Document:

Amendment to First Amended Employment Agreement with Alexis Borisy

 Exhibit 10.7 
 AMENDMENT 
 This Agreement amends the
agreement between CombinatoRx, Incorporated (the “Company”) and Alexis Borisy (the “Employee”) captioned First Amended Employment, Confidentiality and Non-Competition Agreement and dated as of the 1st day of July, 2004 (the “Employment Agreement”). All capitalized terms used in this Agreement shall have the meaning ascribed to them in the
Employment Agreement, unless otherwise expressly provided herein. 
 For good and valuable consideration, the receipt and sufficiency of
which is hereby acknowledged, the parties agree as follows: 
 1. Section 5(d) of the Employment Agreement is amended by striking the
existing Section 5(d) in its entirety and replacing it with the following: 
 “(d) By the Company Other than for
Cause. The Company may terminate the Employee’s employment hereunder other than For Cause at any time upon sixty (60) days’ notice to the Employee or Base Salary in lieu thereof. In the event of termination in accordance with this
Section 5(d), in addition to Final Compensation and any bonus compensation earned but unpaid for the prior fiscal year, the Employee shall be entitled to the same severance pay, benefit premium contributions, accelerated vesting of stock
options and restricted stock, and option exercise period that he would have been entitled to receive had the Employee’s employment been terminated by the Company pursuant to Section 5(g)(i) below.” 
 2. Section 5(e) of the Employment Agreement is amended by striking the existing Section 5(e) in its entirety and replacing it with the
following: 
 “(e) By the Employee for Good Reason. The Employee may terminate his employment hereunder for Good
Reason upon notice to the Company setting forth in reasonable detail the nature of such Good Reason. The following shall constitute Good Reason for termination by the Employee: (i) the Company materially reducing the scope of the
Employee’s duties and responsibilities or materially demoting or reducing the Employee’s authority; (ii) a material change to the Employee’s primary place of employment with the Company, which results in the Company changing the
Employee’s primary place of employment to a location that is more than fifty (50) miles from the Employee’s primary place of employment with the Company immediately prior to such change; or (iii) the Company materially reducing
the Employee’s Base Salary. In the event of termination in accordance with this Section 5(e), in addition to Final Compensation and any bonus compensation earned but unpaid for the prior fiscal year, the Employee shall be entitled to the
same severance pay, benefit premium contributions, accelerated vesting of stock options and restricted stock, and option exercise period that he would have been entitled to receive had the Employee’s employment been terminated by the Company
pursuant to Section 5(g)(i) below.” 
  

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 3. Section 5(g)(i) of the Employment Agreement is amended by striking the existing
Section 5(g)(i) in its entirety and replacing it with the following: 
 “(i) If a Change of Control (as defined
below) occurs and within two (2) years following such Change of Control, the Company terminates the Employee’s employment other than for Cause, or the Employee terminates his employment for Good Reason, the Company (A) shall pay the
Employee, as severance pay, an amount equal to twenty-four (24) months’ Base Salary at the rate in effect on the date of termination of the Employee’s employment, payable in a single lump sum within five (5) business days
following the effective date of the separation agreement required pursuant to Section 6(d) below; (B) shall pay the premium cost of the Employee’s participation in the Company’s group medical and dental plans for a period of
twenty-four (24) months following the date of termination, provided that the Employee is entitled to continue such participation under applicable law and plan terms; (C) shall cause to become vested on the date of termination 100% of the
options granted pursuant to Section 4(c) hereof or otherwise which remain unvested on that date and the Employee shall be entitled to not less than ninety (90) days following the date of termination to exercise all or any portion of such
options, provided that in no event may the exercise date extend beyond the original maximum term of the option; and (D) shall cause to become vested on the date of termination 100% of any restricted stock previously granted to the Employee
which remains unvested on that date.” 
 4. Section 5(g)(ii) of the Employment Agreement is hereby stricken in its entirety, and
the existing Section 5(g)(iii) is hereby renumbered as Section 5(g)(ii). Similarly, any references to Section 5(g)(iii) are hereby amended to refer to the new Section 5(g)(ii). 
 5. Section 6 of the Employment Agreement is amended by adding the following new Section 6(d): 
 “(d) Notwithstanding any other provision of this Agreement, in order to receive any severance pay, benefit premium contributions or
vesting of stock options or restricted stock under Section 5(d), 5(e) or 5(g), the Employee must execute, and not revoke, a separation agreement that includes a general release of claims in a form required by the Company.” 
 6. Section 12 of the Employment Agreement is amended by striking the existing Section 12(b) and replacing it with the following: 
 “(b) A “Change of Control” shall be deemed to have occurred when any of the following events takes place: (i) any
Person is or becomes the beneficial owner (as defined in Rule 13d-3 under the Securities and Exchange Act of 1934, as amended), directly or indirectly, of fifty (50%) percent or more of the outstanding common stock of the Company; (ii) a
sale, merger or consolidation after which securities possessing more than fifty (50%) percent of the total combined voting power of the Company’s outstanding securities have been transferred to or acquired by a Person or Persons 

  

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different from the Persons who held such percentage of the total combined voting power immediately prior to such transaction; (iii) the sale, transfer
or other disposition of all or substantially all of the Company’s assets to one or more Persons (other than a wholly owned subsidiary of the Company or a parent company whose stock ownership after the transaction is the same as the
Company’s ownership before the transaction); or (iv) an acquisition, merger or similar transaction or a divestiture of a substantial portion of the Company’s business after which your role is not substantially the same as such role
prior to the transaction.” 
 7. Add the following new Section 24: 
 “24. Timing of Payments. If at the time of the Employee’s separation from service, the Employee is a “specified
employee,” as hereinafter defined, any and all amounts payable under Section 5 in connection with such separation from service that constitute deferred compensation subject to IRC, § 409A (“Section 409A”), as determined by
the Company in its sole discretion, and that would (but for this sentence) be payable within six months following such separation from service, shall instead be paid on the date that follows the date of such separation from service by six
(6) months. For purposes of the preceding sentence, “separation from service” shall be determined in a manner consistent with subsection (a)(2)(A)(i) of Section 409A and the term “specified employee” shall mean an
individual determined by the Company to be a specified employee as defined in subsection (a)(2)(B)(i) of Section 409A.” 
 Except
as expressly modified herein, the Employment Agreement, and all of its terms and provisions, shall remain unchanged and in full force and effect. This Agreement may be executed in two or more counterparts, each of which shall be an original and all
of which together shall constitute one and the same instrument. 
 Intending to be legally bound, the parties have signed this Agreement to
take effect on the date on which it is signed by the second of the parties. 
  

									
	COMBINATORX, INCORPORATED:	 		 	THE EMPLOYEE:
				
	By:	 	/s/ Robert Forrester	 		 	/s/ Alexis Borisy
	Title:	 	EVP & Chief Financial Officer	 		 	Alexis Borisy
			
	Date: December 12, 2008	 		 	Date: December 12, 2008

  

 3Letter Agreement Re: Retention Bonus with Alexis Borisy

 Exhibit 10.8 
 

 
 December 12, 2008 
 Alexis
Borisy 
 President and Chief Executive Officer 
 c/o CombinatoRx,
Incorporated 
 245 First Street 
 Cambridge, MA 02142 

 

	Re:	Retention Bonus 

 Dear Alexis: 
 As we discussed, subject to the terms and conditions described below, CombinatoRx, Incorporated (the “Company”) is prepared to offer you a bonus of $300,000,
less legally required deductions (the “Retention Bonus”). The Company will pay you $150,000 of the Retention Bonus if you remain continuously employed by the Company through April 1, 2009, and $150,000 of the Retention Bonus if you
remain continuously employed by the Company through January 15, 2010, each such $150,000 amount to be paid to you within five (5) business days following the applicable April 1, 2009 or January 15, 2010 date; provided, however,
that if the Company terminates your employment without Cause (as defined below) or you terminate for Good Reason (as also defined below) prior to either of the payment dates described above, you will still be eligible to receive the unpaid portion
of the Retention Bonus following your termination of employment without Cause or for Good Reason, such unpaid amount to be paid to you within five (5) business days following the effective date of the required General Release of All Claims. If
you resign your employment for any reason other than for Good Reason (as defined below) prior to January 15, 2010 or the Company terminates your employment with Cause (as defined below) prior to January 15, 2010, you will not be eligible
to receive the unpaid portion of the Retention Bonus. 
 For purposes of this letter, Cause shall mean (i) your conviction of a felony; (ii) your
willful failure to perform (other than by reason of disability), or gross negligence in the performance of, your duties and responsibilities as determined by the Board of Directors, which failure or negligence continues or remains uncured after
thirty (30) days’ written notice to you setting forth in reasonable detail the nature of such failure or negligence; (iii) material breach by you of any provision of any agreement between you and the Company, which breach continues or
remains uncured after thirty (30) days’ written notice to you from the Board of Directors setting forth in reasonable detail the nature of such breach; or (iv) material fraudulent conduct by you with respect to the Company as
determined by the Board of Directors. Additionally, for purposes of this letter, Good Reason shall mean your election to terminate employment with the Company as a result of (i) the Company materially reducing the scope of your duties and
responsibilities or materially demoting or reducing your authority; (ii) a material change to your primary place of employment with the Company, which results in the Company changing your primary place of employment to a location that is more
than fifty (50) miles from your 
 245 First Street, Cambridge, MA 02142 
 Ph: 617 301 7000 Fax: 617 301 7010 www.combinatorx.com 

 

 
 primary place of employment with the Company immediately prior to such change; or (iii) the Company materially reducing
your base salary. In the case of a termination by the Company without Cause (as defined above) or by you for Good Reason (as defined above), in order to receive the unpaid portion of the Retention Bonus, you must execute and not revoke a General
Release of All Claims in a form required by the Company. 
 You agree that you will not disclose this Agreement or any of its terms, except to members of
your immediate family and to your legal and tax advisors. This letter agreement shall be binding on all of the Company’s successors or assigns. 
  

	
	Sincerely,
	
	/s/ Robert Forrester
	Robert Forrester
	Executive Vice President and Chief Financial Officer

  

	
	ACKNOWLEDGMENT:
	
	/s/ Alexis Borisy
	Signature

 Dated: December 15, 2008 
 245 First Street, Cambridge, MA 02142 
 Ph: 617 301 7000 Fax: 617 301 7010 www.combinatorx.com

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