Exhibit 10.6

CONSULTING AGREEMENT

THIS CONSULTING AGREEMENT (the “Agreement”) is made and entered into this 1st
day of July, 2009 (the “Effective Date”) by and between CombinatoRx,
Incorporated, a Delaware corporation duly organized under law and having a usual
place of business at 245 First Street, Cambridge, MA 02142 (hereinafter referred
to as the “Company”) and Alexis Borisy.

WHEREAS, the Consultant previously provided services to the Company as its
President and CEO pursuant to that First Amended Employment, Confidentiality and
Non-Competition Agreement, dated as of July 1, 2004, as amended on December 12,
2008 (the “Employment Agreement”),

WHEREAS, the Company and the Consultant have agreed to terminate the
Consultant’s employment relationship with the Company under the Employment
Agreement, and the Company wishes to engage the Consultant to provide the
services described herein and Consultant agrees to provide the services for the
compensation and otherwise in accordance with the terms and conditions contained
in this Agreement,

NOW THEREFORE, in consideration of the foregoing, and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, accepted and agreed to, the Company and the Consultant, intending
to be legally bound, agree to the terms set forth below.

1. TERM. Commencing as of the Effective Date, and continuing until June 30, 2010
(the “Term”), unless earlier terminated pursuant to Section 5 hereof, the
Consultant agrees that he will serve as a member of the Company’s Scientific
Advisory Board and as a consultant to the Company. This Agreement may be renewed
or extended for any period as may be agreed by the parties.

2. DUTIES AND SERVICES.

(a) Consultant’s duties and responsibilities shall be as described in Exhibit
“A,” annexed hereto and made a part hereof (collectively, the “Duties” or
“Services”).

(b) The Consultant represents and warrants to the Company that he is under no
contractual or other restrictions or obligations which are inconsistent with the
execution of this Agreement, or which will interfere with the performance of his
Duties. Consultant represents and warrants that the execution and performance of
this Agreement will not violate any policies or procedures of any other person
or entity for which he performs Services concurrently with those performed
herein. Consultant understands and agrees that he will not bring to the Company
or use in the performance of Consultant’s duties at the Company any materials or
documents rightfully belonging to any other party which are not generally
available to the public. Consultant may bring such materials and documents to
the Company provided Consultant has

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

obtained written authorization from such other party for their possession and
use. Further, Consultant agrees that he will not enter into any agreement
(either written or oral) which would put Consultant in conflict with this
Agreement and/or require that he disclose Confidential Information.

(c) In performing the Services, Consultant shall comply, to the best of his
knowledge, with all business conduct and regulatory and health and safety
guidelines, policies and regulations established by the Company or any
governmental authority with respect to the Company’s business.

(d) Consultant represents that he has not been disbarred and, to the best of his
knowledge, is not under consideration for disbarment by the Food and Drug
Administration from working in or providing services to any pharmaceutical or
biotechnology company under the Generic Drug Enforcement Act of 1992.

3. CONSULTING FEE.

(a) Subject to the provisions hereof, the Company shall pay Consultant a
consulting fee as described in Appendix A. The Consultant shall submit monthly,
on the Company’s standard reporting form, a listing of his hours, the Duties
performed and a summary of his activities. The Consulting Fee shall be paid
within thirty (30) days of the Company’s receipt of the report and invoice.

(b) Consultant shall be entitled to prompt reimbursement for all pre-approved
expenses incurred in the performance of his Duties, upon submission and approval
of written statements and receipts in accordance with the then regular
procedures of the Company. Pre-approval is required for expenses in excess of
$500.00.

4. RELATIONSHIP OF THE PARTIES.

(a) The Consultant agrees that all Services will be rendered by him as an
independent contractor and this Agreement is not to be interpreted as creating
an employment relationship between the Consultant and the Company or any of its
Affiliates. It is agreed that, as an independent contractor, the Consultant will
not attempt to bind the Company or any of its Affiliates to any obligation or
pledge its credit, unless expressly authorized in writing by the CEO or another
expressly authorized representative of the Company. Affiliates means all natural
persons and entities controlling, controlled by or under common control with the
Company, where control may be by management authority, contract or equity
interest.

(b) Because the Consultant is an independent contractor with respect to the
Company, the consulting fees paid under this Agreement are not subject to
withholding for Social Security, unemployment, Medicare, federal, state or local
income or other taxes. All taxes and other legally required payments and any
insurance required by law shall be the sole responsibility of the Consultant.
The Consultant agrees to pay all taxes, including self-employment taxes due in
respect of the Consulting Fee and to indemnify the Company in the event the
Company is required to pay any such taxes on behalf of Consultant.

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

(c) As an independent contractor, neither the Consultant nor anyone claiming
through the Consultant shall be eligible to participate in, or receive benefits
under, any bonus or other compensation plan or any stock option plan, employee
benefit plan or other employee plan, program or arrangement of the Company or
any of its Affiliates.

(d) The Consultant agrees and acknowledges that the Company will not maintain
general liability or other insurance covering him. The Consultant will be solely
responsible for comprehensive general liability, automobile and other insurance
and will assume all risk in connection with the adequacy of any and all such
insurance which the Consultant elects to obtain.

5. EARLY TERMINATION OF THE TERM.

(a) This Agreement may be terminated without cause by either party upon not less
than thirty (30) days’ prior written notice by either party to the other.

(b) Upon termination under Section 5(a), neither party shall have any further
obligations under this Agreement, except for the obligations which by their
terms survive this termination as noted in Section 17 hereof. Upon termination,
and in any case upon the Company’s request, Consultant shall return immediately
to the Company all Confidential Information and copies thereof.

6. CONTINUING OBLIGATIONS. The Consultant acknowledges that he has continuing
obligations to the Company pursuant to the terms of Sections 7, 8, 9 and 10 of
the Employment Agreement and pursuant to the terms of the letter agreement with
the Company dated July 1, 2009. The Consultant acknowledges those continuing
obligations and agrees to abide by them.

7. PROPRIETARY RIGHTS.

(a) Definitions. For the purposes of this Section 7, the terms set forth below
shall have the following meanings:

(i) Concept and Ideas. Those concepts and ideas disclosed by the Company to
Consultant or which are first developed by Consultant during the course of the
performance of Services hereunder and which relate to the Company’s present,
past or prospective business activities, services, and products, all of which
shall remain the sole and exclusive property of the Company. The Consultant
shall have no publication rights, and all of the same shall belong exclusively
to the Company.

(ii) Confidential Information. For the purposes of this Agreement, Confidential
Information shall mean and collectively include all information relating to the
business, plans and/or technology of the Company including but not limited to
technical information, including inventions, methods, plans, processes,
specifications, characteristics, assays, raw data, scientific preclinical or
clinical data, records, databases, formulations, clinical protocols, equipment
design, know-how, experience, and trade secrets; developmental,

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

marketing, sales, customer, supplier, consulting relationship information,
operating, performance, and cost information; computer programming techniques;
microscopy technology and signal identification strategy whether in tangible or
intangible form; and, all record bearing media containing or disclosing the
foregoing information and techniques, including written business plans, patents
and patent applications, grant applications, notes, and memoranda, whether in
writing or presented, stored or maintained in or by electronic, magnetic, or
other means.

Notwithstanding the foregoing, the term “Confidential Information” shall not
include any information which: (a) can be demonstrated to have been in the
public domain or was publicly known or available prior to the date of the
disclosure to Consultant; (b) can be demonstrated in writing to have been
rightfully in the possession of Consultant prior to the disclosure of such
information to Consultant by the Company; (c) becomes part of the public domain
or publicly known or available by publication or otherwise, not due to any
unauthorized act or omission on the part of Consultant; or (d) is supplied to
Consultant by a third party without binder of secrecy, provided, however, that
such third party has no obligation to the Company or any of its Affiliates to
maintain such information in confidence.

(b) Non-Disclosure to Third Parties. Except as required by Consultant’s Duties,
Consultant shall not, at any time now or in the future, directly or indirectly,
use, publish, disseminate or otherwise disclose any Confidential Information,
Concepts, or Ideas to any third party without the prior written consent of the
Company which consent may be denied in each instance and all of the same,
together with publication rights, shall belong exclusively to the Company.

(c) Documents, etc. All documents, diskettes, tapes, procedural manuals, guides,
specifications, plans, drawings, designs and similar materials, lists of
present, past or prospective customers, customer proposals, invitations to
submit proposals, price lists and data relating to the pricing of the Company’s
products and services, records, notebooks and all other materials containing
Confidential Information or information about Concepts or Ideas (including all
copies and reproductions thereof) that come into Consultant’s possession or
control by reason of Consultant’s performance of the relationship, whether
prepared by Consultant or others: (a) are the property of the Company; (b) will
not be used by Consultant in any way other than in connection with the
performance of his Duties; (c) will not be provided or shown to any third party
by Consultant; (d) will not be removed from the Company’s or Consultant’s
premises (except as Consultant’s Duties require); and (e) at the termination
(for whatever reason) of Consultant’s relationship with the Company, or at such
earlier time as requested by the Company, will be left with, or forthwith
returned by Consultant to the Company.

(d) Patents, etc. The Consultant agrees that the Company is and shall remain the
exclusive owner of the Confidential Information and Concepts and Ideas. Any
interest in patents, patent applications, inventions, technological innovations,
trade names, trademarks, service marks, copyrights, copyrightable works,
developments, discoveries, designs, processes, formulas, know-how, data and
analysis, whether registrable or not (“Developments”), which Consultant, as a
result of rendering Services to the Company under this Agreement, may conceive
or develop, shall: (i) forthwith be brought to the attention of the Company by
Consultant and (ii) belong exclusively to the Company. No license or conveyance
of any such rights to the Consultant is granted or implied under this Agreement.

 

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

(e) Assignment. The Consultant hereby assigns and, to the extent any such
assignment cannot be made at present, hereby agrees to assign to the Company,
without further compensation, all of his right, title and interest in and to all
Concepts, Ideas, and Developments. The Consultant will execute all documents and
perform all lawful acts which the Company considers necessary or advisable to
secure its rights hereunder and to carry out the intent of this Agreement.
Consultant’s obligation to assist the Company in effecting such assignment(s),
in any and all countries shall continue beyond the termination or expiration of
this Agreement.

8. EQUITABLE RELIEF. Consultant agrees that any breach of Sections 6 and 7 above
by him would cause irreparable damage to the Company and that, in the event of
such breach, the Company shall have, in addition to any and all remedies of law,
the right to an injunction, specific performance or other equitable relief to
prevent the violation or threatened violation of Consultant’s obligations
hereunder, without the requirement of having to post bond.

9. WAIVER. Any waiver by the Company of a breach of any provision of this
Agreement shall not operate or be construed as a waiver of any subsequent breach
of the same or any other provision hereof. All waivers by the Company shall be
in writing.

10. SEVERABILITY; REFORMATION. In case any one or more of the provisions or
parts of a provision contained in this Agreement shall, for any reason, be held
to be invalid, illegal or unenforceable in any respect, such invalidity,
illegality or unenforceability shall not affect any other provision or part of a
provision of this Agreement; and this Agreement shall, to the fullest extent
lawful, be reformed and construed as if such invalid or illegal or unenforceable
provision, or part of a provision, had never been contained herein, and such
provision or part reformed so that it would be valid, legal and enforceable to
the maximum extent possible. Without limiting the foregoing, if any provision
(or part of a provision) contained in this Agreement shall for any reason be
held to be excessively broad as to duration, activity or subject, it shall be
construed by limiting and reducing it, so as to be enforceable to the fullest
extent compatible with then existing applicable law.

11. ASSIGNMENT. The Company shall have the right to assign its rights and
obligations under this Agreement to a party which assumes the Company’s
obligations hereunder. Consultant shall not have the right to assign his rights
or obligations under this Agreement without the prior written consent of the
Company. This Agreement shall be binding upon and inure to the benefit of the
Consultant’s heirs and legal representatives in the event of his death or
disability.

12. HEADINGS. Headings and subheadings are for convenience only and shall not be
deemed to be a part of this Agreement.

13. AMENDMENTS. This Agreement may be amended or modified, in whole or in part,
only by an instrument in writing signed by all parties hereto.

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

14. NOTICES. Any notices or other communications required hereunder shall be in
writing and shall be deemed given when delivered in person or when mailed, by
certified or registered first class mail, postage prepaid, return receipt
requested, addressed to the parties at their addresses specified in the preamble
to this Agreement or to such other addresses of which a party shall have
notified the others in accordance with the provisions of this Section 14.

15. COUNTERPARTS. This Agreement may be executed in two or more counterparts,
each of which shall constitute an original and all of which shall be deemed a
single agreement.

16. GOVERNING LAW. This Agreement shall be construed in accordance with and
governed for all purposes by the laws of the Commonwealth of Massachusetts
applicable to contracts executed and wholly performed within such jurisdiction.
Any dispute arising hereunder shall be referred to and heard in only a court
located in Massachusetts.

17. SURVIVAL. The provisions of Sections 6 to 10 and 16 to 17 of this Agreement
shall survive the expiration of the Term or the termination of this Agreement.
This Agreement represents the entire agreement of the parties with respect to
the subject matter of this Agreement and supersedes all prior agreements,
written or oral, between the Company and the Consultant relating to the subject
matter of this Agreement.

EXECUTED, under seal, effective as of the Effective Date.

 

COMBINATORX, INCORPORATED    

CONSULTANT

By:  

/s/ Jason F. Cole

   

/s/ Alexis Borisy

Name:   Jason F. Cole     Consultant:   Alexis Borisy Title:   Senior Vice
President and General Counsel      

Hereunto Duly Authorized

     

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

Appendix “A”

(A) Duties and Responsibilities:

During the Term, the Consultant agrees to perform Services of up to no more than
twenty (20) hours per month for the Company, as requested by the Company,
including the following duties and tasks: Consultation in connection with the
Company’s ongoing strategic collaboration with Novartis, and such other duties
and responsibilities, reasonably consistent with his position, as may be
designated from time to time by the Board. The Consultant shall also serve as a
member of the Company’s Scientific Advisory Board.

(B) Scheduling and Completion and Termination Dates:

This agreement will be activated for the Term upon signing by both parties and
can be renewed thereafter if mutually agreed upon.

(C) Fee Schedules and Payment Dates:

The Company agrees to pay the consultant a fee of $350.00 per hour for
consulting requested by the Company. Invoices for hours of service should be
sent monthly to the Company’s Chief Executive Officer or Chief Financial
Officer. The Company may refuse to pay any invoices not provided to the Company
within 60 days of the completion of Services.