EPIMMUNE INC
S-3, 2000-03-17
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1
         AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MARCH 17, 2000
                                                    REGISTRATION NO. 333-
===============================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM S-3
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                                  EPIMMUNE INC.
             (Exact name of Registrant as specified in its charter)

              DELAWARE                                 33-0245076
    (State or other jurisdiction                     (I.R.S. Employer
  of incorporation or organization)                Identification Number)
                             5820 NANCY RIDGE DRIVE
                               SAN DIEGO, CA 92121
                                 (858) 860-2500
       (Address, including zip code, and telephone number, including area
               code, of Registrant's principal executive offices)

                               DEBORAH A. SCHUEREN
         PRESIDENT, CHIEF EXECUTIVE OFFICER AND CHIEF FINANCIAL OFFICER
                                  EPIMMUNE INC.
                             5820 NANCY RIDGE DRIVE
                               SAN DIEGO, CA 92121
                                 (858) 860-2500

            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)

                                   Copies to:
                             FREDERICK T. MUTO, ESQ.
                               COOLEY GODWARD LLP
                        4365 EXECUTIVE DRIVE, SUITE 1100
                               SAN DIEGO, CA 92121
                                 (858) 550-6000

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
     From time to time after this Registration Statement becomes effective.

If the only securities being registered on this Form are being offered pursuant
to dividend or interest reinvestment plans, please check the following box. [ ]
If any of the securities being registered on this Form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered in connection with dividend or interest
reinvestment plans, check the following box. [X]
If this Form is filed to register additional securities for an offering pursuant
to Rule 462(b) under the Securities Act, please check the following box and list
the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ]
If this Form is a post-effective amendment filed pursuant to Rule 462(c) under
the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]
If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]

<TABLE>
<CAPTION>
                          CALCULATION OF REGISTRATION FEE
===============================================================================================================
                                                        PROPOSED MAXIMUM    PROPOSED MAXIMUM
          TITLE OF CLASS OF              AMOUNT TO       OFFERING PRICE        AGGREGATE          AMOUNT OF
     SECURITIES TO BE REGISTERED       BE REGISTERED     PER SHARE (1)     OFFERING PRICE (1)  REGISTRATION FEE
- ---------------------------------------------------------------------------------------------------------------
<S>                                    <C>              <C>                <C>                 <C>
Common Stock, $.01 par value             1,200,000          $10.828           $12,993,750         $3,430.35
===============================================================================================================
</TABLE>

(1) Estimated solely for the purpose of calculating the amount of the
registration fee pursuant to Rule 457(c) of the Securities Act of 1933. The
price per share and aggregate offering price are based upon the average of the
high and low sales price of Epimmune's common stock on March 14, 2000 as
reported on the Nasdaq National Market. It is not known how many shares will be
purchased under this registration statement or at what price such shares will be
purchased.

THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR DATES
AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL FILE
A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION STATEMENT
SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF THE
SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a),
MAY DETERMINE.



<PAGE>   2

        THE INFORMATION IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED.
WE MAY NOT SELL THESE SECURITIES UNTIL THE REGISTRATION STATEMENT FILED WITH THE
SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS PROSPECTUS IS NOT AN OFFER
TO SELL THESE SECURITIES AND IT IS NOT SOLICITING AN OFFER TO BUY THESE
SECURITIES IN ANY STATE WHERE THE OFFER OR SALE IS NOT PERMITTED.


PROSPECTUS



                   SUBJECT TO COMPLETION, DATED MARCH 17, 2000

                                1,200,000 SHARES

                                  EPIMMUNE INC.

                                  COMMON STOCK



We are registering 1,200,000 shares of our common stock for resale by the
selling stockholders identified in this prospectus. We will not receive any of
the proceeds from the sale of shares by the selling stockholders. Our common
stock is listed on the Nasdaq National Market under the symbol "EPMN." The
closing sale price of our common stock, as reported on the Nasdaq National
Market on March 15, 2000, was $15.25 per share.


INVESTING IN OUR COMMON STOCK INVOLVES A HIGH DEGREE OF RISK. SEE "RISK
FACTORS," BEGINNING ON PAGE 5.

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.







                 The date of this prospectus is ________, 2000.



<PAGE>   3

        THIS PROSPECTUS IS PART OF A LARGER REGISTRATION STATEMENT WE FILED WITH
THE SEC. YOU SHOULD RELY ON THE INFORMATION INCORPORATED BY REFERENCE OR
PROVIDED IN THIS PROSPECTUS. WE HAVE NOT AUTHORIZED ANYONE ELSE TO PROVIDE YOU
WITH DIFFERENT INFORMATION. WE ARE NOT MAKING AN OFFER OF THESE SECURITIES IN
ANY STATE WHERE THE OFFER IS NOT PERMITTED. YOU SHOULD NOT ASSUME THAT THE
INFORMATION IN THIS PROSPECTUS IS ACCURATE AS OF ANY DATE OTHER THAN THE DATE ON
THE FRONT OF THE DOCUMENT.

                       WHERE YOU CAN GET MORE INFORMATION

        We are a reporting company and file annual, quarterly and current
reports, proxy statements and other information with the SEC. You may read and
copy these reports, proxy statements and other information at the SEC's public
reference rooms in Washington, D.C., New York, NY and Chicago, IL. You can
request copies of these documents by writing to the SEC and paying a fee for the
copying cost. Please call the SEC at 1-800-SEC-0330 for more information about
the operation of the public reference rooms. Our SEC filings are also available
at the SEC's Web site at "http://www.sec.gov."

    The SEC allows us to "incorporate by reference" information that we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
an important part of this prospectus, and information that we file later with
the SEC will automatically update and supersede this information. We incorporate
by reference the documents listed below and any future filings we will make with
the SEC under Section 13 (a), 13(c), 14 or 15 (d) of the Securities Exchange Act
of 1934:

        -      Annual Report on Form 10-K for the year ended December 31, 1999;
               and

        -      Registration statement on Form 8-A, as amended, which includes a
               description of our common stock.

You may request a copy of these filings at no cost, by writing or telephoning us
at the following address or telephone number:

        Epimmune Inc.
        5820 Nancy Ridge Drive
        San Diego, CA 92121
        Attn:  Investor Relations
        (858) 860-2500



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<PAGE>   4

                                  EPIMMUNE INC.

        Epimmune is developing novel vaccines for infectious diseases and
cancer, building on our expertise and intellectual property in the field of
T-cell recognition and activation. In the cancer field, we are collaborating
with G.D. Searle & Co., a wholly-owned subsidiary of Monsanto Co., to develop
immune stimulating products for the treatment of breast, colon, lung and
prostate cancers. Our first product candidate, which targets breast, colon and
lung cancers, is due to enter human clinical trials by the end of 2000. We are
also in preclinical development with therapeutic vaccines for hepatitis C,
hepatitis B and HIV, and prophylactic vaccines for hepatitis C, HIV and malaria.

        Eliciting a strong cellular, or T cell, immune response is crucial for
treating and preventing certain infectious diseases and tumors. Clinicians have
shown that the cellular immune response is associated with viral clearance and
tumor regression in the subset of patients who spontaneously clear chronic viral
infection and in cancer patients who respond to immunotherapy. This successful
cellular immune response includes cytotoxic T cells, known as CTL, and helper T
cells, known as HTL, which are directed toward specific antigen fragments, known
as epitopes.

        Our vaccines are based on proprietary technology, known as EIS(TM),
which enables the rapid identification of novel epitopes that can stimulate
specific CTL and HTL immune responses. These epitopes can be identified from any
protein or gene sequence, and, to date, we have identified, evaluated and
included in our patent applications more than 10,000 such epitopes, and a small
subset of these epitopes are used in our candidate vaccines. Furthermore, the
EIS enables rapid immunological evaluation of the vast quantities of genomic
data generated, making feasible the development of new vaccine candidates for
such complex diseases as tuberculosis, malaria, herpes simplex virus and
chlamydia.

        The use of epitopes in vaccine development offers several distinct
advantages over traditional vaccine approaches.

        - First, the epitopes are selected from conserved regions of viral or
          tumor-associated antigens, reducing the likelihood of escape mutants.
          When using whole antigens, there is evidence that the immune response
          is directed largely toward variable regions of the antigen, allowing
          immune escape due to mutations.

        - Second, the ability to combine selected epitopes (CTL and HTL) and to
          alter their composition to enhance immunogenicity allows for
          manipulation of the immune response, as appropriate, for the target
          disease. Similar engineering of the response is not possible with
          traditional approaches.

        - Third, a major benefit of epitope-based, immune-stimulating vaccines
          is their safety. The possible pathological side effects caused by
          infectious agents or whole protein antigens, which might have their
          own intrinsic biological activity, is eliminated.

        - Finally, in order to develop the most effective vaccines, multiple
          antigens should be targeted. Combining multiple epitopes into a single
          vaccine offers a simple alternative to traditional combination
          vaccines and enables the design of a well-characterized product which
          contains minimal extraneous biological material.

        Based on our scientists' discoveries in the field, Epimmune has
established a broad intellectual property position directed toward the methods
of epitope identification, epitope compositions and epitope uses in vaccines and
diagnostics products.

        Our executive offices are located at 5820 Nancy Ridge Drive, San Diego,
California 92121, and our telephone number is (858) 860-2500.

        Unless otherwise indicated, all references to "Cytel" are to Cytel
Corporation. Epimmune Inc. was Cytel's majority-owned subsidiary until July 1,
1999, at which time Cytel and Epimmune Inc. merged. All references to "we," "us"
or "our company" are to the combined entity of Cytel and Epimmune Inc.



                                       4.
<PAGE>   5

                                 USE OF PROCEEDS

        We will not receive any proceeds from the sale of the shares of common
stock offered by the selling stockholders.

                                  RISK FACTORS

        An investment in the shares being offered hereby involves a high degree
of risk. In deciding whether to purchase shares of our common stock, you should
carefully consider the following risk factors, in addition to other information
contained in this prospectus, in our most recent quarterly report on Form 10-Q,
in our most recent annual report on Form 10-K, and in any other documents
incorporated by reference into this prospectus from our other SEC filings. This
prospectus also contains forward-looking statements that involve risks and
uncertainties. Our actual results could differ materially from those discussed
here or incorporated by reference. Factors that could cause or contribute to
differences in our actual results include those discussed in this section, as
well as those discussed elsewhere in this prospectus and in other documents
incorporated by reference into this prospectus.

WE ARE AT AN EARLY STAGE OF DEVELOPMENT. IF WE DO NOT SUCCESSFULLY DEVELOP AND
COMMERCIALIZE OUR PRODUCTS, WE MAY NEVER GENERATE SIGNIFICANT REVENUES.

        We are a research and development focused company. In collaboration with
our corporate partner, Searle, we expect that Searle will initiate Phase I/II
human clinical trials by the end of 2000. There are many factors which are
outside of our control that may effect the timing of these trials and we cannot
assure you the trials will commence within the anticipated timeframe. We have
not completed the development of any product and, accordingly, have not begun to
market or generate revenues from the commercialization of any product. We do not
expect to market any of our therapeutic or prophylactic products for a number of
years. If we do not successfully develop and commercialize products we may never
generate significant revenues. Our potential therapies under development will
require time consuming and costly research and development efforts, preclinical
studies, clinical testing, regulatory approvals and additional investment prior
to their commercialization, which may never occur.

        We cannot guarantee that our research and development programs will be
successful or that we can show that our products are safe and effective in
humans. For example, in March 1999, Cytel completed its Phase II/III clinical
trial of Cylexin, its lead cell adhesion inhibitor compound. Based on
disappointing results from this Phase II/III clinical trial, Cytel decided to
terminate the clinical trials of Cylexin and discontinue its therapeutic
anti-inflammatory business. Unacceptable toxicities or side effects may occur at
any time in the course of human clinical trials or during commercial use. Delays
in planned patient enrollment in our clinical trials may result in increased
costs, program delays or both. The appearance of any unacceptable toxicities or
side effects could interrupt, limit, delay or abort the development of any of
our products or, if previously approved, necessitate their withdrawal from the
market.

        We may never obtain FDA or other necessary regulatory approvals to
successfully commercialize any of our products under development. Further, we
may not be able to manufacture any products in commercial quantities in
compliance with regulatory requirements at an acceptable cost. Even if we
successfully develop and obtain approval for our products, we may fail to
achieve the necessary market acceptance of these products. Our failure to
address problems and delays relating to research and development, regulatory
approval, manufacturing and marketing would harm our business.

IF SEARLE TERMINATES ITS COLLABORATION WITH US OR FAILS TO PERFORM AS EXPECTED
UNDER THE COLLABORATION AGREEMENT, IT WILL SIGNIFICANTLY HARM THE DEVELOPMENT OF
OUR CANCER EPITOPE PRODUCTS.

        We have entered into a research and development collaboration with
Searle with respect to the production, use and sale of pharmaceutical products
derived from our cancer epitopes and the use thereof in therapeutic vaccines.
This collaboration is our only significant collaboration, and we are
substantially dependent upon it. The success of the collaboration will depend,
in significant part, on Searle's development, competitive marketing and
strategic considerations, including the relative advantages of alternative
products being developed or marketed by competitors. We expect that
substantially all of our revenues for the foreseeable future will result from
payments



                                       5.
<PAGE>   6

under our existing, and any future, collaborations, including royalties on
product sales and interest income. We cannot be certain that Searle will perform
its obligations under the collaboration or that we will receive any future
milestone payments or other amounts under the collaboration.

        We do not directly control the amount or timing of resources that Searle
will devote to our collaboration, including the decision whether to proceed with
clinical trials. Searle may not commit sufficient resources to our research and
development programs or the commercialization of our products. If Searle fails
to conduct its activities in a timely manner, or at all, our preclinical or
clinical development related to our partnership with Searle could be delayed or
terminated. The suspension or termination of the our collaboration with Searle,
the failure of such collaboration to be successful or the delay in the
development or commercialization of pharmaceutical products pursuant to such
collaboration could harm our business.

IF WE CANNOT OBTAIN COLLABORATION OR LICENSE AGREEMENTS ON ACCEPTABLE TERMS IN
THE FUTURE, WE MAY NOT SUCCESSFULLY DEVELOP SOME OF OUR PRODUCTS.

        We expect to rely on collaborative arrangements both to develop and
commercialize pharmaceutical products. We cannot be certain that we will be able
to enter into collaborative arrangements in the future, that any such
arrangements will be successful or that we will receive royalty revenues,
license fees or milestone payments from any such collaborative arrangements. In
addition, our collaborative partners may pursue alternative technologies or
develop alternative compounds either on their own or in collaboration with
others as a means of developing treatments for the disease targeted by any
collaborative program with us. In addition, we may be required to enter into
licenses or other collaborative agreements with third parties in order to access
technologies that are necessary to successfully develop certain of our products.
We cannot be certain that we will be able to successfully negotiate acceptable
licenses or other collaborative arrangements that will allow us to access such
technologies. In addition, we cannot be certain that any technologies accessed
through such licenses or other collaborations will successfully meet our
requirements.

OUR ADDITIONAL FINANCING REQUIREMENTS AND LIMITED ACCESS TO FINANCING MAY
ADVERSELY AFFECT OUR ABILITY TO DEVELOP PRODUCTS.

        As of December 31, 1999, we had $8.7 million in cash, cash equivalents,
restricted cash and short-term investments. In February 2000, we received $4.3
million from the sale of 1,200,000 shares of our common stock to the selling
stockholders identified in this prospectus. Our future capital requirements will
depend on many factors, including:

        -      our ability to establish and maintain collaborative arrangements;

        -      progress with preclinical testing and clinical trials;

        -      the time and costs involved in obtaining regulatory approvals;

        -      the costs involved in filing, prosecuting and enforcing patent
               claims;

        -      competing technological and market developments;

        -      changes in our existing research relationships;

        -      continued scientific progress in our drug discovery programs;

        -      the magnitude of our drug discovery programs;

        -      the cost of manufacturing scale-up; and

        -      effective commercialization activities and arrangements.



                                       6.
<PAGE>   7
        We intend to seek additional through funding collaborative arrangements
or equity or debt financings. If additional financing is not available, we
anticipate that our existing resources, will enable us to maintain our current
and planned operations through the end of 2001. We may not be able to obtain
financing on favorable terms, if at all, or enter additional collaborations to
reduce our funding requirements. If we acquire funds by issuing securities,
further dilution to existing stockholders may result. If we acquire funds
through additional collaborations, we will likely have to relinquish some or all
of the rights to products or technologies that we may have otherwise developed
ourselves.

OUR HISTORY OF OPERATING LOSSES AND OUR EXPECTATIONS OF CONTINUING LOSSES MAY
HURT OUR ABILITY TO CONTINUE OPERATIONS.

        We have experienced significant operating losses since our inception in
1987. As of December 31, 1999, we had an accumulated deficit of $137.0 million.
We have not generated revenues from the commercialization of any product. All of
our revenues to date have consisted of contract research and development
revenues, license and milestone payments, research grants, certain asset
divestitures and interest income. We expect to incur substantial net operating
losses which may imperil our ability to continue operations. To achieve
profitable operations, we, alone or with partners, must successfully identify,
develop, register and market proprietary products. We may not be able to
generate sufficient product revenue to become profitable on a sustained basis or
at all.

IF WE CANNOT COST-EFFECTIVELY MANUFACTURE OUR PRODUCTS AND THE PRODUCTS OF OUR
PARTNERS IN COMMERCIAL QUANTITIES AND IN COMPLIANCE WITH REGULATORY
REQUIREMENTS, WE MAY NOT BE ABLE TO SUCCESSFULLY COMMERCIALIZE OUR PRODUCTS.

               To be successful, our products and the products of our partners
must be manufactured in commercial quantities in compliance with regulatory
requirements and at an acceptable cost. We have not commercialized any products,
nor have we demonstrated that we can manufacture commercial quantities of our
product candidates or our partners' product candidates in accordance with
regulatory requirements. If we cannot manufacture products in suitable
quantities in accordance with regulatory standards, either on our own our
through contracts with third parties, it may delay clinical trials, regulatory
approvals and marketing efforts for such products. Such delays could adversely
affect our competitive position and our chances of achieving profitability. We
cannot be sure that we can manufacture, either on our own our through contracts
with third parties, such products at a cost or in quantities which are
commercially viable.

THE LENGTHY APPROVAL PROCESS AND UNCERTAINTY OF GOVERNMENT REGULATORY
REQUIREMENTS MAY DELAY OR PREVENT US FROM COMMERCIALIZING PRODUCTS.

        We cannot commercialize our products if we do not receive FDA or foreign
approval for our products. Clinical testing, manufacture, promotion and sale of
our products are subject to extensive regulation by numerous governmental
authorities in the United States, principally the FDA, and corresponding state
and foreign regulatory agencies. These regulations may delay or prevent us from
commercializing products. Noncompliance with applicable requirements can result
in, among other things, fines, injunctions, seizure of products, total or
partial suspension of product marketing, failure of the government to grant
premarket approval, withdrawal of marketing approvals and criminal prosecution.

        The regulatory process for new therapeutic drug products, including the
required preclinical studies and clinical testing, is lengthy and expensive. We
may not receive necessary FDA or foreign clearances for any of our potential
products in a timely manner, or at all. The length of the clinical trial process
and the number of patients the FDA will require to be enrolled in the clinical
trials in order to establish the safety and efficacy of our products is
uncertain. The FDA or Epimmune and its collaborators may decide to discontinue
or suspend clinical trials at any time if the subjects or patients who are
participating in such trials are being exposed to unacceptable health risks or
if the results show no or limited benefit in patients treated with the drug
compared to patients in the control group.

        We may encounter significant delays or excessive costs in our efforts to
secure necessary approvals. Regulatory requirements are evolving and uncertain.
Future United States or foreign legislative or administrative acts could also
prevent or delay regulatory approval of our products. We may not receive the
necessary approvals for clinical trials, manufacturing or marketing of any of
our products under development. Even if we obtain commercial



                                       7.
<PAGE>   8

regulatory approvals, the approvals may significantly limit the indicated uses
for which we may market our products. In addition, the FDA may continually
review a product after its initial approval and commercialization. Later
discovery of previously unknown problems or failure to comply with the
applicable regulatory requirements may result in restrictions on the marketing
of a product or withdrawal of the product from the market, as well as possible
civil or criminal sanctions.

        To market any drug products outside of the United States, we are also
subject to numerous and varying foreign regulatory requirements, implemented by
foreign health authorities, governing the design and conduct of human clinical
trials and marketing approval. The approval procedure varies among countries and
can involve additional testing, and the time required to obtain approval may
differ from that required to obtain FDA approval. The foreign regulatory
approval process includes all of the risks associated with obtaining FDA
approval set forth above, and approval by the FDA does not ensure approval by
the health authorities of any other country, nor does the approval by foreign
health authorities ensure approval be the FDA.

        Among the other requirements for regulatory approval is the requirement
that prospective manufacturers conform to the FDA's Good Manufacturing
Practices, GMP, requirements specifically for biological drugs, as well as for
other drugs. In complying with the FDA's GMP requirements, manufacturers must
continue to expend time, money and effort in production, record keeping and
quality control to assure that the product meets applicable specifications and
other requirements. Failure to comply with the FDA's GMP requirements subjects
the manufacturer to possible FDA regulatory action. If we or our contract
manufacturers, if any, fail to maintain compliance with the FDA's GMP
requirements on a continuing basis, it could materially adversely affect our
operations, commercialization efforts and profitability.

TECHNOLOGICAL CHANGE AND COMPETITION MAY RENDER OUR POTENTIAL PRODUCTS OBSOLETE.

        The biotechnology industry continues to undergo rapid change and
competition is intense and is expected to increase. Our competitors may succeed
in developing technologies and products that are more effective or affordable
than any of the products we are developing or which would render our technology
and products obsolete and noncompetitive. We compete with many public and
private companies, including pharmaceutical companies, chemical companies,
specialized biotechnology companies and academic institutions. Many of our
competitors have substantially greater experience, financial and technical
resources and production, marketing and development capabilities than us. In
addition, many of our competitors have significantly greater experience
conducting preclinical studies and clinical trials of new products, and in
obtaining regulatory approvals for such products. Accordingly, some of our
competitors may succeed in obtaining developing and commercializing products
more rapidly or effectively than us, or in developing technology and products
that would render our technology and products obsolete or noncompetitive. We are
aware of companies that are pursuing the development of novel pharmaceuticals
which target the same diseases that we are targeting. These and other efforts by
potential competitors may be successful, and other technologies may be developed
to compete with our technologies. If we cannot successfully respond to
technological change in a timely manner, our commercialization efforts may be
harmed.

        Our products under development address a range of markets. Our
competition will be determined in part by the potential indications for which
our compounds are developed and ultimately approved by regulatory authorities.
For certain of our potential products, an important factor in competition may be
the timing of market introduction of our products and competitive products.
Accordingly, the relative speed with which we can develop products, compete the
clinical trials and approval processes and supply commercial quantities of the
products to the market are expected to be important competitive factors. We
expect that competition among products approved for sale will be based, among
other things, on product effectiveness, safety, reliability, availability, price
and patent position.

OUR FAILURE TO OBTAIN ISSUED PATENTS AND, CONSEQUENTLY, TO PROTECT OUR
PROPRIETARY TECHNOLOGY, COULD IMPAIR OUR COMPETITIVE POSITION.

        Our success will depend in part on our ability to obtain patent
protection for our products and processes, both in the United States and other
countries. The patent position of biotechnology and pharmaceutical companies is



                                       8.
<PAGE>   9

highly uncertain and involves complex legal and factual questions. There is no
consistent policy regarding the breadth of claims allowed in biotechnology
patents. We intend to file applications and pursue patent prosecution as
appropriate for patents covering both our products and processes. We cannot be
sure that patents will issue from any of the patent applications that we own or
license or that, if patents do issue, that claims allowed will be sufficiently
broad to protect our products and processes. In addition, we cannot be certain
that third parties will not challenge, invalidate or circumvent any patents
issued to us, or that the rights granted under the patents will provide
proprietary protection to us.

        We also protect our proprietary technology and processes in part by
confidentiality agreements with our collaborative partners, employees and
consultants. We cannot be certain that our collaborative partners, employees and
consultants will not breach these agreements, that we will have adequate
remedies for any breach, or that our trade secrets will not otherwise become
known or be independently discovered by competitors.

WE MAY NOT BE ABLE TO COMMERCIALIZE OUR OTHER PRODUCTS UNDER DEVELOPMENT IF THEY
INFRINGE EXISTING PATENTS OR PATENTS THAT HAVE NOT YET ISSUED, WHICH WOULD
MATERIALLY HARM OUR BUSINESS.

        As is typical in the biotechnology industry, our commercial success will
depend in part on our ability to avoid infringing patents issued to competitors
or breaching the technology licenses upon which we might base our products. If
we fail to obtain a license to any technology that we require to commercialize
our products, or to develop an alternative compound and obtain FDA approval
within an acceptable period of time if required to do so, our business would be
harmed. Litigation, which could result in substantial costs to us, may also be
necessary to enforce any patents issued to us or to determine the scope and
validity of others' proprietary rights. In addition, we may have to participate
in interference proceedings declared by the United States Patent and Trademark
Office which could result in substantial costs to determine the priority of
inventions.

OUR FUTURE SUCCESS DEPENDS IN PART ON THE CONTINUED SERVICE OF OUR KEY
SCIENTIFIC AND MANAGEMENT PERSONNEL AND OUR ABILITY TO IDENTIFY, HIRE AND RETAIN
ADDITIONAL PERSONNEL.

        We are highly dependent on the principal members of our scientific and
management staff. We do not maintain key person life insurance on the life of
any employee. Our future success also will depend in part on the continued
service of our key scientific and management personnel and our ability to
identify, hire and retain additional qualified personnel.

        There is intense competition for qualified personnel in the areas of our
activities, and we cannot be sure that we will be able to continue to attract
and retain such personnel necessary for the development of our business. Because
of the intense competition, we cannot be sure that we will be successful in
adding technical personnel as needed to meet the staffing requirements of
additional collaborative relationships. Our failure to attract and retain key
personnel could be significantly detrimental to our product development programs
and could harm our business.

IF WE DO NOT DEVELOP A SUFFICIENT SALES AND MARKETING FORCE, WE MAY NOT BE ABLE
TO SUCCESSFULLY COMMERCIALIZE OUR PRODUCTS.

        We have no experience in sales, marketing or distribution. Before we can
market any of our products directly, we must develop a substantial marketing and
sales force with technical expertise and supporting distribution capability.
Alternatively, we may obtain the assistance of a pharmaceutical company with a
large distribution system and a large direct sales force. Other than our
agreements with Searle and Takara, we do not have any existing distribution
arrangements with any pharmaceutical company for our products under development.
We cannot be sure that we can establish sales and distribution capabilities or
successfully gain market acceptance for our products. If we cannot develop sales
and distribution capabilities, we may not be able to successfully commercialize
our products.



                                       9.
<PAGE>   10

ADVERSE DETERMINATIONS CONCERNING PRODUCT PRICING, REIMBURSEMENT AND RELATED
MATTERS COULD PREVENT US FROM SUCCESSFULLY COMMERCIALIZING PRODUCTS.

        Our ability to successfully commercialize our products may depend in
part on the extent to which reimbursement for the cost of such products and
related treatment will be available from government health administration
authorities, private health insurers and other organizations. Third-party payors
are increasingly challenging the price of medical products and services.
Significant uncertainty exists as to the reimbursement status of newly approved
health care products, and we cannot be certain that adequate third-party
coverage will be available to enable us to maintain price levels sufficient to
realize an appropriate return on our investment in product development. If we
cannot obtain adequate third-party coverage for our products, it could harm our
business.

PRODUCT LIABILITY RISKS MAY EXPOSE US TO SIGNIFICANT LIABILITY.

        Our business exposes us to potential product liability risks which are
inherent in the testing, manufacturing and marketing of human therapeutic
products. While we currently have product liability insurance, we cannot be sure
that we can maintain such insurance on acceptable terms or that our insurance
will provide adequate coverage against potential liabilities.

OUR USE OF HAZARDOUS MATERIALS COULD EXPOSE US TO SIGNIFICANT COSTS.

        Our research and development processes involve the controlled storage,
use and disposal of hazardous materials, chemicals and radioactive compounds. We
are subject to federal, state and local laws and regulations governing the use,
manufacture, storage, handling and disposal of these materials and some waste
products. Although we believe that our safety procedures for handling and
disposing of these materials comply with the standards prescribed by these laws
and regulations, the risk of accidental contamination or injury from these
materials cannot be completely eliminated. In the event of an accident, we could
be held liable for any damages that result, and any liability could exceed our
resources.

        Although we believe that we are in compliance in all material respects
with applicable environmental laws and regulations and currently do not expect
to make material capital expenditures for environmental control facilities in
the near term, we cannot be sure that compliance with environmental laws and
regulations in the future will not entail significant costs, or that our
business will not be harmed by current or future environmental laws or
regulations.

THE VOLATILITY OF THE PRICE OF OUR COMMON STOCK AND OUR DIVIDEND POLICY MAY HURT
OUR STOCKHOLDERS.

        The market prices for securities of biotechnology companies, including
our common stock, have historically been highly volatile and currently are of
new record levels, and the market from time to time has experienced significant
price and volume fluctuations that are unrelated to the operating performance of
such companies. The following factors may have a significant effect on the
market price of our common stock:

        -      announcements of technological innovations or new commercial
               therapeutic products by us or others;

        -      governmental regulation;

        -      developments in patent or other proprietary rights;

        -      developments in our relationships with our collaborative
               partners;

        -      public concern as to the clinical results and/or, the safety of
               drugs developed by us or others; and

        -      general market conditions.

        Fluctuations in financial performance from period to period also may
have a significant impact on the market price of our common stock.



                                      10.
<PAGE>   11

THE SUBORDINATION OF OUR COMMON STOCK TO OUR PREFERRED STOCK COULD HURT COMMON
STOCKHOLDERS.

        Our common stock is expressly subordinate to our Series S and Series S-1
Preferred Stock in the event of our liquidation, dissolution or winding up. If
we were to cease operations and liquidate our assets, there may not be any
remaining value available for distribution to the holders of common stock after
providing for the Series S and Series S-1 Preferred Stock liquidation
preference.

THE EFFECT OF ANTI-TAKEOVER PROVISIONS COULD ADVERSELY AFFECT OUR COMMON
STOCKHOLDERS.

        Our certificate of incorporation includes a provision that requires the
approval of holders of at least 66 2/3% of our voting stock as a condition to a
merger or certain other business transactions with, or proposed by, a holder of
15% or more of our voting stock. This approval is not required in cases where
certain of our directors approve the transaction or where certain minimum price
criteria and other procedural requirements are met. Our certificate of
incorporation also requires the approvals of holders of at least 66 2/3% of our
voting stock to amend or change the provisions mentioned relating to the
transaction approval. Finally, our certificate of incorporation provides that
any action required or permitted to be taken by our stockholders must be
effected at a duly called annual or special meeting rather than by any consent
in writing.

        Further, pursuant to the terms of our stockholder rights plan, we have
distributed a dividend of one right for each outstanding share of common stock.
These rights will cause substantial dilution to the ownership of a person or
group that attempts to acquire us on terms not approved by the Board of
Directors and may have the effect of deterring hostile takeover attempts.

CONCENTRATION OF OWNERSHIP AMONG OUR EXISTING OFFICERS, DIRECTORS AND PRINCIPAL
STOCKHOLDERS MAY PREVENT OTHER STOCKHOLDERS FROM INFLUENCING SIGNIFICANT
CORPORATE DECISIONS AND DEPRESS OUR STOCK PRICE.

        Our officers, directors and stockholders with at least 10% of our stock
will together control approximately 46% of our outstanding common stock and
preferred stock, on a combined, as-converted basis. If these officers,
directors and principal stockholders act together, they will be able to exert a
significant degree of influence over our management and affairs and over matters
requiring stockholder approval, including the election of directors and approval
of mergers or other business combination transactions. The interests of this
concentration of ownership may not always coincide with our interests or the
interests of other stockholders. For instance, officers, directors and principal
stockholders, acting together, could cause us to enter into transactions or
agreements that we would not otherwise consider. Similarly, this concentration
of ownership may have the effect of delaying or preventing a change in control
of our company otherwise favored by our other stockholders. This concentration
of ownership could depress our stock price.

WE HAVE NEVER PAID DIVIDENDS.

        We have never paid any cash dividends and do not anticipate paying cash
dividends in the foreseeable future.



                                      11.
<PAGE>   12

                           FORWARD-LOOKING STATEMENTS

        This prospectus, including the documents that we incorporate by
reference, contains forward-looking statements within the meaning of Section 27A
of the Securities Act and Section 21E of the Exchange Act. Any statements about
our expectations, beliefs, plans, objectives, assumptions or future events or
performance are not historical facts and may be forward-looking. These
statements are often, but not always, made through the use of words or phrases
such as "anticipate," "estimate," "plans," "projects," "continuing," "ongoing,"
"expects," "management believes," "we believe," "we intend" and similar words or
phrases. Accordingly, these statements involve estimates, assumptions and
uncertainties which could cause actual results to differ materially from those
expressed in them. Any forward-looking statements are qualified in their
entirety by reference to the factors discussed in this prospectus or
incorporated by reference.

        Because the factors discussed in this prospectus or incorporated by
reference could cause actual results or outcomes to differ materially from those
expressed in any forward-looking statements made by us or on behalf of the
company, you should not place undue reliance on any such forward-looking
statements. Further, any forward-looking statement speaks only as of the date on
which it is made, and we undertake no obligation to update any forward-looking
statement or statements to reflect events or circumstances after the date on
which such statement is made or to reflect the occurrence of unanticipated
events. New factors emerge from time to time, and it is not possible for us to
predict which will arise. In addition, we cannot assess the impact of each
factor on our business or the extent to which any factor, or combination of
factors, may cause actual results to differ materially from those contained in
any forward-looking statements.



                                      12.
<PAGE>   13

                              SELLING STOCKHOLDERS

        We are registering for resale certain shares of our common stock held by
the selling stockholders identified below. The following table sets forth:

        -  the name of the selling stockholders;

        -  the number and percent of shares of our common stock that the selling
           stockholders beneficially owned prior to the offering for resale of
           any of the shares of our common stock being registered by the
           registration statement of which this prospectus is a part;

        -  the number of shares of our common stock that may be offered for
           resale for the account of the selling stockholders pursuant to this
           prospectus; and

        -  the number and percent of shares of our common stock to be held by
           the selling stockholders after the offering of the resale shares
           (assuming all of the resale shares are sold by the selling
           stockholders).

This information is based upon information provided by each respective selling
stockholder, schedules 13G and other public documents filed with the SEC, and
assumes the sale of all of the resale shares by the selling stockholders. The
term "selling stockholders" includes the stockholders listed below and their
transferees, pledgees, donees or other successors. The applicable percentages of
ownership are based on an aggregate of 7,256,455 shares of common stock issued
and outstanding as of February 16, 2000.


<TABLE>
<CAPTION>
                                         SHARES BENEFICIALLY OWNED                      SHARES BENEFICIALLY OWNED
                                             PRIOR TO OFFERING          NUMBER OF            AFTER OFFERING
                                          -----------------------      SHARES BEING     ------------------------
SELLING STOCKHOLDERS                      NUMBER          PERCENT         OFFERED       NUMBER           PERCENT
- --------------------                      ------          -------         -------       ------           -------
<S>                                    <C>                <C>          <C>              <C>              <C>
State of Wisconsin Investment Board    1,186,427           16.35%         840,000       346,427            4.77%
121 East Wilson Street
Madison, WI 53702

Biotechnology Value Fund II,L.P. (1)     403,500            5.56%         200,000        43,500               *
c/o Grosvenor Capital
Management, L.P.
227 W. Monroe Street, Suite 4800
Chicago, IL 60606

Biotechnology Value Fund, L.P (2)        403,500            5.56%         130,000        43,500               *
c/o Grosvenor Capital
Management, L.P.
227 W. Monroe Street, Suite 4800
Chicago, IL 60606

Investment 10, LLC (3)                   403,500            5.56%          30,000        43,500               *
c/o Grosvenor Capital
Management, L.P.
227 W. Monroe Street, Suite 4800
Chicago, IL 60606
</TABLE>

__________________
* Less than 1%

(1)     Includes 163,614 shares held by the Biotechnology Value Fund, L.P. and
        30,000 shares held by Investment 10, LLC.

(2)     Includes 209,886 held by the Biotechnology Value Fund II, L.P. and
        30,000 shares held by Investment 10, LLC.

(3)     Includes 209,886 held by the Biotechnology Value Fund II, L.P. and
        163,614 shares held by the Biotechnology Value Fund, L.P.



                                      13.
<PAGE>   14

                              PLAN OF DISTRIBUTION

        The shares of common stock may be sold from time to time by the selling
stockholders in one or more transactions at fixed prices, at market prices at
the time of sale, at varying prices determined at the time of sale or at
negotiated prices. The selling stockholders may offer their shares of common
stock in one or more of the following transactions:

        -      on any national securities exchange or quotation service at which
               the common stock may be listed or quoted at the time of sale,
               including the Nasdaq National Market;

        -      in the over-the-counter market;

        -      in private transactions;

        -      through options; and

        -      by pledge to secure debts and other obligations, or a combination
               of any of the above transactions.

        If required, we will distribute a supplement to this prospectus to
describe material changes in the terms of the offering.

        The shares of common stock described in this prospectus may be sold from
time to time directly by the selling stockholders. Alternatively, the selling
stockholders may from time to time offer shares of common stock to or through
underwriters, broker/dealers or agents. The selling stockholders and any
underwriters, broker/dealers or agents that participate in the distribution of
the shares of common stock may be deemed to be "underwriters" within the meaning
of the Securities Act of 1933. Any profits on the resale of shares of common
stock and any compensation received by any underwriter, broker/dealer or agent
may be deemed to be underwriting discounts and commissions under the Securities
Act of 1933.

        Any shares covered by this prospectus which qualify for sale pursuant to
Rule 144 under the Securities Act of 1933 may be sold under rule 144 rather than
under the terms of this prospectus. The selling stockholders may not sell all of
the shares. The selling stockholders may transfer, will or gift such shares by
other means not described in this prospectus.

        To comply with the securities laws of certain jurisdictions, the common
stock must be offered or sold only through registered or licensed brokers or
dealers. In addition, in certain jurisdictions, the common stock may not be
offered or sold unless they have been registered or qualified for sale or an
exemption is available and complied with.

        Under the Securities Exchange Act of 1934, any person engaged in a
distribution of the common stock may not simultaneously engage in market-making
activities with respect to the common stock for nine business days prior to the
start of the distribution. In addition, each selling stockholder and any other
person participating in a distribution will be subject to the Securities
Exchange Act of 1934 which may limit the timing of purchases and sales of common
stock by the selling stockholders or any such other person. These factors may
affect the marketability of the common stock and the ability of brokers or
dealers to engage in market-making activities.

     All expenses of this registration will be paid by Epimmune. These expenses
include the SEC's filing fees and fees under state securities or "blue sky"
laws. We estimate that our expenses in connection with this offering will be
approximately $56,400. All expenses for the issuance of a supplement to this
prospectus, when requested by selling stockholder(s), will be paid by the
requesting stockholder(s).

                                  LEGAL MATTERS

        Cooley Godward LLP will give its opinion that the shares offered in this
prospectus have been validly issued and are fully paid and non-assessable, and
that the shares which will be issued upon the exercise of certain warrants will
be validly issued, fully paid and nonassessable.



                                      14.
<PAGE>   15

                                     EXPERTS

        Ernst & Young LLP, independent auditors, have audited our financial
statements included in our annual report on Form 10-K for the year ended
December 31, 1999 as set forth in their report, which is incorporated by
reference in this prospectus and registration statement. Our financial
statements and schedule are incorporated by reference in reliance on Ernst &
Young LLP's report, given on their authority as experts in accounting and
auditing.




                                      15.
<PAGE>   16


YOU SHOULD RELY ONLY ON THE INFORMATION CONTAINED IN THIS PROSPECTUS. WE HAVE
NOT AUTHORIZED ANYONE TO PROVIDE YOU WITH INFORMATION DIFFERENT FROM THAT
CONTAINED IN THIS PROSPECTUS OR ANY PROSPECTUS SUPPLEMENT. THIS PROSPECTUS IS
NOT AN OFFER OF THESE SECURITIES IN ANY JURISDICTION WHERE AN OFFER AND SALE IS
NOT PERMITTED. THE INFORMATION CONTAINED IN THIS PROSPECTUS IS ACCURATE ONLY AS
OF THE DATE OF THIS PROSPECTUS, REGARDLESS OF THE TIME OF DELIVERY OF THIS
PROSPECTUS OR ANY SALE OF OUR COMMON STOCK.





                                TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                PAGE
                                                                ----
<S>                                                             <C>
WHERE YOU CAN GET MORE INFORMATION ............................  3
EPIMMUNE INC ..................................................  4
USE OF PROCEEDS ...............................................  5
RISK FACTORS ..................................................  5

FORWARD-LOOKING STATEMENTS ....................................  12
SELLING STOCKHOLDERS ..........................................  13
PLAN OF DISTRIBUTION ..........................................  14
LEGAL MATTERS .................................................  14
EXPERTS .......................................................  15
</TABLE>



                            ________________________



                                1,200,000 SHARES


                                  COMMON STOCK



                                  EPIMMUNE INC.



                            ________________________



                                   PROSPECTUS


                            ________________________



                             _________________, 2000






<PAGE>   17

                                     PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

        The expenses in connection with the issuance and distribution of the
securities being registered are set forth in the following table (all amounts
except the registration fee and the listing fee are estimated):

        SEC Registration Fee .............................   $3,430
        Nasdaq National Market Listing Fee ...............  $12,000
        Legal fees and expenses ..........................  $30,000
        Accounting fees and expenses .....................   $6,000
        Transfer agent fees ..............................   $5,000
                                                            -------
                Total ....................................  $56,430
                                                            =======


ITEM 15. INDEMNIFICATION OF OFFICERS AND DIRECTORS.

        The Registrant's Certificate of Incorporation and Bylaws include
provisions to (i) eliminate the personal liability of its directors for monetary
damages resulting from breaches of their fiduciary duty to the extent permitted
by Section 102(b)(7) of the DGCL and (ii) require the Registrant to indemnify
its directors and officers to the fullest extent permitted by applicable law,
including circumstances in which indemnification is otherwise discretionary.
Pursuant to Section 145 of the DGCL, a corporation generally has the power to
indemnify its present and former directors, officers, employees and agents
against expenses incurred by them in connection with any suit to which they are
or are threatened to be made, a party by reason of their serving in such
positions so long as they acted in good faith and in a manner they reasonably
believed to be in or not opposed to, the best interests of the corporation and
with respect to any criminal action, they had no reasonable cause to believe
their conduct was unlawful. The Registrant believes that these provisions are
necessary to attract and retain qualified persons as directors and officers.
These provisions do not eliminate the directors' or officers' duty of care, and,
in appropriate circumstances, equitable remedies such as injunctive or other
forms of non-monetary relief will remain available under the DGCL. In addition,
each director will continue to be subject to liability pursuant to Section 174
of the DGCL, for breach of the director's duty of loyalty to the Registrant, for
acts or omissions not in good faith or involving intentional misconduct, for
knowing violations of law, for acts or omissions that the director believes to
be contrary to the best interests of the Registrant or its stockholders, for any
transaction from which the director derived an improper personal benefit, for
acts or omissions involving a reckless disregard for the director's duty to the
Registrant or its stockholders when the director was aware or should have been
aware of a risk of serious injury to the Registrant or its stockholders, for
acts or omission that constitute an unexcused pattern of inattention that
amounts to an abdication of the director's duty to the Registrant or its
stockholders, for improper transactions between the director and the Registrant
and for improper loans to directors and officers. The provision also does not
affect a director's responsibilities under any other law, such as the federal
securities law or state or federal environmental laws.

       The Registrant has entered into indemnity agreements with each of its
directors and executive officers that require the Registrant to indemnify such
persons against expenses, judgments, fines, settlements and other amounts
incurred (including expenses of a derivative action) in connection with any
proceeding, whether actual or threatened, to which any such person may be made a
party by reason of the fact that such person is or was a director or an
executive officer of the Registrant or any of its affiliated enterprises,
provided such person acted in good faith and in a manner such person reasonably
believed to be in or not opposed to the best interests of the Registrant and,
with respect to any criminal proceeding, had no reasonable cause to believe his
conduct was unlawful. The indemnification agreements also set forth certain
procedures that will apply in the event of a claim for indemnification
thereunder

       At present, there is no pending litigation or proceeding involving a
director or officer of the Registrant as to which indemnification is being
sought nor is the Registrant aware of any threatened litigation that may result
in claims for indemnification by any officer or director.



                                      II-1
<PAGE>   18

The Registrant has an insurance policy covering the officers and directors of
the Registrant with respect to certain liabilities, including liabilities
arising under the Securities Act or otherwise.

ITEM 16. EXHIBITS.

(a)     Exhibits.

<TABLE>
<CAPTION>
Exhibit No.       Description
- -----------       -----------
<S>               <C>
   4.1            Form of Common Stock Purchase Agreement between the Registrant
                  and each selling stockholder dated February 15, 2000(1).

   5.1            Opinion of Cooley Godward LLP.

  10.1            Reference is made to Exhibit 4.1 above.

  23.1            Consent of Ernst & Young, LLP.

  23.2            Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.

  24              Power of Attorney.  Reference is made to page II-4.
</TABLE>

- --------------------
(1) Filed as an exhibit to the Registrant's Annual Report on Form 10-K for the
    fiscal year ended December 31, 1999.

ITEM 17. UNDERTAKINGS.

        The undersigned Registrant hereby undertakes:

        (1) To file, during any period during which offers or sales are being
made, a post-effective amendment to this registration statement;

               (i) To include any prospectus required by Section 10(a)(3) of the
Securities Act of 1933;

               (ii) To reflect in the prospectus any facts or events arising
after the effective date of the registration statement (or the most recent
post-effective amendment thereof) which, individually or in the aggregate,
represent a fundamental change in the information set forth in the registration
statement. Notwithstanding the foregoing, any increase or any decrease in volume
of securities offered (if the total dollar value of securities offered would not
exceed that which was registered) and any deviation from the low end or high end
of the estimated maximum offering range may be reflected in the form of
prospectus filed with the Commission pursuant to Rule 424(b) if, in the
aggregate, the changes in volume and price represent no more than 20% change in
the maximum aggregate offering price set forth in the "Calculation of
Registration Fee" table in the effective registration statement.

               (iii) To include any material information with respect to the
plan of distribution not previously disclosed in the registration statement or
any material change to such information in the registration statement.

provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply if the
information required to be included in a post-effective amendment by those
paragraphs is contained in periodic reports filed with or furnished to the
Commission by the registrant pursuant to Section 13 or 15(d) of the Securities
Exchange Act of 1934 that are incorporated by reference in the registration
statement.

        (2) That, for purposes of determining liability under the Securities Act
of 1933, each such post-effective amendment shall be deemed to be a new
registration statement relating to the securities to be offered therein, and the
offering of such securities at that time shall be deemed to be an initial bona
fide offering thereof.

        (3) To remove from registration by means of a post-effective amendment
any of the securities being registered which shall remain unsold at the
termination of the offering.



                                     II-2.
<PAGE>   19

        The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or 15(d) of the Securities
Exchange Act of 1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of
1934) that is incorporated by reference in the registration statement shall be
deemed to be a new registration statement relating to the securities offered
therein, and the offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

        Insofar as indemnification for liabilities arising under the Securities
Act may be permitted to directors, officers and controlling persons of the
registrant pursuant to provisions described in Item 15, or otherwise, the
registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the
Securities Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrant of expenses incurred or paid by a director, officer or controlling
person of the registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Securities
Act and will be governed by the final adjudication of such issue.



                                     II-3.
<PAGE>   20

                                   SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on March 15, 2000.

EPIMMUNE INC.

By: /S/ Deborah A. Schueren
   -----------------------------------
    Deborah A. Schueren,
    President, Chief Executive Officer
    and Chief Financial Officer


                                POWER OF ATTORNEY

     KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Deborah A. Schueren, his or her true and
lawful attorney-in-fact and agent, with full power of substitution and
resubstitution, for him or her and in his name, place and stead, in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this registration statement, and to file the same, with all exhibits thereto,
and other documents in connection therewith, with the Securities and Exchange
Commission, granting unto said attorneys-in-fact and agents, full power and
authority to do and perform each and every act and thing requisite and necessary
to be done in connection therewith, as fully to all intents and purposes as he
or she might or could do in person, hereby ratifying and confirming all that
said attorney-in-fact and agent or his or her substitutes or substitute, may
lawfully do or cause to be done by virtue hereof.

     Pursuant to the requirements of the Securities Act of 1933, this
registration statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
      Signature                          Title                                       Date
      ---------                          -----                                       ----
<S>                               <C>                                            <C>
  /S/ Deborah A. Schueren         President, Chief Executive Officer             March 15, 2000
- -------------------------------   Chief Financial Officer and Director
Deborah A. Schueren               (Principal Executive Officer,
                                  Principal Financial and Accounting Officer)

  /S/ Howard E. Greene, Jr.       Director                                       March 15, 2000
- ------------------------------
Howard E. Greene, Jr.

  /S/ Nicole Vitullo              Director                                       March 15, 2000
- ------------------------------
Nicole Vitullo

  /S/ Nancy D. Rasmussen          Director                                       March 15, 2000
- ------------------------------
Nancy D. Rasmussen

  /S/ William T. Comer, Ph.D.     Director                                       March 15, 2000
- ------------------------------
William T. Comer, Ph.D.

  /S/ Michael G. Grey             Director                                       March 15, 2000
- ------------------------------
Michael G. Grey
</TABLE>



                                     II-4.
<PAGE>   21

                                  EXHIBIT INDEX


<TABLE>
<CAPTION>
EXHIBIT NO.       DESCRIPTION
- -----------       -----------
<S>               <C>
   4.1            Form of Common Stock Purchase Agreement between the Registrant
                  and each selling stockholder dated February 15, 2000(1).

   5.1            Opinion of Cooley Godward LLP.

  10.1            Reference is made to Exhibit 4.1 above.

  23.1            Consent of Ernst & Young, LLP.

  23.2            Consent of Cooley Godward LLP.  Reference is made to Exhibit
                  5.1.

  24.1            Power of Attorney.  Reference is made to page II-4.
</TABLE>

________________
(1) Filed as an exhibit to the Registrant's Annual Report on Form 10-K for the
    fiscal year ended December 31, 1999.



                                     II-5.

<PAGE>   1

                                                                     EXHIBIT 5.1

                         [Letterhead of Cooley Godward]

March 15, 2000





Epimmune Inc.
5820 Nancy Ridge Drive
San Diego, CA 92121


Ladies and Gentlemen:

        You have requested our opinion with respect to certain matters in
connection with the filing by EPIMMUNE, INC. (the "Company") of a Form S-3
Registration Statement (the "Registration Statement"), including a related
prospectus filed with the Registration Statement (the "Prospectus"), covering
the registration of an aggregate of 1,200,000 shares of Common Stock of the
Company (the "Shares") which were issued to certain purchasers (the
"Purchasers") pursuant to that certain Common Stock Purchase Agreement between
the Company and the Purchasers (the "Agreement").

        In connection with this opinion, we have examined the Registration
Statement and related Prospectus, your Certificate of Incorporation and Bylaws,
as amended, and such other documents, records, certificates, memoranda and other
instruments as we deem necessary as a basis for this opinion. We have assumed
the genuineness and authenticity of all documents submitted to us as originals,
the conformity to originals of all documents submitted to us as copies thereof
and the due execution and delivery of all documents where due execution and
delivery are a prerequisite to the effectiveness thereof.

        In rendering this opinion, we have assumed: the genuineness and
authenticity of all signatures on original documents; the authenticity of all
documents submitted to us as originals; the conformity to originals of all
documents submitted to us as copies; the accuracy, completeness and authenticity
of certificates of public officials; and the due authorization, execution and
delivery of all documents by all of the parties thereto where due authorization,
execution and delivery are prerequisites to the effectiveness of such documents.
We have also assumed that all individuals executing and delivering documents had
the legal capacity to so execute and deliver.

        Our opinion is expressed only with respect to the General Corporation
Law of the State of Delaware.

        On the basis of the foregoing, in reliance thereon, and with the
foregoing qualifications, we are of the opinion that the Shares have been duly
authorized and are validly issued, fully paid and nonassessable.



        We consent to the reference to our firm under the caption "Legal
Matters" in the Prospectus included in the Registration Statement and to the
filing of this opinion as an exhibit to the Registration Statement

        This opinion is intended solely for your benefit and is not to be made
available to or to be relied upon by any other person, firm or entity without
our prior written consent.

Very truly yours,

COOLEY GODWARD LLP

/s/ Frederick T. Muto


Frederick T. Muto





<PAGE>   1
                                                                    EXHIBIT 23.1


               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS

We consent to the reference to our firm under the caption "Experts" in the
Registration Statement (Form S-3) and related Prospectus of Epimmune Inc. for
the registration of 1,200,000 shares of its Common Stock and to the
incorporation by reference therein of our report dated January 21, 2000, except
for Note 11, as to which the date is March 7, 2000, with respect to the
financial statements of Epimmune, Inc. included in its Annual Report (Form 10-K)
for the year ended December 31, 1999, filed with the Securities and Exchange
Commission.

                                         Ernst & Young LLP

San Diego, California
March 16, 2000



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