings, lineal descendants or ancestors of such member or his or her spouse or (iii) by a
Purchaser to an affiliate of such Purchaser, if the prospective transferee agrees in all such instances in writing to be subject to the terms hereof to the same extent as if he or she were an original Purchaser hereunder. 

4.2 Furnishing of Information. As long as the Purchasers beneficially own any of the Securities, the Company
covenants to timely file (or obtain extensions in respect thereof and file within the applicable grace period) all reports required to be filed by the Company after the date hereof pursuant to the Exchange Act. As long as the Purchasers beneficially
own any of the Securities, if the Company is not required to file reports pursuant to the Exchange Act, it will 
  

 20 

 
prepare and furnish to each Purchaser and make publicly available in accordance with Rule 144(c) such information as is required for such Purchaser to sell the Securities under Rule 144. The
Company further covenants that it will take such further action as any holder of Securities may reasonably request, all to the extent required from time to time to enable such Person to sell such Securities without registration under the Securities
Act within the limitation of the exemptions provided by Rule 144. 
 4.3 Integration. None of the
Purchasers, the Company, nor any of their affiliates, nor any Person acting on its or their behalf shall sell, offer for sale or solicit offers to buy or otherwise negotiate in respect of any security (as defined in Section 2 of the Securities
Act) that would be integrated with the offer or sale of the Securities in a manner that would require the registration under the Securities Act of the sale of the Securities to the Purchasers or that would be integrated with the offer or sale of the
Securities for purposes of the rules and regulations of any Trading Market. 
 4.4 Warrant Exercise
Procedures. The forms of Notice of Exercise included in the Common Warrants set forth the totality of the procedures required of a Purchaser in order to exercise such warrants. No additional legal opinion or other information or instructions
shall be required of such Purchaser to exercise their Common Warrants. The Company shall honor exercises of the Common Warrants, and shall deliver Common Warrant Shares, in accordance with the terms, conditions and time periods set forth in the
Transaction Documents. 
 4.5 Securities Laws Disclosure; Publicity. The Company shall, by 5:30 p.m.
Eastern time on the fourth Trading Day following the Closing Date, file a Current Report on Form 8-K, reasonably acceptable to the Purchasers disclosing the material terms of the transactions contemplated hereby. The Company and the Purchasers shall
consult with each other in issuing any other press releases with respect to the transactions contemplated hereby, and neither the Company nor any Purchaser shall issue any such press release without the prior consent of the Company, with respect to
any press release of such Purchaser, or without the prior consent of the Purchasers with respect to any press release of the Company, which consent shall not unreasonably be withheld, except if such disclosure is required by law, in which case the
disclosing party shall promptly provide the other party with prior notice of such public statement or communication. Notwithstanding the foregoing, the Company shall not publicly disclose the name of any Purchaser or any of its affiliates, or
include the name of any Purchaser or any of its affiliates in any filing with the Commission or any regulatory agency or Trading Market, without the prior written consent of such Purchaser, except (i) as required by federal securities law in
connection with the Form 8-K referenced above and the registration statement contemplated by the Registration Rights Agreement and (ii) to the extent such disclosure is required by law or Trading Market regulations, in which case the Company
shall provide such Purchaser with prior notice of such disclosure permitted under subclause (i) or (ii). 

4.6 Use of Proceeds. The Company shall use the net proceeds from the sale of the Securities hereunder for working
capital, research, product development and general corporate purposes and not for the satisfaction of any portion of the Company’s debt (other than payment of trade payables in the ordinary course of the Company’s business and prior
practices), to redeem any Common Stock or Common Stock Equivalents or to settle any outstanding litigation. 
  

 21 

 4.7 Indemnification of Purchasers. Subject to the provisions of this
Section 4.7, the Company will indemnify and hold each Purchaser and its directors, officers, stockholders, members, partners, employees and agents (and any other Persons with a functionally equivalent role of a Person holding such titles
notwithstanding a lack of such title or any other title), each Person who controls such Purchaser (within the meaning of Section 15 of the Securities Act and Section 20 of the Exchange Act), and the directors, officers, agents, members,
partners or employees (and any other Persons with a functionally equivalent role of a Person holding such titles notwithstanding a lack of such title or any other title) of such controlling person (each, a “Purchaser Party”)
harmless from any and all losses, liabilities, obligations, claims, contingencies, damages, costs and reasonable expenses, including all judgments, amounts paid in settlements, court costs and reasonable attorneys’ fees and costs of
investigation that any such Purchaser Party may suffer or incur as a result of or relating to (a) any breach of any of the representations, warranties, covenants or agreements made by the Company in this Agreement or in the other Transaction
Documents or (b) any action instituted against a Purchaser Party, by any third party with respect to any of the transactions contemplated by the Transaction Documents (unless such action is based upon a breach of such Purchaser’s
representations, warranties or covenants under the Transaction Documents or any agreements or understandings such Purchaser may have with any such stockholder or any violations by such Purchaser of state or federal securities laws or any conduct by
such Purchaser which constitutes fraud, gross negligence, willful misconduct or malfeasance). If any action shall be brought against any Purchaser Party in respect of which indemnity may be sought pursuant to this Agreement, such Purchaser Party
shall promptly notify the Company in writing, and the Company shall have the right to assume the defense thereof with counsel of its own choosing. Any Purchaser Party shall have the right to employ separate counsel in any such action and participate
in the defense thereof, but the fees and expenses of such counsel shall be at the expense of such Purchaser Party except to the extent that (i) the employment thereof has been specifically authorized by the Company in writing, (ii) the
Company has failed after a reasonable period of time to assume such defense and to employ counsel or (iii) in such action there is, in the reasonable opinion of such separate counsel, a material conflict on any material issue between the
position of the Company and the position of such Purchaser Party. The Company will not be liable to any Purchaser Party under this Agreement (i) for any settlement by a Purchaser Party effected without the Company’s prior written consent,
which shall not be unreasonably withheld or delayed; or (ii) to the extent, but only to the extent that a loss, claim, damage or liability is attributable to any Purchaser Party’s breach of any of the representations, warranties, covenants
or agreements made by the Purchasers in this Agreement or in the other Transaction Documents. 
 4.8
Reservation and Listing of Securities. 
 (a) The Company shall maintain a reserve from its duly
authorized shares of Common Stock for issuance pursuant to the Transaction Documents in such amount as may be required to fulfill its obligations in full under the Transaction Documents. 

(b) If, on any date, the number of authorized but unissued (and otherwise unreserved) shares of Common Stock is less than
the Required Minimum on such date, then the Board of Directors shall use commercially reasonable efforts to amend the Company’s certificate of incorporation to increase the number of authorized but unissued shares of Common Stock to at least
the Required Minimum at such time, as soon as possible and in any event not later than the 75th day after such date. 
  

 22 

 (c) The Company shall, if applicable: (i) in the time and manner
required by the Trading Market, prepare and file with such Trading Market an additional shares listing application covering a number of shares of Common Stock at least equal to the Required Minimum on the date of such application, (ii) take all
steps necessary to cause such shares of Common Stock to be approved for listing on the Trading Market as soon as possible thereafter, (iii) provide to each Purchaser evidence of such listing, and (iv) maintain the listing of such Common
Stock on any date at least equal to the Required Minimum on such date on such Trading Market or another Trading Market. 

4.9 Short Sales and Confidentiality After The Date Hereof. Each Purchaser covenants that neither it nor any
affiliates acting on its behalf or pursuant to any understanding with it will execute any Short Sales during the period from the date hereof until the earlier of such time as (i) after the transactions contemplated by this Agreement are first
publicly announced or (ii) this Agreement is terminated in full. Each Purchaser covenants that until such time as the transactions contemplated by this Agreement are publicly disclosed by the Company as described in Section 4.5, such
Purchaser will maintain the confidentiality of all disclosures made to it in connection with this transaction (including the existence and terms of this transaction). Each Purchaser understands and acknowledges that the Commission currently takes
the position that coverage of short sales of shares of the Common Stock “against the box” prior to effectiveness of a resale registration statement with securities included in such registration statement would be a violation of
Section 5 of the Securities Act, as set forth in Item 239.10 of the Securities Act Rules Compliance and Disclosure Interpretations compiled by the Office of Chief Counsel, Division of Corporation Finance. 

4.10 Form D: Blue Sky Filings. The Company agrees to timely file a Form D with respect to the Securities as
required under Regulation D and to provide a copy thereof promptly upon request of any Purchaser. The Company shall, on or before the Closing Date, take such action as the Company shall reasonably determine is necessary in order to obtain an
exemption for, or to qualify the Securities for, sale to the Purchasers at the Closing under applicable securities or “Blue Sky” laws of the states of the United States, and shall provide evidence of such actions promptly upon request of
any Purchaser. The Company shall make all filings and reports relating to the offer and sale of the Securities required under applicable securities or “Blue Sky” laws of the states of the United States following the Closing Date.

 4.11 Board of Directors. Following the Closing, the Company shall take any and all actions as may be
required to nominate Nicole Vitullo of Domain Associates, L.L.C. to be elected to the Board of Directors by September 30, 2010, or, if a vacancy should occur on the Board of Directors before that time, to elect Ms. Vitullo to fill that
vacancy. 
 4.12 Section 13(d)(3) of Exchange Act. The parties to this Agreement acknowledge that
the several Purchasers shall not constitute a “group” within the meaning of Section 13(d)(3) of the Exchange Act and the rules and regulations promulgated thereunder. 

 

 23 

 ARTICLE V 

MISCELLANEOUS 

5.1 Termination. This Agreement may be terminated by the Majority Purchasers (on behalf of all Purchasers
hereunder) by written notice to the Company, if the Closing has not been consummated on or before August 27, 2010; provided, however, that no such termination will affect the right of any party to sue for any breach by the other
party (or parties). 
 5.2 Fees and Expenses. Except as expressly set forth herein and in the Transaction
Documents to the contrary, each party shall pay the fees and expenses of its advisers, counsel, accountants and other experts, if any, and all other expenses incurred by such party incident to the negotiation, preparation, execution, delivery and
performance of this Agreement. The Company shall reimburse, at the Closing, the reasonable fees for the Purchasers’ legal counsel, fees to other advisors retained by the Purchasers to represent them in the transactions contemplated by this
Agreement and the Transaction Documents, as well as the Purchasers’ due diligence expenses, in an aggregate amount not to exceed $30,000. The Company shall pay all transfer agent fees, stamp taxes and other taxes and duties levied in connection
with the delivery of any Securities to the Purchasers. 
 5.3 Entire Agreement. The Transaction Documents
and any other written agreement between the Company and the Purchasers dated of even date herewith, together with the exhibits and schedules thereto, contain the entire understanding of the parties with respect to the subject matter hereof and
supersede all prior agreements and understandings, oral or written, with respect to such matters, which the parties acknowledge have been merged into such documents, exhibits and schedules. 

5.4 Notices. Any and all notices or other communications or deliveries required or permitted to be provided
hereunder shall be in writing and shall be deemed given and effective on the earliest of (a) the next Trading Day after delivery, if such notice or communication is delivered via confirmed registered mail, (b) the 2nd Trading Day following
the date of mailing, if sent by U.S. nationally recognized overnight courier service, or (c) upon actual receipt by the party to whom such notice is required to be given. The address for such notices and communications shall be as set forth on
the signature pages attached hereto (unless later updated in writing by the parties hereto to the other parties) and if to the Company, with a copy to: 

Wilmer Cutler Pickering Hale & Dorr LLP 

1100 Winter Street 

Waltham, Massachusetts 02451 

Attention: Susan L. Mazur 

Fax: 781-966-2100 

5.5 Amendments; Waivers. No provision of this Agreement may be waived, modified, supplemented or amended except in
a written instrument signed by the Company and the Majority Purchasers. No waiver of any default with respect to any provision, condition or requirement of this Agreement shall be deemed to be a continuing waiver in the future or a waiver of any
subsequent default or a waiver of any other provision, condition or requirement hereof, nor shall any delay or omission of either party to exercise any right hereunder in any manner impair the exercise of any such right. 

 

 24 

 5.6 Headings. The headings herein are for convenience only, do not
constitute a part of this Agreement and shall not be deemed to limit or affect any of the provisions hereof. The language used in this Agreement will be deemed to be the language chosen by the parties to express their mutual intent, and no rules of
strict construction will be applied against any party. 
 5.7 Successors and Assigns. This Agreement
shall be binding upon and inure to the benefit of the parties and their successors and permitted assigns. The Company may not assign this Agreement or any rights or obligations hereunder without the prior written consent of the Majority Purchasers.
Any Purchaser may assign any or all of its rights under this Agreement to any Person to whom such Purchaser assigns or transfers any Securities, provided the Purchaser obtains the prior written consent of the Company not to be unreasonably withheld
and such transferee agrees in writing to be bound, with respect to the transferred Securities, by the provisions hereof that apply to the “Purchaser”. 

5.8 No Third-Party Beneficiaries. This Agreement is intended for the benefit of the parties hereto and their
respective successors and permitted assigns and is not for the benefit of, nor may any provision hereof be enforced by, any other Person, except as otherwise set forth in Section 4.7. 

5.9 Governing Law. All questions concerning the construction, validity, enforcement and interpretation of the
Transaction Documents shall be governed by and construed and enforced in accordance with the internal laws of the State of New York, without regard to the principles of conflicts of law thereof. Each party agrees that all legal proceedings
concerning the interpretations, enforcement and defense of the transactions contemplated by this Agreement and any other Transaction Documents (whether brought against a party hereto or its respective affiliates, directors, officers, stockholders,
employees or agents) shall be commenced exclusively in the state and federal courts sitting in the City of New York. Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts sitting in the City of New York,
borough of Manhattan for the adjudication of any dispute hereunder or in connection herewith or with any transaction contemplated hereby or discussed herein (including with respect to the enforcement of any of the Transaction Documents), and hereby
irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not personally subject to the jurisdiction of any such court, that such suit, action or proceeding is improper or inconvenient venue for such
proceeding. Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof via registered or certified mail or overnight delivery (with evidence
of delivery) to such party at the address in effect for notices to it under this Agreement and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in
any way any right to serve process in any manner permitted by law. The parties hereby waive all rights to a trial by jury. If either party shall commence an action or proceeding to enforce any provisions of the Transaction Documents, then the
prevailing party in such action or proceeding shall be reimbursed by the other party for its reasonable attorneys’ fees and other costs and expenses incurred with the investigation, preparation and prosecution of such action or proceeding.

  

 25 

 5.10 Survival. The representations, warranties, covenants and other
agreements contained herein shall survive the Closing and the delivery and/or exercise of the Securities, as applicable, for the applicable statue of limitations. 

5.11 Execution. This Agreement may be executed in two or more counterparts, all of which when taken together shall
be considered one and the same agreement and shall become effective when counterparts have been signed by each party and delivered to the other party, it being understood that both parties need not sign the same counterpart. In the event that any
signature is delivered by facsimile transmission (or electronic transmission of PDF file), such signature shall create a valid and binding obligation of the party executing (or on whose behalf such signature is executed) with the same force and
effect as if such facsimile (or PDF file) signature page were an original thereof. 
 5.12 Severability.
If any provision of this Agreement is held to be invalid or unenforceable in any respect, the validity and enforceability of the remaining terms and provisions of this Agreement shall not in any way be affected or impaired thereby and the parties
will attempt to agree upon a valid and enforceable provision that is a reasonable substitute therefor, and upon so agreeing, shall incorporate such substitute provision in this Agreement. 

5.13 Replacement of Securities. If any certificate or instrument evidencing any Securities is mutilated, lost,
stolen or destroyed, the Company shall issue or cause to be issued in exchange and substitution for and upon cancellation thereof, or in lieu of and substitution therefor, a new certificate or instrument, but only upon receipt of evidence reasonably
satisfactory to the Company of such loss, theft or destruction and customary and reasonable indemnity, if requested. The applicants for a new certificate or instrument under such circumstances shall also pay any reasonable third-party costs
associated with the issuance of such replacement Securities. 
 5.14 Remedies. In addition to being
entitled to exercise all rights provided herein or granted by law, including recovery of damages, each Purchaser and the Company will be entitled to specific performance under the Transaction Documents. The parties agree that monetary damages may
not be adequate compensation for any loss incurred by reason of any breach of obligations described in the foregoing sentence and hereby agrees to waive in any action for specific performance of any such obligation the defense that a remedy at law
would be adequate. 
 5.15 Liquidated Damages. The Company’s obligations to pay any partial
liquidated damages or other amounts owing under the Transaction Documents is a continuing obligation of the Company and shall not terminate until all unpaid partial liquidated damages and other amounts have been paid notwithstanding the fact that
the instrument or security pursuant to which such partial liquidated damages or other amounts are due and payable shall have been canceled. 

5.16 Construction. The parties agree that each of them and/or their respective counsel has reviewed and had an
opportunity to revise the Transaction Documents and, therefore, the normal rule of construction to the effect that any ambiguities are to be resolved against the drafting party shall not be employed in the interpretation of the Transaction Documents
or any amendments hereto. 
  

 26 

 5.17 Aggregation of Stock. All Securities held or acquired by
affiliated Persons or Persons under common management or control shall be aggregated together for the purpose of determining the availability of any rights under this Agreement and the Transaction Documents. 

[Signature Pages Follow] 
  

 27 

 IN WITNESS WHEREOF, the parties hereto have caused this Securities Purchase
Agreement to be duly executed by their respective authorized signatories as of the date first indicated above. 
  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	 /s/ Michael Kishbauch

		 	Name: Michael Kishbauch
		 	Title: President / CEO

  

			
	Address for Notice:
	
	Achillion Pharmaceuticals, Inc.
	300 George Street
	New Haven, CT 06511
	Attn:	 	Michael D. Kishbauch
	Fax:	 	203-624-6003

 [REMAINDER OF PAGE
INTENTIONALLY LEFT BLANK 
 SIGNATURE PAGES FOR PURCHASERS FOLLOW] 

 

 28 

 IN WITNESS WHEREOF, the parties hereto have caused this Securities Purchase
Agreement to be duly executed by their respective authorized signatories as of the date first indicated above. 
  

			
	DOMAIN PARTNERS VIII, L.P.
		
	By:	 	One Palmer Square Associates VIII, L.L.C.
	Its:	 	General Partner
		
	By:	 	 /s/ Kathleen Schoemaker

		 	Name: Kathleen Schoemaker
		 	Title: Managing Member
	
	Address for Notice of Purchaser:
	
	One Palmer Square, Suite 515
	Princeton, NJ 08542
	
	Address for Delivery of Securities for Purchaser (if not same as above):
	
	  

	
	  

	
	EIN Number:

  

 29 

			
	DP VIII ASSOCIATES, L.P.
		
	By:	 	One Palmer Square Associates VIII, L.L.C.
	Its:	 	General Partner
		
	By:	 	 /s/ Kathleen Schoemaker

		 	Name: Kathleen Schoemaker
		 	Title: Managing Member
	
	Address for Notice of Purchaser:
	
	One Palmer Square, Suite 515
	Princeton, NJ 08542
	
	Address for Delivery of Securities for Holder (if not same as above):
	
	  

	
	  

	
	EIN Number:

  

 30 

			
	CLARUS LIFESCIENCES II, L.P.
		
	By:	 	Clarus Ventures II GP, LP
	Its:	 	General partner
		
	By:	 	Clarus Ventures, II LLC
	Its:	 	General partner
		
	By:	 	 /s/ Robert Liptak

		 	Name: Robert Liptak
		 	Title: Managing Director
	
	Address for Notice of Holder:
	
	c/o Clarus Ventures, LLC
	101 Main Street, Suite 1210
	Cambridge, MA 02142
	
	Address for Delivery of Securities for Holder (if not same as above):
	
	  

	
	  

	
	EIN Number:

  

 31 

			
	QUAKER BIOVENTURES II, L.P.
		
	By:	 	 Quaker Bioventures Capital II, L.P.

its general partner

		
	By:	 	 Quaker Bioventures Capital II, L.L.C.

its general partner

		
	By:	 	 /s/ Adele C. Oliva

		 	Name: Adele C. Oliva
		 	Title: Vice President
	
	Address for Notice of Holder:
	
	Cira Centre
	2929 Arch Street
	Philadelphia, PA 19104-2868
	
	Address for Delivery of Securities for Holder (if not same as above):
	
	  

	
	  

	
	EIN Number:

  

 32 

			
	A.M. PAPPAS LIFE SCIENCE VENTURES IV, L.P.
		
	By:	 	AMP&A Management IV, LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Ford S. Worthy

		 	Name: Ford S. Worthy
		 	Title: Partner & CFO
	
	Address for Notice of Holder:
	
	c/o Pappas Ventures
	P. O. Box 110287
	Research Triangle Park, NC 27709
	
	Address for Delivery of Securities for Holder (if not same as above):
	
	2520 Meridian Parkway, Suite 400
	Durham, NC 27713
	
	EIN Number:

  

 33 

			
	PV IV CEO FUND, L.P.
		
	By:	 	AMP&A Management IV, LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Ford S. Worthy

		 	Name: Ford S. Worthy
		 	Title: Partner & CFO
	
	Address for Notice of Holder:
	
	c/o Pappas Ventures
	P. O. Box 110287
	Research Triangle Park, NC 27709
	
	Address for Delivery of Securities for Holder (if not same as above):
	
	2520 Meridian Parkway, Suite 400
	Durham, NC 27713
	
	EIN Number:

  

 34 

 EXHIBIT A 

Schedule of Purchasers 
  

									
	 Purchaser Name and Address
	  	Number of
Shares to be
Purchased	  	Number of
Common
Warrants to
be Purchased	  	Number of
Common
Warrant
Shares
Underlying
Common
Warrants
Purchased	  	Aggregate
Purchase Price
of
Closing
Securities
	 Domain Partners VIII, L.P.
 One
Palmer Square
 Suite 515
 Princeton, NJ
08542
 Attn:
 Tel:
	  	7,972,968	  	1	  	2,790,539	  	$20,201,507.67
					
	 DP VIII Associates, L.P.
 One
Palmer Square
 Suite 515
 Princeton, NJ
08542
 Attn:
 Tel:
	  	59,161	  	1	  	20,706	  	$149,899.18
					
	 Clarus Lifesciences II, L.P.

c/o Clarus Ventures, LLC
 101 Main Street, Suite
1210
 Cambridge, MA 02142

Attn:
 Tel:
	  	4,875,502	  	1	  	1,706,426	  	$12,353,303.20
					
	 Quaker Bioventures II, L.P.

Cira Centre
 2929 Arch Street

Philadelphia, PA 19104-2868
 Attn:

Tel:
	  	4,859,438	  	1	  	1,700,803	  	$12,312,601.04
					
	 A.M. Pappas Life Science

Ventures IV, L.P.
 c/o Pappas Ventures

P.O. Box 110287
 Research Triangle Park, NC 27709

 Attn: Ford S. Worthy
 Tel: (919)
998-3300
	  	1,916,799	  	1	  	670,880	  	$4,856,689.64
					
	 PV IV CEO Fund L.P.
 c/o Pappas
Ventures
 P.O. Box 110287
 Research
Triangle Park, NC
 27709
 Attn: Ford S.
Worthy
 Tel: (919) 998-3300
	  	91,233	  	1	  	31,932	  	$231,161.43

  

 35 

 EXHIBIT B 

Form of Common Warrant 
  

 36 

 EXHIBIT C 

Registration Rights Agreement 
  

 37 

 EXHIBIT D 

Form of Opinion of Company Counsel 
  

 38 

 EXHIBIT E 

Representation Letter 
  

 39Form of Common Stock Warrant pursuant to the Securities Purchase Agreement

 Exhibit 10.2 

NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE
COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN
EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OR PURSUANT TO AN AVAILABLE EXEMPTION FROM, OR IN A TRANSACTION NOT SUBJECT TO, THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT AND IN ACCORDANCE WITH APPLICABLE STATE SECURITIES LAWS AS
EVIDENCED BY A LEGAL OPINION OF COUNSEL TO THE TRANSFEROR TO SUCH EFFECT, THE SUBSTANCE OF WHICH SHALL BE REASONABLY ACCEPTABLE TO THE COMPANY. 

Void after 5:00 p.m. (New York time) on the    th day
of             , 2017. 
  

			
	Number of Warrants:	  	Warrant Certificate No.

ACHILLION PHARMACEUTICALS, INC. 

(A corporation existing under the laws of the State of Delaware) 

THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value
received,                     (the “Holder”), is entitled, upon the terms and subject to the limitations on exercise and the
conditions hereinafter set forth, including without limitation Section 3(c), at any time on or after the date hereof and on or prior to 5:00 p.m. (New York time) on            , 2017
(the “Expiry Time”) but not thereafter, to subscribe for and purchase from Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), up
to                    shares (the “Warrant Shares”) of Common Stock, par value $0.001 per share, of the Company (the “Common
Stock”), subject to adjustment as provided herein. The purchase price of one share of Common Stock under this Warrant shall be equal to the Exercise Price, as defined in Section 2(b). 

Section 1. Definitions. Capitalized terms used and not otherwise defined herein shall have the
meanings set forth in that certain Securities Purchase Agreement (the “Securities Purchase Agreement”), dated August 18, 2010, among the Company and the purchasers signatory thereto. 

Section 2. Exercise. 

a) Exercise of Warrant. Exercise of the purchase rights represented by this Warrant may be made, in whole or in
part, at any time or times on or after the date of issuance of this Warrant and on or before the Expiry Time by delivery to the principal office of the Company of a duly executed copy of the Notice of Exercise Form annexed hereto (or to such other
office or agency of the Company as it may designate by notice in writing to the registered Holder at the address of such Holder appearing on the books of the Company) and the Company shall have received payment of the aggregate Exercise Price of the
shares thereby purchased by wire transfer or cashier’s check drawn on a United States bank (the “Exercise Date”); provided, however, if this Warrant is exercised in full, the Holder shall have surrendered this Warrant to

 
the Company within three (3) business days of the date the Notice of Exercise is delivered to the Company. Notwithstanding anything herein to the contrary, the Holder shall not be required
to physically surrender this Warrant to the Company until the Holder has purchased all of the Warrant Shares available hereunder and the Warrant has been exercised in full. Partial exercises of this Warrant resulting in purchases of a portion of the
total number of Warrant Shares available hereunder shall have the effect of lowering the outstanding number of Warrant Shares purchasable hereunder in an amount equal to the applicable number of Warrant Shares purchased. The Holder and the Company
shall maintain records showing the number of Warrant Shares purchased and the date of such purchases. The Company shall deliver any objection to any Notice of Exercise Form within two (2) Business Days of receipt of such notice. The Holder and
any assignee, by acceptance of this Warrant, acknowledge and agree that, by reason of the provisions of this paragraph, following the purchase of a portion of the Warrant Shares hereunder, the number of Warrant Shares available for purchase
hereunder at any given time may be less than the amount stated on the face hereof. 
 Immediately prior to the
Expiry Time, the portion of this Warrant not exercised prior thereto shall automatically be deemed to be exercised in full in the manner set forth in Section 2(c), without any further action on behalf of the Holder; provided, however, that in
the event that the cashless exercise formula set forth in Section 2(c) yields a result that is less than or equal to zero, then the unexercised portion of this Warrant shall automatically terminate and become void. The Company may not call or
redeem any portion of this Warrant without the prior written consent of the affected Holder. 
 b) Exercise
Price. The exercise price of the Common Stock under this Warrant shall be $3.1125 per share, subject to adjustment hereunder. 

c) Cashless Exercise. This Warrant may also be exercised by means of a “cashless exercise” in which the
Holder shall be entitled to receive a certificate for the number of Warrant Shares equal to the quotient obtained by dividing [(A-B)*(X)] by (A), where: 
  

			
	(A) =	 	the VWAP on the trading day immediately preceding the date of such election;
		
	(B) =	 	the Exercise Price of this Warrant, as adjusted; and
		
	(X) =	 	the number of Warrant Shares issuable upon exercise of this Warrant in accordance with the terms of this Warrant by means of a cash exercise rather than a cashless
exercise.

 The “VWAP” means, for any date, the price determined by the first of
the following clauses that applies: (a) if the Common Stock is then listed or quoted on a Trading Market, the daily volume weighted average price of the Common Stock for such date (or the nearest preceding date) on the Trading Market on which
the Common Stock is then listed or quoted as reported by Bloomberg Financial L.P. (based on a Trading Day from 9:30 a.m. Eastern Time to 4:02 p.m. Eastern Time); (b) the volume weighted average price of the Common Stock for such date (or the
nearest preceding date) on the OTC Bulletin Board or (c) if the Common Stock is not then listed or quoted on the OTC Bulletin Board and if prices for the Common Stock are then 

 

 2 

 
reported in the “Pink Sheets” published by the Pink Sheets, LLC (or a similar organization or agency succeeding to its functions of reporting prices), the most recent bid price per
share of the Common Stock so reported; or (d) in all other cases, the fair market value of a share of Common Stock as determined by a good faith determination of the Company’s Board of Directors. 

d) Percentage Limitation. Notwithstanding anything herein to the contrary, the Company shall not issue to any
Holder any shares of Common Stock, including pursuant to any rights herein, including, without limitation, any exercise rights, to the extent such shares, when added to the number of shares of Common Stock then beneficially owned by such Holder and
any Persons whose beneficial ownership of Common Stock would be aggregated with such Holder for purposes of Section 13(d) of the Securities Exchange Act, would cause the total number of shares of Common Stock beneficially owned by such Holder
and any such Persons to exceed 19.999% of the total number of outstanding shares of Common Stock of the Company at the time of such issuance (the “Maximum Aggregate Share Amount”), provided, however, that this Section 2(d)
shall not apply to the exercise of this Warrant in connection with any Fundamental Transaction (as defined below) in which the Company is acquired by a third party, whether by merger or stock purchase. For purposes of this Section 2(d),
beneficial ownership shall be determined in accordance with Section 13(d) of the Exchange Act and the rules and regulations promulgated thereunder. If on any attempted exercise of this Warrant other than in connection with a Fundamental
Transaction, the issuance of Warrant Shares would exceed the Maximum Aggregate Share Amount, then the Company shall issue to the Holder requesting a Warrant exercise such number of Warrant Shares as may be issued below the Maximum Aggregate Share
Amount and, with respect to the remainder of the aggregate number of Warrant Shares, this Warrant shall remain exercisable, subject to this Section 2(d). Notwithstanding anything to the contrary contained in this Section 2(d), the
limitations contained herein shall not apply unless (i) such limitations are required under Nasdaq Global Market Rule 5635 or (ii) the Holder has, by providing the Company with written notice, lowered the Maximum Aggregate Share Amount to
a percentage below 19.999% of the total number of outstanding shares of Common Stock (such amount being the “Adjusted Maximum Aggregate Share Amount”). Upon providing the Company with at least 61 days prior written notice, the
Holder may increase the Adjusted Maximum Aggregate Share Amount up to 19.999% of the shares of Common Stock outstanding immediately after giving effect to such exercise, provided, however, that in the event that Nasdaq Global Market Rule 5635 does
not require the limitations contained in this Section 2(c), the Holder may increase the Adjusted Maximum Aggregate Share Amount above 19.999% of the shares Common Stock outstanding immediately after giving effect to such exercise. 

e) Mechanics of Exercise. 

i. Authorization of Warrant Shares. The Company covenants that all Warrant Shares which may be issued upon the
exercise of the purchase rights represented by this Warrant will, upon exercise of the purchase rights represented by this Warrant and payment to the Company of the purchase price therefor, be duly authorized, validly issued, fully paid and
nonassessable and free from all taxes, liens and charges in respect of the issue thereof (other than taxes in respect of any transfer occurring contemporaneously with such issue). 

 

 3 

 ii. Delivery of Certificates Upon Exercise. Certificates for shares
purchased hereunder shall be transmitted by the transfer agent of the Company to the Holder by crediting the account of the Holder’s prime broker with the Depository Trust Company through its Deposit Withdrawal Agent Commission
(“DWAC”) system if the Company is a participant in such system, and otherwise by physical delivery to the address specified by the Holder in the Notice of Exercise within three (3) Trading Days from the delivery to the Company
of the Notice of Exercise Form, surrender of this Warrant (if required) and payment of the aggregate Exercise Price (unless exercised by means of a cashless exercise pursuant to Section 2(c)) (“Warrant Share Delivery Date”).
This Warrant shall be deemed to have been exercised on the date the Exercise Price is received by the Company (or in the case of a cashless exercise pursuant to Section 2(c), the date this Warrant is surrendered). If all or any part of a
Warrant is exercised at a time when there is an effective registration statement to cover the issuance or resale of the Warrant Shares and if the legend is not required under applicable securities laws, such Warrant Shares shall be issued free of
all legends on or before the Warrant Share Delivery Date. The Warrant Shares shall be deemed to have been issued, and Holder or any other Person so designated to be named therein shall be deemed to have become a holder of record of such shares for
all purposes, as of the Exercise Date irrespective of the date such Warrant Shares are credited to the Holder’s DWAC account, or the date of delivery of certificates evidencing the Warrant Shares, as the case may be. 

iii. Delivery of New Warrants Upon Exercise. If this Warrant shall have been exercised in part, the Company
shall, at the request of a Holder and upon surrender of this Warrant certificate, at the time of delivery of the certificate or certificates representing Warrant Shares, deliver to Holder a new Warrant evidencing the rights of Holder to purchase the
unpurchased Warrant Shares called for by this Warrant, which new Warrant shall in all other respects be identical with this Warrant. 

iv. No Fractional Shares or Scrip. No fractional shares or scrip representing fractional shares shall be issued
upon the exercise of this Warrant. As to any fraction of a share that Holder would otherwise be entitled to purchase upon such exercise, the Company shall pay a cash adjustment in respect of such final fraction in an amount equal to such fraction
multiplied by the Exercise Price. 
 v. Charges, Taxes and Expenses. Issuance of certificates for
Warrant Shares shall be made without charge to the Holder for any issue or transfer tax or other incidental expense in respect of the issuance of such certificate, all of which taxes and expenses shall be paid by the Company, and such certificates
shall be issued in the name of the Holder or in such name or names as may be directed by the Holder; provided, however, that in the event certificates for Warrant Shares are to be issued in a name other than the name of the Holder, this Warrant when
surrendered for exercise shall be accompanied by the Assignment Form attached hereto duly executed by the Holder; and the Company may require, as a condition thereto, the payment of a sum sufficient to reimburse it for any transfer tax incidental
thereto. 
 f) The Company’s obligations to issue and deliver Warrant Shares in accordance with the terms
hereof are absolute and unconditional, irrespective of any action or inaction by the Holder to enforce the same, any waiver or consent with respect to any provision hereof, the recovery of any judgment against any Person or any action to enforce the
same, or any setoff, counterclaim, recoupment, limitation or termination, or any breach or alleged breach by the Holder or any other Person of any obligation to the Company or any violation or alleged

  

 4 

 
violation of law by the Holder or any other Person, and irrespective of any other circumstance which might otherwise limit such obligation of the Company to the Holder in connection with the
issuance of Warrant Shares. Nothing herein shall limit a Holder’s right to pursue any other remedies available to it hereunder, at law or in equity including, without limitation, a decree of specific performance and/or injunctive relief with
respect to the Company’s failure to timely deliver the Warrant Shares upon exercise of the Warrant as required pursuant to the terms hereof. 

Section 3. Certain Adjustments. 

a) Stock Dividends and Splits. If the Company, at any time while this Warrant is outstanding: (A) pays a stock
dividend or otherwise makes a distribution or distributions on shares of its Common Stock or any other equity or equity equivalent securities payable in shares of Common Stock (which, for avoidance of doubt, shall not include any shares of Common
Stock issued by the Company pursuant to this Warrant), (B) subdivides outstanding shares of Common Stock into a larger number of shares, (C) combines (including by way of reverse stock split) outstanding shares of Common Stock into a
smaller number of shares, or (D) issues by reclassification of shares of the Common Stock any shares of capital stock of the Company, then in each case the Exercise Price shall be multiplied by a fraction, of which the numerator shall be the
number of shares of Common Stock (excluding treasury shares, if any) outstanding immediately before such event and of which the denominator shall be the number of shares of Common Stock outstanding immediately after such event and the number of
shares issuable upon exercise of this Warrant shall be proportionately adjusted in an inverse manner (e.g., an increase in the Exercise Price shall result in a decrease in the number of shares of Common Stock). Any adjustment made pursuant to
this Section 3(a) shall become effective immediately after the record date for the determination of stockholders entitled to receive such dividend or distribution and shall become effective immediately after the effective date in the case of a
subdivision, combination or re-classification. 
 b) Pro Rata Distributions. If the Company, at any time
prior to the Expiry Time, shall declare, or distribute any dividend or other distribution to all holders of Common Stock (and not to Holders of the Warrants) evidences of its indebtedness or assets (including cash and cash dividends) or rights or
warrants to subscribe for or purchase any security other than the Common Stock, then in each such case the Exercise Price shall be adjusted by multiplying the Exercise Price in effect immediately prior to the record date fixed for determination of
stockholders entitled to receive such distribution by a fraction, of which the denominator shall be the VWAP determined as of the record date mentioned above, and of which the numerator shall be such VWAP on such record date less the then per share
fair market value at such record date of the portion of such assets or evidence of indebtedness so distributed applicable to one outstanding share of the Common Stock as determined by the Board of Directors of the Company in good faith. The
adjustment shall be described in a statement provided to the Holder. Such adjustment shall be made whenever any such distribution is made and shall become effective immediately after the record date mentioned above. 

c) Fundamental Transaction; Automatic Exercise. If, at any time while this Warrant is outstanding, the Company
effects (A) any merger or consolidation of the Company with or into another Person (an “Acquisition”), (B) any sale of all or substantially all of its assets in one or a series of related transactions (an “Asset
Sale”), (C) any tender offer or exchange offer 
  

 5 

 
(whether by the Company or another Person) pursuant to which holders of Common Stock are permitted to tender or exchange their shares for other securities, cash or property (a “Tender
Offer”), or (D) any reclassification of the Common Stock or any compulsory share exchange pursuant to which the Common Stock is effectively converted into or exchanged for other securities, cash or property (in any such case, a
“Fundamental Transaction”), then, this Warrant shall remain outstanding according to its terms except that, upon any subsequent exercise of this Warrant, the Holder shall have the right to receive, for each Warrant Share that would
have been issuable upon such exercise immediately prior to the occurrence of such Fundamental Transaction, the number of shares of Common Stock of the successor or acquiring corporation or of the Company, if it is the surviving corporation, and any
additional consideration (the “Alternate Consideration”) receivable upon or as a result of such reorganization, reclassification, merger, consolidation or disposition of assets by a Holder of the number of shares of Common Stock for
which this Warrant is exercisable immediately prior to such event. Notwithstanding the foregoing, in the event the Fundamental Transaction is in the form of an Acquisition, Asset Sale or Tender Offer, and the consideration payable with respect to
such transaction is cash (a “Cash Transaction”), then Holder shall exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Cash
Transaction, and, if Holder does not so exercise, this Warrant shall automatically be exercised pursuant to Section 2(c) hereof, without any action by Holder immediately prior to the consummation of such Cash Transaction. The Company shall
provide the Holder with written notice of its request relating to the foregoing (together with such reasonable information as the Holder may request in connection with such contemplated Acquisition giving rise to such notice), which is to be
delivered to Holder not less than ten (10) days prior to the closing of the proposed Cash Transaction. The provisions of Section 2(d) shall apply to any such exercise. To the extent necessary to effectuate the foregoing provisions, any
successor to the Company or surviving entity in such Fundamental Transaction shall issue to the Holder a new warrant consistent with the foregoing provisions and evidencing the Holder’s right to exercise such warrant for the Alternate
Consideration. The terms of any agreement pursuant to which a Fundamental Transaction is effected shall include terms requiring any such successor or surviving entity to comply with the provisions of this Section 3(c) and insuring that this
Warrant (or any such replacement security) will be similarly adjusted upon any subsequent transaction analogous to a Fundamental Transaction. 

d) Calculations. All calculations under this Section 3 shall be made to the nearest cent or the nearest
1/100th of a share, as the case may be. For purposes of this Section 3, the number of shares of Common Stock deemed to be issued and outstanding as of a given date shall be the sum of the number of shares of Common Stock (excluding treasury
shares, if any) issued and outstanding. 
 e) Notice to Holders. 

i. Adjustment to Exercise Price. Whenever the Exercise Price is adjusted pursuant to this Section 3, the
Company shall promptly mail to each Holder a notice setting forth the Exercise Price after such adjustment and setting forth a brief statement of the facts requiring such adjustment. 

 

 6 

 ii. Notice to Allow Exercise by Holder. If (A) the Company
shall declare a dividend (or any other distribution) on the Common Stock; (B) the Company shall declare a special nonrecurring cash dividend on or a redemption of the Common Stock; (C) the Company shall authorize the granting to all
holders of the Common Stock rights or warrants to subscribe for or purchase any shares of capital stock of any class or of any rights; (D) the approval of any stockholders of the Company shall be required in connection with any Fundamental
Transaction; (E) the Company shall authorize the voluntary or involuntary dissolution, liquidation or winding up of the affairs of the Company; then, in each case, the Company shall cause to be mailed to the Holder at its last address as it
shall appear upon the Warrant Register of the Company, at least 10 calendar days prior to the applicable record or effective date hereinafter specified, a notice stating (x) the date on which a record is to be taken for the purpose of such
dividend, distribution, redemption, rights or warrants, or if a record is not to be taken, the date as of which the holders of the Common Stock of record to be entitled to such dividend, distributions, redemption, rights or warrants are to be
determined or (y) the date on which such reclassification, consolidation, merger, sale, transfer or share exchange is expected to become effective or close, and the date as of which it is expected that holders of the Common Stock of record
shall be entitled to exchange their shares of the Common Stock for securities, cash or other property deliverable upon such reclassification, consolidation, merger, sale, transfer or share exchange; provided, in each case that such information shall
be made known to the public through a press release, filing with the Commission, or other public announcement prior to or in conjunction with such notice being provided to the Holder, and provided further that the failure to mail such notice or any
defect therein or in the mailing thereof shall not affect the validity of the corporate action required to be specified in such notice. The Holder is entitled to exercise this Warrant during the 10-day period commencing on the date of such notice to
the effective date of the event triggering such notice. 
 Section 4. Transfer of Warrant.

 a) Transferability. This Warrant and all rights hereunder are transferable, in whole or in part, upon
surrender of this Warrant at the principal office of the Company, together with a written assignment of this Warrant substantially in the form attached hereto duly executed by the Holder or its agent or attorney and funds sufficient to pay any
transfer taxes payable upon the making of such transfer. Upon such surrender and, if required, such payment, the Company shall execute and deliver a new Warrant or Warrants in the name of the assignee or assignees and in the denomination or
denominations specified in such instrument of assignment, and shall issue to the assignor a new Warrant evidencing the portion of this Warrant not so assigned, and this Warrant shall promptly be cancelled. A Warrant, if properly assigned, may be
exercised by a new holder for the purchase of Warrant Shares without having a new Warrant issued. The Holder represents that by accepting this Warrant it understands that this Warrant and any securities obtainable upon exercise of this Warrant have
not been registered for sale under Federal or state securities laws and are being offered and sold to the Holder pursuant to one or more exemptions from the registration requirements of such securities laws. In the absence of an effective
registration of such securities or an exemption therefrom, any certificates for such securities shall bear the legend set forth on the first page hereof. The Holder understands that it must bear the economic risk of its investment in this Warrant
and any securities obtainable upon exercise of this Warrant for an indefinite period of time, as this Warrant and such securities have not been registered under Federal or state securities laws and therefore cannot be sold unless subsequently
registered under such laws, unless an exemption from such registration is available. 
  

 7 

 b) New Warrants. This Warrant may be divided or combined with other
Warrants upon presentation hereof at the aforesaid office of the Company, together with a written notice specifying the names and denominations in which new Warrants are to be issued, signed by the Holder or its agent or attorney. Subject to
compliance with Section 4(a), as to any transfer which may be involved in such division or combination, the Company shall execute and deliver a new Warrant or Warrants in exchange for the Warrant or Warrants to be divided or combined in
accordance with such notice. 
 c) Warrant Register. The Company shall register this Warrant, upon
records to be maintained by the Company for that purpose (the “Warrant Register”), in the name of the record Holder hereof. The Company may deem and treat the registered Holder of this Warrant as the absolute owner hereof for the
purpose of any exercise hereof or any distribution to the Holder, and for all other purposes, absent actual notice to the contrary. 

Section 5. Miscellaneous. 

a) No Rights as Stockholder Until Exercise. This Warrant does not entitle the Holder to any voting rights or other
rights as a stockholder of the Company prior to the exercise hereof. Upon the surrender of this Warrant and the payment of the aggregate Exercise Price (or by means of a cashless exercise), the Warrant Shares so purchased shall be and be deemed to
be issued to such Holder as the record owner of such shares as of the close of business on the later of the date of such surrender or payment. 

b) Loss, Theft, Destruction or Mutilation of Warrant. The Company covenants that upon receipt by the Company of
evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this Warrant or any stock certificate relating to the Warrant Shares, and in case of loss, theft or destruction, of indemnity or security reasonably satisfactory
to it (which, in the case of the Warrant, shall not include the posting of any bond), and upon surrender and cancellation of such Warrant or stock certificate, if mutilated, the Company will make and deliver a new Warrant or stock certificate of
like tenor and dated as of such cancellation, in lieu of such Warrant or stock certificate. 
 c) Saturdays,
Sundays, Holidays, etc. If the last or appointed day for the taking of any action or the expiration of any right required or granted herein shall be a Saturday, Sunday or a legal holiday, then such action may be taken or such right may be
exercised on the next succeeding day not a Saturday, Sunday or legal holiday. 
 d) Authorized Shares.
The Company covenants that during the period the Warrant is outstanding, it will maintain a reserve, free from preemption rights, from its duly authorized shares of Common Stock for issuance pursuant to the Transaction Documents in such amount as
may be required to fulfill its obligations in full under the Transaction Documents. The Company further covenants that its issuance of this Warrant shall constitute full authority to its officers who are charged with the duty of executing stock
certificates to execute and issue the necessary certificates for the Warrant Shares upon the exercise of the purchase rights under this 

 

 8 

 
Warrant. The Company will take all such reasonable action as may be necessary to assure that such Warrant Shares may be issued as provided herein without violation of any applicable law or
regulation, or of any requirements of the Trading Market upon which the Common Stock may be listed. If at any time prior to the Expiry Time the number of authorized but unissued shares of Common Stock shall not be sufficient to permit exercise of
this Warrant, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock (or other securities as provided herein) to such number of shares as shall
be sufficient for such purposes. 
 Except and to the extent as waived or consented to by the Holder, the
Company hereby covenants to not by any action, including, without limitation, amending its certificate of incorporation, bylaws or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any
other voluntary action, avoid or seek to avoid the observance or performance of any of the terms of this Warrant, and will at all times in good faith assist in the carrying out of all such terms and in the taking of all such actions as may be
necessary or appropriate to protect the rights of Holder as set forth in this Warrant against impairment. Without limiting the generality of the foregoing, the Company will (a) not increase the par value of any Warrant Shares above the Exercise
Price then in effect and (b) take all such action as may be necessary or appropriate in order that the Company may validly and legally issue fully paid and nonassessable Warrant Shares upon the exercise of this Warrant. 

e) Jurisdiction. All questions concerning the construction, validity, enforcement and interpretation of this
Warrant shall be determined in accordance with the provisions of the Securities Purchase Agreement. 
 f)
Restrictions. The Holder acknowledges that the Warrant Shares acquired upon the exercise of this Warrant, if not registered, will contain a legend to that effect. 

g) Nonwaiver and Expenses. No course of dealing or any delay or failure to exercise any right hereunder on the
part of Holder shall operate as a waiver of such right or otherwise prejudice Holder’s rights, powers or remedies, notwithstanding the fact that all rights hereunder terminate on the Expiry Time. If the Company willfully and knowingly fails to
comply with any provision of this Warrant, which results in any material damages to the Holder, the Company shall pay to Holder such amounts as shall be sufficient to cover any costs and expenses incurred by Holder in collecting any amounts due
pursuant hereto or in otherwise enforcing any of its rights, powers or remedies hereunder. 
 h) Notices.
Any notice, request or other document required or permitted to be given or delivered to the Holder by the Company shall be delivered in accordance with the notice provisions of the Securities Purchase Agreement. 

i) Limitation of Liability. No provision hereof, in the absence of any affirmative action by Holder to exercise
this Warrant or purchase Warrant Shares, and no enumeration herein of the rights or privileges of Holder, shall give rise to any liability of Holder for the purchase price of any Common Stock or as a stockholder of the Company, whether such
liability is asserted by the Company or by creditors of the Company. 
  

 9 

 j) Remedies. The remedies provided in this Warrant shall be
cumulative and in addition to all other remedies available or granted by law, including recovery of damages. Each of the parties hereto will be entitled to specific performance of its rights under this Warrant. The Company acknowledges that a breach
by it of its obligations hereunder will cause irreparable harm to the Holder and agrees that monetary damages would not be adequate compensation for any loss incurred by reason of a breach or threatened breach by it of the provisions of this Warrant
and hereby agrees to waive the defense in any action for specific performance that a remedy at law would be adequate including making a showing of economic loss and the posting of a bond or other security. 

k) Successors and Assigns. Subject to applicable securities laws, this Warrant and the rights and obligations
evidenced hereby shall inure to the benefit of and be binding upon the successors of the Company and the successors and permitted assigns of Holder. The provisions of this Warrant are intended to be for the benefit of all Holders from time to time
of this Warrant and shall be enforceable by any such Holder or holder of Warrant Shares. 
 l) Amendment.
This Warrant may be modified or amended or the provisions hereof waived only with the written consent of the Company and the Holder. 

m) Severability. Wherever possible, each provision of this Warrant shall be interpreted in such manner as to be
effective and valid under applicable law, but if any provision of this Warrant shall be prohibited by or invalid under applicable law, such provision shall be ineffective to the extent of such prohibition or invalidity, without invalidating the
remainder of such provisions or the remaining provisions of this Warrant. 
 n) Headings. The headings
used in this Warrant are for the convenience of reference only and shall not, for any purpose, be deemed a part of this Warrant. 
  

 10 

 IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by
its officer thereunto duly authorized. 
 Dated:             , 2010

  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	  

		 	Name:
		 	Title:

 NOTICE OF EXERCISE 

TO: ACHILLION PHARMACEUTICALS, INC. 

(1) The undersigned hereby elects to purchase             
Warrant Shares of the Company pursuant to the terms of the attached Warrant (only if exercised in full), and tenders herewith payment of the Exercise Price in full, together with all applicable transfer taxes, if any. 

(2) Payment shall take the form of (check applicable box): 

 

	 	 ̈	 in lawful money of the United States; or (if available) 

 

	 	 ̈	 the cancellation of such number of Warrant Shares as is necessary, in accordance with the formula set forth in subsection 2(c), to exercise this
Warrant with respect to the maximum number of Warrant Shares purchasable pursuant to the cashless exercise procedure set forth in subsection 2(c). 

(3) Please issue a certificate or certificates representing said Warrant Shares in the name of the undersigned or in such
other name as is specified below: 
  

					
		  	  
	  	

 The Warrant Shares shall be delivered to the following: 

 

					
		  	  
	  	
		  	  
	  	
		  	  
	  	

 (4) Accredited Investor. The undersigned is an “accredited investor”
as defined in Regulation D promulgated under the Securities Act of 1933, as amended. 
 Name of Investing Entity:
                                         
                                         
                                         
                                      

Signature of Authorized Signatory of Investing Entity:
                                         
                                         
                                  

Name of Authorized Signatory:
                                         
                                         
                                         
                             

Title of Authorized Signatory:
                                         
                                         
                                         
                               

Date:
                                         
                                         
                                         
                                         
                              

 ASSIGNMENT FORM 

(To assign the foregoing warrant, execute 

this form and supply required information. 

Do not use this form to exercise the warrant.) 

FOR VALUE RECEIVED, the foregoing Warrant and all rights evidenced thereby are hereby assigned to: 

                      
                                         
                                  

whose address is: 

                      
                                         
                                  

                      
                                         
                                  

Dated:             ,
         
 Holder’s Signature:
                                         
                                      

Holder’s Address:
                                         
                                        

                   
                                         
                     

Signature Guaranteed:
                                         
                                         
   
 NOTE: The signature to this Assignment Form must correspond with the name as it appears on the face of the
Warrant, without alteration or enlargement or any change whatsoever, and must be guaranteed by a bank or trust company. Officers of corporations and those acting in a fiduciary or other representative capacity should file proper evidence of
authority to assign the foregoing Warrant.

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