<PAGE>

                                                                     EXHIBIT 4.3

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

                                  EPIMMUNE INC.

                        WARRANT TO PURCHASE COMMON STOCK

NO. CW-__                                                         APRIL __, 2004
                            VOID AFTER APRIL __, 2007

         THIS CERTIFIES THAT, for value received, __________________________,
with its principal office at __________________________, or assigns (the
"HOLDER"), is entitled to subscribe for and purchase at the Exercise Price
(defined below) from Epimmune Inc., a Delaware corporation, with its principal
office at 5820 Nancy Ridge Drive, Suite 100 San Diego, CA 92121 (the "COMPANY")
up to __________ shares of the Common Stock of the Company (the "COMMON STOCK").
This Warrant is being issued pursuant to the terms of the Unit Purchase
Agreement, dated April __, 2004.

         1. DEFINITIONS. As used herein, the following terms shall have the
following respective meanings:

                  (a) "EXERCISE PERIOD" shall mean the period commencing with
the date hereof and ending three years later, unless sooner terminated as
provided below.

                  (b) "EXERCISE PRICE" shall mean $2.655 per share, subject to
adjustment pursuant to Section 5 below.

                  (c) "EXERCISE SHARES" shall mean the shares of the Company's
Common Stock issuable upon exercise of this Warrant, subject to adjustment
pursuant to the terms herein, including but not limited to adjustment pursuant
to Section 5 below.

         2. EXERCISE OF WARRANT. The rights represented by this Warrant may be
exercised in whole or in part at any time during the Exercise Period, by
delivery of the following to the Company at its address set forth above (or at
such other address as it may designate by notice in writing to the Holder):

                  (a) An executed Notice of Exercise in the form attached
hereto;

                  (b) Payment of the Exercise Price either (i) in cash or by
check, or (ii) by cancellation of indebtedness; and

                  (c) This Warrant.

                                       1.
<PAGE>

         Upon the exercise of the rights represented by this Warrant, a
certificate or certificates for the Exercise Shares so purchased, registered in
the name of the Holder or persons affiliated with the Holder, if the Holder so
designates, shall be issued and delivered to the Holder within a reasonable time
after the rights represented by this Warrant shall have been so exercised.

         The person in whose name any certificate or certificates for Exercise
Shares are to be issued upon exercise of this Warrant shall be deemed to have
become the holder of record of such shares on the date on which this Warrant was
surrendered and payment of the Exercise Price was made, irrespective of the date
of delivery of such certificate or certificates, except that, if the date of
such surrender and payment is a date when the stock transfer books of the
Company are closed, such person shall be deemed to have become the holder of
such shares at the close of business on the next succeeding date on which the
stock transfer books are open.

         3. COVENANTS OF THE COMPANY.

                  3.1 COVENANTS AS TO EXERCISE SHARES. The Company covenants and
agrees that all Exercise Shares that may be issued upon the exercise of the
rights represented by this Warrant will, upon issuance, be validly issued and
outstanding, fully paid and nonassessable, and free from all taxes, liens and
charges with respect to the issuance thereof. The Company further covenants and
agrees that the Company will at all times during the Exercise Period, have
authorized and reserved, free from preemptive rights, a sufficient number of
shares of its Common Stock to provide for the exercise of the rights represented
by this Warrant. If at any time during the Exercise Period the number of
authorized but unissued shares of Common Stock shall not be sufficient to permit
exercise of this Warrant, the Company will take such corporate action as may, in
the opinion of its counsel, be necessary to increase its authorized but unissued
shares of Common Stock to such number of shares as shall be sufficient for such
purposes.

                  3.2 NO IMPAIRMENT. Except and to the extent as waived or
consented to by the Holder, the Company will not, by amendment of its Amended
and Restated Certificate of Incorporation, as amended, or through any
reorganization, transfer of assets, consolidation, merger, dissolution, issue or
sale of securities or any other voluntary action, avoid or seek to avoid the
observance or performance of any of the terms to be observed or performed
hereunder by the Company, but will at all times in good faith assist in the
carrying out of all the provisions of this Warrant and in the taking of all such
action as may be necessary or appropriate in order to protect the exercise
rights of the Holder against impairment.

                  3.3 NOTICES OF RECORD DATE. In the event of any taking by the
Company of a record of the holders of any class of securities for the purpose of
determining the holders thereof who are entitled to receive any dividend (other
than a cash dividend which is the same as cash dividends paid in previous
quarters) or other distribution, the Company shall mail to the Holder, at least
ten days prior to the date specified herein, a notice specifying the date on
which any such record is to be taken for the purpose of such dividend or
distribution.

         4. REPRESENTATIONS OF HOLDER.

                  4.1 ACQUISITION OF WARRANT FOR PERSONAL ACCOUNT. The Holder
represents and warrants that it is acquiring the Warrant and the Exercise Shares
solely for its account for

                                       2.
<PAGE>

investment and not with a view to or for sale or distribution of said Warrant or
Exercise Shares or any part thereof. The Holder also represents that the entire
legal and beneficial interests of the Warrant and Exercise Shares the Holder is
acquiring is being acquired for, and will be held for, its account only.

                  4.2 SECURITIES ARE NOT REGISTERED.

                           (a) The Holder understands that the Warrant and the
Exercise Shares have not been registered under the Securities Act of 1933, as
amended (the "ACT") on the basis that no distribution or public offering of the
stock of the Company is to be effected. The Holder realizes that the basis for
the exemption may not be present if, notwithstanding its representations, the
Holder has a present intention of acquiring the securities for a fixed or
determinable period in the future, selling (in connection with a distribution or
otherwise), granting any participation in, or otherwise distributing the
securities. The Holder has no such present intention.

                           (b) The Holder recognizes that the Warrant and the
Exercise Shares must be held indefinitely unless they are subsequently
registered under the Act or an exemption from such registration is available.
The Holder recognizes that the Company has no obligation to register the Warrant
or the Exercise Shares of the Company, or to comply with any exemption from such
registration.

                           (c) The Holder is aware that neither the Warrant nor
the Exercise Shares may be sold pursuant to Rule 144 adopted under the Act
unless certain conditions are met, including, among other things, the existence
of a public market for the shares, the availability of certain current public
information about the Company, the resale following the required holding period
under Rule 144 and the number of shares being sold during any three month period
not exceeding specified limitations. Holder is aware that the conditions for
resale set forth in Rule 144 have not been satisfied.

                  4.3 DISPOSITION OF WARRANT AND EXERCISE SHARES.

                           (a) The Holder further agrees not to make any
disposition of all or any part of the Warrant or Exercise Shares in any event
unless and until:

                                    (i) The Company shall have received a letter
secured by the Holder from the Securities and Exchange Commission stating that
no action will be recommended to the Commission with respect to the proposed
disposition;

                                    (ii) There is then in effect a registration
statement under the Act covering such proposed disposition and such disposition
is made in accordance with said registration statement; or

                                    (iii) The Holder shall have notified the
Company of the proposed disposition and shall have furnished the Company with a
detailed statement of the circumstances surrounding the proposed disposition,
and if reasonably requested by the Company, the Holder shall have furnished the
Company with an opinion of counsel, reasonably satisfactory to the Company, for
the Holder to the effect that such disposition will not require

                                       3.
<PAGE>

registration of such Warrant or Exercise Shares under the Act or any applicable
state securities laws.

                           (b) The Holder understands and agrees that all
certificates evidencing the Exercise Shares to be issued to the Holder may bear
a legend in substantially the following form:

         THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
         1933, AS AMENDED (THE "ACT"). THEY MAY NOT BE SOLD, OFFERED FOR SALE,
         PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION
         STATEMENT AS TO THE SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL
         SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

         5. ADJUSTMENT OF EXERCISE PRICE. In the event of changes in the
outstanding Common Stock of the Company by reason of stock dividends, split-ups,
recapitalizations, reclassifications, combinations or exchanges of shares,
separations, reorganizations, liquidations, or the like, the number and class of
shares available under the Warrant in the aggregate and the Exercise Price shall
be correspondingly adjusted to give the Holder of the Warrant, on exercise for
the same aggregate Exercise Price, the total number, class, and kind of shares
as the Holder would have owned had the Warrant been exercised prior to the event
and had the Holder continued to hold such shares until after the event requiring
adjustment; provided, however, that such adjustment shall not be made with
respect to, and this Warrant shall terminate if not exercised prior to, the
events set forth in Section 7 below. The form of this Warrant need not be
changed because of any adjustment in the number of Exercise Shares subject to
this Warrant.

         6. FRACTIONAL SHARES. No fractional shares shall be issued upon the
exercise of this Warrant as a consequence of any adjustment pursuant hereto. All
Exercise Shares (including fractions) issuable upon exercise of this Warrant may
be aggregated for purposes of determining whether the exercise would result in
the issuance of any fractional share. If, after aggregation, the exercise would
result in the issuance of a fractional share, the Company shall, in lieu of
issuance of any fractional share, pay the Holder otherwise entitled to such
fraction a sum in cash equal to the product resulting from multiplying the then
current fair market value of an Exercise Share by such fraction.

         7. EARLY TERMINATION. In the event of, at any time during the Exercise
Period, any capital reorganization, or any reclassification of the capital stock
of the Company (other than a change in par value or from par value to no par
value or no par value to par value or as a result of a stock dividend or
subdivision, split-up or combination of shares), or the consolidation or merger
of the Company with or into another corporation (other than a merger solely to
effect a reincorporation of the Company into another state), or the sale or
other disposition of all or substantially all the properties and assets of the
Company in its entirety to any other person, the Company shall provide to the
Holder 20 days advance written notice of such reorganization, reclassification,
consolidation, merger or sale or other disposition of the Company's assets, and
this Warrant shall terminate unless exercised prior to the occurrence of such
reorganization, reclassification, consolidation, merger or sale or other
disposition of the Company's assets.

                                       4.
<PAGE>

         8. NO STOCKHOLDER RIGHTS. This Warrant in and of itself shall not
entitle the Holder to any voting rights or other rights as a stockholder of the
Company.

         9. TRANSFER OF WARRANT. Subject to applicable laws and the restriction
on transfer set forth on the first page of this Warrant, this Warrant and all
rights hereunder are transferable, by the Holder in person or by duly authorized
attorney, upon delivery of this Warrant and the form of assignment attached
hereto to any transferee designated by Holder. The transferee shall sign an
investment letter in form and substance satisfactory to the Company.

         10. LOST, STOLEN, MUTILATED OR DESTROYED WARRANT. If this Warrant is
lost, stolen, mutilated or destroyed, the Company may, on such terms as to
indemnity or otherwise as it may reasonably impose (which shall, in the case of
a mutilated Warrant, include the surrender thereof), issue a new Warrant of like
denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed.
Any such new Warrant shall constitute an original contractual obligation of the
Company, whether or not the allegedly lost, stolen, mutilated or destroyed
Warrant shall be at any time enforceable by anyone.

         11. NOTICES, ETC. All notices required or permitted hereunder shall be
in writing and shall be deemed effectively given: (a) upon personal delivery to
the party to be notified, (b) when sent by confirmed telex or facsimile if sent
during normal business hours of the recipient, if not, then on the next business
day, (c) five days after having been sent by registered or certified mail,
return receipt requested, postage prepaid, or (d) one day after deposit with a
nationally recognized overnight courier, specifying next day delivery, with
written verification of receipt. All communications shall be sent to the Company
at the address listed on the signature page and to the Holders at the addresses
on the Company records, or at such other address as the Company or Holder may
designate by ten days advance written notice to the other parties hereto.

         12. ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute
acceptance of and agreement to all of the terms and conditions contained herein.

         13. GOVERNING LAW. This Warrant and all rights, obligations and
liabilities hereunder shall be governed by the laws of the State of California
without regard to the principles of conflict of laws.

                                       5.
<PAGE>

         IN WITNESS WHEREOF, the Company has caused this Warrant to be executed
by its duly authorized officer as of April __, 2004.

                                EPIMMUNE INC.

                                By: ___________________________________________

                                Name: Robert De Vaere

                                Title: Vice President, Finance & Admin., CFO

                                Address: 5820 Nancy Ridge Drive, Suite 100
                                         San Diego, CA 92121
                                         Facsimile: (858) 860-2600

                                       6.
<PAGE>

                               NOTICE OF EXERCISE

TO:  EPIMMUNE INC.

         (1) The undersigned hereby elects to purchase ________ shares of the
Common Stock of Epimmune (the "COMPANY") pursuant to the terms of the attached
Warrant, and tenders herewith payment of the exercise price in full, together
with all applicable transfer taxes, if any.

         (2) Please issue a certificate or certificates representing said shares
of Common Stock in the name of the undersigned or in such other name as is
specified below:

                            _________________________
                                     (Name)

                            _________________________
                            _________________________
                                    (Address)

         (3) The undersigned represents that (i) the aforesaid shares of Common
Stock 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; (ii) the undersigned is aware of the Company's business affairs and
financial condition and has acquired sufficient information about the Company to
reach an informed and knowledgeable decision regarding its investment in the
Company; (iii) the undersigned is experienced in making investments of this type
and has such knowledge and background in financial and business matters that the
undersigned is capable of evaluating the merits and risks of this investment and
protecting the undersigned's own interests; (iv) the undersigned understands
that the shares of Common Stock issuable upon exercise of this Warrant have not
been registered under the Securities Act of 1933, as amended (the "SECURITIES
ACT"), by reason of a specific exemption from the registration provisions of the
Securities Act, which exemption depends upon, among other things, the bona fide
nature of the investment intent as expressed herein, and, because such
securities have not been registered under the Securities Act, they must be held
indefinitely unless subsequently registered under the Securities Act or an
exemption from such registration is available; (v) the undersigned is aware that
the aforesaid shares of Common Stock may not be sold pursuant to Rule 144
adopted under the Securities Act unless certain conditions are met and until the
undersigned has held the shares for the number of years prescribed by Rule 144,
that among the conditions for use of the Rule is the availability of current
information to the public about the Company and the Company has not made such
information available and has no present plans to do so; and (vi) the
undersigned agrees not to make any disposition of all or any part of the
aforesaid shares of Common Stock unless and until there is then in effect a
registration statement under the Securities Act covering such proposed
disposition and such disposition is made in accordance with said registration
statement, or the undersigned has provided the Company with an opinion of
counsel satisfactory to the Company, stating that such registration is not
required.

_________________________                         _________________________
(Date)                                            (Signature)

                                                  _________________________
                                                  (Print name)

<PAGE>

                                 ASSIGNMENT FORM

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

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

Name: __________________________________________________________________________
                                (Please Print)

Address: _______________________________________________________________________
                                  (Please Print)

Dated:  __________, 20__

Holder's
Signature: ___________________________________________________

Holder's
Address: ___________________________________________________

NOTE: The signature to this Assignment Form must correspond with the name as it
appears on the face of the Warrant, 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.