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

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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

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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

 

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