Document:

SECURITY AGREEMENT

 Exhibit 10.1 
  
 SECURITY AGREEMENT 
  
 This Agreement, dated as of November 17, 2003 is between GeneSoft Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and
Genome Therapeutics Corp., a Massachusetts corporation (the “Secured Party”). The parties agree as follows: 
  
 1. Security Interest. 
  
 1.1. Collateral. As security for the payment and performance of the Company’s obligations to the Secured Party under the Promissory Note (as
amended, restated, modified or supplemented from time to time, the “Note”) dated the date hereof and issued by the Company to the Secured Party in the aggregate principal amount of $6,200,000 (the “Secured
Obligations”), the Company hereby creates a security interest in favor of the Secured Party in all of the Company’s right, title and interest in and to (but none of its obligations or liabilities with respect to) all items and types of
present and future property described in clauses (a) through (f) below, whether now owned or hereafter acquired, all of which shall be included in the term “Collateral”: 
  
 (a) All goods and equipment now owned or hereafter acquired, including, without limitation, all laboratory
equipment, computer equipment, office equipment, machinery, fixtures, vehicles (including motor vehicles and trailers), and any interest in any of the foregoing, and all attachments, accessories, accessions, replacements, substitutions, additions,
and improvements to any of the foregoing, wherever located. 
  
 (b) All inventory now owned or hereafter acquired, including, without limitation, all merchandise, raw materials, parts, supplies, packing and shipping materials, work in process and finished products including such
inventory as is temporarily out of the Company’s custody or possession or in transit and including any returns upon any accounts or other proceeds, including insurance proceeds, resulting from the sale or disposition of any of the foregoing and
any documents of title representing any of the above, and the Company’s books relating to any of the foregoing. 
  
 (c) All contact rights and general intangibles, now owned or hereafter acquired or developed, including, without limitation, goodwill,
license agreements, franchise agreements, patents, patent rights (and applications and registrations therefor), trademarks and service marks (and applications and registrations therefor), inventions, copyrights, trade names, trade styles, trade
secrets, methods, processes, know how, all notes and records with respect to any research and development, blueprints, drawings, purchase orders, customer lists, route lists, infringements, claims, computer programs, computer disks, computer tapes,
literature, reports, catalogs, design rights, income tax refunds, payments of insurance and rights to payment of any kind. 
  
 (d) All now existing and hereafter arising accounts, contract rights, royalties, license rights and all other forms of obligations owing
to the Company arising out of the sale or lease of goods, the licensing of technology or the rendering of services by the Company (subject, in each case, to the contractual rights of third parties to require funds received by the Company to be
expended in a particular manner), whether or not earned by performance, and any and all credit insurance, guaranties, and other security therefor, as well as merchandise returned to or reclaimed by the Company and the Company’s books relating
to any of the foregoing. 
  
 (e) All documents,
cash, deposit accounts, letters of credit, certificates of deposit, instruments, chattel paper and investment property, including, without limitation, all securities, whether certificated or uncertificated, security entitlements, securities
accounts, commodity contracts and commodity accounts, and all financial assets held in any securities account or otherwise, wherever located, now owned or hereafter acquired and the Company’s books relating to the foregoing. 

 (f) Any and all claims, rights and interests in any of the above and all substitutions
for, additions and accessions to and proceeds thereof, including, without limitation, insurance, condemnation, requisition or similar payments and proceeds of the sale or licensing of Intellectual Property. 
  
 1.2. Perfection of Collateral. The Secured Party may at any time and
from time to time execute and file Uniform Commercial Code (“UCC”) financing statements, continuation statements and amendments thereto that describe the Collateral and contain any information required by the UCC or the applicable
filing office with respect to any such UCC financing statement, continuation statement or amendment thereof. Upon the Secured Party’s reasonable request from time to time, the Company will execute and deliver, and file and record in the proper
filing and recording places, all such instruments, including, without limitation, UCC financing statements, and will take all such other action, as the Secured Party deems reasonably necessary for perfecting or otherwise confirming to it the
security interest granted by the Company to the Secured Party in the Collateral pursuant to this Agreement. 
  
 1.3. No Liens or Dispositions. All Collateral shall be free and clear of any liens and restrictions on the transfer thereof, including, without
limitation, contractual provisions which prohibit the assignment of rights under contracts, except for (a) nonconsensual liens imposed by law; (b) liens and restrictions on transfer approved in writing by the Secured Party, and (c) liens existing on
the date hereof. Except with the Secured Party’s prior written consent, the Company will not sell, lease or otherwise dispose of any of the Collateral, except in each case in the ordinary course of business consistent with past practice.

  
 2. Right to Realize upon Collateral. Except to the extent prohibited by
applicable law that cannot be waived, this Section 2 shall govern the Secured Party’s rights to realize upon the Collateral if any default by the Company in respect of the Secured Obligations shall have occurred and be continuing (a
“Default”). The provisions of this Section 2 are in addition to any rights and remedies available at law or in equity. 
  
 2.1. Assembly of Collateral; Receiver. The Company shall, upon the Secured Party’s written request, assemble the Collateral and otherwise make
it available to the Secured Party. The Secured Party may have a receiver appointed for all or any portion of the Company’s assets or business which constitutes the Collateral in order to manage, protect, preserve, sell and otherwise dispose of
all or any portion of the Collateral. 
  
 2.2. Waiver. To
the extent it may lawfully do so, the Company waives and relinquishes the benefit and advantage of, and covenants not to assert against the Secured Party, any valuation, stay, appraisement, extension, redemption or similar laws now or hereafter
existing which, but for this Section 2.2, might be applicable to the sale of any Collateral made under the judgment, order or decree of any court, or privately under the power of sale conferred by this Agreement, or otherwise. 
  
 2.3. Foreclosure Sale. All or any part of the Collateral may be sold
for cash or other value in any number of lots at public or private sale, without demand, advertisement or notice; provided, however, that unless the Collateral to be sold threatens to decline speedily in value or is of a type
customarily sold on a recognized market, the Secured Party shall give the Company 10 days’ prior written notice of the time and place of any public sale, or the time after which a private sale may be made, which notice each of the Company and
the Secured Party agrees to be reasonable. At any sale or sales of Collateral, the Secured Party or any of its assigns may bid for and purchase all or any part of the property and rights so sold and may use all or any portion of the Secured
Obligations owed to the Secured Party as payment for the property or rights so purchased, and upon compliance with the terms of such sale may hold and dispose of such property and rights without further accountability to the Company, except for the
proceeds of such sale or sales pursuant to Section 2.4. 
  
 2.4.
Application of Proceeds. The proceeds of all sales and collections in respect of any Collateral or other assets of the Company, all funds collected from the Company and any cash contained in the Collateral, the application of which is not
otherwise specifically provided for herein, shall be applied as follows: 

 (a) first, to the payment of the costs and expenses of such sales and collections, the
reasonable expenses of the Secured Party and the reasonable fees and expenses of its counsel; 
  
 (b) second, any surplus then remaining to the payment of the Secured Obligations in such order and manner as the Secured Party may in its
reasonable discretion determine; and 
  
 (c)
third, any surplus then remaining shall be paid to the Company, subject, however, to any rights of the holder of any then existing lien who has duly presented to the Secured Party an authenticated demand for proceeds before the Secured Party’s
distribution of the proceeds is completed. 
  
 3. Custody of Collateral.
Except as provided by applicable law that cannot be waived, the Secured Party will have no duty as to the custody and protection of the Collateral, the collection of any part thereof or of any income thereon or the preservation or exercise of any
rights pertaining thereto, including, without limitation, rights against prior parties, except for the use of reasonable care in the custody and physical preservation of any Collateral in its possession. The Secured Party will not be liable or
responsible for any loss or damage to any Collateral, or for any diminution in the value thereof, by reason of the act or omission of any agent selected by the Secured Party acting in good faith. 
  
 4. General. This Agreement shall bind and inure to the benefit of the parties hereto
and their respective successors and assigns; provided, however, that the Company may not assign its rights or obligations hereunder without the prior written consent of the Secured Party. Notices shall be furnished in writing to each
party at such party’s address appearing on the signature page hereof or as such party may otherwise direct in writing actually received by the other party. The invalidity or unenforceability of any provision hereof shall not affect the validity
or enforceability of any other provision hereof, and any invalid or unenforceable provision shall be modified so as to be enforceable to the maximum extent of its validity or enforceability. The headings in this Agreement are for convenience of
reference only and shall not limit, alter or otherwise affect the meaning hereof. This Agreement constitutes the entire understanding of the parties with respect to the subject matter hereof and supersedes all prior and current understandings and
agreements, whether written or oral, with respect to such subject matter. This Agreement may be executed in any number of counterparts, which together shall constitute one instrument. This Agreement shall be governed by and construed in accordance
with the laws (other than the conflict of laws rules) of the State of New York, except as may be required by the UCC of other jurisdictions with respect to matters involving the perfection of the Secured Party’s lien on the Collateral located
in such other jurisdictions. 
  
 [The remainder of this page is
intentionally blank.] 

 Each of the undersigned has caused this Security Agreement to be executed and delivered by its duly
authorized officer as an agreement under seal as of the date first written above. 
  

	 COMPANY:
	  	 GENESOFT, INC.

		
	 	  	 By

	 	  	       Title:

		
	 SECURED PARTY:
	  	 GENOME THERAPEUTICS CORP.

		
	 	  	 By:

	 	  	       Name:

	 	  	       Title:WARRANT TO PURCHASE

 Exhibit 10.2 
  

	    	THIS WARRANT AND THE SECURITIES ISSUABLE UPON THE EXERCISE HEREOF HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. THEY MAY NOT BE SOLD, OFFERED FOR SALE,
PLEDGED, HYPOTHECATED, OR OTHERWISE TRANSFERRED EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT REGISTRATION IS NOT REQUIRED UNDER SUCH
ACT OR UNLESS SOLD PURSUANT TO RULE 144 UNDER SUCH ACT. 

  

	 Date of Issuance
	  	Void after
	 November 17, 2003
	  	November 17, 2008

  
 GENESOFT
PHARMACEUTICALS, INC. 
 WARRANT TO PURCHASE SHARES OF COMMON STOCK 
  
 FOR VALUE RECEIVED, this Warrant is issued to Genome Therapeutics Corp., a
Massachusetts corporation, or its assigns (the “Holder”) by GeneSoft Pharmaceuticals, Inc., a Delaware corporation (the “Company”). 
  
 This Warrant is issued pursuant to that certain Promissory Note issued by the Company to the Holder and dated as of the date hereof (the “Promissory
Note”). The Company, the Holder and the other parties thereto have entered into an Agreement and Plan of Merger and Reorganization dated the date hereof (the “Merger Agreement”), and capitalized terms not defined herein shall have the
meaning set forth in the Merger Agreement. 
  
 For purposes of
this Warrant, an “Adverse Termination Event” shall be deemed to have occurred if the Merger Agreement is terminated by Holder pursuant to (i) Section 8.01(b) of the Merger Agreement, but only if the primary reason that the Effective Time
has not occurred prior to April 30, 2004 is a result of the failure by the Company to satisfy a condition set forth in Sections 7.02(c), (f), (g), (i), (l), (m) or (n) of the Merger Agreement; (ii) Section 8.01(d) of the Merger Agreement; (iii)
Section 8.01(f) of the Merger Agreement; or (iv) Section 8.01(h) of the Merger Agreement. 
  
 ARTICLE VIPurchase of Shares. 
  
 (a) Number of Shares of Company Stock. Subject to the terms and conditions set forth herein, the Holder is entitled, upon surrender of this Warrant at the principal office of the Company (or at such other place
as the Company shall notify the Holder in writing), to purchase from the Company up to 457,838 fully paid and nonassessable shares of common stock, $0.0001 par value, of the Company (“Company Stock”), as adjusted pursuant to Section
6 hereof. 
  
 (b) Exercise Price. The purchase price for
the shares of Company Stock issuable pursuant to this Section 1 shall be $3.39 per share of Company Stock. The number of shares of Company Stock purchasable under this Warrant and the purchase price of such Company Stock shall be subject to
adjustment pursuant to Section 6 hereof. Such purchase price, as adjusted from time to time, is herein referred to as the “Exercise Price.” 
  
 ARTICLE VIIExercise Period. This Warrant shall be exercisable at any time following an Adverse Termination Event and shall expire on the
fifth anniversary of the date hereof; provided, however, that, subject to Section 3(d), this Warrant shall no longer be exercisable and shall become null and void upon the consummation of a Corporate Transaction (as defined below) or
the closing of the issuance and sale of shares of equity securities of the Company in the Company’s first underwritten public offering pursuant to an effective registration statement under the Securities Act of 1933, as amended (the
“Initial Public Offering”). In the event of a Corporate Transaction or Initial Public Offering, the Company shall notify the Holder at least ten (10) days prior to 

 
the consummation of such Corporate Transaction or Initial Public Offering. For purposes of this Warrant, a “Corporate Transaction” shall mean (i)
any acquisition of the Company by means of merger or other form of corporate reorganization in which outstanding shares of the Company are exchanged for securities or other consideration issued, or caused to be issued, by the acquiring corporation
or its subsidiary (other than a mere reincorporation transaction) and pursuant to which the holders of the outstanding voting securities of the Company as constituted immediately prior to such consolidation, merger or other transaction fail to hold
equity securities representing a majority of the voting power of the Company or surviving entity immediately following such consolidation, merger or other transaction, or (ii) a sale of all or substantially all of the assets of the Company.

  
 ARTICLE VIIIMethod of Exercise. 
  
 (a) While this Warrant remains outstanding and exercisable in accordance
with Section 2 above, the Holder may exercise, in whole or in part, the purchase rights evidenced hereby. Such exercise shall be effected by: 
  
 VIII.01.a.1 the surrender of the Warrant, together with a duly executed copy of the Notice of Exercise attached hereto, to the Secretary of the Company
at its principal office (or at such other place as the Company shall notify the Holder in writing); and 
  
 VIII.01.a.2 the payment to the Company of an amount equal to the aggregate Exercise Price for the number of shares of Company Stock being purchased.

  
 (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 is surrendered to the Company as provided in Section 3(a) above. At such time, the person or persons in whose name or names any certificate for the Company Stock
shall be issuable upon such exercise as provided in Section 3(c) below shall be deemed to have become the holder or holders of record of the Company Stock represented by such certificate. 
  
 (c) As soon as practicable after the exercise of this Warrant in whole or in part, the Company at its expense will cause to
be issued in the name of, and delivered to, the Holder, or as such Holder (upon payment by such Holder of any applicable transfer taxes) may direct: 
  
 VIII.01.c.1 a certificate or certificates for the number of shares of Company Stock to which such Holder shall be entitled, and 
  
 VIII.01.c.2 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 shares of Company Stock equal to the number of such shares of Company Stock called for on the face of this Warrant minus the number of
shares of Company Stock purchased by the Holder upon all exercises made in accordance with Section 3(a) above or Section 4 below. 
  
 (d) Notwithstanding the provisions of Section 2, if the Holder has not exercised this Warrant prior to the closing of a Corporate Transaction or an
Initial Public Offering, this Warrant shall automatically be deemed to be exercised in full in the manner set forth in Section 4, without any further action on behalf of the Holder, immediately prior to the closing of any such transaction.

  
 ARTICLE IXNet Exercise. In lieu of exercising
this Warrant for cash, the Holder may elect to receive shares equal to the value of this Warrant (or the portion thereof being exercised) by surrender of this Warrant at the principal office of the Company together with notice of such election (a
“Net Exercise”). A Holder who Net Exercises shall have the rights described in Sections 3(b) and 3(c) hereof, and the Company shall issue to such Holder the number of shares of Company Stock computed using the following formula:

  

	 X=
	  	 Y(A-B)

	  	A

 Where 
  

	 X  =
	  	The number of shares of Company Stock to be issued to the Holder.
		
	 Y  =
	  	The number of shares of Company Stock purchasable under this Warrant or, if only a portion of the Warrant is being exercised, the portion of the Warrant being exercised (at the
date of such calculation).
		
	 A  =
	  	The fair market value of one (1) share of Company Stock (at the date of such calculation).
		
	 B  =
	  	The Exercise Price (as adjusted to the date of such calculations).

  
 For purposes of this
Section 4, the fair market value of a share of Company Stock shall mean the average of the closing price of Company Stock quoted in the over-the-counter market in which the Company Stock is traded or the closing price quoted on any exchange or
electronic securities market on which the Company Stock is listed, whichever is applicable, as published in the Western Edition of The Wall Street Journal for the thirty (30) trading days prior to the date of determination of fair market
value (or such shorter period of time during which such Company Stock was traded over-the-counter or on such exchange). In the event that this Warrant is exercised pursuant to this Section 4 in connection with the Company’s Initial Public
Offering, the fair market value per share of Company Stock shall be the per share offering price to the public of the Company’s Initial Public Offering. If the Company Stock is not traded on the over-the-counter market, an exchange or an
electronic securities market, the fair market value shall be the price per share of Company Stock that the Company could obtain from a willing buyer for Company Stock sold by the Company from authorized but unissued Company Stock, as such prices
shall be determined in good faith by the Company’s Board of Directors. 
  
 ARTICLE XCovenants of the Company. 
  
 (a) Notices of Record Date. In the event of any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to receive any
dividend (other than a cash dividend which is the same as cash dividends paid in previous quarters or a stock dividend) or other distribution, the Company shall mail to the Holder, at least ten (10) days prior to such record date, a notice
specifying the date on which any such record is to be taken for the purpose of such dividend or distribution. 
  
 (b) Covenants as to Exercise Shares. The Company covenants and agrees that all shares of Company Stock that may be issued upon the exercise of the
rights represented by this Warrant will, upon issuance in accordance with the terms hereof, be validly issued and outstanding, fully paid and nonassessable, and free from all preemptive rights, taxes, liens and charges with respect to the issuance
thereof. The Company further covenants and agrees that the Company will, at all times after the issuance but prior to the expiration of this Warrant, have authorized and reserved, free from preemptive rights, a sufficient number of shares of its
Company Stock to provide for the exercise of the rights represented by this Warrant. If, at any time after the issuance but prior to the expiration of this Warrant, the number of authorized but unissued shares of Company Stock shall not be
sufficient to permit exercise of this Warrant, the Company will take such corporate action as may, in the reasonable opinion of its counsel, be necessary to increase its authorized but unissued shares of Company Stock to such number of shares as
shall be sufficient for such purposes. 
  
 (c) No
Impairment. Except and to the extent waived or consented to by the Holder, or as otherwise permitted under the terms hereof, the Company will not, by amendment of its Certificate of Incorporation 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 to be observed or performed hereunder by the Company, but will at all
times in good faith assist in the carrying out of all the provisions of this Warrant and in the taking of all such action as may be necessary or appropriate in order to protect the exercise rights of the Holder against impairment. 

 ARTICLE XIAdjustment of Exercise Price and Number of Shares. The number and kind of shares
purchasable upon exercise of this Warrant and the Exercise Price shall be subject to adjustment from time to time as follows: 
  
 (a) Subdivisions, Combinations and Other Issuances. If the Company shall at any time after the issuance but prior to the expiration of this Warrant
subdivide its Company Stock, by split-up or otherwise, or issue additional shares of its Company Stock as a dividend with respect to any shares of its Company Stock, the number of shares of Company Stock issuable on the exercise of this Warrant
shall forthwith be proportionately increased in the case of a subdivision or stock dividend, or proportionately decreased in the case of a combination. Appropriate adjustments shall also be made to the Exercise Price payable per share, but the
aggregate Exercise Price payable for the total number of shares of Company Stock purchasable under this Warrant (as adjusted) shall remain the same. Any adjustment under this Section 6(a) shall become effective at the close of business on the date
the subdivision or combination becomes effective, or as of the record date of such dividend, or in the event that no record date is fixed, upon the making of such dividend. 
  
 (b) Adjustment for Other Dividends and Distributions. In case the Company shall make or issue, or shall fix a record
date for the determination of eligible holders entitled to receive, a dividend or other distribution payable with respect to the shares purchasable upon exercise of this Warrant that is payable in (i) securities of the Company (other than issuances
with respect to which adjustment is made under Section 6(a)), or (ii) assets (other than cash dividends paid or payable solely out of retained earnings), then, and in each such case, the Holder, upon exercise of this Warrant at any time after the
consummation, effective date or record date of such event, shall receive, in addition to the shares of Company Stock issuable upon such exercise prior to such date, the securities or such other assets of the Company to which the Holder would have
been entitled upon such date if the Holder had exercised this Warrant immediately prior thereto (all subject to further adjustment as provided in this Warrant). 
  

(c) Reclassification, Reorganization and Consolidation. In case of any reclassification, capital reorganization or change in the capital stock
of the Company (other than as a result of a subdivision, combination or stock dividend provided for in Section 6(a) above), then, as a condition of such reclassification, reorganization or change, lawful provision shall be made, and duly executed
documents evidencing the same from the Company or its successor shall be delivered to the Holder, so that the Holder shall have the right at any time prior to the expiration of this Warrant to purchase, at a total price equal to that payable upon
the exercise of this Warrant, the kind and amount of shares of stock and other securities or property receivable in connection with such reclassification, reorganization or change by a holder of the same number and type of securities as were
purchasable by the Holder immediately prior to such reclassification, reorganization or change. In any such case appropriate provisions shall be made with respect to the rights and interest of the Holder so that the provisions hereof shall
thereafter be applicable with respect to any shares of stock or other securities or property deliverable upon exercise hereof, and appropriate adjustments shall be made to the Exercise Price per share of Company Stock payable hereunder, provided the
aggregate Exercise Price shall remain the same. 
  
 (d) Notice
of Adjustment. When any adjustment is required to be made in the number or kind of shares purchasable upon exercise of the Warrant, or in the Exercise Price, the Company shall promptly notify the Holder of such event and of the number of shares
of Company Stock or other securities or property thereafter purchasable upon exercise of this Warrant. 
  
 ARTICLE XIINo Fractional Shares or Scrip. No fractional shares or scrip representing fractional shares shall be issued upon the exercise of
this Warrant, but in lieu of such fractional shares the Company shall make a cash payment therefor on the basis of the Exercise Price then in effect. 
  
 ARTICLE XIIINo Stockholder Rights. Prior to exercise of this Warrant and pursuant to the terms of this Warrant, the Holder shall not be
entitled to any rights of a stockholder with respect to the Company Stock, including (without limitation) the right to vote such Company Stock, receive dividends or other distributions thereon, exercise preemptive rights or be notified of
stockholder meetings, and except as otherwise provided in this Warrant, such Holder shall not be entitled to any stockholder notice or other communication concerning the business or affairs of the Company. Nothing in this Section 8 shall be deemed
to modify any rights Holder may have pursuant to any other agreement with the Company, including, without limitation, the Promissory note and the Merger Agreement. 

 ARTICLE XIVTransfer of Warrant. Subject to compliance with applicable federal and state
securities laws and any other contractual restrictions between the Company and the Holder contained in the Merger Agreement, this Warrant and all rights hereunder are transferable in whole or in part by the Holder to any person or entity upon
written notice to the Company. Within a reasonable time after the Company’s receipt of an executed Assignment Form in the form attached hereto, the transfer shall be recorded on the books of the Company upon the surrender of this Warrant,
properly endorsed, to the Company at its principal offices, and the payment to the Company of all transfer taxes and other governmental charges imposed on such transfer. In the event of a partial transfer, the Company shall issue to the new holders
one or more appropriate new warrants. 
  
 ARTICLE
XVGoverning Law. This Warrant shall be governed by and construed under the laws (other than the conflict of laws rules) of the State of New York. 
  
 ARTICLE XVISuccessors and Assigns. The terms and provisions of this Warrant shall inure to the
benefit of, and be binding upon, the Company and the holders hereof and their respective successors and assigns. 
  
 ARTICLE XVIITitles and Subtitles. The titles and subtitles used in this Warrant are used for convenience only and are not to
be considered in construing or interpreting this Warrant. 
  
 ARTICLE XVIIINotices. All notices and other communications given or made pursuant hereto shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when
sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient, and if not so confirmed, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt
requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the respective parties at the
following addresses (or at such other addresses as shall be specified by notice given in accordance with this Section 13): 
  
 If to the Company: 
  
 GeneSoft Pharmaceuticals, Inc. 
 7300
Shoreline Court 
 South San Francisco, CA 94080 
 Attention: David B. Singer 
  
 If
to Holders: 
  
 Genome Therapeutics Corp. 
 100 Beaver Street 
 Waltham, MA 02453

 Attention: Chief Financial Officer 
 Facsimile No.: (781) 893-8277 
  
 with a copy to:

  
 Ropes & Gray LLP 
 One International Place 
 Boston, MA 02110

 Attention: Patrick O’Brien 
 Facsimile No.: (617) 951-7050 
  
 ARTICLE
XIXAmendments and Waivers. Any term of this Warrant may be amended and the observance of any term of this Warrant may be waived (either generally or in a particular instance and either retroactively or prospectively), with the written
consent of the Company and the Holder. Any waiver or amendment effected in accordance with this Section shall be binding upon the parties hereto, their successors and assigns. 

 ARTICLE XXSeverability. If any provision of this Warrant is held to be unenforceable under
applicable law, such provision shall be excluded from this Warrant and the balance of the Warrant shall be interpreted as if such provision were so excluded and shall be enforceable in accordance with its terms. 
  
 ARTICLE XXIRepresentations and Warranties of the Holder. In
connection with the transactions provided for herein, the Holder hereby represents and warrants to the Company that: 
  
 (a) Purchase Entirely for Own Account. The Holder acknowledges that this Warrant is entered into by the Company in reliance upon the Holder’s
representation to the Company that the Warrant and the Company Stock issuable upon exercise of the Warrant (collectively, the “Securities”) will be acquired for investment for the Holder’s own account, not as a nominee or agent, and
not with a view to the resale or distribution of any part thereof, and that the Holder has no present intention of selling, granting any participation in or otherwise distributing the same. By acknowledging this Warrant, the Holder further
represents that the Holder does not have any contract, undertaking, agreement, or arrangement with any person to sell, transfer or grant participations to such person or to any third person, with respect to the Securities. 
  
 (b) Disclosure of Information. The Holder acknowledges that it has
received all the information it considers necessary or appropriate for deciding whether to acquire the Securities. The Holder further represents that it has had an opportunity to ask questions and receive answers from the Company regarding the terms
and conditions of the offering of the Securities. 
  
 (c)
Investment Experience. The Holder acknowledges that it is able to fend for itself, can bear the economic risk of its investment, and has such knowledge and experience in financial or business matters that it is capable of evaluating the
merits and risks of the investment in the Securities. The Holder also represents it has not been organized solely for the purpose of acquiring the Securities. 
  

(d) Restricted Securities. The Holder understands that the Securities are characterized as “restricted securities” under the federal
securities laws inasmuch as they are being acquired from the Company in a transaction not involving a public offering and that under such laws and applicable regulations such securities may be resold without registration under the Securities Act of
1933, as amended (the “Act”), only in certain limited circumstances. In this connection, the Holder represents that it is familiar with Rule 144, as presently in effect, as promulgated by the SEC under the Act (“Rule 144”), and
understands the resale limitations imposed thereby and by the Act. 
  
 (e) Further Limitations on Disposition. Unless there is then in effect a registration statement under the Act covering a proposed disposition of Securities and such disposition is made in accordance with such registration statement,
the Holder agrees not to make any disposition of all or any portion of the Securities unless and until the transferee has agreed in writing for the benefit of the Company to be bound by the terms of this Section 16 (and, only in the event of a
transfer of this Warrant, agreed in writing to be bound by the terms of this Warrant) and the Holder shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances
surrounding the proposed disposition, and if reasonably requested by the Company, the Holder shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, that such disposition will not require registration of
such shares under the Act. It is agreed that the Company will not require opinions of counsel for transactions made pursuant to Rule 144 except in extraordinary circumstances. 
  
 (f) Legends. It is understood that the Securities may bear the following legend: 
  
 “THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED. THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, HYPOTHECATED, OR OTHERWISE TRANSFERRED EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933, 

 
AS AMENDED, OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT REGISTRATION IS NOT REQUIRED UNDER SUCH ACT OR UNLESS SOLD PURSUANT TO RULE 144 UNDER
SUCH ACT.” 
  

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

	 	 	GENESOFT PHARMACEUTICALS, INC.
			
	 	 	 By:
	 	  

	 	 	 	 	 David B. Singer

	 	 	 	 	 Chairman and Chief Executive Officer

		
	 Address:
	 	 7300 Shoreline Court

	 	 	 South San Francisco, CA 94080

  

	ACKNOWLEDGED AND AGREED:
	
	GENOME THERAPEUTICS CORP.
	
	 By:

	 Name:

	 Title:

 NOTICE OF EXERCISE 
  
 GeneSoft Pharmaceuticals, Inc. 
 Attention:
Corporate Secretary 
  
 The undersigned hereby elects to purchase,
pursuant to the provisions of the Warrant, as follows: 
  
                       shares of Company Stock pursuant to the terms of the attached Warrant, and tenders herewith payment in
cash of the Exercise Price of such Company Stock in full, together with all applicable transfer taxes, if any. 
  
          Net Exercise the attached Warrant with respect to
             shares of Company Stock. 
  

	 	 	 HOLDER:

		
	 Date:

	 	 By:

		
	 	 	 Address:

  

  

	 Name in which shares should be registered:
  

	 	 

 ASSIGNMENT FORM 
  
 (To assign the foregoing Warrant, execute 
 this form and supply required information. 
 Do not use this form to purchase shares.) 
  
 FOR VALUE
RECEIVED, the foregoing Warrant and all rights evidenced thereby are hereby assigned to: 
  

	 Name:

	(Please Print)
	 Address:

	(Please Print)

  

	 Dated:
	 	  

		
	 Holder’s
 Signature:
	 	  
  

		
	 Holder’s
 Address:
	 	  
  

  
 NOTE: The signature to this
Assignment Form must correspond with the name as it appears on the face of the Warrant. Officers of corporations and those acting in a fiduciary or other representative capacity should provide proper evidence of authority to assign the foregoing
Warrant.

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