EX-10.3



 Exhibit 10.3 

EXECUTION VERSION 
 STOCK
PURCHASE AGREEMENT 
 By and Between 

JOHNSON & JOHNSON INNOVATION-JJDC, INC. 

AND 
 ACHILLION
PHARMACEUTICALS, INC. 
 Dated as of May 19, 2015 







 TABLE OF CONTENTS 

 

									
	 	  	 	  	 	  	Page	 
			
	 1.
	  	 Definitions
	  	 	1	  
				
		  	 1.1
	  	 Defined Terms
	  	 	1	  
				
		  	 1.2
	  	 Additional Defined Terms
	  	 	4	  
			
	 2.
	  	 Purchase and Sale of Common Stock
	  	 	5	  
			
	 3.
	  	 Closing Date; Deliveries
	  	 	5	  
				
		  	 3.1
	  	 Closing Date
	  	 	5	  
				
		  	 3.2
	  	 Deliveries
	  	 	5	  
			
	 4.
	  	 Representations and Warranties of the Company
	  	 	6	  
				
		  	 4.1
	  	 Organization, Good Standing and Qualification
	  	 	6	  
				
		  	 4.2
	  	 Capitalization and Voting Rights
	  	 	6	  
				
		  	 4.3
	  	 Subsidiaries
	  	 	7	  
				
		  	 4.4
	  	 Authorization
	  	 	7	  
				
		  	 4.5
	  	 No Defaults
	  	 	8	  
				
		  	 4.6
	  	 No Conflicts
	  	 	8	  
				
		  	 4.7
	  	 No Governmental Authority or Third Party Consents
	  	 	8	  
				
		  	 4.8
	  	 Valid Issuance of Shares
	  	 	8	  
				
		  	 4.9
	  	 Litigation
	  	 	9	  
				
		  	 4.10
	  	 Licenses and Other Rights; Compliance with Laws
	  	 	9	  
				
		  	 4.11
	  	 Company SEC Documents; Financial Statements; Nasdaq Stock Market
	  	 	9	  
				
		  	 4.12
	  	 Absence of Certain Changes
	  	 	11	  
				
		  	 4.13
	  	 Offering
	  	 	11	  
				
		  	 4.14
	  	 No Integration
	  	 	11	  
				
		  	 4.15
	  	 Brokers’ or Finders’ Fees
	  	 	11	  
				
		  	 4.16
	  	 Investment Company
	  	 	11	  
				
		  	 4.17
	  	 No General Solicitation
	  	 	11	  
				
		  	 4.18
	  	 Foreign Corrupt Practices
	  	 	12	  
				
		  	 4.19
	  	 Regulation M Compliance
	  	 	12	  
				
		  	 4.20
	  	 Office of Foreign Assets Control
	  	 	12	  
				
		  	 4.21
	  	 Intellectual Property
	  	 	12	  
				
		  	 4.22
	  	 Full Disclosure
	  	 	12	  









									
	 5.
	  	 Representations and Warranties of the Investor
	  	 	13	  
				
		  	 5.1
	  	 Organization; Good Standing
	  	 	13	  
				
		  	 5.2
	  	 Authorization
	  	 	13	  
				
		  	 5.3
	  	 No Conflicts
	  	 	13	  
				
		  	 5.4
	  	 No Governmental Authority or Third Party Consents
	  	 	14	  
				
		  	 5.5
	  	 Purchase Entirely for Own Account
	  	 	14	  
				
		  	 5.6
	  	 Disclosure of Information
	  	 	14	  
				
		  	 5.7
	  	 Investment Experience and Accredited Investor Status
	  	 	14	  
				
		  	 5.8
	  	 Acquiring Person
	  	 	14	  
				
		  	 5.9
	  	 Restricted Securities
	  	 	14	  
				
		  	 5.10
	  	 Legends
	  	 	15	  
				
		  	 5.11
	  	 Financial Assurances
	  	 	15	  
				
		  	 5.12
	  	 Stock Ownership
	  	 	15	  
			
	 6.
	  	 Investor’s Conditions to Closing
	  	 	15	  
				
		  	 6.1
	  	 Representations and Warranties
	  	 	15	  
				
		  	 6.2
	  	 Representations and Warranties in the Collaboration Agreement
	  	 	16	  
				
		  	 6.3
	  	 Covenants
	  	 	16	  
				
		  	 6.4
	  	 Investor Agreement
	  	 	16	  
				
		  	 6.5
	  	 Collaboration Agreement
	  	 	16	  
				
		  	 6.6
	  	 No Material Adverse Effect
	  	 	16	  
				
		  	 6.7
	  	 Listing
	  	 	16	  
			
	 7.
	  	 Company’s Conditions to Closing
	  	 	16	  
				
		  	 7.1
	  	 Representations and Warranties
	  	 	16	  
				
		  	 7.2
	  	 Covenants
	  	 	17	  
				
		  	 7.3
	  	 Investor Agreement
	  	 	17	  
				
		  	 7.4
	  	 Collaboration Agreement
	  	 	17	  
			
	 8.
	  	 Mutual Conditions to Closing
	  	 	17	  
				
		  	 8.1
	  	 HSR Act Qualification
	  	 	17	  
				
		  	 8.2
	  	 Absence of Litigation
	  	 	17	  
				
		  	 8.3
	  	 No Prohibition
	  	 	17	  
			
	 9.
	  	 Termination
	  	 	17	  
				
		  	 9.1
	  	 Ability to Terminate
	  	 	17	  
				
		  	 9.2
	  	 Effect of Termination
	  	 	18	  


  
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	 10.
	  	 Additional Covenants and Agreements
	  	 	18	  
				
		  	 10.1
	  	 Market Listing
	  	 	18	  
				
		  	 10.2
	  	 Notification under the HSR Act
	  	 	19	  
				
		  	 10.3
	  	 Assistance and Cooperation
	  	 	20	  
				
		  	 10.4
	  	 Form D; Blue Sky Filings
	  	 	20	  
				
		  	 10.5
	  	 Legend Removal
	  	 	20	  
				
		  	 10.6
	  	 Conduct of Business
	  	 	21	  
			
	 11.
	  	 Miscellaneous
	  	 	21	  
				
		  	 11.1
	  	 Governing Law; Submission to Jurisdiction
	  	 	21	  
				
		  	 11.2
	  	 Waiver
	  	 	21	  
				
		  	 11.3
	  	 Notices
	  	 	22	  
				
		  	 11.4
	  	 Entire Agreement
	  	 	22	  
				
		  	 11.5
	  	 Amendments
	  	 	22	  
				
		  	 11.6
	  	 Headings; Nouns and Pronouns; Section References
	  	 	22	  
				
		  	 11.7
	  	 Severability
	  	 	22	  
				
		  	 11.8
	  	 Assignment
	  	 	22	  
				
		  	 11.9
	  	 Successors and Assigns
	  	 	23	  
				
		  	 11.10
	  	 Counterparts
	  	 	23	  
				
		  	 11.11
	  	 Third Party Beneficiaries
	  	 	23	  
				
		  	 11.12
	  	 No Strict Construction
	  	 	23	  
				
		  	 11.13
	  	 Survival of Warranties
	  	 	23	  
				
		  	 11.14
	  	 Remedies
	  	 	23	  
				
		  	 11.15
	  	 Expenses
	  	 	23	  
				
		  	 11.16
	  	 No Publicity
	  	 	23	  
				
		  	 11.17
	  	 Limitation of Liability
	  	 	23	  
		
	 Exhibit A – Form of Investor Agreement
	  			
	 Exhibit B – Notices
	  			


  
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 STOCK PURCHASE AGREEMENT 

THIS STOCK PURCHASE AGREEMENT (this “Agreement”), dated as of May 19, 2015, by and between Johnson &
Johnson Innovation-JJDC, Inc. (the “Investor”), a New Jersey corporation with its principal place of business at 410 George Street, New Brunswick, New Jersey 08901, and Achillion Pharmaceuticals, Inc. (the
“Company”), a Delaware corporation, with its principal place of business at 300 George Street, New Haven, CT 06511. 

WHEREAS, pursuant to the terms and subject to the conditions set forth in this Agreement, the Company desires to issue and sell to the
Investor, and the Investor desires to subscribe for and purchase from the Company, certain shares of common stock, par value $0.01 per share, of the Company (the “Common Stock”); and 

WHEREAS, simultaneously with the execution of this Agreement, the Company and Janssen Pharmaceuticals, Inc.
(“Janssen”), an Affiliate of the Investor, are entering into the Collaboration Agreement. 
 NOW, THEREFORE, in
consideration of the following mutual promises and obligations, and for good and valuable consideration, the adequacy and sufficiency of which are hereby acknowledged, the Investor and the Company agree as follows: 

1. Definitions. 
 1.1
Defined Terms. When used in this Agreement, the following terms shall have the respective meanings specified therefor below: 

“Affiliate” shall mean, with respect to any Person, another Person that controls, is controlled by or is under common control
with such Person; provided, that with respect to the Investor, “Affiliate” shall mean the Investor’s subsidiaries that are wholly-owned directly or indirectly, by the Investor and any Person that wholly-owns, directly or
indirectly, the Investor. A Person shall be deemed to control another Person if such Person possesses, directly or indirectly, the power to direct or cause the direction of the management and policies of such Person, whether through the ownership of
voting securities, by contract or otherwise. Without limiting the generality of the foregoing, a Person shall be deemed to control another Person if any of the following conditions is met: (i) in the case of corporate entities, direct or
indirect ownership of more than fifty percent (50%) of the stock or shares having the right to vote for the election of directors, and (ii) in the case of non-corporate entities, direct or indirect ownership of more than fifty percent
(50%) of the equity interest with the power to direct the management and policies of such non-corporate entities. For the purposes of this Agreement, in no event shall the Investor or any of its Affiliates be deemed Affiliates of the Company or
any of its Affiliates, nor shall the Company or any of its Affiliates be deemed Affiliates of the Investor or any of its Affiliates. 

“Agreement” shall have the meaning set forth in the Preamble, including all Exhibits attached hereto. 







 “Business Day” shall mean a weekday on which banking institutions in the United
States are generally open for business. 
 “Collaboration Agreement” shall mean the Collaboration and License Agreement, of
even date herewith, between Janssen and the Company. 
 “Collaboration Assets” shall mean the Achillion Background IP (as
defined in the Collaboration Agreement) licensed by the Company to Janssen pursuant to Section 2.1.1 or 2.1.2 of the Collaboration Agreement. 

“Collaboration Material Adverse Effect” shall mean any effect that, individually or when taken together with all other
Effects, has had, or would reasonably be expected to have, (i) a material adverse effect on the Collaboration Assets, taken as a whole, or (ii) a material adverse effect on the Company’s ability to perform its obligations under the
Collaboration Agreement. 
 “DOJ” means the U.S. Department of Justice. 

“Effect” shall have the meaning set forth in the definition of “Material Adverse Effect.” 

“FTC” means the U.S. Federal Trade Commission. 

“Governmental Authority” shall mean any court, agency, authority, department, regulatory body or other instrumentality of any
government or country or of any national, federal, state, provincial, regional, county, city or other political subdivision of any such government or country or any supranational organization of which any such country is a member. 

“Intellectual Property” shall mean trademarks, trade names, trade dress, service marks, copyrights, and similar rights
(including registrations and applications to register or renew the registration of any of the foregoing), patents and patent applications, trade secrets, and any other similar intellectual property rights. 

“Intellectual Property License” shall mean any license, permit, authorization, approval, contract or consent granted, issued
by or with any Person relating to the use of Intellectual Property. 
 “Investor Agreement” shall mean that certain
Investor Agreement between the Investor and the Company, to be dated as of the Closing Date, in substantially the form of Exhibit A attached hereto, as the same may be amended from time to time. 

“Law” or “Laws” shall mean all laws, statutes, rules, regulations, orders, judgments, injunctions and/or
ordinances of any Governmental Authority. 
 “Material Adverse Effect” shall mean any change, event or occurrence (each, an
“Effect”) that, individually or when taken together with all other Effects, has had, or would reasonably be expected to have, (i) a material adverse effect on the business, financial condition, assets or results of operations
of the Company and its subsidiaries, taken as a whole, or (ii) a 

  
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material adverse effect on the Company’s ability to perform its obligations, or consummate the Transaction, in accordance with the terms of this Agreement, except in the case of (i) to
the extent that any such Effect results from or arises out of: (A) changes in conditions in the United States or global economy or capital or financial markets generally, including changes in interest or exchange rates, (B) changes in
general legal, regulatory, political, economic or business conditions or changes in generally accepted accounting principles in the United States or interpretations thereof, (C) acts of war, sabotage or terrorism, or any escalation or worsening
of any such acts of war, sabotage or terrorism, (D) earthquakes, hurricanes, floods or other natural disasters, (E) the announcement of this Agreement or the Transaction, (F) any change in the Company’s stock price or trading
volume or any failure to meet internal projections or forecasts or published revenue or earnings projections of industry analysts (provided that the underlying events giving rise to any such change shall not be excluded), (G) any breach,
violation or non-performance by the Investor or any of its Affiliates under the Collaboration Agreement, provided, however, that the Effects excluded in clauses (A), (B), (C) and (D) shall only be excluded to the extent such
Effects are not disproportionately adverse on the Company and its subsidiaries as compared to other companies operating in the Company’s industry. 

“Organizational Documents” shall mean (i) the Restated Certificate of Incorporation of the Company, as amended through
the date of this Agreement and (ii) the Amended and Restated By-laws of the Company, as amended through the date of this Agreement. 

“Per Share Purchase Price” shall mean $12.25; provided, however, that in the event of any stock dividend, stock
split, combination of shares, recapitalization or other similar change in the capital structure of the Company after the date hereof and on or prior to the Closing which affects or relates to the Common Stock, the Per Share Purchase Price shall be
appropriately adjusted. 
 “Person” shall mean any individual, partnership, limited liability company, firm, corporation,
trust, unincorporated organization, government or any department or agency thereof or other entity, as well as any syndicate or group that would be deemed to be a Person under Section 13(d)(3) of the Exchange Act. 

“Third Party” shall mean any Person (other than a Governmental Authority) other than the Investor, the Company or any
Affiliate of the Investor or the Company. 
 “Trading Market” means The Nasdaq Stock Market. 

“Transaction” means the issuance and sale of the Shares by the Company, and the purchase of the Shares by the Investor, in
accordance with the terms hereof. 
 “Transaction Agreements” shall mean this Agreement and the Investor Agreement. 

  
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 1.2 Additional Defined Terms. In addition to the terms defined in Section 1.1, the
following terms shall have the respective meanings assigned thereto in the sections indicated below: 
  

			
	 Defined Term
	  	 Section

		
	Aggregate Purchase Price	  	Section 2
		
	Closing	  	Section 3.1
		
	Closing Date	  	Section 3.1
		
	Common Stock	  	Preamble
		
	Company	  	Preamble
		
	Company Rights	  	Section 4.21(b)
		
	Company SEC Documents	  	Section 4.11(a)
		
	Exchange Act	  	Section 4.11(a)
		
	GAAP	  	Section 4.11(c)
		
	HSR Act	  	Section 4.7
		
	Investor	  	Preamble
		
	LAS	  	Section 4.7
		
	Permits	  	Section 4.10
		
	Proprietary Rights	  	Section 4.21(b)
		
	Rule 144	  	Section 5.9
		
	SEC	  	Section 4.7
		
	Securities Act	  	Section 4.11(a)
		
	Shares	  	Section 2
		
	Subsidiaries	  	Section 4.3
		
	Termination Date	  	Section 9.1(b)
		
	Transfer Agent	  	Section 10.5(c)


  
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 2. Purchase and Sale of Common Stock. Subject to the terms and conditions of this
Agreement, at the Closing, the Company shall issue and sell to the Investor, free and clear of all liens, other than any liens arising as a result of any action by the Investor, and the Investor shall purchase from the Company, a number of shares of
Common Stock (the “Shares”) equal to the amount obtained by dividing the aggregate purchase price of US $225,000,000 (the “Aggregate Purchase Price”) by the Per Share Purchase Price. 

3. Closing Date; Deliveries. 

3.1 Closing Date. Subject to the satisfaction or waiver of all the conditions to the Closing set forth in Sections 6, 7 and 8 hereof,
the closing of the purchase and sale of the Shares hereunder (the “Closing”) shall be held on the third (3rd) Business Day after the satisfaction of the conditions to Closing
set forth in Sections 6, 7 and 8 (other than those conditions that by their nature are to be satisfied at the Closing, but subject to the satisfaction at such time of such conditions), at 9:00 a.m. Boston time, at the offices of Wilmer Cutler
Pickering Hale and Dorr LLP, 60 State Street, Boston, Massachusetts 02109, or at such other time, date and location as the parties may agree. The date the Closing occurs is hereinafter referred to as the “Closing Date.” 

3.2 Deliveries. 
 (a)
Deliveries by the Company. At the Closing, the Company shall deliver to the Investor the Shares, registered in the name of the Investor, and the Company shall instruct its transfer agent to register such issuance at the time of such issuance.
The Company shall also deliver at the Closing: (i) a certificate in form and substance reasonably satisfactory to the Investor and duly executed on behalf of the Company by an authorized executive officer of the Company, certifying that the
conditions to Closing set forth in Sections 6 and 8.2 of this Agreement have been fulfilled; (ii) a duly executed Investor Agreement; and (iii) a certificate of the secretary of the Company dated as of the Closing Date certifying
(A) that attached thereto is a true and complete copy of the Amended and Restated By-laws of the Company as in effect at the time of the actions by the Board of Directors of the Company referred to in clause (B) below, and on the Closing
Date; (B) that attached thereto is a true and complete copy of all resolutions adopted by the Board of Directors of the Company authorizing the execution, delivery and performance of the Transaction Agreements and the Transaction and that all
such resolutions are in full force and effect and are all the resolutions adopted in connection with the transactions contemplated hereby as of the Closing Date; (C) that attached thereto is a true and complete copy of the Company’s
Restated Certificate of Incorporation as in effect at the time of the actions by the Board of Directors of the Company referred to in clause (B) above, and on the Closing Date; and (D) as to the incumbency and specimen signature of any
officer of the Company executing a Transaction Agreement on behalf of the Company. 
 (b) Deliveries by the Investor. At the
Closing, the Investor shall deliver, or cause to be delivered, to the Company the Aggregate Purchase Price by wire transfer of immediately available United States funds to an account designated by the Company. The Company shall notify the Investor
in writing of the wiring instructions for such account not less than five (5) Business Days before the Closing Date. The Investor shall also deliver, or cause to be 

  
 - 5 - 








 
delivered, at the Closing: (i) a certificate in form and substance reasonably satisfactory to the Company duly executed by an authorized executive officer of the Investor certifying that the
conditions to Closing set forth in Section 7 of this Agreement have been fulfilled; (ii) a duly executed Investor Agreement; and (iii) a certificate of the secretary or assistant secretary of the Investor dated as of the Closing Date
certifying as to the incumbency and specimen signature of any officer executing a Transaction Agreement on behalf of the Investor. 
 4.
Representations and Warranties of the Company. The Company hereby represents and warrants to the Investor that: 
 4.1
Organization, Good Standing and Qualification. 
 (a) The Company is a corporation duly incorporated or otherwise organized, validly
existing and in good standing under the laws of the jurisdiction of its incorporation or organization, with the requisite power and authority to own and use its properties and assets and to carry on its business as currently conducted. The Company
has all requisite corporate power and corporate authority to own, lease and operate its properties and assets, to carry on its business as now conducted, and as proposed to be conducted as described in the Company SEC Documents, the Company has all
requisite corporate power and corporate authority to enter into the Transaction Agreements and the Collaboration Agreement, to issue and sell the Shares and to perform its obligations under and to carry out the other transactions contemplated by the
Transaction Agreements and the Collaboration Agreement. 
 (b) The Company is qualified to transact business and is in good standing in
each jurisdiction in which the character of the properties owned, leased or operated by the Company, or the nature of the business conducted by the Company, makes such qualification necessary, except where the failure to be so qualified would not
have a Material Adverse Effect. 
 4.2 Capitalization and Voting Rights. 

(a) The authorized capital of the Company as of the date hereof consists of: (i) 200,000,000 shares of Common Stock of which, as of the
date of this Agreement, (x) 117,972,461 shares are issued and outstanding, (y) 10,680,711 shares are reserved for issuance pursuant to the Company’s stock incentive and employee stock purchase plans, of which 8,733,997 shares are
issuable upon the exercise of stock options outstanding on the date hereof, and (z) 2,832,612 shares are reserved for issuance upon the exercise of warrants to purchase Common Stock that are outstanding on the date hereof, and
(ii) 5,000,000 shares of preferred stock, par value $0.01 per share, of which no shares are issued and outstanding as of the date of this Agreement. All of the issued and outstanding shares of Common Stock (A) have been duly authorized and
validly issued, (B) are fully paid and nonassessable and (C) were issued in compliance with all applicable federal and state securities Laws and not in violation of any preemptive rights. 

(b) All of the authorized shares of Common Stock are entitled to one (1) vote per share. 

  
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 (c) Except as described or referred to in Section 4.2(a) above and as provided in the
Investor Agreement, as of the date hereof, there are not: (i) any outstanding equity securities, options, warrants, rights (including conversion or preemptive rights) or other agreements pursuant to which the Company is or may become obligated
to issue, sell or repurchase any shares of its capital stock or any other securities of the Company or (ii) any restrictions on the transfer of capital stock of the Company other than pursuant to state and federal securities Laws. 

(d) Except as provided in the Investor Agreement or as disclosed in the Company SEC Documents, the Company is not a party to or subject to
any agreement or understanding relating to the voting of shares of capital stock of the Company or the giving of written consents by a stockholder or director of the Company. 

(e) Except as provided in the Investor Agreement or disclosed in the Company SEC Documents, no Person has any right to cause the Company to
effect the registration under the Securities Act of any securities of the Company. 
 (f) The Common Stock is registered pursuant to
Section 12(b) or 12(g) of the Exchange Act, and the Company has taken no action designed to, or which to its knowledge is likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act nor has the Company
received any notification that the SEC is contemplating terminating such registration. 
 4.3 Subsidiaries. The Company has no
subsidiaries. 
 4.4 Authorization. 

(a) All requisite corporate action on the part of the Company, its directors and stockholders required by applicable Law for the
authorization, execution and delivery by the Company of the Transaction Agreements and the Collaboration Agreement, and the performance of all obligations of the Company hereunder and thereunder, including the authorization, issuance and delivery of
the Shares, has been taken. 
 (b) This Agreement and the Collaboration Agreement have been, and upon the execution and delivery of the
Investor Agreement by the Company at the Closing, the Investor Agreement will be, duly executed and delivered by the Company, and upon the due execution and delivery of this Agreement by the Investor and the Collaboration Agreement by Janssen, this
Agreement and the Collaboration Agreement will constitute, and upon the due execution and delivery of the Investor Agreement by the Investor, the Investor Agreement will constitute, valid and legally binding obligations of the Company, enforceable
against the Company in accordance with their respective terms (except with respect to the Investor Agreement and the Collaboration Agreement as such enforceability may be limited by (i) applicable bankruptcy, insolvency, reorganization,
moratorium or other Laws of general application relating to or affecting enforcement of creditors’ rights and (ii) rules of Law governing specific performance, injunctive relief or other equitable remedies and limitations of public
policy). 
 (c) No stop order or suspension of trading of the Common Stock has been imposed by Nasdaq, the SEC or any other Governmental
Authority and remains in effect. 

  
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 4.5 No Defaults. The Company is not in default under or in violation of (a) its
Organizational Documents, (b) any provision of applicable Law or any ruling, writ, injunction, order, Permit, judgment or decree of any Governmental Authority or (c) any agreement, arrangement or instrument, whether written or oral, by
which the Company or any of its assets are bound, except, in the case of subsections (b) and (c), as would not have a Material Adverse Effect. There exists no condition, event or act which after notice, lapse of time, or both, would constitute
a default or violation by the Company under any of the foregoing, except, in the case of subsections (b) and (c), as would not have a Material Adverse Effect. 

4.6 No Conflicts. The execution, delivery and performance of the Transaction Agreements and the Collaboration Agreement, and compliance
with the provisions hereof and thereof by the Company do not and shall not: (a) violate any provision of applicable Law or any ruling, writ, injunction, order, permit, judgment or decree of any Governmental Authority, (b) constitute a
breach of, or default under (or an event which, with notice or lapse of time or both, would become a default under) or conflict with, or give rise to any right of termination, cancellation or acceleration of, any agreement, arrangement or
instrument, whether written or oral, by which the Company or any of its assets are bound, (c) violate or conflict with any of the provisions of the Company’s Organizational Documents or (d) result in any encumbrance upon any of the
Shares, other than restrictions pursuant to the Investor Agreement or securities Laws, or on any of the properties or assets of the Company, except, in the case of subsections (a) and (b), as would not have a Material Adverse Effect with
respect to this Agreement or the Investor Agreement or a Collaboration Material Adverse Effect with respect to the Collaboration Agreement. 

4.7 No Governmental Authority or Third Party Consents. No consent, approval, authorization or other order of, or filing with, or notice
to, any Governmental Authority or other Third Party is required to be obtained or made by the Company in connection with the authorization, execution and delivery by the Company of any of the Transaction Agreements or the Collaboration Agreement, or
with the authorization, issue and sale by the Company of the Shares, except (i) such filings as may be required to be made with the Securities and Exchange Commission (the “SEC”) and with any state blue sky or securities
regulatory authority, which filings shall be made in a timely manner in accordance with all applicable Laws, (ii) as required pursuant to the Hart-Scott-Rodino Antitrust Improvements Act, as amended (the “HSR Act”) and
(iii) with respect to the Shares, the filing with The Nasdaq Stock Market LLC of, and the absence of unresolved issues with respect to, a Notification Form: Listing of Additional Shares (the “LAS”). 

4.8 Valid Issuance of Shares. When issued, sold and delivered at the Closing in accordance with the terms hereof for the Aggregate
Purchase Price, the Shares shall be duly authorized, validly issued, fully paid and nonassessable, free from any liens, encumbrances or restrictions on transfer, including preemptive rights, rights of first refusal or other similar rights, other
than as arising pursuant to the Transaction Agreements, as a result of any action by the Investor or under federal or state securities Laws. 

  
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 4.9 Litigation. Except as set forth in the Company SEC Documents filed prior to the date
of this Agreement, there is no action, suit, proceeding or investigation pending (of which the Company has received notice or otherwise has knowledge) or, to the Company’s knowledge, threatened, against the Company or which the Company intends
to initiate which has had or is reasonably likely to have a Material Adverse Effect. 
 4.10 Licenses and Other Rights; Compliance with
Laws. The Company has all franchises, permits, licenses and other rights and privileges (“Permits”) necessary to permit it to own its properties and to conduct its business as presently conducted and is in compliance thereunder,
except where the failure to be in compliance does not and would not have a Material Adverse Effect. The Company has not taken any action that would interfere with the Company’s ability to renew all such Permit(s), except where the failure to
renew such Permit(s) would not have a Material Adverse Effect. The Company is and has been in compliance with all Laws applicable to its business, properties and assets, and to the products and services sold by it, except where the failure to be in
compliance does not and would not have a Material Adverse Effect. 
 4.11 Company SEC Documents; Financial Statements; Nasdaq Stock
Market. 
 (a) Since January 1, 2014, the Company has timely filed all required reports, schedules, forms, statements and other
documents (including exhibits and all other information incorporated therein), and any required amendments to any of the foregoing, with the SEC (the “Company SEC Documents”). As of their respective filing dates, each of the Company
SEC Documents complied in all material respects with the requirements of the Securities Act of 1933, as amended (the “Securities Act”), and the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and
the rules and regulations of the SEC promulgated thereunder applicable to such Company SEC Documents, and no Company SEC Documents when filed, declared effective or mailed, as applicable, 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 light of the circumstances under which they were made, not misleading. 

(b) As of the date of this Agreement, there are no outstanding or unresolved comments in comment letters received from the SEC or its staff.

 (c) The financial statements of the Company included in its Annual Report on Form 10-K for the fiscal year ended December 31, 2014
and in its quarterly report on Form 10-Q for the quarterly period ended March 31, 2015 comply as to form in all material respects with applicable accounting requirements and the published rules and regulations of the SEC with respect thereto,
have been prepared in accordance with United States generally accepted accounting principles (“GAAP”) applied on a consistent basis during the periods involved (except as may be indicated in the notes thereto) and fairly present in
all material respects the financial position of the Company as of the dates thereof and the results of its operations and cash flows for the periods then ended. Except (i) as set forth in the Company SEC Documents or (ii) for liabilities


  
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incurred in the ordinary course of business subsequent to the date of the most recent balance sheet contained in the Company SEC Documents, the Company has no liabilities, whether absolute or
accrued, contingent or otherwise, other than those that would not, individually or in the aggregate, have a Material Adverse Effect. There are no material unconsolidated subsidiaries of the Company or any material off-balance sheet arrangements of
any type (including any off balance sheet arrangements required to be disclosed pursuant to Item 303(a)(4) of Regulation S-K promulgated under the Securities Act) that have not been so described in the Company SEC Reports filed prior to the
date hereof nor any obligations to enter into any such arrangements. 
 (d) The Common Stock is listed on The Nasdaq Global Select Market,
and the Company has taken no action designed to, or which is likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act or delisting the Common Stock from The Nasdaq Global Select Market. The Company has
not received any notification that, and has no knowledge that, the SEC or The Nasdaq Stock Market LLC is contemplating terminating such listing or registration. 

(e) The Company has implemented and maintains a system of internal control over financial reporting (to the extent required by Rule 13a-15(a)
under the Exchange Act) that is designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of consolidated financial statements for external purposes, and, to the knowledge of the Company, such
system of internal control over financial reporting is effective. For purposes of this Section 4.11(e), “knowledge of the Company” means the actual knowledge of the Chief Executive Officer and the Chief Financial Officer of the
Company. The Company has implemented and maintains disclosure controls and procedures (to the extent required by Rule 13a-15(a) of the Exchange Act) that are designed to ensure that information required to be disclosed by the Company in the reports
it files or submits under the Exchange Act is recorded, processed, summarized and reported within the timeframes specified by the SEC’s rules and forms (and such disclosure controls and procedures are effective), and has disclosed, based on its
most recent evaluation of its system of internal control over financial reporting prior to the date of this Agreement, to the Company’s outside auditors and the audit committee of the Company Board (i) any significant deficiencies and
material weaknesses known to it in the design or operation of its internal control over financial reporting (as defined in Rule 13a-15(f) of the Exchange Act) that would reasonably be expected to adversely affect the Company’s ability to
record, process, summarize and report financial information and (ii) any fraud known to it, that involves management or other employees who have a significant role in the Company’s internal control over financial reporting. 

(f) To the knowledge of the Company, as of the date hereof, no employee of the Company has provided since January 1, 2013 or is
providing information to any law enforcement agency regarding the violation of any applicable Law of the type described in Section 806 of the Sarbanes-Oxley Act by the Company. The Company has not discharged, demoted or suspended an employee of
the Company in the terms and conditions of employment because of any lawful act of such employee described in Section 806 of the Sarbanes-Oxley Act. 

  
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 4.12 Absence of Certain Changes. 

(a) Except as disclosed in the Company SEC Documents, since December 31, 2013, there has not occurred any event that has caused or would
reasonably be expected to cause a Material Adverse Effect. 
 (b) Except as set forth in the Company SEC Documents filed prior to the date
hereof, since December 31, 2013, the Company has not (i) declared or paid any dividends, or authorized or made any distribution upon or with respect to any class or series of its capital stock, or (ii) sold, exchanged or otherwise
disposed of any of its material assets or rights. 
 (c) Since December 31, 2013, the Company has not admitted in writing its
inability to pay its debts generally as they become due, filed or consented to the filing against it of a petition in bankruptcy or a petition to take advantage of any insolvency act, made an assignment for the benefit of creditors, consented to the
appointment of a receiver for itself or for the whole or any substantial part of its property, or had a petition in bankruptcy filed against it, been adjudicated a bankrupt, or filed a petition or answer seeking reorganization or arrangement under
the federal bankruptcy laws or any other laws of the United States or any other jurisdiction. 
 4.13 Offering. Subject to the
accuracy of the Investor’s representations set forth in Sections 5.5, 5.6, 5.7, 5.9 and 5.10, the offer, sale and issuance of the Shares to be issued in conformity with the terms of this Agreement constitute transactions which are exempt from
the registration requirements of the Securities Act and from all applicable state registration or qualification requirements. Neither the Company nor any Person acting on its behalf will take any action that would cause the loss of such exemption.

 4.14 No Integration. The Company has not, directly or through any agent, sold, offered for sale, solicited offers to buy or
otherwise negotiated in respect of, any security (as defined in the Securities Act) which is or will be integrated with the Shares sold pursuant to this Agreement in a manner that would require the registration of the Shares under the Securities
Act. 
 4.15 Brokers’ or Finders’ Fees. Other than Centerview Partners LLC, no broker, finder, investment banker or other
Person is entitled to any brokerage, finder’s or other fee or commission from the Company in connection with the transactions contemplated by the Transaction Agreements and the Collaboration Agreement. 

4.16 Investment Company. The Company is not, and is not an Affiliate of, and immediately after receipt of payment for the Shares, 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 an “investment company”
subject to registration under the Investment Company Act of 1940, as amended. 
 4.17 No General Solicitation. Neither the Company
nor any person acting on behalf of the Company has offered or sold any of the Shares by any form of general solicitation or general advertising. The Company has offered the Shares for sale only to the Investor. 

  
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 4.18 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 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 or (iv) violated in any material respect any provision of the Foreign Corrupt Practices Act of 1977, as amended, or any applicable non-U.S.
anti-bribery Law. 
 4.19 Regulation M Compliance. The Company has not, and to its knowledge no one acting on its behalf has,
(i) taken, 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 Shares, (ii) sold, bid for,
purchased, or paid any compensation for soliciting purchases of, any of the Shares, or (iii) paid or agreed to pay to any Person any compensation for soliciting another to purchase any other securities of the Company. 

4.20 Office of Foreign Assets Control. Neither the Company nor, to the Company’s knowledge, any director, officer, agent, employee
or Affiliate of the Company is currently subject to any U.S. sanctions administered by the Office of Foreign Assets Control of the U.S. Treasury Department. 

4.21 Intellectual Property. 

(a) The Intellectual Property that is owned by the Company is owned free from any liens or restrictions (other than any restrictions set
forth in any Intellectual Property License relating to such Intellectual Property), and all of the Company’s material Intellectual Property Licenses are in full force and effect in accordance with their terms, are, to the Company’s
knowledge, free of any liens or restrictions, and neither the Company nor to the Company’s knowledge any other party thereto, is in material breach of any such material Intellectual Property License, and no event has occurred that with notice
or lapse of time or both would constitute such a breach or default thereunder or would result in the termination thereof or would cause or permit the acceleration or other change of any right or obligation of the loss of any benefit thereunder by
the Company except (i) for such failures to be in full force and effect, such liens or restrictions, and such material breaches that would not reasonably be expected to have a Material Adverse Effect, or (ii) as set forth in any such
Intellectual Property License. Except as set forth in the Company SEC Documents filed prior to the date hereof, there is no material legal claim or demand of any Person pertaining to, or any proceeding which is pending (of which the Company has
received notice or otherwise has knowledge) or, to the knowledge of the Company, threatened, (i) challenging the right of the Company in respect of any Company Intellectual Property, or (ii) that claims that any default exists under any
Intellectual Property License, except, in the case of (i) and (ii) above, where any such claim, demand or proceeding would not have or reasonably be expected to have a Material Adverse Effect. 

(b) Except as set forth in the Company’s SEC Documents: (i) the Company owns, free and clear of any lien or encumbrance, or has a
valid license to, or has an enforceable right to use, as it is used or held for use, all U.S. and non-U.S. patents, trade secrets, know-how, trademarks, service marks, copyrights, and other proprietary and intellectual property rights, and all
grants and applications with respect to the foregoing (collectively, the “Proprietary Rights”) necessary for the conduct of the Company’s business, the absence of which would not have or reasonably be expected to have a
Material Adverse Effect (such Proprietary Rights owned by or licensed to the Company collectively, the “Company Rights”); and (ii) the Company has taken reasonable measures to protect the Company Rights, consistent with prudent
commercial practices in the biotechnology industry, except where failure to take such measures would not have or reasonably be expected to have a Material Adverse Effect. 

4.22 Full Disclosure. As of the date hereof, and other than the transactions that are the subject of this Agreement and the
Collaboration Agreement, no material fact or circumstance exists that would be required to be disclosed in a current report on Form 8-K or in a registration statement filed under the Securities Act, were
such a registration statement filed on the date hereof, that has not been disclosed in an SEC Report filed on or after March 5, 2013. 

  
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 5. Representations and Warranties of the Investor. The Investor hereby represents and
warrants to the Company that: 
 5.1 Organization; Good Standing. The Investor is a corporation duly organized, validly existing and
in good standing under the laws of New Jersey. The Investor has or will have all requisite power and authority to enter into the Transaction Agreements, to purchase the Shares and to perform its obligations under and to carry out the other
transactions contemplated by the Transaction Agreements. 
 5.2 Authorization. All requisite action on the part of the Investor and
its directors and stockholders, required by applicable Law for the authorization, execution and delivery by the Investor of the Transaction Agreements, and the performance of all of its obligations thereunder, including the subscription for and
purchase of the Shares, has been taken. This Agreement has been, and upon the execution and delivery of the Investor Agreement at the Closing by the Investor, the Investor Agreement will be, duly executed and delivered by the Investor and upon the
due execution and delivery thereof by the Company, will constitute valid and legally binding obligations of the Investor, enforceable against the Investor in accordance with their respective terms (except as such enforceability may be limited by
(a) applicable bankruptcy, insolvency, reorganization, moratorium or other Laws of general application relating to or affecting enforcement of creditors’ rights and (b) rules of Law governing specific performance, injunctive relief or
other equitable remedies and limitations of public policy). 
 5.3 No Conflicts. The execution, delivery and performance of the
Transaction Agreements and compliance with the provisions thereof by the Investor do not and shall not: (a) violate any provision of applicable Law or any ruling, writ, injunction, order, permit, judgment or decree of any Governmental
Authority, (b) constitute a breach of, or default under (or an event which, with notice or lapse of time or both, would become a default under) or conflict with, or give 

  
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rise to any right of termination, cancellation or acceleration of, any agreement, arrangement or instrument, whether written or oral, by which the Investor or any of its assets, are bound, or
(c) violate or conflict with any of the provisions of the Investor’s organizational documents (including any articles or memoranda of organization or association, charter, bylaws or similar documents), except as would not impair or
adversely affect the ability of the Investor to consummate the Transactions and perform its obligations under the Transaction Agreements and except, in the case of subsections (a) and (b) as would not have a material adverse effect on the
Investor’s ability to perform its obligations or consummate the Transaction in accordance with the terms of this Agreement. 
 5.4
No Governmental Authority or Third Party Consents. No consent, approval, authorization or other order of any Governmental Authority or other Third Party is required to be obtained by the Investor in connection with the authorization,
execution and delivery of any of the Transaction Agreements or with the subscription for and purchase of the Shares, except as required pursuant to the HSR Act. 

5.5 Purchase Entirely for Own Account. The Shares shall be acquired for investment for the Investor’s own account, not as a
nominee or agent, and not with a view to the resale or distribution of any part thereof, and the Investor has no present intention of selling, granting any participation or otherwise distributing the Shares. The Investor does not have and will not
have as of the Closing any contract, undertaking, agreement or arrangement with any Person to sell, transfer or grant participation to a Person any of the Shares. 

5.6 Disclosure of Information. The Investor has received all the information from the Company and its management that the Investor
considers necessary or appropriate for deciding whether to purchase the Shares hereunder. The Investor further represents that it has had an opportunity to ask questions and receive answers from the Company regarding the Company, its financial
condition, results of operations and prospects and the terms and conditions of the offering of the Shares sufficient to enable it to evaluate its investment. 

5.7 Investment Experience and Accredited Investor Status. The Investor is an “accredited investor” (as defined in Regulation
D under the Securities Act). The Investor has such knowledge and experience in financial or business matters that it is capable of evaluating the merits and risks of the investment in the Shares to be purchased hereunder. 

5.8 Acquiring Person. As of the date of this Agreement and immediately prior to the Closing, neither the Investor nor any of its
Affiliates beneficially owns, or will beneficially own (as determined pursuant to Rule 13d-3 under the Exchange Act without regard for the number of days in which a Person has the right to acquire such beneficial ownership, and without regard to
Investor’s rights under this Agreement), any securities of the Company, except for securities that may be owned by employee benefit plans of the Investor or any of its Affiliates. 

5.9 Restricted Securities. The Investor understands that the Shares, when issued, shall be “restricted securities” under the
federal securities Laws inasmuch as they are being acquired from the Company in a transaction not involving a public offering and that under such 

  
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Laws the Shares may be resold without registration under the Securities Act only in certain limited circumstances. The Investor represents that it is familiar with Rule 144 of the Securities Act
(“Rule 144”), as presently in effect. 
 5.10 Legends. The Investor understands that any certificates representing
the Shares shall bear the following legends: 
 (a) “These securities have not been registered under the Securities Act of 1933. They
may not be sold, offered for sale, pledged or hypothecated in the absence of a registration statement in effect with respect to the securities under the Securities Act or an opinion of counsel (which counsel shall be reasonably satisfactory to the
Company) that such registration is not required or unless sold pursuant to Rule 144 of the Securities Act.”; 
 (b) any legend
required by applicable state securities Laws; and 
 (c) “The securities represented by this certificate are subject to and shall be
transferable only upon the terms and conditions of an Investor Agreement dated as of                  , 2015, by and between Achillion Pharmaceuticals, Inc. and
Johnson & Johnson Innovation-JJDC, Inc., a copy of which is on file with the Secretary of Achillion Pharmaceuticals, Inc.” 

5.11 Financial Assurances. As of the date hereof and as of the Closing Date, the Investor has and will have access to cash in an amount
sufficient to pay to the Company the Aggregate Purchase Price. 
 5.12 Stock Ownership. As of the date hereof, neither the Investor
nor any of its Affiliates (excluding for this purpose any employee benefit plan of the Investor) own any shares of capital stock of the Company. 

6. Investor’s Conditions to Closing. The Investor’s obligation to purchase the Shares at the Closing is subject to the
fulfillment as of the Closing of the following conditions (unless waived in writing by the Investor): 
 6.1 Representations and
Warranties. The representations and warranties made by the Company in Section 4 hereof shall be true and correct as of the date of this Agreement and as of the Closing Date as though made on and as of such Closing Date, except to the extent
such representations and warranties are specifically made as of a particular date, in which case such representations and warranties shall be true and correct as of such date; provided, however, that for purposes of this
Section 6.1, all such representations and warranties of the Company (other than Sections 4.1(a), 4.2, 4.3, 4.4, 4.5(a), 4.6(c), 4.8, and 4.11 of this Agreement) shall be deemed to be true and correct for purposes of this Section 6.1 unless
the failure or failures of such representations and warranties to be so true and correct, without regard to any “material,” “materiality” or “Material Adverse Effect” qualifiers set forth therein, constitute a Material
Adverse Effect. 

  
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 6.2 Representations and Warranties in the Collaboration Agreement. The representations and
warranties made by the Company in Article XII (Sections 12.1 through 12.6 and 12.8 through 12.10) of the Collaboration Agreement shall be true and correct as of the Closing Date as though made on and as of such Closing Date, except to the extent
such representations and warranties are specifically made as of a particular date, in which case such representations and warranties shall be true and correct as of such date; provided, however, that for purposes of this
Section 6.2, all such representations and warranties of the Company shall be deemed to be true and correct for purposes of this Section 6.2 unless the failure or failures of such representations and warranties to be so true and correct,
without regard to any “material” or “materiality” qualifiers set forth therein, individually or in the aggregate, has had or would reasonably be expected to have a Collaboration Material Adverse Effect. 

6.3 Covenants. All covenants and agreements contained in this Agreement to be performed or complied with by the Company on or prior to
the Closing Date shall have been performed or complied with in all material respects. 
 6.4 Investor Agreement. The Company shall
have duly executed and delivered to the Investor, pursuant to Section 3.2(a) of this Agreement, the Investor Agreement, and (subject to execution by the Investor) such agreement shall be in full force and effect. 

6.5 Collaboration Agreement. The Company shall have duly executed and delivered to the Investor the Collaboration Agreement, and there
shall have been no termination of the Collaboration Agreement that, as of the Closing, is effective. 
 6.6 No Material Adverse
Effect. From and after the date of this Agreement until the Closing Date, there shall have occurred no event that has caused a Material Adverse Effect or a Collaboration Material Adverse Effect. 

6.7 Listing. The Shares shall be eligible and approved for listing on the Nasdaq Global Select Market. 

7. Company’s Conditions to Closing. The Company’s obligation to issue and sell the Shares at the Closing is subject to the
fulfillment as of the Closing of the following conditions (unless waived in writing by the Company): 
 7.1 Representations and
Warranties. The representations and warranties made by the Investor in Section 5 hereof shall be true and correct as of the date of this Agreement and as of the Closing Date as though made on and as of such Closing Date, except to the
extent such representations and warranties are specifically made as of a particular date, in which case such representations and warranties shall be true and correct as of such date, in the case of Sections 5.1-5.4, and 5.11, except where any
failure to be true and correct would not have a material adverse effect on the Investor’s ability to perform its obligations, or consummate the Transaction in accordance with the terms of this Agreement, in the case of Section 5.5, 5.6 and
5.7, except where any inaccuracy would not result in the issuance of the Shares hereunder failing to qualify as an offering of securities not involving any public offering under the federal securities Laws, and in


  
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the case of Section 5.8, except where any inaccuracy would not be material on the Investor’s ability to perform its obligations, or consummate the Transaction in accordance with the
terms of this Agreement. 
 7.2 Covenants. All covenants and agreements contained in this Agreement to be performed or complied with
by the Investor on or prior to the Closing Date shall have been performed or complied with in all material respects. 
 7.3 Investor
Agreement. The Investor shall have duly executed and delivered to the Company, pursuant to Section 3.2(b) of this Agreement, the Investor Agreement, and (subject to execution by the Company) such agreement shall be in full force and effect.

 7.4 Collaboration Agreement. Janssen shall have duly executed and delivered to the Company the Collaboration Agreement, and there
shall have been no termination of the Collaboration Agreement that, as of the Closing, is effective. 
 8. Mutual Conditions to
Closing. The obligations of the Investor and the Company to consummate the Closing are subject to the fulfillment as of the Closing Date of the following conditions: 

8.1 HSR Act Qualification. The filings required under the HSR Act in connection with this Agreement shall have been made and the
required waiting period shall have expired or been terminated as of the Closing Date. 
 8.2 Absence of Litigation. There shall be no
action, suit, proceeding or investigation by a Governmental Authority pending or currently threatened in writing against the Company or the Investor that questions the validity of any of the Transaction Agreements, the right of the Company or the
Investor to enter into any Transaction Agreement or to consummate the transactions contemplated hereby or thereby or which, if determined adversely, would impose substantial monetary damages on the Company or the Investor as a result of the
consummation of the transactions contemplated by any Transaction Agreement. 
 8.3 No Prohibition. No provision of any applicable Law
and no judgment, injunction (preliminary or permanent), order or decree that prohibits, makes illegal or enjoins the consummation of the Transaction shall be in effect. 

9. Termination. 
 9.1
Ability to Terminate. This Agreement may be terminated at any time prior to the Closing by: 
 (a) mutual written consent of the
Company and the Investor; 
 (b) either the Company or the Investor, upon written notice to the other no earlier than August 31, 2015
(the “Termination Date”), if the Transaction shall not have been consummated by the Termination Date; 

  
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 (c) either the Company or the Investor, upon written notice to the other, if any of the mutual
conditions to the Closing set forth in Section 8 shall have become incapable of fulfillment by the Termination Date and shall not have been waived in writing by the other party within ten business days after receiving receipt of written notice
of an intention to terminate pursuant to this clause (c) provided, however, that the right to terminate this Agreement under this Section 9.1(c) shall not be available to any party whose failure to fulfill any obligation under this
Agreement has been the cause of, or resulted in, the failure to consummate the transactions contemplated hereby prior to the Termination Date; 

(d) the Company, upon written notice to the Investor, so long as the Company is not then in breach of its representations, warranties,
covenants or agreements under this Agreement such that any of the conditions set forth in Section 6.1 or 6.2, as applicable, could not be satisfied by the Termination Date, (i) upon a material breach of any covenant or agreement on the
part of the Investor set forth in this Agreement, or (ii) if any representation or warranty of the Investor shall have been or become untrue, in each case such that any of the conditions set forth in Section 7.1, 7.2, 7.3 or 7.4, as
applicable, could not be satisfied by the Termination Date; 
 (e) the Investor, upon written notice to the Company, so long as the
Investor is not then in breach of its representations, warranties, covenants or agreements under this Agreement such that any of the conditions set forth in Section 7.1, 7.2 or 7.3, as applicable, could not be satisfied by the Termination Date,
(i) upon a breach of any covenant or agreement on the part of the Company set forth in this Agreement, or (ii) if any representation or warranty of the Company shall have been or become untrue, in each case such that any of the conditions
set forth in Section 6.1, 6.2, 6.3 or 6.4, as applicable, could not be satisfied by the Termination Date. 
 9.2 Effect of
Termination. In the event of the termination of this Agreement pursuant to Section 9.1 hereof, (a) this Agreement (except for this Section 9.2 and Section 11 hereof (other than Section 11.13), and any definitions set
forth in this Agreement and used in such sections) shall forthwith become void and have no effect, without any liability on the part of any party hereto or its Affiliates, and (b) all filings, applications and other submissions made pursuant to
this Agreement, to the extent practicable, shall be withdrawn from the agency or other Person to which they were made or appropriately amended to reflect the termination of the transactions contemplated hereby; provided, however, that
nothing contained in this Section 9.2 shall relieve any party from liability for fraud or any intentional or willful breach of this Agreement. 

10. Additional Covenants and Agreements. 

10.1 Market Listing. From the date hereof through the Closing Date, Company shall use all reasonable efforts to (a) maintain the
listing and trading of the Common Stock on The Nasdaq Global Select Market and (b) effect the listing of the Shares on The Nasdaq Global Select Market, including submitting the LAS to The Nasdaq Stock Market LLC no later than fifteen
(15) calendar days prior to the Closing Date. 

  
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 10.2 Notification under the HSR Act. 

(a) As a result of the aggregate consideration being paid by the Investor under this Agreement and the Collaboration Agreement, which
satisfies the size of transaction jurisdictional threshold under the HSR Act, the parties shall, as soon as practicable, and, in any event, no later than ten (10) Business Days after the date of this Agreement, file or cause to be filed with
the Federal Trade Commission and the Department of Justice the notifications required to be filed under the HSR Act and the rules and regulations promulgated thereunder with respect to the transactions contemplated by this Agreement. The parties
will use all reasonable efforts to respond on a timely basis to any requests for additional information made by either of such agencies. 

(b) Each of Investor and Company shall: (i) reasonably cooperate with each other in connection with any investigation or other inquiry
relating to the transactions contemplated by the Transaction Agreements and the Collaboration Agreement; (ii) reasonably keep the other party informed of any communication received by such party from, or given by such party to, the FTC, the DOJ
or any other Merger Control Authority and of any communication received or given in connection with any proceeding by a private party, in each case regarding the transactions contemplated by the Transaction Agreements or the Collaboration Agreement;
(iii) promptly respond to and certify substantial compliance with any inquiries or requests received from the FTC or the DOJ for additional information or documentation; (iv) reasonably consult with each other in advance of any meeting or
conference with the FTC, the DOJ or any other Merger Control Authority, and to the extent permitted by the FTC, the DOJ or such other Merger Control Authority and reasonably determined by such party to be appropriate under the circumstances, give
the other party or their counsel the opportunity to attend and participate in such meetings and conferences; and (v) permit the other party or their counsel to the extent reasonably practicable to review in advance, and in good faith consider
the views of the other party or their counsel concerning, any submission, filing or communication (and documents submitted therewith) intended to be given by it to the FTC, the DOJ or any other Merger Control Authority; provided,
however, such party shall be under no obligation to reschedule any meetings or conferences with the FTC, the DOJ or any other Merger Control Authority to enable the other party to attend. 

(c) Notwithstanding anything to the contrary in this Agreement, the terms “commercially reasonable efforts” or “reasonable
efforts” do not require that either party (i) offer, negotiate, commit to or effect, by consent decree, hold separate order, trust or otherwise, the sale, divestiture, license or other disposition of any capital stock, assets, rights,
products or businesses of Investor, Company or their respective Affiliates, (ii) agree to any restrictions on the activities of Investor, Company or their respective Affiliates, or (iii) pay any material amount or take any other action to
prevent, effect the dissolution of, vacate, or lift any decree, order, judgment, injunction, temporary restraining order, or other order in any suit or proceeding that would otherwise have the effect of preventing or delaying any of the transactions
contemplated by the Transaction Agreements or the Collaboration Agreement. 

  
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 10.3 Assistance and Cooperation. Prior to the Closing, upon the terms and subject to the
conditions set forth in this Agreement, each of the parties agrees to use all reasonable efforts to take, or cause to be taken, all actions and to do, or cause to be done, and to assist and cooperate with the other party in doing, all things
necessary, proper or advisable to consummate and make effective, in the most expeditious manner practicable, the transactions contemplated by this Agreement, including using all reasonable efforts to accomplish the following: (a) taking all
reasonable acts necessary to cause the conditions precedent set forth in Sections 6, 7 and 8 to be satisfied (including, in the case of the Company, promptly notifying the Investor of any notice from The Nasdaq Stock Market LLC with respect to the
LAS); (b) taking all reasonable actions necessary to obtain all necessary actions or non-actions, waivers, consents, approvals, orders and authorizations from Governmental Authorities and the making of all necessary registrations, declarations
and filings (including registrations, declarations and filings with Governmental Authorities, if any); (c) taking all reasonable actions necessary to obtain all necessary consents, approvals or waivers from Third Parties; and (d) except as
otherwise provided for in Section 10.2, defending any suits, claims, actions, investigations or proceedings, whether judicial or administrative, challenging this Agreement or the consummation of the transactions contemplated hereby, including
seeking to have any stay or temporary restraining order entered by any court or other Governmental Authority vacated or reversed. 
 10.4
Form D; Blue Sky Filings. The Company agrees to timely file a Form D with respect to the Shares as required under Regulation D and to provide a copy thereof, promptly upon request of the Investor. The Company shall take such action as the
Company shall reasonably determine is necessary in order to obtain an exemption for, or to qualify the Shares for, sale to the Investor 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 the Investor. 
 10.5 Legend Removal. 

(a) Certificates evidencing the Shares shall not contain the legend set forth in Section 5.10(a): (i) following a sale of such
Shares pursuant to a registration statement covering the resale of such Shares, while such registration statement is effective under the Securities Act, (ii) following any sale of such Shares pursuant to Rule 144, (iii) if such Shares are
eligible for sale under Rule 144, without the requirement for the Company to be in compliance with the current public information required under Rule 144 as to such Shares and without volume or manner-of-sale restrictions under Rule 144 or
(iv) if such legend is not required under applicable requirements of the Securities Act (including judicial interpretations and pronouncements issued by the staff of the SEC). 

(b) Certificates evidencing the Shares shall not contain the legend set forth in Section 5.10(c) following: (i) a sale of such
Shares pursuant to a registration statement covering the resale of such Shares, while such registration statement is effective under the Securities Act, (ii) any sale of such Shares pursuant to Rule 144 or (iii) the expiration of the
Standstill Term (as defined in the Investor Agreement), the Lock-Up Term (as defined in the Investor Agreement) and the Voting Agreement (as defined in the Investor Agreement); provided that any transfer described in clause (i) or
(ii) above shall have been in compliance with all applicable provisions of the Investor Agreement. 
 (c) The Company agrees that at
such time as any legend set forth in Section 5.10 is no longer required under this Section 10.5, the Company will, no later than three (3) Business Days following the delivery by the Investor to the Company or the Company’s
transfer agent (the “Transfer Agent”) of a certificate representing Shares issued with such legend, deliver or cause to be delivered to the Investor a certificate representing such Shares that is free from such legend, or, in the
event that such shares are uncertificated, remove any such legend in the Company’s stock records. The Company may not make any notation on its records or give instructions to the Transfer Agent that enlarge the restrictions on transfer set
forth in Section 5.10. 

  
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 10.6 Conduct of Business. During the period from the date hereof until the Closing, except
as consented to in writing by the Investor, the Company shall not (i) declare, set aside or pay any dividend or make any other distribution or payment (whether in cash, stock or property or any combination thereof) in respect of its capital
stock, or establish a record date for any of the foregoing, or (ii) make any other actual, constructive or deemed distribution in respect of any shares of its capital stock or otherwise make any payments to stockholders in their capacity as
such, except pursuant to repurchases of equity pursuant to the terms of its equity compensation plans. 
 11. Miscellaneous. 

11.1 Governing Law; Submission to Jurisdiction. This Agreement shall be governed by and construed in accordance with the Laws of the
State of Delaware, without regard to the conflict of laws principles thereof that would require the application of the Law of any other jurisdiction. Any action brought, arising out of, or relating to this Agreement shall be brought in the Court of
Chancery of the State of Delaware. Each party hereby irrevocably submits to the exclusive jurisdiction of said Court in respect of any claim relating to the validity, interpretation and enforcement of this Agreement, and hereby waives, and agrees
not to assert, as a defense in any action, suit or proceeding in which any such claim is made that it is not subject thereto or that such action, suit or proceeding may not be brought or is not maintainable in such courts, or that the venue thereof
may not be appropriate or that this agreement may not be enforced in or by such courts. The parties hereby consent to and grant the Court of Chancery of the State of Delaware jurisdiction over such parties and over the subject matter of any such
claim and agree that mailing of process or other papers in connection with any such action, suit or proceeding in the manner provided in Section 11.3 or in such other manner as may be permitted by law, shall be valid and sufficient thereof.

 11.2 Waiver. Waiver by a party of a breach hereunder by the other party shall not be construed as a waiver of any subsequent
breach of the same or any other provision. No delay or omission by a party in exercising or availing itself of any right, power or privilege hereunder shall preclude the later exercise of any such right, power or privilege by such party. No waiver
shall be effective unless made in writing with specific reference to the relevant provision(s) of this Agreement and signed by a duly authorized representative of the party granting the waiver. 

  
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 11.3 Notices. All notices, instructions and other communications hereunder or in
connection herewith shall be in writing, shall be sent to the address of the relevant party set forth on Exhibit B attached hereto and shall be (a) delivered personally, (b) sent by registered or certified mail, return receipt requested,
postage prepaid, (c) sent via a reputable nationwide overnight courier service or (d) sent by facsimile transmission or electronic mail, with a confirmation copy to be sent by registered or certified mail, return receipt requested, postage
prepaid. Any such notice, instruction or communication shall be deemed to have been delivered upon receipt if delivered by hand, three (3) Business Days after it is sent by registered or certified mail, return receipt requested, postage
prepaid, one (1) Business Day after it is sent via a reputable nationwide overnight courier service or when transmitted with electronic confirmation of receipt, if transmitted by facsimile or electronic mail (if such transmission is made during
regular business hours of the recipient on a Business Day; or otherwise, on the next Business Day following such transmission). Either party may change its address by giving notice to the other party in the manner provided above. 

11.4 Entire Agreement. This Agreement, the Investor Agreement (once executed) and the Collaboration Agreement, contain the entire
agreement among the parties with respect to the subject matter hereof and thereof and supersede all prior and contemporaneous arrangements or understandings, whether written or oral, with respect hereto and thereto. 

11.5 Amendments. No provision in this Agreement shall be supplemented, deleted or amended except in a writing executed by an authorized
representative of each of the Investor and the Company. 
 11.6 Headings; Nouns and Pronouns; Section References. Headings in this
Agreement are for convenience of reference only and shall not be considered in construing this Agreement. Whenever the context may require, any pronouns used herein shall include the corresponding masculine, feminine or neuter forms, and the
singular form of names and pronouns shall include the plural and vice-versa. References in this Agreement to a section or subsection shall be deemed to refer to a section or subsection of this Agreement unless otherwise expressly stated. 

11.7 Severability. If, under applicable Laws, any provision hereof is invalid or unenforceable, or otherwise directly or indirectly
affects the validity of any other material provision(s) of this Agreement in any jurisdiction (“Modified Clause”), then, it is mutually agreed that this Agreement shall endure and that the Modified Clause shall be enforced in such
jurisdiction to the maximum extent permitted under applicable Laws in such jurisdiction; provided that the parties shall consult and use all reasonable efforts to agree upon, and hereby consent to, any valid and enforceable modification of this
Agreement as may be necessary to avoid any unjust enrichment of either party and to match the intent of this Agreement as closely as possible, including the economic benefits and rights contemplated herein. 

11.8 Assignment. Except for an assignment of this Agreement or any rights hereunder by the Investor to an Affiliate, neither this
Agreement nor any of the rights or obligations hereunder may be assigned by either the Investor or the Company without (a) the prior written consent of Company in the case of any assignment by the Investor or (b) the prior written consent
of the Investor in the case of an assignment by the Company. 

  
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 11.9 Successors and Assigns. This Agreement shall be binding upon and inure to the benefit
of the parties hereto and their respective successors and permitted assigns. 
 11.10 Counterparts. This Agreement may be executed in
counterparts, each of which shall be deemed an original but which together shall constitute one and the same instrument. 
 11.11 Third
Party Beneficiaries. None of the provisions of this Agreement shall be for the benefit of or enforceable by any Third Party, including any creditor of any party hereto. No Third Party shall obtain any right under any provision of this Agreement
or shall by reason of any such provision make any claim in respect of any debt, liability or obligation (or otherwise) against any party hereto. 

11.12 No Strict Construction. This Agreement has been prepared jointly and will not be construed against either party. 

11.13 Survival of Warranties. The representations and warranties of the Company and the Investor contained in this Agreement shall
survive the Closing and the delivery of the Shares. 
 11.14 Remedies. The rights, powers and remedies of the parties under this
Agreement are cumulative and not exclusive of any other right, power or remedy which such parties may have under any other agreement or Law. No single or partial assertion or exercise of any right, power or remedy of a party hereunder shall preclude
any other or further assertion or exercise thereof. 
 11.15 Expenses. Each party shall pay its own fees and expenses in connection
with the preparation, negotiation, execution and delivery of the Transaction Agreements. 
 11.16 No Publicity. The parties hereto
agree that the provisions of Section 11.5 of the Collaboration Agreement shall be applicable to the parties to this Agreement with respect to any public disclosures regarding the proposed transactions contemplated by the Purchase Agreement and
the Collaboration Agreement or regarding the parties hereto or their Affiliates (it being understood that the provisions of Section 11.5 of the Collaboration Agreement shall be read to apply to disclosures of information relating to this
Agreement and the transactions contemplated hereby). 
 11.17 Limitation of Liability. IN NO EVENT WILL EITHER PARTY BE LIABLE TO THE
OTHER PARTY (OR THE OTHER PARTY’S AFFILIATES OR SUBLICENSEES) IN CONNECTION WITH THIS AGREEMENT FOR LOST REVENUE, LOST PROFITS, LOST SAVINGS, LOSS OF USE, DAMAGE TO GOODWILL, OR ANY CONSEQUENTIAL, INCIDENTAL, SPECIAL, EXEMPLARY, PUNITIVE OR
INDIRECT DAMAGES UNDER ANY THEORY, INCLUDING CONTRACT, NEGLIGENCE, OR STRICT LIABILITY, EVEN IF THAT PARTY HAS BEEN PLACED ON NOTICE OF THE POSSIBILITY OF SUCH DAMAGES. 

  
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 (Signature Page Follows) 

  
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 IN WITNESS WHEREOF, the parties have executed and delivered this Agreement as of the date first
above written. 
  

					
	JOHNSON & JOHNSON INNOVATION-JJDC, INC.
		
	By:	 	 Marian T. Nakada

		 	Name:	 	Marian T. Nakada
		 	Title:	 	VP Venture Investments
	
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	 /s/ Milind Deshpande

	Name:	 	Milind Deshpande
	Title:	 	President & CEO


 (Signature Page to Stock Purchase Agreement) 







 EXHIBIT A 

FORM OF INVESTOR AGREEMENT 
 Incorporated
by reference to Exhibit 10.4 to the Company’s Quarterly Report on Form 10-Q for the fiscal period ended June 30, 2015