Document:

AMENDMENT TO EMPLOYMENT AGREEMENT

 Exhibit 10.7 
  
 Amendment to Employment Agreement 
  
 This AMENDMENT (this “Amendment”) TO THE EMPLOYMENT AGREEMENT referred to below is dated
February 5 , 2004 and entered into between Genome Therapeutics Corp., a Massachusetts corporation with its principal place of business and chief executive office at 100 Beaver St., Waltham, Massachusetts 02154 (the “Company”) and
Steven M. Rauscher with an address at 47 Cary Avenue, Lexington, Massachusetts 02451 (the “Executive”). 
  
 RECITALS: 
  
 WHEREAS, the Company and Executive entered into an Amended and Restated Employment Agreement dated as of May 9, 2001 (the “Employment
Agreement”), 
  
 WHEREAS, in connection with the
Company’s merger with GeneSoft Pharmaceuticals, Inc., the Company and Executive have agreed to amend the Employment Agreement as provided hereunder. 
  
 NOW, THEREFORE, in consideration of the premises and the agreements, provisions and covenants herein contained, the parties hereto agree as follows:

  

	Section 1.	AMENDMENT TO EMPLOYMENT AGREEMENT 

  

	(a)	Paragraph 4(d) is hereby amended by deleting such paragraph in its entirety and replacing it with a new Paragraph 4(d) as follows: 

  
 If within two years of a Change of Control (as defined below) of the Company
or the closing of the Genesoft Merger (as defined below), (i) you are terminated other than for Cause, or (ii) you terminate your employment with the surviving company due to the fact that (a) the surviving company takes any action that results in a
material diminution in your position, authority or duties as such position, authority or duties existed immediately prior to the Change of Control or the Genesoft Merger, as the case may be, provided, however, that your ceasing to serve as the
Chairman of the Board of Directors of the Company following the Genesoft Merger shall not constitute a material diminution in your position, authority or duties with the Company, or (b) the surviving company takes any action that would require you
to have your principal place of work changed to any location outside a thirty-five mile radius of the City of Boston, then, in the case of either (i) or (ii), the Company will continue to pay your Base Salary in effect on the Termination Date and
provide you with the benefits set forth in paragraph 2 of this agreement for a period of eighteen (18) months from the Termination Date. The Company will also pay you on the Termination Date any Base Salary earned but not paid through the
Termination Date. In addition, upon such termination, your remaining unvested options and non-exercisable restricted shares will immediately fully vest and all your options shall remain exercisable for a period equal to the lesser of two years from
the Termination Date or until the final exercise date of the options as determined in the applicable stock option agreement between yourself and the Company. All severance payments will be payable in accordance with the normal payroll practices of
the Company. If you are eligible for severance payments under this paragraph 4(d), then the provisions of paragraph 4(c) above shall not apply to such termination. 

	(b)	Paragraph 4(e) is hereby amended by adding the following definition in appropriate alphabetic order: 

  
 “Genesoft Merger” shall mean the consummation of the transactions pursuant to the Agreement and Plan of Merger and
Reorganization, dated as of November 17, 2003, among the Company, Guardian Acquisition, Inc., a wholly-owned subsidiary of the Company, GeneSoft Pharmaceutics, Inc. (“Genesoft”), and Luke Evnin, as the representative of the Genesoft
stockholders. 
  

	(c)	Paragraph 4(e)(iv) is hereby amended by inserting the following words at the end of clause (i) thereof: “provided, however, that your ceasing to serve as the Chairman of the
Board of Directors of the Company following the Genesoft Merger shall not constitute a material diminution in your position, authority or duties with the Company;”. 

  

	Section 2.	AFFIRMATION OF OTHER TERMS AND PROVISIONS 

  
 Except as expressly set forth herein, or amended hereby, the parties hereby ratify, acknowledge, confirm, and agree that all other terms and provisions of
the Employment Agreement shall remain in full force and effect. 
  

	Section 3.	EFFECTIVENESS 

  
 This Amendment shall become effective as of the date hereof. 
  

	Section 4.	MISCELLANEOUS 

  
 This Amendment may be executed in any number of counterparts, which together shall constitute one instrument, and delivery of an executed signature page
by facsimile transmission shall be effective as delivery of a manually executed counterpart. 
  

	Section 5.	GOVERNING LAW 

  
 This Amendment shall be governed and construed in accordance with the laws of the Commonwealth of Massachusetts, without regard to the conflict of laws
principles thereof. 
  

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 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly executed and delivered as of
the date first written above. 
  

					
	GENOME THERAPEUTICS CORP. 	 	 	 	 Accepted and Agreed: 

			
	/s/    NORBERT RIEDEL	 	 	 	/s/    STEVEN M. RAUSCHER
	
	 	 	 	

	 Norbert Riedel
 Chairman of the Stock Option

and Compensation Committee
	 	 	 	Steven M. Rauscher

  

 -3-LETTER AGREEMENT

 Exhibit 10.8 
  
 [Genome Therapeutics Corporation] 
  
 March 15, 2004 
  
 Dear Martin: 
  
 You have advised
us that you wish to leave Genome Therapeutics Corp. (the “Company”) no later than June 30, 2004, and we have agreed that it is in our mutual interests for there to be a transition period prior to a separation of your employment with the
Company. The purpose of this letter is to confirm the agreement between you and the Company concerning the remainder of your employment and your separation arrangements, as follows: 
  
 1.    Remaining Period of Employment and Employment Termination. 
  
 (a)    The Company will continue to
employ you in your current position, at a base rate of pay of $260,000 per year, retroactive to January 1, 2004, and will continue your participation in those of its benefit plans in which you are currently enrolled, during the remainder of your
employment with the Company. 
  
 (b)    The Company will pay you a bonus for 2003 of Seventy Two Thousand Seven Hundred and Fifty Dollars ($72,750) at the time 2003 bonuses are paid to other executives of the Company in the normal course. 
  
 (c)    You agree to continue to work to
accomplish the goals to which you and the Company have agreed (as set forth on Attachment A to this Agreement) and to otherwise cooperate to assure a smooth winding down or transition, as applicable, of your duties and responsibilities for
the Company. You will continue to provide services on a full-time basis until the termination of your employment, unless a reduced work schedule is initiated or approved by the Company. It is understood that the Company may hire your replacement
while your employment continues and, at the Company’s election, such replacement may begin employment and may assume the regular duties of your position and the management of personnel currently reporting to you. Further, in that event, the
Company may elect to assign you responsibility for assisting your replacement to fully assume your former responsibilities for a period not to exceed thirty (30) calendar days. 
  
 (d)    Your employment with the Company will terminate on June 30, 2004 (the
“Separation Date”). The Company, at its option, may relieve you of performing any further responsibilities for the Company prior to the Separation Date, but notwithstanding any such action, you will continue to be an employee through the
Separation Date with respect to your right to receive salary, accrue vacation, and receive or participate in all other employment benefits and 

 programs to which you are currently entitled, including but not limited to, participation in the Employee Stock Purchase
Program. You hereby resign all positions and offices held with the Company or any of its Affiliates (as hereafter defined), effective as of the earlier of the Separation Date or the date your performance obligations with the Company terminate. It is
understood that the Company will take actions in reliance on your resignation and that it is irrevocable. 
  
 (e)    The Company will fully fund its required match to your 401(k) plan contributions and accelerate the vesting of
all such Company matching funds, through the Separation Date, to the extent necessary to fully vest those contributions by the Separation Date, provided that such funding and vesting are permissible under plan terms and applicable law. 

 
 2.    Final Salary and Vacation Pay. You will
receive, no later than the Separation Date, pay for all work you have performed for the Company during the final payroll period of your employment, through the Separation Date, to the extent not previously paid. You will also receive pay, no later
than the Separation Date, for all vacation time you have earned but not used as of the Separation Date, as determined in accordance with the policies of the Company. 
  
 3.    Severance Payments and Benefits. Provided that you reasonably meet your obligations under
Section 1(c) hereof and the Employee Agreement (as defined in Section 7 hereof) to the reasonable satisfaction of the Company and otherwise meet the conditions set forth herein, including your obligation to sign an effective release of claims in the
form attached hereto and marked Attachment B (the “Release”), the Company will provide you the following severance payments and benefits: 
  
 (a)    The Company will pay you severance payments at the annual base rate set forth in Section 1(a) from the day
immediately following the Separation Date until the earlier of the expiration of 45 weeks or the date you commence new employment in a comparable position with equivalent compensation; provided, however, that if you obtain such other employment
prior to receiving 32 weeks of severance payments, the Company will nonetheless continue severance payments hereunder until you have received a total of 32 weeks of such payments. (The period of weeks of severance pay to which you are entitled
hereunder is referred to hereinafter as the “Severance Period.”) Severance payments will be made at the Company’s regular paydays, beginning on the Company’s next regular payday which is at least fifteen (15) business days
following the later of the effective date of the Release or the date it is received by the Company, but the first payment will be retroactive to the day immediately following the Separation Date. 
  
 (b)    (i) Following the Separation Date,
you and your eligible dependents may continue participation in the Company’s group health and dental plans under the federal law known as COBRA in compliance with COBRA regulations. If you elect to do so, then, from the day immediately
following the Separation Date until the sooner of the last day of the Severance Period or the date you become eligible for coverage under the group health and dental plans of another employer, the Company will contribute to the premium cost of that
participation at the same rate that it is contributing to the premium cost of active full-time employees (that is, 80% of the premium cost), provided that you pay the remainder of the premium cost by authorized deduction from your severance payments
and provided further that you notify the Company promptly when you become eligible for coverage from other employment. After the Company’s obligation hereunder to contribute to the premium cost of your coverage under its group health and dental

  

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 plans ceases, you and your eligible dependents may continue participation for any remaining period
permitted under COBRA by paying the full premium cost plus a small administrative fee no greater than the amount authorized by COBRA. (ii) Alternatively, if you do not elect continuing health and/or dental coverage under COBRA as of the Separation
Date, or if you elect not to continue such coverage, then, in lieu of the contributions to premium costs that the Company would otherwise be obligated to make under Section 3(c)(i), the Company will pay you seventy-five percent (75%) of such
contributions, from the later of the Separation Date or the date on which you elect to discontinue COBRA coverage through the last day of the Severance Period, such payment to be made in a single lump sum payable within fifteen (15) business days
following the Company’s receipt of your written notification that you have opted not to elect continuing coverage or to discontinue such coverage or, if later, your notice of whether you are electing cash or stock options pursuant to the
following sentence. You may elect to take any payment due you under the preceding sentence in cash or in a grant of options for shares of the Company’s common stock of equivalent cash value, with the price of such shares being discounted by 70%
of fair market value (“Discounted Stock Options”). All Discounted Stock Options granted to you under this Agreement shall be fully exercisable on the date of grant. 
  
 (c)    The Company will pay you a bonus for 2004 of not less than Thirty Thousand
Dollars ($30,000) and not more than thirty percent (30%) of your base salary, as set forth in Section l(a) hereof, with the amount of any bonus in excess of the minimum being determined by the Company based on its reasonable assessment of your
achievement of the transition goals set forth on Attachment A. Your bonus for 2004 will be paid within fifteen (15) business days of the Separation Date. You may elect to receive the bonus in cash or a grant of Discounted Stock Options.

  
 (e)    To assist you in
your search for other employment, the Company will provide you an additional lump sum payment in the amount of $8,500, payable within fifteen (15) business days following the later of the effective date of the Release or the date it is received by
the Company. 
  
 (f)    Any
stock options granted to you by the Company which are not exercisable on the Separation Date and not then exercised, expired or cancelled, shall continue to vest through the last day of the Severance Period, including the accelerated vesting process
specified in the letter agreement between you and the Company concerning your employment amended and restated as of March 31, 2003 (the “Employment Agreement”). You may exercise any vested stock options, provided that you do so within
ninety (90) days following the last day of the Severance Period. Any stock options not exercised prior to the end of that ninety (90) day period shall be cancelled. Your elections under this Section 3(f), including without limitation your decision
to delay the exercise of options vested on the Separation Date to a date more than three months from the Separation Date, may have tax consequences and the Company recommends that you consult your tax advisor. 
  
 (g)    As a condition of your eligibility
to receive the severance payments and other severance benefits set forth in this Section 3, you must sign and return the Release no earlier than the day immediately following the Separation Date and no later than 21 days thereafter, and having
signed and returned the Release, you must not revoke it in a timely manner thereafter. The Release creates legally binding obligations and the Company advises you to consult an attorney before signing it. 
  

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 4.    Withholding. All payments made by the Company under this Agreement shall
be reduced by any tax or other amounts required to be withheld by the Company under applicable law. 
  
 5.    Acknowledgement of Full Payment. You acknowledge and agree that the payments and benefits to be provided you in
accordance with Sections 1 and 2 of this Agreement are in complete satisfaction of any and all compensation due to you from the Company or any of its Affiliates, whether for services provided or otherwise, through the Separation Date and that,
except as expressly provided under this Agreement, no further compensation of any kind, in cash or equity or otherwise, is owed to you. 
  
 6.    Status of Employee Benefits and Paid Time Off. Except as otherwise expressly provided in Section 3(b) and 3(f) of this
Agreement, your participation in all employee benefit plans of the Company will end as of the Separation Date, in accordance with the terms of those plans. You will not continue to earn vacation or other paid time off after the Separation Date.

  
 7.    Continuing Obligations. You
agree to continue to honor all of your obligations under the agreement captioned “Invention Assignment, Non-Disclosure and Covenant Not to Compete” which you entered into with the Company in 2001 (the “Employee Agreement”);
provided, however, that the Company hereby waives Section 7(b)(ii) and Section 7(c) of that agreement with respect to your search for and acceptance of new employment, and the exercise of your responsibilities for a new employer, except to the
extent that you are directly employed by a company selling an oral quinolone antibiotic directly competitive with Factive and an oral non-absorbed antibiotic directly competitive with ramoplanin, as the senior vice president of marketing in direct
control of the marketing of such products. 
  
 8.    Mutual Non-Disparagement. You agree not to disparage the Company or its Affiliates, their business, products or management, publicly or to Company employees or to those with whom the Company does business.
The Company agrees that it will instruct its directors and senior officers (meaning those holding the office of vice president or above) not to speak disparagingly about you internally or publicly or to persons outside the Company who are within the
biotechnology industry. 
  
 9.    Cooperation with regard to Litigation. You agree, during the remainder of your employment and thereafter for a period of two (2) years (unless extended in a particular instance by legal mandate such as a
valid and binding subpoena or discovery request), to reasonably cooperate with the Company with respect to all matters arising during or related to your employment with the Company, including without limitation all matters in connection with any
governmental investigation, litigation or regulatory or other proceeding which may have arisen or which may arise following the signing of this Agreement. The Company will reimburse your reasonable out-of-pocket expenses incurred in complying with
its requests hereunder, subject to such substantiation and documentation as the Company may reasonably require. In addition, for all time spent complying with your obligations under this Section 9 at the request of the Company after the Separation
Date, the Company will pay you at your prevailing consulting rate. 
  
 10.    Definition of Affiliates. For purposes of this Agreement, “Affiliates” means all persons and entities directly or indirectly controlling, controlled by or under common control with the Company,
where control may be by management authority, equity interest or otherwise. 
  

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 11.    Indemnification and Insurance. The Company agrees that following the
termination of your employment, (i) any rights that you currently have to indemnification and contribution as an officer and employee of the Company under the Articles of Incorporation or By-Laws of the Company or any of its Affiliates will remain
in full force and effect; (ii) the Company will honor its obligations, if any, to indemnify and hold you harmless as a former officer, director and employee of the Company and any of its Affiliates, and will enforce any obligations of other parties
to do so, pursuant to the merger agreement and other documents executed in connection with the completed merger by and between the Company and Genesoft Pharmaceuticals, and pursuant to any joint venture, collaboration, licensing, and other
agreements executed by the Company in connection with any activities in which you were involved during the course of your employment with the Company; and (iii) you will continue to be covered as a former officer and employee of the Company under
the Company’s Directors and Officers liability insurance policy(ies) it elects to maintain for your actions while an officer, director and employee of the Company and its Affiliates. 
  
 12.    Complete Agreement and Amendment. This Agreement constitutes the entire agreement between
you and the Company and replaces all prior and contemporaneous agreements, communications and understandings, whether oral or written, with respect to your employment and its termination and all related matters, excluding only the Employee Agreement
to which reference is made in Section 7 above. This Agreement may not be modified or amended, and no breach shall be deemed to be waived, unless agreed to in writing by you and the Chief Executive Officer of the Company or his expressly authorized
designee. 
  
 13.    Captions and
Counterparts. The captions and headings in this Agreement are for convenience only and in no way define or describe the scope or content of any provision of this Agreement. This Agreement may be signed in two or more counterparts, each of which
shall be an original and all of which together shall constitute one and the same instrument. 
  
 If the terms of this Agreement are acceptable to you, please promptly sign, date and return it to me. At the time you sign and return it, this letter will take effect as a legally-binding agreement between you and the
Company on the basis set forth above. The enclosed counterpart of this Agreement, which you should also sign and date, is for your own records. 
  

			
	 Sincerely,
  
 GENOME THERAPEUTICS CORPORATION

		
	By:	 	 /s/    JOSEPH A. PANE

		
	Title:	 	 V.P. – Human Resources

		
	Date:	 	 March 15, 2004

  

			
	Accepted and agreed:
		
	Signature:	 	/s/    MARTIN D. WILLIAMS
	 	 	

	 	 	Martin D. Williams

			
		
	Date:	 	March 15, 2004
	 	 	

  

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 ATTACHMENT A 
 Transition Performance Objectives 
  

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