<PAGE>
                                                                     Exhibit 4.3

      THIS WARRANT AND THE SHARES OBTAINABLE UPON ITS EXERCISE HAVE NOT BEEN
      REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE
      SECURITIES LAWS (COLLECTIVELY, THE "ACTS"), AND MAY NOT BE OFFERED, SOLD
      OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL
      REGISTERED UNDER ALL APPLICABLE ACTS OR UNLESS AN OPINION OF COUNSEL IS
      DELIVERED TO THE ISSUER IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER
      TO THE EFFECT THAT AN EXEMPTION FROM REGISTRATION IS AVAILABLE UNDER ALL
      APPLICABLE ACTS.

No. CS-1                                                        October 30, 2003

                      PREDIX PHARMACEUTICALS HOLDINGS, INC.

                          WARRANT FOR NEW COMMON STOCK

      THIS CERTIFIES THAT, for value received, RRD International, LLC, or its
registered assigns (the "Holder"), is entitled, subject to the vesting
provisions set forth herein, to subscribe for and purchase from Predix
Pharmaceuticals Holdings, Inc., a Delaware corporation (the "Company"), at any
time prior to or upon October 30, 2008, or, in the event such date is a
Saturday, Sunday or United States holiday, the next business day (the
"Expiration Date"), up to one hundred eighty thousand (180,000) shares (the
"Shares") of the Company's New Common Stock, $0.01 par value (the "Common
Stock"), at an exercise price of $1.00 per share (the "Exercise Price").

      This Warrant is subject to the following terms and conditions:

      1. Vesting.

      (a) Upon the terms and subject to the conditions set forth herein, this
Warrant shall vest and Warrants shall be exercisable in five equal installments
upon the execution of this Agreement and the achievement of certain milestones
set forth below in accordance with the following vesting schedule:

            (i) 20% of this Warrant (representing 36,000 Shares) shall vest upon
execution of this Agreement by both parties hereto.

            (ii) 20% of this Warrant (representing 36,000 Shares) shall vest
immediately upon completion of the pre-IND meetings for the Company's PRX-00023
product with the FDA or similar meetings with a foreign equivalent agency;
provided, however, that if such pre-IND meetings or foreign equivalent meetings
are not required, the portion of the Warrant subject to vesting under this
clause (ii) shall vest upon completion of the milestone set forth in clause
(iii) below.

                                       1
<PAGE>

            (iii) 20% of this Warrant (representing 36,000 Shares) shall vest
immediately upon filing of the IND for the Company's PRX-00023 product with the
FDA or upon an equivalent filing with a foreign agency.

            (iv) 20% of this Warrant (representing 36,000 Shares) shall vest
immediately upon enrollment of the first subject/patient in clinical trials for
the Company's PRX-00023 product.

            (v) 20% of this Warrant (representing 36,000 Shares) shall vest on
July 31, 2004.

Notwithstanding anything herein to the contrary, the milestones set forth above
and the vesting provisions of this Warrant Agreement may be accelerated pursuant
to the provisions of the Master Services Agreement and any Work Orders thereto
entered into between the Company and the Holder of this Warrant as of October
30, 2003.

      2. Exercise; Payment.

      (a) Cash Exercise. The purchase rights represented by this Warrant may be
exercised by the Holder, in whole or in part, at any time, or from time to time,
by the surrender of this Warrant (together with a duly executed notice of
exercise (the "Notice of Exercise") in the form attached hereto as Exhibit A) at
the address of the Company's principal corporate offices set forth in Section 6
hereof, and by payment to the Company of an amount equal to the Exercise Price
multiplied by the number of the Shares being purchased, which amount may be paid
by the Holder by wire transfer or check payable to the order of the Company. The
Person in whose name any certificate representing the Shares issuable upon any
exercise of this Warrant shall be deemed to have become the holder of record of,
and shall be treated for all purposes as the record holder of the Shares
represented thereby (and such Shares shall be deemed to have been issued)
immediately prior to the close of business on the date or dates upon which such
surrender and payment are made. As used herein, the term "Person" means any
individual or any corporation, partnership, trust, limited liability company or
other entity or organization of any kind.

      (b) Stock Certificates. In the event of any exercise of the rights
represented by this Warrant, as promptly as practicable on or after the date of
exercise and in any event within thirty days thereafter, the Company at its
expense shall issue and deliver to the Person or Persons entitled to receive the
same a certificate or certificates representing the number of Shares issued upon
such exercise. In the event that this Warrant is exercised in part, as promptly
as practicable on or after the date of exercise and in any event within thirty
days thereafter, the Company at its sole expense will execute and deliver a new
Warrant of like tenor exercisable for the number of Shares for which this
Warrant may then be exercised.

      (c) Taxes. The issuance of the Shares upon the exercise of this Warrant,
and the delivery of certificates or other instruments representing such Shares,
shall be made

                                       2
<PAGE>

without charge to the Holder for any tax or other charge of whatever nature in
respect of such issuance and the Company shall bear any such taxes in respect of
such issuance.

      3. Stock Fully Paid; Reservation of Shares. All of the Shares issuable
upon the exercise of the rights represented by this Warrant will, upon issuance
and receipt of the Exercise Price therefor, be fully paid and nonassessable, and
free from all preemptive rights, rights of first refusal or first offer, taxes,
liens and charges of whatever nature, with respect to the issuance thereof.
During the period within which the rights represented by this Warrant may be
exercised, the Company shall use its best efforts, including soliciting its
stockholders for requisite approval, to at all times have authorized and
reserved for issuance a sufficient number of shares of its Common Stock to
provide for the full exercise of the rights represented by this Warrant. In
connection with any amendment to the Company's Certificate of Incorporation (the
"Certificate of Incorporation") to effect the foregoing, the Holder will vote
all shares of the Company's capital stock held by such Holder in favor of such
amendment. The Company hereby agrees that the issuance of this Warrant shall
constitute full authority to its officers who are charged with the duty of
executing stock certificates to execute and issue the proper certificates for
Shares upon the full or each partial exercise of this Warrant and shares of
Common Stock issuable upon any conversion of all or any portion of such Shares.

      4. Adjustment of Exercise Price and Number of Shares. The number and class
or series of Shares purchasable upon the exercise of this Warrant and the
Exercise Price therefor shall be subject to adjustment from time to time upon
the occurrence of certain events, as follows:

      (a) Adjustment for Reclassification, Consolidation or Merger. If while
this Warrant, or any portion hereof, remains outstanding and unexpired there
shall be (i) a reorganization or recapitalization (other than a combination,
reclassification, exchange or subdivision of shares otherwise provided for
herein), (ii) a merger or consolidation of the Company with or into another
Person in which the Company is not the surviving entity, or a reverse merger in
which the Company is the surviving entity but the shares of the Company's
capital stock outstanding immediately prior to the merger are converted by
virtue of the merger into other property, whether in the form of securities,
cash, or otherwise, or (iii) a sale or transfer of the Company's properties and
assets as, or substantially as, an entirety to any other Person in one
transaction or a series of related transactions, then, as a part of such
reorganization, recapitalization, merger, consolidation, sale or transfer,
unless otherwise directed by the Holder, all necessary or appropriate lawful
provisions shall be made so that the Holder shall thereafter be entitled to
receive upon exercise of this Warrant, during the period specified herein and
upon payment of the Exercise Price then in effect, the greatest number of shares
of stock or other securities or property that a holder of the Shares deliverable
upon exercise of this Warrant would have been entitled to receive in such
reorganization, recapitalization, consolidation, merger, sale or transfer if
this Warrant had been exercised immediately prior to such reorganization,
recapitalization, merger, consolidation, sale or transfer, all subject to
further adjustment as provided in this Section 4. If the per Share consideration
payable to the Holder for Shares in connection with any such transaction is in a
form other than cash or marketable securities, then the value of such
consideration shall be

                                       3
<PAGE>

determined in good faith by the Company's Board of Directors. The foregoing
provisions of this paragraph shall similarly apply to successive
reorganizations, recapitalizations, consolidations, mergers, sales and transfers
and to the stock or securities of any other corporation that are at the time
receivable upon the exercise of this Warrant. In all events, appropriate
adjustment shall be made in the application of the provisions of this Warrant
(including adjustment of the Exercise Price and number of Shares purchasable
pursuant to the terms and conditions of this Warrant) with respect to the rights
and interests of the Holder after the transaction, to the end that the
provisions of this Warrant shall be applicable after that event, as near as
reasonably may be, in relation to any shares or other property deliverable or
issuable after such reorganization, recapitalization, merger, consolidation,
sale or transfer upon exercise of this Warrant.

      (b) Adjustments for Split, Subdivision or Combination of Shares. If the
Company at any time while this Warrant, or any portion hereof, remains
outstanding and unexpired shall split or subdivide any class of securities as to
which purchase rights under this Warrant exist, into a different number of
securities of the same class, the number of shares of such class issuable upon
exercise of this Warrant immediately prior to such split or subdivision shall be
proportionately adjusted and the Exercise Price for such class of securities
shall be proportionately adjusted. If the Company at any time while this
Warrant, or any portion hereof, remains outstanding and unexpired shall combine
any class of securities as to which purchase rights under this Warrant exist,
into a different number of securities of the same class, the number of shares of
such class issuable upon exercise of this Warrant immediately prior to such
combination shall be proportionately adjusted and the Exercise Price for such
class of securities shall be proportionately adjusted.

      (c) Adjustments for Dividends in Stock or Other Securities or Property. If
while this Warrant, or any portion hereof, remains outstanding and unexpired,
the holders of any class of securities as to which purchase rights under this
Warrant exist at the time shall have received, or, on or after the record date
fixed for the determination of eligible stockholders, shall have become entitled
to receive, without payment therefor, other or additional stock or other
securities or property (other than cash) of the Company by way of dividend, then
and in each case, this Warrant shall represent the right to acquire, in addition
to the number of shares of such class of security receivable upon exercise of
this Warrant, and without payment of any additional consideration therefor, the
amount of such other or additional stock or other securities or property (other
than cash) of the Company that such holder would hold on the date of such
exercise had it been the holder of record of the class of security receivable
upon exercise of this Warrant on the date hereof and had thereafter, during the
period from the date hereof to and including the date of such exercise, retained
such shares and/or all other additional stock available by it as aforesaid
during said period, giving effect to all adjustments called for during such
period by the provisions of this Section 4.

      (d) Further Adjustments. In case at any time or from time to time the
Company shall take any action that affects the Shares, other than an action
described herein, then, unless such action will not have a materially adverse
effect upon the rights

                                       4
<PAGE>

of the Holder, the number of Shares into which this Warrant is exercisable shall
be adjusted in such a manner and at such time as shall be equitable in the
circumstances.

      (e) Notice of Adjustments. Upon any adjustment of the Exercise Price and
any increase or decrease in the number of Shares purchasable upon the exercise
of this Warrant, then, and in each such case, the Company, within 30 days
thereafter, shall give written notice thereof to the Holder at the address of
such Holder as shown on the books of the Company which notice shall state the
Exercise Price as adjusted and, if applicable, the increased or decreased number
of Shares purchasable upon the exercise of this Warrant, setting forth in
reasonable detail the method of calculation of each.

      5. Transfers, etc.

      (a) At any time prior to the Expiration Date, the Warrants shall only be
transferable to Affiliates (as defined below) (each transferee shall be referred
to as a "Permitted Transferee"); and, provided further, that any such transfer
does not increase the total number of holders of Warrants by more than one
(taking into account all prior transfers of any one Warrant) and will not
increase the total number of stockholders of the Company by more than one
(taking into account all prior transfers of any one Warrant). For purposes of
this Warrant, "Affiliate" of a Holder shall mean any of the stockholders,
subsidiaries, officers, directors, members or partners of such Holder, and any
other corporation, partnership or other business entity which directly or
indirectly controls, is controlled by or is under common control with, such
Holder.

      (b) Any transfer pursuant to Section 5(a) shall be effected upon surrender
of this Warrant with a properly executed assignment (in the form attached hereto
as Exhibit B) at the principal office of the Company (or, if another office or
agency has been designated by the Company for such purpose, then at such other
office or agency).

      6. Notices.

      (a) All notices, requests, consents, and other communications under this
Warrant shall be in writing and shall be deemed delivered (i) seven business
days after being sent by registered or certified mail, return receipt requested,
postage prepaid or (ii) three business days after being sent via a reputable
nationwide overnight courier service guaranteeing next business day delivery, in
each case to the intended recipient as set forth below:

      If to the Company, at 10 K Gill Street, Woburn, Massachusetts 01801,
Attention: Chief Financial Officer, or at such other address as may have been
furnished in writing by the Company to the Holder, with a copy to Hale and Dorr
LLP, 650 College Road East, Princeton, New Jersey 08540, Attention: Richard S.
Mattessich, Esq.; or

      If to a Holder, at 11 North Washington Street, Suite 310, Rockville,
Maryland 20850, Attention: Joseph P. Clancy, or at such other address as may be
furnished in writing by the Holder to the Company, with a copy to Curtin, Law,
Roberson, Dunigan & Salans, 900 M Street, NW, Washington, DC 20036, Attn: Thomas
Dunigan, Esq.

                                       5
<PAGE>

      (b) Either party may give any notice, request, consent or other
communication under this Warrant using any other means (including, without
limitation, personal delivery, messenger service, telecopy, first class mail or
electronic mail), but no such notice, request, consent or other communication
shall be deemed to have been duly given unless and until it is actually received
by the party for whom it is intended. Either party may change the address to
which notices, requests, consents or other communications hereunder are to be
delivered by giving the other party notice in the manner set forth in this
Section.

      7. Legends. Each certificate evidencing the Shares issued upon exercise of
this Warrant, or transfer of such Shares (other than a transfer registered under
the Securities Act, or any subsequent transfer of Shares so registered) shall be
stamped or imprinted with a legend substantially in the following forms:

      THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
      UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"), OR THE
      SECURITIES LAWS OF ANY STATE. THE SECURITIES MAY NOT BE TRANSFERRED EXCEPT
      PURSUANT TO AN EFFECTIVE REGISTRATION STATEMENT UNDER SUCH ACT AND
      APPLICABLE STATE SECURITIES LAWS OR PURSUANT TO AN APPLICABLE EXEMPTION
      FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND SUCH LAWS.

      8. Fractional Shares. No fractional Shares will be issued in connection
with any exercise hereunder. Instead, the Company shall pay to such Holder an
amount in cash equal to any fractional share to which such Holder would be
entitled, multiplied by the Fair Market Value of a Share, as determined in good
faith by the Company's Board of Directors. For purposes of this Section 8, the
Fair Market Value of one Share shall equal: (a) the average of the closing sale
price of the Common Stock (or any other security for which this Warrant is then
exercisable) as quoted on the Nasdaq Stock Market or in the Over-The-Counter
Market Summary or the closing price quoted on any national securities exchange
on which such securities are listed, whichever is applicable, as reported in The
Wall Street Journal for the ten trading days immediately prior to the date of
determination of Fair Market Value (or, if no sales take place on any such
trading day, the average of the closing bid and asked prices on such trading
day); or (b) if the Common Stock (or any other security for which this Warrant
is then exercisable) is not quoted on the Nasdaq Stock Market or
Over-The-Counter or on a national securities exchange, the Fair Market Value of
a Share shall be established in good faith by the Company's Board of Directors.

      9. Representations and Warranties of the Company. The Company hereby
represents and warrants to the Holder as follows:

      (a) This Warrant has been duly authorized and executed by the Company and
is a valid and binding obligation of the Company enforceable in accordance with
its terms;

                                       6
<PAGE>

      (b) The Company shall use its best efforts to ensure that the Shares have
been duly authorized and reserved for issuance by the Company and, when issued
in accordance with the terms hereof, will be validly issued, fully paid and
nonassessable, and free from all preemptive rights, rights of first refusal or
first offer, taxes, liens and charges of whatever nature; and

      (c) The execution and delivery of this Warrant are not, and the issuance
of the Shares upon exercise of this Warrant in accordance with the terms hereof
will not be, inconsistent with the Company's Certificate of Incorporation, as
then in effect, and the Company's by-laws (the "By-Laws"), as then in effect.

      10. Representations and Warranties by the Holder. The Holder represents
and warrants to the Company as follows:

      (a) This Warrant is being acquired for its own account, for investment and
not with a view to, or for resale in connection with, any distribution thereof
within the meaning of the Securities Act. Upon exercise of this Warrant, the
Holder shall, if so requested by the Company, confirm in writing, in a form
reasonably satisfactory to the Company, that the Shares issuable upon exercise
of this Warrant are being acquired for investment and not with a view toward
distribution or resale that would violate the Securities Act.

      (b) The Holder understands that the Warrant and the Shares have not been
registered under the Securities Act by reason of their issuance in a transaction
exempt from the registration and prospectus delivery requirements of the
Securities Act pursuant to Section 4(2) thereof, and that they must be held by
the Holder indefinitely, and that the Holder must therefore bear the economic
risk of such investment indefinitely, unless a subsequent disposition thereof is
registered under the Securities Act or is exempted from such registration.

      (c) The Holder has such knowledge and experience in financial and business
matters that it is capable of evaluating the merits and risks of the purchase of
this Warrant and the Shares purchasable pursuant to the terms of this Warrant
and of protecting its interests in connection therewith.

      (d) The Holder is able to bear the economic risk of the purchase of the
Shares pursuant to the terms of this Warrant.

      (e) The Holder is an "accredited investor" within the meaning of Rule 501
of Regulation D under the Securities Act.

      11. Rights of Stockholders. Subject to Section 4 hereof, no Holder, as
such, shall be entitled to vote or receive dividends or be deemed the holder of
the Shares or any other securities of the Company that may at any time be
issuable on the exercise hereof for any purpose, nor shall anything contained
herein be construed to confer upon the Holder, as such, any of the rights of a
stockholder of the Company or any right to vote for the election of directors or
upon any matter submitted to stockholders at any meeting thereof, or to give or
withhold consent to any corporate action (whether upon

                                       7
<PAGE>

any recapitalization, issuance of stock, reclassification of stock, change of
par value, consolidation, merger, conveyance, or otherwise) or to receive notice
of meetings, or to receive dividends or subscription rights or otherwise until
this Warrant shall have been exercised and the Shares purchasable upon the
exercise hereof shall have become issuable, as provided herein.

      12. Expiration of Warrant. This Warrant shall expire and shall no longer
be exercisable as of 5:00 p.m., Eastern Time, on October 30, 2008.

      13. Miscellaneous.

      (a) This Warrant shall be governed by and construed for all purposes under
and in accordance with the laws of the State of Delaware without regard to
principles of conflicts of law.

      (b) The headings in this Warrant are for purposes of reference only, and
shall not limit or otherwise affect any of the terms hereof.

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

      (d) The terms of this Warrant shall be binding upon and shall inure to the
benefit of any successors or assigns of the Company and of the Holder and of the
Shares issued or issuable upon the exercise hereof.

      (e) This Warrant and the other documents delivered pursuant hereto
constitute the full and entire understanding and agreement between the parties
with regard to the subjects hereof and thereof.

      (f) The Company shall not, by amendment of its Certificate of
Incorporation or By-Laws, or through any other means, directly or indirectly,
avoid or seek to avoid the observance or performance of any of the terms of this
Warrant and shall at all times in good faith assist in the carrying out of all
such terms and in the taking of all such action as may be necessary or
appropriate in order to protect the rights of the Holder against impairment.

      (g) Upon receipt of evidence reasonably satisfactory to the Company of the
loss, theft, destruction or mutilation of this Warrant and, in the case of any
such loss, theft or destruction, upon delivery of an indemnity agreement
reasonably satisfactory in form and amount to the Company or, in the case of any
such mutilation, upon surrender and cancellation of such Warrant, the Company,
at its expense, will execute and deliver to the Holder, in lieu thereof, a new
Warrant of like date and tenor.

      (h) This Warrant and any provision hereof may be amended, waived or
terminated only by an instrument in writing signed by the Company and the
Holder.

                                       8
<PAGE>

      (i) The Warrant Shares shall be registered under the Securities Act to the
extent provided in the certain Registration Rights Agreement, of even date
herewith, by and between the Company and the Holder of this Warrant.

                            [Signature Page Follows]

                                       9
<PAGE>

      IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by
its duly authorized officer.

                                       Predix Pharmaceuticals Holdings, Inc.

                                       By: /s/ NIK HAYES
                                           ------------------------------------
                                           Name: Nik Hayes
                                           Title: Chief Financial Officer

Acknowledged and Accepted:

RRD INTERNATIONAL, LLC

By: /s/ JOSEPH P. CLANCY
    -------------------------------
Name: Joseph P. Clancy
Title: Chief Executive Officer
Address: 11 North Washington Street, Ste 310
         Rockville, MD 20850

                                       10
<PAGE>

                                                                       EXHIBIT A

                               NOTICE OF EXERCISE

TO: Predix Pharmaceuticals Holdings, Inc.
    Attention: Chief Financial Officer

      1. The undersigned hereby elects to purchase _________________ shares of
Common Stock of Predix Pharmaceuticals Holdings, Inc. pursuant to the terms of
this Warrant, and tenders herewith payment of the purchase price of such shares
in full.

      2. Please issue a certificate or certificates representing said securities
in the name of the undersigned or in such other name as is specified below:

                              ___________________________
                                        (Name)

                              ___________________________

                              ___________________________
                                       (Address)

      3. The undersigned hereby represents and warrants that the aforesaid
securities are being acquired for the account of the undersigned for investment
and not with a view to, or for resale, in connection with the distribution
thereof, and that the undersigned has no present intention of distributing or
reselling such shares and all representations and warranties of the undersigned
set forth in Section 10 of the attached Warrant are true and correct as of the
date hereof.
                                           ___________________________
                                           (Signature and Date)

                                       11
<PAGE>

                                                                       EXHIBIT B

                               FORM OF ASSIGNMENT

                  (To be executed by the Holder if such Holder
                        desires to transfer the Warrant)

FOR VALUE RECEIVED __________________________________ (the "Transferor") hereby
sells, assigns and transfers unto _____________________________ (the
"Transferee")

                  (Please print name and address of transferee)

this Warrant, together with all right, title and interest therein, and does
hereby irrevocably constitute and appoint ___________________________ as its
Attorney to transfer such Warrant on the books of Predix Pharmaceuticals
Holdings, Inc., with full power of substitution. The Transferor has provided a
written instrument to the Company notifying the Company of such transfer and
pursuant to which the Transferee hereunder has agreed in writing to be bound by
the terms of the Warrant dated October 30, 2003 issued by Predix Pharmaceuticals
Holdings, Inc., a Delaware corporation, a copy of which has been provided to the
Transferee by the Transferor.

Dated:                                 Signature ______________________________
                                       (Signature must conform in all respects
                                       to name of Holder as specified on the
                                       face of the Warrant)

                                       _________________________________________
                                       (Insert Social Security or other
                                       Identifying Number of Holder)

                                       12