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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

Under the Securities Exchange Act of 1934
(Amendment No. 1)*

EPIX PHARMACEUTICALS, INC.
(Name of Issuer)
Common Stock, par value $0.01 per share
(Title of Class of Securities)
26881Q101
(CUSIP Number)
August 16, 2006
(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

     þ Rule 13d-1(b)

     o Rule 13d-1(c)

     o Rule 13d-1(d)

* The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page.

The information required in the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB control number.

 
 

1


 

                     
CUSIP No.
 
26881Q101 

 

           
1   NAMES OF REPORTING PERSONS:
Prescott Group Capital Management, L.L.C.
   
  I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY): 
   
     
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS):

  (a)   o
  (b)   o
     
3   SEC USE ONLY:
   
   
     
4   CITIZENSHIP OR PLACE OF ORGANIZATION:
   
  State of Oklahoma
       
  5   SOLE VOTING POWER:
     
NUMBER OF   0
       
SHARES 6   SHARED VOTING POWER:
BENEFICIALLY    
OWNED BY   0
       
EACH 7   SOLE DISPOSITIVE POWER:
REPORTING    
PERSON   0
       
WITH: 8   SHARED DISPOSITIVE POWER:
     
    0
     
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON:
   
  0
     
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (SEE INSTRUCTIONS):
   
  o
     
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9):
   
  0%**
     
12   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS):
   
  IA

**SEE ITEM 4(b).

2


 

                     
CUSIP No.
 
26881Q101 

 

           
1   NAMES OF REPORTING PERSONS:
Prescott Group Aggressive Small Cap, L.P.
   
  I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY): 
   
     
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS):

  (a)   o
  (b)   o
     
3   SEC USE ONLY:
   
   
     
4   CITIZENSHIP OR PLACE OF ORGANIZATION:
   
  State of Oklahoma
       
  5   SOLE VOTING POWER:
     
NUMBER OF   0
       
SHARES 6   SHARED VOTING POWER:
BENEFICIALLY    
OWNED BY   0
       
EACH 7   SOLE DISPOSITIVE POWER:
REPORTING    
PERSON   0
       
WITH: 8   SHARED DISPOSITIVE POWER:
     
    0
     
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON:
   
  0
     
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (SEE INSTRUCTIONS):
   
  o
     
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9):
   
  0%**
     
12   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS):
   
  PN

**SEE ITEM 4(b).

3


 

                     
CUSIP No.
 
26881Q101 

 

           
1   NAMES OF REPORTING PERSONS:
Prescott Group Aggressive Small Cap II, L.P.
   
  I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY): 
   
     
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS):

  (a)   o
  (b)   o
     
3   SEC USE ONLY:
   
   
     
4   CITIZENSHIP OR PLACE OF ORGANIZATION:
   
  State of Oklahoma
       
  5   SOLE VOTING POWER:
     
NUMBER OF   0
       
SHARES 6   SHARED VOTING POWER:
BENEFICIALLY    
OWNED BY   0
       
EACH 7   SOLE DISPOSITIVE POWER:
REPORTING    
PERSON   0
       
WITH: 8   SHARED DISPOSITIVE POWER:
     
    0
     
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON:
   
  0
     
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (SEE INSTRUCTIONS):
   
  o
     
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9):
   
  0%**
     
12   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS):
   
  PN

**SEE ITEM 4(b).

4


 

                     
CUSIP No.
 
26881Q101 

 

           
1   NAMES OF REPORTING PERSONS:
Phil Frohlich
   
  I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY): 
   
     
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS):

  (a)   o
  (b)   o
     
3   SEC USE ONLY:
   
   
     
4   CITIZENSHIP OR PLACE OF ORGANIZATION:
   
  U.S. Citizen
       
  5   SOLE VOTING POWER:
     
NUMBER OF   0
       
SHARES 6   SHARED VOTING POWER:
BENEFICIALLY    
OWNED BY   0
       
EACH 7   SOLE DISPOSITIVE POWER:
REPORTING    
PERSON   0
       
WITH: 8   SHARED DISPOSITIVE POWER:
     
    0
     
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON:
   
  0
     
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (SEE INSTRUCTIONS):
   
  o
     
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9):
   
  0%**
     
12   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS):
   
  IN

**SEE ITEM 4(b).

5


 

SCHEDULE 13G/A
     This Amendment No. 1 to Schedule 13G (the “Schedule 13G”) is being filed on behalf of Prescott Group Capital Management, L.L.C., an Oklahoma limited liability company (“Prescott Capital”), Prescott Group Aggressive Small Cap, L.P., an Oklahoma limited partnership (“Prescott Small Cap”), Prescott Group Aggressive Small Cap II, L.P., an Oklahoma limited partnership (“Prescott Small Cap II” and together with Prescott Small Cap, the “Small Cap Funds”) and Mr. Phil Frohlich the principal of Prescott Capital, relating to shares of common stock of EPIX Pharmaceuticals, Inc., a Delaware corporation (the “Issuer”).
     This Schedule 13G relates to shares of common stock, $0.01 par value, (the “Common Stock”) of the Issuer purchased by the Small Cap Funds through the account of Prescott Group Aggressive Small Cap Master Fund, G.P., an Oklahoma general partnership (“Prescott Master Fund”), of which the Prescott Small Cap Funds are general partners. Prescott Capital serves as the general partner of the Small Cap Funds and may direct the Small Cap Funds, the general partners of Prescott Master Fund, to direct the vote and disposition of the 0 shares of Common Stock held by the Master Fund. As the principal of Prescott Capital, Mr. Frohlich may direct the vote and disposition of the 0 shares of Common Stock held by Prescott Master Fund and 0 shares of Common Stock held by himself, individually.
     The Schedule 13G is hereby amended in its entirety as follows:
     
Item 1(a)
  Name of Issuer.
 
   
 
  EPIX Pharmaceuticals, Inc.
 
   
Item 1(b)
  Address of Issuer’s Principal Executive Offices.
 
   
 
  161 First Street
 Cambridge, Massachusetts 02142
 
   
Item 2(a)
  Name of Person Filing.
 
   
 
  Prescott Group Capital Management, L.L.C. (“Prescott Capital”), Prescott Group Aggressive Small Cap, L.P. (“Prescott Small Cap”), Prescott Group Aggressive Small Cap II, L.P. (“Prescott Small Cap II” and together with Prescott Small Cap, the “Small Cap Funds”), and Mr. Phil Frohlich.
 
   
Item 2(b)
  Address of Principal Business Office, or, if none, Residence.
 
   
 
  1924 South Utica, Suite 1120
 Tulsa, Oklahoma 74104-6529

6


 

     
Item 2(c)
  Citizenship or Place of Organization.
 
   
 
  Prescott Capital is an Oklahoma limited liability company. The Small Cap Funds are Oklahoma limited partnerships. Mr. Phil Frohlich is the principal of Prescott Capital and is a U.S. citizen.
 
   
Item 2(d)
  Title of Class of Securities.
 
   
 
  Common Stock, par value $0.01 per share (the “Common Stock”).
 
   
Item 2(e)
  CUSIP Number.
 
   
 
  26881Q101 
 
   
Item 3
  Reporting Person.
 
   
 
  Inapplicable.
 
   
Item 4
  Ownership.
  (a)   Prescott Capital is the beneficial owner of 0 shares of Common Stock and Mr. Phil Frohlich is the beneficial owner of 0 shares of Common Stock.
 
  (b)   Prescott Capital and Mr. Phil Frohlich are the beneficial owners of 0% and 0%, respectively, of the outstanding shares of Common Stock.
 
  (c)   Prescott Capital, as the general partner of the Small Cap Funds, general partners of Prescott Master Fund, may direct them to direct the vote and disposition of the 0 shares of Common Stock held by Prescott Master Fund. As the principal of Prescott Capital, Mr. Phil Frohlich may direct the vote and disposition of the 0 shares of Common Stock held by Prescott Master Fund and 0 shares of Common Stock held by himself, individually.
     
Item 5
  Ownership of Five Percent or Less of a Class.
 
   
 
  If this statement is being filed to report the fact that as of the date hereof the person reporting has ceased to be the beneficial owner of more than five percent of the class of securities, check the following þ.
 
   
Item 6
  Ownership of More Than Five Percent on Behalf of Another Person.
 
   
 
  Inapplicable.
 
   
Item 7
  Identification and Classification of the Subsidiary which Acquired the Security Being Reported On by the Parent Holding Company.
 
   
 
  Inapplicable.

7


 

     
Item 8
  Identification and Classification of Members of the Group.
 
   
 
  Inapplicable.
 
   
Item 9
  Notice of Dissolution of Group.
 
   
 
  Inapplicable.
 
   
Item 10
  Certification.
 
   
 
  By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.
 
   
Exhibits
  Exhibit 1
 
   
 
  Joint Filing Agreement dated September 29, 2006, between Prescott Capital, Prescott Small Cap and Mr. Phil Frohlich.

8


 

SIGNATURE
     After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.
     Date: September 29, 2006
         
    Prescott Group Capital Management, L.L.C.
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    Prescott Group Aggressive Small Cap, L.P.
 
       
    By: Prescott Group Capital Management, L.L.C., its
general partner
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    Prescott Group Aggressive Small Cap II, L.P.
 
       
    By: Prescott Group Capital Management, L.L.C., its
general partner
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    /s/ Phil Frohlich
     
    Phil Frohlich

9


 

EXHIBIT 1
JOINT FILING AGREEMENT
     In accordance with Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended, the undersigned agree to the joint filing on behalf of each of them of a Statement on Schedule 13G (including any and all amendments thereto) with respect to the Common Stock, par value $0.01 per share, of EPIX Pharmaceuticals, Inc., and further agree that this Joint Filing Agreement shall be included as an Exhibit to such joint filings.
     The undersigned further agree that each party hereto is responsible for the timely filing of such Statement on Schedule 13G and any amendments thereto, and for the accuracy and completeness of the information concerning such party contained therein; provided, however, that no party is responsible for the accuracy or completeness of the information concerning any other party, unless such party knows or has reason to believe that such information is inaccurate.
     This Joint Filing Agreement may be signed in counterparts with the same effect as if the signature on each counterpart were upon the same instrument.
     IN WITNESS WHEREOF, the undersigned have executed this Agreement as of September 29, 2006.
         
    Prescott Group Capital Management, L.L.C.
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    Prescott Group Aggressive Small Cap, L.P.
 
       
    By: Prescott Group Capital Management, L.L.C., its
general partner
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    Prescott Group Aggressive Small Cap II, L.P.
 
       
    By: Prescott Group Capital Management, L.L.C., its
general partner
 
       
 
  By:   /s/ Phil Frohlich
 
       
 
      PHIL FROHLICH, Managing Member
 
       
    /s/ Phil Frohlich
     
    Phil Frohlich

10