Exhibit 10.1


4156674-006


NEITHER THIS PROMISSORY NOTE NOR THE MASTER SECURITY
AGREEMENT TO WHICH THIS NOTE IS TIED HAVE BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED.  NO SALE OR
DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH RULE 144 UNDER SAID
ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN
OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION
LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION


PROMISSORY NOTE


March 29, 2007


(Date)


FOR
VALUE RECEIVED, CombinatoRx, Incorporated
a corporation located at the address stated below (“Maker”) promises, jointly and severally if more than one, to
pay to the order of General Electric Capital
Corporation or any subsequent holder hereof (each, a “Payee”) at its office located at 83 Wooster Heights Road, Danbury, CT 06810
or at such other place as Payee or the holder hereof may designate, the
principal sum One Million One Hundred One Thousand
One Hundred Seventy-Seven and 18/100  Dollars ($1,101,177.18), with interest on the unpaid principal
balance, from the date hereof through and including the dates of payment, at a
fixed interest rate of Ten and Twelve Hundredths percent (10.12%) per annum, to
be paid in lawful money of the United States, in Forty-Eight (48) consecutive
monthly  installments of principal and
interest as follows:


	
     Periodic

  	
   

  	
   

  	
   

  
	
  Installment

  	
   

  	
   

  	
   

  	
  Amount

  	
   

  
	
  Thirty-Six (36)

  	
   

  	
  $

  	
  32,755.43

  	
   

  
	
  Eleven (11)

  	
   

  	
  $

  	
  10,452.41

  	
   

  
							



 


each
(“Periodic Installment”) and a final installment which shall be in the amount
of the total outstanding principal and interest.  The first Periodic Installment shall be due
and payable on May 1, 2007
and the following Periodic Installments and the final installment shall be due
and payable on the same day of each succeeding month (each, a “Payment Date”).  Such installments have been calculated on the
basis of a 360 day year of twelve 30-day months.  Each payment may, at the option of the Payee,
be calculated and applied on an assumption that such payment would be made on
its due date.


The
acceptance by Payee of any payment which is less than payment in full of all
amounts due and owing at such time shall not constitute a waiver of Payee’s
right to receive payment in full at such time or at any prior or subsequent
time.


The Maker hereby expressly
authorizes the Payee to insert the date value is actually given in the blank
space on the face hereof and on all related documents pertaining hereto.


This Note may be secured by a security agreement, chattel mortgage,
pledge agreement or like instrument (each of which is hereinafter called a “Security Agreement”).


Time is of the essence
hereof.  If any installment or any other
sum due under this Note or any Security Agreement is not received within ten
(10) days after its due date, the Maker agrees to pay, in addition to the
amount of each such installment or other sum, a late payment charge of five
percent (5%) of the amount of said installment or other sum, but not exceeding
any lawful maximum.  If (i) Maker fails
to make payment of any amount due hereunder within ten (10) days after the same
becomes 











due and payable; or  (ii) Maker is in default under, or fails to
perform under any term or condition contained in any Security Agreement after
ten (10) days written notice, then the entire principal sum remaining unpaid,
together with all accrued interest thereon and any other sum payable under this
Note or any Security Agreement, at the election of Payee, shall immediately become
due and payable, with interest thereon at the lesser of eighteen percent (18%)
per annum or the highest rate not prohibited by applicable law from the date of
such accelerated maturity until paid (both before and after any judgment).


The Maker may prepay
in full, but not in part, its entire indebtedness hereunder upon payment of the
outstanding principal amount plus all accrued interest to the date of
prepayment, plus an additional sum as a premium equal to the following
percentages of the remaining principal balance for the indicated period

Months 1 —12: No Prepayment Allowed

Months 13 — 24:  6% premium

Months 25 — 36: 5% premium


It is the intention of the
parties hereto to comply with the applicable usury laws; accordingly, it is
agreed that, notwithstanding any provision to the contrary in this Note or any
Security Agreement, in no event shall this Note or any Security Agreement
require the payment or permit the collection of interest in excess of the
maximum amount permitted by applicable law. 
If any such excess interest is contracted for, charged or received under
this Note or any Security Agreement, or if all of the principal balance shall
be prepaid, so that under any of such circumstances the amount of interest
contracted for, charged or received under this Note or any Security Agreement
on the principal balance shall exceed the maximum amount of interest permitted
by applicable law, then in such event 
(a) the provisions of this paragraph shall govern and control,  (b) neither Maker nor any other person or
entity now or hereafter liable for the payment hereof shall be obligated to pay
the amount of such interest to the extent that it is in excess of the maximum
amount of interest permitted by applicable law, 
(c) any such excess which may have been collected shall be either
applied as a credit against the then unpaid principal balance or refunded to
Maker, at the option of the Payee, and 
(d) the effective rate of interest shall be automatically reduced to the
maximum lawful contract rate allowed under applicable law as now or hereafter
construed by the courts having jurisdiction thereof.  It is further agreed that without limitation
of the foregoing, all calculations of the rate of interest contracted for, charged
or received under this Note or any Security Agreement which are made for the
purpose of determining whether such rate exceeds the maximum lawful contract
rate, shall be made, to the extent permitted by applicable law, by amortizing,
prorating, allocating and spreading in equal parts during the period of the
full stated term of the indebtedness evidenced hereby, all interest at any time
contracted for, charged or received from Maker or otherwise by Payee in
connection with such indebtedness; provided, however, that if any applicable
state law is amended or the law of the United States of America preempts any
applicable state law, so that it becomes lawful for the Payee to receive a
greater interest per annum rate than is presently allowed, the Maker agrees
that, on the effective date of such amendment or preemption, as the case may
be, the lawful maximum hereunder shall be increased to the maximum interest per
annum rate allowed by the amended state law or the law of the United States of
America.


The Maker and all sureties,
endorsers, guarantors or any others (each such person, other than the Maker, an
“Obligor”) who may at any time
become liable for the payment hereof jointly and severally consent hereby to
any and all extensions of time, renewals, waivers or modifications of, and all
substitutions or releases of, security or of any party primarily or secondarily
liable on this Note or any Security Agreement or any term and provision of
either, which may be made, granted or consented to by Payee, and agree that
suit may be brought and maintained against any one or more of them, at the
election of Payee without joinder of any other as a party thereto, and that
Payee shall not be required first to foreclose, proceed against, or exhaust any
security hereof in order to enforce payment of this Note.  The Maker and each Obligor hereby waives
presentment, demand for payment, notice of nonpayment, protest, notice of
protest, notice of dishonor, and all other notices in connection herewith, as
well as filing of suit (if permitted by law) and diligence in collecting this
Note or enforcing any of the security hereof, and agrees to pay (if permitted
by law) all expenses incurred in collection, including Payee’s actual attorneys’
fees.  Maker and each Obligor agrees that
fees not in excess of twenty percent (20%) of the amount then due shall be
deemed reasonable.


THE MAKER
HEREBY UNCONDITIONALLY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE
OF ACTION BASED UPON OR ARISING OUT OF, DIRECTLY OR INDIRECTLY, THIS NOTE, ANY
OF THE RELATED DOCUMENTS, ANY DEALINGS BETWEEN MAKER AND PAYEE RELATING TO THE
SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE
RELATIONSHIP THAT IS BEING ESTABLISHED BETWEEN MAKER AND PAYEE.  THE SCOPE OF THIS WAIVER IS INTENDED TO BE
ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN 











ANY COURT
(INCLUDING, WITHOUT LIMITATION, CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY
CLAIMS, AND ALL OTHER COMMON LAW AND STATUTORY CLAIMS.)  THIS WAIVER IS IRREVOCABLE MEANING THAT IT
MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING, AND THE WAIVER SHALL APPLY TO
ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS NOTE,
ANY RELATED DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS
TRANSACTION OR ANY RELATED TRANSACTION. 
IN THE EVENT OF LITIGATION, THIS NOTE MAY BE FILED AS A WRITTEN CONSENT
TO A TRIAL BY THE COURT.


This Note and any Security Agreement constitute the
entire agreement of the Maker and Payee with respect to the subject matter
hereof and supercedes all prior understandings, agreements and representations,
express or implied.


No variation or modification
of this Note, or any waiver of any of its provisions or conditions, shall be
valid unless in writing and signed by an authorized representative of Maker and
Payee.  Any such waiver, consent,
modification or change shall be effective only in the specific instance and for
the specific purpose given.


Any provision in this Note or
any Security Agreement which is in conflict with any statute, law or applicable
rule shall be deemed omitted, modified or altered to conform thereto.


	
  

  	
   

  	
  CombinatoRx, Incorporated

  
	
   

  	
   

  	
   

  
	
  /s/ Jason F.
  Cole

  	
   

  	
  By:

  	
  /s/ Justin Renz

  
	
  (Witness)

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
   

  
	
  Jason F. Cole

  	
   

  	
  Name:

  	
  Justin Renz

  
	
  (Print name)

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
   

  
	
  245 First
  Street, Cambridge, MA 02142

  	
   

  	
  Title:

  	
  VP, Finance, Treasurer

  
	
  (Address)

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
  Federal Tax ID #04-3514457

  
	
   

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
  Address: 245 First Street, Cambridge, MA 02142