Document:

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                                                                  EXHIBIT 4.1

                                     [LOGO]

              INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE

                                         SEE REVERSE FOR CERTAIN DEFINITIONS

COMMON STOCK
PAR VALUE $.01 PER SHARE

                                CUSIP 739421 10 5

This Certifies That
is the owner of

           FULLY PAID AND NONASSESSABLE SHARES OF THE COMMON STOCK OF

                      PRAECIS PHARMACEUTICALS INCORPORATED

(HEREINAFTER CALLED THE "CORPORATION") TRANSFERABLE ON THE BOOKS OF THE
CORPORATION BY SAID OWNER IN PERSON OR BY DULY AUTHORIZED ATTORNEY, UPON
SURRENDER OF THIS CERTIFICATE PROPERLY ENDORSED. THE CORPORATION WILL FURNISH
WITHOUT CHARGE TO EACH STOCKHOLDER WHO SO REQUESTS, A STATEMENT OF THE POWERS,
DESIGNATIONS, PREFERENCES AND RELATIVE, PARTICIPATING, OPTIONAL, OR OTHER
SPECIAL RIGHTS OF EACH CLASS OF STOCK OR SERIES THEREOF AND THE QUALIFICATIONS,
LIMITATIONS OR RESTRICTIONS OF SUCH PREFERENCES AND/OR RIGHTS. THIS CERTIFICATE
AND THE SHARES REPRESENTED HEREBY ARE ISSUED AND SHALL BE HELD SUBJECT TO ALL
THE PROVISIONS OF THE CERTIFICATE OF INCORPORATION AND ALL AMENDMENTS THERETO,
COPIES OF WHICH ARE ON FILE AT THE OFFICE OF THE TRANSFER AGENT, AND THE HOLDER
HEREOF, BY ACCEPTANCE OF THIS CERTIFICATE, CONSENTS TO AND AGREES TO BE BOUND BY
ALL OF SAID PROVISIONS. THIS CERTIFICATE IS NOT VALID UNLESS COUNTERSIGNED AND
REGISTERED BY THE TRANSFER AGENT AND REGISTRAR.

        WITNESS, THE FACSIMILE SEAL OF THE CORPORATION AND BY FACSIMILE THE
SIGNATURES OF ITS DULY AUTHORIZED OFFICERS.

Dated:

/s/ Kevin F. McLaughlin                                 /s/ Malcolm L. Gefter
    SECRETARY                                               PRESIDENT

Countersigned and Registered:

                     AMERICAN STOCK TRANSFER & TRUST COMPANY
                              (NEW YORK, NEW YORK)

                                                                  Transfer Agent
                                                                   and Registrar

By:

                                                            Authorized Signature

<PAGE>

                      PRAECIS PHARMACEUTICALS INCORPORATED

      The following abbreviations, when used in the inscription on the face of
this certificate, shall be construed as though they were written out in full
according to applicable laws or regulations:

TEN COM - as tenants in common
TEN ENT - as tenants by the entireties
JT TEN - as joint tenants with right of survivorship
         and not as tenants in common

UNIF GIFT MIN ACT-                   Custodian
                   -----------------           -------------------
                         (Cust)                      (Minor)
                   under Uniform Gifts to Minors Act
                   Act
                       -------------------
                            (State)

     Additional abbreviations may also be used though not in the above list.

     For Value Received ___________________________________________ hereby sell,
assign and transfer unto

      PLEASE INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE

________________________________________________________________________________
  (PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING ZIP CODE, OF ASSIGNEE)
________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________

________________________________________________________________________________

_________________________________________________________________________ Shares
of the capital stock represented by the within certificate, and do hereby
irrevocably constitute and appoint

________________________________________________________________________________

______________________________________________________________________  Attorney
to transfer the said stock on the books of the within named Corporation with
full power of substitution in the premises.

Dated ________________________________________________________________________

_________________________________________________________________

NOTICE: The signature to this assignment must correspond with the name as
written upon the face of the certificate in every particular, without alteration
or enlargement or any change whatever.

Signature(s) Guaranteed:
                        -----------------------------------------------------

THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE GUARANTOR INSTITUTION
(BANKS, STOCK-BROKERS, SAVINGS AND LOAN ASSOCIATIONS AND CREDIT UNIONS WITH
MEMBERSHIP IN AN APPROVED SIGNATURE GUARANTEE MEDALLION PROGRAM), PURSUANT TO
S.E.C. RULE 17Ad-15.

KEEP THIS CERTIFICATE IN A SAFE PLACE. IF IT IS LOST, STOLEN, MUTILATED OR
DESTROYED, THE CORPORATION WILL REQUIRE A BOND OF INDEMNITY AS A CONDITION TO
THE ISSUANCE OF A REPLACEMENT CERTIFICATE.<PAGE>
                                                                     EXHIBIT 4.2

      THIS WARRANT AND SECURITIES ACQUIRED UPON THE EXERCISE OF THIS WARRANT
      HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
      "1933 ACT"). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, OR
      HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT RELATED
      THERETO OR AN OPINION OF COUNSEL (WHICH MAY BE COMPANY COUNSEL) REASONABLY
      SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED UNDER
      THE 1933 ACT).

                                WARRANT AGREEMENT

        To Purchase Shares of the Series A Convertible Preferred Stock of

                 PRAECIS PHARMACEUTICALS INCORPORATED (formerly
                         Pharmaceutical Peptides, Inc.)

                Dated as of March 29, 1995 (the "Effective Date")
                         Re-Issued as of August 12, 1998

      WHEREAS, PRAECIS PHARMACEUTICALS INCORPORATED (formerly known as
Pharmaceutical Peptides, Inc.) a Delaware corporation (the "Company"), has
entered into a Master Lease Agreement dated as of February 28, 1995, Equipment
Schedules No. VL-1 and VL-2, and related Schedules (collectively the "Leases")
with Comdisco, Inc., a Delaware corporation (the "Warrantholder"); and

      WHEREAS, in consideration for such leases, the Company entered into a
Warrant Agreement dated as of March 29, 1995 (the "Original Warrant Agreement"),
whereby the Company granted the Warrantholder the right to purchase 14,925
shares of its Series A Convertible Preferred Stock; and

      WHEREAS, pursuant to and in accordance with the Original Warrant
Agreement, the Warrantholder has transferred to Gregory Stento, effective as of
August 12, 1998, the Warrantholder's rights under the Original Warrant Agreement
with respect to the purchase of 1,703 shares of the Company's Series A
Convertible Preferred Stock (the "Warrant Transfer"); and

      WHEREAS, the Company and the Warrantholder acknowledge the Warrant
Transfer and, accordingly, the Company is reissuing, as of August 12, 1998, the
Warrant provided for in the Original Warrant Agreement, and the Company and the
Warrantholder are entering into this Warrant Agreement, to reflect the Warrant
Transfer and the Warrantholder's right to purchase 13,222 shares of Series A
Convertible Preferred Stock as set forth herein;

      NOW THEREFORE, in consideration of the foregoing, and the mutual covenants
and agreements contained herein, the Company and Warrantholder agree as follows:
<PAGE>

1.    GRANT OF THE RIGHT TO PURCHASE PREFERRED STOCK.

      The Company hereby grants to the Warrantholder, and the Warrantholder is
entitled, upon the terms and subject to the conditions hereinafter set forth, to
subscribe to and purchase, from the Company, 13,222 fully paid and
non-assessable shares of the Company's Series A Convertible Preferred Stock, par
value $.01 per share ("Preferred Stock") at a purchase price of $10.085 per
share (the "Exercise Price"). The number and purchase price of such shares are
subject to adjustment as provided in Section 8 hereof.

2.    TERM OF THE WARRANT AGREEMENT.

      Except as otherwise provided for herein, the term of this Warrant
Agreement and the right to purchase Preferred Stock as granted herein shall
commence on the Effective Date and shall be exercisable for a period commencing
on the Effective Date and ending on the later of (i) the date ten (10) years
after the Effective Date, or (ii) the date two (2) years from the effective date
of the Company's initial public offering.

      In the event the Company converts all of its shares of Preferred Stock
into Common Stock (the "Preferred Conversion" pursuant to Section (4)(f) of
Article Fifth of the Company's Amended and Restated Certificate of Incorporation
filed with the Secretary of State of the State of Delaware on April 30, 1998
(hereinafter the "Certificate"), then notwithstanding any other provision hereof
this Warrant to purchase shares of Preferred Stock shall automatically convert
to a Warrant to purchase a number of shares of Common Stock of the Company, par
value $.01 per share ("Common Stock") equal to the number of shares of Common
Stock into which the number of shares of Preferred Stock for which this Warrant
was exercisable as of immediately prior to the Preferred Conversion was
convertible as of such time, and from and after such conversion of this Warrant
the Exercise Price per share of Common Stock shall equal the Conversion Price
(as defined in the Certificate) for the Preferred Stock, and the number and
purchase price of such shares of Common Stock shall be subject to adjustment in
accordance with Section 8 herein. In the event of such conversion, all
references to "Preferred" Stock herein shall be deemed to be references to
"Common" Stock.

3.    EXERCISE OF THE PURCHASE RIGHTS.

      The purchase rights set forth in this Warrant Agreement are exercisable by
the Warrantholder, in whole or in part, at any time, or from time to time, prior
to the expiration of the term set forth in Section 2 above, by tendering to the
Company at its principal office a notice of exercise in the form attached hereto
as Exhibit I (the "Notice of Exercise"), duly completed and executed. Promptly
upon receipt of the Notice of Exercise and the payment of the purchase price in
accordance with the terms set forth below, and in no event later than twenty-one
(21) days thereafter, the Company shall issue to the Warrantholder a certificate
for the number of shares of Preferred Stock purchased and shall execute the
Acknowledgment of Exercise in the form attached hereto as Exhibit II indicating
the number of shares which remain subject to future purchases, if any.

                                       2
<PAGE>

In the event of an initial public offering, and if specifically requested by the
Underwriter(s), Warrantholder will agree to lockup provisions equivalent to but
not to exceed those required of the other preferred shareholders.

      The Exercise Price may be paid at the Warrantholder's election either (i)
by cash or check, or (ii) by surrender of Warrants ("Net Issuance") as
determined below. If the Warrantholder elects the Net Issuance method, the
Company will issue Preferred Stock in accordance with the following formula:

            X = Y(A-B)
                ------
                   A

Where:      X = the number of shares of Preferred Stock to be issued to the
                Warrantholder.

            Y = the number of shares of Preferred Stock as to which the
                Warrants are being exercised under this Warrant Agreement.

            A = the fair market value of one (1) share of Common Stock.

            B = the Exercise Price.

      As used herein, current fair market value of Common Stock shall mean with
respect to each share of Common Stock:

      (i) if the exercise is in connection with an initial public offering, and
      if the Company's Registration Statement relating to such public offering
      has been declared effective by the Securities and Exchange Commission (the
      "SEC"), then the initial "Price to Public" specified in the final
      prospectus with respect to the offering;

      (ii) if this Warrant is exercised after, and not in connection with the
      Company's initial public offering, and:

            (a) if traded on a securities exchange, the fair market value shall
            be deemed to be the average of the closing prices over a twenty-one
            (21) day period ending three days before the day the current fair
            market value of the securities is being determined; or

            (b) if actively traded over-the-counter, the fair market value shall
            be deemed to be the average of the closing bid and asked prices
            quoted on the NASDAQ system (or similar system) over the twenty-one
            (21) day period ending three days before the day the current fair
            market value of the securities is being determined;

                                       3
<PAGE>

      (iii) if at any time the Common Stock is not listed on any securities
      exchange or quoted in the NASDAQ System or the over-the-counter market,
      the current fair market value of Common Stock shall be the highest price
      per share which the Company could obtain from a willing buyer (not a
      current employee or director) for shares of Common Stock sold by the
      Company, from authorized but unissued shares, as determined in good faith
      by its Board of Directors, unless the Company shall become subject to a
      merger, acquisition or other consolidation pursuant to which the Company
      is not the surviving party, in which case the fair market value of Common
      Stock shall be deemed to be the value received by the holders of the
      Company's Preferred Stock on a common equivalent basis pursuant to such
      merger or acquisition.

      Upon partial exercise by either cash or Net Issuance, the Company shall
promptly issue an amended Warrant Agreement representing the remaining number of
shares purchasable hereunder. All other terms and conditions of such amended
Warrant Agreement shall be identical to those contained herein, including, but
not limited to the Effective Date hereof.

4.    RESERVATION OF SHARES.

      (a) Authorization and Reservation of Shares. During the term of this
Warrant Agreement, the Company will at all times have authorized and reserved a
sufficient number of shares of its Preferred Stock to provide for the exercise
of the rights to purchase Preferred Stock as provided for herein.

      (b) Registration or Listing. If any shares of Preferred Stock required to
be reserved hereunder require registration with or approval of any governmental
authority under any Federal or State law (other than any registration under the
1933 Act, as then in effect, or any similar Federal statute then enforced, or
any state securities law, required by reason of any transfer involved in such
conversion), or listing on any domestic securities exchange, before such shares
may be issued upon conversion, the Company will, at its expense and as
expeditiously as possible, use its reasonable best efforts to cause such shares
to be duly registered, listed or approved for listing on such domestic
securities exchange, as the case may be.

5.    NO FRACTIONAL SHARE OR SCRIP.

      No fractional shares or scrip representing fractional shares shall be
issued upon the exercise of the Warrant, but in lieu of such fractional shares
the Company shall make a cash payment therefor upon the basis of the Exercise
Price then in effect.

6.    NO RIGHTS AS SHAREHOLDER.

      This Warrant Agreement does not entitle the Warrantholder to any voting
rights or other rights as a shareholder of the Company prior to the exercise of
the Warrant.

                                       4
<PAGE>

7.    WARRANTHOLDER REGISTRY.

      The Company shall maintain a registry showing the name and address of the
registered holder of this Warrant Agreement.

8.    ADJUSTMENT RIGHTS.

      The purchase price per share and the number of shares of Preferred Stock
purchasable hereunder are subject to adjustment, as follows:

      (a) Merger and Sale of Assets. If at any time there shall be a capital
reorganization reclassifying or otherwise altering shares of Preferred Stock
(other than a combination, reclassification, exchange or subdivision of shares
otherwise provided for herein), or a merger or consolidation of the Company with
or into another corporation when the Company is not the surviving corporation,
or the sale of all or substantially all of the Company's properties and assets
to any other person (hereinafter referred to as a "Merger Event"), then, as a
part of such Merger Event, lawful provision shall be made so that the
Warrantholder shall thereafter be entitled to receive, upon exercise of the
Warrant, the number of shares of preferred stock or other securities of the
successor corporation resulting from such Merger Event, equivalent in value to
that which would have been issuable if Warrantholder had exercised this Warrant
immediately prior to the Merger Event. In any such case, appropriate adjustment
(as determined in good faith by the Company's Board of Directors) shall be made
in the application of the provisions of this Warrant Agreement with respect to
the rights and interest of the Warrantholder after the Merger Event to the end
that the provisions of this Warrant Agreement (including adjustments of the
Exercise Price and number of shares of Preferred Stock purchasable) shall be
applicable to the greatest extent possible.

      (b) Reclassification of Shares. If the Company at any time shall, by
combination, reclassification, exchange or subdivision of securities or
otherwise, change any of the securities as to which purchase rights under this
Warrant Agreement exist into the same or a different number of securities of any
other class or classes, this Warrant Agreement shall thereafter represent the
right to acquire such number and kind of securities as would have been issuable
as the result of such change with respect to the securities which were subject
to the purchase rights under this Warrant Agreement immediately prior to such
combination, reclassification, exchange, subdivision or other change.

      (c) Subdivision or Combination of Shares. If the Company at any time shall
combine or subdivide its Preferred Stock, the Exercise Price shall be
proportionately decreased in the case of a subdivision, or proportionately
increased in the case of a combination.

      (d) Stock Dividends. If the Company at any time shall issue any shares of
Preferred Stock by means of a dividend or other distribution on the Preferred
Stock (except any distribution specifically provided for in the foregoing
subsections (a) or (b)), then the Exercise Price shall be adjusted, from and
after the record date of such dividend or distribution, to that price determined
by

                                       5
<PAGE>

multiplying the Exercise Price in effect immediately prior to such record date
by a fraction (i) the numerator of which shall be the total number of shares of
Preferred Stock outstanding immediately prior to such dividend or distribution,
and (ii) the denominator of which shall be the total number shares of Preferred
Stock outstanding immediately after such dividend or distribution. The
Warrantholder shall thereafter be entitled to purchase, at the Exercise Price
resulting from such adjustment, the number of shares of Preferred Stock
(calculated to the nearest whole share) obtained by multiplying the Exercise
Price in effect immediately prior to such adjustment by the number of shares of
Preferred Stock issuable upon the exercise hereof immediately prior to such
adjustment and dividing the product thereof by the Exercise Price resulting from
such adjustment.

      (e) Right to Purchase Additional Stock. If, the Warrantholder's total cost
of equipment leased pursuant to Equipment Schedule VL-1 and Equipment Schedule
VL-2/Part I under the Leases exceeds $1,500,000.00, Warrantholder shall have the
right to purchase from the Company, upon the terms and subject to the conditions
herein at the Exercise Price (adjusted as set forth herein), an additional
number of shares, which number shall be determined by (i) multiplying the amount
by which the Warrantholder's total equipment cost exceeds $1,500,000.00 by 9%,
and (ii) dividing the product thereof by the Exercise Price per share referenced
above.

      If, the Warrantholder's total cost of equipment leased pursuant to
Equipment Schedule VL-2/Part II under the Leases exceeds $1,000,000.00,
Warrantholder shall have the right to purchase from the Company, at the Exercise
Price (adjusted as set forth herein), an additional number of shares, which
number shall be determined by (i) multiplying the amount by which the
Warrantholder's total equipment cost exceeds $1,000,000.00 by 3%, and (ii)
dividing the product thereof by the Exercise Price per share referenced above.

      (f) Antidilution Rights. A true and correct copy of the Certificate, as
amended through the Re-Issue Date, is attached hereto as Annex A. The Company
shall promptly provide the Warrantholder with any restatement, amendment,
modification or waiver of the Certificate.

      (g) Notice of Adjustments. If: (i) the Company shall declare any dividend
or distribution upon its Preferred Stock, whether in cash, property, stock or
other securities; (ii) the Company shall offer for subscription prorata to the
holders of any class of its Preferred or other convertible stock any additional
shares of stock of any class or other rights; (iii) there shall be any Merger
Event; or (iv) there shall be any voluntary or involuntary dissolution,
liquidation or winding up of the Company; then, in connection with each such
event, the Company shall send to the Warrantholder: (A) at least twenty (20)
days' prior written notice of the date on which the books of the Company shall
close or a record shall be taken for such dividend, distribution, subscription
rights (specifying the date on which the holders of Preferred Stock shall be
entitled thereto) or for determining rights to vote in respect of such Merger
Event, dissolution, liquidation or winding up; and (B) in the case of any such
Merger Event, dissolution, liquidation or winding up, at least twenty (20) days'
prior written notice of the date when the same shall take place (and specifying
the date on which the holders of Preferred Stock shall be entitled to exchange
their Preferred Stock for securities or other property deliverable upon such
Merger Event, dissolution, liquidation or winding up). In the case

                                       6
<PAGE>

of a public offering, the Company shall give Warrantholder at least twenty (20)
days written notice prior to the effective date thereof.

      Each such written notice shall set forth, in reasonable detail, (i) the
event requiring an adjustment (if any adjustment is required), (ii) the amount
of the adjustment (if any adjustment is required), (iii) the method by which
such adjustment was calculated (if any adjustment is required), (iv) the
Exercise Price after giving effect to such adjustment (if any adjustment is
required), and (v) the number of shares subject to purchase hereunder after
giving effect to such adjustment (if any adjustment is required), and shall be
given by first class mail, postage prepaid, addressed to the Warrantholder, at
the address as shown on the books of the Company.

      (h) Timely Notice. Failure to timely provide such notice required by
subsection (g) above shall entitle Warrantholder to retain the benefit of the
applicable notice period notwithstanding anything to the contrary contained in
any insufficient notice received by Warrantholder. The notice period shall begin
on the date Warrantholder actually receives a written notice containing all the
information specified above.

9.    REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY.

      (a) Reservation of Preferred Stock. The Preferred Stock issuable upon
exercise of the Warrantholder's rights has been (or, in the case of Preferred
Stock issuable pursuant to Section 8(e), will be) duly and validly reserved and,
when issued in accordance with the provisions of this Warrant Agreement, will be
validly issued, fully paid and non-assessable, and will be free of any taxes,
liens, charges or encumbrances of any nature whatsoever; provided, however, that
the Preferred Stock issuable pursuant to this Warrant Agreement may be subject
to restrictions on transfer under state and/or Federal securities laws. The
Company has made available to the Warrantholder true, correct and complete
copies of its Charter, as heretofore amended. The issuance of certificates for
shares of Preferred Stock upon exercise of the Warrant shall be made without
charge to the Warrantholder for any issuance tax in respect thereof, or other
cost incurred by the Company in connection with such exercise and the related
issuance of shares of Preferred Stock. The Company shall not be required to pay
any tax which may be payable in respect of any transfer involved and the
issuance and delivery of any certificate in a name other than that of the
Warrantholder.

      (b) Due Authority. The execution and delivery by the Company of this
Warrant Agreement and the performance of all obligations of the Company
hereunder, including the issuance to Warrantholder of the right to acquire the
shares of Preferred Stock, have been duly authorized by all necessary corporate
action on the part of the Company, and the Leases and this Warrant Agreement are
not inconsistent with the Company's Charter or Bylaws, do not contravene any law
or governmental rule, regulation or order applicable to it, do not and will not
contravene any provision of, or constitute a default under, any indenture,
mortgage, contract or other instrument to which it is a party or by which it is
bound, and the Leases and this Warrant Agreement constitute legal, valid and
binding agreements of the Company, enforceable in accordance with their
respective terms.

                                       7
<PAGE>

      (c) Consents and Approvals. No consent or approval of, giving of notice
to, registration with, or taking of any other action in respect of any state,
Federal or other governmental authority or agency is required with respect to
the execution, delivery and performance by the Company of its obligations under
this Warrant Agreement, except for the filing of notices pursuant to Regulation
D under the 1933 Act if such Regulation is being relied upon, which filing will
be effective by the time required thereby.

      (d) Issued Securities. All issued and outstanding shares of Common Stock,
Preferred Stock or any other securities of the Company have been duly authorized
and validly issued and are fully paid and nonassessable. All outstanding shares
of Common Stock, Preferred Stock and any other securities were issued in full
compliance with all Federal and state securities laws. In addition as of the
Effective Date:

      (i) The authorized capital of the Company consists of (A) 3,000,000 shares
of Common Stock, of which 417,044 shares are issued and outstanding, and the
Company has commitments to issue an additional 3,472 shares and (B) 2,000,000
shares of Preferred Stock, of which 1,104,866 shares are issued and outstanding
and are currently convertible into 1,104,866 shares of Common Stock at $10.085
per share.

      (ii) The Company has reserved (A) 450,000 shares of Common Stock for
issuance under its 1995 Stock Plan, under which 389,206 options are outstanding
at an average price of $1.00 per share. There are no other options, warrants,
conversion privileges or other rights presently outstanding to purchase or
otherwise acquire any authorized but unissued shares of the Company's capital
stock or other securities of the Company.

      (iii) Except as set forth in Section 5 of the Company's Amended
Certificate of Designation, no shareholder of the Company has preemptive rights
to purchase new issuances of the Company's capital stock pursuant to the
Company's Certificate of Incorporation.

      (e) Insurance. The Company has in full force and effect insurance
policies, with extended coverage, insuring the Company and its property and
business against such losses and risks, and in such amounts, as are customary
for corporations engaged in a similar business and similarly situated and as
otherwise may be required pursuant to the terms of any other contract or
agreement.

      (f) Commitments to Register Securities. As of the Effective Date, except
as set forth in the Stockholders Agreement dated as of December 23, 1993, and
supplemented by Supplement Number 1, dated as of March 1, 1994, the Company is
not, pursuant to the terms of any other agreement currently in existence, under
any obligation to register under the 1933 Act any of its presently outstanding
securities or any of its securities which may hereafter be issued.

                                       8
<PAGE>

      (g) Exempt Transaction. Subject to the accuracy of the Warrantholder's
representations in Section 10 hereof and assuming no circumstances at the time
of the exercise of this Warrant which would render unavailable the exemption
referred to in clause (i) of this subparagraph (g), the issuance of the
Preferred Stock upon exercise of this Warrant will constitute a transaction
exempt from (i) the registration requirements of Section 5 of the 1933 Act, in
reliance upon Section 4(2) thereof, and (ii) the qualification requirements of
the Illinois Securities Law, in reliance upon Section 4. c. thereof, and of the
Massachusetts Uniform Securities Act, in reliance upon Section 402(b)(8).

      (h) Compliance with Rule 144. If the Company shall have filed a
registration statement pursuant to the requirements of Section 12 of the
Securities Exchange Act of 1934, as amended (the "1934 Act") or a registration
statement pursuant to the requirements of the 1933 Act, at the written request
of the Warrantholder, who proposes to sell Preferred Stock issuable upon the
exercise of the Warrant in compliance with Rule 144 promulgated by the SEC, the
Company shall furnish to the Warrantholder, within ten days after receipt of
such request, a written statement confirming the Company's compliance with the
filing requirements of the SEC as set forth in such Rule, as such Rule may be
amended from time to time.

10.   REPRESENTATIONS AND COVENANTS OF THE WARRANTHOLDERS.

      This Warrant Agreement has been entered into by the Company in reliance
upon the following representations and covenants of the Warrantholder:

      (a) Investment Purpose. The right to acquire Preferred Stock represented
by this Warrant Agreement and the Preferred Stock issuable upon exercise of the
Warrantholder's rights contained herein will be acquired for investment and not
with a view to the sale or distribution of any part thereof, and the
Warrantholder has no present intention of selling or engaging in any public
distribution of the same except pursuant to a registration or exemption from the
registration requirements of Section 5 of the 1933 Act.

      (b) Private Issue. The Warrantholder understands (i) that the issuance of
this Warrant and the Preferred Stock issuable upon exercise of this Warrant is
not registered under the 1933 Act or qualified under applicable state securities
laws on the ground that the issuances are or will be exempt from the
registration and qualifications requirements thereof, and (ii) that the
Company's reliance on such exemption is predicated on the representations set
forth in this Section 10. In addition, the Warrantholder consents to the
placement of a legend on any certificate or other document evidencing this
Warrant, the Preferred Stock issuable upon exercise of this Warrant or any
Common Stock issuable upon conversion of the Preferred Stock, such legend
stating that such securities have not been registered under the 1933 Act or
under any state securities or "blue sky" laws and setting forth or referring to
the restrictions on transferability and sale thereof, including the restrictions
set forth herein, until such time as such restrictions are not longer
applicable.

      (c) Disposition of Warrantholder's Rights. In no event will the
Warrantholder make a disposition of any of its rights to acquire Preferred Stock
or Preferred Stock issuable upon exercise

                                       9
<PAGE>

of such rights unless and until (i) it shall have notified the Company of the
proposed disposition, and (ii) if requested by the Company, it shall have
furnished the Company with an opinion of counsel (which counsel may either be
inside or outside counsel to the Warrantholder) satisfactory to the Company and
its counsel to the effect that (A) appropriate action necessary for compliance
with the 1933 Act has been taken, or (B) an exemption from the registration
requirements of the 1933 Act is available. Notwithstanding the foregoing, the
restrictions imposed upon the transferability of any of its rights to acquire
Preferred Stock or Preferred Stock issuable on the exercise of such rights do
not apply to transfers from the beneficial owner of any of the aforementioned
securities to its nominee or from such nominee to its beneficial owner, and
shall terminate as to any particular share of Preferred Stock when (1) such
security shall have been effectively registered under the 1933 Act and sold by
the holder thereof in accordance with such registration or (2) such security
shall have been sold without registration in compliance with Rule 144 under the
1933 Act, or (3) a letter shall have been issued to the Warrantholder at its
request by the staff of the SEC or a ruling shall have been issued to the
Warrantholder at its request by the SEC stating that no action shall be
recommended by such staff or taken by the SEC, as the case may be, if such
security is transferred without registration under the 1933 Act in accordance
with the conditions set forth in such letter or ruling and such letter or ruling
specifies that no subsequent restrictions on transfer are required. Whenever the
restrictions imposed hereunder shall terminate, as hereinabove provided, the
Warrantholder or holder of a share of Preferred Stock then outstanding as to
which such restrictions have terminated shall be entitled to receive from the
Company, without expense to such holder, one or more new certificates for the
Warrant or for such shares of Preferred Stock not bearing any restrictive
legend.

      (d) Financial Risk. The Warrantholder has such knowledge and experience in
financial and business matters as to be capable of evaluating the merits and
risks of its investment, and has the ability to bear the economic risks of its
investment.

      (e) Risk of No Registration. The Warrantholder understands that if the
Company does not register with the SEC pursuant to Section 12 of the 1933 Act,
or file reports pursuant to Section 15(d), of the 1934 Act, or if a registration
statement covering the securities under the 1933 Act is not in effect when it
desires to sell (i) the rights to purchase Preferred Stock pursuant to this
Warrant Agreement, or (ii) the Preferred Stock issuable upon exercise of the
right to purchase, it may be required to hold such securities for an indefinite
period. The Warrantholder also understands that any sale of its rights as the
Warrantholder to purchase Preferred Stock or Preferred Stock which might be made
by it in reliance upon Rule 144 under the 1933 Act may be made only in
accordance with the terms and conditions of that Rule.

11.   TRANSFERS.

      Subject to the terms and conditions contained in Section 10 hereof, this
Warrant Agreement and all rights hereunder are transferable in whole or in part
by the Warrantholder and any successor transferee, provided, however, in no
event shall the number of transfers of the rights and interests in all of the
Warrants exceed a total of three (3) transfers. The transfer shall be recorded
on the

                                       10
<PAGE>

books of the Company upon receipt by the Company of a notice of transfer in the
form attached hereto as Exhibit III (the "Transfer Notice"), at its principal
offices and the payment to the Company of all transfer taxes and other
governmental charges imposed on such transfer.

12.   MISCELLANEOUS.

      (a) Effective Date. The provisions of this Warrant Agreement (except for
references to instruments dated after the Effective Date) shall be construed and
shall be given effect in all respects as if it had been executed and delivered
by the Company as of the Effective Date. This Warrant Agreement shall be binding
upon any successors or assigns of the Company.

      (b) Attorney's Fees. In any litigation, arbitration or court proceeding
between the Company and the Warrantholder relating hereto, the prevailing party
shall be entitled to attorneys' fees and expenses and all costs of proceedings
incurred in enforcing this Warrant Agreement.

      (c) Governing Law. This Warrant Agreement shall be governed by and
construed for all purposes under and in accordance with the laws of the State of
Illinois.

      (d) Counterparts. This Warrant Agreement may be executed in counterparts,
each of which shall be deemed an original, but both of which together shall
constitute one and the same instrument.

      (e) Notices. Any notice required or permitted hereunder shall be given in
writing and shall be deemed effectively given upon personal delivery, facsimile
transmission (provided that the original is sent by personal delivery or mail as
hereinafter set forth) or seven (7) days after deposit in the United States
mail, by registered or certified mail, addressed (i) to the Warrantholder at
6111 North River Road, Rosemont, Illinois 60018, attention: James Labe, Venture
Leasing Director, cc: Legal Department, (and/or, if by facsimile, (847)
518-5465) and (ii) to the Company at 1 Hampshire Street, Cambridge,
Massachusetts 02139-1572, attention: President (and/or if by facsimile, (617)
494-8414) or at such other address as any such party may subsequently designate
by written notice to the other party.

      (f) Remedies. In the event of any default hereunder, the non-defaulting
party may proceed to protect and enforce its rights either by suit in equity
and/or by action at law, including but not limited to an action for damages as a
result of any such default, and/or an action for specific performance for any
default where a party will not have an adequate remedy at law and where damages
will not be readily ascertainable. The Company expressly agrees that it shall
not oppose, on the grounds that on adequate remedy at law exists, an application
by the Warrantholder or any other person entitled to the benefit of this
Agreement requiring specific performance of any or all provisions hereof or
enjoining the Company from continuing to commit any such breach of this
Agreement.

                                       11
<PAGE>

      (g) No Impairment of Rights. The Company will not, by amendment of its
Charter or through any other means, avoid or seek to avoid the observance or
performance of any of the terms of this Warrant, but will at all times in good
faith assist in the carrying out of all such terms.

      (h) Survival. The representations, warranties, covenants and conditions of
the respective parties contained herein or made pursuant to this Warrant
Agreement shall survive the execution and delivery of this Warrant Agreement.

      (i) Severability. In the event any one or more of the provisions of this
Warrant Agreement shall for any reason be held invalid, illegal or
unenforceable, the remaining provisions of this Warrant Agreement shall be
unimpaired, and the invalid, illegal or unenforceable provision shall be
replaced by a mutually acceptable valid, legal and enforceable provision, which
comes closest to the intention of the parties underlying the invalid, illegal or
unenforceable provision.

      (j) Amendments. Any provision of this Warrant Agreement may be amended by
a written instrument signed by the Company and by the Warrantholder.

      (k) Additional Documents. The Company, upon execution of this Warrant
Agreement, shall provide the Warrantholder with certified resolutions with
respect to the Company's authorization of the execution, delivery, and
performance by the Company of the Warrant Agreement. The Company shall also
supply such other documents as may be reasonably necessary to confirm the
Company's compliance with its obligation hereunder (subject to reasonable
confidentiality restrictions) as the Warrantholder may from time to time
reasonably request.

      IN WITNESS WHEREOF, the parties hereto have caused this Warrant Agreement
to be executed by its officers thereunto duly authorized as of the Effective
Date.

                                             Company: PRAECIS PHARMACEUTICALS
                                                      INCORPORATED

                                             By: /s/Malcolm L. Gefter
                                                 -------------------------------

                                             Title: Chairman of the Board
                                                   -----------------------------

                                             Warrantholder:  COMDISCO, INC.

                                             By: /s/John J. Vosicky
                                                 -------------------------------

                                             Title: Executive Vice President and
                                                    ----------------------------
                                                     Chief Financial Officer
                                                     ---------------------------

                                       12
<PAGE>

                                    EXHIBIT I

                               NOTICE OF EXERCISE

To: ___________________

(1)   The undersigned Warrantholder hereby elects to purchase ____________
      shares of the [Series A Convertible Preferred Stock] [Common Stock, if the
      Warrant has been converted pursuant to Section 2 of the Warrant Agreement
      referred to below] of PRAECIS PHARMACEUTICALS INCORPORATED (the
      "Company"), pursuant to the terms of the Warrant Agreement originally
      dated as of the 29th day of March, 1995, reissued as of August 12, 1998
      (the "Warrant Agreement"), between the Company and the Warrantholder, and
      tenders herewith payment of the purchase price for such shares in full,
      together with all applicable transfer taxes, if any.

(2)   In exercising its rights to purchase the [Series A Convertible Preferred
      Stock] [Common Stock] of the Company, the undersigned hereby confirms and
      acknowledges the invest ment representations and warranties made in
      Section 10 of the Warrant Agreement.

(3)   Please issue a certificate or certificates representing said shares of
      [Series A Convertible Preferred Stock] [Common Stock] in the name of the
      undersigned or in such other name as is specified below.

-----------------------------
(Name)

-----------------------------
(Address)

Warrantholder: COMDISCO, INC.

By:__________________________

Title:_______________________

Date:________________________

                                       13
<PAGE>

                                   EXHIBIT II

                           ACKNOWLEDGMENT OF EXERCISE

      The undersigned _______________________, hereby acknowledges receipt of
the "Notice of Exercise" from Comdisco, Inc., to purchase _____________ shares
of the [Series A Convertible Preferred Stock] [Common Stock] of PRAECIS
PHARMACEUTICALS INCORPORATED, pursuant to the terms of the Warrant Agreement,
and further acknowledges that ___________ shares remain subject to purchase
under the terms of the Warrant Agreement.

                                                Company: PRAECIS PHARMACEUTICALS
                                                         INCORPORATED

                                                By:_____________________________

                                                Title:__________________________

                                                Date:___________________________

                                       14
<PAGE>

                                   EXHIBIT III

                                 TRANSFER NOTICE

(To transfer or assign the foregoing Warrant Agreement execute this form and
supply required information. Do not use this form to purchase shares.)

      FOR VALUE RECEIVED, the foregoing Warrant Agreement and all rights
evidenced thereby are hereby transferred and assigned to

--------------------------------------------------------------------------------
                                 (Please Print)

whose address is _______________________________________________________________

________________________________________________________________________________

                                    Dated_______________________________________

                                    Holder's Signature__________________________

                                    Holder's Address____________________________

________________________________________________________________________________

Signature Guaranteed:___________________________________________________________

        NOTE:         The signature to this Transfer Notice must correspond with
                      the name as it appears on the face of the Warrant
                      Agreement, without alteration or enlargement or any change
                      whatever. Officers of corporations and those acting in a
                      fiduciary or other representative capacity should file
                      proper evidence of authority to assign the foregoing
                      Warrant Agreement.

                                       15

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