##### Table of Contents



U.S. SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-K/A
 Amendment No. 1
 (Mark One)
 þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2005
 OR
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934
 For the transition period fromto
 Commission file number: 0-21863
 EPIX PHARMACEUTICALS, INC.
  Delaware
(State or other jurisdiction
of incorporation or organization)
    
    04-3030815
(I.R.S. Employer Identification No.)161 First Street, Cambridge, Massachusetts
(Address of principal executive offices)
    
    02142
(Zip Code)
 (617) 250-6000
 NONE
  Common Stock, $.01 Par Value Per Share
 (Title of class)
 o þ
 o þ
 þ o
 þ
  o þ o
 o þ




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EXPLANATORY NOTE
  2




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TABLE OF CONTENTS  PART IIIITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANTITEM 11. EXECUTIVE COMPENSATIONITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERSITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONSITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICESPART IVITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULESSIGNATURESEXHIBIT INDEXEX-31.1 SECTION 302 CERTIFICATION OF MICHAEL J. ASTRUEEX-31.2 SECTION 302 CERTIFICATION OF ROBERT B. PELLETIEREX-32 SECTION 906 CERTIFICATION OF MICHAEL J. ASTRUE AND ROBERT B. PELLETIER    Table of Contents  
 PART III
 
 ITEM 10.     DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT
 (a) Identification of Directors
    Name
    
    Age
    
    Position with the CompanyChristopher F.O. Gabrieli
    
    46
    
    Chairman of the BoardMichael Gilman, Ph.D.
    
    51
    
    DirectorMark Leuchtenberger
    
    49
    
    DirectorGregory D. Phelps
    
    57
    
    DirectorPeter Wirth, Esq.
    
    55
    
    Director
 Christopher F.O. Gabrieli
Chairman of the Board
 Mr. Gabrieli
 Michael Gilman, Ph.D.
Director
 Dr. Gilman
 3




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##### Table of Contents



Mark Leuchtenberger
Director
 Mr. Leuchtenberger
 Gregory D. Phelps
Director
 Mr. Phelps
 Peter Wirth, Esq.
Director
 Mr. Wirth
 (b) Identification of Executive Officers
  Name
    
    Age
    
    Position with the CompanyMichael J. Astrue
    
    49
    
    Interim Chief Executive OfficerAndrew C.G.
Uprichard, M.D.
    
    49
    
    President and Chief Operating OfficerRobert Pelletier, CPA
    
    53
    
    Executive Director of Finance and
Principal Accounting Officer
 Michael J. Astrue
Interim Chief Executive Officer
 Mr. Astrue
 Andrew C.G. Uprichard, M.D.
President and Chief Operating Officer
 Dr. Uprichard
 4




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##### Table of Contents



Robert Pelletier, CPA
Executive Director of Finance and Principal Accounting Officer
 Mr. Pelletier
 (c) Identification of Certain Significant Employees.
  (d) Family Relationships.
  (e) Business Experience.
   (f) Involvement in Certain Legal Proceedings.
  (g) Promoters and Control Persons.
  (h) and (i) Audit Committee and Audit Committee Financial Expert.
  5




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##### Table of Contents



(j) Procedures for Stockholder Nominations to our Board of Directors.
  Code of Conduct and Ethics
  Section 16(a) Beneficial Ownership Reporting Compliance
  
 ITEM 11.     EXECUTIVE COMPENSATION
 Summary Compensation Table
  Long-TermCompensationAnnual Compensation
    
    
    AwardsOther
    
    
    SecuritiesAnnual
    
    
    Underlying
    
    
    All OtherName and Principal Position
    
    Year
    
    
    Salary
    
    
    Bonus (1)
    
    
    Compensation
    
    
    Options (#)
    
    
    CompensationMichael J. Astrue (2)
    
    
    2005
    
    
    $
    112,308
    
    
    $
    
    
    
    
    
    
    
    
    
    
    
    $
    Interim
Chief Executive Officer
    
    
    2004
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    2003
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Andrew C.G. Uprichard, M.D.
    
    
    2005
    
    
    
    309,872
    
    
    
    14,002
    
    
    
    
    
    
    
    52,500
    
    
    
    2,803
    (3)President and
    
    
    2004
    
    
    
    137,308
    
    
    
    54,878
    (4)
    
    
    
    
    
    
    175,000
    
    
    
    2,677
    (3)Chief Operating Officer
    
    
    2003
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Robert Pelletier, CPA
    
    
    2005
    
    
    
    175,188
    
    
    
    25,835
    
    
    
    
    
    
    
    23,281
    
    
    
    4,591
    (3)Executive Director of Finance
    
    
    2004
    
    
    
    157,961
    
    
    
    34,609
    
    
    
    
    
    
    
    7,288
    
    
    
    4,078
    (3)and Principal Accounting
Officer
    
    
    2003
    
    
    
    124,038
    
    
    
    40,050
    
    
    
    
    
    
    
    40,000
    
    
    
    3,539
    (3)Michael D. Webb
    
    
    2005
    
    
    
    356,517
    (6)
    
    
    
    
    
    
    
    
    
    
    50,000
    
    
    
    6,300
    (5)Former Chief Executive Officer
    
    
    2004
    
    
    
    334,286
    
    
    
    49,125
    
    
    
    
    
    
    
    62,500
    
    
    
    8,620
    (5)2003
    
    
    
    313,351
    
    
    
    137,722
    
    
    
    
    
    
    
    66,500
    
    
    
    6,225
    (5)Peyton J. Marshall, Ph.D. (7)
    
    
    2005
    
    
    
    129,635
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    4,972
    (3)Former Senior Vice President
    
    
    2004
    
    
    
    238,933
    
    
    
    36,114
    
    
    
    
    
    
    
    35,625
    
    
    
    4,883
    (3)and Chief Financial Officer
    
    
    2003
    
    
    
    225,000
    
    
    
    80,156
    
    
    
    
    
    
    
    
    
    
    
    3,404
    (3)
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(1)
    
    Bonuses were earned in the year indicated and are generally paid in the subsequent year.(2)
    
    Mr. Astrue intends to resign as Interim Chief Executive Officer in May 2006.(3)
    
    Consists of matching 401(k) contributions.(4)
    
    Dr. Uprichard joined the Company in July 2004 and the bonus compensation amount includes a
$20,000 signing bonus.(5)
    
    Consists of matching 401(k) contributions of $6,300, $6,000 and $6,000 in 2005, 2004 and 2003,
respectively, and life insurance premiums paid by us on behalf of Mr. Webb on a policy for the
benefit of Mr. Webb of $2,620 in 2004 and $225 in 2003.(6)
    
    Effective September 14, 2005, Mr. Webb resigned as Chief Executive Officer and member of the
board of directors. This figure represents $254,435 earned by Mr. Webb as Chief Executive Officer
through September 14, 2005, and $102,082 in fees and expense reimbursements, paid to Mr. Webb in
connection with consulting services he provided to us from September 14, 2005 through December 31,
2005.(7)
    
    Effective July 1, 2005, Mr. Marshall resigned as Senior Vice President, Finance and
Administration and Chief Financial Officer. Employment and Severance Agreements
   7




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Option Grants in Our Last Fiscal Year
  Individual Grants (1)Number of
    
    
    % of Total
    
    
    
    
    
    
    
    
    
    
    Potential RealizableSecurities
    
    
    Options
    
    
    Exercise
    
    
    
    
    
    
    Value at Assumed Annual RatesUnderlying
    
    
    Granted to
    
    
    or Base
    
    
    
    
    
    
    of Stock Price AppreciationOptions
    
    
    Employees in
    
    
    Price
    
    
    Expiration
    
    
    for Option Term (2)Name
    
    Granted (1)
    
    
    Fiscal Year
    
    
    ($/Share)
    
    
    Date
    
    
    5%
    
    
    10%Michael J. Astrue
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Andrew C.G. Uprichard,
M.D.
    
    
    52,500
    
    
    
    8.83
    %
    
    $
    7.15
    
    
    
    3/17/2015
    
    
    $
    236,071
    
    
    $
    598,251Robert Pelletier, CPA
    
    
    8,281
    
    
    
    1.39
    %
    
    
    7.15
    
    
    
    3/17/2015
    
    
    
    37,236
    
    
    
    94,36415,000
    
    
    
    2.52
    %
    
    
    8.69
    
    
    
    6/24/2015
    
    
    
    81,976
    
    
    
    207,744Michael D. Webb (3)
    
    
    50,000
    
    
    
    8.41
    %
    
    
    7.15
    
    
    
    3/17/2015
    
    
    
    224,830
    
    
    
    569,763Peyton J. Marshall, Ph.D.
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
 
 (1)
    
    These options were granted under our Amended and Restated 1992 Equity Incentive Plan, or the
Equity Plan, at an exercise price equal to the fair market value of our common stock at the date of
grant. All of the options granted vest in five equal annual installments and began vesting on March
17, 2006 except for one of the grants to Mr. Pelletier which begins vesting on June 24, 2006. With
the exception of Mr. Pelletiers option for 8,281 shares, which is an incentive stock option, each of the
options cited above consists of a combination of non-qualified stock options and incentive stock
options as follows: Dr. Uprichards option consists of 41,992 non-qualified stock options and
10,508 incentive stock options; Mr. Pelletiers grant of 15,000 options consists of 7,907
non-qualified stock options and 7,093 incentive stock options, and Mr. Webbs option consists of
39,998 non-qualified options and 10,002 incentive stock options. The options are not transferable,
except by will or by laws of descent and distribution. The
post-termination exercise period for exercisable options is generally three months. If an
acquisition event also 8




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constitutes a change in control, or, if there is a change in control that
does not also constitute an acquisition event, unless provided to the contrary in an agreement
between us and the optionee, the options or such assumed or substituted options shall become
immediately exercisable in full, if within 18 months of the change in control, a termination
event (as defined below) with respect to the optionee occurs. If the acquiring or succeeding
corporation does not agree to assume or issue substitute options for the options issued by us, the
options issued by us shall become immediately exercisable in full. If the acquisition event
involves a cash payment to our stockholders, the optionee shall receive a cash payment for each
option equal to the amount by which the price to be paid in the acquisition exceeds the option
exercise price.An acquisition event means (a) any merger or consolidation of us with or into another entity as a
result of which our common stock is converted into or exchanged for the right to receive cash,
securities or other property; (b) any exchange of our shares for cash, securities or other property
pursuant to a statutory share exchange transaction; (c) any sale or exchange of all or
substantially all of our assets in one transaction or in a series of transactions; or (d) a
reorganization or liquidation of us.A change in control means either (a) (i) a merger or consolidation of us, whether or not approved
by the board of directors, other than a merger or consolidation in which our voting securities
continue to represent at least 50% of the total voting power represented by our voting securities
of the surviving entity outstanding immediately after the merger or consolidation, or (ii) the
approval by our stockholders of an agreement for the sale or disposition by us of all or
substantially all of our assets; or (b) any person becoming the beneficial owner of our securities
representing 50% or more of our total outstanding voting power (excluding us or our affiliates or
any of our employee benefit plans) pursuant to a transaction or a series of related transactions
which the board of directors does not approve.A termination event means the termination of the optionees employment (a) by us or the acquiring
or succeeding corporation without cause; or (b) by the optionee upon written notice given promptly
after our or the acquiring or succeeding corporations taking any of the following actions, which
actions shall not have been cured within a 30-day period following such notice: (i) the principal
place of the performance of the optionees responsibilities, or the Principal Location, is changed
to a location outside of a 30 mile radius from the Principal Location immediately prior to the
change in control; (ii) there is a material reduction in the optionees salary; or (iii) there is a
material diminution in the scope of the optionees responsibilities without the optionees
agreement or without cause.(2)
    
    In accordance with the rules of the Securities and Exchange Commission, we show in these
columns the potential realizable value over the term of the option (the period from the grant date
to the expiration date). We calculate this assuming that the fair market value of our common stock
on the date of grant appreciates at the indicated annual rate, 5% and 10% compounded annually, for
the entire term of the option and that the option is exercised and sold on the last day of its term
for the appreciated stock price. These amounts are based on assumed rates of appreciation and do
not represent an estimate of our future stock price. Actual gains, if any, on stock option
exercises will depend on the future performance of our common stock, the optionholders continued
employment with us through the option exercise period, and the date on which the option is
exercised.(3)
    
    Effective September 14, 2005, Mr. Webb resigned as Chief Executive Officer and member of the
board of directors, but continued to provide consulting services to us through December 31, 2005.
In connection with his departure these options have now been cancelled. Aggregated Option Exercises in Last Fiscal Year and Fiscal Year-End Option Values
  9




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Shares
    
    
    
    
    
    
    Number of Securities Underlying
    
    
    Value of the UnexercisedAcquired
    
    
    
    
    
    Unexercised Options
    
    
    In-The-Money Optionson
    
    
    Value
    
    
    at Fiscal Year-End
    
    
    at Fiscal Year-EndName
    
    Exercise
    
    

Realized (1)
    
    
    Exercisable
    
    
    Unexercisable
    
    
    Exercisable
    
    
    UnexercisableMichael J. Astrue
    
    
    
    
    
    $
    
    
    
    
    
    
    
    
    
    
    
    $
    
    
    
    $
    Andrew C.G. Uprichard,
M.D.
    
    
    
    
    
    
    
    
    
    
    35,000
    
    
    
    192,500
    
    
    
    
    
    
    
    Robert Pelletier, CPA
    
    
    
    
    
    
    
    
    
    
    9,457
    
    
    
    53,112
    
    
    
    
    
    
    
    Michael D. Webb
    
    
    30,000
    
    
    
    66,600
    
    
    
    467,794
    
    
    
    
    
    
    
    
    
    
    
    Peyton J. Marshall, Ph.D.
    
    
    20,500
    
    
    
    52,682
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
 
 (1)
    
    Amounts shown in this column do not necessarily represent actual value realized from the sale
of the shares acquired upon exercise of the option because in many cases the shares are not sold on
exercise but continue to be held by the executive officer exercising the option. The amounts shown
represent the difference between the option exercise price and the market price on the date of
exercise, which is the amount that would have been realized if the shares had been sold immediately
upon exercise. Compensation of Our Directors
  Compensation Committee Interlocks and Insider Participation
  10




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ITEM 12.
    
    SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER
MATTERS Principal Stockholders
  Shares Beneficially OwnedName and Address **
    
    Number
    
    
    PercentPrescott Group Capital Management, L.L.C. (1)
    
    
    1,712,334
    
    
    
    7.35
    %1924 South Utica, Suite 1120Tulsa, Oklahoma 74104-6529Michael J. Astrue
    
    
    
    
    
    
    
    *Andrew C.G. Uprichard, M.D. (2)
    
    
    45,500
    
    
    
    
    *Robert Pelletier, CPA (3)
    
    
    22,131
    
    
    
    
    *Michael D. Webb (4)
    
    
    32,666
    
    
    
    
    *Peyton J. Marshall, Ph.D. (5)
    
    
    64,000
    
    
    
    
    *Christopher F.O. Gabrieli (6)
    
    
    217,450
    
    
    
    
    *Gregory D. Phelps (7)
    
    
    8,334
    
    
    
    
    *Mark Leuchtenberger (8)
    
    
    8,334
    
    
    
    
    *Peter Wirth, Esq. (9)
    
    
    55,000
    
    
    
    
    *Michael Gilman, Ph.D.
    
    
    
    
    
    
    
    *All current directors and executive officers
as a group (8 persons) (10)
    
    
    356,749
    
    
    
    1.53
    %
 
 *
    
    Represents beneficial ownership of less than 1% of the outstanding shares of our common
stock.**
    
    Addresses are given for beneficial owners of more than 5% of our outstanding common stock
only.(1)
    
    Includes (a) 1,630,334 shares of our common stock held by the Prescott Group Aggressive Small
Cap Master Fund, G.P., of which Prescott Group Aggressive Small Cap,
L.P. and Prescott Group Aggressive Small Cap II, L.P. are general partners, and (b) 82,000 shares of our common stock held
by Phil Frohlich. Prescott Group Capital Management, L.L.C. serves as the general partner of
Prescott Group Aggressive Small Cap, L.P. and Prescott Group 11




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Aggressive Small Cap II, L.P. and may
direct Prescott Group Aggressive Small Cap, L.P. and Prescott Group Aggressive Small Cap II, L.P.,
the general partners of Prescott Group Aggressive Small Cap Master Fund, G.P., in connection with
the voting and disposition of the 1,630,334 shares of our common stock held by Prescott Group
Aggressive Small Cap Master Fund, G.P. As principal of Prescott Group Capital Management, L.L.C.,
Mr. Frohlich may direct the vote and disposition of the 1,630,334 shares of our common stock held
by Prescott Group Aggressive Small Cap Master Fund, G.P. and the 82,000 shares of our common stock
held by himself, individually. This information is based solely on a Schedule 13G filed by Prescott
Group Capital Management, L.L.C. with the Securities and Exchange Commission on January 30, 2006,
which reported ownership as of October 10, 2005.(2)
    
    Represents shares of our common stock subject to options exercisable by Dr. Uprichard within
the 60-day period following March 31, 2006.(3)
    
    Consists of 1,561 shares of our common stock owned of record by and 20,570 shares of our common
stock subject to options exercisable by Mr. Pelletier within the 60-day period following March 31,
2006.(4)
    
    Consists of 14,166 shares of our common stock owned of record by Mr. Webb and 18,500 shares of
our common stock held by Mr. Webbs wife as to which Mr. Webb disclaims beneficial ownership.
Effective September 14, 2005, Mr. Webb resigned as Chief Executive Officer and member of the board
of directors, but continued to serve as a consultant to us through December 31, 2005.(5)
    
    Represents 64,000 shares of our common stock owned of record by Mr. Marshall. Effective July 1,
2005, Mr. Marshall resigned as Senior Vice President, Finance and Administration and Chief
Financial Officer.(6)
    
    Consists of 152,450 shares of our common stock owned of record by Mr. Gabrieli and 65,000
shares of our common stock subject to options exercisable by Mr. Gabrieli within the 60-day period
following March 31, 2006.(7)
    
    Represents shares of our common stock subject to options exercisable by Mr. Phelps within the
60-day period following March 31, 2006.(8)
    
    Represents shares of our common stock subject to options exercisable by Mr. Leuchtenberger
within the 60-day period following March 31, 2006.(9)
    
    Represents shares of our common stock subject to options exercisable by Mr. Wirth within the
60-day period following March 31, 2006.(10)
    
    Includes 202,738 shares of our common stock subject to options exercisable within the 60-day
period following March 31, 2006. See also footnotes (2), (3) and (6) through (9) above. Equity Compensation Plan Information
  Number of SecuritiesRemaining Available forFuture Issuance UnderEquity CompensationPlansNumber of Securities to be
    
    
    Weighted-Average
    
    
    (Excluding SecuritiesIssued Upon Exercise of
    
    
    Exercise Price of
    
    
    Reflected in the FirstPlan Category
    
    Outstanding Options
    
    

Outstanding Options
    
    
    Column)Equity Compensation
Plans
    
    
    3,271,909
    
    
    $
    11.39
    
    
    1,519,165Approved by
Securityholders (1)
    
    
    
    
    
    
    
    
    
    (2)(3)(4)(5)Equity Compensation
Plans
not Approved by
Securityholders
    
    
    N/A
    
    
    
    N/A
    
    

N/ATotal
    
    
    3,271,909
    
    
    $
    11.39
    
    
    1,519,165
 12




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##### Table of Contents



(1)
    
    These plans consist of our Amended and Restated 1992 Equity Incentive Plan, or the Equity Plan,
the Amended and Restated 1996 Director Stock Option Plan, or the Director Plan, and the Amended and
Restated 1996 Employee Stock Purchase Plan, or the Employee Plan.(2)
    
    Includes options to purchase 1,032,521 shares of our common stock issued under the Equity Plan
that were cancelled after December 31, 2005.(3)
    
    Does not include options to purchase 300,562 shares of our common stock issued under the Equity
Plan that were granted to employees after December 31, 2005.(4)
    
    Includes options to purchase 53,334 shares of our common stock issued under the Director Plan
that were cancelled after December 31, 2005.(5)
    
    Does not include 149,916 shares of our common stock issued to date under the Employee Plan.
Shares of our common stock that are set aside within the Employee Plan immediately become
outstanding common stock when purchased by employees. 
 ITEM 13.     CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
    
 ITEM 14.     PRINCIPAL ACCOUNTANT FEES AND SERVICES
  13




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Year
EndedDecember 31, 2005
    
    
    December 31, 2004Audit Fees:(1)
    
    $
    265,500
    
    
    $
    393,000Audit-Related Fees:(2)
    
    
    
    
    
    
    Tax Fees:(3)
    
    
    17,700
    
    
    
    27,872All Other Fees:(4)
    
    
    
    
    
    
    Total
    
    
    283,200
    
    
    
    420,872
 
 (1)
    
    Audit Fees consist of fees for professional services rendered for the audit of our annual
financial statements, a review of the interim financial statements included in the quarterly
reports, a review of internal controls of financial reporting (Section 404) and services normally
provided by Ernst & Young LLP in connection regulatory filings, as well as work generally only the
independent auditor can reasonably be expected to provide, such as statutory audits.(2)
    
    Audit-Related Fees consist of fees for assurance and related services that are reasonably
related to the performance of an audit or review of our financial statements and are not reported
under Audit Fees. The category includes fees for the review of our employee benefit plans. In
2004, we hired an accounting firm other than Ernst & Young LLP
to audit the employee benefit plans.(3)
    
    Tax Fees consist of fees for professional services rendered in preparing the federal and state
tax returns, and for providing tax compliance, tax advice and tax planning assistance.(4)
    
    All Other Fees consist of fees for services other than the services reported above. Policy on Audit Committee Pre-Approval of Audit and Permissible
Non-audit Services of Independent Auditors
   Audit
 Audit-Related
 Tax
 Other Fees
  14




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PART IV
 
 ITEM 15.     EXHIBITS, FINANCIAL STATEMENT SCHEDULES
   ExhibitNumber
    
    Description31.1
    
    Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 for Michael J. Astrue.31.2
    
    Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 for Robert B. Pelletier.32
    
    Certification pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (Subsections(a) and(b)
of Section 1350, Chapter 63 of Title 18, U.S. Code).
 15




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SIGNATURES
  EPIX Pharmaceuticals, Inc.By:
    
    /s/ Michael J. AstrueMichael J. AstrueInterim Chief Executive Officer
 16




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EXHIBIT INDEX
 ExhibitNumber
    
    Description31.1
    
    Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 for Michael J. Astrue.31.2
    
    Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 for Robert B. Pelletier.32
    
    Certification pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (Subsections(a) and(b)of Section 1350, Chapter 63 of Title 18, U.S. Code)
 17