exh10_1.htm


     

    
      Exhibit
10.1

      


      June 1,
2009

      


      


      Lexicon
Pharmaceuticals, Inc.

      8800
Technology Forest Place

      The
Woodlands, Texas 77381-1160

      Attention:                      Arthur
Sands, President & CEO

      


      
        	
                 
      

              	
                Re:

              	
                Second
      Amended and Restated Collaboration and License
  Agreement

              


      

      


      Dear Dr.
Sands:

       

      
        This
letter agreement (“Letter Agreement”) relates to the Second Amended and Restated
Collaboration and License Agreement between Genentech, Inc. and Lexicon
Pharmaceuticals, Inc. effective as of November 30, 2005
(“Agreement”).  All capitalized terms not otherwise defined herein
shall have the meanings defined in the Agreement.

         

        For good
and valuable consideration, the receipt and sufficiency of which is hereby
acknowledged, Genentech and Lexicon hereby agree, as of the date of this Letter
Agreement above (“Letter Agreement Date”), as follows:

         

      

      
        	
                1.

              	
                Waiver of Genentech Opt-In
      Rights to UNQ171 Products and UNQ153 Products.  Genentech
      hereby waives its rights to exercise either an IND Opt-In pursuant to
      Section 4.6(a) or a Phase II Opt-In pursuant to Section 4.6(b) with
      respect those Lexicon Advanced Research Products that are UNQ171 Products
      or UNQ153 Products and, in each case, do not contain as an active
      pharmaceutical ingredient a Protein other than the Protein produced by
      UNQ171 or UNQ153 (collectively, “UNQ171/UNQ153
      Products”).  Accordingly, the period during which Genentech may
      otherwise have had the right to exercise an IND Opt-In or Phase II Opt-In
      with respect to any UNQ171/UNQ153 Product shall be deemed to have expired
      on the Letter Agreement Date.  In addition, Genentech hereby
      waives its rights under Section 4.15(b) and Section 4.15(c) of the
      Agreement with respect to UNQ171/UNQ153 Products.  For clarity,
      Section 4.15(a) shall continue to apply to UNQ171/UNQ153
      Products.

              


      

       

      
        	
                2.

              	
                Waiver of Certain Diligence
      Requirements Applicable to UNQ171 Products and UNQ153
      Products.  In addition, Genentech hereby waives its
      rights under Section 4.5(a) and Section 4.5(b) of the Agreement with
      respect to UNQ171/UNQ153 Products; provided that Lexicon
      (together with any Lexicon (sub)licensee(s)) shall use Commercially
      Reasonable Efforts to develop at least one Lexicon Advanced Research
      Product that is a UNQ171/UNQ153 Product.  For clarity, the
      Parties acknowledge that, in light of the preceding paragraph of this
      Letter Agreement, Section 4(c) of the Agreement does not apply to
      UNQ171/UNQ153 Products.

              


      

       

      
        	
                3.

              	
                Waiver of Lexicon Rights with
      Respect to Selection of Draft Candidates.  Lexicon hereby
      waives its rights under Section 3.7(c) of the Agreement, with the result
      that the Proteins produced by all Draft Candidates are hereby designated
      as Genentech Advanced Research Protein
  Candidates.

              


      

       

      
        	
                4.

              	
                Waiver of Lexicon Rights to
      Payment of Certain IND Filing Milestones.  Lexicon hereby
      waives its rights to receive, and Genentech shall not be required to pay,
      the milestone payment that would otherwise be due under Section
      8.10(a)(i), 8.11(a)(i), 8.12(a)(i) or 8.13(a)(i), as applicable, with
      respect to the first two (2) Genentech Licensed Products for which an IND
      is filed.

              


      

       

       

      
        
          
          

        

        
          
          

          
            

          

        

        
          
          

        

      

       

      
        	
                5.

              	
                Agreement of Lexicon to Provide
      Overexpression Materials.  Lexicon hereby agrees to
      provide Genentech with purified virus for each Overexpression Mouse
      produced by Lexicon under Section 3.8 of the Agreement.  Such
      purified virus shall be provided to Genentech within sixty (60 days) of
      the Letter Agreement Date at Lexicon’s sole
  expense.

              


      

       

      
        	
                6.

              	
                Execution of Material Transfer
      Agreement with UC Davis. The Parties shall execute or have
      executed, on the Letter Agreement Date, a Material Transfer Agreement
      (“MTA”) pursuant to which Lexicon agrees to transfer certain mice and
      frozen biological material to the University of California, Davis for the
      purposes of propagation and distribution to parties specified in the
      MTA.

              


      

       

      Genentech
hereby acknowledges and agrees that Lexicon timely completed Advanced Phenotypic
Analysis on the requisite percentages of Project Genes specified in Section 11.2
of the Agreement, and that Genentech has no right to terminate the Agreement
thereunder.

       

      Except as
expressly modified by this Letter Agreement, all of the terms and conditions of
the Agreement shall remain in full force and effect (including those rights and
obligations related to UNQ171 Products and UNQ153 Products not expressly
modified by this Letter Agreement) and continues to constitutes the entire
understanding of the Parties with respect to the subject matter
thereof.

       

      If you
are in agreement with the foregoing, please have an authorized representative
sign both originals of this Letter Agreement in the space provided below, and
return one signed original to Genentech.  Thank you.

       

       

      
        
          
            
              	 	Sincerely,	 
	 	for Genentech, Inc.	 
	 	 	 	 
	
                       

                    	
                      By:
      

                    	/s/ Roy
      Hardiman	 
	 	 Name: 	Roy
      Hardiman	 
	 	 Title: 	VP,
      Alliance Management	 
	 	 	 	 


            

          

        



      
        
          
            
              
                
                  	Agreed
      to by:	 
	 	 
	Lexicon Pharmaceuticals,
      Inc.	 
	 	 	 
	
                           By:
      

                        	/s/ Arthur
      T. Sands	 
	 Name:	Arthur
      T. Sands, M.D., Ph.D.	 
	 Title: 	President
      and CEO	 
	 Date:	June
      8, 2009