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.

 

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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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