CUBIST PHARMACEUTICALS INC
DEF 14A, 2000-04-03
PHARMACEUTICAL PREPARATIONS
Previous: CUBIST PHARMACEUTICALS INC, S-3/A, 2000-04-03
Next: FEDERATED INSURANCE SERIES, 485APOS, 2000-04-03



<PAGE>
                            SCHEDULE 14A INFORMATION

                  Proxy Statement Pursuant to Section 14(a) of
                      the Securities Exchange Act of 1934

<TABLE>
      <S>        <C>
      Filed by the Registrant /X/
      Filed by a Party other than the Registrant / /

      Check the appropriate box:
      / /        Preliminary Proxy Statement
      /X/        Definitive Proxy Statement
      / /        Definitive Additional Materials
      / /        Soliciting Material Pursuant to Section240.14a-11(c) or
                 Section240.14a-12
      / /        Confidential, for Use of the Commission Only (as permitted
                 by Rule 14a-6(e)(2))

                   CUBIST PHARMACEUTICALS, INC.
      -----------------------------------------------------------------------
                 (Name of Registrant as Specified In Its Charter)
</TABLE>

Payment of Filing Fee (Check the appropriate box):

<TABLE>
<S>        <C>  <C>
/X/        No fee required.
/ /        Fee computed on table below per Exchange Act Rules 14a-6(i)(2)
           and 0-11.
           (1)  Title of each class of securities to which transaction
                applies:
                ----------------------------------------------------------
           (2)  Aggregate number of securities to which transaction
                applies:
                ----------------------------------------------------------
           (3)  Per unit price or other underlying value of transaction
                computed pursuant to Exchange Act Rule 0-11 (Set forth the
                amount on which the filing fee is calculated and state how
                it was determined):
                ----------------------------------------------------------
           (4)  Proposed maximum aggregate value of transaction:
                ----------------------------------------------------------
           (5)  Total fee paid:
                ----------------------------------------------------------
/ /        Fee paid previously with preliminary materials.
/ /        Check box if any part of the fee is offset as provided by
           Exchange Act Rule 0-11(a)(2) and identify the filing for which
           the offsetting fee was paid previously. Identify the previous
           filing by registration statement number, or the Form or
           Schedule and the date of its filing.
           (1)  Amount Previously Paid:
                ----------------------------------------------------------
           (2)  Form, Schedule or Registration Statement No.:
                ----------------------------------------------------------
           (3)  Filing Party:
                ----------------------------------------------------------
           (4)  Date Filed:
                ----------------------------------------------------------
</TABLE>
<PAGE>
                          CUBIST PHARMACEUTICALS, INC.
                                24 EMILY STREET
                              CAMBRIDGE, MA 02139
                 NOTICE OF 2000 ANNUAL MEETING OF STOCKHOLDERS

TO THE STOCKHOLDERS OF CUBIST PHARMACEUTICALS, INC.:

    NOTICE IS HEREBY GIVEN that the 2000 Annual Meeting of Stockholders of
Cubist Pharmaceuticals, Inc. will be held at our corporate offices, 125 Sidney
Street, Cambridge, MA 02139, on Tuesday, May 16, 2000, at 9:00 A.M., local time,
for the following purposes:

    1.  To elect three Class I directors to hold office for a three year term
       and until their successors have been duly elected and qualified;

    2.  To consider and vote upon a proposal to ratify the adoption and approval
       by the Board of Directors of the Fourth Amendment to our Amended and
       Restated 1993 Stock Option Plan to provide for (i) an increase in the
       number of shares of common stock that are issuable upon exercise of
       options granted under the plan from 3,000,000 to 4,000,000 shares; and
       (ii) an increase in the maximum aggregate number of shares of common
       stock that may be issued pursuant to the exercise of incentive stock
       options granted under the plan from 3,000,000 to 6,000,000 shares.

    3.  To transact such other business as may properly come before the annual
       meeting or any adjournments or postponements thereof.

    The Board of Directors has fixed April 3, 2000 as the record date for the
determination of stockholders entitled to notice of, and to vote at, the 2000
Annual Meeting of Stockholders. Accordingly, only stockholders of record at the
close of business on April 3, 2000 will be entitled to notice of, and to vote
at, such meeting or any adjournments thereof.

    To ensure your representation at the meeting, however, you are urged to vote
by proxy by following one of these steps as promptly as possible:

       (a) Complete, date, sign and return the enclosed proxy card (a
           postage-prepaid envelope is enclosed for that purpose); or

       (b) Vote via the Internet (see instructions on the enclosed proxy card);
           or

       (c) Vote via telephone (toll-free) in the United States or Canada (see
           instructions on the enclosed proxy card).

    The Internet and telephone voting procedures are designed to authenticate
shareholders' identities, to allow shareholders to vote their shares and to
confirm that their instructions have been properly recorded. Specific
instructions to be followed by any registered shareholder interested in voting
via the Internet or telephone are set forth in the proxy card and must be
completed by 6 p.m. on May 15, 2000. Your shares cannot be voted unless you
date, sign, and return the enclosed proxy card, vote via the Internet or
telephone or attend the annual meeting in person. Regardless of the number of
shares you own, your careful consideration of, and vote on, the matters before
the shareholders is important.

                                       2
<PAGE>
                                          By order of the Board of Directors
                                          JUSTIN P. MORREALE
                                          SECRETARY

April 4, 2000

NOTE: THE BOARD OF DIRECTORS SOLICITS THE EXECUTION AND PROMPT RETURN OF THE
      ACCOMPANYING PROXY. WHETHER OR NOT YOU EXPECT TO BE PRESENT AT THE
      MEETING, PLEASE VOTE VIA THE INTERNET OR TELEPHONE OR COMPLETE, DATE, SIGN
      AND MAIL THE ACCOMPANYING PROXY CARD AND PROMPTLY RETURN IT IN THE
      PRE-ADDRESSED ENVELOPE PROVIDED FOR THAT PURPOSE. IF YOU ATTEND THE
      MEETING, YOU MAY WITHDRAW ANY PROXY GIVEN BY YOU AND VOTE YOUR SHARES IN
      PERSON.

                                       3
<PAGE>
                          CUBIST PHARMACEUTICALS, INC.
                                24 EMILY STREET
                              CAMBRIDGE, MA 02139

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

                                PROXY STATEMENT
                            ------------------------

                              GENERAL INFORMATION

PROXY SOLICITATION

    This proxy statement is furnished to the holders of the common stock, $.001
par value per share, of Cubist Pharmaceuticals, Inc. in connection with the
solicitation of proxies on behalf of our Board of Directors for use at the
annual meeting of stockholders to be held on May 16, 2000, or at any adjournment
or postponement of the meeting, pursuant to the accompanying Notice of 2000
Annual Meeting of Stockholders. The purposes of the annual meeting and the
matters to be acted upon are set forth in the accompanying Notice of 2000 Annual
Meeting of Stockholders. The Board of Directors knows of no other business that
will come before the annual meeting.

    This proxy statement and proxies for use at the meeting will be first mailed
to stockholders on or about April 4, 2000 and such proxies will be solicited
chiefly by mail, but additional solicitations may be made by telephone or
telegram by our officers or regular employees. We may enlist the assistance of
brokerage houses in soliciting proxies. We shall bear all solicitation expenses,
including costs of preparing, assembling and mailing proxy material.

REVOCABILITY AND VOTING OF PROXY

    Registered shareholders can vote their shares via (1) a toll-free telephone
call from the U.S. or Canada, or (2) the Internet or (3) by mailing their signed
proxy card. The telephone and Internet voting procedures are designed to
authenticate shareholders' identities, to allow shareholders to vote their
shares and to confirm that their instructions have been properly recorded. We
have been advised by counsel that the procedures that have been put in place are
consistent with the requirements of applicable law. Specific instructions to be
followed by any registered shareholder interested in voting via telephone or the
Internet are set forth on the enclosed proxy card.

    Stockholders may revoke the authority granted by their execution of proxies
at any time before the effective exercise of such authority by filing with our
Secretary a written revocation or a duly executed proxy bearing a later date or
by voting in person at the annual meeting. Shares represented by executed and
unrevoked proxies will be voted in accordance with the choice or instructions
specified thereon. If no specifications are given, the proxies intend to vote
the shares represented thereby to approve Proposals No. 1 and 2 as set forth in
the accompanying Notice of 2000 Annual Meeting of Stockholders and in accordance
with their best judgment on any other matters that may properly come before the
Meeting.

RECORD DATE AND VOTING RIGHTS

    Only stockholders of record at the close of business on April 3, 2000, are
entitled to notice of, and to vote, at the annual meeting or any adjournment or
postponement thereof. We had outstanding on April 3, 2000, 23,543,385 shares of
common stock, each of which is entitled to one vote upon the matters to be

                                       4
<PAGE>
presented at the annual meeting. The presence, in person or by proxy, of a
majority of the issued and outstanding shares of common stock will constitute a
quorum for the transaction of business at the annual meeting. Votes withheld
from any nominee, abstentions and broker "non-votes" are counted as present or
represented for purposes of determining the presence or absence of a quorum for
the annual meeting. A broker "non-vote" occurs when a nominee holding shares for
a beneficial owner does not vote on one or more proposals because the nominee
does not have discretionary voting power and has not received instructions from
the beneficial owner. Abstentions are included in the number of shares present
or represented and voting on each matter. Broker "non-votes" are not so
included.

                             PRINCIPAL STOCKHOLDERS

    The following table sets forth certain information with respect to each
person known to us to be the beneficial owner of more than 5% of the issued and
outstanding common stock as of March 3, 2000 or other date noted below. As of
March 3, 2000, 23,485,940 shares of common stock were outstanding.

<TABLE>
<CAPTION>
                                                            NUMBER OF SHARES
                                                           BENEFICIALLY OWNED             PERCENTAGE
                                                   -----------------------------------    OF SHARES
                                                   OUTSTANDING   RIGHT TO      TOTAL     BENEFICIALLY
NAME AND ADDRESS OF BENEFICIAL OWNER                 SHARES       ACQUIRE     NUMBER        OWNED
- -------------------------------------------------  -----------   ---------   ---------   ------------
<S>                                                <C>           <C>         <C>         <C>
Sofinov Societe Financiere D'Innovation Inc......   1,029,823    1,113,424   2,143,247       8.7%
  1981 Avenue McGill College
  7e etage
  Montreal, Quebec H3A 3C7
Entities Affiliated with Hambrecht & Quist          1,113,005      333,334   1,446,339       6.1%
  Capital Management Incorporated................
  50 Rowes Wharf
  Boston, MA 02110
</TABLE>

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

With respect to the foregoing table, you should note that:

- - We filed a registration statement with the SEC on March 10, 2000 and a
  Pre-Effective Amendment No. 1 on April 3, 2000, in connection with a proposed
  public offering by us. The proposed public offering will be underwritten on a
  firm-commitment basis. As of the date of this proxy statement, this proposed
  public offering had not been consummated. None of the shares proposed to be
  sold are reflected in the foregoing table.

- - Beneficial ownership is determined in accordance with the rules and
  regulations of the SEC. In computing the number of shares beneficially owned
  by a person and the percentage ownership of that person, shares of common
  stock subject to options held by that person that are currently exercisable or
  exercisable within 60 days of March 3, 2000 are deemed outstanding. These
  shares, however, are not deemed outstanding for the purposes of computing the
  percentage ownership of any other person. Except as indicated above and
  pursuant to the applicable community property laws, each stockholder named in
  the table has sole voting and investment power with respect to the shares set
  forth opposite such stockholder's name. Shares included in the table under
  "Right to Acquire" represent shares subject to outstanding common stock
  purchase warrants currently exercisable.

- - Sofinov Societe Financiere D'Innovation Inc. is a wholly-owned subsidiary of
  Caisse De Depot et Placement du Quebec. Because of such relationship, Caisse
  is the indirect beneficial owner of the shares

                                       5
<PAGE>
  attributable to Sofinov and may be deemed to beneficially own all of the
  shares owned by Sofinov. In addition, the shares Sofinov has the right to
  acquire includes the shares Ms. Trudie Resch has the right to acquire.
  Ms. Resch is a member of the board of directors and holds the position of
  Director at Sofinov.

- - The shares attributable to entities affiliated with Hambrecht & Quist Capital
  Management Inc. includes shares and warrants held by H&Q Healthcare Investors
  and shares and warrants held by H&Q Life Sciences Investors. Hambrecht & Quist
  Capital Management Inc. is the Investment Adviser of H&Q Healthcare Investors
  and H&Q Life Sciences Investors and therefore has voting and investment power
  with respect to the shares owned by H&Q Healthcare Investors and H&Q Life
  Sciences Investors. Hambrecht & Quist Capital Management Inc. may be deemed to
  beneficially own all of the shares owned by H&Q Healthcare Investors and H&Q
  Life Sciences Investors although Hambrecht & Quist Capital Management Inc.
  disclaims beneficial ownership.

                                 PROPOSAL NO. 1
                             ELECTION OF DIRECTORS

NOMINEES FOR ELECTION AS DIRECTORS

    The Board of Directors is divided into three classes, with one class of
directors elected each year at the annual meeting of stockholders for a three
year term of office. All directors of a class hold their positions until the
annual meeting of stockholders at which their terms of office expire and until
their successors have been duly elected and qualified.

    The term of office of the Class I directors will expire at the annual
meeting. The Board of Directors has nominated John Zabriskie, Ph.D., Ms. Trudie
Resch and David Martin, Ph.D., for reelection as Class I directors to hold
office until the annual meeting of stockholders to be held in 2003 and until
their respective successors have been duly elected and qualified. In the event
any of the nominees shall be unable or unwilling to serve as a director,
discretionary authority is reserved to vote for a substitute or substitutes. The
Board of Directors has no reason to believe that any of the nominees will be
unable or unwilling to serve. Proxies cannot be voted for any persons other than
the nominees.

    The affirmative vote of a plurality of the shares of common stock present at
the annual meeting, in person or by proxy, is required for the election of the
Class I directors. Unless authority to do so is withheld, the persons named in
each proxy will vote the shares represented thereby "FOR" the election of the
nominees.

INFORMATION AS TO DIRECTORS AND NOMINEES FOR DIRECTOR

    The names of our directors (including the nominees for reelection as
Class I directors at the annual meeting), their ages, their position(s) with
Cubist, the year in which each first became a director, the expiration of the
term of office of each, the class of director of each, the principal occupation
and

                                       6
<PAGE>
employment of each over at least the last five years, and other directorships,
if any, of each are listed below.

<TABLE>
<CAPTION>
                                                                           DIRECTOR     TERM     CLASS OF
NAME                              AGE             POSITION(S) HELD          SINCE     EXPIRES    DIRECTOR
- ----                            --------   ------------------------------  --------   --------   --------
<S>                             <C>        <C>                             <C>        <C>        <C>
Scott M. Rocklage, Ph.D.......     45      Chairman of the Board of          1994       2002      III
                                             Directors, Chief Executive
                                             Officer and President
John K. Clarke................     46      Director                          1992       2002      III
Paul R. Schimmel, Ph.D........     59      Director                          1992       2002      III
Barry Bloom, Ph.D.............     71      Director                          1993       2001      II
Walter Maupay.................     61      Director                          1999       2001      II
David W. Martin, Jr., M.D.....     59      Director                          1997       2000       I
Trudie Resch..................     39      Director                          1999       2000       I
John Zabriskie, Ph.D..........     60      Director                          1999       2000       I
</TABLE>

    DR. ROCKLAGE was elected Chairman of the Board of Directors in March 2000.
Dr. Rocklage has served as our President and Chief Executive Officer and as a
member of the board of directors since July 1994. From 1990 to 1994,
Dr. Rocklage served as President and Chief Executive Officer of Nycomed
Salutar, Inc., a diagnostic imaging company. From 1992 to 1994, he also served
as President and Chief Executive Officer and Chairman of Nycomed
Interventional, Inc., a medical device company. From 1986 to 1990, he served in
various positions at Nycomed Salutar, Inc. and was responsible for designing and
implementing research and development programs that resulted in three drug
products in human clinical trials, including the approved drugs Omniscan and
Teslascan. Dr. Rocklage received his B.S. in Chemistry from the University of
California, Berkeley and his Ph.D. in Chemistry from the Massachusetts Institute
of Technology.

    MR. CLARKE is one of our founders and served as Chairman of the Board of
Directors from our incorporation to March 2000. Mr. Clarke has served as one of
our directors since our incorporation. From 1992 to 1994, Mr. Clarke served as
our acting President and Chief Executive Officer. Since 1982, he has been a
general partner of DSV Management in Princeton, New Jersey, the general partner
of DSV Partners IV. He is a founder and director of Alkermes, Inc. and a
director of Plastic Surgeons of America Inc. Mr. Clarke is the Managing General
Partner for Cardinal Health Partners, founded in 1997. Mr. Clarke received his
B.A. in Biology and Economics from Harvard College and his M.B.A. from The
Wharton School of the University of Pennsylvania.

    DR. SCHIMMEL is one of our scientific founders and has served as one of our
directors since our incorporation. From 1967 to 1998, Dr. Schimmel served as a
Professor of Biochemistry and Biophysics at the Massachusetts Institute of
Technology and as the John D. and Catherine T. MacArthur Professor of
Biochemistry and Biophysics at the Massachusetts Institute of Technology from
1992 to 1997. He has been a Professor and member of the Skaggs Institute for
Chemical Biology of the Scripps Research Institute since 1997. Dr. Schimmel is
an expert in molecular biology, protein translation and aminoacyl-tRNA
synthetases. He is a member of the National Academy of Sciences and the American
Academy of Arts and Sciences. Dr. Schimmel was a founder and is a director of
Repligen Corporation and Alkermes, Inc., each a biotechnology company.
Dr. Schimmel received his A.B. in Pre-Medicine from Ohio Wesleyan University and
his Ph.D. in Biochemistry from the Massachusetts Institute of Technology.

                                       7
<PAGE>
    DR. BLOOM has served as a one of our directors since September 1993.
Dr. Bloom has more than 40 years experience in the pharmaceutical industry. From
1952 to 1993, Dr. Bloom served in various positions at Pfizer Inc., including
Executive Vice President of Research & Development. He is a director of Vertex
Pharmaceuticals, Inc. and Neurogen Corp., biotechnology companies; Microbia, a
biotechnology company; Catalytica Pharmaceuticals, Inc., a chemical manufacturer
and supplier, and Incyte Pharmaceuticals, Inc., a genomics company. Dr. Bloom
received his S.B. in Chemistry and his Ph.D. in Organic Chemistry from the
Massachusetts Institute of Technology.

    MR. MAUPAY has served as one of our directors since June 1999. Since 1988,
Mr. Maupay has served as President of Calgon Vestal Laboratories, a division of
Merck & Co., Inc. until January 1995, when it was sold to Bristol-Myers Squibb.
Since June 1995, Mr. Maupay has also served as Group Executive of Calgon Vestal
Laboratories after the sale to Bristol-Myers Squibb. From 1984 to 1988
Mr. Maupay served as Vice-President, Healthcare at Calgon Vestal Laboratories.
Mr. Maupay is a director of Life Medical Sciences, Inc., a medical device
company, Kensey Nash Corporation, a medical device company, Neshaminy Golf
Club, Inc. and Warwick Golf Farm. Mr. Maupay received his Bachelor of Science in
Pharmacy from Temple University and his M.B.A. from Lehigh University.

    DR. MARTIN has served as one of our directors since October 1997. Since
July 1997, Dr. Martin has served as President, Chief Executive Officer and a
founder of Eos Biotechnology, Inc. Dr. Martin was a Professor of Medicine,
Professor of Biochemistry and an Investigator of the Howard Hughes Medical
Institute at the University of California San Francisco until 1983 when he
became the First Vice President and subsequently Senior Vice President of
Research and Development at Genentech, Inc., a position he held until 1990. He
was Executive Vice President of DuPont Merck Pharmaceutical Company from 1991
through 1993 and then returned to California in 1994 where he was Senior
Vice-President of Chiron Corp., a biotechnology company, and President of Chiron
Therapeutics. In May 1995, he assumed the position of President and Chief
Executive Officer of Lynx Therapeutics, Inc., a biotechnology company, and
served until November 1996. Dr. Martin is also a Director of Varian
Associates, Inc., a medical equipment supplier.

    MS. RESCH has served as one of our directors since June 1999. Since
June 1998, Ms. Resch has served as Director at Sofinov Societe Financiere
d'Innovation Inc. From June 1998 to June 1999, she served as Manager at Sofinov.
From June 1997 to December 1997, Ms. Resch was a consultant, principally working
with Sofinov.

    DR. ZABRISKIE has served as one of our directors since June 1999. Since
July 1997, Dr. Zabriskie has served as Chairman of the Board of NEN Life Science
Products, Inc., a laboratory supply company. From July 1997 to December 1999,
Dr. Zabriskie also served as President and Chief Executive Officer of NEN Life
Science Products, Inc. From November 1995 to January 1997, he was President and
Chief Executive Officer of Pharmacia & Upjohn. From 1994 to November 1995, he
served as President, Chief Executive Officer and Chairman of UpJohn Co.

    Walter Maupay was elected as a Class II Director to fill the vacancy created
by the resignation of Julius Rebek, effective June 1, 1999; Dr. John Zabriskie
was elected as a Class I Director to fill the vacancy created by the resignation
of Ellen Feeney, effective June 1, 1999; and Ms. Trudie Resch was elected as a
Class I Director to fill the vacancy created by the resignation of Terrance
McGuire, effective June 1, 1999. John Clarke resigned his position as Chairman
of the Board of Directors, effective March 3, 2000, and the Board of Directors
appointed Scott Rocklage as successor, effective March 3, 2000.

                                       8
<PAGE>
OWNERSHIP OF EQUITY SECURITIES BY MANAGEMENT

    The table below sets forth information as of March 3, 2000, as reported to
us, with respect to the beneficial ownership of the common stock by each
director and each named executive officer, and by all directors and executive
officers as a group. Beneficial ownership is determined in accordance with the
rules and regulations of the SEC. In computing the number of shares beneficially
owned by a person and the percentage ownership of that person, shares of common
stock subject to options held by that person that are currently exercisable or
exercisable within 60 days of March 3, 2000 are deemed outstanding. These
shares, however, are not deemed outstanding for the purposes of computing the
percentage ownership of any other person. Except as indicated below and pursuant
to applicable community property laws, each stockholder named in the table has
sole voting and investment power with respect to the shares set forth opposite
such stockholder's name. Shares included below under "Right to Acquire"
represent shares subject to outstanding stock options currently exercisable or
exercisable within 60 days of March 3, 2000.

<TABLE>
<CAPTION>
                                                              NUMBER OF SHARES
                                                             BENEFICIALLY OWNED            PERCENTAGE
                                                     ----------------------------------    OF SHARES
                                                     OUTSTANDING   RIGHT TO     TOTAL     BENEFICIALLY
NAME                                                   SHARES      ACQUIRE     NUMBER        OWNED
- ----                                                 -----------   --------   ---------   ------------
<S>                                                  <C>           <C>        <C>         <C>
Scott M. Rocklage, Ph.D............................    208,908     220,991      429,899       1.8%
Francis P. Tally, M.D..............................    102,857      44,296      147,153      *
Alan D. Watson, Ph.D, M.B.A........................     52,000      15,937       67,937      *
Thomas A. Shea, M.B.A..............................      7,142      38,424       45,566      *
Michael F. DeBruin, M.D............................                  9,375        9,375      *
Dennis D. Keith, Ph.D..............................     22,116      64,999       87,115      *
Frederick B. Oleson, Jr., D.Sc.....................                 60,312       60,312      *
George H. Shimer, Jr., Ph.D........................                  4,687        4,687      *
Thomas J. Slater...................................                 17,500       17,500      *
John K. Clarke.....................................                  9,130        9,130      *
Paul R. Schimmel, Ph.D.............................    295,713      26,272      321,985      *
Barry Bloom, Ph.D..................................      7,142      16,272       23,414      *
David W. Martin, Jr., M.D..........................                  5,856        5,856      *
Trudie Resch.......................................                  2,312        2,312      *
Walter Maupay......................................      6,000       2,312        8,312      *
John Zabriskie.....................................      4,000       2,312        6,312      *
All directors and executive officers as a group
  (16 persons).....................................    705,878     540,987    1,246,865       5.2%
</TABLE>

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

*   Less than 1% of the issued and outstanding shares of Common Stock.

- - We filed a registration statement with the SEC on March 10, 2000 and a
  Pre-Effective Amendment No. 1 on April 3, 2000, in connection with a proposed
  public offering by us. The proposed public offering will be underwritten on a
  firm-commitment basis. As of the date of this proxy statement, this proposed
  public offering had not been consummated. None of the shares proposed to be
  sold are reflected in the foregoing table.

- - A portion of the shares attributable to Dr. Schimmel are held by the Paul R.
  Schimmel Profit-Sharing Plan.

                                       9
<PAGE>
THE BOARD OF DIRECTORS AND COMMITTEES OF THE BOARD

    The Board of Directors has an Audit Committee, which met one time during the
1999 fiscal year. The functions of the Audit Committee include (1) making
recommendations to the Board of Directors with respect to the engagement of the
independent auditors; (2) reviewing the audit plans developed by the independent
auditors for the annual audit of our books and records and the results of such
audit; (3) reviewing the annual financial statements; (4) reviewing the
professional services provided by the independent auditors and the auditors'
independence; and (5) reviewing the adequacy of our system of internal controls
and the responses to management letters issued by the independent auditors. The
Board of Directors have not, as of the date of this proxy statement, adopted a
written charter for the audit committee. The members of the Audit Committee
during the 1999 fiscal year were Dr. Barry Bloom, Dr. John Zabriskie,
Ms. Trudie Resch and Mr. Terrance McGuire. Terrance McGuire resigned his
position as Director, effective February 5, 1999. Dr. John Zabriskie and
Ms. Trudie Resch became members of the Audit Committee as of June 1, 1999.

    The Board of Directors has a Compensation Committee, which met two times
during the 1999 fiscal year. The Compensation Committee's principal functions
are to review and approve salary plans and bonus awards, as well as other forms
of compensation, and to administer our 1993 Amended and Restated Stock Option
Plan, pursuant to the terms of such plan. The members of the Compensation
Committee during the 1999 fiscal year were Mr. John K. Clarke, Mr. George
Conrades and Mr. Walter Maupay. Mr. Walter Maupay became a member of the
compensation Committee as of June 1, 1999. Mr. George Conrades resigned his
position as a director, effective as of December 20, 1999. The Board of
Directors has not appointed a new member to the Compensation Committee to fill
the vacancy created by his resignation.

    During the 1999 fiscal year, the Board of Directors held four meetings. Each
director attended more than seventy-five percent (75%) of the Board meetings,
and the meetings of Board committees on which he or she served, except
Mr. Conrades and Dr. Zabriskie who attended fifty percent (50%) of the Board
meetings.

COMPENSATION OF DIRECTORS

    Dr. Rocklage is Chairman of the Board of Directors and one of our full-time
officers; he receives no additional compensation for serving on the Board of
Directors or its committees. No other director is a full-time officer. We paid
$1,000 to Dr. Bloom, Dr. Martin, Mr. Maupay, Mr. Conrades and Dr. Zabriskie,
each for each meeting of the Board of Directors they attended. No other director
received cash compensation during the 1999 fiscal year for his or her service on
the Board of Directors or any committee thereof. In 2000, Dr. Bloom,
Dr. Martin, Mr. Maupay and Dr. Zabriskie will receive a fee of $1,000 for each
Board meeting attended and will be reimbursed for expenses incurred in
connection with their attendance. No other director will receive cash
compensation during the 2000 fiscal year for his or her service on the Board of
Directors or any committee thereof.

    Pursuant to our stock option plan, upon first joining the Board of
Directors, each director who is not one of our officers or employees is granted
automatically a stock option exercisable for 15,000 shares of common stock at
fair market value, and each time that he or she is serving as a director on the
business day immediately following an annual meeting of stockholders, such
director is automatically granted on such business day a stock option
exercisable for 2,000 shares of common stock at fair market value.

    Pursuant to a consulting agreement, Dr. Schimmel received $48,000, for
consulting services during 1999.

                                       10
<PAGE>
                             EXECUTIVE COMPENSATION

SUMMARY COMPENSATION TABLE

    The table below sets forth certain compensation information for the fiscal
years ended December 31, 1999, 1998 and 1997 with respect to our Chief Executive
Officer and those other executive officers whose 1999 total annual compensation
exceeded $100,000.

<TABLE>
<CAPTION>
                                                                                      LONG-TERM
                                                                                 COMPENSATION AWARDS
                                                                             ----------------------------
                                                    ANNUAL COMPENSATION        RESTRICTED      SECURITIES    ALL OTHER
               NAME AND                          -------------------------        STOCK        UNDERLYING   COMPENSATION
          PRINCIPAL POSITION            YEAR     SALARY($)(1)     BONUS($)      AWARDS($)      OPTIONS(#)      ($)(2)
  ----------------------------------  --------   ------------     --------   ---------------   ----------   ------------
  <S>                                 <C>        <C>              <C>        <C>               <C>          <C>
  Scott M. Rocklage, Ph.D. (3)......    1999       $284,100       $185,000   $           --      85,000        $ 8,858
  Chairman of the Board of              1998       $258,923       $ 63,500   $           --     175,000        $ 8,076
  Directors, Chief Executive Officer    1997       $225,000       $ 90,000   $           --      35,000        $27,154
  and President

  Francis P. Tally, MD..............    1999       $233,263       $ 34,040   $           --      41,500        $16,067
  Executive Vice President;             1998       $220,000       $ 40,000   $           --      65,398        $ 9,258
  Scientific Affairs                    1997       $220,000       $ 11,000   $           --          --        $ 9,308

  Thomas A. Shea, M.B.A. ...........    1999       $134,221       $     --   $           --      25,500        $ 5,763
  Vice President Finance & Admin.       1998       $111,807       $     --   $           --      44,500        $  1000
  Chief Financial Officer, Treasurer    1997       $ 89,587       $     --   $           --          --        $  1050

  Dennis D. Keith, Ph.D. ...........    1999       $167,723       $ 15,000   $           --      15,000        $ 7,901
  Vice President; Drug Discovery        1998       $160,000       $     --   $           --      35,000        $ 1,000
                                        1997       $ 27,692(4)    $     --   $           --      75,000        $   110

  Frederick B. Oleson, Jr.,             1999       $150,096       $ 28,400   $           --      40,000        $ 7,002
    D.Sc. ..........................    1998       $140,000       $     --   $           --      35,000        $   500
  Vice President; Drug Development      1997       $ 17,231(5)    $     --   $           --      55,000        $    83
</TABLE>

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

(1) Salary includes amounts deferred pursuant to the Company's 401(k) Plan.

(2) All other compensation includes (i) the forgiveness of principal and accrued
    interest owed by Dr. Rocklage in 1997 and 1996, (ii) long-term disability
    insurance premiums paid by Cubist and (iii) Cubist's matching contributions
    under the Company's 401(k) Plan.

(3) Dr. Rocklage was appointed Chairman of the Board of Directors on March 3,
    2000.

(4) Reflects compensation from October 20, 1997 to December 31, 1997.
    Dr. Keith's employment commenced on October 20, 1997.

(5) Reflects compensation from November 6, 1997 to December 31, 1997.
    Dr. Oleson's employment commenced on November 6, 1997.

                                       11
<PAGE>
OPTION GRANTS IN LAST FISCAL YEAR

    The following table sets forth information regarding grants of stock options
under the Amended and Restated 1993 Stock Option Plan to the named executive
officers during the fiscal year ended December 31, 1999.

<TABLE>
<CAPTION>
                                            NUMBER OF      PERCENT
                                           SECURITIES      OF TOTAL
                                           UNDERLYING      OPTIONS
                                             OPTIONS      GRANTED TO    EXERCISE                GRANT DATE
                                             GRANTED     EMPLOYEES IN   OR BASE    EXPIRATION    PRESENT
NAME                                       (SHARES)(1)   FISCAL 1999     PRICE        DATE       VALUE(2)
- ----                                       -----------   ------------   --------   ----------   ----------
<S>                                        <C>           <C>            <C>        <C>          <C>
Scott M. Rocklage, Ph.D. ................    60,000          6.9%        $3.813     01/01/09     $167,934
                                             25,000          2.9%        $4.375     01/01/09     $ 69,973
Thomas A. Shea, M.B.A. ..................    25,500          2.9%        $3.813     01/01/09     $ 71,316
Francis P. Tally, M.D. ..................    41,500          4.7%        $3.813     01/01/09     $116,154
Dennis D. Keith, Ph.D. ..................    15,000          1.7%        $3.813     01/01/09     $ 41,984
Frederick B. Oleson, D.Sc. ..............    40,000          4.6%        $3.813     01/01/09     $111,868
</TABLE>

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

(1) Each option is exercisable in 16 equal quarterly installments, and has a
    maximum term of 10 years from the date of grant, subject to earlier
    termination in the event of the optionee's cessation of service with Cubist.
    The options are exercisable during the holder's lifetime only by the holder
    and they are exercisable by the holder only while the holder is an employee
    of Cubist and for certain limited periods of time thereafter in the event of
    termination of employment.

(2) Based on the Black-Scholes pricing model suggested by the Securities and
    Exchange Commission. The estimated values under that model are based on
    arbitrary assumptions as to variables such as stock price volatility,
    projected future dividend yield and interest rates, discounted for lack of
    marketability and potential forfeiture due to vesting schedule. The
    estimated values above use the following significant assumptions:
    volatility--74%; dividend yield--0%; the average life of the options--
    7.2 years; risk-free interest rate--yield to maturity of 10-year treasury
    note at grant date--4.67%. The actual value, if any, an executive may
    realize will depend on the excess of the stock price over the exercise price
    on the date the option is exercised. There is no assurance that the value
    realized by an executive will be at or near the value estimated using a
    modified Black-Scholes model.

                                       12
<PAGE>
AGGREGATE OPTION EXERCISES IN LAST FISCAL YEAR AND FISCAL YEAR-END OPTION VALUES

    The following table sets forth information with respect to the stock options
exercised during the fiscal year ended December 31, 1999, and the unexercised
stock options held at the end of such fiscal year by the named executive
officers.

<TABLE>
<CAPTION>
                                                                       NUMBER OF UNEXERCISED       VALUE OF UNEXERCISED IN-
                                                                          OPTIONS HELD AT              THE-MONEY OPTIONS
                                                                         DECEMBER 31, 1999           DECEMBER 31, 1999(1)
                                 SHARES ACQUIRED                    ---------------------------   ---------------------------
NAME                               ON EXERCISE     VALUE REALIZED   EXERCISABLE   UNEXERCISABLE   EXERCISABLE   UNEXERCISABLE
- ----                             ---------------   --------------   -----------   -------------   -----------   -------------
<S>                              <C>               <C>              <C>           <C>             <C>           <C>
Scott M. Rocklage, Ph.D........      14,285           $107,387        169,937        221,101      $2,760,153     $3,486,563
Thomas A. Shea, M.B.A..........          --           $     --         41,355         52,460      $  683,915     $  821,777
Francis Tally, M.D.............          --           $     --         29,356         77,787      $  447,931     $1,217,655
Dennis D. Keith, Ph.D..........          --           $     --         49,062         75,938      $  650,169     $1,089,676
Frederick B. Oleson, D.Sc......          --           $     --         43,750         86,250      $  648,163     $1,328,858
</TABLE>

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

(1) Based on the difference between the exercise price of each option and the
    last reported sales price of the Company's Common Stock on the NASDAQ-NMS on
    December 31, 1999 of $19.25.

EXECUTIVE EMPLOYMENT AGREEMENTS

    Dr. Rocklage, our Chairman of the Board, Chief Executive Officer and
President is employed pursuant to an employment agreement with Cubist, dated
June 20, 1994. Under the terms of that agreement, Dr. Rocklage's annual base
salary was set at $175,000 subject to annual review and increase by the Board of
Directors, and he is entitled to a performance bonus upon our achievement of
certain milestones for each fiscal year that have been mutually agreed upon by
Dr. Rocklage and the Board of Directors prior to the commencement of that
particular fiscal year. Dr. Rocklage received a base salary in 1999 of $285,000
and a performance bonus of $115,000. We can terminate Dr. Rocklage's employment
at any time by giving written notice of termination and may be terminated by
Dr. Rocklage at any time upon thirty days' written notice of termination. Upon
any termination of Dr. Rocklage's employment by us without cause, Dr. Rocklage
is entitled to severance pay in an amount equal to six months of his then
current annual base salary.

    None of our other executive officers has entered into an employment
agreement with Cubist.

                                       13
<PAGE>
                         COMPENSATION COMMITTEE REPORT
                       ON EXECUTIVE OFFICER COMPENSATION

COMPENSATION PHILOSOPHY AND OBJECTIVES

    Our compensation philosophy for executive officer compensation is to reflect
the value created and protected for shareholders, while furthering our short and
long-term strategic goals and values by aligning compensation with business
objectives and individual performance. Short and long-term compensation should
motivate and reward high levels of performance and are geared to attract and
retain qualified executive officers. Accordingly, our executive officer
compensation consists of three primary components intended to further our
overall compensation philosophy to achieve our compensation objectives. The
components include: base salary, annual bonuses and grants of stock options.

    In evaluating our executive officer's performance, we generally follow the
process outlined below:

    - Prior to or shortly after the beginning of each fiscal year, we set goals
      and objectives, which are reviewed with, and ultimately approved by, the
      full Board of Directors. Dr. Rocklage reports to the Board on Cubist's
      progress toward the achievement of these goals and objectives throughout
      the year at Board meetings and at other times as necessary.

    - Twice a year, generally in July and December, the Compensation Committee
      meets with Dr. Rocklage. The July meeting is to address Dr. Rocklage's
      personal goals and objectives along with Cubist's goals and objectives and
      approves a first half bonus payment accordingly. The December meeting is a
      comprehensive review of goals and objectives achieved during the year
      along with a review of Dr. Rocklage's full compensation package against
      compensation packages of Chief Executive Officers in similar companies.
      Dr. Rocklage's compensation is then set accordingly for the next fiscal
      year.

    - In December of each year, Dr. Rocklage evaluates the performance of the
      remainder of Cubist's executive officers against their goals and
      objectives set the prior year and recommends an annual base salary, stock
      option grant and bonus to the Compensation Committee commensurate with
      performance.

COMPENSATION FOR FISCAL 1999

CHIEF EXECUTIVE OFFICER COMPENSATION

    In December 1999, the Compensation Committee set Dr. Rocklage's annual base
salary at $325,000 effective on January 1, 2000. This increase represented a
$39,000 increase or 13.6% over the prior years base salary. The Compensation
Committee performed a comprehensive review of the compensation paid to chief
executive officers in other companies and has concluded this increase positions
Dr. Rocklage fairly within the range of base salaries paid to other chief
executive officers of comparable companies.

    In July 1999, the Compensation Committee determined that Dr. Rocklage
achieved the majority of milestone objectives for the first six months of 1999
and awarded Dr. Rocklage a bonus in the amount of $50,000 in July and an
additional $25,000 in September. In December 1999, the Compensation Committee
awarded Dr. Rocklage $40,000 in bonus funds and set an additional $162,500 as
the potential bonus amount payable upon achievement of goals for 2000.

                                       14
<PAGE>
    In December 1999, the Compensation Committee authorized a company-wide
distribution of stock options to employees based on performance. Dr. Rocklage's
stock options awarded relating to this distribution amounted to 70,000 common
shares.

REPORT ON EXECUTIVE COMPENSATION

    In December 1999, Dr. Rocklage recommended and the Compensation Committee
accepted base salary increases for the executive staff ranging from 0% to 7%.
The increases were determined after reviewing performance against goals and
objectives set for the year and also against salaries of similar positions in
comparable companies.

    The Compensation Committee also authorized bonuses in the amount of $117,365
for Cubist's seven executive officers, excluding Dr. Rocklage.

    In December 1999, the Compensation Committee authorized a company-wide
distribution of stock options to employees based on performance. The executive
officer's stock options awards relating to this distribution amounted to 150,000
common shares, excluding Dr. Rocklage.

CONCLUSION

    The Compensation Committee believes that the total 2000-related compensation
of the Chief Executive Officer and each of the executive officers, as described
above, is fair and is within the range of compensation for executive officers in
similar positions at comparable companies.

                                          COMPENSATION COMMITTEE
                                          John Clarke
                                          Walter Maupay

                                       15
<PAGE>
                          CORPORATE PERFORMANCE GRAPH

    The following graph compares the performance of our common stock to the
Nasdaq Stock Market (U.S. Companies) Index and to the Nasdaq Pharmaceutical
Index since October 25, 1996. The comparison assumes $100 was invested on
October 25, 1996 in Cubist's common stock and in each of the foregoing indices
and assumes reinvestment of dividends.

                          CORPORATE PERFORMANCE GRAPH

<TABLE>
<CAPTION>
                                                    CUBIST(1)    NAS(2)     NAP(3)
                                                    ---------   --------   --------
<S>                                                 <C>         <C>        <C>
10/25/96..........................................    $100        $100       $100
  12/96...........................................    $ 95        $106       $100
  12/97...........................................    $ 90        $130       $103
  12/98...........................................    $ 59        $183       $132
  12/99...........................................    $298        $338       $246
</TABLE>

(1) CUBIST PHARMACEUTICALS, INC.

(2) NASDAQ STOCK MARKET (U.S.)

(3) NASDAQ PHARMACEUTICAL

                              CERTAIN TRANSACTIONS

    On September 25, 1999, in consideration for the performance of services by
Alan Watson, our Senior Vice President, Corporate Development, we issued to
Mr. Watson 50,000 restricted shares of common stock, at a purchase price of
$10.125 per share, the fair market value of the common stock as determined by
the board of directors. Mr. Watson purchased the shares by executing a
promissory note in the amount of $506,250 with a 4% annual interest rate. This
note is secured by the 50,000 shares of common stock. The principal and interest
on the promissory note will be forgiven in three equal installments on
September 25, 2000, September 25, 2001, and September 25, 2002.

    We have adopted a policy, that all transactions between Cubist and its
officers, directors and affiliates must (i) be approved by a majority of those
members of our Board of Directors that are not parties, directly or indirectly
through affiliates, to such transactions and (ii) be on terms no less favorable
to Cubist than could be obtained from unrelated third parties.

    For a description of certain transactions and certain employment and other
arrangements between Cubist and certain of its directors and executive officers,
see "Compensation of Directors" and "Executive Employment Agreements."

                                       16
<PAGE>
            SECTION 16(A) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

    Under Section 16(a) of the Securities Exchange Act of 1934, as amended,
Cubist's directors, its executive (and certain other) officers, and any persons
holding more than ten percent of the common stock are required to report their
ownership of the common stock and any changes in that ownership to the
Securities and Exchange Commission. Specific due dates for these reports have
been established and we are required to report in this proxy statement any
failure to file by these dates during 1999. To our knowledge, all of these
filing requirements were satisfied by its directors, officers and ten percent
holders. In making these statements, the Company has relied upon the written
representations of its directors, officers and its ten percent holders and
copies of the reports that they have filed with the Commission.

                                       17
<PAGE>
                                 PROPOSAL NO. 2
                    RATIFICATION OF ADOPTION AND APPROVAL OF
                       AMENDMENT TO AMENDED AND RESTATED
                             1993 STOCK OPTION PLAN

    On March 3, 2000 our Board of Directors, subject to stockholder approval,
adopted and approved an amendment to our Amended and Restated 1993 Stock Option
Plan for the purpose of (i) increasing the number of shares of common stock
issuable upon exercise of options granted under our plan from 3,000,000 to
4,000,000; and (ii) increasing the maximum aggregate number of shares of common
stock that may be issued pursuant to the exercise of incentive stock options
granted under our plan from 3,000,000 to 6,000,000.

    The Board of Directors believes that an increase in the number of shares
available for issuance under the plan will enable us to continue our general
practice of making annual grants of stock options to key employees, officers and
directors, thereby encouraging stock ownership by our key employees, officers
and directors and our subsidiaries and providing additional incentives for them
to promote the success of our business.

    The discussion below provides a summary description of certain provisions of
our plan, as amended, and a brief and general description of the Federal income
tax rules applicable to incentive stock options and nonqualified stock options
granted under our plan.

    Our plan provides for grants of incentive stock options intended to qualify
for preferential tax treatment under Section 422 of the Internal Revenue Code of
1986, as amended, and nonstatutory stock options that do not qualify for such
treatment. All of our employees are eligible for stock options under our plan in
amounts and at prices determined by the Compensation Committee, provided that,
in the case of incentive stock options, the price will not be less than 100% of
the fair market value of the common stock on the date of grant, or not less than
110% of the fair market value of the stock on the grant date if the optionee
owns, directly or indirectly, more than 10% of the total combined voting power
of all classes of stock.

    Each director who is not one of our officers or employees and who is first
elected to the Board of Directors during the term of the plan will receive, on
the director's election date, an option to purchase 15,000 shares of common
stock. In addition, each time that a non-employee director is serving as a
director on the business day immediately following an annual meeting of
stockholders, he or she will be automatically granted on such business day a
stock option exercisable for 2,000 shares of common stock at fair market value,
which will become exercisable in four installments on the last day of each
fiscal quarter if the optionee remains a director on that date.

    The plan is administered by the Compensation Committee or the entire Board
of Directors. The entire Board or the Compensation Committee selects
participants (other than for automatic grants to non-employee directors as set
forth in the plan) and, in a manner consistent with the terms of the plan,
determines the number and duration of the options to be granted and the terms
and conditions of the option agreements. The entire Board of Directors or the
Compensation Committee has the right to alter, amend or revoke the plan.

    The plan provides that each outstanding option will immediately become fully
exercisable upon a "Change in Corporate Control" of Cubist, as defined in our
plan. A "Change in Corporate Control" includes the acquisition by any third
party (as hereinafter defined), directly or indirectly, of more than 80%

                                       18
<PAGE>
of the common stock outstanding at the time, without the prior approval of our
Board of Directors. With respect to options granted after January 1, 1999, the
Committee administering the plan has the discretion to exclude any event from
being deemed a "Change in Corporate Control". A "third party" for purposes of
the foregoing means any person other than Cubist or a subsidiary or employee
benefit plan or trust maintained by Cubist or any of its subsidiaries together
with any of such person's "affiliates" and "associates" as defined in
Rule 12b-2 under the Securities Exchange Act of 1934, as amended.

    The plan states that the maximum number of shares reserved for issuance
under the plan will increase, effective as of January 1, 1998 and each
January 1 thereafter during the term of the plan, by an additional number of
shares of common stock equal to fifteen percent (15%) of the excess, if any, of
(i) the total number of shares of common stock and common stock equivalents
issued and outstanding as of the close of business on December 31 of the
preceding year over (ii) the total number of shares of common stock and common
stock equivalents issued and outstanding as of the close of business on
December 31 of the year prior to such preceding year. The maximum number of
shares that may be subject to incentive stock options granted under the plan is
currently 3,000,000 shares, and the maximum number of shares that may be subject
to stock options granted to any person (including non-employee directors) under
the plan in a given year is 500,000 shares.

    Pursuant to the plan provision described above, on January 1, 1999 the
number of shares of common stock of the Company reserved for issuance under the
plan increased from 2,155,427 to 3,000,000. Upon approval of this proposal,
therefore, the number of shares of common stock reserved for issuance under the
plan will be 4,000,000 and the maximum number of shares that may be subject to
incentive stock options granted under the plan will be 6,000,000.

    Incentive stock options granted under the plan are not transferable except
by will or the laws of descent and distribution and may be exercised during the
life of the optionee only by the optionee. Nonstatutory stock options granted
under the plan are not transferable except by will of the laws of descent and
distribution and except that nonstatutory stock options may be transferred if
and to the extent authorized by the Compensation Committee.

    The following table sets forth information as of April 3, 2000 with respect
to stock options which have been received since the plan was adopted by
(i) each of our Chief Executive Officer and our other executive officers named
in the Summary Compensation Table, (ii) all current executive officers as a
group, (iii) all current directors, (iv) all current directors, other than those
who are executive officers, as a group, and (v) all employees and consultants,
excluding executive officers and directors, as a group since the plan was
adopted.

                         OPTION GRANTS UNDER 1993 PLAN

<TABLE>
<CAPTION>
NAME                                                          OPTIONS (SHARES)
- ----                                                          ----------------
<S>                                                           <C>
Scott M. Rocklage, Ph.D.....................................        675,322
Francis P. Tally, M.D.......................................        225,000
Alan D. Watson, Ph.D., M.B.A................................        130,000
Thomas A. Shea, M.B.A.......................................        120,957
Michael F. DeBruin, M.D.....................................        100,000
Dennis D. Keith, Ph.D.......................................        130,000
Frederick B. Oleson, Jr., D.Sc..............................        135,000
George H. Shimer, Jr., Ph.D.................................         75,000
</TABLE>

                                       19
<PAGE>

<TABLE>
<CAPTION>
NAME                                                          OPTIONS (SHARES)
- ----                                                          ----------------
<S>                                                           <C>
Thomas J. Slater............................................        100,000
John K. Clarke..............................................         17,100
Paul R. Schimmel, Ph.D......................................         17,100
Barry Bloom, Ph.D...........................................         31,384
David W. Martin, Jr., M.D...................................         16,400
Trudie Resch................................................         15,000
Walter Maupay...............................................         15,000
John Zabriskie, Ph.D........................................         15,000
All executive officers as a group...........................      1,691,279
All directors, as a group...................................        802,306
All directors, excluding executive officers, as a group.....        126,984
All employees and consultants, excluding executive officers
  and directors, as a group.................................      1,142,126
</TABLE>

    The affirmative vote of the holders of a majority of the shares of common
stock voted on the issue at the annual meeting, in person or by proxy, is
required to ratify the adoption and approval by the Board of Directors of the
amendment to the Amended and Restated 1993 Stock Option Plan. If the proposal to
ratify the amendment to the plan is not approved at the annual meeting, the
plan, as previously adopted by the Board of Directors and ratified by the
shareholders, will remain in full force and effect.

    THE BOARD OF DIRECTORS DEEMS PROPOSAL NO. 2 TO BE IN THE BEST INTERESTS OF
CUBIST AND ITS STOCKHOLDERS AND RECOMMENDS A VOTE "FOR" APPROVAL THEREOF. Unless
authority to do so is withheld, the persons named in each proxy will vote the
shares represented thereby "FOR" the ratification of the adoption and approval
by the Board of Directors of the amendment to the plan.

                             STOCKHOLDER PROPOSALS

    All stockholder proposals that are intended to be presented at the 2001
Annual Meeting of Stockholders of Cubist must be received by Cubist not later
than December 31, 2000, for inclusion in the Board of Directors' proxy statement
and form of proxy relating to the annual meeting.

                                 OTHER BUSINESS

    Representatives of PricewaterhouseCoopers LLP are expected to be present at
the annual meeting and will have the opportunity to make a statement if they
desire to do so and to respond to appropriate questions.

    The Board of Directors knows of no other business to be acted upon at the
annual meeting. However, if any other business properly comes before the annual
meeting, it is the intention of the persons named in the enclosed proxy to vote
on such matters in accordance with their judgment.

    The prompt return of your proxy will be appreciated and helpful in obtaining
the necessary vote. Therefore, whether or not you expect to attend the annual
meeting, please sign the proxy and return it in the enclosed envelope, or vote
by telephone or on the Internet by following the instructions on the enclosed
proxy card.

                                       20
<PAGE>
                                  [Back Cover]

                          [Code for Boston EquiServe]

                                    1596PS00
<PAGE>
                                                                        APPENDIX

                          CUBIST PHARMACEUTICALS, INC.
                  AMENDED AND RESTATED 1993 STOCK OPTION PLAN

    This Amended and Restated 1993 Stock Option Plan hereby further amends and
restates the Company's current Amended and Restated 1993 Stock Option Plan, as
heretofore amended, to read in its entirety as follows:

    1.  DEFINITIONS.  As used in this Amended and Restated 1993 Stock Option
Plan of Cubist Pharmaceuticals, Inc., the following terms shall have the
following meanings:

    1.1.  AWARDED GRANT DATE means the date as of which an Awarded Option is
granted, as determined under Section 7.1.

    1.2.  AWARDED OPTION means Options granted pursuant to Section 7 hereof.

    1.3.  BOARD means the Company's Board of Directors.

    1.4  CHANGE IN CORPORATE CONTROL means (1) the time of approval by the
shareholders of the Company of (A) any consolidation or merger of the Company in
which the Company is not the continuing or surviving corporation or pursuant to
which Shares would be converted into cash, securities or other property, other
than a merger in which the holders of Stock immediately prior to the merger will
have the same proportionate ownership of common stock of the surviving
corporation immediately after the merger as before the merger, (B) any sale,
lease, exchange, or other transfer (in one transaction or a series of related
transactions) of all or substantially all the assets of the Company, or
(C) adoption of any plan or proposal for the liquidation or dissolution of the
Company, or (2) the date on which any "person" (as defined in Section 13(d) of
the Exchange Act), other than the Company or a Subsidiary or employee benefit
plan or trust maintained by the Company or any of its Subsidiaries shall become
(together with its "affiliates" and "associates," as defined in Rule 12b-2 under
the Exchange Act) the "beneficial owner" (as defined in Rule 13d-3 under the
Exchange Act), directly or indirectly, of more than 25% of the Stock outstanding
at the time, without the prior approval of the Board of Directors of the
Company.

    1.5.  CODE means the federal Internal Revenue Code of 1986, as amended.

    1.6.  COMMITTEE means a committee comprised of two or more Outside
Directors, appointed by the Board of Directors, responsible for the
administration of the Plan, as provided in Section 5; provided, that the Board
of Directors itself may at any time, in its sole discretion, exercise any or all
functions and authority of the Committee.

    1.7.  COMPANY means Cubist Pharmaceuticals, Inc., a Delaware corporation.

    1.8.  EXCHANGE ACT means the Securities Exchange Act of 1934, as amended.

    1.9.  ELIGIBLE DIRECTOR means a director of one or more of the Company and
its Subsidiaries who is not also an employee or officer of one or more of the
Company and its Subsidiaries.

    1.10.  FAIR MARKET VALUE means on any date (i) if the Stock is traded on a
stock exchange or on the Nasdaq National Market, the closing price on the date
in question or, if no trades were reported on such date, the closing price on
the most recent trading day preceding such date on which a trade occurred, and

                                      A-1
<PAGE>
(ii) if the Stock is not traded on a stock exchange or on the Nasdaq National
Market, the value of a Share on such date as determined by the Committee.

    1.11.  FORMULA GRANT means the grant of a Formula Option.

    1.12.  FORMULA GRANT DATE shall have the meaning specified in Section 8.1
hereof.

    1.13.  FORMULA OPTIONS means Options granted pursuant to Section 8 hereof.

    1.14  HOLDER means, with respect to any Option, (i) the Optionee to whom
such Option shall have been granted under the Plan, or (ii) any transferee of
such Option to whom such Option shall have been transferred in accordance with
the provisions of Section 14.

    1.15.  INCENTIVE OPTION means an Awarded Option which by its terms is to be
treated as an "incentive stock option" within the meaning of Section 422 of the
Code.

    1.16.  NONSTATUTORY OPTION means any Option that is not an Incentive Option.

    1.17.  OPTION means an Awarded Option or Formula Option granted under the
Plan to purchase Shares.

    1.18.  OPTION AGREEMENT means an agreement between the Company and an
Optionee, setting forth the terms and conditions of an Option.

    1.19.  OPTION PRICE means the price paid by an Optionee for a Share upon
exercise of an Option.

    1.20.  OPTIONEE means a person eligible to receive an Option, as provided in
Section 6, to whom an Option shall have been granted under the Plan.

    1.21.  OUTSIDE DIRECTOR shall mean a member of the Board who is not an
officer, employee or consultant of the Company or any Subsidiary.

    1.22.  PLAN means this Amended and Restated 1993 Stock Option Plan of the
Company, as amended from time to time.

    1.23.  RETIREMENT means, with respect to any Optionee that is an employee or
director of the Company, the voluntary retirement of such Optionee as an
employee and/or director, as the case may be, of the Company at any time after
age 65 or such earlier age as the Committee shall determine.

    1.24.  SECURITIES ACT means the Securities Act of 1933, as amended.

    1.25.  SHARES means shares of Stock.

    1.26.  STOCK means common stock, $.001 par value per share, of the Company.

    1.27.  SUBSIDIARY means any corporation which qualifies as a subsidiary of
the Company under the definition of "subsidiary corporation" in Section 424(f)
of the Code.

    1.28.  TEN PERCENT OWNER means a person who owns, or is deemed within the
meaning of Section 422(b)(6) of the Code to own, stock possessing more than 10%
of the total combined voting power of all classes of stock of the Company (or
its parent or Subsidiaries). Whether a person is a Ten Percent Owner shall be
determined with respect to each Incentive Option based on the facts existing
immediately prior to the applicable grant date thereof.

                                      A-2
<PAGE>
    1.29.  VESTING YEAR for any portion of any Incentive Option means the
calendar year in which that portion of the Incentive Option first becomes
exercisable.

    2.  PURPOSE.  This Plan is intended to encourage ownership of Stock by
officers, employees and directors of and consultants to the Company and its
Subsidiaries and to provide additional incentives for them to promote the
success of the Company's business. The Plan is intended to be an incentive stock
option plan within the meaning of Section 422 of the Code but not all Options
granted hereunder are required to be Incentive Options.

    3.  TERM OF THE PLAN.  Options may be granted hereunder at any time in the
period commencing upon the effectiveness of the Plan pursuant to Section 21 and
ending on May 6, 2003.

    4.  STOCK SUBJECT TO THE PLAN.  Subject to the provisions of Section 15 of
the Plan, at no time shall the number of Shares then outstanding which are
attributable to the exercise of Options granted under the Plan, plus the number
of Shares then issuable upon exercise of outstanding Options granted under the
Plan exceed 1,500,000 Shares, which aggregate number of Shares, automatically
and without further action, shall increase, on January 1, 1998, and each
January 1 thereafter during the term of the Plan, by an additional number of
Shares equal to fifteen percent (15%) of the difference between (i) the total
number of Shares and Stock equivalents (other than Options) issued and
outstanding as of the close of business on December 31 of the immediately
preceding year and (ii) the total number of Shares and Stock equivalents (other
than Options) issued and outstanding as of the close of business on December 31
of the year prior to such immediately preceding year. Notwithstanding the
foregoing, no more than an aggregate of 3,000,000 Shares (subject to adjustment
pursuant to the provisions of Section 15 hereof) may be issued pursuant to the
exercise of Incentive Stock Options granted under the Plan. Shares to be issued
upon the exercise of Options granted under the Plan may be either authorized but
unissued Shares or Shares held by the Company in its treasury. If any Option
expires or terminates for any reason without having been exercised in full, the
Shares not purchased thereunder shall again be available for Options thereafter
to be granted.

    5.  ADMINISTRATION.  The Plan shall be administered by the Committee.
Subject to the provisions of the Plan, the Committee shall have complete
authority, in its discretion, to make or to select the manner of making the
following determinations with respect to each Awarded Option to be granted by
the Company: (a) the officer, employee or consultant to receive such Awarded
Option; (b) whether the Awarded Option (if granted to an employee) will be an
Incentive Option or Nonstatutory Option; (c) the time of granting the Awarded
Option; (d) the number of Shares subject to the Awarded Option; (e) the Option
Price; (f) the option period; (g) the exercise date or dates or, if the Awarded
Option is immediately exercisable in full on its grant date, the vesting
schedule, if any, applicable to the Shares issuable upon the exercise of the
Awarded Option; (h) the effect of termination of employment, consulting or
association with the Company on the subsequent exercisability of the Awarded
Option; and (i) if the Awarded Option is a Nonstatutory Option, whether such
Nonstatutory Option may be transferred by the Holder to a third party. Subject
to the provisions of the Plan, the Committee shall have complete authority, in
its discretion, to determine whether any Formula Option may be transferred by
the Holder to a third party. In making such determinations, the Committee may
take into account the nature of the services rendered by the respective
officers, employees and consultants, their present and potential contributions
to the success of the Company and its Subsidiaries, and such other factors as
the Committee in its discretion shall deem relevant. Subject to the provisions
of the Plan, the Committee shall also have complete authority to interpret the
Plan, to prescribe, amend and rescind rules and regulations relating to it, to
determine the terms and provisions of the respective Option Agreements (which
need not be identical), and to make all

                                      A-3
<PAGE>
other determinations necessary or advisable for the administration of the Plan.
The Committee's determinations on the matters referred to in this Section 5
shall be conclusive.

    6.  ELIGIBILITY.  An Awarded Option may be granted only to an employee or
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. Eligible Directors may not be granted Awarded Options in their
capacities as directors of the Company, but those Eligible Directors that are
also consultants to the Company may be granted Awarded Options in their
capacities as consultants. Subject to adjustment pursuant to Section 15 hereof,
no person in any year may be granted Options with respect to more than 500,000
Shares.

    7.  AWARDED OPTIONS.

    7.1.  TIME OF GRANTING AWARDED OPTIONS.  The granting of an Awarded Option
shall take place at the time specified by the Committee. Only if expressly so
provided by the Committee, shall the Awarded Grant Date be the date on which an
Option Agreement shall have been duly executed and delivered by the Company and
the Optionee.

    7.2.  OPTION PRICE.  The Option Price under each Awarded Option shall be
determined by the Committee but, in the case of any Incentive Option, shall be
not less than 100% of the Fair Market Value of Stock on the Awarded Grant Date,
or not less than 110% of the Fair Market Value of Stock on the Awarded Grant
Date if the Optionee is a Ten Percent Owner. The Option Price under each
Nonstatutory Option shall not be so limited solely by reason of this
Section 7.2.

    7.3.  AWARDED OPTION PERIOD.  No Incentive Option may be exercised later
than the tenth (10th) anniversary of the Awarded Grant Date but in any case not
later than the fifth (5th) anniversary of the Awarded Grant Date if the Optionee
is a Ten Percent Owner. The option period under each Nonstatutory Option shall
not be so limited solely by reason of this Section 7.3.

    7.4.  VESTING.  An Awarded Option may become exercisable in such
installments, cumulative or non-cumulative, as the Committee may determine. In
the case of an Awarded Option not otherwise immediately exercisable in full, the
Committee may accelerate the exercisability of such Awarded Option in whole or
in part at any time, provided the acceleration of the exercisability of any
Incentive Option would not cause the Awarded Option to fail to comply with the
provisions of Section 422 of the Code.

    7.5.  LIMIT ON INCENTIVE OPTION CHARACTERIZATION.  No Incentive Option shall
be considered an Incentive Option to the extent pursuant to its terms it would
permit the Optionee to purchase for the first time in any Vesting Year under
that Incentive Option more than the number of Shares calculated by dividing the
current limit by the Option Price. The current limit for any Optionee for any
Vesting Year shall be $100,000 minus the aggregate Fair Market Value (determined
as of the respective Awarded Grant Dates) of the number of Shares available for
purchase for the first time in the Vesting Year under each other Incentive
Option granted to the Optionee under the Plan and each other incentive stock
option granted to the Optionee after December 31, 1986 under any other incentive
stock option plan of the Company (and any parent corporation and Subsidiaries).
Any Shares subject to an Incentive Option in excess of the foregoing limitation
shall be treated as if granted under a Nonstatutory Option with otherwise
identical terms.

                                      A-4
<PAGE>
    8.  FORMULA OPTIONS.

    8.1.  DIRECTORS ELECTED FOR FIRST TIME.  Subject to the Plan's effectiveness
as set forth in Section 21, each Eligible Director who is elected to the Board,
and was never before a member of the Board, and who is elected to the Board
during the term of the Plan (whether elected at an annual or special
stockholders' meeting or by action of the Board or written consent of
stockholders without a meeting), shall be granted, on the date of such meeting
or other appointment (as used in or with reference to this Section 8.1, a
"FORMULA GRANT DATE"), a Nonstatutory Option to purchase 7,000 Shares. Grants of
Formula Options under this Section 8.1 occur automatically without any action
being required of the Optionee, the Committee, the Board of Directors, the
Company or any other person, entity or body.

    8.2.  ANNUAL FORMULA GRANTS.  Subject to the Plan's effectiveness as set
forth in Section 21, on the date of each annual meeting of stockholders of the
Company commencing with the 1997 Annual Meeting of Stockholders of the Company,
each Eligible Director who continues to be a director of the Company on the
business day immediately following such annual meeting of stockholders shall be
granted a Nonstatutory Option on such business day (also referred to as a
"Formula Grant Date"), to purchase 700 Shares. Grants of Formula Options under
this Section 8.2 occur automatically without any action being required of the
Optionee, the Committee, the Board of Directors, the Company or any other
person, entity or body.

    8.3.  CERTAIN TERMS OF FORMULA OPTIONS.  Each Formula Option granted to an
Optionee under this Section 8 shall have an exercise price equal to 100% of the
Fair Market Value of the Stock on the applicable Formula Grant Date. No Formula
Option granted pursuant to this Section 8 is intended to qualify as an incentive
stock option within the meaning of Section 422 of the Code. The Formula Grants
shall be evidenced by Option Agreements containing provisions that are in all
respects consistent with this Section 8. All of such Option Agreements shall
contain identical terms and conditions, except as otherwise required or
permitted by this Section 8.

    8.4.  OPTION PERIOD.  The option period for any Formula Option granted
pursuant to this Section 8 shall be ten years from the date of grant.

    8.5.  EXERCISABILITY.  Each Formula Option granted to an Eligible Director
pursuant to Section 8.1 hereof (a "Section 8.1 Formula Option") shall become
exercisable in twelve (12) equal installments, with the first installment
becoming exercisable on the last day of the first full fiscal quarter following
the Formula Grant Date applicable to such Section 8.1 Formula Option and an
additional installment becoming exercisable on the last day of each of the
eleven successive fiscal quarters following such first fiscal quarter; PROVIDED,
HOWEVER, that if the Optionee with respect to such Section 8.1 Formula Option
shall cease to be a director of the Company and each of its Subsidiaries, then,
notwithstanding anything in this Section 8.5 to the contrary and subject to
Sections 8.6 and 13 hereof, such Section 8.1 Formula Option shall thereafter be
exercisable only with respect to those of such installments for which such
Section 8.1 Formula Option is exercisable, pursuant to this Section 8.5, at the
time of such cessation. Each Formula Option granted to an Eligible Director
pursuant to Section 8.2 hereof (a "Section 8.2 Formula Option") shall become
exercisable in four (4) equal installments, with the first installment becoming
exercisable on the last day of the first full fiscal quarter following the
Formula Grant Date applicable to such Section 8.2 Formula Option and an
additional installment becoming exercisable on the last day of each of the three
successive fiscal quarters following such first fiscal quarter; PROVIDED,
HOWEVER, that if the Optionee with respect to such Section 8.2 Formula Option
shall cease to be a director of the Company and each of its Subsidiaries, then,
notwithstanding anything in this Section 8.5 to the contrary and subject to
Sections 8.6 and 13 hereof, such Section 8.2 Formula Option shall thereafter be
exercisable only with respect to those

                                      A-5
<PAGE>
of such installments for which such Section 8.2 Formula Option is exercisable,
pursuant to this Section 8.5, at the time of such cessation.

    8.6.  CERTAIN MODIFICATIONS OF FORMULA OPTIONS.  Notwithstanding anything in
this Section 8 or any applicable Option Agreement to the contrary, the Board or
any committee of two or more Outside Directors that are disinterested in the
matter may (i) accelerate the exercisability of any Formula Option in whole or
in part at any time or (ii) determine and alter at any time the effect that the
termination of any Optionee's position as a director of the Company shall have
on the exercisability of any Formula Option held by a Holder.

    9.  EXERCISE OF OPTION.

           (a) An Option may be exercised only by giving written notice, in the
       manner provided in Section 20 hereof, specifying the number of Shares as
       to which the Option is being exercised, accompanied (except as otherwise
       provided in paragraph (b) of this Section 9) by full payment for such
       Shares in the form of a check or bank draft payable to the order of the
       Company or other Shares with a current Fair Market Value equal to the
       Option Price of the Shares to be purchased. Receipt by the Company of
       such notice and payment shall constitute the exercise of the Option or a
       part thereof. Subject to the provisions of the Plan (including, without
       limitation, Sections 10, 11 and 12) or any applicable Option Agreement,
       within 30 days after receipt of such notice and payment, the Company
       shall deliver or cause to be delivered to the Holder a certificate or
       certificates for the number of Shares then being purchased by the Holder.
       Such Shares shall be fully paid and nonassessable. If such Shares are not
       at that time effectively registered under the Securities Act, the Holder
       shall include with such notice a letter, in form and substance
       satisfactory to the Company, confirming that such Shares are being
       purchased for the Holder's own account for investment and not with a view
       to distribution.

           (b) In lieu of payment by check, bank draft or other Shares
       accompanying the written notice of exercise as described in
       paragraph (a) of this Section 9, a Holder may, unless prohibited by
       applicable law, elect to effect payment by including with the written
       notice referred to in paragraph (a) of this Section 9 irrevocable
       instructions to deliver for sale to a registered securities broker
       acceptable to the Company that number of Shares subject to the Option
       being exercised sufficient, after brokerage commissions, to cover the
       aggregate exercise price of such Option and, if the Holder further
       elects, the withholding obligations of the Optionee and/or such Holder
       pursuant to Section 12 with respect to such exercise, together with
       irrevocable instructions to such broker to sell such Shares and to remit
       directly to the Company such aggregate exercise price and, if the Holder
       has so elected, the amount of such withholding obligation. The Company
       shall not be required to deliver to such securities broker any stock
       certificate for such Shares until it has received from the broker such
       exercise price and, if the Holder has so elected, the amount of such
       withholding obligation.

           (c) The right of the Holder to exercise an Option pursuant to any
       provision of this Section 9, and the obligation of the Company to issue
       Shares upon any exercise of an Option pursuant to this Section 9, is
       subject to compliance with all of the other provisions of the Plan
       (including, without limitation, Sections 10, 11 and 12) or any applicable
       Option Agreement.

                                      A-6
<PAGE>
    10.  RESTRICTIONS ON ISSUE OF SHARES.

           (a) Notwithstanding any other provision of the Plan, if, at any time,
       in the reasonable opinion of the Company the issuance of Shares covered
       by the exercise of any Option may constitute a violation of law, then the
       Company may delay such issuance and the delivery of a certificate for
       such Shares until (i) approval shall have been obtained from such
       governmental agencies, other than the Securities and Exchange Commission,
       as may be required under any applicable law, rule, or regulation; and
       (ii) in the case where such issuance would constitute a violation of a
       law administered by or a regulation of the Securities and Exchange
       Commission, one of the following conditions shall have been satisfied:

        (1)  the Shares with respect to which such Option has been exercised are
    at the time of the issue of such Shares effectively registered under the
    Securities Act; or

        (2)  a no-action letter in form and substance reasonably satisfactory to
    the Company with respect to the issuance of such Shares shall have been
    obtained by the Company from the Securities and Exchange Commission.

The Company shall make all reasonable efforts to bring about the occurrence of
said events.

           (b) Each certificate representing Shares issued upon the exercise of
       an Option will bear restrictive legends which may refer to this Plan.

    11.  PURCHASE FOR INVESTMENT; SUBSEQUENT REGISTRATION.

           (a) Without limiting the generality of Section 10 hereof, if the
       Shares to be issued upon exercise of an Option granted under the Plan
       have not been effectively registered under the Securities Act, the
       Company shall be under no obligation to issue any Shares covered by any
       Option unless the person who exercises such Option, in whole or in part,
       shall give a written representation to the Company which is satisfactory
       in form and substance to its counsel and upon which the Company may
       reasonably rely, that he or she is acquiring the Shares issued pursuant
       to such exercise of the Option as an investment and not with a view to,
       or for sale in connection with, the distribution of any such Shares.

           (b) Each Share issued pursuant to the exercise of an Option granted
       pursuant to this Plan may bear a reference to the investment
       representation made in accordance with this Section 11 and to the fact
       that no registration statement has been filed with the Securities and
       Exchange Commission in respect to said Stock.

           (c) If the Company shall deem it necessary or desirable to register
       under the Securities Act or other applicable statutes any Shares with
       respect to which an Option shall have been granted, or to qualify any
       such Shares for exemption from the Securities Act or other applicable
       statutes, then the Company shall take such action at its own expense. The
       Company may require from each Option holder, or each holder of Shares
       acquired pursuant to the Plan, such information in writing for use in any
       registration statement, prospectus, preliminary prospectus or offering
       circular as is reasonably necessary for such purpose and may require
       reasonable indemnity to the Company and its officers and directors from
       such holder against all losses, claims, damage and liabilities arising
       from such use of the information so furnished and caused by any untrue
       statement of any material fact therein or caused by the omission to state
       a material fact required

                                      A-7
<PAGE>
       to be stated therein or necessary to make the statements therein not
       misleading in the light of the circumstances under which they were made.

    12.  WITHHOLDING; NOTICE OF DISPOSITION OF STOCK PRIOR TO EXPIRATION OF
SPECIFIED HOLDING PERIOD.

           (a) Whenever Shares are to be issued in satisfaction of an Option
       granted hereunder, the Company shall have the right to require the
       Optionee and/or any subsequent Holder to remit to the Company an amount
       sufficient to satisfy federal, state, local, employment or other tax
       withholding requirements if and to the extent required by law (whether so
       required to secure for the Company an otherwise available tax deduction
       or otherwise) prior to the delivery of any certificate or certificates
       for such Shares.

           (b) The Company may require as a condition to the issuance of Shares
       covered by any Incentive Option that the party exercising such Option
       give a written representation to the Company which is satisfactory in
       form and substance to its counsel and upon which the Company may
       reasonably rely, that he or she will report to the Company any
       disposition of such Shares prior to the expiration of the holding periods
       specified by Section 422(a)(1) of the Code. If and to the extent that the
       realization of income in such a disposition imposes upon the Company
       federal, state, local or other withholding tax requirements, or any such
       withholding is required to secure for the Company an otherwise available
       tax deduction, the Company shall have the right to require that the
       recipient remit to the Company an amount sufficient to satisfy those
       requirements; and the Company may require as a condition to the issuance
       of Shares covered by an Incentive Option that the party exercising such
       Incentive Option give a satisfactory written representation promising to
       make such a remittance.

           (c) The Committee may, at or after grant, permit an Optionee and/or
       subsequent Holder to satisfy any tax withholding requirements pertaining
       to the exercise of an Option by delivery to the Company of Shares
       (including, without limitation, Shares retained from the Option exercise
       that is creating the tax obligation) having a value equal to the amount
       to be withheld. The value of Shares to be so delivered shall be based on
       the Committee's determination of the Fair Market Value of a Share on the
       date the amount of tax to be withheld is to be determined.

    13.  TERMINATION OF ASSOCIATION WITH THE COMPANY.  If an Optionee ceases to
be an employee, director or consultant of the Company and its Subsidiaries for
any reason other than Retirement or death of such Optionee, any Option held by
such Optionee and/or any subsequent Holder may be exercised by such Optionee
and/or such subsequent Holder at any time within 90 days after the termination
of such relationship, but only to the extent exercisable at termination and in
no event after the applicable option period. If an Optionee enters Retirement or
dies, any Option held by such Optionee and/or any subsequent Holder may be
exercised by such Optionee, such subsequent Holder and/or the executor or
administrator of such Optionee or such subsequent Holder at any time within the
shorter of the applicable option period or 12 months after the date of the
Optionee's Retirement or death, but only to the extent exercisable at the time
of such Optionee's Retirement or death. Options which are not exercisable at the
time of termination of such relationship between the Company and the Optionee or
which are so exercisable but are not exercised within the time periods described
above shall terminate. Notwithstanding the foregoing, in the event that (i) the
applicable Option Agreement with respect to an Option shall contain specific
provisions governing the effect that any such termination shall have on the
exercisability of such Option or (ii) the Board, the Committee or any other
committee of the Board composed of Outside Directors that are disinterested on
the matter, as appropriate, shall at any time adopt specific provisions

                                      A-8
<PAGE>
governing the effect that any such termination shall have on the exercisability
of such Option, then such provisions shall, to the extent that they are
inconsistent with the provisions of this Section 13, control and be deemed to
supersede the provisions of this Section 13. For purposes of this Section 13,
military or sick leave shall not be deemed a termination of employment, PROVIDED
that it does not exceed the longer of 90 days or the period during which the
absent Optionee's reemployment rights, if any, are guaranteed by statute or by
contract.

    14.  TRANSFERABILITY OF OPTIONS.  Incentive Options shall not be
transferable, otherwise than by will or the laws of descent and distribution,
and may be exercised during the life of the Optionee only by the Optionee.
Nonstatutory Options shall not be transferable; PROVIDED, HOWEVER, that
Nonstatutory Options shall be transferable by will or the laws of descent and
distribution; and PROVIDED, FURTHER, that Nonstatutory Options may be
transferred to a third party if and to the extent authorized and permitted by
the Compensation Committee. In granting its authorization and permission to any
proposed transfer of a Nonstatutory Option to a third party, the Compensation
Committee may impose conditions or requirements that must be satisfied by the
transferor or the third party transferee prior to or in connection with such
transfer, including, without limitation, any conditions or requirements that may
be necessary or desirable, in the sole and absolute discretion of the Committee,
to ensure that such proposed transfer complies with applicable securities laws
or to prevent the Company, such transferor or such third party transferee from
violating or otherwise not be in compliance with applicable securities laws as a
result of such transfer. For purposes of this Section 14, the term Nonstatutory
Option shall include an Option that was an Incentive Option at the time of
grant, but that has been subsequently been disqualified or otherwise lost its
status as an Incentive Option. The restrictions on transferability set forth in
this Section 14 shall in no way preclude any Holder from effecting "cashless"
exercises of an Option pursuant to, and in accordance with, Section 9(b) hereof.

    15.  ADJUSTMENT OF NUMBER OF OPTION SHARES.  In the event of any stock
dividend payable in Stock or any split-up or contraction in the number of Shares
prior to the exercise in full of an Option, the number of Shares subject to the
Option and the price to be paid for each Share subject to the Option shall be
proportionately adjusted. In the event of any reclassification or change of
outstanding Stock or in case of any consolidation or merger of the Company with
or into another company or in case of any sale or conveyance to another company
or entity of the property of the Company as a whole or substantially as a whole,
shares of stock or other securities equivalent in kind and value to those shares
a Holder would have received if he or she had held the full number of Shares
subject to the Option immediately prior to such reclassification, change,
consolidation, merger, sale or conveyance and had continued to hold those shares
(together with all other shares, stock and securities thereafter issued in
respect thereof) to the time of the exercise of the Option shall thereupon be
subject to the Option. Upon dissolution or liquidation of the Company, the
Option shall terminate, but the Holder (if at the time the Optionee is in the
employ or retained as a consultant or serving as a director of the Company or
any of its Subsidiaries) shall have the right, immediately prior to such
dissolution or liquidation, to exercise the Option to the extent not theretofore
exercised. No fraction of a share shall be purchasable or deliverable upon
exercise, but in the event that any adjustment hereunder of the number of Shares
covered by the Option shall cause such number to include a fraction of a Share,
such number of Shares shall be adjusted to the nearest smaller whole number of
shares. In the event of changes in the outstanding Stock by reason of any stock
dividend, split-up, contraction, reclassification, or change of outstanding
Shares of the nature contemplated by this Section 15, the number of Shares
available for the purpose of the Plan as stated in Section 4 hereof shall be
correspondingly adjusted.

                                      A-9
<PAGE>
    16.  CHANGE IN CORPORATE CONTROL.  Upon a Change in Corporate Control, each
outstanding Option shall immediately become fully exercisable.

    17.  RESERVATION OF STOCK.  The Company shall at all times during the term
of the Plan and, without duplication, of any outstanding Options reserve or
otherwise keep available such number of Shares as will be sufficient to satisfy
the requirements of the Plan (if not then terminated) and such outstanding
Options and shall pay all fees and expenses necessarily incurred by the Company
in connection therewith.

    18.  LIMITATION OF RIGHTS IN STOCK; NO SPECIAL EMPLOYMENT OR OTHER
RIGHTS.  A Holder shall not be deemed for any purpose to be a stockholder of the
Company with respect to any of the Shares covered by an Option, except to the
extent that the Option shall have been exercised with respect thereto and, in
addition, a certificate shall have been issued therefor and delivered to the
Holder or his agent. Any Stock issued pursuant to the Option shall be subject to
all restrictions upon the transfer thereof which may be now or hereafter imposed
by the Certificate of Incorporation, and the By-laws of the Company, if any.
Nothing contained in the Plan or in any Option shall confer upon any Optionee
any right with respect to the continuation of his or her employment with, or
retention as a consultant, director or advisor to, the Company (or any
Subsidiary), or interfere in any way with the right of the Company (or any
Subsidiary), subject to the terms of any separate employment or consulting
agreement or provision of law or corporate articles or by-laws to the contrary,
at any time to terminate such employment, consulting, directorship or advisory
relationship or to increase or decrease the compensation of the Optionee from
the rate in existence at the time of the grant of an Option.

    19.  TERMINATION AND AMENDMENT OF THE PLAN.  The Board may at any time
terminate the Plan or make such modifications of the Plan as it shall deem
advisable. No termination or amendment of the Plan may, without the consent of
the Holder of any Option, adversely affect the rights of such Holder under such
Option.

    20.  NOTICES AND OTHER COMMUNICATIONS.  All notices and other communications
required or permitted under the Plan shall be effective if in writing and if
delivered or sent by certified or registered mail, return receipt requested
(a) if to the Holder, at his or her residence address last filed with the
Company, and (b) if to the Company, at 24 Emily Street, Cambridge, Massachusetts
02139, Attention: President or to such other persons or addresses as the Holder
or the Company may specify by a written notice to the other from time to time.
Copies of all notices sent to any Holder that is not the Optionee shall also be
sent to the Optionee in the manner set forth in this Section 20.

    21.  EFFECTIVENESS.  This Amended and Restated 1993 Stock Option Plan was
approved by the Board of Directors on June 11, 1996, but shall not become
effective until and unless the later of (i) the ratification and approval of
this Amended and Restated 1993 Stock Option Plan by the stockholders of the
Company and (ii) the consummation of the Company's proposed initial public
offering. Prior to the effectiveness of this Amended and Restated 1993 Stock
Option Plan, the Company's existing Amended and Restated 1993 Stock Option Plan,
as amended from time to time prior to the effectiveness of this Amended and
Restated 1993 Stock Option Plan, shall remain in full force and effect.

                                      A-10
<PAGE>
                          CUBIST PHARMACEUTICALS, INC.

                                FIRST AMENDMENT
                                       TO
                  1993 AMENDED AND RESTATED STOCK OPTION PLAN

    This FIRST AMENDMENT (this "Amendment") to the Amended and Restated 1993
Stock Option Plan (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 October 30, 1997 (the "Effective Date"), subject
to the approval of the stockholders of the Company within one year from the
Effective Date. Effective from and after the Effective Date, and subject to
obtaining the required stockholder approval, the Plan is hereby amended as
follows:

    1. Section 4 of the Plan hereby is amended by replacing the number
"1,500,000" in the fifth (5th) line thereof with the number "2,000,000", said
amendment being for the purpose of increasing the total number of shares of
common stock, $.001 par value per share, that may be subject to options granted
under the Plan from 1,500,000 shares to 2,000,000 shares.

    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.

                                      A-11
<PAGE>
                          CUBIST PHARMACEUTICALS, INC.

                                SECOND AMENDMENT
                                       TO
                  1993 AMENDED AND RESTATED STOCK OPTION PLAN

    This SECOND 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 December 11, 1998 (the "Effective
Date"). Effective from and after the Effective Date, the Plan is hereby amended
as follows:

        1. Section 16 of the Plan hereby is amended by adding the following
    sentence at the end of the paragraph: "With respect to Options granted after
    January 1, 1999, the Committee shall have the discretion to exclude any
    event from being deemed a Change in Corporate Control for the purposes of
    the preceding sentence."

    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.

                                      A-12
<PAGE>
                          CUBIST PHARMACEUTICALS, INC.

                                THIRD AMENDMENT
                                       TO
                  1993 AMENDED AND RESTATED STOCK 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 in its 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 Section 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.

                                      A-13


<PAGE>

                              [FORM OF PROXY CARD]

                          CUBIST PHARMACEUTICALS, INC.
                  PROXY SOLICITED BY THE BOARD OF DIRECTORS FOR

               2000 ANNUAL MEETING OF STOCKHOLDERS ON MAY 16, 2000

         The undersigned hereby appoints Scott M. Rocklage and Justin P.
Morreale and each of them proxies, each with power of substitution, to vote at
the 2000 Annual Meeting of Stockholders of CUBIST PHARMACEUTICALS, INC. to be
held on May 16, 2000 (including any adjournments or postponements thereof), with
all the powers the undersigned would possess if personally present, as specified
on the ballot on the reverse side on the matters listed on the reverse side and,
in accordance with their discretion, on any other business that may come before
the meeting, and revokes all proxies previously given by the undersigned with
respect to the shares covered hereby.

         THIS PROXY WHEN PROPERLY EXECUTED WILL BE VOTED IN THE MANNER DIRECTED
HEREIN BY THE STOCKHOLDER. IF NO CONTRARY SPECIFICATION IS MADE, THIS PROXY WILL
BE VOTED FOR THE ELECTION OF THE NOMINEES OF THE BOARD OF DIRECTORS AND FOR THE
RATIFICATION OF ADOPTION AND APPROVAL OF THE AMENDMENT TO THE CORPORATION'S
AMENDED AND RESTATED 1993 STOCK OPTION PLAN AND UPON SUCH OTHER BUSINESS AS MAY
PROPERLY COME BEFORE THE MEETING IN THE APPOINTED PROXIES' DISCRETION.

<TABLE>
<S>                                       <C>                                                            <C>
- -------------------------                                                                                ----------------------
      SEE REVERSE                          CONTINUED AND TO BE SIGNED ON REVERSE SIDE                    SEE REVERSE
          SIDE                                                                                                   SIDE
- -------------------------                                                                                ----------------------
</TABLE>



<PAGE>


<TABLE>
<CAPTION>

- ------------------------------------                             ------------------------------
VOTE BY TELEPHONE                                                VOTE BY INTERNET

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

<S>                                                             <C>
It's fast, convenient, and immediate!                            It's fast, convenient, and your vote is
immediately Call Toll-Free on a Touch-Tone Phone                 confirmed and posted.

1-877-PRX-VOTE (1-877-779-8683)

Follow these four easy steps:                                    Follow these four easy steps:

   1. Read the accompanying Proxy                                     1. Read the accompanying Proxy
Statement/Prospectus and Proxy Card.                                  Statement/Prospectus and Proxy Card.

   2.    Call the toll-free number                                    2. Go to the website: 1-877-PRX-VOTE
         (1-877-779-8683)                                                http://www.eproxyvote.com/cbst

   3. Enter your 14-digit Voter Control Number                        3. Enter your 14-digit Voter Control Number located on your
      located on your Proxy Card above your name.                        Proxy Card above your name.

   4. Follow the recorded instructions.                               4. Follow the recorded instructions.

YOUR VOTE IS IMPORTANT!                                          YOUR VOTE IS IMPORTANT!
CALL 1-877-PRX-VOTE ANYTIME!                                     GO TO HTTP://WWW.EPROXYVOTE.COM/CBST!
</TABLE>

    DO NOT RETURN YOUR PROXY CARD IF YOU ARE VOTING BY TELEPHONE OR INTERNET

THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE PROPOSAL TO RATIFY THE ADOPTION
AND APPROVAL OF THE AMENDMENT TO THE CORPORATION'S AMENDED AND RESTATED 1993
STOCK OPTION PLAN.

1.    Class I Directors

      Nominees:   John Zabriskie, Ph.D.,  Trudie Resch
                           David M. Martin, Jr., Ph.D.

         /_/ FOR all nominees listed above  /_/ WITHHELD from all nominees

         /_/

                  For all nominees except as noted above

2.                    Ratification of the adoption and approval of amendment to
                      the Corporation's Amended and Restated 1993 Stock Option
                      Plan.

                      FOR           AGAINST          ABSTAIN

                        / /                      / /                         / /

         The undersigned hereby acknowledge(s) receipt of a copy of the
accompanying Notice of 2000 Annual Meeting of Stockholders and related Proxy
Statement.

Please date, sign as name appears below, and return this proxy in the enclosed
envelope, whether or not you expect to attend the meeting. You may nevertheless
vote in person if you do attend.

<PAGE>

Executors, administrators, trustees, custodians, etc. should indicate capacity
in which signing. When stock is held in the name of more than one person, each
person should sign the proxy.

MARK HERE FOR ADDRESS CHANGE AND NOTE AT LEFT                 |_|

                                            Date:                         , 2000
                                                 _________________________

                                            Please
                                            Sign

                                            Here:
                                                 _________________________


© 2022 IncJournal is not affiliated with or endorsed by the U.S. Securities and Exchange Commission