Exhibit
10.1


 


AMENDMENT NO. 2 TO
ASSIGNMENT AND LICENSE AGREEMENT


 


THIS
AMENDMENT NO. 2 TO ASSIGNMENT AND LICENSE AGREEMENT (this “Amendment”) dated
this 3rd day of March, 2005 (the “Effective Date”), is entered into between
Cubist Pharmaceuticals Incorporated, a Delaware corporation having its
principal place of business at 65 Hayden Avenue, Lexington, MA 02421 and its
Affiliates (collectively “CUBIST”) and Eli Lilly and Company, an Indiana
corporation having an office and principal place of business at Lilly Corporate
Center, Indianapolis, Indiana 46285 and its Affiliates (“LILLY”).


 


WITNESSETH:


 


WHEREAS,
the parties entered into an ASSIGNMENT AND LICENSE AGREEMENT effective as of
October 20, 2000, and an AMENDMENT No. 1 to the ASSIGNMENT AND LICENSE AGREEMENT
dated as of July 1, 2003 (as amended, the “Agreement”).


 


WHEREAS,
the parties have entered into a STOCK PURCHASE AGREEMENT and a REGISTRATION
RIGHTS AGREEMENT on even date herewith whereby CUBIST will transfer to LILLY
twenty million dollars ($20,000,000) worth of shares of CUBIST common stock
(the “Shares”) and cause such Shares to be registered under applicable
securities laws in return for a reduction of two percent (2%) on all royalties
to be paid under the Agreement.


 


WHEREAS,
the parties desire to amend the Agreement in accordance with Section 17.04
thereof in certain respects as set forth below.


 


NOW,
THEREFORE, in consideration of the foregoing premises and the mutual covenants
set forth below, the parties amend the Agreement and agree as follows:


 


AMENDMENT


 


The
Parties have reached mutual agreement that as of the Amendment Effective Date
(as defined below),  each of the specific
royalty rates set forth in Sections 4.01, 4.02 and 4.03 of the Agreement, shall
be deleted and shall be replaced with a specific royalty rate that is equal to
(a) the previous royalty rate minus
(b) two percentage points. For avoidance of doubt, upon the Amendment Effective
Date, the aggregate royalty reduction to date, including the royalty reduction
set forth in Amendment No. 1 to the ASSIGNMENT AND LICENSE AGREEMENT, shall be
equivalent to three percentage points.


 


AMENDMENT
EFFECTIVE DATE


 


The
amendments referred to above shall become effective upon the closing of the
stock purchase contemplated by the STOCK PURCHASE AGREEMENT; provided however,
that if such closing occurs prior to the effective date of the Registration
Statement contemplated by the REGISTRATION RIGHTS AGREEMENT, then the
amendments referred to above shall become effective upon the earlier of: (a) the
date on which the Registration Statement


 


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contemplated
by the REGISTRATION RIGHTS AGREEMENT shall have been declared effective by the
Securities and Exchange Commission; (b) the date on which Lilly makes its first
sale of any Shares, which date shall be provided to Cubist in writing within
five (5) days of such sale, provided that Lilly’s failure to notify Cubist
thereof shall not impact the determination of the Amendment Effective Date for
purposes of this clause (b); or (c) one (1) year from the  date of closing of the stock purchase
contemplated by the STOCK PURCHASE AGREEMENT (the date on which the amendments
become effective being the “Amendment Effective Date”). In the event the STOCK
PURCHASE AGREEMENT is terminated pursuant to Section 5.3 thereof prior to the
consummation of the stock purchase contemplated thereby, this Amendment shall
be deemed terminated and of no further force or effect, and the royalty
reduction contemplated herein shall not occur.


 


MISCELLANEOUS


 


1.1           Defined Terms.  All terms used, but not defined, herein shall
have the respective meanings set forth in the Agreement.


 


1.2           Continuing Effect.  This Amendment shall be effective for all
purposes as of the Amendment Effective Date. 
Except as otherwise expressly modified by this Amendment, the Agreement
shall remain in full force and effect in accordance with its terms.


 


1.3           Counterparts.  This Amendment may be executed in two or more
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.


 


[Remainder of page
intentionally left blank.]


 


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IN
WITNESS WHEREOF, the parties have executed this Amendment as of the date first
written above.


 


 


ELI
LILLY AND COMPANY


 


 


	
  By

  	
   

  	
  /s/John C. Lechleiter

  	
   

  
	
   

  	
   

  	
   

  
	
  Title

  	
   

  	
  Executive VP Pharma
  Operations

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  CUBIST
  PHARMACEUTICALS, INC.

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By

  	
   

  	
  /s/David W.J. McGirr

  	
   

  
	
   

  	
   

  	
   

  
	
  Title

  	
   

  	
  Senior VP, Chief
  Financial Officer

  	
   

  
							



 


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