Document:

<PAGE>

                                                         EXHIBIT 10.44

                          CUBIST PHARMACEUTICALS, INC.
                                 24 Emily Street
                               Cambridge, MA 02139

                               September 25, 1999

Alan D. Watson, Ph.D., MBA

Dear Alan:

     On September 25, 1999, the Board of Directors Cubist Pharmaceuticals, Inc.,
a Delaware corporation (the "Company"), granted to you the right to purchase
50,000 restricted shares (the "Shares") of the Company's common stock, $.001 par
value per share, for a purchase price of $10.3125 per share.

     You and the Company hereby agree as follows:

     1.   PURCHASE OF SHARES. You hereby elect to purchase the Shares. Subject
to the terms and provisions of this letter agreement, the Company hereby sells
and issues to you, and you hereby purchase from the Company, the Shares at a
purchase price of $10.3125 per share.

     2.   PAYMENT OF PURCHASE PRICE. You hereby make payment of the aggregate
purchase price for all of the Shares by executing and delivering to the Company
a Secured Promissory Note, substantially in the form of EXHIBIT A attached
hereto, in the principal amount of $515,625 (the "Note"). Your obligation to pay
any and all amounts due under the Note will be secured by a Stock Pledge
Agreement, substantially in the form of EXHIBIT B attached hereto (the "Pledge
Agreement"), which Pledge Agreement is being executed contemporaneously
herewith.

     3.   FORGIVENESS OF PRINCIPAL OF NOTE. On each of the dates set forth in
EXHIBIT C hereto, the Company shall forgive that portion of the original
principal amount under the Note equal to the product of (i) such original
principal amount and (ii) the percentage set forth opposite to such date on
EXHIBIT C hereto, PROVIDED that your employment with the Company shall not have
been terminated on or prior to such date. Notwithstanding anything in the
foregoing provisions of this Section 3 or in EXHIBIT C hereto to the contrary,
the Company's obligation to forgive any portion of the original principal amount
of the Note shall terminate on the effective date of termination of your
employment with the Company (the "Employment Termination Date"). From and after
the Employment Termination Date, you shall remain liable for all amounts then
still owing under the Note or that otherwise become due and payable under the
Note, all subject to and upon the terms and conditions of the Note.

     4.   FORGIVENESS OF INTEREST. On the first anniversary of the Note, the
Company will forgive that portion of the interest accruing under the Note that
has become due and payable on such date, PROVIDED that your employment with the
Company shall not have been terminated on or prior to such date.

     5.   RESTRICTIONS ON TRANSFER OF SHARES.

<PAGE>

Alan D. Watson
September 25, 1999
Page 2

          (a)  SECURITIES LAWS RESTRICTIONS. You acknowledge and agree that you
shall have no right at any time to sell, assign, pledge, transfer, or otherwise
dispose of or encumber the Exercised Shares (except by will or by the laws of
descent and distribution) unless such sale, assignment, pledge, transfer, or
other disposition is either registered under the Securities Act of 1933, as
amended (the "Act"), or is exempt from registration under the Act and any
applicable state securities laws.

          (b)  RESTRICTIVE LEGENDS. You acknowledge that the stock certificate
for the Exercised Shares will bear restrictive legends which may refer to the
restrictions on transfer referred to in this Section 6.

     6.   MISCELLANEOUS. This letter agreement shall be governed by the internal
substantive laws of the Commonwealth of Massachusetts and shall be binding upon
the heirs, personal representatives, executors, administrators, successors and
permitted assigns of the parties. The rights and obligations of either party
under this letter agreement may only be assigned with the prior written consent
of the other party hereto. This letter agreement supersedes all prior written
and oral agreements and understandings between the parties and represents the
entire agreement between the parties with respect to the subject matter hereof
and may only be modified or amended pursuant to a written instrument signed by
both parties. The Company is not by reason of this letter agreement obligated to
continue your employment.

     If the foregoing accurately reflects our understanding, please so
acknowledge by countersigning this letter agreement in the space provided for
your signature below.

                                        Very truly yours,
                                        CUBIST PHARMACEUTICALS, INC.

                                        By: /s/ Scott M. Rocklage
                                           --------------------------------
                                              Scott M. Rocklage, Ph.D.
                                              President and CEO

Agreed and Accepted as of this 25th day of
September, 1999:

/s/ Alan D. Watson
--------------------------------
Alan D. Watson, Ph.D., MBA

<PAGE>

                                                                      EXHIBIT C

<TABLE>
<CAPTION>
            DATE                              PERCENTAGE
            ----                              ----------
<S>                                          <C>
     September 25, 2000                        33.33%
     September 25, 2001                        33.33%
     September 25, 2002                        33.34%
</TABLE><PAGE>

                                                             EXHIBIT 10.45

                             SECURED PROMISSORY NOTE

$515,625                                                     September 25, 1999

     FOR VALUE RECEIVED, the undersigned, ALAN D. WATSON, PH.D., MBA (the
"MAKER"), by this Secured Demand Promissory Note (this "NOTE"), absolutely
and unconditionally promises to pay to the order of CUBIST PHARMACEUTICALS,
INC., a Delaware corporation (the "COMPANY") or its successors or assigns or
any such successor or assign, as the case may be, being hereinafter referred
to as (the "PAYEE"), the aggregate principal amount of Five Hundred Fifteen
Thousand Six Hundred Twenty Five Dollars ($515,625) on September 25, 2002
(the "MATURITY DATE"), and to pay interest on the principal amount
outstanding from time to time hereunder, from the date hereof through and
including the date on which such principal amount is paid in full, at a rate
of four percent (4%) per annum simple interest. Interest hereunder shall be
payable annually on the first anniversary hereof, the second anniversary
hereof and on the Maturity Date.

     The Maker shall have the right to prepay the unpaid principal amount of
this Note in full at any time, or in part from time to time, without premium or
prepayment penalty, provided that there is paid with each such principal
prepayment all accrued and unpaid interest to the date of prepayment (calculated
on the basis of a 365-day year for the actual number of days for which the same
is due).

     All payments of interest and principal hereunder shall be made at the
business address of the holder hereof. All payments hereunder shall be applied
FIRST to any unpaid accrued interest, SECOND to payment of all, if any, other
amounts except principal due under or in respect of this Note, and THIRD to
repayment of principal.

     The obligations of the Maker under this Note are secured by a pledge of
among other things, 50,000 shares (the "SHARES") of the Common Stock, par value
$.001 per share of the Company pursuant to the provisions of a certain Stock
Pledge Agreement, dated of even date herewith, between the Maker and the Payee
(the "PLEDGE AGREEMENT").

     Anything implied herein to the contrary notwithstanding, in the event that
(1) the Maker shall fail to pay when due all or any portion of the principal of
or interest on this Note, (2) the Maker shall breach any provision of the Pledge
Agreement, (3) the Maker shall make an assignment of the whole or a substantial
part of his assets for the benefit of creditors, or (4) there shall be commenced
by or against the Maker any proceeding under any bankruptcy, insolvency,
readjustment of debt or similar law of any jurisdiction, (each event referred to
in clauses (1) through (4) above being hereinafter referred to herein as an
"EVENT OF DEFAULT"), then without notice to or demand upon the Maker the entire
unpaid principal of this Note, and all interest accrued thereon, shall (if not
already due and payable) immediately become and be due and payable to the order
of the holder hereof.

<PAGE>

     The Maker hereby, to the fullest extent permitted by applicable law: (a)
waives presentment, demand, notice, protest, and all other demands and notices
in connection with delivery, acceptance, performance, default, acceleration or
enforcement of or under this Note; (b) assents to any extension or postponement
of the time of payment or any other indulgence, and to any substitution,
exchange or release of collateral; and (c) agrees to pay to the holder, on
demand, all costs and expenses of collection, including, without limitation,
reasonable attorneys' fees and legal expenses, incurred by the holder in
enforcing this Note, whether or not litigation is commenced.

     No failure by the holder to exercise, or delay by the holder in exercising,
any right or remedy hereunder shall operate as a waiver thereof, or of any other
right or remedy, and no single or partial exercise of any right or remedy shall
preclude any other or further exercise thereof or of any other right or remedy.
Acceptance by the holder of any payment after the maturity of this Note has been
accelerated shall not constitute a waiver of such acceleration.

     This Note shall take effect as an instrument under seal and shall be
governed by and construed in accordance with the law of the Commonwealth of
Massachusetts.

                                                /s/ Alan D. Watson
                                                --------------------------
                                                Alan D. Watson, Ph.D., MBA

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00003-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00003-of-00352.parquet"}]]