Document:

Form of Common Stock Warrant

 EXHIBIT 10.14 
 NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH RULE 144 UNDER SAID
ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL FOR HOLDER, SATISFACTORY TO COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE
COMMISSION. 
 WARRANT TO PURCHASE 21,368 SHARES OF COMMON STOCK 
 February 26, 2008 
 THIS CERTIFIES THAT, for value received, Oxford Finance Corporation
(“Holder”) is entitled to subscribe for and purchase Twenty-One Thousand Three Hundred Sixty-Eight (21,368) shares of fully paid and nonassessable Common Stock of Achillion Pharmaceuticals, Inc., a Delaware corporation (the
“Company”), at the Warrant Price (as hereinafter defined), subject to the provisions and upon the terms and conditions hereinafter set forth. As used herein, the term “Common Stock” shall mean Company’s presently
authorized common stock and any stock into which such common stock may hereafter be converted or exchanged and the term “Warrant Shares” shall mean the shares of Common Stock which Holder may acquire pursuant to this Warrant and any other
shares of stock into which such shares of Common Stock may hereafter be converted or exchanged. 
 1. Warrant Price. The “Warrant
Price” shall initially be Four and 68/100 dollars ($4.68) per share, subject to adjustment as provided in Section 7 below. 
 2.
Conditions to Exercise. The purchase right represented by this Warrant may be exercised at any time, or from time to time, in whole or in part during the term commencing on the date hereof and ending at 5:00 P.M. Pacific time on the
tenth anniversary of the date of this Warrant (the “Expiration Date”). 
 3. Method of Exercise or Conversion; Payment; Issuance of
Shares; Issuance of New Warrant. 
 (a) Cash Exercise. Subject to Section 2 hereof, the purchase right represented by this
Warrant may be exercised by Holder hereof, in whole or in part, by the surrender of this Warrant (with a duly executed Notice of Exercise in the form attached hereto) at the principal office of Company (as set forth in Section 19 below) and by
payment to Company, by check, of an amount equal to the then applicable Warrant Price per share multiplied by the number of shares then being purchased. In the event of any exercise of the rights represented by this Warrant, certificates for the
shares of stock so purchased shall be in the name of, and delivered to, Holder hereof, or as such Holder may direct (subject to the terms of transfer contained herein and upon payment by such Holder hereof of any applicable transfer taxes). Such
delivery shall be made within 30 days after exercise of this Warrant and at Company’s expense and, unless this Warrant has been fully exercised or expired, a new Warrant having terms and conditions substantially identical to this Warrant
and representing the portion of the Shares, if any, with respect to which this Warrant shall not have been exercised, shall also be issued to Holder hereof within 30 days after exercise of this Warrant. 

 (b) Conversion. In lieu of exercising this Warrant as specified in Section 3(a), Holder may
from time to time convert this Warrant, in whole or in part, into Warrant Shares by surrender of this Warrant (with a duly executed Notice of Exercise in the form attached hereto) at the principal office of Company, in which event Company shall
issue to Holder the number of Warrant Shares computed using the following formula: 
  

							
	X	 	=	 	Y (A-B)	  	
		 		 	A	  	
	
	Where:
			
	X	 	=	 	the number of Warrant Shares to be issued to Holder.
			
	Y	 	=	 	the number of Warrant Shares purchasable under this Warrant (at the date of such calculation).
			
	A	 	=	 	the Fair Market Value of one share of Company’s Common Stock (at the date of such calculation).
			
	B	 	=	 	Warrant Price (as adjusted to the date of such calculation).

 (c) Fair Market Value. For purposes of this Section 3, Fair Market Value of one share
of Company’s Common Stock shall mean: 
 (i) If Company’s common stock is listed on the Nasdaq Global Market or another national
securities exchange, the average of the high and low sale prices of Common Stock quoted on the Nasdaq Global Market or on any other national securities exchange on which the Common Stock is listed for the three (3) trading days prior to
the date of exercise; or 
 (ii) In the event of an exercise in connection with a merger, acquisition or other consolidation in which Company
is not the surviving entity, the per share Fair Market Value for the Common Stock shall be the value to be received per share of Common Stock by all holders of the Common Stock in such transaction as determined by the Board of Directors; or

 (iii) In any other instance, the per share Fair Market Value for the Common Stock shall be as determined in the reasonable good faith
judgment of Company’s Board of Directors. 
 In the event of 3(c)(ii) or 3(c)(iii), above, Company’s Board of Directors shall
prepare a certificate, to be signed by an authorized officer of Company, setting forth in reasonable detail the basis for and method of determination of the per share Fair Market Value of the Common Stock. The Board of Directors will also certify to
Holder that this per share Fair Market Value will be applicable to all holders of Company’s Common Stock. Such certification must be made to Holder at least thirty (30) business days prior to the proposed effective date of the merger,
consolidation, sale, or other triggering event as defined in 3(c)(ii) or 3(c)(iii). 
 (d) Automatic Exercise. To the extent this
Warrant is not previously exercised, it shall be automatically exercised in accordance with Sections 3(b) and 3(c) hereof (even if not surrendered) immediately before its expiration, involuntary termination or cancellation unless Holder
notifies Company in writing to the contrary prior to such automatic exercise. 
  

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 (e) Treatment of Warrant Upon Acquisition of Company. 
 (i) Certain Definitions. For the purpose of this Warrant, “Acquisition” means any sale, license, or other disposition of all or
substantially all of the assets of Company, or any reorganization, consolidation, or merger of Company, or sale of Company securities, where the holders of Company’s securities before the transaction beneficially own less than 50% of the
outstanding voting securities of the surviving entity after the transaction, and “Affiliate” shall mean any person or entity that owns or controls directly or indirectly ten (10) percent or more of the stock of Company, any person or
entity that controls or is controlled by or is under common control with such persons or entities, and each of such person’s or entity’s officers, directors, joint venturers or partners, as applicable. 
 (ii) Cash Acquisition. In the event of an Acquisition in which the sole consideration is cash, Holder may either (a) exercise its conversion
or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) permit the Warrant to expire upon the consummation of such Acquisition. Company shall provide
Holder with written notice of any proposed Acquisition together with such reasonable information as 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) business days prior to the closing of the proposed Acquisition. 
 (iii) Asset Sale. In the event of an Acquisition that is
an arms length sale of all or substantially all of Company’s assets (and only its assets) to a third party that is not an Affiliate of Company (a “True Asset Sale”), Holder may either (a) exercise its conversion or
purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) permit the Warrant to continue until the Expiration Date if Company continues as a going concern
following the closing of any such True Asset Sale. Company shall provide Holder with written notice of any proposed asset sale together with such reasonable information as Holder may request in connection with such asset sale giving rise to such
notice, which is to be delivered to Holder not less than ten (10) business days prior to the closing of the proposed asset sale. 
 (iv)
Assumption of Warrant. Upon the closing of any Acquisition other than those particularly described in subsections (ii) and (iii) above, the successor entity shall assume the obligations of this Warrant, and this Warrant shall be
exercisable for the same securities, cash, and property as would be payable for the Warrant Shares issuable upon exercise of the unexercised portion of this Warrant as if such Warrant Shares were outstanding on the record date for the Acquisition
and subsequent closing. The Warrant Price and/or number of Warrant Shares shall be adjusted accordingly. 
 4. Representations and Warranties of Holder
and Company. 
 (a) Representations and Warranties by Holder. Holder represents and warrants to Company with respect to this
purchase as follows: 
 (i) Evaluation. Holder has substantial experience in evaluating and investing in private placement transactions
of securities of companies similar to Company so that Holder is capable of evaluating the merits and risks of its investment in Company and has the capacity to protect its interests. 
 (ii) Resale. Except for transfers to an affiliate of Holder, Holder is acquiring this Warrant 

  

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and the Warrant Shares issuable upon exercise of this Warrant (collectively the “Securities”) for investment for its own account and not
with a view to, or for resale in connection with, any distribution thereof. Holder understands that the Securities have not been registered under the Securities Act of 1933, as amended (the “Act”) by reason of a specific exemption
from the registration provisions of the Act which depends upon, among other things, the bona fide nature of the investment intent as expressed herein. 
 (iii) Rule 144. Holder acknowledges that the Securities must be held indefinitely unless subsequently registered under the Act or an exemption from such registration is available. Holder is aware of the
provisions of Rule 144 promulgated under the Act. 
 (iv) Accredited Investor. Holder is an “accredited investor” within
the meaning of Regulation D promulgated under the Act. 
 (v) Opportunity To Discuss. Holder has had an opportunity to discuss
Company’s business, management and financial affairs with its management and an opportunity to review Company’s facilities. Holder understands that such discussions, as well as the written information issued by Company, were intended to
describe the aspects of Company’s business and prospects which Company believes to be material but were not necessarily a thorough or exhaustive description. 
 (b) Representations and Warranties by Company. Company hereby represents and warrants to Holder that the statements in the following paragraphs of this Section 4(b) are true and correct (a) as of the
date hereof and (b) except where any such representation and warranty relates specifically to an earlier date, as of the date of any exercise of this Warrant. 
 (i) Corporate Organization and Authority. Company (a) is a corporation duly organized, validly existing, and in good standing in its jurisdiction of incorporation, (b) has the corporate power and
authority to own and operate its properties and to carry on its business as now conducted and as proposed to be conducted; and (c) is qualified as a foreign corporation in all jurisdictions where such qualification is required. 
 (ii) Corporate Power. Company has all requisite legal and corporate power and authority to execute, issue and deliver this Warrant, to issue the
Warrant Shares issuable upon exercise or conversion of this Warrant, and to carry out and perform its obligations under this Warrant and any related agreements. 
 (iii) Authorization; Enforceability. All corporate action on the part of Company, its officers, directors and shareholders necessary for the authorization, execution, delivery and performance of its obligations
under this Warrant and for the authorization, issuance and delivery of this Warrant and the Warrant Shares issuable upon exercise of this Warrant has been taken and this Warrant constitutes the legally binding and valid obligation of Company
enforceable in accordance with its terms. 
 (iv) Valid Issuance of Warrant and Warrant Shares. This Warrant has been validly issued
and is free of restrictions on transfer other than restrictions on transfer set forth herein and under applicable state and federal securities laws. The Warrant Shares issuable upon conversion of this Warrant, when issued, sold and delivered in
accordance with the terms of this Warrant for the consideration expressed herein, will be duly and validly issued, fully paid and nonassessable, and will be free of restrictions on transfer other than restrictions on transfer under this Warrant and
under applicable state and federal securities laws. Subject to 

  

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applicable restrictions on transfer, the issuance and delivery of this Warrant and the Warrant Shares issuable upon exercise or conversion of this Warrant
are not subject to any preemptive or other similar rights or any liens or encumbrances except as specifically set forth in Company’s Certificate of Incorporation or this Warrant. The offer, sale and issuance of the Warrant Shares, as
contemplated by this Warrant, are exempt from the prospectus and registration requirements of applicable United States federal and state security laws, and neither Company nor any authorized agent acting on its behalf has or will take any action
hereafter that would cause the loss of such exemption. 
 (v) No Conflict. The execution, delivery, and performance of this Warrant
will not result in (a) any violation of, be in conflict with, or constitute a default under, with or without the passage of time or the giving of notice (1) any provision of Company’s Certificate of Incorporation or by-laws;
(2) any provision of any judgment, decree, or order to which Company is a party, by which it is bound, or to which any of its material assets are subject; (3) any contract, obligation, or commitment to which Company is a party or by which
it is bound; or (4) any statute, rule, or governmental regulation applicable to Company, or (b) the creation of any lien, charge or encumbrance upon any assets of Company. 
 (vi) Reports. Company has previously furnished or made available to Holder complete and accurate copies, as amended or supplemented, of its
(a) Annual Report on Form 10-K for the fiscal year ended December 31, 2006, as filed with the Securities and Exchange Commission (the “SEC”), and (b) all other reports filed by Company under Section 13
or subsections (a) or (c) of Section 14 of the Securities Exchange Act of 1934 (as amended, the “Exchange Act”) with the SEC since December 31, 2006 (such reports are collectively referred to herein as
the “Company Reports”). The Company Reports constitute all of the documents required to be filed by Company under Section 13 or subsections (a) or (c) of Section 14 of the Exchange Act with the SEC from
December 31, 2006 through the date of this Warrant. 
 5. Legends. 
 (a) Legend. Each certificate representing the Warrant Shares shall be endorsed with the following legend: 
 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 AND MAY NOT BE TRANSFERRED UNLESS COVERED BY AN EFFECTIVE REGISTRATION
STATEMENT UNDER SAID ACT, A “NO ACTION” LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER MEETING THE REQUIREMENTS OF RULE 144 OF THE SECURITIES AND EXCHANGE COMMISSION, OR (IF REASONABLY
REQUIRED BY COMPANY) AN OPINION OF COUNSEL SATISFACTORY TO COMPANY TO THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 Company need not enter into its stock records a transfer of Warrant Shares unless the conditions specified in the foregoing legend are satisfied. Company may also instruct its transfer agent not to allow the transfer of any of the Warrant
Shares unless the conditions specified in the foregoing legend are satisfied. 
 (b) Removal of Legend and Transfer Restrictions. The
legend relating to the Act endorsed on a certificate pursuant to paragraph 5(a) of this Warrant shall be removed and Company shall issue a certificate without such legend to Holder if (i) the Securities are registered under the Act and a
prospectus meeting the requirements of Section 10 of the Act is available or (ii) Holder provides to 

  

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Company an opinion of counsel for Holder reasonably satisfactory to Company, a no-action letter or interpretive opinion of the staff of the SEC reasonably
satisfactory to Company, or other evidence reasonably satisfactory to Company, to the effect that public sale, transfer or assignment of the Securities may be made without registration and without compliance with any restriction such as
Rule 144. 
 6. Condition of Transfer or Exercise of Warrant. It shall be a condition to any transfer or exercise of this Warrant that at the
time of such transfer or exercise, Holder shall provide Company with a representation in writing that Holder or transferee is acquiring this Warrant and the shares of Common Stock to be issued upon exercise for investment purposes only and not with
a view to any sale or distribution, or will provide Company with a statement of pertinent facts covering any proposed distribution. As a further condition to any transfer of this Warrant or any or all of the shares of Common Stock issuable upon
exercise of this Warrant, other than a transfer registered under the Act, Company may request a legal opinion, in form and substance satisfactory to Company and its counsel, reciting the pertinent circumstances surrounding the proposed transfer and
stating that such transfer is exempt from the registration and prospectus delivery requirements of the Act. Company shall not require Holder to provide an opinion of counsel if the transfer is to an affiliate of Holder. Each certificate evidencing
the Warrant Shares issued upon exercise of this Warrant or upon any transfer of the Warrant Shares (other than a transfer registered under the Act or any subsequent transfer of shares so registered) shall, at Company’s option, if the Warrant
Shares are not freely saleable under Rule 144(b)(1)(ii) under the Act, contain a legend in form and substance satisfactory to Company and its counsel, restricting the transfer of the Warrant Shares to sales or other dispositions exempt from the
requirements of the Act. As further condition to each transfer, at the request of Company, Holder shall surrender this Warrant to Company and the transferee shall receive and accept a Warrant, of like tenor and date, executed by Company. 

7. Adjustment for Certain Events. The number and kind of securities purchasable upon the exercise of this Warrant and the Warrant Price shall be subject to
adjustment from time to time upon the occurrence of certain events, as follows: 
 (a) Reclassification or Merger. In case of
(i) any reclassification or change of securities of the class issuable upon exercise of this Warrant (other than a change in par value, or from par value to no par value, or from no par value to par value, or as a result of a subdivision or
combination), (ii) any merger of Company with or into another corporation (other than a merger with another corporation in which Company is the acquiring and the surviving corporation and which does not result in any reclassification or change
of outstanding securities issuable upon exercise of this Warrant), or (iii) any sale of all or substantially all of the assets of Company, Company, or such successor or purchasing corporation, as the case may be, shall duly execute and deliver
to Holder a new Warrant (in form and substance satisfactory to Holder of this Warrant), or Company shall make appropriate provision without the issuance of a new Warrant, so that Holder shall have the right to receive, at a total purchase price not
to exceed that payable upon the exercise of the unexercised portion of this Warrant, and in lieu of the Warrant Shares theretofore issuable upon exercise or conversion of this Warrant, the kind and amount of shares of stock, other securities, money
and property receivable upon such reclassification, change, merger or sale by a holder of the number of shares of Common Stock then purchasable under this Warrant, or in the case of such a merger or sale in which the consideration paid consists all
or in part of assets other than securities of the successor or purchasing corporation, at the option of Holder, the securities of the successor or purchasing corporation having a value at the time of the transaction equivalent to the value of the
Warrant Shares purchasable upon exercise of this Warrant at the time of the transaction. Any new Warrant shall provide for adjustments that shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section 7.
The provisions of this subparagraph (a) shall similarly apply to successive reclassifications, changes, mergers and transfers. 
  

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 (b) Stock Splits and Combinations of Common Stock. If outstanding shares of Company’s Common
Stock shall be subdivided into a greater number of shares or a dividend in Common Stock shall be paid in respect of Common Stock, the Warrant Price in effect immediately prior to such subdivision or at the record date of such dividend shall
simultaneously with the effectiveness of such subdivision or immediately after the record date of such dividend be proportionately reduced and if outstanding shares of Common Stock shall be combined into a smaller number of shares, the Warrant Price
with respect to such shares of Common Stock in effect immediately prior to such combination shall, simultaneously with the effectiveness of such combination, be proportionately increased. When any adjustment is required to be made in the Warrant
Price pursuant to this Section 7(b), the number of Shares purchasable upon the exercise of this Warrant shall be changed to the number determined by dividing (i) an amount equal to the number of shares issuable upon the exercise of this
Warrant immediately prior to such adjustment, by (ii) the Warrant Price in effect immediately after such adjustment. 
 8. Notice of Adjustments.
Whenever any Warrant Price or the kind or number of securities issuable under this Warrant shall be adjusted pursuant to Section 7 hereof, Company shall prepare a certificate signed by an officer of Company setting forth, in reasonable detail,
the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the Warrant Price and number or kind of shares issuable upon exercise of this Warrant after giving effect to such adjustment,
and shall cause copies of such certificate to be mailed (by certified or registered mail, return receipt required, postage prepaid) within thirty (30) days of such adjustment to Holder as set forth in Section 19 hereof. 
 9. Financial and Other Reports. From time to time up to the earlier of the Expiration Date or the complete exercise of this Warrant, Company shall furnish to
Holder (i) within 90 days after the close of each fiscal year of Company an audited balance sheet and statement of changes in financial position at and as of the end of such fiscal year, together with an audited statement of income for such
fiscal year; and (ii) within 45 days after the close of each fiscal quarter of Company, an unaudited balance sheet and statement of cash flows at and as of the end of such quarter, together with an unaudited statement of income for such
quarter; provided, however, that so long as Company remains subject to and in compliance with the Exchange Act, Company will be deemed to have complied with such requirements upon the timely filing of annual and quarterly reports as required by the
Exchange Act. 
 10. Transferability of Warrant. This Warrant is transferable on the books of Company at its principal office by the registered Holder
hereof upon surrender of this Warrant properly endorsed, subject to compliance with Section 6 and applicable federal and state securities laws. Company shall issue and deliver to the transferee a new Warrant representing the Warrant so
transferred. Upon any partial transfer, Company will issue and deliver to Holder a new Warrant with respect to the Warrant not so transferred. Holder shall not have any right to transfer any portion of this Warrant to any direct competitor of
Company. 
 11. No Fractional Shares. No fractional share of Common Stock will be issued in connection with any exercise or conversion hereunder, but
in lieu of such fractional share Company shall make a cash payment therefor upon the basis of the Warrant Price then in effect. 
 12. Charges, Taxes and
Expenses. Issuance of certificates for shares of Common Stock upon the exercise or conversion of this Warrant shall be made without charge to Holder for any United States or state of the United States documentary stamp tax or other incidental
expense with respect to the issuance of such certificate, all of which taxes and expenses shall be paid by Company, and such certificates shall be issued in the name of Holder. 
  

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 13. No Shareholder Rights Until Exercise. Except as expressly provided herein, this Warrant does not entitle
Holder to any voting rights or other rights as a shareholder of Company prior to the exercise hereof. 
 14. Registry of Warrant. Company shall
maintain a registry showing the name and address of the registered Holder of this Warrant. This Warrant may be surrendered for exchange or exercise, in accordance with its terms, at such office or agency of Company. 
 16. Loss, Theft, Destruction or Mutilation of Warrant. Upon receipt by Company of evidence reasonably satisfactory to it of the loss, theft, destruction or
mutilation of this Warrant, and, in the case of loss, theft, or destruction, of indemnity reasonably satisfactory to it, and, if mutilated, upon surrender and cancellation of this Warrant, Company will execute and deliver a new Warrant, having terms
and conditions substantially identical to this Warrant, in lieu hereof. 
 17. Miscellaneous. 
 (a) Issue Date. The provisions of this Warrant shall be construed and shall be given effect in all respect as if it had been issued and delivered
by Company on the date hereof. 
 (b) Successors. This Warrant shall be binding upon any successors or assigns of Company. 

(c) Headings. The headings used in this Warrant are used for convenience only and are not to be considered in construing or interpreting this
Warrant. 
 (d) Saturdays, Sundays, Holidays. 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 or a Sunday or shall be a legal holiday in the State of Connecticut, then such action may be taken or such right may be exercised on the next succeeding day not a legal holiday. 
 (e) Attorney’s Fees. In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the party prevailing
in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorney’s fees. 
 18. No
Impairment. Company will not, by amendment of its Certificate of Incorporation or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms of this Warrant, but will at all times in good faith assist in
the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of Holder hereof against impairment. 
 19. Addresses. Any notice required or permitted hereunder shall be in writing and shall be mailed by overnight courier, registered or certified mail, return receipt requested, and postage prepaid, or otherwise
delivered by hand or by messenger, addressed as set forth below, or at such other address as Company or Holder hereof shall have furnished to the other party in accordance with the delivery instructions set forth in this Section 19. 

 

					
	If to Company:	 	Achillion Pharmaceuticals, Inc.
		 	300 George Street
		 	New Haven, CT 06511
		 	Attn: Mary Kay Fenton, Chief Financial Officer

  

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	With a copy to:	 	Wilmer Cutler Pickering Hale and Dorr, LLP
		 	WilmerHale Venture Group
		 	Bay Colony Corporate Center
		 	 1100 Winter Street
 Waltham, MA
02451

		 	Attn: Susan Mazur, Esq.
		
	If to Holder:	 	Oxford Finance Corporation
		 	 133 North Fairfax Street
 Alexandria, VA
22314

		 	Attention:	 	Timothy A. Lex
		 		 	Executive Vice President & Chief Operating Officer

 If mailed by registered or certified mail, return receipt requested, and postage prepaid, notice
shall be deemed to be given five (5) days after being sent, and if sent by overnight courier, by hand or by messenger, notice shall be deemed to be given when delivered (if on a business day, and if not, on the next business day). 

20. WAIVER OF JURY TRIAL. EACH OF THE PARTIES HERETO HEREBY WAIVES TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY RIGHT IT MAY HAVE TO A TRIAL BY JURY
IN RESPECT OF ANY LITIGATION DIRECTLY OR INDIRECTLY ARISING OUT OF, UNDER OR IN CONNECTION WITH THIS WARRANT OR THE WARRANT SHARES. 
 21. GOVERNING
LAW. THIS WARRANT SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF DELAWARE. 
  

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

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	  

	Name:	 	Mary Kay Fenton
	Title:	 	Chief Financial Officer
	
	Dated as of February 26, 2008.

 SIGNATURE PAGE 
 OXFORD WARRANT 

 NOTICE OF EXERCISE 
  

			
	To:	 	
	Achillion Pharmaceuticals, Inc.
	 300 George Street
 New Haven, CT
06511

	Attn:	 	Mary Kay Fenton, Chief Financial Officer

  

	1.	The undersigned Warrantholder (“Holder”) elects to acquire shares of the Common Stock (the “Common Stock”) of Achillion Pharmaceuticals, Inc. (the
“Company”), pursuant to the terms of the Stock Purchase Warrant dated February 26, 2008 (the “Warrant”). 

  

	2.	Holder exercises its rights under the Warrant as set forth below: 

  

	 	(            )	Holder elects to purchase                      shares of Common Stock as
provided in Section 3(a) and tenders herewith a check in the amount of $                     as payment of the purchase price.

  

	 	(            )	Holder elects to convert the purchase rights into shares of Common Stock as provided in Section 3(b) of the Warrant. 

  

	3.	Holder surrenders the Warrant with this Notice of Exercise. 

 Holder
represents that it is acquiring the aforesaid shares of Common Stock for investment and not with a view to or for resale in connection with distribution and that Holder has no present intention of distributing or reselling the shares. 
 Please issue a certificate representing the shares of the Common Stock in the name of Holder or in such other name as is specified below: 
  

					
	Name:	 	  
	 	
	Address:	 	  
	 	
	Taxpayer I.D.:	 	  
	 	

  

			
	OXFORD FINANCE CORPORATION
	By:	 	  

	Name:	 	  

	Title:	 	  

	Date:	 	                 ,200Promissory Notes & Master Security Agreement

 Exhibit 10.28 
 PROMISSORY NOTE 
 June 30, 2003 
 (Date) 
 FOR VALUE RECEIVED, Achillion Pharmaceuticals, Inc., a corporation located at
the address stated below (“Maker”) promises, jointly and severally if more than one, to pay to the order of Webster Bank or any subsequent holder hereof (each, a “Payee”) at its office located at 80 Elm
Street, New Haven, CT 06510 or at such other place as Payee or the holder hereof may designate, the principal sum of one hundred ten thousand, two hundred seventy-two dollars and four cents ($110,272.04), pursuant to that certain Master
Security Agreement (“MSA”) by and between Webster Bank and Achillion Pharmaceuticals, Inc., dated as of May 15, 2003 as amended, and in effect from time to time, together with interest on the unpaid principal balance, from the
date hereof through and including the dates of payment, at a fixed interest rate of 6.72% per annum, to be paid in lawful money of the United States, in thirty-six (36) consecutive monthly installments of principal and interest as follows:

  

			
	 Periodic Installment
	  	 Amount

	 1-36
	  	$3,372.12

 each (“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest. The first Periodic Installment shall be due and payable on July 1, 2003 and the following Periodic Installments and the final installment shall be due and payable on the first day of each succeeding month
(each, a “Payment Date”); notwithstanding the foregoing, in the event this Note is dated other than the first day of a month, the interest accruing from the date hereof through and including the date of the first Periodic
Installment shall be paid in addition to, and together with, the first Periodic Installment. The Periodic Installments have been calculated on the basis of a 360 day year of twelve 30-day months. Each payment may, at the option of the Payee, be
calculated and applied on an assumption that such payment would be made on its due date. All terms and conditions of the MSA are incorporated herein, except that in the event there are any conflicting terms and conditions, the terms and conditions
of this Note shall prevail. 
 The acceptance by Payee of any payment which is less than payment in full of all amounts due and owing at such time shall not
constitute a waiver of Payee’s right to receive payment in full at such time or at any prior or subsequent time. 
 The Maker hereby expressly
authorizes the Payee to insert the date value is actually given in the blank space on the face hereof and on all related documents pertaining hereto. 
 This
Note may be secured by a security agreement, chattel mortgage, pledge agreement or like instrument (each of which is hereinafter called a “Security Agreement”). 

 Time is of the essence hereof. If any installment or any other sum due under this Note or any Security Agreement is not
received within ten (10) days after its due date, the Maker agrees to pay, in addition to the amount of each such installment or other sum, a late payment charge of five percent (5%) of the amount of said installment or other sum, but not
exceeding any lawful maximum. If (i) Maker fails to make payment of any amount due hereunder within ten (10) days after the same becomes due and payable; or (ii) Maker is in default under, or fails to perform under any term or
condition contained in any Security Agreement, then the entire principal sum remaining unpaid, together with all accrued interest thereon and any other sum payable under this Note or any Security Agreement, at the election of Payee, shall
immediately become due and payable, with interest thereon at the lesser of eighteen percent (18%) per annum or the highest rate not prohibited by applicable law from the date of such accelerated maturity until paid (both before and after any
judgment). 
 The Maker may prepay its indebtedness hereunder, subject to a yield maintenance fee computed as follows. The current rate at the time of the
prepayment for US Treasury Bills with a maturity date closest to the maturity date of this Note shall be subtracted from the interest rate in effect at the time of the prepayment. If the result is zero or negative, there shall be no yield
maintenance fee. If the result is a positive number, then the resulting percentage shall be multiplied by the amount of the principal balance being repaid, divided by 360 and multiplied by the number of days remaining to the maturity date of this
Note. Said amount shall be reduced to present value by using the above-referenced US Treasury Bill rate and the number of days remaining to the maturity date of the term of this Note as of the date of repayment. The resulting amount is the yield
maintenance fee. 
 It is the intention of the parties hereto to comply with the applicable usury laws; accordingly, it is agreed that, notwithstanding any
provision to the contrary in this Note or any Security Agreement, in no event shall this Note or any Security Agreement require the payment or permit the collection of interest in excess of the maximum amount permitted by applicable law. If any such
excess interest is contracted for, charged or received under this Note or any Security Agreement, or if all of the principal balance shall be prepaid, so that under any of such circumstances the amount of interest contracted for, charged or received
under this Note or any Security Agreement on the principal balance shall exceed the maximum amount of interest permitted by applicable law, then in such event (a) the provisions of this paragraph shall govern and control, (b) neither Maker
nor any other person or entity now or hereafter liable for the payment hereof shall be obligated to pay the amount of such interest to the extent that it is in excess of the maximum amount of interest permitted by applicable law, (c) any such
excess which may have been collected shall be either applied as a credit against the then unpaid principal balance or refunded to Maker, at the option of the Payee, and (d) the effective rate of interest shall be automatically reduced to the
maximum lawful contract rate allowed under applicable law as now or hereafter construed by the courts having jurisdiction thereof. It is further agreed that without limitation of the foregoing, all calculations of the rate of interest contracted
for, charged or received under this Note or any Security Agreement which are made for the purpose of determining whether such rate exceeds the maximum lawful contract rate, shall be made, to the extent permitted by applicable law, by amortizing,
prorating, allocating and spreading in equal parts during the period of the full stated term of the indebtedness evidenced hereby, all interest at any time contracted for, charged or received from Maker or otherwise by Payee in connection with such
indebtedness; provided, however, that if any applicable state law is amended or the law of the United States of America preempts any applicable state law, so that it becomes lawful for the Payee to receive a greater interest per annum rate than is
presently 

 
allowed, the Maker agrees that, on the effective date of such amendment or preemption, as the case may be, the lawful maximum hereunder shall be increased to
the maximum interest per annum rate allowed by the amended state law or the law of the United States of America. 
 The Maker and all sureties, endorsers,
guarantors or any others (each such person, other than the Maker, an “Obligor”) who may at any time become liable for the payment hereof jointly and severally consent hereby to any and all extensions of time, renewals, waivers or
modifications of, and all substitutions or releases of, security or of any party primarily or secondarily liable on this Note or any Security Agreement or any term and provision of either, which may be made, granted or consented to by Payee, and
agree that suit may be brought and maintained against any one or more of them, at the election of Payee without joinder of any other as a party thereto, and that Payee shall not be required first to foreclose, proceed against, or exhaust any
security hereof in order to enforce payment of this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith,
as well as filing of suit (if permitted by law) and diligence in collecting this Note or enforcing any of the security hereof, and agrees to pay (if permitted by law) all expenses incurred in collection, including Payee’s actual attorneys’
fees. Maker and each Obligor agrees that fees not in excess of twenty percent (20%) of the amount then due shall be deemed reasonable. 
 THE MAKER
HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT
MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT
(INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL
APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE
MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 
 This Note and any Security Agreement constitute the entire agreement of the Maker and Payee
with respect to the subject matter hereof and supercedes all prior understandings, agreements and representations, express or implied. 
 No variation or
modification of this Note, or any waiver of any of its provisions or conditions, shall be valid unless in writing and signed by an authorized representative of Maker and Payee. Any such waiver, consent, modification or change shall be effective only
in the specific instance and for the specific purpose given. 

 Any provision in this Note or any Security Agreement which is in conflict with any statute, law or applicable rule shall
be deemed omitted, modified or altered to conform thereto. 
  

									
		 		 	Achillion Pharmaceuticals, Inc.
				
	/s/ Melissa Donnarummo	 		 	By:	 	/s/ Mary Kay Fenton
	(Witness)	 		 		 	
	Melissa Donnarummo	 		 	Name:	 	Mary Kay Fenton
	(Print Name)	 		 		 	
	300 George St., New Haven, CT 06511	 		 	Title:	 	Senior Director, Finance
	(Address)	 		 		 	
			
		 		 	Federal Tax ID#: 52-2113479
			
		 		 	 Address:  300 George Street, New Haven,
                  New Haven County, CT 06511

 PROMISSORY NOTE #2 
 September 26, 2003 
 (Date) 
 FOR VALUE RECEIVED, Achillion Pharmaceuticals, Inc., a corporation located at the address stated below (“Maker”) promises, jointly and severally if more than one, to pay to the order of
Webster Bank or any subsequent holder hereof (each, a “Payee”) at its office located at 80 Elm Street, New Haven, CT 06510 or at such other place as Payee or the holder hereof may designate, the principal sum of two
hundred thirty-nine thousand, two hundred forty-five dollars ($239,245.00), pursuant to that certain Master Security Agreement (“MSA”) by and between Webster Bank and Achillion Pharmaceuticals, Inc., dated as of May 15,
2003 as amended, and in effect from time to time, together with interest on the unpaid principal balance, from the date hereof through and including the dates of payment, at a fixed interest rate of 7.16% per annum, to be paid in lawful money
of the United States, in thirty-six (36) consecutive monthly installments of principal and interest as follows: 
  

			
	 Periodic Installment
	  	Amount
	 1-36
	  	$7,360.78

 each (“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest. The first Periodic Installment shall be due and payable on October 1, 2003 and the following Periodic Installments and the final installment shall be due and payable on the first day of each succeeding
month (each, a “Payment Date”); notwithstanding the foregoing, in the event this Note is dated other than the first day of a month, the interest accruing from the date hereof through and including the date of the first Periodic
Installment shall be paid in addition to, and together with, the first Periodic Installment. The Periodic Installments have been calculated on the basis of a 360 day year of twelve 30-day months. Each payment may, at the option of the Payee, be
calculated and applied on an assumption that such payment would be made on its due date. All terms and conditions of the MSA are incorporated herein, except that in the event there are any conflicting terms and conditions, the terms and conditions
of this Note shall prevail. 
 The acceptance by Payee of any payment which is less than payment in full of all amounts due and owing at such time shall not
constitute a waiver of Payee’s right to receive payment in full at such time or at any prior or subsequent time. 
 The Maker hereby expressly
authorizes the Payee to insert the date value is actually given in the blank space on the face hereof and on all related documents pertaining hereto. 
 This
Note may be secured by a security agreement, chattel mortgage, pledge agreement or like instrument (each of which is hereinafter called a “Security Agreement”). 
 Time is of the essence hereof. If any installment or any other sum due under this Note or any Security Agreement is not received within ten (10) days after its due date, the Maker agrees to 

 
pay, in addition to the amount of each such installment or other sum, a late payment charge of five percent (5%) of the amount of said installment or
other sum, but not exceeding any lawful maximum. If (i) Maker fails to make payment of any amount due hereunder within ten (10) days after the same becomes due and payable; or (ii) Maker is in default under, or fails to perform under
any term or condition contained in any Security Agreement, then the entire principal sum remaining unpaid, together with all accrued interest thereon and any other sum payable under this Note or any Security Agreement, at the election of Payee,
shall immediately become due and payable, with interest thereon at the lesser of eighteen percent (18%) per annum or the highest rate not prohibited by applicable law from the date of such accelerated maturity until paid (both before and after
any judgment). 
 The Maker may prepay its indebtedness hereunder, subject to a yield maintenance fee computed as follows. The current rate at the time of
the prepayment for US Treasury Bills with a maturity date closest to the maturity date of this Note shall be subtracted from the interest rate in effect at the time of the prepayment. If the result is zero or negative, there shall be no yield
maintenance fee. If the result is a positive number, then the resulting percentage shall be multiplied by the amount of the principal balance being repaid, divided by 360 and multiplied by the number of days remaining to the maturity date of this
Note. Said amount shall be reduced to present value by using the above-referenced US Treasury Bill rate and the number of days remaining to the maturity date of the term of this Note as of the date of repayment. The resulting amount is the yield
maintenance fee. 
 It is the intention of the parties hereto to comply with the applicable usury laws; accordingly, it is agreed that, notwithstanding any
provision to the contrary in this Note or any Security Agreement, in no event shall this Note or any Security Agreement require the payment or permit the collection of interest in excess of the maximum amount permitted by applicable law. If any such
excess interest is contracted for, charged or received under this Note or any Security Agreement, or if all of the principal balance shall be prepaid, so that under any of such circumstances the amount of interest contracted for, charged or received
under this Note or any Security Agreement on the principal balance shall exceed the maximum amount of interest permitted by applicable law, then in such event (a) the provisions of this paragraph shall govern and control, (b) neither Maker
nor any other person or entity now or hereafter liable for the payment hereof shall be obligated to pay the amount of such interest to the extent that it is in excess of the maximum amount of interest permitted by applicable law, (c) any such
excess which may have been collected shall be either applied as a credit against the then unpaid principal balance or refunded to Maker, at the option of the Payee, and (d) the effective rate of interest shall be automatically reduced to the
maximum lawful contract rate allowed under applicable law as now or hereafter construed by the courts having jurisdiction thereof. It is further agreed that without limitation of the foregoing, all calculations of the rate of interest contracted
for, charged or received under this Note or any Security Agreement which are made for the purpose of determining whether such rate exceeds the maximum lawful contract rate, shall be made, to the extent permitted by applicable law, by amortizing,
prorating, allocating and spreading in equal parts during the period of the full stated term of the indebtedness evidenced hereby, all interest at any time contracted for, charged or received from Maker or otherwise by Payee in connection with such
indebtedness; provided, however, that if any applicable state law is amended or the law of the United States of America preempts any applicable state law, so that it becomes lawful for the Payee to receive a greater interest per annum rate than is
presently 

 
allowed, the Maker agrees that, on the effective date of such amendment or preemption, as the case may be, the lawful maximum hereunder shall be increased to
the maximum interest per annum rate allowed by the amended state law or the law of the United States of America. 
 The Maker and all sureties, endorsers,
guarantors or any others (each such person, other than the Maker, an “Obligor”) who may at any time become liable for the payment hereof jointly and severally consent hereby to any and all extensions of time, renewals, waivers or
modifications of, and all substitutions or releases of, security or of any party primarily or secondarily liable on this Note or any Security Agreement or any term and provision of either, which may be made, granted or consented to by Payee, and
agree that suit may be brought and maintained against any one or more of them, at the election of Payee without joinder of any other as a party thereto, and that Payee shall not be required first to foreclose, proceed against, or exhaust any
security hereof in order to enforce payment of this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith,
as well as filing of suit (if permitted by law) and diligence in collecting this Note or enforcing any of the security hereof, and agrees to pay (if permitted by law) all expenses incurred in collection, including Payee’s actual attorneys’
fees. Maker and each Obligor agrees that fees not in excess of twenty percent (20%) of the amount then due shall be deemed reasonable. 
 THE MAKER
HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT
MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT
(INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL
APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE
MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 
 This Note and any Security Agreement constitute the entire agreement of the Maker and Payee
with respect to the subject matter hereof and supercedes all prior understandings, agreements and representations, express or implied. 
 No variation or
modification of this Note, or any waiver of any of its provisions or conditions, shall be valid unless in writing and signed by an authorized representative of Maker and Payee. Any such waiver, consent, modification or change shall be effective only
in the specific instance and for the specific purpose given. 

 Any provision in this Note or any Security Agreement which is in conflict with any statute, law or applicable rule shall
be deemed omitted, modified or altered to conform thereto. 
  

									
		 		 	Achillion Pharmaceuticals, Inc.
				
	 	 		 	By:	 	 
	(Witness)	 		 		 	
		 		 	Name:	 	
	(Print Name)	 		 		 	
		 		 	Title:	 	
	(Address)	 		 		 	
			
		 		 	Federal Tax ID#: 52-2113479
			
		 		 	 Address:  300 George Street, New Haven,
                  New Haven County, CT 06511

 PROMISSORY NOTE #3 
 October 29, 2004 
 (Date) 
 FOR VALUE RECEIVED, Achillion Pharmaceuticals, Inc., a corporation located at the address stated below (“Maker”) promises, jointly and severally if more than one, to pay to the order of
Webster Bank or any subsequent holder hereof (each, a “Payee”) at its office located at 80 Elm Street, New Haven, CT 06510 or at such other place as Payee or the holder hereof may designate, the principal sum of
ninety-two thousand, one hundred thirty-nine dollars and ninety cents ($92,139.90), pursuant to that certain Master Security Agreement (“MSA”) by and between Webster Bank and Achillion Pharmaceuticals, Inc., dated as of
May 15, 2003 as amended, and in effect from time to time, together with interest on the unpaid principal balance, from the date hereof through and including the dates of payment, at a fixed interest rate of 7.79% per annum, to be paid in
lawful money of the United States, in thirty-six (36) consecutive monthly installments of principal and interest as follows: 
  

			
	 Periodic Installment
	  	Amount
	 1-36
	  	$2,859.85

 each (“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest. The first Periodic Installment shall be due and payable on November 1, 2004 and the following Periodic Installments and the final installment shall be due and payable on the first day of each
succeeding month (each, a “Payment Date”); notwithstanding the foregoing, in the event this Note is dated other than the first day of a month, the interest accruing from the date hereof through and including the date of the first
Periodic Installment shall be paid in addition to, and together with, the first Periodic Installment. The Periodic Installments have been calculated on the basis of a 360 day year of twelve 30-day months. Each payment may, at the option of the
Payee, be calculated and applied on an assumption that such payment would be made on its due date. All terms and conditions of the MSA are incorporated herein, except that in the event there are any conflicting terms and conditions, the terms and
conditions of this Note shall prevail. 
 The acceptance by Payee of any payment which is less than payment in full of all amounts due and owing at such time
shall not constitute a waiver of Payee’s right to receive payment in full at such time or at any prior or subsequent time. 
 The Maker hereby expressly
authorizes the Payee to insert the date value is actually given in the blank space on the face hereof and on all related documents pertaining hereto. 
 This
Note may be secured by a security agreement, chattel mortgage, pledge agreement or like instrument (each of which is hereinafter called a “Security Agreement”). 
 Time is of the essence hereof. If any installment or any other sum due under this Note or any Security Agreement is not received within ten (10) days after its due date, the Maker agrees to 

 
pay, in addition to the amount of each such installment or other sum, a late payment charge of five percent (5%) of the amount of said installment or
other sum, but not exceeding any lawful maximum. If (i) Maker fails to make payment of any amount due hereunder within ten (10) days after the same becomes due and payable; or (ii) Maker is in default under, or fails to perform under
any term or condition contained in any Security Agreement, then the entire principal sum remaining unpaid, together with all accrued interest thereon and any other sum payable under this Note or any Security Agreement, at the election of Payee,
shall immediately become due and payable, with interest thereon at the lesser of eighteen percent (18%) per annum or the highest rate not prohibited by applicable law from the date of such accelerated maturity until paid (both before and after
any judgment). 
 The Maker may prepay its indebtedness hereunder, subject to a yield maintenance fee computed as follows. The current rate at the time of
the prepayment for US Treasury Bills with a maturity date closest to the maturity date of this Note shall be subtracted from the interest rate in effect at the time of the prepayment. If the result is zero or negative, there shall be no yield
maintenance fee. If the result is a positive number, then the resulting percentage shall be multiplied by the amount of the principal balance being repaid, divided by 360 and multiplied by the number of days remaining to the maturity date of this
Note. Said amount shall be reduced to present value by using the above-referenced US Treasury Bill rate and the number of days remaining to the maturity date of the term of this Note as of the date of repayment. The resulting amount is the yield
maintenance fee. 
 It is the intention of the parties hereto to comply with the applicable usury laws; accordingly, it is agreed that, notwithstanding any
provision to the contrary in this Note or any Security Agreement, in no event shall this Note or any Security Agreement require the payment or permit the collection of interest in excess of the maximum amount permitted by applicable law. If any such
excess interest is contracted for, charged or received under this Note or any Security Agreement, or if all of the principal balance shall be prepaid, so that under any of such circumstances the amount of interest contracted for, charged or received
under this Note or any Security Agreement on the principal balance shall exceed the maximum amount of interest permitted by applicable law, then in such event (a) the provisions of this paragraph shall govern and control, (b) neither Maker
nor any other person or entity now or hereafter liable for the payment hereof shall be obligated to pay the amount of such interest to the extent that it is in excess of the maximum amount of interest permitted by applicable law, (c) any such
excess which may have been collected shall be either applied as a credit against the then unpaid principal balance or refunded to Maker, at the option of the Payee, and (d) the effective rate of interest shall be automatically reduced to the
maximum lawful contract rate allowed under applicable law as now or hereafter construed by the courts having jurisdiction thereof. It is further agreed that without limitation of the foregoing, all calculations of the rate of interest contracted
for, charged or received under this Note or any Security Agreement which are made for the purpose of determining whether such rate exceeds the maximum lawful contract rate, shall be made, to the extent permitted by applicable law, by amortizing,
prorating, allocating and spreading in equal parts during the period of the full stated term of the indebtedness evidenced hereby, all interest at any time contracted for, charged or received from Maker or otherwise by Payee in connection with such
indebtedness; provided, however, that if any applicable state law is amended or the law of the United States of America preempts any applicable state law, so that it becomes lawful for the Payee to receive a greater interest per annum rate than is
presently 

 
allowed, the Maker agrees that, on the effective date of such amendment or preemption, as the case may be, the lawful maximum hereunder shall be increased to
the maximum interest per annum rate allowed by the amended state law or the law of the United States of America. 
 The Maker and all sureties, endorsers,
guarantors or any others (each such person, other than the Maker, an “Obligor”) who may at any time become liable for the payment hereof jointly and severally consent hereby to any and all extensions of time, renewals, waivers or
modifications of, and all substitutions or releases of, security or of any party primarily or secondarily liable on this Note or any Security Agreement or any term and provision of either, which may be made, granted or consented to by Payee, and
agree that suit may be brought and maintained against any one or more of them, at the election of Payee without joinder of any other as a party thereto, and that Payee shall not be required first to foreclose, proceed against, or exhaust any
security hereof in order to enforce payment of this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith,
as well as filing of suit (if permitted by law) and diligence in collecting this Note or enforcing any of the security hereof, and agrees to pay (if permitted by law) all expenses incurred in collection, including Payee’s actual attorneys’
fees. Maker and each Obligor agrees that fees not in excess of twenty percent (20%) of the amount then due shall be deemed reasonable. 
 THE MAKER
HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT
MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT
(INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL
APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE
MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 
 This Note and any Security Agreement constitute the entire agreement of the Maker and Payee
with respect to the subject matter hereof and supercedes all prior understandings, agreements and representations, express or implied. 
 No variation or
modification of this Note, or any waiver of any of its provisions or conditions, shall be valid unless in writing and signed by an authorized representative of Maker and Payee. Any such waiver, consent, modification or change shall be effective only
in the specific instance and for the specific purpose given. 

 Any provision in this Note or any Security Agreement which is in conflict with any statute, law or applicable rule shall
be deemed omitted, modified or altered to conform thereto. 
  

									
		 		 	Achillion Pharmaceuticals, Inc.
				
	/s/ Marita Kheim	 		 	By:	 	/s/ Mary Kay Fenton
	(Witness)	 		 		 	
	Marita Kheim	 		 	Name:	 	Mary Kay Fenton
	(Print Name)	 		 		 	
	300 George St., New Haven, CT 06511	 		 	Title:	 	Senior Director, Finance
	(Address)	 		 		 	
			
		 		 	Federal Tax ID#: 52-2113479
			
		 		 	 Address:  300 George Street, New Haven,
                  New Haven County, CT 06511

 PROMISSORY NOTE #4 
 May 13, 2005 
 (Date) 
 FOR VALUE RECEIVED, Achillion Pharmaceuticals, Inc., a corporation located at the address stated below (“Maker”) promises, jointly and severally if more than one, to pay to the order of
Webster Bank or any subsequent holder hereof (each, a “Payee”) at its office located at 80 Elm Street, New Haven, CT 06510 or at such other place as Payee or the holder hereof may designate the principal sum of one
hundred forty nine thousand nine hundred seventy two dollars and seventy seven cents ($149,972.77), pursuant to that certain Master Security Agreement (“MSA”) by and between Webster Bank and Achillion Pharmaceuticals, Inc. dated
as of May 15, 2003 as amended, and in effect from time to time, together with interest on the unpaid principal balance, from the date hereof through and including the dates of payment, at a fixed interest rate of 8.72% per annum, to be
paid in lawful money of the United States, in thirty-six (36) consecutive monthly installments of principal and interest as follows: 
  

			
	 Periodic Installment
	  	Amount
	 1-36
	  	$4,715.31

 each (“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest. The first Periodic Installment shall be due and payable on June 1, 2005 and the following Periodic Installments and the final installment shall be due and payable on the first day of each succeeding
month (each, a “Payment Date”); notwithstanding the foregoing, in the event this Note is dated other than the first day of a month, the interest accruing from the date hereof through and including the date of the first Periodic
Installment shall be paid in addition to, and together with, the first Periodic Installment. The Periodic Installments have been calculated on the basis of a 360 day year of twelve 30-day months. Each payment may, at the option of the Payee, be
calculated and applied on an assumption that such payment would be made on its due date. All terms and conditions of the MSA are incorporated herein, except that in the event there are any conflicting terms and conditions, the terms and conditions
of this Note shall prevail. 
 The acceptance by Payee of any payment which is less than payment in full of all amounts due and owing at such time shall not
constitute a waiver of Payee’s right to receive payment in full at such time or at any prior or subsequent time. 
 The Maker hereby expressly
authorizes the Payee to insert the date value is actually given in the blank space on the face hereof and on all related documents pertaining hereto. 
 This
Note may be secured by a security agreement, chattel mortgage, pledge agreement or like instrument (each of which is hereinafter called a “Security Agreement”). 
 Time is of the essence hereof. If any installment or any other sum due under this Note or any Security Agreement is not received within ten (10) days after its due date, the Maker agrees to 

 
pay, in addition to the amount of each such installment or other sum, a late payment charge of five percent (5%) of the amount of said installment or
other sum, but not exceeding any lawful maximum. If (i) Maker fails to make payment of any amount due hereunder within ten (10) days after the same becomes due and payable; or (ii) Maker is in default under, or fails to perform under
any term or condition contained in any Security Agreement then the entire principal sum remaining unpaid, together with all accrued interest thereon and any other sum payable under this Note or any Security Agreement, at the election of Payee, shall
immediately become due and payable, with interest thereon at the lesser of eighteen percent (18%) per annum or the highest rate not prohibited by applicable law from the date of such accelerated maturity until paid (both before and after any
judgment). 
 The Maker may prepay its indebtedness hereunder, subject to a yield maintenance fee computed as follows. The current rate at the time of the
prepayment for US Treasury Bills with a maturity date closest to the maturity date of this Note shall be subtracted from the interest rate in effect at the time of the prepayment. If the result is zero or negative, there shall he no yield
maintenance fee. If the result is a positive number, then the resulting percentage shall be multiplied by the amount of the principal balance being repaid, divided by 360 and multiplied by the number of days remaining to the maturity date of this
Note. Said amount shall be reduced to present value by using the above-referenced US Treasury Bill rate and the number of days remaining to the maturity date of the term of this Note as of the date of repayment. The resulting amount is the yield
maintenance fee. 
 It is the intention of the parties hereto to comply with the applicable usury laws; accordingly, it is agreed that, notwithstanding any
provision to the contrary in this Note or any Security Agreement, in no event shall this Note or any Security Agreement require the payment or permit the collection of interest in excess of the maximum amount permitted by applicable law. If any such
excess interest is contracted for, charged or received under this Note or any Security Agreement, or if all of the principal balance shall be prepaid, so that under any of such circumstances the amount of interest contracted for, charged or received
under this Note or any Security Agreement on the principal balance shall exceed the maximum amount of interest permitted by applicable law, then in such event (a) the provisions of this paragraph shall govern and control, (b) neither Maker
nor any other person or entity now or hereafter liable for the payment hereof shall be obligated to pay the amount of such interest to the extent that it is in excess of the maximum amount of interest permitted by applicable law, (c) any such
excess which may have been collected shall be either applied as a credit against the then unpaid principal balance or refunded to Maker, at the option of the Payee, and (d) the effective rate of interest shall be automatically reduced to the
maximum lawful contract rate allowed under applicable law as now or hereafter construed by the courts having jurisdiction thereof. It is further agreed that without limitation of the foregoing, all calculations of the rate of interest contracted
for, charged or received under this Note or any Security Agreement which are made for the purpose of determining whether such rate exceeds the maximum lawful contract rate, shall be made, to the extent permitted by applicable law, by amortizing,
prorating, allocating and spreading in equal parts during the period of the full stated term of the indebtedness evidenced hereby, all interest at any time contracted for, charged or received from Maker or otherwise by Payee in connection with such
indebtedness; provided, however, that if any applicable state law is amended or the law of the United States of America preempts any applicable state law, so that it becomes lawful for the Payee to receive a greater interest per annum rate than is
presently 

 
allowed, the Maker agrees that, on the effective date of such amendment or preemption, as the can may be, the lawful maximum hereunder shall be increased to
the maximum interest per annum rate allowed by the amended state law or the law of the United States of America. 
 The Maker and all sureties, endorsers,
guarantors or any others (each such person, other than the Maker, an “Obligor”) who may at any time become liable for the payment hereof jointly and severally consent hereby to any and all extensions of time, renewals, waivers or
modifications of, and all substitutions or releases of, security or of any party primarily or secondarily liable on this Note or any Security Agreement or any term and provision of either, which may be made, granted or consented to by Payee, and
agree that suit may be brought and maintained against any one or more of them, at the election of Payee without joinder of any other as a party thereto, and that Payee shall not be required first to foreclose, proceed against, or exhaust any
security hereof in order to enforce payment of this Note. The Maker and each Obligor hereby waives presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith,
as well as filing of suit (if permitted by law) and diligence in collecting this Note or enforcing any of the security hereof, and agrees to pay (if permitted by law) all expenses incurred in collection, including Payee’s actual attorneys’
fees. Maker and each Obligor agrees that fees not in excess of twenty percent (20%) of the amount then due shall be deemed reasonable. 
 THE MAKER
HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT
MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT
(INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL
APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE
MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 
 This Note and any Security Agreement constitute the entire agreement of the Maker and Payee
with respect to the subject matter hereof and supercedes all prior understandings, agreements and representations, express or implied. 
 No variation or
modification of this Note, or any waiver of any of its provisions or conditions, shall be valid unless in writing and signed by an authorized representative of Maker and Payee. Any such waiver, consent, modification or change shall be effective only
in the specific instance and for the specific purpose given. 

 Any provision in this Note or any Security Agreement which is in conflict with any statute, law or applicable rule shall
be deemed omitted, modified or altered to conform thereto. 
  

									
		 		 	Achillion Pharmaceuticals, Inc.
				
	/s/ Melissa Donnarummo	 		 	By:	 	/s/ Mary Kay Fenton
	(Witness)	 		 		 	
	Melissa Donnarummo	 		 	Name:	 	Mary Kay Fenton
	(Print Name)	 		 		 	
	300 George St., New Haven, CT 06511	 		 	Title:	 	VP, Finance
	(Address)	 		 		 	
			
		 		 	Federal Tax ID#: 52-2113479
			
		 		 	 Address:  300 George Street, New Haven,
                  New Haven County, CT 06511

 MASTER SECURITY AGREEMENT 
 dated as of May 15, 2003 (“Agreement”) 
 THIS AGREEMENT is
between Webster Bank (together with its successors and assigns, if any, “Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). Secured Party has an office at 80 Elm Street, New Haven, CT
06510. Debtor is a corporation organized and existing under the laws of the state of Delaware. Debtor’s mailing address and chief place of business is 300 George Street, New Haven, CT 06511. 
 1. CREATION OF SECURITY INTEREST. 
 Debtor grants to
Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future annexed to or made a part of this Agreement (“Collateral Schedule”), and in and
against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or exchanges therefor, and all insurance and/or other proceeds thereof (all such property is individually and collectively called the
“Collateral”). This security interest is given to secure the payment and performance of all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing or arising in the future, including but
not limited to the payment and performance of certain Promissory Notes from time to time identified on any Collateral Schedule (collectively “Notes” and each a “Note”), and any renewals, extensions and modifications
of such debts, obligations and liabilities (such Notes, debts, obligations and liabilities are called the “Indebtedness”). Unless otherwise provided by applicable law, notwithstanding anything to the contrary contained in this
Agreement, to the extent that Secured Party asserts a purchase money security interest in any items of Collateral (“PMSI Collateral”): (i) the PMSI Collateral shall secure only that portion of the Indebtedness which has been
advanced by Secured Party to enable Debtor to purchase, or acquire rights in or the use of such PMSI Collateral (the “PMSI Indebtedness”), and (ii) no other Collateral shall secure the PMSI Indebtedness. 
 2. REPRESENTATIONS, WARRANTIES AND COVENANTS OF DEBTOR. 
 Debtor represents, warrants and covenants as of the date of this Agreement and as of the date of each Collateral Schedule that: 
 (a) Debtor’s exact legal name is as set forth in the preamble of this Agreement and Debtor is, and will remain, duly organized, existing and in good standing under the laws of the State set forth in the preamble of this Agreement, has
its chief executive offices at the location specified in the preamble, and is, and will remain, duly qualified and licensed in every jurisdiction wherever necessary to carry on its business and operations; 
 (b) Debtor has adequate power and capacity to enter into, and to perform its obligations under this Agreement, each Note and any other documents
evidencing, or given in connection with, any of the Indebtedness (all of the foregoing are called the “Debt Documents”); 
 (c) This Agreement and the other Debt Documents have been duly authorized, executed and delivered by Debtor and constitute legal, valid and binding agreements enforceable in accordance with their terms, except to the extent that the
enforcement of remedies may be limited under applicable bankruptcy and insolvency laws; 
 (d) No approval, consent or withholding of
objections is required from any governmental authority or instrumentality with respect to the entry into, or performance by Debtor of any of the Debt Documents, except any already obtained; 
 (e) The entry into, and performance by, Debtor of the Debt Documents will not (i) violate any of the organizational documents of Debtor or any
judgment, order, law or regulation applicable to Debtor, or (ii) result in any breach of or constitute a default under any contract to which Debtor is a party, or result in the creation of any lien, claim or encumbrance on any of Debtor’s
property (except for liens in favor of Secured Party) pursuant to any indenture, mortgage, deed of trust, bank loan, credit agreement, or other agreement or instrument to which Debtor is a party; 
 (f) There are no suits or proceedings pending in court or before any commission, board or other administrative agency against or affecting Debtor which
could, in the aggregate, have a material adverse effect on Debtor, its business or operations, or its ability to perform its obligations under the Debt Documents, nor does Debtor have reason to believe that any such suits or proceedings are
threatened; 

 (g) All financial statements delivered to Secured Party in connection with the Indebtedness have been
prepared in accordance with generally accepted accounting principles, and since the date of the most recent financial statement, there has been no material adverse change in Debtors financial condition; 
 (h) The Collateral is not, and will not be, used by Debtor for personal, family or household purposes; 
 (i) The Collateral is, and will remain, in good condition and repair and Debtor will not be negligent in its care and use; 
 (j) Debtor is, and will remain, the sole and lawful owner, and in possession of, the Collateral, and has the sole right and lawful authority to grant the
security interest described in this Agreement; and 
 (k) The Collateral is, and will remain, free and clear of all liens, claims and
encumbrances of any kind whatsoever, except for (i) liens in favor of Secured Party, (ii) liens for taxes not yet due or for taxes being contested in good faith and which do not involve, in the judgment of Secured Party, any risk of the
sale, forfeiture or loss of any of the Collateral, and (iii) inchoate materialmen’s, mechanic’s, repairmen’s and similar liens arising by operation of law in the normal course of business for amounts which are not delinquent (all
of such liens are called “Permitted Liens”). 
 3. COLLATERAL. 
 (a) Until the declaration of any default, Debtor shall remain in possession of the Collateral; except that Secured Party shall have the right to possess
(i) any chattel paper or instrument that constitutes a part of the Collateral, and (ii) any other Collateral in which Secured Party’s security interest may be perfected only by possession. Secured Party may inspect any of the
Collateral during normal business hours after giving Debtor reasonable prior notice. If Secured Party asks, Debtor will promptly notify Secured Party in writing of the location of any Collateral. 
 (b) Debtor shall (i) use the Collateral only in its trade or business, (ii) maintain all of the Collateral in good operating order and repair,
normal wear and tear excepted, (iii) use and maintain the Collateral only in compliance with manufacturers recommendations and all applicable laws, and (iv) keep all of the Collateral free and clear of all liens, claims and encumbrances
(except for Permitted Liens). 
 (c) Secured Party does not authorize and Debtor agrees it shall not (i) part with possession of any of
the Collateral (except to Secured Party or for maintenance and repair), (ii) remove any of the Collateral from the continental United States, or (iii) sell, rent, lease, mortgage, license, grant a security interest in or otherwise transfer
or encumber (except for Permitted Liens) any of the Collateral. 
 (d) Debtor shall pay promptly when due all taxes, license fees,
assessments and public and private charges levied or assessed on any of the Collateral, on its use, or on this Agreement or any of the other Debt Documents. At its option. Secured Party may discharge taxes, liens, security interests or other
encumbrances at any time levied or placed on the Collateral and may pay for the maintenance, insurance and preservation of the Collateral and effect compliance with the terms of this Agreement or any of the other Debt Documents. Debtor agrees to
reimburse Secured Party, on demand, all costs and expenses incurred by Secured Party in connection with such payment or performance and agrees that such reimbursement obligation shall constitute Indebtedness. 
 (e) Debtor shall, at all times, keep accurate and complete records of the Collateral, and Secured Party shall have the right to inspect and make copies
of all of Debtor’s books and records relating to the Collateral during normal business hours, after giving Debtor reasonable prior notice. 
 (f) Debtor agrees and acknowledges that any third person who may at any time possess all or any portion of the Collateral shall be deemed to hold, and shall hold, the Collateral as the agent of, and as pledge holder for, Secured Party.
Secured Party may at any time give notice to any third person described in the preceding sentence that such third person is holding the Collateral as the agent of, and as pledge holder for, the Secured Party. 
 4. INSURANCE. 
 (a) Debtor shall at all times bear the
entire risk of any loss, theft, damage to, or destruction of, any of the Collateral from any cause whatsoever. 
 (b) Debtor agrees to keep
the Collateral insured against loss or damage by fire and extended coverage perils, theft, burglary, and for 

 any or all Collateral which are vehicles, for risk of loss by collision, and if requested by Secured Party, against such
other risks as Secured Party may reasonably require. The insurance coverage shall be in an amount no less than the full replacement value of the Collateral, and deductible amounts, insurers and policies shall be acceptable to Secured Party. Debtor
shall deliver to Secured Party policies or certificates of insurance evidencing such coverage. Each policy shall name Secured Party as a loss payee, shall provide for coverage to Secured Party regardless of the breach by Debtor of any warranty or
representation made therein, shall not be subject to co-insurance, and shall provide that coverage may not be canceled or altered by the insurer except upon thirty (30) days prior written notice to Secured Party. Debtor appoints Secured Party
as its attorney-in-fact to make proof of loss, claim for insurance and adjustments with insurers, and to receive payment of and execute or endorse all documents, checks or drafts in connection with insurance payments. Secured Party shall not act as
Debtor’s attorney-in-fact unless Debtor is in default. Proceeds of insurance shall be applied, at the option of Secured Party, to repair or replace the Collateral or to reduce any of the Indebtedness. 
 5. REPORTS. 
 (a) Debtor shall promptly notify Secured
Party of (i) any change in the name of Debtor, (ii) any change in the state of its incorporation or registration, (iii) any relocation of its chief executive offices, (iv) any relocation of any of the Collateral, (v) any of
the Collateral being lost, stolen, missing, destroyed, materially damaged or worn out, or (vi) any lien, claim or encumbrance other than Permitted Liens attaching to or being made against any of the Collateral. 
 (b) Debtor will deliver to Secured Party Debtor’s complete financial statements, certified by a recognized firm of certified public accountants,
within ninety (90) days of the close of each fiscal year of Debtor. If Secured Party requests, Debtor will deliver to Secured Party copies of Debtor’s quarterly financial reports certified by Debtor’s chief financial officer, within
ninety (90) days after the close of each of Debtor’s fiscal quarter. Debtor will deliver to Secured Party copies of all Forms 10-K and 10-Q, if any, within 30 days after the dates on which they are filed with the Securities and Exchange
Commission. 
 6. FURTHER ASSURANCES. 
 (a) Debtor shall, upon request of Secured Party, furnish to Secured Party such further information, execute and deliver to Secured Party such documents and instruments (including, without limitation, Uniform Commercial Code financing
statements) and shall do such other acts and things as Secured Party may at any time reasonably request relating to the perfection or protection of the security interest created by this Agreement or for the purpose of carrying out the intent of this
Agreement. Without limiting the foregoing, Debtor shall cooperate and do all acts deemed necessary or advisable by Secured Party to continue in Secured Party a perfected first security interest in the Collateral, and shall obtain and furnish to
Secured Party any subordinations, releases, landlord waivers, lessor waivers, mortgagee waivers, or control agreements, and similar documents as may be from time to time requested by, and in form and substance satisfactory to, Secured Party.

 (b) Debtor authorizes Secured Party to file a financing statement and amendments thereto describing the Collateral and containing any
other information required by the applicable Uniform Commercial Code. Debtor irrevocably grants to Secured Party the power to sign Debtor’s name and generally to act on behalf of Debtor to execute and file applications for title, transfers of
title, financing statements, notices of lien and other documents pertaining to any or all of the Collateral; this power is coupled with Secured Party’s interest in the Collateral. Debtor shall, if any certificate of title be required or
permitted by law for any of the Collateral, obtain and promptly deliver to Secured Party such certificate showing the lien of this Agreement with respect to the Collateral. Debtor ratifies its prior authorization for Secured Party to file financing
statements and amendments thereto describing the Collateral and containing any other information required by the Uniform Commercial Code if filed prior to the date hereof. 
 (c) Debtor shall indemnify and defend the Secured Party, its successors and assigns, and their respective directors, officers and employees, from and
against all claims, actions and suits (including, without limitation, related attorneys’ fees) of any kind whatsoever arising, directly or indirectly, in connection with any of the Collateral. 
 7. DEFAULT AND REMEDIES. 
 (a) Debtor shall be in
default under this Agreement and each of the other Debt Documents if: 
 (i) Debtor breaches its obligation to pay when due any installment or
other amount due or coming due under any of the Debt Documents; 

 (ii) Debtor, without the prior written consent of Secured Party, attempts to or does sell, rent, lease,
license, mortgage, grant a security interest in, or otherwise transfer or encumber (except for Permitted Liens) any of the Collateral; 
 (iii) Debtor breaches any of its insurance obligations under Section 4; 
 (iv) Debtor breaches any of its other obligations
under any of the Debt Documents and fails to cure that breach within thirty (30) days after written notice from Secured Party; 
 (v)
Any warranty, representation or statement made by Debtor in any of the Debt Documents or otherwise in connection with any of the Indebtedness shall be false or misleading in any material respect; 
 (vi) Any of the Collateral is subjected to attachment, execution, levy, seizure or confiscation in any legal proceeding or otherwise, or if any legal or
administrative proceeding is commenced against Debtor or any of the Collateral, which in the good faith judgment of Secured Party subjects any of the Collateral to a material risk of attachment, execution, levy, seizure or confiscation and no bond
is posted or protective order obtained to negate such risk; 
 (vii) Debtor breaches or is in default under any other agreement between
Debtor and Secured Party; 
 (viii) Debtor or any guarantor or other obligor for any of the Indebtedness (collectively
“Guarantor”) dissolves, terminates its existence, becomes insolvent or ceases to do business as a going concern; 
 (ix) If
Debtor or any Guarantor is a natural person, Debtor or any such Guarantor dies or becomes incompetent; 
 (x) A receiver is appointed for all
or of any part of the property of Debtor or any Guarantor, or Debtor or any Guarantor makes any assignment for the benefit of creditors; 
 (xi) Debtor or any Guarantor files a petition under any bankruptcy, insolvency or similar law, or any such petition is filed against Debtor or any Guarantor and is not dismissed within forty-five (45) days; or 
 (xii) Debtor’s improper filing of an amendment or termination statement relating to a filed financing statement describing the Collateral.

 (b) If Debtor is in default, the Secured Party, at its option, may declare any or all of the Indebtedness to be immediately due and
payable, without demand or notice to Debtor or any Guarantor. The accelerated obligations and liabilities shall bear interest (both before and after any judgment) until paid in full at the lower of eighteen percent (18%) per annum or the
maximum rate not prohibited by applicable law. 
 (c) After default, Secured Party shall have all of the rights and remedies of a Secured
Party under the Uniform Commercial Code, and under any other applicable law. Without limiting the foregoing, Secured Party shall have the right to (i) notify any account debtor of Debtor or any obligor on any instrument which constitutes part
of the Collateral to make payment to the Secured Party, (ii) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from the premises or store it on the premises,
(iii) sell the Collateral at public or private sale, in whole or in part, and have the right to bid and purchase at said sale, or (iv) lease or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to
the obligations then in default. If requested by Secured Party, Debtor shall promptly assemble the Collateral and make it available to Secured Party at a place to be designated by Secured Party which is reasonably convenient to both parties. Secured
Party may also render any or all of the Collateral unusable at the Debtor’s premises and may dispose of such Collateral on such premises without liability for rent or costs. Any notice that Secured Party is required to give to Debtor under the
Uniform Commercial Code of the time and place of any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed to constitute reasonable notice if such notice is given to the
last known address of Debtor at least five (5) days prior to such action. 
 (d) Proceeds from any sale or lease or other disposition
shall be applied: first, to all costs of repossession, storage, and disposition including without limitation attorneys’, appraisers’, and auctioneers’ fees; second, to discharge the obligations then in default; third, to discharge any
other Indebtedness of Debtor to Secured Party, whether as obligor, endorser, guarantor, surety or indemnitor; fourth, to expenses incurred in paying or settling liens and claims against the Collateral; and lastly, to Debtor, if there exists any
surplus. Debtor shall remain fully liable for any deficiency. 

 (e) Debtor agrees to pay all reasonable attorneys’ fees and other costs incurred by Secured Party in
connection with the enforcement, assertion, defense or preservation of Secured Party’s rights and remedies under this Agreement, or if prohibited by law, such lesser sum as may be permitted. Debtor further agrees that such fees and costs shall
constitute Indebtedness. 
 (f) Secured Party’s rights and remedies under this Agreement or otherwise arising are cumulative and may be
exercised singularly or concurrently. Neither the failure nor any delay on the part of the Secured Party to exercise any right, power or privilege under this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right,
power or privilege preclude any other or further exercise of that or any other right, power or privilege. SECURED PARTY SHALL NOT BE DEEMED TO HAVE WAIVED ANY OF ITS RIGHTS UNDER THIS AGREEMENT OR UNDER ANY OTHER AGREEMENT, INSTRUMENT OR PAPER
SIGNED BY DEBTOR UNLESS SUCH WAIVER IS EXPRESSED IN WRITING AND SIGNED BY SECURED PARTY. A waiver on any one occasion shall not be construed as a bar to or waiver of any right or remedy on any future occasion. 
 (g) DEBTOR AND SECURED PARTY UNCONDITIONALLY WAIVE THEIR RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS
AGREEMENT, ANY OF THE OTHER DEBT DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS BETWEEN DEBTOR AND SECURED PARTY RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING
ESTABLISHED BETWEEN DEBTOR AND SECURED PARTY. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR IN
WRITING. THE WAIVER ALSO SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT, ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION.
THIS AGREEMENT MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 
 8. MISCELLANEOUS. 
 (a) This Agreement, any Note and/or any of the other Debt Documents may be assigned, in whole or in part, by Secured Party without notice to Debtor, and
Debtor agrees not to assert against any such assignee, or assignee’s assigns, any defense, set-off, recoupment claim or counterclaim which Debtor has or may at any time have against Secured Patty for any reason whatsoever. Debtor agrees that if
Debtor receives written notice of an assignment from Secured Party, Debtor will pay all amounts payable under any assigned Debt Documents to such assignee or as instructed by Secured Party. Debtor also agrees to confirm in writing receipt of the
notice of assignment as may be reasonably requested by Secured Party or assignee. 
 (b) All notices to be given in connection with this
Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth in this Agreement (unless and until a different address may be specified in a written notice to the other party), and shall be deemed given
(i) on the date of receipt if delivered in hand or by facsimile transmission, (ii) on the next business day after being sent by express mail, and (iii) on the fourth business day after being sent by regular, registered or certified
mail. As used herein, the term “business day” shall mean and include any day other than Saturdays, Sundays, or other days on which commercial banks in New York, New York are required or authorized to be closed. 
 (c) Secured Party may correct patent errors and fill in all blanks in this Agreement or in any Collateral Schedule consistent with the agreement of the
parties. 
 (d) Time is of the essence of this Agreement. This Agreement shall be binding, jointly and severally, upon all parties described
as the “Debtor” and their respective heirs, executors, representatives, successors and assigns, and shall inure to the benefit of Secured Party, its successors and assigns. 
 (e) This Agreement and its Collateral Schedules constitute the entire agreement between the parties with respect to the subject matter of this Agreement
and supersede all prior understandings (whether written, verbal or implied) with respect to such subject matter. THIS 

 AGREEMENT AND ITS COLLATERAL SCHEDULES SHALL NOT BE CHANGED OR TERMINATED ORALLY OR BY COURSE OF CONDUCT, BUT ONLY BY A
WRITING SIGNED BY BOTH PARTIES. Section headings contained in this Agreement have been included for convenience only, and shall not affect the construction or interpretation of this Agreement. 
 (f) This Agreement shall continue in full force and effect until all of the Indebtedness has been indefeasibly paid in full to Secured Party or its
assignee. The surrender, upon payment or otherwise, of any Note or any of the other documents evidencing any of the Indebtedness shall not affect the right of Secured Party to retain the Collateral for such other Indebtedness as may then exist or as
it may be reasonably contemplated will exist in the future. This Agreement shall automatically be reinstated if Secured Party is ever required to return or restore the payment of all or any portion of the Indebtedness (all as though such payment had
never been made). 
 (g) THIS AGREEMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL IN ALL RESPECTS BE GOVERNED BY AND
CONSTRUED IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE STATE OF CONNECTICUT (WITHOUT REGARD TO THE CONFLICT OF LAWS PRINCIPLES OF SUCH STATE), INCLUDING ALL MATTERS OF CONSTRUCTION, VALIDITY AND PERFORMANCE, REGARDLESS OF THE LOCATION OF THE
EQUIPMENT. 

 IN WITNESS WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have duly
executed this Agreement in one or more counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid. 
  

							
	SECURED PARTY:	 	DEBTOR:
		
	Webster Bank	 	Achillion Pharmaceuticals, Inc.
				
	By:	 	 /s/John E. Rossi
	 	By:	 	 /s/Mary Kay Fenton

	Name:	 	/s/John E. Rossi	 	Name:	 	Mary Kay Fenton
	Title:	 	Senior Vice President	 	Title:	 	Sr. Director, Finance

 AMENDMENT 
 THIS AMENDMENT is made as of the 15th day of May, 2003, between Webster Bank (“Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”) in connection with that certain Master
Security Agreement of even date herewith (“Agreement”). The terms of this Amendment are hereby incorporated into the Agreement as though fully set forth therein. Section references below refer to the section numbers of the
Agreement. The Agreement is hereby amended as follows: 
 I. SECTION 1 
  

	 	A.	This Section is hereby amended and replaced with the following: 

 “1. EQUIPMENT LOAN ADVANCES; NOTES, CONDITIONS PRECEDENT; CONTINGENCY; CREATION OF SECURITY INTEREST. 
 (a) Equipment Loan Advances. Subject to the terms and condition set forth in this Agreement, Secured Party agrees to make advances for the purchase of Eligible Equipment (defined below) (each an
“Equipment Loan Advance” and collectively “Equipment Loan Advances”) to Debtor from time to time on any business day during the period from the date of this Agreement up to, but not including, the first anniversary
date of this Agreement (the “Drawdown Period”); provided, however, that at no time shall the aggregate amount of all Equipment Loan Advances exceed One Million Dollars ($1,000,000) (the “Committed
Amount”). “Eligible Equipment” for the purposes of this Agreement may include new lab and test equipment provided, however, that computer, office automation equipment and furnishings may not exceed fifteen
percent (15%) of the Committed Amount and software may not exceed five percent (5%) of the Committed Amount. Notwithstanding anything to the contrary contained in this Agreement, (i) the initial Equipment Loan Advance will include
purchases made within ninety (90) days of the closing date of the initial Equipment Loan Advance; (ii) future Equipment Loan Advances, if any, will be made within sixty (60) days of Debtor’s purchase date provided,
that such purchase amount is equal to or greater than Two Hundred Thousand Dollars ($200,000); (iii) Debtor is limited to a total of five (5) Equipment Loan Advances during the Drawdown Period; and (iv) any amounts repaid with
respect to any Equipment Loan Advance may not be reborrowed. 
 (b) Equipment Loan Notes. Equipment Loan Advances shall
be evidenced by, and repaid with interest in accordance with, promissory notes of Debtor in the form of Exhibit A hereto, duly completed, executed and delivered to Secured Party, the aggregate of which shall not exceed the Committed
Amount, payable to Secured Party in accordance with its terms (each such promissory note a “Note” and collectively, the “Notes”). Debtor hereby authorizes Secured Party to record on each Note or in its internal
computerized records the amount of each Equipment Loan Advance and of each payment of principal received by Secured 
  

 - 1 - 

 Party on account of the advances evidenced by the Notes (individually, an “Equipment Loan”
and collectively, the “Equipment Loans”), which recordation shall, in the absence of manifest error, be conclusive as to the outstanding principal balance of the Equipment Loans and shall be considered correct and binding on
Debtor; provided, however, that the failure to make such recordation with respect to any Equipment Loan Advance or payment shall not limit or otherwise affect the obligations of Debtor under this Agreement or the Equipment Loan Notes.

 (c) Conditions Precedent. 
 (i) As a condition precedent to the execution and delivery of this Agreement by Secured Party, as of the date hereof, Debtor’s cash
and cash equivalents, including the Equipment Loan proceeds, shall be greater than or equal to Debtor’s projected cash burn during the Drawdown Period. 
 (ii) As a condition precedent to each closing of an Equipment Loan Advance, Debtor shall have (A) delivered duly executed and
completed copies of this Agreement (in the case of the initial Equipment Loan Advance), each Note and any other documents evidencing, or given in connection with, any of the Indebtedness (defined below) (all of the foregoing are referred to herein
as the “Debt Documents”); (B) certified that the all representations and warranties contained in the debt documents are true, complete and correct as of the closing date of each Equipment Loan Advance; and (C) certified
that each covenant required to be performed or competed as of each Equipment Loan Advance closing date has been duly performed or completed. 
 (d) Creation of Security Interest. Debtor grants to Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future annexed to
or made a part of this Agreement (“Collateral Schedule”), and in and against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or exchanges therefor, and all insurance and/or
other proceeds thereof (all such property is individually and collectively called the “Collateral”). This security interest is given to secure the payment and performance of all debts, obligations and liabilities of any kind
whatsoever (other than with respect to any preferred stock of Debtor) of Debtor to Secured Party now existing or arising in the future, including but not limited to the payment and performance of the Notes identified on any Collateral Schedule, and
any renewals, extensions and modifications of such debts, obligations and liabilities (such Notes, debts, obligations and liabilities are called the “Indebtedness”). Unless otherwise provided by applicable law, notwithstanding
anything to the contrary contained in this Agreement, to the extent that Secured Party asserts a purchase money security interest in any items of Collateral (“PMSI Collateral”): (i) the PMSI Collateral shall secure only that
portion of the Indebtedness which has been advanced by Secured Party to enable Debtor to purchase, or acquire rights in or the use of such PMSI Collateral (the “PMSI Indebtedness”), and (ii) no other Collateral shall secure the
PMSI Indebtedness. 
  

 - 2 - 

 (e) Stipulated Loss Value. If a unit of equipment is lost, stolen, destroyed or
seized by a government authority, Debtor will pay to Secured Party the applicable Stipulated Loss Value (a percentage) times Secured Party’s advance on the unit. A table of Stipulated Loss Value, substantially in the form of Exhibit B,
will be included in each advance schedule.” . 
 II. SECTION 2 
 A. The first sentence of this Section is hereby amended and replaced with the following: 
 “Debtor represents, warrants and covenants as of the date of this Agreement and as of the date of each Collateral Schedule, unless specifically otherwise disclosed in writing, that:” . 
 B. Subsection (b) is hereby amended and replaced with the following: 
 “Debtor has adequate power and capacity to enter into, and to perform its obligations under the Debt Documents;” . 
 C. Subsection (c) is hereby amended and replaced with the following: 
 “This Agreement and the other Debt Documents have been duly authorized, executed and delivered by Debtor and constitute legal, valid and binding
agreements enforceable in accordance with their terms, except to the extent that the enforcement of remedies may be limited under applicable bankruptcy and insolvency laws and equitable remedies;” . 
 D. Subsection (j) is hereby amended by deleting after the semi-colon the word “and” 
 E. Subsection (k) is hereby amended by deleting at the end of this subsection the period “.” and replacing it with “;
and” . 
  

 - 3 - 

 F. This Section is hereby amended by adding subsection (l) as follows: 
 “(l) Debtor shall maintain all of its operating accounts (other than Debtor’s payroll account with ADP or other similar payroll services
provider) with Secured Party.” . 
 III. SECTION 3 
 A. Subsection (a) is hereby amended and replaced with the following: 
 “Until the occurrence
and during the continuance of any default under Section 7, Debtor shall remain in possession of the Collateral; except that Secured Party shall have the right to possess (i) any chattel paper or instrument that constitutes a part of the
Collateral, and (ii) any other Collateral in which Secured Party’s security interest may be perfected only by possession. Secured Party may inspect any of the Collateral during normal business hours after giving Debtor reasonable prior
notice. If Secured Party asks, Debtor will promptly notify Secured Party in writing of the location of any Collateral.” . 
 B.
Subsection 3(c)(ii) is hereby amended and replaced with the following: 
 “(ii) move any of the Collateral to a new location without
the express, prior written consent of Secured Party, or” . 
 C. Subsection (d) is hereby amended and replaced with the
following: 
 “Debtor shall pay promptly when due all taxes, license fees, assessments and public and private charges levied or assessed
on any of the Collateral, on its use, or on this Agreement or any of the other Debt Documents. At its option, Secured Party may discharge taxes, liens, security interests or other encumbrances at any time levied or placed on the Collateral and may
pay for the maintenance, insurance and preservation of the Collateral and effect compliance with the terms of this Agreement or any of the other Debt Documents. Debtor agrees to reimburse Secured Party, on demand, all reasonable costs and expenses
incurred by Secured Party in connection with such payment or performance and agrees that such reimbursement obligation shall constitute Indebtedness.” . 
 IV. SECTION 5 
 A. Subsection (b) is hereby amended and replaced with the following: 
 “(b) Debtor will deliver to Secured Party Debtor’s complete audited financial statements, certified by a recognized firm of certified public
accountants, within one hundred twenty (120) days of the close of each fiscal year of Debtor. In addition, Debtor will deliver to Secured Party (i) Debtor’s monthly management prepared financial statements within thirty (30) days
after the end of each month and (ii) Debtor’s annual projected financial statements, including statement of cash flows prepared on a monthly or quarterly basis as presented or provided to Borrower’s Board of Directors.”.

  

 - 4 - 

 V. SECTION 7. 
 A. This Section is hereby amended by deleting the title of this Section and replacing it with “1. DEFAULT AND REMEDIES; RIGHT TO SET OFF.”. 
 B. Section (a) is hereby amended and replaced with the following: 
 “Debtor shall be in default under this Agreement and each of the other Debt Documents if (and so long as is continuing):” . 
 C. Section (a)(i) is hereby amended and replaced with the following: 
 “Debtor breaches its obligation to pay when due any installment or other amount due or coming due under any of the Debt Documents unless such failure to pay on the required due date is as a result of the error or
malfunction of any electronic payment system or other system established for the electronic transfer of funds. If the error or malfunction of any electronic payment system or other system persists for more than three (3) days, Debtor agrees to
immediately send payment to Secured Party via wire transfer or overnight mail” . 
 D. Subsection (a)(v) is hereby amended and
replaced with the following: 
 “Any warranty, representation or statement made by Debtor in any of the Debt Documents or otherwise in
connection with any of the Indebtedness shall be false or misleading in any material respect when made;” . 
 E. Subsection
(a)(vii) is hereby amended and replaced with the following: 
 “Debtor shall (A) fail to pay any indebtedness for borrowed money,
including interest or premium thereon, when due (whether by scheduled maturity, required prepayment, acceleration, demand, or otherwise), (B) fail to perform or observe any term, covenant, or condition on its part to be performed or observed
under any agreement or instrument relating to any such indebtedness, when required to be performed or observed (including any applicable grace periods) if the effect of such failure to perform or observe is to accelerate, or to permit the
acceleration after the giving of notice or passage of time, or both, of the maturity of such indebtedness, whether or not such failure to perform or observe shall be waived by the holder of such indebtedness; or any such indebtedness shall be
declared to be due and payable, or required to be prepaid (other than by a regularly scheduled required prepayment), prior to the stated maturity thereof, or (C) be in default under any other indebtedness of Debtor to Secured Party.” .

 F. Subsection (a)(xi) is hereby amended and replaced with the following: 
 “Debtor or any Guarantor files a petition under any bankruptcy, insolvency or similar law, or any such petition is filed against Debtor or any
Guarantor and is not dismissed within sixty (60) days; or” . 
  

 - 5 - 

 G. Subsection (c) is hereby amended and replaced with the following: 
 “After default, Secured Party shall have all of the rights and remedies of a Secured Party under the Uniform Commercial Code, and under any other
applicable law. Without limiting the foregoing, Secured Party shall have the right to (i) notify any account debtor of Debtor or any obligor on any instrument which constitutes part of the Collateral to make payment to the Secured Party,
(ii) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from the premises or store it on the premises, (iii) sell the Collateral at public or private sale, in
whole or in part, and have the right to bid and purchase at said sale, or (iv) lease or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to the obligations then in default. If requested by Secured
Party, Debtor shall promptly assemble the Collateral and make it available to Secured Party at a place to be designated by Secured Party which is reasonably convenient to both parties. Secured Party may also render any or all of the Collateral
unusable at the Debtor’s premises and may dispose of such Collateral on such premises without liability for rent or costs. Any notice that Secured Party is required to give to Debtor under the Uniform Commercial Code of the time and place of
any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed to constitute reasonable notice if such notice is given to the last known address of Debtor at least ten
(10) days prior to such action.” . 
 H. This Section is hereby amended by adding a new subsection (h) as follows:

 “(h) Set Off. Debtor hereby grants to Secured Party a lien on, a security interest in, and during the existence of an event of
default, an option to set off against, any and all property, including deposits of Debtor, now or hereafter in the possession or control of Secured Party (inclusive of such property as may be in transit by mail or carrier to or from Secured Party),
or that of any third party acting on behalf of Debtor against any and all Indebtedness due under the Master Security Agreement, although otherwise unmatured, without prior demand or notice regardless of the adequacy of any collateral securing all or
part of the Indebtedness, and without resort to legal process or judicial proceeding or other authorization.” . 
  

 - 6 - 

 VI. SECTION 8 
 A. Subsection (b) is hereby amended and replaced with the following: 
 “All notices to be given in connection with
this Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth in this Agreement (unless and until a different address may be specified in a written notice to the other party), and shall be deemed given
(i) on the date of receipt if delivered in hand or by facsimile transmission, (ii) on the next business day after being sent by express mail, and (iii) on the fourth business day after being sent by regular, registered or certified
mail. As used herein, the term “business day” shall mean and include any day other than Saturdays, Sundays, or other days on which commercial banks in New Haven, Connecticut are required or authorized to be closed.” . 
 TERMS USED, BUT NOT OTHERWISE DEFINED HEREIN SHALL HAVE THE MEANINGS GIVEN TO THEM IN THE AGREEMENT. EXCEPT AS EXPRESSLY AMENDED HEREBY, THE AGREEMENT
SHALL REMAIN IN FULL FORCE AND EFFECT. IF THERE IS ANY CONFLICT BETWEEN THE PROVISIONS OF THE AGREEMENT AND THIS AMENDMENT, THEN THIS AMENDMENT SHALL CONTROL. 
  

 - 7 - 

 IN WITNESS WHEREOF, the parties hereto have executed this Amendment simultaneously with the
Agreement by signature of their respective authorized representative set forth below. 
  

							
	Webster Bank	 	Achillion Pharmaceuticals, Inc.
				
	By:	 	 /s/John E. Rossi
	 	By:	 	 /s/ Mary Kay Fenton

	Name:	 	John E. Rossi	 	Name:	 	Mary Kay Fenton
	Title:	 	Senior Vice President	 	Title:	 	Sr. Director, Finance

  

 - 8 - 

 SECOND AMENDMENT TO MASTER SECURITY AGREEMENT 
 This Second Amendment to Master Security Agreement (this “Second Amendment”) is made as of the 29th day of October, 2004 between Webster Bank
(“Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). 
 WHEREAS, Secured Party and
Debtor entered into a Master Security Agreement dated as of May 15, 2003 (the “Original Agreement”) and an Amendment dated May 15, 2003 (the “Amendment” and together with the Original Agreement and this Second
Amendment, the “Agreement”); and 
 WHEREAS, Secured Party and Debtor desire to amend the Agreement in certain respects and
to ratify and confirm the portions of the Agreement that are not being amended by this Second Amendment; and 
 WHEREAS, Secured Party
desires to signify its consent to the extension of the Drawdown Period from the date of this Second Amendment through and including December 31, 2004, for a Committed Amount of $250,000. 
 NOW THEREFORE, in consideration of the foregoing and the mutual covenants set forth below and intending to be legally bound, the parties hereby
agree as follows: 
 (1) Amendment to Master Security Agreement. The following amendments to the Agreement shall be made: 
 (a) Section l(a) “Equipment Loan Advances” is hereby deleted in its entirety and replaced with the following: 
 “(a) Equipment Loan Advances. Subject to the terms and conditions set forth in this Agreement, Secured Party agrees to make advances for the
purchase of Eligible Equipment (defined below) (each an “Equipment Loan Advance” and collectively “Equipment Loan Advances”) to Debtor from time to time on any business day during the period from October 29,
2004 up to and including, December 31, 2004 (the “Drawdown Period”); provided, however, that at no time shall the aggregate amount of all Equipment Loan Advances exceed Two Hundred Fifty Thousand Dollars
($250,000) (the “Committed Amount”). “Eligible Equipment” for the purposes of this Agreement may include new lab and test equipment provided, however, that computer, office automation equipment and
furnishings may not exceed fifteen percent (15%) of the Committed Amount. Notwithstanding anything to the contrary contained in this Agreement, (i) the initial Equipment Loan Advance may include purchases made no later than April 1,
2004 provided, that, such initial advance shall not exceed $100,000, (ii) future Equipment Loan Advances, if any, will be made within sixty (60) clays of Debtor’s purchase and (iii) any amounts repaid with respect
to any Equipment Loan Advance may not be reborrowed. 

 (2) Ratification of Original Agreement. Except as expressly amended hereby, the Agreement shall remain in full
force and effect, and is hereby ratified and confirmed in all respects. 
 (3) Miscellaneous 
 (a) Successors and Assigns. This Second Amendment shall inure to the benefit of and shall be binding upon the parties hereto and their respective
successors and assigns. 
 (b) Severability. If any provision of this Second Amendment shall be held invalid or unenforceable by any
court of competent jurisdiction, such holding shall not invalidate or render unenforceable any other provision hereof. 
 (c) Modifications
in Writing. Amendments or modifications of any provision of this Second Amendment (including this paragraph) or any documents delivered in connection herewith shall in no event be effective unless the same shall be in writing and signed by the
party against whom enforcement is sought. 
 (d) Execution and Counterparts. This Second Amendment may be executed in several
counterparts, each of which shall be an original and all of which shall constitute one and the same document. 
 (e) Captions. The
captions and headings in this Second Amendment are for convenience only and do not define, limit or describe the intent of any provisions hereof. 
 (f) Definitions. Capitalized terms used herein, but not otherwise defined herein shall have the meanings given to them in the Agreement. 
 [Signature Page to Follow] 
  

 2 

 IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment to Master Security
Agreement by signature of their respective authorized representative set forth below. 
  

							
	Webster Bank	 	Achillion Pharmaceuticals, Inc.
				
	By:	 	 /s/ John R. Strahley
	 	By:	 	 /s/ Mary Kay Fenton

	Name:	 	John R. Strahley	 	Name:	 	Mary Kay Fenton
	Title:	 	Vice President	 	Title:	 	Vice President, Finance

  

 3 

 Execution Copy 
 THIRD AMENDMENT TO MASTER SECURITY AGREEMENT 
 This Third Amendment to Master Security Agreement
(this “Third Amendment”) is made as of the 24th day of March, 2005 between Webster Bank, National Association (“Secured Party”) and Achillion Pharmaceuticals, Inc. (“Debtor”). 
 WHEREAS, Secured Party and Debtor entered into that certain Master Security Agreement dated as of May 15, 2003 (the “Original
Agreement”), an Amendment dated May 15, 2003 (the “First Amendment”) and most recently, a Second Amendment dated October 29, 2004 (the “Second Amendment” and together with the Original Agreement, the First
Amendment and this Second Amendment, the “Agreement”); and 
 WHEREAS, Secured Party and Debtor desire to amend the
Agreement in certain respects and to ratify and confirm the portions of the Agreement that are not being amended by this Third Amendment; and 
 WHEREAS, Secured Party desires to signify its consent to the extension of the Drawdown Period from the date of this Third Amendment through and including December 31, 2005, for a Committed Amount of $500,000. 
 NOW THEREFORE, in consideration of the foregoing and the mutual covenants set forth below and intending to be legally bound, the parties hereby
agree as follows: 
 (1) Amendment to Master Security Agreement. The following amendments to the Agreement shall be made: 
 (a) Section l(a) “Equipment Loan Advances” is hereby deleted in its entirety and replaced with the following: 
 “(a) Equipment Loan Advances. Subject to the terms and conditions set forth in this Agreement, Secured Party agrees to make advances for the
purchase of Eligible Equipment (defined below) (each an “Equipment Loan Advance” and collectively “Equipment Loan Advances”) to Debtor from time to time on any business day during the period from March 24, 2005 up to and
including, December 31, 2005 (the “Drawdown Period”); provided, however, that at no time shall the aggregate amount of all Equipment Loan Advances exceed Five Hundred Thousand Dollars ($500,000) (the “Committed
Amount”), exclusive of amounts currently outstanding under previous advances. “Eligible Equipment” for the purposes of this Agreement may include new lab and test equipment provided, however, that computer, office
automation equipment and furnishings may not exceed fifteen percent (15%) of the Committed Amount. Notwithstanding anything to the contrary contained in this Agreement, (i) the initial Equipment Loan Advance may include purchases of
Eligible Equipment 
  

 4 

 made within ninety (90) days prior to the date of such Equipment Loan Advance,
(ii) future Equipment Loan Advances, if any, will be made within sixty (60) days of Debtor’s purchase of Eligible Equipment, (iii) each Equipment Loan Advance must be equal to or greater than $50,000 and (iv) the Equipment
Loan Advances are limited to five (5) in total. Any amounts repaid with respect to any Equipment Loan Advance may not be reborrowed. 
 (b) Subsection l(c) “Conditions Precedent” is amended as follows: 
  

	 	(i)	Subsection l(c)(i) is hereby deleted and replaced with the following: 

 “(i) as a condition precedent to the execution and delivery of this Amendment by Secured Party, as of the date hereof, Debtor’s cash and cash equivalents, including the Equipment Loan proceeds AND TAKING
INTO ACCOUNT THE ASSUMPTIONS SET FORTH IN THE FORECAST AS PREVIOUSLY DELIVERED BY DEBTOR TO SECURED PARTY, shall be a minimum of twelve (12) months projected cash burn.” 
 (2) Ratification of Original Agreement. Except as expressly amended hereby, the Agreement shall remain in full force and effect, and is hereby ratified and confirmed in all respects. 
 (3) Miscellaneous 
 (a) Successors and Assigns. This
Third Amendment shall inure to the benefit of and shall be binding upon the parties hereto and their respective successors and assigns. 
 (b)
Severability. If any provision of this Third Amendment shall be held invalid or unenforceable by any court of competent jurisdiction, such holding shall not invalidate or render unenforceable any other provision hereof. 
 (c) Modifications in Writing. Amendments or modifications of any provision of this Third Amendment (including this paragraph) or any documents
delivered in connection herewith shall in no event be effective unless the same shall be in writing and signed by the party against whom enforcement is sought. 
 (d) Execution and Counterparts. This Third Amendment may be executed in several counterparts, each of which shall be an original and all of which shall constitute one and the same document. 
  

 5 

 (e) Captions. The captions and headings in this Third Amendment are for convenience only and do
not define, limit or describe the intent of any provisions hereof. 
 (f) Definitions. Capitalized terms used herein, but not otherwise
defined herein shall have the meanings given to them in the Agreement. 
 [Signature Page to Follow] 
  

 6 

 IN WITNESS WHEREOF, the parties hereto have executed this Third Amendment to Master Security Agreement by
signature of their respective authorized representative set forth below. 
  

							
	Webster Bank, National Association	 	Achillion Pharmaceuticals, Inc.
				
	By:	 	 /s/ John E. Rossi
	 	By:	 	 /s/ Mary Kay Fenton

	Name:	 	John E. Rossi	 	Name:	 	Mary Kay Fenton
	Title:	 	Senior Vice President	 	Title:	 	Vice President, Finance

  

 7 

 FOURTH AMENDMENT TO MASTER SECURITY AGREEMENT 
 This Fourth Amendment to Master Security Agreement (this “Fourth Amendment”) is made as
of the 7th day of August, 2006 between Webster Bank, National Association (“Secured Party”) and Achillion Pharmaceuticals, Inc.
(“Debtor”). 
 WHEREAS, Secured Party and Debtor entered into that certain Master Security Agreement dated as of
May 15, 2003 (the “Original Agreement”), an Amendment, dated May 15, 2003 (the “First Amendment”), a Second Amendment dated October 29, 2004 (the “Second Amendment”) and most recently, a Third Amendment
dated March 24, 2005 (the “Third Amendment” and together with the Original Agreement, the First Amendment, and the Second Amendment, the “Agreement”); and 
 WHEREAS, Secured Party and Debtor desire to amend the Agreement in certain respects and to ratify and confirm the portions of the Agreement that
are not being amended by this Fourth Amendment; and 
 WHEREAS, Secured Party desires to signify its consent to the extension of the
Drawdown Period from the date of this Fourth Amendment through and including August 7, 2007, for a Committed Amount of $630,405.69. 
 NOW THEREFORE, in consideration of the foregoing and the mutual covenants set forth below and intending to be legally bound, the parties hereby agree as follows: 
 (1) Amendment to Master Security Agreement. The following amendments to the Agreement shall be made: 
 (a) Section l(a) “Equipment Loan Advances” is hereby deleted in its entirety and replaced with the following: 
 “(a) Equipment Loan Advances. Subject to the terms and conditions set forth in this Agreement, Secured Party agrees to make
advances for the purchase of Eligible Equipment (defined below) (each an “Equipment Loan Advance” and collectively “Equipment Loan Advances”) to Debtor from time to time on any business day during the period from August 7,
2006 up to and including, August 7, 2007 (the “Drawdown Period”); provided, however, that at no time shall the aggregate amount of all Equipment Loan Advances exceed the lesser of (i) one hundred percent
(100%) of the documented cost of the Eligible Equipment and (ii) Six Hundred Thirty Thousand Four Hundred Five Dollars and 69/100 ($630,405.69) (the “Committed Amount”), inclusive of amounts currently outstanding under previous
advances. “Eligible Equipment” for the purposes of this Agreement may include new lab and test equipment. Notwithstanding anything to the contrary contained in this Agreement, (i) any and all Equipment Loan Advances must be made
within ninety (90) days of Debtor’s purchase of Eligible Equipment, (ii) each Equipment Loan Advance must be equal to or greater than $50,000 and (iii) the Equipment Loan Advances are limited to five (5) in total. Any
amounts repaid with respect to any Equipment Loan Advance may not be reborrowed. 
 (b) Section 5(b) is hereby deleted in
its entirety and replaced with the following: 
 “(b) Debtor will deliver to Secured Party Debtor’s complete audited
financial statements, certified by a recognized firm of certified public accountants, within ninety (90) days of the close of each fiscal year of Debtor. In addition, Debtor will deliver to Secured Party Debtor’s quarterly management
prepared financial statements within thirty (30) days after the end of each fiscal quarter.” 
 (2) Ratification of Original
Agreement. Except as expressly amended hereby, the Agreement shall remain in full force and effect, and is hereby ratified and confirmed in all respects. 

 (3) Material Adverse Change. Secured Party’s obligation to enter into this Fourth Amendment
shall terminate if, in Secured Party’s sole discretion, there has been a material adverse change in the general affairs, management, results, operations, condition (financial or otherwise) of Debtor, whether or not arising from transactions in
the ordinary course of business, or if there has been any material adverse deviation by Debtor from the business plan of Debtor presented to and accepted by Secured Party prior to the execution of this Fourth Amendment. 
 (4) Miscellaneous 
 (a) Successors and Assigns. This Fourth Amendment shall inure to the benefit of and shall be binding upon the parties hereto and their respective successors and assigns. 
 (b) Severability. If any provision of this Fourth Amendment shall be held invalid or unenforceable by any court of competent
jurisdiction, such holding shall not invalidate or render unenforceable any other provision hereof. 
 (c) Modifications in
Writing. Amendments or modifications of any provision of this Fourth Amendment (including this paragraph) or any documents delivered in connection herewith shall in no event be effective unless the same shall be in writing and signed by the
party against whom enforcement is sought. 
 (d) Execution and Counterparts. This Fourth Amendment may be executed in
several counterparts, each of which shall be an original and all of which shall constitute one and the same document. 
 (e)
Captions. The captions and headings in this Fourth Amendment are for convenience only and do not define, limit or describe the intent of any provisions hereof. 
 (f) Definitions. Capitalized terms used herein, but not otherwise defined herein shall have the meanings given to them in the
Agreement. 
 [Signature Page to Follow] 

 IN WITNESS WHEREOF, the parties hereto have executed this Fourth Amendment to Master Security
Agreement by signature of their respective authorized representative set forth below. 
  

									
	Webster Bank, National Association	 		 	Achillion Pharmaceuticals, Inc.
					
	By:	 	/s/    JOHN E. ROSSI        	 		 	By:	 	/s/    MARY KAY FENTON        

	Name:	 	John E. Rossi	 		 	Name:	 	Mary Kay Fenton
	Title:	 	Senior Vice President	 		 	Title:	 	Vice President, Finance and CFO

 FIFTH AMENDMENT TO MASTER SECURITY AGREEMENT 
 This Fifth Amendment to Master Security Agreement (this “Fifth Amendment”) is made as of
the 7th of December, 2007 between Webster Bank, National Association (“Secured Party”) and Achillion Pharmaceuticals, Inc.
(“Debtor”). 
 WHEREAS, Secured Party and Debtor entered into that certain Master Security Agreement dated as of
May 15, 2003 (the “Original Agreement”), an Amendment dated May 15, 2003 (the “First Amendment”), a Second Amendment dated October 29, 2004 (the “Second Amendment”) a Third Amendment dated March 24,
2005 (the “Third Amendment”) and most recently a Fourth Amendment dated August     , 2006 (the “Fourth Amendment” and together with the Original Agreement, the First Amendment, the Second Amendment
and the Third Amendment, the “Agreement”); and 
 WHEREAS, Secured Party and Debtor desire to amend the Agreement in certain
respects and to ratify and confirm the portions of the Agreement that are not being amended by this Fifth Amendment; and 
 WHEREAS, Secured Party desires to signify its consent to the extension of the Drawdown from
the date of this Fifth Amendment through and including December 7th, 2008, for a Committed Amount of $500,000. 
 NOW THEREFORE, in consideration of the foregoing and the mutual covenants set forth below and intending to be legally bound, the parties hereby
agree as follows: 
 (1) Amendment to Master Security Agreement. The following amendments to the Agreement shall be made: 
 (a) Section 1(a) “Equipment Loan Advances” is hereby deleted in its entirety and replaced with the following: 
 “(a) Equipment Loan Advances. Subject to the terms and conditions set forth in this Agreement, Secured Party agrees to make
advances for the purchase of Eligible Equipment (defined below) (each an “Equipment Loan Advance” and collectively “Equipment Loan Advances”) to Debtor from time to time on any business day during the period from
December     , 2007 up to and including, December     , 2008 (the “Drawdown Period”); provided, however, that at no time shall the aggregate amount of all
Equipment Loan Advances exceed the lesser of (i) one hundred percent (100%) of the documented cost of the Eligible Equipment and (ii) Five Hundred Thousand Dollars and 00/100 ($500,000) (the “Committed Amount”), exclusive of
amounts currently outstanding under previous advances. “Eligible Equipment” for the purposes of this Agreement includes new lab and test equipment plus soft costs provided, however, that soft costs may not exceed twenty
percent (20%) of each Equipment Loan Advance. Notwithstanding anything to the contrary contained in this Agreement; (i) any and all Equipment Loan Advances must be made (A) no later than fifteen (15) days after or (B) ninety
(90) days prior to Debtor’s purchase of Eligible Equipment, (ii) each Equipment Loan Advance must be equal to or 

 
greater than $50,000 and (iii) the Equipment Loan Advances are limited to five (5) in total. Any amounts repaid with respect to any Equipment Loan
Advance may not be reborrowed. 
 (b) Exhibit A to the Agreement (the form of Note) is replaced in its entirety with Exhibit A
attached hereto. 
 (2) Ratification of Original Agreement. Except as expressly amended hereby, the Agreement shall remain in full force and effect,
and is hereby ratified and confirmed in all respects. 
 (3) Material Adverse Change. Secured Party’s obligation to enter into this Fifth
Amendment shall terminate if, in Secured Party’s sole discretion, there has been a material adverse change in the general affairs, management, results, operations, condition (financial or otherwise) of Debtor, whether or not arising from
transactions in the ordinary course of business, or if there has been any material adverse deviation by Debtor from the business plan of Debtor presented to and accepted by Secured Party prior to the execution of this Fifth Amendment. 
 (4) Miscellaneous 
 (a) Successors and Assigns.
This Fifth Amendment shall inure to the benefit of and shall be binding upon the parties hereto and their respective successors and assigns. 
 (b) Severability. If any provision of this Fifth Amendment shall be held invalid or unenforceable by any court of competent jurisdiction, such holding shall not invalidate or render unenforceable any other provision hereof.

 (c) Modifications in Writing. Amendments or modifications of any provision of this Fifth Amendment (including this paragraph) or any
documents delivered in connection herewith shall in no event be effective unless the same shall be in writing and signed by the party against whom enforcement is sought. 
 (d) Execution and Counterparts. This Fifth Amendment may be executed in several counterparts, each of which shall be an original and all of which shall constitute one and the same document. 
 (e) Captions. The captions and headings in this Fifth Amendment are for convenience only and do not define, limit or describe the intent of any
provisions hereof. 
 (f) Definitions. Capitalized terms used herein, but not otherwise defined herein shall have the meanings given to
them in the Agreement. 
 [Signature Page to Follow] 

 IN WITNESS WHEREOF, the parties hereto have executed this Fifth Amendment to Master Security Agreement by
signature of their respective authorized representative set forth below. 
  

									
	Webster Bank, National Association	 		 	Achillion Pharmaceuticals, Inc.
					
	By:	 	 /s/ Peter R. Hicks
	 		 	By:	 	 /s/ Mary Kay Fenton

	Name:	 	Peter R. Hicks	 		 	Name:	 	Mary Kay Fenton
	Title:	 	Vice President	 		 	Title:	 	Chief Financial Officer

 PROMISSORY NOTE 
 December 10, 2007 
 FOR VALUE RECEIVED, Achillion Pharmaceuticals, Inc. a corporation located at
the address stated below (“Maker”) promises, jointly and severally if more than one, to pay to the order of Webster Bank, National Association or any subsequent holder hereof (each, a “Payee”) at its office
located at 80 Elm Street, New Haven, CT 06510 or at such other place as Payee or the holder hereof may designate, the principal sum of Four Hundred Fourteen Thousand Six Hundred Twenty Three Dollars and forty five cents
($414,623.45), pursuant to that certain Master Security Agreement (“MSA”) by and between Webster Bank and Achillion Pharmaceuticals, Inc., dated as of May 15, 2003 as amended, and in effect from time to time, together with
interest on the unpaid principal balance, from the date hereof through and including the dates of payment, at a fixed interest rate [3 year US Treasury yield plus 450 basis points] of (7.46% ) per annum, to be paid in lawful money of
the United States, in thirty-six (36) consecutive monthly installments of principal and interest as follows: 
 Periodic 

 Installment Amount $12,889.75 
 each (“Periodic Installment”) and a final installment which shall be in the amount of the total
outstanding principal and interest. The first Periodic Installment shall be due and payable on January 1st, 2008 and the following Periodic
Installments and the final installment shall be due and payable on the first day of each succeeding month (each, a “Payment Date”); notwithstanding the foregoing, in the event this Note is dated other than the first day of a month,
the interest accruing from the date hereof through and including the date of the first Periodic Installment shall be paid in addition to, and together with, the first Periodic Installment. The Periodic Installments have been calculated on the basis
of a 360 day year of twelve 30-day months. Each payment may, at the option of the Payee, be calculated and applied on an assumption that such payment would be made on its due date. All terms and conditions of the MSA are incorporated herein, except
that in the event there are any conflicting terms and conditions, the terms and conditions of this Note shall prevail. 
 The acceptance by Payee of any
payment which is less than payment in full of all amounts due and owing at such time shall not constitute a waiver of Payee’s right to receive payment in full at such time or at any prior or subsequent time. 
 The Maker hereby expressly authorizes the Payee to insert the date value is actually given in the blank space on the face hereof and on all related documents pertaining
hereto. 
 This Note may be secured by a security agreement, chattel mortgage, pledge agreement or like instrument (each of which is hereinafter called a
“Security Agreement”). 
 Time is of the essence hereof. If any installment or any other sum due under this Note or any Security Agreement
is not received within ten (10) days after its due date, the Maker agrees to pay, in addition to the amount of each such installment or other sum, a late payment charge of five percent (5%) of the amount of said installment or other sum,
but not exceeding any lawful maximum. If (i) Maker fails to make payment of any amount due hereunder within ten (10) days 

 
after the same becomes due and payable; or (ii) Maker is in default under, or fails to perform under any term or condition contained in any Security
Agreement, then the entire principal sum remaining unpaid, together with all accrued interest thereon and any other sum payable under this Note or any Security Agreement, at the election of Payee, shall immediately become due and payable, with
interest thereon at the lesser of eighteen percent (18%) per annum or the highest rate not prohibited by applicable law from the date of such accelerated maturity until paid (both before and after any judgment). 
 The Maker may prepay its indebtedness hereunder, subject to a yield maintenance fee computed as follows. The current rate at the time of the prepayment for US Treasury
Bills with a maturity date closest to the maturity date of this Note shall be subtracted from the interest rate in effect at the time of the prepayment. If the result is zero or negative, there shall be no yield maintenance fee. If the result is a
positive number, then the resulting percentage shall be multiplied by the amount of the principal balance being repaid, divided by 360 and multiplied by the number of days remaining to the maturity date of this Note. Said amount shall be reduced to
present value by using the above-referenced US Treasury Bill rate and the number of days remaining to the maturity date of the term of this Note as of the date of repayment. The resulting amount is the yield maintenance fee. 
 It is the intention of the parties hereto to comply with the applicable usury laws; accordingly, it is agreed that, notwithstanding any provision to the contrary in this
Note or any Security Agreement, in no event shall this Note or any Security Agreement require the payment or permit the collection of interest in excess of the maximum amount permitted by applicable law. If any such excess interest is contracted
for, charged or received under this Note or any Security Agreement, or if all of the principal balance shall be prepaid, so that under any of such circumstances the amount of interest contracted for, charged or received under this Note or any
Security Agreement on the principal balance shall exceed the maximum amount of interest permitted by applicable law, then in such event (a) the provisions of this paragraph shall govern and control, (b) neither Maker nor any other person
or entity now or hereafter liable for the payment hereof shall be obligated to pay the amount of such interest to the extent that it is in excess of the maximum amount of interest permitted by applicable law, (c) any such excess which may have
been collected shall be either applied as a credit against the then unpaid principal balance or refunded to Maker, at the option of the Payee, and (d) the effective rate of interest shall be automatically reduced to the maximum lawful contract
rate allowed under applicable law as now or hereafter construed by the courts having jurisdiction thereof. It is further agreed that without limitation of the foregoing, all calculations of the rate of interest contracted for, charged or received
under this Note or any Security Agreement which are made for the purpose of determining whether such rate exceeds the maximum lawful contract rate, shall be made, to the extent permitted by applicable law, by amortizing, prorating, allocating and
spreading in equal parts during the period of the full stated term of the indebtedness evidenced hereby, all interest at any time contracted for, charged or received from Maker or otherwise by Payee in connection with such indebtedness; provided,
however, that if any applicable state law is amended or the law of the United States of America preempts any applicable state law, so that it becomes lawful for the Payee to receive a greater interest per annum rate than is presently allowed, the
Maker agrees that, on the effective date of such amendment or preemption, as the case may be, the lawful maximum hereunder shall be increased to the maximum interest per annum rate allowed by the amended state law or the law of the United States of
America. 

 The Maker and all sureties, endorsers, guarantors or any others (each such person, other than the Maker, an
“Obligor”) who may at any time become liable for the payment hereof jointly and severally consent hereby to any and all extensions of time, renewals, waivers or modifications of, and all substitutions or releases of, security or of
any party primarily or secondarily liable on this Note or any Security Agreement or any term and provision of either, which may be made, granted or consented to by Payee, and agree that suit may be brought and maintained against any one or more of
them, at the election of Payee without joinder of any other as a party thereto, and that Payee shall not be required first to foreclose, proceed against, or exhaust any security hereof in order to enforce payment of this Note. The Maker and each
Obligor hereby waives presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith, as well as filing of suit (if permitted by law) and diligence in collecting
this Note or enforcing any of the security hereof, and agrees to pay (if permitted by law) all expenses incurred in collection, including Payee’s actual attorneys’ fees. Maker and each Obligor agrees that fees not in excess of twenty
percent (20%) of the amount then due shall be deemed reasonable. 
 THE MAKER HEREBY UNCONDITIONALLY WANES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR
CAUSE OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE
RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT (INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH
OF DUTY CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.) THIS WAIVER IS IRREVOCABLE MEANING THAT IT MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR
MODIFICATIONS TO THIS NOTE, ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. IN THE EVENT OF LITIGATION, THIS NOTE MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 

 This Note and any Security Agreement constitute the entire agreement of the Maker and Payee with respect to the subject matter hereof and supercedes all
prior understandings, agreements and representations, express or implied. 
 No variation or modification of this Note, or any waiver of any of its
provisions or conditions, shall be valid unless in writing and signed by an authorized representative of Maker and Payee. Any such waiver, consent, modification or change shall be effective only in the specific instance and for the specific purpose
given. 
 Any provision in this Note or any Security Agreement which is in conflict with any statute, law or applicable rule shall be deemed omitted,
modified or altered to conform thereto. 

									
		 		 	Achillion Pharmaceuticals, Inc.
				
	 /s/ Marita Kheim
	 		 	By:	 	 /s/ Mary Kay Fenton

	(Witness)	 		 	Name:	 	Mary Kay Fenton
	  
 Marita Kheim
	 		 	Title:	 	CFO
	(Print Name)	 		 	Federal Tax ID #:	 	 52-2113479

				
	 300 George St., New Haven, CT 06511
	 		 	Address:	 	300 George Street, New Haven, New Haven County,
	(Address)	 		 		 	CT 06511

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