Document:

Exhibit 4.1

 

DISCOVERY
PARTNERS INTERNATIONAL, INC.

 

FIRST
AMENDMENT TO RIGHTS AGREEMENT

 

THIS FIRST AMENDMENT TO RIGHTS AGREEMENT
(this “Amendment”) is made as of April
10, 2006 between DISCOVERY PARTNERS INTERNATIONAL, INC., a
Delaware corporation (the “Company”),
and AMERICAN STOCK TRANSFER & TRUST COMPANY, as
rights agent (the “Rights
Agent”).

 

WHEREAS, the Company and the
Rights Agent entered into that certain Rights Agreement dated as of February 13,
2003 (the “Rights Agreement”)
(capitalized terms used but not defined herein shall have the meaning assigned
to them in the Rights Agreement); and

 

WHEREAS, the Company and the
Rights Agent desire to irrevocably amend the Rights Agreement as provided
below.

 

NOW, THEREFORE, in consideration
of the foregoing premises and the mutual covenants and conditions set forth
below, and for other good and valuable consideration, the receipt of which is
hereby acknowledged, the parties to this First Amendment to Rights Agreement
hereby agree as follows:

 

AMENDMENT

 

1.                                      Amendment
of the Rights Agreement.

 

1.1          A new Section 35 of
the Rights Agreement is hereby added as follows:

 

“Section 35. Permitted Transactions. Reference
is made to (a) the Agreement and Plan of Merger and Reorganization by and among
the Company, Infinity Pharmaceuticals, Inc., a Delaware corporation (“Infinity”), and Darwin Corp., a
wholly-owned corporate subsidiary of the Company organized under Delaware law (“Merger Sub”), to be dated as of a
date occurring on or after April 10, 2006 and on or before April 14, 2006 (such
date, the “Execution Date”), as it may
be amended from time to time (the “Merger Agreement”)
and (b) the Voting Agreements by and between the Company and certain
stockholders of Infinity, to be dated as of the Effective Date, as each may be
amended from time to time (the “Voting Agreements”).
Notwithstanding any other provision of this Agreement, the term “Acquiring
Person” as used throughout this Agreement shall not include the stockholders of
Infinity, or any of such stockholder’s Affiliates or Associates, in each case
to the extent, but only to the extent, that any such stockholder or any of such
Affiliates or Associates, becomes or shall become the Beneficial Owner of 15%
or more of the shares of Common Stock of the Company then outstanding as a
result of the execution, delivery or performance of the Merger Agreement or the
Voting Agreements (or any of them) or the consummation of the Merger (as such
term is defined in the Merger Agreement) or the transactions contemplated
thereby, in each case in accordance with the terms thereof, as such terms may
be amended by the parties thereto. In addition, notwithstanding any other
provision

 

1

 

of this Agreement, neither a Distribution Date nor a Share
Acquisition Date shall be deemed to occur, and the Rights will not separate
from the Common Stock, as a result of the execution, delivery or performance of
the Merger Agreement or the Voting Agreements (or any of them) or the
consummation of the Merger (as such term is defined in the Merger Agreement) or
the transactions contemplated thereby, in accordance with the terms thereof, as
such terms may be amended by the parties thereto.”

 

2.             No Other Amendment.
Except as modified by this Amendment, the Rights Agreement shall remain in full
force and effect without any modification. By executing this Amendment below,
the Company certifies that this Amendment has been executed and delivered in
compliance with the terms of Section 27 of the Rights Agreement. This Amendment
shall be deemed an amendment to the Rights Agreement and shall become effective
when executed and delivered by the Company and the Rights Agent as provided
under Section 27 of the Rights Agreement. This Amendment shall be irrevocable.

 

3.             Counterparts.  This Amendment may be
executed in several counterparts, each of which shall constitute an original
and all of which, when taken together, shall constitute one agreement.

 

 

[THIS SPACE INTENTIONALLY LEFT BLANK]

 

2

 

The foregoing
Amendment is hereby executed as of the date first above written.

 

THE COMPANY:

 

DISCOVERY PARTNERS INTERNATIONAL, INC.

 

 

	
  By:

  	
  /s/ Michael C. Venuti

  	
   

  
	
   

  	
  Michael C. Venuti

  
	
   

  	
  Acting Chief Executive Officer

  
	
   

  
	
   

  
	
  RIGHTS AGENT:

  
	
   

  
	
  AMERICAN STOCK TRANSFER & TRUST COMPANY

  
	
   

  
	
   

  
	
  By:

  	
  /s/ Herbert J. Lemmer

  	
   

  
	
  Name:

  	
  Herbert J. Lemmer

  	
   

  
	
  Title:

  	
  Vice President

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By:

  	
   

  	
   

  	 

	
  Name:

  	
   

  	
   

  
	
  Title:LOAN MODIFICATION AND EXTENSION AGREEMENT

    EXHIBIT
      10.3.4

    

    Loan
      Number 610050161

    

    Date: April
      5,
      2006

    

    LOAN
      MODIFICATION AND EXTENSION AGREEMENT

    AND

    AMENDMENT
      TO PROMISSORY NOTE

    

    

    
      	1.  	
              The
                Loan.
                DICON FIBEROPTICS, INC., a California corporation (“Borrower”), is
                indebted to CATHAY BANK, a California banking corporation (“Lender”),
                under the terms of a Promissory Note dated November 20, 2001 in the
                original principal amount of $27,000,000.00 (the “Loan”) and issued under
                the terms of a Term Loan Agreement dated November 20, 2001, which
                Promissory Note and Term Loan Agreement were modified pursuant to
                the Loan
                Modification and Extension Agreement and Amendment to Promissory
                Note
                dated June 28, 2004 (such Promissory Note as so amended is hereinafter
                referred to as the “Note” and such Term Loan Agreement as so amended is
                hereinafter referred to as the “Term Loan Agreement”). The Note is an
                extension and renewal of a Construction Loan Promissory Note dated
                August
                24, 2000. As of March 23, 2006, the unpaid principal balance of the
                Loan
                is $9,957,051.51, and interest has been paid to March 20, 2006. The
                Loan
                is evidenced by the Note and is secured by a Construction Trust Deed
                dated
                August 24, 2000 that was recorded in the Official Records of Contra
                Costa
                County, California (the “Official Records”), on August 25, 2000 as
                Document No. 2000-0182834-00, as modified by a Modification of
                Construction Trust Deed dated November 20, 2001 and recorded in the
                Official Records on November 27, 2001 as Document No. 2001-0361073-00
                and
                a Modification of Construction Trust Deed dated June 28, 2004 and
                recorded
                in the Official Records on September 3, 2004 as Document No.
                2004-0342993-00 (such Construction Trust Deed as so modified, hereinafter
                referred to as the “Trust Deed”).

            

    

    

    
      	2.  	
              Extension
                of Maturity Date.
                Borrower and Lender hereby agree to extend the Final Payment Date
                of the
                Loan under the terms of the Note from October 20, 2007 to October
                20,
                2017, with a corresponding increase in the number of monthly
                payments.

            

    

    

    
      	3.  	
              Decrease
                in Interest Rate.
                The interest rate to be applied to the unpaid principal balance of
                the
                Note is changed from the Index to the Index minus
                1.0%. There shall be no floor rate of interest; all other interest
                rates
                remain unchanged.

            

    

    

    
      	4.  	
              Partial
                Release and Reconveyance from Trust Deed.
                Notwithstanding anything in the Term Loan Agreement, the Note or
                the Trust
                Deed to the contrary, simultaneously with the execution and delivery
                of
                this Agreement Lender will grant a partial reconveyance from the
                lien or
                charge of the Trust Deed with respect to that parcel of vacant land
                of
                approximately 5.88 acres described as Lot 1 of Parcel Map MS 753-04
                filed
                December 14, 2005, Book 195 of Maps, page 26, Official Records, together
                with all appurtances thereto. Borrower shall pay all costs of executing
                and recording the reconveyance. 

            

    

    

    
      	5.  	
              Modification
                to the Trust Deed.
                The Trust Deed shall be further modified to contain partial release
                provisions in accordance with paragraph 4
                above.

            

    

    

    
      	6.  	
              No
                Waiver. By
                entering into this Agreement and except as set forth herein, Lender
                does
                not waive any default, now existing or hereafter occurring, in the
                loan
                documents. Any waiver or forbearance granted by Lender does not obligate
                Lender to grant any other or further waiver or forbearance. Consent
                by
                Lender to this Agreement does not waive Lender’s right to require
                performance of Borrower’s obligations as modified
                hereby.

            

    

    

    
      	7.  	
              Continuing
                Validity and Liability.
                Except as expressly modified or changed by this Agreement, the obligations
                under the Note and loan documents, including all agreements evidencing
                or
                securing the Note and loan documents, remain in full force and effect.
                This Agreement modifies the terms of an existing Note and loan documents
                and is not a novation.

            

    

    

    
      	8.  	
              General.
                This Agreement and the existing loan documents constitute a single
                integrated written contract expressing the entire agreement of the
                parties
                relative to the subject matter hereof. If any provision of this Agreement
                is found to be illegal, invalid or unenforceable under present or
                future
                laws effective during the term of this Agreement, such provisions
                shall be
                fully severable; this Agreement shall be construed and enforced as
                if such
                provision never comprised a part of this Agreement; and the remaining
                provisions hereof shall not be affected by the illegal, invalid or
                unenforceable provision or by its severance. At request of Lender,
                Borrower shall execute and deliver such further documents and do
                such
                other things, as Lender may reasonably require, in order to effect
                the
                purposes and enforceability of this Agreement and the loan documents
                and
                to obtain and continue any security interests and the perfection
                and
                priority of any security interests in the collateral. All terms,
                which are
                not defined in this Agreement, have the meaning given them in the
                existing
                loan documents. In the event of any conflict or inconsistency between
                the
                terms, conditions and provisions of this Agreement and the loan documents,
                this Agreement shall prevail. Headings in this Agreement are for
                convenience only and shall not affect the construction or interpretation
                of this Agreement.

            

    

    

    THIS
      LOAN MODIFICATION AND EXTENSION AGREEMENT AND AMENDMENT TO PROMISSORY NOTE
      IS
      ENTERED INTO AS OF THE DATE FIRST SET FORTH ABOVE.

     

    

    

    Borrower: DICON
      FIBEROPTICS, INC.,

    a
      California corporation

    

    

    By:
      /s/
      Ho-Shang Lee 

    Name:
      Ho-Shang Lee 

    Title:
      President

    

    

    

    Lender: CATHAY
      BANK,

    a
      California banking corporation

    

    

    By:
      /s/
      Eddie Chang    

    Name:
      Eddie Chang    

    Title:
      S.V.P. & Manager

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