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FORM 10-Q
 SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
  þ
    
    Quarterly Report Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934
 For the quarterly period ended June 30, 2005,
 or
 o
    
    Transition Period Pursuant to Section 13 or 15(d) of the Securities Exchange Act
of 1934
 For the Transition Period From  to.
 Commission file number 0-19591
 EPIMMUNE INC.
  Delaware
    
    33-0245076(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification No.)
 San Diego, California 92121
 (858) 860-2500
 þ o
 o þ




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EPIMMUNE INC.
 QUARTERLY REPORT
FORM 10-Q
 COVER PAGE
    
    
    1TABLE OF CONTENTS
    
    
    2PART I. FINANCIAL INFORMATIONITEM 1.
    
    Financial StatementsCondensed Balance Sheets as of June 30, 2005 (unaudited) and December 31, 2004
    
    
    3Condensed Statements of Operations (unaudited) for the Three and Six Months Ended June 30, 2005 and 2004
    
    
    4Condensed Statements of Cash Flows (unaudited) for the Six Months Ended June 30, 2005 and 2004
    
    
    5Notes to Condensed Financial Statements (unaudited)
    
    
    6ITEM 2.
    
    Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    10ITEM 3.
    
    Quantitative and Qualitative Disclosures about Market Risk
    
    
    16Risk Factors
    
    
    17ITEM 4.
    
    Controls and Procedures
    
    
    30PART II. OTHER INFORMATIONITEM 1.
    
    Legal Proceedings
    
    
    31ITEM 2.
    
    Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    *ITEM 3.
    
    Defaults upon Senior Securities
    
    
    *ITEM 4.
    
    Submission of Matters to a Vote of Security Holders
    
    
    *ITEM 5.
    
    Other Information
    
    
    *ITEM 6.
    
    Exhibits
    
    
    31SIGNATURE
    
    
    34EXHIBIT 31.1EXHIBIT 31.2EXHIBIT 32.1
  
 * No information provided due to inapplicability of item. 2




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PART I. FINANCIAL INFORMATION
 
 ITEM I. FINANCIAL STATEMENTS
 EPIMMUNE INC.
 
 CONDENSED BALANCE SHEETS
(in thousands, except share and per share data)
 June 30,
    
    December 31,2005
    
    2004(unaudited)ASSETSCurrent assets:Cash and cash equivalents
    
    $
    3,038
    
    
    $
    7,006Accounts receivable
    
    
    758
    
    
    
    2,667Prepaids and other current assets
    
    
    280
    
    
    
    221Total current assets
    
    
    4,076
    
    
    
    9,894Restricted long-term cash
    
    
    354
    
    
    
    354Property and equipment, net
    
    
    899
    
    
    
    1,032Patents and other assets, net
    
    
    3,388
    
    
    
    3,527TOTAL ASSETS
    
    $
    8,717
    
    
    $
    14,807LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable, trade
    
    $
    420
    
    
    $
    1,013Accrued liabilities
    
    
    421
    
    
    
    1,700Deferred contract revenues
    
    
    382
    
    
    
    607Accrued payroll and related expenses
    
    
    192
    
    
    
    161Total current liabilities
    
    
    1,415
    
    
    
    3,481Deferred rent
    
    
    202
    
    
    
    210Stockholders equity:Preferred stock, $.01 par value, 10,000,000 shares authorized,
1,409,288 shares issued and outstanding of Series S and S-1 convertible
preferred stock at June 30, 2005 and December 31, 2004. Liquidation
preference of $10,000,000 at June 30, 2005 and December 31, 2004.
    
    
    14
    
    
    
    14Common stock, $.01 par value, 40,000,000 shares authorized,
16,039,992 shares and 16,011,655 shares issued and outstanding
at June 30, 2005 and December 31, 2004, respectively.
    
    
    160
    
    
    
    160Additional paid-in capital
    
    
    172,952
    
    
    
    172,933Deferred compensation
    
    
    (150
    )
    
    
    (184
    )Accumulated deficit
    
    
    (165,876
    )
    
    
    (161,807
    )Total stockholders equity
    
    
    7,100
    
    
    
    11,116TOTAL LIABILITIES AND STOCKHOLDERS EQUITY
    
    $
    8,717
    
    
    $
    14,807
 See accompanying notes.
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EPIMMUNE INC.
 
 CONDENSED STATEMENTS OF OPERATIONS
(unaudited)
(in thousands, except per share data)
 Three months ended June 30,
    
    Six months ended June 30,2005
    
    2004
    
    2005
    
    2004RevenuesLicense fees and milestones
    
    $
    116
    
    
    $
    127
    
    
    $
    230
    
    
    $
    224Research grants and contract revenue
    
    
    1,132
    
    
    
    1,736
    
    
    
    2,851
    
    
    
    3,190Related party revenue
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    1,026Total revenues
    
    
    1,248
    
    
    
    1,863
    
    
    
    3,081
    
    
    
    4,440Costs and expenses:Research and development
    
    
    1,972
    
    
    
    2,232
    
    
    
    4,658
    
    
    
    4,639General and administrative
    
    
    412
    
    
    
    522
    
    
    
    880
    
    
    
    1,180Transaction costs for business
combination
    
    
    574
    
    
    
    
    
    
    
    1,662
    
    
    
    Total costs and expenses
    
    
    2,958
    
    
    
    2,754
    
    
    
    7,200
    
    
    
    5,819Loss from operations
    
    
    (1,710
    )
    
    
    (891
    )
    
    
    (4,119
    )
    
    
    (1,379
    )Interest income, net
    
    
    22
    
    
    
    22
    
    
    
    58
    
    
    
    26Other expense, net
    
    
    (3
    )
    
    
    (3
    )
    
    
    (8
    )
    
    
    (4
    )Net loss
    
    $
    (1,691
    )
    
    $
    (872
    )
    
    $
    (4,069
    )
    
    $
    (1,357
    )Net loss per share  basic and diluted
    
    $
    (0.11
    )
    
    $
    (0.06
    )
    
    $
    (0.25
    )
    
    $
    (0.09
    )Shares used in computing net loss per
share
    
    
    16,024
    
    
    
    15,782
    
    
    
    16,020
    
    
    
    14,619
 See accompanying notes.
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EPIMMUNE INC.
 
 CONDENSED STATEMENTS OF CASH FLOWS
(unaudited)
(in thousands)
 Six months ended June 30,2005
    
    2004OPERATING ACTIVITIESNet loss
    
    $
    (4,069
    )
    
    $
    (1,357
    )Adjustments to reconcile net loss to net cash used in operating
activities:Depreciation and amortization
    
    
    413
    
    
    
    440Stock-based compensation
    
    
    32
    
    
    
    57Deferred rent
    
    
    (8
    )
    
    
    1Deferred revenue
    
    
    (225
    )
    
    
    (356
    )Write-off of abandoned patents
    
    
    111
    
    
    
    29Change in operating assets and liabilities:Accounts receivable
    
    
    1,909
    
    
    
    51Prepaids and other current assets
    
    
    (59
    )
    
    
    (61
    )Change in restricted cash
    
    
    
    
    
    
    118Accounts payable, trade
    
    
    (593
    )
    
    
    198Accrued liabilities
    
    
    (1,271
    )
    
    
    (395
    )Accrued payroll and related expenses
    
    
    31
    
    
    
    15Net cash used in operating activities
    
    
    (3,729
    )
    
    
    (1,260
    )INVESTING ACTIVITIESPurchase of property and equipment
    
    
    (8
    )
    
    
    (81
    )Patents and other assets
    
    
    (244
    )
    
    
    (434
    )Net cash used in investing activities
    
    
    (252
    )
    
    
    (515
    )FINANCING ACTIVITIESNet proceeds from issuance of common stock
    
    
    13
    
    
    
    5,011Net cash provided by financing activities
    
    
    13
    
    
    
    5,011(Decrease) increase in cash and cash equivalents
    
    
    (3,968
    )
    
    
    3,236Cash and cash equivalents at beginning of year
    
    
    7,006
    
    
    
    6,416Cash and cash equivalents at end of period
    
    $
    3,038
    
    
    $
    9,652SUPPLEMENTAL DISCLOSURE OF CASH FLOW
INFORMATIONInterest paid
    
    $
    1
    
    
    $
    2Reclassification of unvested common shares from liabilities to equity
    
    $
    7
    
    
    $
    89
 See accompanying notes.
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EPIMMUNE INC.
 
 NOTES TO CONDENSED FINANCIAL STATEMENTS
(unaudited)
June 30, 2005
 1. Basis of Presentation
     Earnings per Share
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2005
    
    2004Common stock outstanding
    
    
    16,039,992
    
    
    
    16,004,263Preferred shares, as converted
    
    
    1,787,572
    
    
    
    1,787,572Options outstanding
    
    
    2,390,271
    
    
    
    2,561,931Warrants outstanding
    
    
    2,275,426
    
    
    
    2,275,426Fully diluted shares
    
    
    22,493,261
    
    
    
    22,629,192
 Accounting for Stock-based Compensation Accounting for Stock Issued to Employees
 Accounting for Stock-Based Compensation -
Transition and Disclosure
  Three months ended June 30,
    
    Six months ended June 30,2005
    
    2004
    
    2005
    
    2004Net loss as reported
    
    ($
    1,691,000
    )
    
    ($
    872,000
    )
    
    ($
    4,069,000
    )
    
    ($
    1,357,000
    )Add: stock-based employee
compensation expense included
in reported net loss
    
    
    15,000
    
    
    
    32,000
    
    
    
    30,000
    
    
    
    32,000Deduct: stock-based employee
compensation expense
determined under fair value based
method for all awards
    
    
    (190,000
    )
    
    
    (601,000
    )
    
    
    (479,000
    )
    
    
    (817,000
    )Pro forma net loss
    
    ($
    1,866,000
    )
    
    ($
    1,441,000
    )
    
    ($
    4,518,000
    )
    
    ($
    2,142,000
    )Net loss per share:Basic and diluted  as reported
    
    ($
    0.11
    )
    
    ($
    0.06
    )
    
    ($
    0.25
    )
    
    ($
    0.09
    )Basic and diluted  pro forma
    
    ($
    0.12
    )
    
    ($
    0.09
    )
    
    ($
    0.28
    )
    
    ($
    0.15
    )
 Share-Based
Payments
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2. Proposed Business Combination with IDM S.A.
      8




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3. Subsequent Events
  9




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ITEM 2.
    
    MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS
  ® ®
   Critical Accounting Policies
  Revenue Recognition
 Revenue Recognition.
 10




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Patents
  Investment Policy
  Results of Operations
 Three months ended June 30, 2005, as compared with three months ended June 30, 2004.
   11




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Six months ended June 30, 2005 as compared with six months ended June 30, 2004.
    12




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Three months ended June 30,
    
    Six months ended June 30,2005
    
    2004
    
    2005
    
    2004Cancer Programs
    
    $
    731,000
    
    
    $
    366,000
    
    
    $
    1,673,000
    
    
    $
    818,000HIV Programs
    
    
    642,000
    
    
    
    1,123,000
    
    
    
    1,572,000
    
    
    
    2,319,000Collaborations
    
    
    270,000
    
    
    
    359,000
    
    
    
    674,000
    
    
    
    711,000Other Programs
    
    
    329,000
    
    
    
    384,000
    
    
    
    739,000
    
    
    
    791,000$
    1,972,000
    
    
    $
    2,232,000
    
    
    $
    4,658,000
    
    
    $
    4,639,000
  Three months ended June 30,
    
    Six months ended June 30,2005
    
    2004
    
    2005
    
    2004Cancer Programs
    
    $
    160,000
    
    
    $
    156,000
    
    
    $
    343,000
    
    
    $
    272,000HIV Programs
    
    
    631,000
    
    
    
    938,000
    
    
    
    1,567,000
    
    
    
    2,087,000Collaborations
    
    
    270,000
    
    
    
    359,000
    
    
    
    674,000
    
    
    
    711,000Other Programs
    
    
    107,000
    
    
    
    173,000
    
    
    
    216,000
    
    
    
    366,000$
    1,168,000
    
    
    $
    1,626,000
    
    
    $
    2,800,000
    
    
    $
    3,436,000
     Liquidity and Capital Resources
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
    
    whether our proposed transaction with IDM is successfully completed;
    
    whether we are able to secure additional financing on favorable terms, or at all;
    
    the costs associated with our ongoing Phase I/II clinical trial for our vaccine
targeting HIV, which began in September 2002, including the status of our contract with the
NIH;
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
    
    the costs associated with our Phase II clinical trial for our vaccine targeting
non-small cell lung cancer, or NSCLC, which began in December 2004;
    
    progress with other preclinical testing and clinical trials in the future;
    
    our ability to establish and maintain collaboration and license agreements and any
government contracts and grants;
    
    the actual revenue we receive under our collaboration and license agreements;
    
    the actual costs we incur under our research collaboration with Bavarian Nordic;
    
    the time and costs involved in obtaining regulatory approvals;
    
    the costs involved in filing, prosecuting, enforcing and defending patent claims and any
other proprietary rights;
    
    competing technological and market developments;
    
    changes in our existing research relationships;
    
    continued scientific progress in our drug discovery programs; and
    
    the magnitude of our drug discovery and development programs.
  15




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ITEM 3.
    
    QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
  16




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RISK FACTORS
 We wish to caution readers that the following important factors, among others, in some cases have
affected our results and in the future could cause our actual results and needs to vary materially
from forward-looking statements made from time to time by us on the basis of managements
then-current expectations. The business in which we are engaged is rapidly changing and competitive
and involves a high degree of risk.
 Our substantial additional financing requirements and limited access to financing, which will
likely be even more limited in the absence of the proposed combination with IDM, may adversely
affect our ability to develop products and fund our operations.
  
    
    whether our proposed transaction with IDM is successfully completed;
    
    whether we are able to secure additional financing on favorable terms, or at all;
    
    the costs associated with our ongoing Phase I/II clinical trial for our vaccine
targeting HIV, which began in September 2002, including the status of our contract with the
NIH;
    
    the costs associated with our Phase II clinical trial for our vaccine targeting NSCLC,
which began in December 2004;
    
    progress with other preclinical testing and clinical trials in the future;
    
    our ability to establish and maintain collaboration and license agreements and any
government contracts and grants;
    
    the actual revenue we receive under our collaboration and license agreements;
    
    the actual costs we incur under our research collaboration with Bavarian Nordic;
    
    the time and costs involved in obtaining regulatory approvals;
    
    the costs involved in filing, prosecuting, enforcing and defending patent claims and any
other proprietary rights;
    
    competing technological and market developments;
    
    changes in our existing research relationships;
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
    
    continued scientific progress in our drug discovery programs; and
    
    the magnitude of our drug discovery and development programs.
  We presently do not meet all of The Nasdaq National Markets continued listing requirements and we
may be delisted, which could reduce the liquidity of our common stock and adversely affect our
ability to raise additional necessary capital.
   18




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The process of developing therapeutic products requires significant research and development,
preclinical testing and clinical trials, all of which are extremely expensive and time-consuming
and may not result in a commercial product.
  
    
    the results of preclinical studies may be inconclusive, or they may not be
indicative of results that will be obtained in human clinical trials;
    
    after reviewing test results, we or our collaborators may abandon projects that
we might previously have believed to be promising;
    
    we, our collaborators or regulators may suspend or terminate clinical trials if
the participating subjects or patients are being exposed to unacceptable health risks;
    
    we may have to delay clinical trials as a result of scheduling conflicts with
participating clinicians and clinical institutions, or difficulties in identifying and
enrolling patients who meet trial eligibility criteria;
    
    safety and efficacy results attained in early human clinical trials may not be
indicative of results that are obtained in later clinical trials; and
    
    the effects our vaccine candidates have may not be the desired effects or may
include undesirable side effects or other characteristics that preclude regulatory approval
or limit their commercial use if ever approved.
  Some of our programs are funded by the U.S. government and the government may not allocate funds
for these programs in future fiscal years.
  Our history of operating losses and our expectations of continuing losses may hurt our ability to
reach profitability or continue operations.
  19




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We are at an early stage of development, and we may experience delays and other problems in
entering clinical trials.
  Unexpected side effects or other characteristics of our technology may delay or otherwise hurt the
development of our vaccine candidates.
  There are no therapeutic vaccines that have been approved for use by the FDA and our vaccines may
not work, which would prevent us from ever becoming profitable.
  Adverse publicity regarding the safety or side effects of the technology approach or products of
others could reduce our revenues and cause our stock price to fall.
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Our research and development programs may not yield effective product candidates, which could
prevent us from developing our products.
  We may not identify the correct epitopes and, therefore, not develop a safe or effective vaccine.
  Our business is based on a novel technology, which has not been used in any commercial drugs, and
may not work.
  Our failure to obtain issued patents and, consequently, to protect our proprietary technology,
could hurt our competitive position.
   
    
    the pending patent applications we have filed or to which we have exclusive rights may
not result in issued patents or may take longer than we expect to result in issued patents;
    
    the allowed claims of any patents that issue may not provide meaningful protection;
    
    we may be unable to develop additional proprietary technologies that are patentable;
    
    the patents licensed or issued to us may not provide a competitive advantage;
    
    other companies may challenge patents licensed or issued to us;
    
    disputes may arise regarding inventions and corresponding ownership rights in inventions
and know-how resulting from the joint creation or use of intellectual property by us, our
licensors, or
collaborators; and
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
    
    other companies may design around our patented technologies.
 Our competitors may develop products that are more effective and that render our potential products
obsolete.
  If we are unable to compete effectively in the highly competitive biotechnology industry, our
business will fail.
  
    
    pharmaceutical companies;
    
    chemical companies;
    
    specialized biotechnology companies;
    
    academic institutions; and
    
    research organizations.
  PhRMA PhRMA
 Litigation regarding intellectual property rights owned or used by us may be costly and
time-consuming.
  22




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
    
    assert against others or defend ourselves against claims of infringement;
    
    enforce patents in our portfolio owned by us or licensed from another party;
    
    protect our trade secrets or know-how; or
    
    determine the enforceability, scope and validity of the proprietary rights of ours or others.
 If we cannot obtain and maintain strategic collaborations on acceptable terms in the future, we may
not be able to develop products in markets where it would be too costly or complex to do so on our
own.
  If our collaboration or license arrangements are unsuccessful, our revenues and product development
may be limited.
  
    
    collaborators and licensees may not pursue further development and commercialization of
potential products resulting from our collaborations or may elect not to renew research and
development programs;
    
    collaborators and licensees may delay clinical trials, under-fund a clinical trial
program, stop a clinical trial or abandon a product candidate, repeat or conduct new
clinical trials or require new formulation of a product candidate for clinical testing;
    
    expected revenue might not be generated because milestones may not be achieved and
product candidates may not be developed;
    
    collaborators and licensees could independently develop, or develop with third parties,
products that could compete with our future products;
    
    the terms of our contracts with our current or future collaborators and licensees may
not be
favorable to us in the future;
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
    
    a collaborator or licensee with marketing and distribution rights to one or more of our
products may not commit enough resources to the marketing and distribution of our products,
limiting our potential revenues from the commercialization of a product;
    
    disputes may arise delaying or terminating the research, development or
commercialization of our product candidates, or result in significant and costly litigation
or arbitration; and
    
    collaborations and licensee arrangements may be terminated and we will experience
increased operating expenses and capital requirements if we elect to pursue further
development of the product candidate.
 We may not be able to obtain licenses to technology that is necessary for us to develop products.
  We may not be able to commercialize our products under development if they infringe claims in
existing patents or patents that have not yet issued, and this would materially harm our ability to
operate.
  If we, or our collaborators cannot cost-effectively manufacture vaccines in commercial quantities
and for clinical trials in compliance with regulatory requirements, we, or our collaborators may
not be able to successfully commercialize the products.
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If we do not successfully develop and commercialize our products, we may never generate significant
revenues or become profitable
  The lengthy approval process and uncertainty of government regulatory requirements may impair our
ability to develop, manufacture and sell any vaccines.
   
    
    fines and penalties;
    
    injunctions;
    
    seizure of products;
    
    total or partial suspension of product marketing;
    
    failure of the government to grant a new drug application;
    
    withdrawal of marketing approvals; and
    
    criminal prosecution.
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The approval process outside the United States is also uncertain and may limit our ability to
develop, manufacture and sell our products internationally.
  Even if we obtain regulatory approval, we may be required to perform additional clinical trials or
change the labeling of our products if we, or others identify side effects after our products are
on the market, which could harm sales of the affected products.
  
    
    regulatory approval may be withdrawn;
    
    reformulation of our products, additional clinical trials, changes in labeling of our
products or changes to or re-approvals of our manufacturing facilities may be required;
    
    sales of the affected products may drop significantly;
    
    our reputation in the marketplace may suffer; and
    
    lawsuits, including costly and lengthy class action suits, may be brought against us.
  If we are unable to protect our trade secrets, we may be unable to protect from competitors our
interests in proprietary know-how that is not patentable or for which we have elected not to seek
patent protection.
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If we lose our key scientific and management personnel or are unable to attract and retain
qualified personnel, it could delay or hurt our epitope identification and vaccine development
efforts.
  We out-license technology outside of our core area of focus, and these licensees may not develop
any products using our technology, which may limit our revenue.
  Some of our programs are funded by the U.S. government and, therefore, the government may have
rights to certain of our technology and could require us to grant licenses of our technology to
third parties.
  Adverse determinations concerning product pricing, reimbursement and related matters could prevent
us from successfully commercializing products and impair our ability to generate revenues.
  Product liability risks may expose us to significant liability that could cause us to incur
significant costs or cease developing our products.
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Our use of hazardous materials could expose us to significant costs.
  The subordination of our common stock to our preferred stock could hurt common stockholders and,
upon conversion, our preferred stock will further dilute our holders of common stock.
  The volatility of the price of our common stock may hurt our stockholders.
  
    
    whether we are able to secure additional financing on favorable terms, or at all;
    
    announcements of technological innovations or new commercial vaccines or other
therapeutic products by us or others;
    
    governmental regulation that affects the biotechnology and pharmaceutical industries;
    
    developments in patent or other proprietary rights;
    
    receipt of funding under collaboration and license agreements and government grants;
    
    developments in, or termination of, our relationships with our collaborators and licensees;
    
    public concern as to the clinical results and/or the safety of drugs developed by us or
others; and
    
    announcements related to the sale of our stock.
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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.
  Compliance with the Sarbanes-Oxley Act of 2002 and other changing regulations of corporate
governance and public disclosure may result in additional expenses.
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ITEM 4. CONTROLS AND PROCEDURES
     30




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PART II. OTHER INFORMATION
 
 ITEM 1. LEGAL PROCEEDINGS
  
 ITEM 6. EXHIBITS
 Exhibit 3.1
    
    Amended and Restated Certificate of Incorporation filed with the
Secretary of State of Delaware on December 2, 1991.(1)Exhibit 3.2
    
    Certificate of Designation of Series A Junior Participating Preferred
Stock filed with the Secretary of State of Delaware on April 2, 1993.(2)Exhibit 3.3
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 5, 1995.(3)Exhibit 3.4
    
    Certificate of Increase of Series A Junior Participating Preferred Stock
filed with the Secretary of State of Delaware on July 5, 1995.Exhibit 3.5
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 2, 1998.(4)Exhibit 3.6
    
    Certificate of Increase of Series A Junior Participating Preferred Stock
filed with the Secretary of State of Delaware on July 2, 1998.(4)Exhibit 3.7
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on November 12,
1998.(5)Exhibit 3.8
    
    Certificate of Designations of the Series S and Series S-1 Preferred
Stock filed with the Secretary of State of Delaware on June 29, 1999.(6)Exhibit 3.9
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 1, 1999.(7)Exhibit 3.10
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on September 23,
1999.(8)Exhibit 3.11
    
    Certificate of Decrease of Series A Junior Participating Preferred
Stock filed with the Secretary of State of Delaware on September 23, 1999.(8)Exhibit 3.12
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on June 17,
2004.(9)Exhibit 3.13
    
    Amended and Restated Bylaws of the Registrant.(10)Exhibit 4.1
    
    Reference is made to Exhibits 3.1 through 3.13.
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Exhibit 4.2
    
    Specimen certificate of the common stock.(1)Exhibit 10.1
    
    Share Exchange Agreement dated March 15, 2005 among Epimmune Inc. and
certain shareholders of IDM S.A.(11)Exhibit 10.3
    
    Amendment No. 1 (to the Share Exchange Agreement) dated March 15, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(11)Exhibit 10.4
    
    Voting Agreement dated March 15, 2005 among Epimmune Inc., Hélène
Ploix, as the Shareholder Representative, and certain stockholders of Epimmune
Inc.(11)Exhibit 10.5
    
    Preferred Exchange Agreement dated March 15, 2005.(11)Exhibit 10.6
    
    Employment Agreement with Emile Loria, M.D. dated March 17, 2005.(11)Exhibit 10.7
    
    Employment Agreement with Mark Newman, Ph.D. dated March 17, 2005.(11)Exhibit 10.8
    
    Employment Agreement with Robert De Vaere dated March 17, 2005.(11)Exhibit 10.9
    
    Amended and Restated Preferred Exchange Agreement dated April 12,
2005.(12)Exhibit 10.10
    
    Amendment No. 2 (to the Share Exchange Agreement) dated April 21, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(13)Exhibit 10.11
    
    Amendment No. 3 (to the Share Exchange Agreement) dated May 31, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(14)Exhibit 10.11
    
    Amendment No. 4 (to the Share Exchange Agreement) dated June 30, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(15)Exhibit 31.1
    
    Certification of Principal Executive Officer pursuant to Rule 13a-14(a)
or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.Exhibit 31.2
    
    Certification of Principal Financial Officer pursuant to Rule 13a-14(a)
or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.Exhibit 32.1
    
    Certification pursuant to Rule 13a-14(b) or Rule 15d-14(b) of the
Securities Exchange Act of 1934, as amended, and Section 1350 of Chapter 63 of
Title 18 of the United States Code (18 U.S.C. § 1350).
 
 (1)
    
    Incorporated by reference to the Companys Form S-1
Registration Statement and Amendments thereto filed with Securities and
Exchange Commission (the SEC) (File No. 33-43356).(2)
    
    Incorporated by reference to the Companys Form 8-K, filed with
the SEC on March 22, 1993. 32




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(3)
    
    Incorporated by reference to the Companys Annual Report on
Form 10-K for the fiscal year ended December 31, 1994, filed with the SEC on
March 31, 1995.(4)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended June 30, 1998, filed with the SEC on
August 14, 1998.(5)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended September 30, 1998, filed with the SEC
on November 16, 1998.(6)
    
    Incorporated by reference to the Companys Form 8-K, filed with
the SEC on July 16, 1999.(7)
    
    Incorporated by reference to the Companys Definitive Proxy
Statement, filed with the SEC on Form DEF 14A on July 28, 1999.(8)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended September 30, 1999, filed with the SEC
on November 15, 1999.(9)
    
    Incorporated by reference to the Companys Registration
Statement on Form S-8, filed with the SEC on July 2, 2004.(10)
    
    Incorporated by reference to the Companys Annual Report on
Form 10-K for the fiscal year ended December 31, 2001, filed with the SEC on
March 29, 2002.(11)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on March 18, 2005.(12)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on April 18, 2005.(13)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on April 22, 2005.(14)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on June 2, 2005.(15)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on July 7, 2005. 33




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EPIMMUNE INC.
 
 SIGNATURES
  EPIMMUNE INC.Dated: August 9, 2005
    By:
    /s/ Emile LoriaEmile Loria, M.D.President, Chief Executive Officer and Director
(Principal Executive Officer) Dated: August 9, 2005
    By:
    /s/ Robert De VaereRobert De VaereVice President, Finance and Administration,
Chief Financial Officer and Secretary
(Principal Financial and Accounting Officer) 34