Document:

FORM OF WARRANT ISSUED BY THE COMPANY

 Exhibit 4.1 
  

THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY
NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED OR EXERCISED UNLESS AND UNTIL SUCH WARRANT AND/OR SHARES OF COMMON STOCK IS REGISTERED UNDER SUCH ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY IS OBTAINED TO THE
EFFECT THAT SUCH REGISTRATION IS NOT REQUIRED. THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUABLE UPON EXERCISE OF THIS WARRANT ARE SUBJECT TO THE RESTRICTIONS ON TRANSFER SET FORTH IN SECTIONS 4 AND 10 OF THIS WARRANT. 
  

	 Warrant No. [    ] 
	 Number of Shares: [    ] 

 (subject to adjustment) 
  
 Date of Issuance: As of September 29, 2003 
  
 GENOME THERAPEUTICS CORP. 
  
 Common Stock Purchase Warrant 
  
 (Void after five years) 
  
 GENOME THERAPEUTICS CORP., a Massachusetts corporation (the “Company”), for value received, hereby certifies that [INVESTOR], or its
registered assigns (the “Registered Holder”), is entitled, subject to the terms and conditions set forth below, to purchase from the Company, at any time after March 29, 2004 and on or before 5:00 p.m. (Eastern time) on September 29, 2008,
[NUMBER (    )] shares of Common Stock, of the Company, at a purchase price of $3.48 per share. The shares purchasable upon exercise of this Warrant, and the purchase price per share, each as adjusted
from time to time pursuant to the provisions of this Warrant, are hereinafter referred to as the “Warrant Shares” and the “Purchase Price,” respectively. 
  
 1.    Exercise. 
  
 (a) This Warrant may be exercised by the Registered Holder, in whole or in part, by surrendering this Warrant, with the purchase form appended hereto as
Exhibit I duly executed by the Registered Holder or by the Registered Holder’s duly authorized attorney, at the principal office of the Company, or at such other office or agency as the Company may designate, accompanied by payment in full, in
lawful money of the United States, of the Purchase Price payable in respect of the number of Warrant Shares purchased upon such exercise. 
  
 (b) Each exercise of this Warrant shall be deemed to have been effected immediately prior to the close of business on the day on which this Warrant shall
have been surrendered to the Company as provided in subsection 1(a) above accompanied by payment in full of the Purchase Price (the “Exercise Date”). At such time, the person or persons in whose name or names any certificates for Warrant
Shares shall be issuable upon such exercise as provided in subsection 1(d) below shall be deemed to have become the holder or holders of record of the Warrant Shares represented by such certificates. 

 (c) As soon as practicable after the exercise of this Warrant in full or in part, and in any event within
3 business days thereafter, the Company, at its expense, will cause to be issued in the name of, and delivered to, the Registered Holder, or as such Holder (upon payment by such Holder of any applicable transfer taxes) may direct: 
  
 (i) a certificate or certificates for the number of full
Warrant Shares to which the Registered Holder shall be entitled upon such exercise plus, in lieu of any fractional share to which the Registered Holder would otherwise be entitled, cash in an amount determined pursuant to Section 3 hereof; and

  
 (ii) in case such exercise is in part only, a
new warrant or warrants (dated the date hereof) of like tenor, calling in the aggregate on the face or faces thereof for the number of remaining Warrant Shares. 
  

2.    Adjustments. 
  
 (a) Adjustment for Stock Splits and Combinations.    If the Company shall at any time or from time to time after September 29,
2003 (the “Original Issue Date”) effect a subdivision of the outstanding Common Stock, the Purchase Price then in effect immediately before that subdivision shall be proportionately decreased. If the Company shall at any time or from time
to time after the Original Issue Date combine the outstanding shares of Common Stock, the Purchase Price then in effect immediately before the combination shall be proportionately increased. Any adjustment under this paragraph shall become effective
at the close of business on the date the subdivision or combination becomes effective. 
  
 (b) Adjustment for Certain Dividends and Distributions.    In the event the Company at any time, or from time to time after the Original Issue Date, shall make or issue, or fix a record date
for the determination of holders of Common Stock entitled to receive, a dividend or other distribution payable in additional shares of Common Stock, then and in each such event the Purchase Price then in effect immediately before such event shall be
decreased as of the time of such issuance or, in the event such a record date shall have been fixed, as of the close of business on such record date, by multiplying the Purchase Price then in effect by a fraction: 
  

	 	(1)	 	the numerator of which shall be the total number of shares of Common Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such
record date, and 

  

	 	(2)	 	the denominator of which shall be the total number of shares of Common Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such
record date plus the number of shares of Common Stock issuable in payment of such dividend or distribution; 

  
 provided, however, if such record date shall have been fixed and such dividend is not fully paid or if such distribution is not fully made on the date fixed therefore,
the Purchase Price shall be recomputed accordingly as of the close of business on such record date and thereafter the Purchase Price shall be adjusted pursuant to this paragraph as of the time of actual payment of such dividends or distributions.

  

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 (c) Adjustment in Number of Warrant Shares.    When any adjustment is required
to be made in the Purchase Price pursuant to subsections 2(a) or 2(b), the number of Warrant 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, multiplied by the Purchase Price in effect immediately prior to such adjustment, by (ii) the Purchase Price in effect immediately after such adjustment. 
  
 (d) Adjustments for Other Dividends and
Distributions.    In the event the Company at any time or from time to time after the Original Issue Date shall make or issue, or fix a record date for the determination of holders of Common Stock entitled to receive, a
dividend or other distribution payable in securities of the Company (other than shares of Common Stock) or in cash or other property (other than cash out of earnings or earned surplus, determined in accordance with generally accepted accounting
principles), then and in each such event provision shall be made so that the Registered Holder shall receive upon exercise hereof, in addition to the number of shares of Common Stock issuable hereunder, the kind and amount of securities of the
Company and/or cash and other property which the Registered Holder would have been entitled to receive had this Warrant been exercised into Common Stock on the date of such event and had the Registered Holder thereafter, during the period from the
date of such event to and including the Exercise Date, retained any such securities receivable, giving application to all adjustments called for during such period under this Section 2 with respect to the rights of the Registered Holder. 

 
 (e) Adjustment for Mergers or Reorganizations,
etc.    If there shall occur any reorganization, recapitalization, consolidation or merger involving the Company in which the Common Stock is converted into or exchanged for securities, cash or other property (other than a
transaction covered by subsections 2(a), 2(b) or 2(d)), then, following any such reorganization, recapitalization, consolidation or merger, the Registered Holder shall receive upon exercise hereof the kind and amount of securities, cash or other
property which the Registered Holder would have been entitled to receive if, immediately prior to such reorganization, recapitalization, consolidation or merger, the Registered Holder had held the number of shares of Common Stock subject to this
Warrant. The Company shall not effect any such reorganization, recapitalization, consolidation or merger unless prior to or simultaneously with the consummation thereof the successor company (if other than the Company) resulting from such
consolidation or merger or the corporation purchasing or otherwise acquiring such assets or other appropriate corporation or entity shall assume, by written instrument executed and delivered to the Company, the obligation to deliver to the holder of
this Warrant such shares of securities, cash or other property as, in accordance with the foregoing provisions, the Registered Holder may be entitled to purchase and the other obligations under this Warrant. 
  
 (f) Certificate as to Adjustments.    Upon the
occurrence of each adjustment or readjustment of the Purchase Price pursuant to this Section 2, the Company at its expense shall promptly compute such adjustment or readjustment in accordance with the terms hereof and furnish to the Registered
Holder a certificate setting forth such adjustment or readjustment (including the kind and amount of securities, cash or other property for which this Warrant shall be exercisable and the Purchase Price) and showing in detail the facts upon which
such adjustment or readjustment is based. The Company shall, upon the written request at any time of the Registered Holder, furnish or cause to be furnished to the Registered Holder a certificate 
  

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 setting forth (i) the Purchase Price then in effect and (ii) the number of shares of Common Stock and the amount, if any,
of other securities, cash or property which then would be received upon the exercise of this Warrant. 
  
 3.    Fractional Shares.    The Company shall not be required upon the exercise of this Warrant to issue any fractional shares, but shall make an adjustment
therefor in cash on the basis of the Fair Market Value per share of Common Stock. The Fair Market Value per share of Common Stock shall be determined as follows: 
  
 (i) If the Common Stock is listed on a national securities exchange, the Nasdaq National Market or another
nationally recognized trading system (including, without limitation, the OTC Bulletin Board and the Pink Sheets) as of the Exercise Date, the Fair Market Value per share of Common Stock shall be deemed to be the average of the high and low reported
sale prices per share of Common Stock thereon on the trading day immediately preceding the Exercise Date (provided that if no such price is reported on such day, the Fair Market Value per share of Common Stock shall be determined pursuant to clause
(ii)). 
  
 (ii) If the Common Stock is not listed
on a national securities exchange, the Nasdaq National Market or another nationally recognized trading system as of the Exercise Date, the Fair Market Value per share of Common Stock shall be deemed to be the amount most recently determined by the
Board of Directors to represent the fair market value per share of the Common Stock (including without limitation a determination for purposes of granting Common Stock options or issuing Common Stock under an employee benefit plan of the Company);
and, upon request of the Registered Holder, the Board of Directors (or a representative thereof) shall promptly notify the Registered Holder of the Fair Market Value per share of Common Stock. Notwithstanding the foregoing, if the Board of Directors
has not made such a determination within the three-month period prior to the Exercise Date, then (A) the Board of Directors shall make a determination of the Fair Market Value per share of the Common Stock within 15 days of a request by the
Registered Holder that it do so, and (B) the exercise of this Warrant pursuant to this subsection 1(b) shall be delayed until such determination is made. 
  
 4.    Requirements for Transfer. 
  
 (a) This Warrant and the Warrant Shares shall not be sold or transferred unless either (i) they first shall have been registered under the Securities Act
of 1933, as amended (the “Act”), or (ii) the Company first shall have been furnished with an opinion of legal counsel, reasonably satisfactory to the Company, to the effect that such sale or transfer is exempt from the registration
requirements of the Act. 
  
 (b) Notwithstanding the foregoing, no
registration or opinion of counsel shall be required for (i) a transfer by a Registered Holder which is a corporation to a wholly owned subsidiary of such corporation, a transfer by a Registered Holder which is a partnership to a partner of such
partnership or a retired partner of such partnership or to the estate of any such partner or retired partner, a transfer by a Registered Holder which is a limited liability company to a member of 
  

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 such limited liability company or a retired member or to the estate of any such member or retired member, or a transfer
by a Registered Holder which is a member of the National Association of Securities Dealers (the “NASD”) to an officer or employee of the Registered Holder as permitted by NASD rules, provided that the transferee in each case agrees in
writing to be subject to the terms of this Section 4, or (ii) a transfer made in accordance with Rule 144 under the Act. In no event shall the Company be required to accept any transfer which would result in there being more than five holders of
record of this Warrant. 
  
 (c) Each certificate representing
Warrant Shares shall bear a legend substantially in the following form: 
  
 “The securities represented by this certificate have not been registered under the Securities Act of 1933, as amended, and may not be offered, sold or otherwise transferred, pledged or hypothecated unless and until such securities are
registered under such Act or an opinion of counsel satisfactory to the Company is obtained to the effect that such registration is not required.” 
  
 The foregoing legend shall be removed from the certificates representing any Warrant Shares, at the request of the holder thereof, at such time as they become eligible
for resale pursuant to Rule 144(k) under the Act or if an effective registration statement is then in effect permitting the resale of the Warrant Shares. 
  
 5.    No Impairment.    The Company will not, by amendment of its charter or through any reorganization, transfer of
assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms of this Warrant, 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 the holder of this Warrant against impairment. 
  
 6.    Notices of Record Date, etc. In the event: 
  
 (a) the Company shall take a record of the holders of its Common Stock (or
other stock or securities at the time deliverable upon the exercise of this Warrant) for the purpose of entitling or enabling them to receive any dividend or other distribution, or to receive any right to subscribe for or purchase any shares of
stock of any class or any other securities, or to receive any other right; or 
  
 (b) of any capital reorganization of the Company, any reclassification of the Common Stock of the Company, any consolidation or merger of the Company with or into another corporation (other than a consolidation or
merger in which the Company is the surviving entity and its Common Stock is not converted into or exchanged for any other securities or property), or any transfer of all or substantially all of the assets of the Company, or the voluntary or
involuntary dissolution, liquidation or winding-up of the Company, then, and in each such case, the Company will mail or cause to be mailed to the Registered Holder a notice specifying, as the case may be, (i) the record date for such dividend,
distribution or right, and the amount and character of such dividend, distribution or right, or (ii) the effective date on which such reorganization, reclassification, consolidation, merger, transfer, dissolution, liquidation or 
  

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 winding-up is to take place, and the time, if any is to be fixed, as of which the holders of record of Common Stock (or
such other stock or securities at the time deliverable upon the exercise of this Warrant) shall be entitled to exchange their shares of Common Stock (or such other stock or securities) for securities or other property deliverable upon such
reorganization, reclassification, consolidation, merger, transfer, dissolution, liquidation or winding-up. Such notice shall be mailed at least ten days prior to the record date or effective date for the event specified in such notice. 

 
 7.    Reservation of Stock.    The
Company will at all times reserve and keep available, solely for issuance and delivery upon the exercise of this Warrant, such number of Warrant Shares and other securities, cash and/or property, as from time to time shall be issuable upon the
exercise of this Warrant. 
  
 8.    Exchange of
Warrants.    Upon the surrender by the Registered Holder, properly endorsed, to the Company at the principal office of the Company, the Company will, subject to the provisions of Section 4 hereof, issue and deliver to or upon
the order of such Holder, at the Company’s expense, a new Warrant or Warrants of like tenor, in the name of the Registered Holder or as the Registered Holder (upon payment by the Registered Holder of any applicable transfer taxes) may direct,
calling in the aggregate on the face or faces thereof for the number of shares of Common Stock (or other securities, cash and/or property) then issuable upon exercise of this Warrant. 
  
 9.    Replacement of Warrants.    Upon receipt of evidence reasonably satisfactory to
the Company of the loss, theft, destruction or mutilation of this Warrant and (in the case of loss, theft or destruction) upon delivery of an indemnity agreement (with surety if reasonably required) in an amount reasonably satisfactory to the
Company, or (in the case of mutilation) upon surrender and cancellation of this Warrant, the Company will issue, in lieu thereof, a new Warrant of like tenor. 
  

10.    Transfers, etc. 
  
 (a) The Company will maintain a register containing the name and address of the Registered Holder of this Warrant. The Registered Holder may change its or
his address as shown on the warrant register by written notice to the Company requesting such change. 
  
 (b) Subject to the provisions of Section 4 hereof, this Warrant and all rights hereunder are transferable, in whole or in part, upon surrender of this
Warrant with a properly executed assignment (in the form of Exhibit II hereto) at the principal office of the Company. 
  
 (c) Until any transfer of this Warrant is made in the warrant register, the Company may treat the Registered Holder as the absolute owner hereof for all
purposes; provided, however, that if and when this Warrant is properly assigned in blank, the Company may (but shall not be obligated to) treat the bearer hereof as the absolute owner hereof for all purposes, notwithstanding any notice to the
contrary. 
  
 11.    Representations of the
Registered Holder.    The Registered Holder of this Warrant represents and warrants to the Company as follows: 
  

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 (a) Investment.    The Registered Holder is acquiring this Warrant and the
Warrant Shares issuable upon the exercise of this Warrant, for its own account for investment and not with a view to, or for sale in connection with, any distribution thereof, nor with any present intention of distributing or selling the same,
except as otherwise may be permitted under applicable securities laws. 
  
 (b) Authority.    The Registered Holder has full power and authority to enter into and to perform this Warrant in accordance with its terms. The Registered Holder has not been organized specifically for the
purpose of investing in the Company. 
  
 (c) Accredited
Investor.    The Registered Holder is an Accredited Investor within the definition set forth in Rule 501(a) promulgated under the Securities Act. 
  
 12.    Mailing of Notices, etc.    All notices and other communications from the
Company to the Registered Holder shall be mailed by first-class certified or registered mail, postage prepaid, to the address last furnished to the Company in writing by the Registered Holder. All notices and other communications from the Registered
Holder or in connection herewith to the Company shall be mailed by first-class certified or registered mail, postage prepaid, to the Company at its principal office set forth below. If the Company should at any time change the location of its
principal office to a place other than as set forth below, it shall give prompt written notice to the Registered Holder and thereafter all references in this Warrant to the location of its principal office at the particular time shall be as so
specified in such notice. 
  
 13.    No Rights as
Stockholder.    Until the exercise of this Warrant, the Registered Holder shall not have or exercise any rights by virtue hereof as a stockholder of the Company. 
  
 14.    Change or Waiver.    Any term of this Warrant may be changed or waived only by
an instrument in writing signed by the party against which enforcement of the change or waiver is sought. 
  
 15.    Section Headings.    The section headings in this Warrant are for the convenience of the parties and in no way alter, modify, amend, limit or restrict the
contractual obligations of the parties. 
  
 16.    Governing Law.    This Warrant will be governed by and construed in accordance with the internal laws of The Commonwealth of Massachusetts (without reference to the conflicts of
law provisions thereof). 
  
 EXECUTED as of the Date of Issuance
indicated above. 
  
  
 GENOME THERAPEUTICS CORP. 
  
  
 By: ___________________________ 
  
  
 Title: __________________________ 
  
  
 ATTEST: 
  
 _____________________________ 
  

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 EXHIBIT I 
  
 PURCHASE FORM 
  

	 To: _______________ 
	 Dated:______________ 

  
  
 The undersigned, pursuant to the provisions set forth in the
attached Warrant (No.     ), hereby irrevocably elects to purchase          shares of the Common Stock covered by such Warrant. 
  
 The undersigned herewith makes payment of the full purchase price for such shares at the
price per share provided for in such Warrant, which is $            . Such payment takes the form of $            
in lawful money of the United States. 
  
  
 Signature: ____________________ 
  
  
 Address: _____________________ 
  
  
 _____________________ 
  

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 EXHIBIT II 
  
 ASSIGNMENT FORM 
  
 FOR VALUE RECEIVED,
                                        
                                        
                                        
     hereby sells, assigns and transfers all of the rights of the undersigned under the attached Warrant (No.     ) with respect to the number of shares of Common Stock covered thereby set forth
below, unto: 
  
 Name of
Assignee                                       
                                 
Address                                       
                      No. of Shares 
  
  
  
 Dated:
_____________________ 
  
 Signature: __________________________________

  
 Signature Guaranteed: 
  
 By: ______________________________ 
  
 The signature should be guaranteed 
 by an eligible guarantor institution 
 (banks, stockbrokers, savings and

 loan associations and credit unions 
 with membership in an
approved 
 signature guarantee medallion 
 program) pursuant to
Rule 17Ad-15 
 under the Securities Act of 1934. 
  

 -9-FORM OF SUBSCRIPTION AGREEMENT

 Exhibit 10.1 
  
 SUBSCRIPTION AGREEMENT 
  
 Genome Therapeutics Corp. 
 100 Beaver Street 
 Waltham, MA 02453 
  
 Ladies and Gentlemen: 
  
 The
undersigned subscriber (“Subscriber”) hereby tenders this Subscription Agreement (this “Agreement”) in accordance with and subject to the terms and conditions set forth herein: 
  
 1.    Subscription. 
  
 1.1.    Subscriber hereby subscribes for and agrees to
purchase the number of shares (the “Shares”) of common stock, par value $.10 per share (the “Common Stock”) of Genome Therapeutics Corp., a Massachusetts corporation (the “Company”) and warrants to purchase shares of
Common Stock (the “Warrants”), indicated on the signature page attached hereto at the purchase price set forth on such signature page (the “Purchase Price”). Subscriber has made or, prior to the Closing Date (as defined below),
will make payment by wire transfer of funds in accordance with instructions from the Company in the full amount of the Purchase Price of the Shares and Warrants for which Subscriber is subscribing (the “Payment”). 
  
 1.2.    This Agreement is part of an offering of Shares
and Warrants being conducted by Life Science Group, Inc. (the “Placement Agent”) on behalf of the Company (the “Offering”). 
  
 1.3.    Subscriber understands that it will not earn interest on any funds held by the Company prior to the date of closing of the
Offering. The Placement Agent and the Company will hold the closing of the Offering (the “Closing”) to occur on or before September 29, 2003. The date of the Closing is hereinafter referred to as the “Closing Date.” Subscriber
acknowledges that the Company has the obligation, subsequent to the Closing, to offer an aggregate of up to 1,408,480 Shares and 704,240 Warrants on the same terms as the Offering to the Tail Wind Fund, Ltd and Smithfield Fiduciary LLC in accordance
with the terms of the Company’s Amendment, Redemption and Exchange Agreements dated June 4, 2003. 
  
 1.4.    Subscriber agrees to be bound hereby upon (i) execution and delivery to the Company of the signature page to this Agreement,
(ii) written acceptance on the Closing Date by the Company of Subscriber’s subscription, which shall be confirmed by faxing to the Subscriber the signature page to this Agreement that has been executed by the Company (the
“Subscription”) and (iii) fulfillment by the Company of the conditions set forth in Section 3 hereof. 
  
 1.5.    Prior to acceptance of this Agreement by the Company, Subscriber agrees that the Company and Placement Agent may, as they
mutually agree in their sole and absolute discretion, reduce the size of Subscriber’s Subscription by giving notice by telephone to Subscriber; provided, however, that if Subscriber’s Subscription is so reduced, Subscriber may withdraw its

 entire Subscription. Subscriber hereby irrevocably constitutes and appoints the Placement Agent and each officer of the
Placement Agent, each of the foregoing acting singularly, in each case with full power of substitution, the true and lawful agent and attorney-in-fact of Subscriber, with full power and authority in Subscriber’s name, place and stead to amend
this Agreement, including, in each case, Subscriber’s signature page thereto, to effect any of the foregoing provisions of this Section 1.5. 
  
 1.6.    Upon receipt by the Company from the Subscriber of the Purchase Price for the Shares and the Warrants and the Company’s
acceptance of the Subscriber’s subscription in accordance with Section 1.4, a stock certificate for the Shares and a certificate for the Warrants so purchased will be issued in the name of such Subscriber, and the name of such Subscriber will
be registered on the stock transfer books of the Company as the record owner of such Shares and Warrants. 
  
 2.    Offering Material. Subscriber represents and warrants that it is in receipt of and that it has carefully read the following items: 
  
 (a)    The Company’s Annual Report on Form 10-K for
the period ended December 31, 2002 (the “Form 10-K”); 
  
 (b)    The Company’s Current Reports on Form 10-Q for the periods ended March 29, 2003 and June 28, 2003; 
  
 (c)    The Company’s Current Report on Form 8-K filed on August 13, 2003; 
  
 (d)    The Risk Factors set forth in the Company’s
Registration Statement on Form S-3/A filed on September 12, 2003; and 
  
 (e)    All other documents filed by the Company with the Securities and Exchange Commission (the “SEC”) subsequent to the Company’s Form 10-K and prior to the Closing Date. 
  
 The documents listed in this Section 2 shall be referred to herein as the
“Disclosure Documents.” 
  
 3.    Conditions to
Subscriber’s Obligations. 
  
 The obligation of
Subscriber to close the transaction contemplated by this Agreement (the “Transaction”) is subject to the satisfaction on or prior to the Closing Date of the following conditions set forth in Sections 3.1 through 3.4 hereof. 
  
 3.1.    The Company shall have executed this Agreement
and the Registration Rights Agreement attached hereto as Exhibit A (the “Registration Rights Agreement”) and delivered the same to Subscriber. 
  
 3.2.    Subscriber shall have received copies of all documents and information which it may have reasonably requested in connection
with the Offering. 
  

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 3.3.    The Company shall have caused its legal counsel to deliver to Subscriber a
legal opinion in substantially the form attached hereto as Exhibit B. 
  
 3.4.    No stop order or suspension of trading shall have been imposed by the Nasdaq National Market (“Nasdaq”), the SEC, or any other governmental regulatory body with respect to public trading in shares of
Common Stock of the Company. 
  
 4.    Representations and
Warranties. The Company represents and warrants to Subscriber as follows: 
  
 4.1.    The Company and each of its subsidiaries are corporations duly incorporated, validly existing and in good standing under the laws of their states of incorporation, with all requisite
corporate power and authority to carry on the business in which they are engaged and to own the properties they own, and the Company has all requisite power and authority to execute and deliver this Agreement and to consummate the transactions
contemplated hereby. The Company and each of its subsidiaries are duly qualified and licensed to do business and are in good standing in all jurisdictions where the nature of their business makes such qualification necessary, except where the
failure to be so qualified or licensed would not reasonably be expected to have a material adverse effect on the business or financial condition of the Company and its subsidiaries, taken as a whole (a “Material Adverse Effect”).

  
 4.2.    There are no legal actions or
administrative proceedings or investigations instituted, or to the knowledge of the Company, threatened, against the Company that would reasonably be expected to have a Material Adverse Effect, or which concerns the transactions contemplated by this
Agreement. 
  
 4.3.    The Company’s
audited consolidated financial statements as of December 31, 2002, contained in the Form 10-K, including the notes contained therein, fairly present the consolidated financial position of the Company at the respective dates thereof and the results
of its consolidated operations for the periods purported to be covered thereby. Such financial statements have been prepared in conformity with United States generally accepted accounting principles consistently applied with prior periods subject to
any comments and notes contained therein. All liabilities, contingent and other, of the Company and its subsidiaries, are set forth in the financial statements contained in the Form 10-Q for the quarter ended June 28, 2003, excepting only
liabilities incurred in the ordinary course of business subsequent to June 28, 2003, and liabilities of the type not required under generally accepted accounting principles to be reflected in such financial statements. Since June 28, 2003 there has
been no material adverse change in the financial condition of the Company from the financial condition stated in such financial statements. 
  
 4.4.    Schedule 4.4 hereto sets forth the authorized capital stock of the Company, the number of shares of the Company’s capital
stock issued and outstanding (prior to the issuance of the Shares), the number of shares of the Company’s capital stock issuable and reserved for issuance pursuant to the Company’s equity incentive plans, the number of shares of the
Company’s capital stock issuable and reserved for issuance pursuant to securities exercisable for, 
  

 -3- 

 or convertible into or exchangeable for any shares of the Company’s capital stock (prior to issuance of the
Warrants) as of the Closing Date.  
  
 4.5.    The Company has, or will have prior to the Closing, taken all corporate actions necessary to duly authorize the execution of this Agreement, the Registration Rights Agreement and the issuance and delivery of the
Shares and Warrants. The Company has, or will have prior to the Closing, reserved a sufficient number of shares of Common Stock for the issuance of Common Stock upon conversion of the Warrants. The Shares and Warrants are not subject to preemptive,
anti-dilution or other rights of any stockholders of the Company, except as set forth in Schedule 4.5 hereto, and when issued in accordance with the terms of this Agreement and the Articles of Organization of the Company, as amended (the
“Charter”), the Shares will be validly issued, fully paid and nonassessable and free and clear of all pledges, liens and encumbrances. 
  
 4.6.    Performance of this Agreement and compliance with the provisions hereof will not violate any provision of any applicable law
or of the Charter or Bylaws of the Company, or of any of its subsidiaries, and, will not conflict with or result in any breach of any of the terms, conditions or provisions of, or constitute a default under, or result in the creation or imposition
of any lien, charge or encumbrance upon, any of the properties or assets of the Company, or of any of its subsidiaries, pursuant to the terms of any indenture, mortgage, deed of trust or other agreement or instrument binding upon the Company, or any
of its subsidiaries, other than such breaches, defaults or liens which would not reasonably be expected to have a Material Adverse Effect. 
  
 4.7.    On their respective dates of filing, the Disclosure Documents (a) complied in all material respects with the requirements of
the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and the rules and regulations of the SEC thereunder, and (b) did not include any untrue statement of a material fact or omit to state a material fact required to be
stated therein or necessary to make the statements made therein, in light of the circumstances in which they were made, not misleading. 
  
 4.8.    This Agreement and the Registration Rights Agreement have been duly executed and delivered by the Company and constitute valid
and binding obligations of the Company, enforceable against the Company in accordance with their terms, subject to laws of general application relating to bankruptcy, insolvency and the relief of debtors and rules of law governing specific
performance, injunctive relief or other equitable remedies, and to limitations of public policy. 
  
 4.9.    Other than the filing of a Form D with the SEC and any state Blue Sky filings, which shall in each case be made prior to the
Closing Date, if so required, or if not so required, as soon after the Closing Date as is reasonably practicable, no registration, authorization, approval, qualification or consent of any court or governmental authority or agency is necessary in
connection with the execution and delivery of this Agreement or the offering, issuance or sale of the Shares and Warrants under this Agreement. 
  
 4.10.    The Company is not now, and after the sale of the Shares and the Warrants under this Agreement and the application of the net
proceeds from the sale of the Shares and the 
  

 -4- 

 Warrants will not be, an “investment company” within the meaning of the Investment Company Act of 1940, as
amended. 
  
 4.11.    Subject to the accuracy
of the Subscriber’s’ representations and warranties in Section 5 of this Agreement, the offer, sale, and issuance of the Shares and the Warrants in conformity with the terms of this Agreement constitute transactions exempt from the
registration requirements of Section 5 of the Securities Act of 1933, as amended (the “Securities Act”) and from the registration or qualification requirements of the laws of any applicable state or United States jurisdiction. 

 
 4.12.    Neither the Company, nor any of its
affiliates, nor any person acting on its or their behalf, has directly or indirectly made any offers or sales in any security or solicited any offers to buy any security under circumstances that would require registration under the Securities Act of
the issuance of the Shares and the Warrants to the Subscriber. The issuance of the Shares and the Warrants to the Subscribers will not be integrated with any other issuance of the Company’s securities (past, current or future) for purposes of
the Securities Act or any applicable rules of Nasdaq. 
  
 4.13.    The Company is eligible, and will take all action required to continue to be eligible, to register the Shares and the shares of Common Stock underlying the Warrants (the “Underlying Common Stock”) for
resale with the SEC on Form S-3 promulgated under the Securities Act. 
  
 4.14.    The Company owns or possesses adequate rights or licenses to use the inventions, know-how, patents, patent rights, copyrights, trademarks, trade names, licenses, trade secrets confidential information and other
intellectual property rights (collectively, “Intellectual Property Rights”) necessary to conduct the business now operated by it. To the knowledge of the Company, the Company’s patents and other Intellectual Property Rights and the
present activities of the Company do not infringe any patent, copyright, trademark, trade name or other proprietary rights of any third party, except where such infringement would not reasonably be expected to cause Material Adverse Effect, and
there is no claim, action or proceeding being made or brought against, or to the Company’s knowledge, being threatened against, the Company or its subsidiaries regarding its Intellectual Property Rights (other than as set forth in the
Company’s filings under the Exchange Act). The Company has no knowledge of the material infringement of its Intellectual Property Rights by third parties. The Company and its subsidiaries have taken reasonable security measures to protect the
secrecy, confidentiality and value of the Intellectual Property.  
  
 4.15.    The Underlying Common Shares have been duly authorized and reserved for issuance by all necessary corporate action on the part of the Company; and the shares of Common Stock issued in
connection with the Subscription Agreement and the Warrants, in each case, when issued, sold and delivered against payment therefore in accordance with the provisions of the Subscription Agreement, and the Underlying Shares, when issued against
payment therefore in accordance with the provisions of the Warrants, will be duly and validly issued, fully paid and non-assessable. 
  

 -5- 

 5.    Subscriber Representations. Subscriber hereby represents and warrants to the Company as
follows: 
  
 5.1.    Subscriber has been
furnished with and has carefully read the Disclosure Documents as set forth in Section 2 hereto and is familiar with the terms of the Offering. With respect to tax and other economic considerations involved in this investment, Subscriber is not
relying on the Company or the Placement Agent (or any agent or representative of any of them). Subscriber has carefully considered and has, to the extent Subscriber believes such discussion necessary, discussed with Subscriber’s legal, tax,
accounting and financial advisers the suitability of an investment in the Shares and the Warrants for Subscriber’s particular tax and financial situation. 
  

5.2.    Subscriber has had an opportunity to inspect relevant documents relating to the organization and operations of the Company.
Subscriber acknowledges that all documents, records and books pertaining to this investment which Subscriber has requested have been made available for inspection by Subscriber and Subscriber’s attorney, accountant or other advisor(s).

  
 5.3.    Subscriber and/or
Subscriber’s advisor(s) has/have had a reasonable opportunity to ask questions of and receive answers and to request additional relevant information from a person or persons acting on behalf of the Company concerning the Offering. 

 
 5.4.    Subscriber is not subscribing for the Shares
and the Warrants as a result of or subsequent to any advertisement, article, notice or other communication published in any newspaper, magazine or similar media or broadcast over television or radio or presented at any seminar. 
  
 5.5.    Subscriber is an “accredited investor,”
within the meaning of Rule 501 of Regulation D under the Securities Act (“Regulation D”). Subscriber, by reason of Subscriber’s business or financial experience or the business or financial experience of Subscriber’s professional
advisers who are unaffiliated with and who are not compensated by the Company or the Placement Agent or any affiliate of either of them, directly or indirectly, can be reasonably assumed to have the capacity to protect Subscriber’s own
interests in connection with the transaction. Subscriber further acknowledges that he has read the written materials provided by the Company. 
  
 5.6.    Subscriber has adequate means of providing for Subscriber’s current financial needs and contingencies, is able to bear
the substantial economic risks of an investment in the Shares and the Warrants for an indefinite period of time, has no need for liquidity in such investment and, at the present time, could afford a complete loss of such investment. 
  
 5.7.    Subscriber has such knowledge and experience in
financial, tax and business matters so as to enable Subscriber to use the information made available to Subscriber in connection with the Offering to evaluate the merits and risks of an investment in the Shares and the Warrants and to make an
informed investment decision with respect thereto. 
  

 -6- 

 5.8.    Subscriber acknowledges that the Shares, the Warrants and the Underlying
Common Stock herein subscribed for have not been registered under the Securities Act or under any state securities law. Subscriber understands further that in absence of an effective Registration Statement, the Shares, the Warrants and the
Underlying Common Stock can only be sold pursuant to an exemption from registration, such as Rule 144 promulgated under the Securities Act, which requires, among other conditions, that the Common Stock must be held for a minimum of one (1) year.
Subscriber shall not sell or otherwise transfer the Shares, the Warrants or the Underlying Common Stock unless such subsequent disposition is pursuant to an effective registration statement under the Securities Act or is exempt from registration.

  
 5.9.    Subscriber recognizes that
investment in the Shares and the Warrants involves substantial risks. Subscriber further recognizes that no federal or state agencies have passed upon this offering of the Shares and the Warrants or made any finding or determination as to the
fairness of this investment. 
  
 5.10.    Subscriber acknowledges that each certificate representing the Shares and the Underlying Common Stock shall contain a legend substantially in the following form: 
  
 THESE SHARES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933
(THE “SECURITIES ACT”) OR UNDER APPLICABLE STATE SECURITIES LAWS AND MAY NOT BE SOLD, TRANSFERRED OR OTHERWISE DISPOSED OF UNLESS REGISTERED UNDER THE SECURITIES ACT AND ANY APPLICABLE STATE SECURITIES LAWS OR PURSUANT TO AVAILABLE
EXEMPTIONS FROM SUCH REGISTRATION, PROVIDED THAT THE SELLER DELIVERS TO THE COMPANY AN OPINION OF COUNSEL (WHICH OPINION AND COUNSEL ARE SATISFACTORY TO THE COMPANY) CONFIRMING THE AVAILABILITY OF SUCH EXEMPTION. INVESTORS SHOULD BE AWARE THAT THEY
MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR AN INDEFINITE PERIOD OF TIME. 
  
 The foregoing legend shall be removed from the certificates representing any Shares, at the request of the holder thereof, at such time as they become eligible for resale pursuant to Rule 144(k) under the Act or if an
effective registration statement is then in effect permitting the resale of the Shares. 
  
 5.11.    The Subscriber has full power and authority (corporate, statutory and otherwise) to execute and deliver this Agreement and to purchase the Shares and the Warrants. This Agreement
constitutes the legal, valid and binding obligation of the Subscriber, enforceable against such Subscriber in accordance with its terms, subject to laws of general application relating to bankruptcy, insolvency and the relief of debtors and rules of
law governing specific performance, injunctive relief or other equitable remedies, and to limitations of public policy. 
  
 5.12.    No person or entity acting on behalf, or under the authority, of Subscriber is or will be entitled to any broker’s,
finder’s or similar fee or commission in connection with this Subscription. 
  

 -7- 

 5.13.    If Subscriber is a retirement plan or is investing on behalf of a retirement
plan, Subscriber acknowledges that investment in the Shares and the Warrants poses risks in addition to those associated with other investments, including the inability to use losses generated by an investment in the Shares and the Warrants to
offset taxable income. 
  
 5.14.    The
information furnished by Subscriber in the subscriber questionnaire attached hereto as Exhibit C (the “Subscriber Questionnaire”) signed by Subscriber is true and accurate as of the date thereof and as of the Closing Date of the
Subscription. 
  
 6.    Understandings. 
  
 6.1.    Subscriber hereby acknowledges and agrees that,
upon acceptance of its Subscription by the Company in accordance with the provisions of Section 1.4, the Subscription hereunder is irrevocable and binding on Subscriber. If the Subscriber executing this Subscription Agreement is more than one
natural person, the obligations of Subscriber hereunder shall be joint and several and the agreements, representations, warranties and acknowledgments herein contained shall be deemed to be made by and be binding upon each such person and his or her
heirs, executors, administrators, successors, legal representatives and permitted assigns. 
  
 6.2.    The Offering is intended to be exempt from registration under the Securities Act by virtue of Section 4(2) of the Securities Act and the provisions of Rule 506 of Regulation D thereunder,
which is in part dependent upon the truth, completeness and accuracy of the statements made by Subscriber herein and in the Subscriber Questionnaire. 
  
 6.3.    It is understood that in order not to jeopardize the Offering’s exempt status under Section 4(2) of the Securities Act
and Regulation D, any transferee may, at a minimum, be required to fulfill the investor suitability requirements thereunder. 
  
 6.4.    The Placement Agent will receive compensation from the Company in connection with the Offering but is not guaranteeing or
assuming responsibility for the operation or possible liability of the Company, including, without limitation, compliance by the Company with the agreements entered into in connection with the Offering, and the Placement Agent will not supervise or
participate in the operation or management of the Company. 
  
 6.5.    IN MAKING AN INVESTMENT DECISION, SUBSCRIBER MUST RELY ON ITS OWN EXAMINATION OF THE, COMPANY AND THE TERMS OF THE OFFERING, INCLUDING THE MERITS AND RISKS INVOLVED. THE SHARES AND THE WARRANTS HAVE NOT BEEN
RECOMMENDED BY ANY FEDERAL OR STATE SECURITIES COMMISSION OR REGULATORY AUTHORITY. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL OFFENSE. 
  
 6.6.    The Company will use its best efforts to cause the Shares to be listed on the principal national securities exchange, or
included in an inter-dealer quotation system of a registered national securities association, on or in which securities of the same class or series issued by the Company are then listed or included. 
  

 -8- 

 7.    Miscellaneous. 
  
 7.1.    Except as set forth elsewhere herein, any notice or demand to be given or served in connection
herewith shall be deemed to be sufficiently given or served for all purposes if made in writing by hand-delivery, registered first class mail, facsimile or reputable delivery service, such as Federal Express, by overnight delivery: 
  
 If to the Company, to it at: 
  
 Genome Therapeutics Corp. 
 100 Beaver Street 
 Waltham, Massachusetts
02453 
 Attention: Stephen Cohen 
 Title: Sr. Vice President and Chief Financial Officer 
 Facsimile #: 781-893-8277 
  
 If to the Subscriber, to it at the address set forth on the signature page
hereto. 
  
 7.2.    This Agreement shall be
enforced, governed and construed in all respects in accordance with the laws of The Commonwealth of Massachusetts, without giving effect to any choice or conflict of law provision or rule of any state that would cause the application of the laws of
any jurisdiction other than The Commonwealth of Massachusetts. 
  
 7.3.    Each party to this Agreement, by its execution hereof, (i) hereby irrevocably submits to the exclusive jurisdiction of the state courts of The Commonwealth of Massachusetts or the United States District Court
located in the District of Massachusetts for the purpose of any action or claim arising out of or based upon this Agreement or relating to the subject matter hereof, (ii) hereby waives to the extent not prohibited by applicable law, and agrees not
to assert by way of motion, as a defense or otherwise, in any such action, any claim that it is not subject personally to the jurisdiction of the above-named courts, that its property is exempt or immune from attachment or execution, that any such
proceeding brought in one of the above-named courts is improper, or that this Agreement or the subject matter hereof may not be enforced in or by such court, and (iii) hereby agrees not to commence any action or claim arising out of or based upon
this Agreement or relating to the subject matter hereof other than before one of the above-named courts nor to make any motion or take any other action seeking or intending to cause the transfer or removal of any such action or claim to any court
other than one of the above-named courts whether on the grounds of inconvenient forum or otherwise. Each party hereby consents to service of process in any such proceeding in any manner permitted by Massachusetts law. 
  
 7.4.    This Agreement, the Registration Rights
Agreement, the Warrants and the Subscriber Questionnaire constitute the entire agreement among the parties hereto with respect to the subject matter hereof. There are no restrictions, promises, warranties or undertakings, other than those set forth
herein or therein. This Agreement supercedes all prior agreements and understandings among the parties hereto with respect to the subject matter hereof. 
  

 -9- 

 7.5.    This Agreement shall be binding upon and inure to the benefit of the parties
named herein and their respective successors and permitted assigns. No party may assign either this Agreement or any of its rights, interests, or obligations hereunder without the prior written approval of the other party. 
  
 7.6.    This Agreement may be executed in one or more
counterparts, each of which shall be deemed an original but all of which together will constitute one and the same instrument. This Agreement may be delivered in facsimile. 
  
 7.7.    No amendment of any provision of this Agreement shall be valid unless the same shall be in
writing and signed by the Company and the Subscriber. No waiver by either party of any default, misrepresentation, or breach of warranty or covenant hereunder, whether intentional or not, shall be deemed to extend to any prior or subsequent default,
misrepresentation, or breach of warranty or covenant hereunder or affect in any way any rights arising by virtue of any prior or subsequent such occurrence. 
  
 7.8.    Any term or provision of this Agreement that is invalid or unenforceable in any situation in any jurisdiction shall not affect
the validity or enforceability of the remaining terms and provisions hereof or the validity or enforceability of the offending term or provision in any other situation or in any other jurisdiction. 
  
 [Remainder of Page Intentionally Left Blank] 
  

 -10- 

 IN WITNESS WHEREOF, the Company and the Subscriber have caused this Agreement to be duly executed as of
the date first above written. 
  
 GENOME
THERAPEUTICS CORP. 
  
 By:
                                        
                 
 Name: 
 Title: 
  
 [Subscriber] 
  
 By:
                                        
                 
 Name: 
 Title: 
  
 Subscriber’s Address: 
  
 ___________________________ 
  
 ___________________________ 
  
 ___________________________ 
 Facsimile #:
                                        

  
 Number of Shares of Common Stock 

To Be Purchased:
                     
 Warrants to Purchase                
 Shares of Common Stock 
  
 Purchase
Price: $

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