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                                                                EXHIBIT 10.42

                         CUBIST PHARMACEUTICALS, INC.

                               THIRD AMENDMENT
                                      TO
                  1993 AMENDED AND RESTATED SOCK OPTION PLAN

     This THIRD AMENDMENT (this "Amendment") to the Amended and Restated 1993
Stock Option Plan, as amended (the "Plan"), of Cubist Pharmaceuticals, Inc.,
a Delaware corporation (the "Company"), is being adopted by resolution of the
board of Directors at a meeting held on September 25, 1999 (the "Effective
Date"). Effective from and after the Effective Date, the Plan is hereby
amended as follows:

     1.  Section 6 of the Plan hereby is amended by deleting Section 6 in its
entirety and inserting inits place the following, said amendment being for
the purpose of making directors eligible to receive Awarded Options.

               6.  ELIGIBILITY.  An Awarded Option may be granted only to an
         employee or Eligible Director of officer of or consultant to one or
         more of the Company and its Subsidiaries, PROVIDED that Incentive
         Options may be granted only to an employee (including an officer that
         is an employee) of the Company or one or more of its Subsidiaries.
         Each Eligible Director shall receive Formula Options pursuant to
         Section 8 hereof. Subject to adjustment pursuant to Secion 15 hereof,
         no person in any year may be granted Options with respect to more than
         500,000 Shares.

     2.  Section 8.1 of the Plan hereby is amended by replacing the reference
therein to "7,000 Shares" with "15,000 Shares", said amendment being for the
purpose of increasing the number of Shares subject to the Nonstatutory Option
granted to Directors elected for the first on the Formula Grant Date.

     3.  Section 8.2 of the Plan hereby is amended by replacing the reference
therein to "700 Shares" with "2,000 Shares", said amendment being for the
purpose of increasing the number of Shares subject to the Nonstatutory Option
granted to Directors on the business day immediately following the annual
meeting of stockholders of the Company.

     Except to the extent amended hereby, all of the terms, provisions and
conditions set forth in the Plan are hereby ratified and confirmed and shall
remain in full force and effect. The Plan and this Amendment shall be read
and construed together as a single instrument.<PAGE>

                                                            EXHIBIT 10.43

                             STOCK PLEDGE AGREEMENT

     This STOCK PLEDGE AGREEMENT (this "Agreement") is made as of this 25th day
of September, 1999 by and between Alan D. Watson, Ph.D., MBA (the "Pledgor"),
and Cubist Pharmaceuticals, Inc. a Delaware corporation (the "Company").

     WHEREAS, the Company has agreed to issue and sell to the Pledgor 50,000
restricted shares (the "Shares") of the Company's Common Stock, $.001 par value
per share (the "Common Stock") at a purchase price of $10.3125 per share.

     WHEREAS, the Pledgor wishes to purchase the Shares, such purchase to be
upon the terms and conditions set forth in that certain letter agreement, dated
as of the date hereof, by and between the Company and the Pledgor (the "Letter
Agreement");

     WHEREAS, the Company has agreed to sell the Shares to the Pledgor pursuant
to the terms of the Letter Agreement;

     WHEREAS, the Letter Agreement provides that the Pledgor shall make payment
of the aggregate purchase price for the Shares by delivering to the Company a
promissory note, the principal amount of which shall be equal to such aggregate
purchase price (the "Note"); and

     WHEREAS, it is a condition precedent to the Company's obligation to
consummate the sale of the Shares to the Pledgor that the Pledgor shall have
executed and delivered this Agreement.

     NOW, THEREFORE, in consideration of the premises contained herein and for
other good and valuable consideration, the receipt and sufficiency of which are
hereby acknowledged, the parties hereto hereby agree as follows:

     1.   PLEDGE OF STOCK, ETC. The Pledgor hereby pledges, assigns, grants a
security interest in, and delivers to the Company, to secure the Obligations (as
defined below), all of his right, title and interest in and to the Shares to be
held by the Company subject to the terms and conditions hereinafter set forth.
The certificates for such Shares, accompanied by stock powers or other
appropriate instruments of assignment thereof duly executed in blank by the
Pledgor, are being delivered to the Company contemporaneously herewith. The
Pledgor also hereby pledges, assigns, grants a security interest in, and
delivers to the Company, to secure the Obligations, all of his right, title and
interest in and to any and all sums or other property (including, without
limitation, any additional shares of the capital stock of the Company and any
shares of the capital stock of any issuer) paid or distributed upon or with
respect to any of the shares of the capital stock of the Company or any other
issuer pledged hereunder from time to time, regardless of whether any such sums
or other property are paid or distributed by dividend or redemption, upon
liquidation or dissolution, or otherwise.

     2.   DEFINITIONS. The following terms shall have the following meanings:

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          EVENT OF DEFAULT shall have the meaning ascribed to such term in the
     Note.

          STOCK. The Shares, together with any additional shares of capital
     stock of any issuer pledged to the Company from time to time pursuant to
     Section 1 hereof.

          STOCK COLLATERAL. The property at any time pledged to the Company
     hereunder (whether described herein or not) and all income therefrom,
     increases therein and proceeds thereof, but excluding from the definition
     of "Stock Collateral" any income, increases or proceeds received by the
     Pledgor to the extent expressly permitted by Section 6.

     3.   SECURITY FOR OBLIGATIONS. This Agreement and the security interest in
and pledge of the Stock Collateral hereunder are made with and granted to the
Company as security for the payment and performance in full of all of the
obligations of the Pledgor under the Note (all of such obligations being
collectively referred to herein as the "Obligations").

     4.   LIQUIDATION, RECAPITALIZATION, ETC. Any sums or other property
(including, without limitation, any shares of the capital stock of any issuer,
including the Company, or any securities exchangeable for or convertible into
shares of such capital stock) paid or distributed upon or with respect to any of
the Stock, whether by dividend or redemption or upon the liquidation or
dissolution of the issuer thereof or otherwise, shall, except to the limited
extent provided in Section 6, be paid over and delivered to the Company to be
held by the Company, pursuant to the terms of this Agreement, as security for
the payment and performance in full of all of the Obligations. In the event
that, pursuant to the recapitalization or reclassification of the capital of the
issuer thereof or pursuant to the reorganization thereof, any distribution of
capital shall be made on or in respect of any of the Stock or any property shall
be distributed upon or with respect to any of the Stock, the property so
distributed shall be delivered to the Company to be held by it as security for
the Obligations. Except to the limited extent provided in Section 6, all sums of
money and property paid or distributed in respect of the Stock, whether as a
dividend or upon such a liquidation, dissolution, recapitalization or
reclassification or otherwise, that are received by the Pledgor shall, until
paid or delivered to the Company, be held in trust for the Company as security
for the payment and performance in full of all of the Obligations.

     5.   WARRANTY OF TITLE; AUTHORITY. The Pledgor hereby represents and
warrants that: (a) the Pledgor has good and marketable title to the Shares,
subject to no pledges, liens, security interests, charges, options, restrictions
or other encumbrances except the pledge and security interest created by this
Agreement, and except for any restrictions imposed by the Securities Act of
1933, as amended (the "Securities Act"), (b) the Pledgor has full power,
authority and legal right to execute, deliver and perform its obligations under
this Agreement and to pledge and grant a security interest in all of the Stock
Collateral pursuant to this Agreement, and (c) the execution, delivery and
performance of this Agreement by the Pledgor and the pledge of and grant of a
security interest in the Stock Collateral hereunder do not contravene any law,
rule or regulation or any provision of the charter or by-laws of the issuer or
issuers thereof or of any judgment, decree or order of any tribunal or of any
agreement or instrument to which the Pledgor is a party or by which he or any of
his property is bound or affected or constitute a default

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thereunder. The Pledgor further warrants that he will have good and marketable
title to any and all Stock Collateral hereafter pledged to the Company
hereunder, subject to no pledges, liens, security interests, charges, options,
restrictions or other encumbrances except the pledge and security interest
created by this Agreement, and except for any restrictions imposed by the
Securities Act. The Pledgor covenants that he shall defend the Company's rights
and security interest in such Stock Collateral against the claims and demands of
any and all third parties. The Pledgor further covenants that he shall not enter
into any agreement that conflicts with this Agreement.

     6.   DIVIDENDS, VOTING, ETC., PRIOR TO MATURITY. So long as no Event of
Default shall have occurred and be continuing, the Pledgor shall be entitled to
receive all cash dividends paid in respect of the Stock, to vote the Stock and
to give consents, waivers and ratifications in respect of the Stock; PROVIDED,
HOWEVER, that no vote shall be cast or consent, waiver or ratification given by
the Pledgor if the effect thereof would impair any of the Stock Collateral. All
such rights of the Pledgor to receive cash dividends shall cease in case an
Event of Default shall have occurred and be continuing. All such rights of the
Pledgor to vote and give consents, waivers and ratifications with respect to the
Stock shall, at the Company's option, as evidenced by the Company's notifying
the Pledgor of such election, cease in case an Event of Default shall have
occurred and be continuing.

     7.   REMEDIES.

          7.1. IN GENERAL. If an Event of Default shall have occurred and be
     continuing, the Company shall thereafter have the following rights and
     remedies (to the extent permitted by applicable law) in addition to the
     rights and remedies of a secured party under the Uniform Commercial Code of
     Massachusetts, all such rights and remedies being cumulative, not
     exclusive, and enforceable alternatively, successively or concurrently, at
     such time or times as the Company deems expedient:

               (a)  if the Company so elects and gives notice of such election
          to the Pledgor, the Company may vote any or all shares of the Stock
          (whether or not the same shall have been transferred into its name or
          the name of its nominee or nominees) for any lawful purpose,
          including, without limitation, if the Company so elects, for the
          liquidation of the assets of the issuer thereof, and give all
          consents, waivers and ratifications in respect of the Stock and
          otherwise act with respect thereto as though it were the outright
          owner thereof (the Pledgor hereby irrevocably constituting and
          appointing the Company as his proxy and attorney-in-fact, with full
          power of substitution, to do so);

               (b)  the Company may demand, sue for, collect or make any
          compromise or settlement the Company deems suitable in respect of any
          Stock Collateral;

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               (c)  the Company may sell, resell, assign and deliver, or
          otherwise dispose of, any or all of the Stock Collateral, for cash or
          credit or both and upon such terms, at such place or places, at such
          time or times and to such entities or other persons as the Company
          thinks expedient, all without demand for performance by the Pledgor or
          any notice or advertisement whatsoever except as expressly provided
          herein or as may otherwise be required by law; and

               (d)  the Company may cause all or any part of the Stock held by
          it to be transferred into its name or the name of its nominee or
          nominees.

          7.2. SALE OF STOCK COLLATERAL. In the event of any disposition of the
     Stock Collateral as provided in clause (c) of Section 7.1, the Company
     shall give to the Pledgor at least five business days' prior written notice
     of the time and place of any public sale of the Stock Collateral or of the
     time after which any private sale or any other intended disposition is to
     be made. The Pledgor hereby acknowledges that five business days prior
     written notice of such sale or sales shall be reasonable notice. The
     Company may enforce its rights hereafter without any other notice and
     without compliance with any other condition precedent now or hereunder
     imposed by statute, rule of law or otherwise (all of which are hereby
     expressly waived by the Pledgor, to the fullest extent permitted by law).
     The Company may buy any part or all of the Stock Collateral at any public
     sale and if any part or all of the Stock Collateral is of a type
     customarily sold in a recognized market or is of the type which is the
     subject of widely-distributed standard price quotations, the Company may
     buy at private sale and may make payments thereof by any means. The Company
     may apply the cash proceeds actually received from any sale or other
     disposition to the reasonable expenses of retaking, holding, preparing for
     sale, selling and the like, to reasonable attorneys' fees, travel and all
     other expenses which may be incurred by the Company in attempting to
     collect the Obligations or to enforce this Agreement or in the prosecution
     or defense of any action or proceeding related to the subject matter of
     this Agreement, and then to the Obligations in such order or preference as
     the Company may determine after proper allowance for Obligations not then
     due. Only after such applications, and after payment by the Company of any
     amount required by Section 9-504(1)(c) of the Uniform Commercial Code of
     the Commonwealth of Massachusetts, need the Company account to the Pledgor
     for any surplus.

          7.3. THE PLEDGOR'S AGREEMENTS, ETC. The Pledgor further agrees to do
     or cause to be done all such other acts and things as may be reasonably
     necessary to make any sales of any portion or all of the Stock pursuant to
     this Section 7 valid and binding and in compliance with any and all
     applicable laws (including, without limitation, the Securities Act, the
     Securities Exchange Act of 1934, as amended, the rules and regulations of
     the Securities and Exchange Commission applicable thereto and all
     applicable state securities or "Blue Sky" laws), regulations, orders,
     writs, injunctions, decrees or awards of any and all courts, arbitrators or
     governmental instrumentalities, domestic or foreign, having jurisdiction
     over any such sale or sales, all at the Pledgor's expense. The Pledgor
     further agrees that a breach of any of the covenants contained in this
     Section 7 will cause irreparable

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     injury to the Company, that the Company has no adequate remedy at law in
     respect of such breach and, as a consequence, agrees that each and every
     covenant contained in this Section 7 shall be specifically enforceable
     against the Pledgor and the Pledgor hereby waives and agrees not to assert
     any defenses against an action for specific performance of such covenants.

     8.   MARSHALLING. The Company shall not be required to marshal any present
or future security for (including, but not limited to, this Agreement and the
Stock Collateral pledged hereunder), or guaranties of, the Obligations or any of
them, or to resort to such security or guaranties in any particular order; and
all of its rights hereunder and in respect to such security and guaranties shall
be cumulative and in addition to all other rights, however existing or arising.
To the extent that he lawfully may, the Pledgor hereby agrees that he will not
invoke any law relating to the marshalling of collateral which might cause delay
in or impede the enforcement of the Company's rights under this Agreement, and,
to the extent that he lawfully may, the Pledgor hereby irrevocably waives the
benefits of all such laws.

     9.   PLEDGOR'S OBLIGATIONS NOT AFFECTED. To the extent permitted by law,
the obligations of the Pledgor hereunder shall remain in full force and effect
without regard to, and shall not be impaired by (a) any bankruptcy, insolvency,
reorganization, arrangement, readjustment, composition, liquidation or the like
of the Pledgor; (b) any exercise or nonexercise, or any waiver, by the Company
of any right, remedy, power or privilege under or in respect of any of the
Obligations or any security therefor (including this Agreement); (c) any
amendment to or modification of any of the Obligations; (d) any amendment to or
modification of any instrument (other than this Agreement) securing any of the
Obligations; or (e) the taking of additional security for, or any guaranty of,
any of the Obligations or the release or discharge or termination of any
security or guaranty for any of the Obligations; whether or not the Pledgor
shall have notice or knowledge of any of the foregoing.

     10.  TRANSFER, ETC., BY THE PLEDGOR. Without the prior written consent of
the Company, the Pledgor will not sell, assign, transfer or otherwise dispose
of, grant any option with respect to, or pledge or grant any security interest
in or otherwise encumber or restrict any of the Stock Collateral or any interest
therein, except for the pledge thereof and security interest therein provided
for in this Agreement.

     11.  FURTHER ASSURANCES. The Pledgor will do all such acts, and will
furnish to the Company all such financing statements, certificates, legal
opinions and other documents and will obtain all such governmental consents and
corporate approvals and will do or cause to be done all such other things as the
Company may reasonably request from time to time in order to give full effect to
this Agreement and to secure the rights of the Company hereunder, all without
any cost or expense to the Company. If the Company so elects, a photocopy of
this Agreement may at any time and from time to time be filed by the Company as
a financing statement in any recording office in any jurisdiction.

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                                      -6-

     12.  COMPANY'S EXONERATION. Under no circumstances shall the Company be
deemed to assume any responsibility for or obligation or duty with respect to
any part or all of the Stock Collateral of any nature or kind or any matter or
proceedings arising out of or relating thereto, other than (a) to exercise
reasonable care in the physical custody of the Stock Collateral and (b) after an
Event of Default shall have occurred and be continuing to act in a commercially
reasonable manner. The Company shall not be required to take any action of any
kind to collect, preserve or protect its or the Pledgor's rights in the Stock
Collateral or against other parties thereto. The Company's prior recourse to any
part or all of the Stock Collateral shall not constitute a condition of any
demand, suit or proceeding for payment or collection of any of the Obligations.

     13.  OVERDUE AMOUNTS. Until paid, all amounts due and payable by the
Pledgor hereunder shall be a debt secured by the Stock Collateral and shall
bear, whether before or after judgment, interest at the rate of interest set
forth in the Note.

     14.  NO WAIVER, ETC. No act, failure or delay by the Company shall
constitute a waiver of its rights and remedies hereunder or otherwise. No single
or partial waiver by the Company of any default or right or remedy that it may
have shall operate as a waiver of any other default, right or remedy or of the
same default, right or remedy on a future occasion. The Pledgor hereby waives
presentment, notice of dishonor and protest of all instruments, included in or
evidencing any of the Obligations or the Stock Collateral, and any and all other
notices and demands whatsoever (except as expressly provided herein).

     15.  NOTICES, ETC. Any communication to be made hereunder shall (a) be made
in writing, but unless otherwise stated, may be made by telex, facsimile
transmission or letter, and (b) be made or delivered to the address of the party
receiving notice which is identified with its signature below (unless such party
has by five (5) days' written notice specified another address), and shall be
deemed made or delivered, when dispatched, left at that address, or five (5)
days after being mailed, postage prepaid, to such address.

     16.  TERMINATION. Upon final payment and performance in full of the
Obligations, this Agreement shall terminate and the Company shall, at the
Pledgor's request and expense, return such Stock Collateral in the possession or
control of the Company as has not theretofore been disposed of pursuant to the
provisions hereof, together with any moneys and other property at the time held
by the Company hereunder.

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     17.  AMENDMENT. Neither this Agreement nor any term hereof may be amended,
modified, waived, discharged or terminated except by a written instrument
expressly referring to this Agreement and to the provisions so amended,
modified, waived, discharged or terminated, and executed by the party to be
charged.

     18.  SUCCESSORS AND ASSIGNS. This Agreement and all obligations of the
Pledgor hereunder shall be binding upon the heirs, successors and assigns of the
Pledgor, and shall, together with the rights and remedies of the Company
hereunder, inure to the benefit of the Company, its successors in title and
assigns.

     19.  GOVERNING LAW; CONSENT TO JURISDICTION. THIS AGREEMENT IS INTENDED TO
TAKE EFFECT AS A SEALED INSTRUMENT AND SHALL BE GOVERNED BY, AND CONSTRUED IN
ACCORDANCE WITH, THE LAWS OF THE COMMONWEALTH OF MASSACHUSETTS. To the fullest
extent permitted by law, the Pledgor hereby absolutely and irrevocably consents
and submits to the jurisdiction of the courts of the Commonwealth of
Massachusetts and of any Federal court located in the said Commonwealth in
connection with any actions or proceedings brought against the Pledgor by the
Company arising out of or relating to this Agreement or any of the agreements or
transactions contemplated hereby and hereby irrevocably agrees that all claims
in respect of any such action or proceeding may be heard and determined in any
such court. The Pledgor hereby waives any objection that it may now or hereafter
have to the venue of any such suit or any such court or that such suit is
brought in an inconvenient court.

     20.  WAIVER OF JURY TRIAL. THE PLEDGOR WAIVES HIS RIGHT TO A JURY TRIAL
WITH RESPECT TO ANY ACTION OR CLAIM ARISING OUT OF ANY DISPUTE IN CONNECTION
WITH THIS AGREEMENT, ANY RIGHTS OR OBLIGATIONS HEREUNDER OR THE PERFORMANCE OF
ANY SUCH RIGHTS OR OBLIGATIONS. Except as prohibited by law, the Pledgor waives
any right which he may have to claim or recover in any litigation referred to in
the preceding sentence any special, exemplary, punitive or consequential damages
or any damages other than, or in addition to, actual damages.

     21.  HEADINGS. The descriptive section headings have been inserted for
convenience of reference only and do not define or limit the provisions hereof.

     22.  SEVERABILITY, ETC. If any term of this Agreement shall be held to be
invalid, illegal or unenforceable, the validity of all other terms hereof shall
be in no way affected thereby, and this Agreement shall be construed and be
enforceable as if such invalid, illegal or unenforceable term had not been
included herein. The Pledgor acknowledges receipt of a copy of this Agreement.

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     IN WITNESS WHEREOF, intending to be legally bound, the Pledgor and the
Company have caused this Agreement to be executed as of the date first above
written.

                                         CUBIST PHARMACEUTICALS, INC.

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

                                         Address: 24 Emily Street
                                                  Cambridge, MA 02139

                                         PLEDGOR

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

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