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. 
  

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