exv4w1







Exhibit 4.1




SECOND SUPPLEMENTAL INDENTURE




     THIS
SECOND SUPPLEMENTAL INDENTURE, dated as of May 7, 2009 (this “Second Supplemental
Indenture”), to the Indenture (as defined below), is hereby entered into by and between EPIX
Pharmaceuticals, Inc. (f/k/a EPIX Medical, Inc.), a Delaware corporation (the “Issuer”) and
U.S. Bank National Association, a national banking association organized under the laws of the
United States, as Trustee (the “Trustee”).



RECITALS




     WHEREAS, the Issuer has issued its 3% Convertible Senior Notes due June 15, 2024 (the
“Notes”) in the aggregate principal amount of $100,000,000 under and pursuant to the
Indenture, dated as of June 7, 2004, by and between the Issuer and the Trustee (the
“Indenture”).



     WHEREAS, unless the context requires otherwise, all capitalized terms used but not otherwise
defined herein will have the meanings ascribed thereto in the Indenture.



     WHEREAS, the Board of Directors of the Issuer has authorized the Issuer to make an offer to
purchase any and all of the outstanding Notes from each Holder thereof and solicit the consent of
the Holders to amend the Indenture to, among other things, eliminate several of the restrictive
covenants of the Notes thereunder (the “Tender Offer and Consent Solicitation”);



     WHEREAS, in connection with the Tender Offer and Consent Solicitation, Holders of a majority
in aggregate principal amount of the Notes have consented to this Second Supplemental Indenture.



     WHEREAS, pursuant to Section 8.2 of the Indenture, the Issuer and the Trustee may enter into
this Second Supplemental Indenture.



     WHEREAS, the Issuer hereby directs the Trustee to enter into this Second Supplemental
Indenture.



AGREEMENT




     NOW, THEREFORE, for and in consideration of the premises and the mutual covenants and
agreements hereinafter set forth, the parties hereto agree as follows:



SECTION 1. Amendments.




     Section 1.01. Deletion of Certain Sections. Each of the following Sections of the
Indenture is hereby amended by deleting the text of such Section in its entirety and
replacing such text, in each case, with the words “Intentionally Omitted”:



     Section 10.3 Money for Security Payments to Be Held in Trust



     Section 10.4 Existence



     Section 10.7 Registration and Listing



     Section 10.10 Resale of Certain Securities



     Section 10.11 Registration Rights



 









 





     Section 1.02. Amendment to Section 10.8. Section 10.8 of the Indenture is hereby
amended by deleting the text of such Section in its entirety and replacing such text with
the following: “The Company shall, so long as any of the Notes are outstanding, comply with
Section 314 of the Trust Indenture Act.”



SECTION 2. Miscellaneous.




     Section 2.01. Duplicates. Each party may sign any number of copies of this Second
Supplemental Indenture. Each signed copy or counterpart shall be an original, but all of
them together shall represent the same agreement.



     Section 2.02. Successors and Assigns. All agreements of the Issuer and the Trustee
in this Second Supplemental Indenture shall bind their respective successors.



     Section 2.03. Severability. To the extent permitted by applicable law, in case any
one or more of the provisions in this Second Supplemental Indenture shall be held invalid,
illegal or unenforceable, in any respect for any reason, the validity, legality and
enforceability of any such provision in every other respect and of the remaining provisions
shall not in any way be affected or impaired thereby, it being intended that all of the
provisions hereof shall be enforceable to the full extent permitted by law.



     Section 2.04. Governing Law. This Second Supplemental Indenture will be governed by
and construed in accordance with the laws of the State of New York.



     Section 2.05. Effectiveness of Second Supplemental Indenture. Notwithstanding
anything to the contrary contained herein, this Second Supplemental Indenture shall become
operative upon the acceptance by the Issuer of the Notes tendered in connection with the
Tender Offer and Consent Solicitation, provided, however, that this Second Supplemental
Indenture will cease to be operative if the Issuer fails to purchase outstanding Notes
comprising a majority in aggregate principal amount of the outstanding Notes issued under
the Indenture.



[The remainder of this page has been intentionally left blank.]




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     IN WITNESS WHEREOF, the parties hereto have caused this Second Supplemental Indenture to be
duly executed all as of the date first written above.



	 	 	 	 	 	 	 
	 	 	EPIX PHARMACEUTICALS, INC.

(f/k/a EPIX MEDICAL, INC.)	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Kim C. Drapkin	 	 
	 

	 	Name:
	 	 

Kim C. Drapkin
	 	 
	 

	 	Title:
	 	 CFO	 	 
	 
	 	 	 	 	 	 
	 	 	U.S. BANK NATIONAL ASSOCIATION, as
Trustee	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Karen R. Beard	 	 
	 

	 	Name:
	 	 

Karen R. Beard
	 	 
	 

	 	Title:
	 	Vice President	 	 






Signature Page to Second Supplemental Indenture