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.”

 

1

--------------------------------------------------------------------------------

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

 

2

--------------------------------------------------------------------------------

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

 

3