Document:

Waiver and Amendment to Series D-1 Warrants, dated as of April 18, 2007

 EXHIBIT 4.13 
 WAIVER AND AMENDMENT TO 
 WARRANTS TO PURCHASE SHARES OF PREFERRED STOCK OF 
 PHARMASSET, INC. 
 THIS WAIVER AND
AMENDMENT (this “Waiver and Amendment”) TO WARRANTS TO PURCHASE SHARES OF PREFERRED STOCK OF PHARMASSET, INC., each dated as of August 4, 2004, entitling its holders to purchase a specified number of shares of the
Company’s Series D-1 Preferred Stock (the “Warrants”), is entered into as of April 18, 2007 (the “Effective Date”) by and among Pharmasset, Inc., a Delaware corporation (the “Company”),
and the undersigned holders of the Company’s Warrants (collectively, the “Warrantholders”). Capitalized terms used but not otherwise defined in this Waiver and Amendment shall have the meanings set forth in the Warrants.

 RECITALS 
 WHEREAS, the
Company intends to issue and sell shares of its common stock, par value $.001 per share, in an underwritten public offering (the “Offering”) and has filed a Registration Statement (No. 333-133907) with the Securities and Exchange
Commission (the “Commission”) related to the Offering (the “Registration Statement”); and 
 WHEREAS, the
Company and the Warrantholders desire to amend the definition of “Qualified IPO” contained in Section 5 of each Warrant; 
 NOW, THEREFORE, in consideration of the mutual promises and covenants hereinafter set forth, the receipt, sufficiency and adequacy of which are hereby acknowledged, the parties hereto agree as follows: 
 1. Amendment of Definition of “Qualified IPO”. The definition of the term “Qualified IPO” set forth in Section 5
of the Warrants is hereby amended in its entirety as follows: 
 “Qualified IPO” means a fully underwritten, firm commitment
public offering that is consummated pursuant to an effective registration statement under the Securities Act covering the offer and sale by the Company of Common Stock in which the aggregate offering amount equals or exceeds US$30,000,000 and in
which the price per share of the Common Stock offered to the public equals or exceeds US$5.00 (such price to be equitably adjusted in the event of any share dividend, share split, reverse split, combination, recapitalization or other similar event).

 2. Waiver. Solely with respect to the Offering, each of the undersigned hereby waives its respective rights to notice of the
Offering by the Company pursuant to Section 2(a) of the Warrants. 
 3. Governing Law. This Waiver and Amendment shall be
construed in accordance with and governed by the laws of the State of Delaware (without giving effect to any conflicts or choice of laws provisions thereof). 

 4. Effective Date. This Waiver and Amendment shall become effective on the Effective Date.

 5. Termination of Amendment. This Waiver and Amendment shall terminate and have no further effect in the event that the
Registration Statement has not been declared effective by the Commission and the Company terminates the Offering. 
 6. Miscellaneous.
From and after the Effective Date of this Waiver and Amendment, unless otherwise terminated pursuant to Section 5 hereof, each reference in the Warrants to “this Warrant”, “hereof”, “hereunder”, or words of like
import in any and all agreements, instruments, documents, notes, certificates and other writings of any kind and nature shall be deemed to refer to the Warrants as amended by this Waiver and Amendment. This Waiver and Amendment may be executed in
any number of counterparts, each of which shall be an original, but all of which together constitute one instrument. The headings in this Waiver and Amendment are for purposes of reference only and shall not limit or otherwise effect the meaning
hereof. 
 [Signatures on Following Pages] 
 WAIVER AND AMENDMENT TO 
 SERIES
D-1 WARRANTS 
  

 2 

 IN WITNESS WHEREOF, the parties hereto have executed this Waiver and Amendment to the Warrant to Purchase
Shares of Preferred Stock as of the Effective Date. 
  

			
	COMPANY:
	
	PHARMASSET, INC.
		
	By:	 	/s/ P. Schaefer Price
	Name:	 	P. Schaefer Price
	Title:	 	President and Chief Executive Officer

  

			
	WARRANTHOLDERS:
	
	 BURRILL LIFE SCIENCES
 CAPITAL
FUND, L.P.

		
	By:	 	/s/ G. Steven Burrill
	Name:	 	G. Steven Burrill
	Title:	 	Member

  

			
	 BURRILL INDIANA LIFE SCIENCES
 CAPITAL FUND, L.P.

	
	 By: Burrill and Company (Indiana GP),
 LLC,
its General Partner

		
	By:	 	/s/ G. Steven Burrill
	Name:	 	G. Steven Burrill
	Title:	 	Member

  

			
	 MDS LIFE SCIENCES TECHNOLOGY
 FUND
II NC LIMITED PARTNERSHIP

		
	By:	 	/s/ Stephen Cummings  /s/ Graysanne Bedell
	Name:	 	Stephen Cummings  Graysanne Bedell
	Title:	 	Vice-President Finance V.P. & Secretary

 SIGNATURE PAGE TO WAIVER
AND AMENDMENT TO 
 SERIES D-1 WARRANTS 

			
	WARRANTHOLDERS (Cont’d):
	
	 MDS LIFE SCIENCES TECHNOLOGY
 FUND
II NC QUEBEC LIMITED
 PARTNERSHIP, by its General Partner,
 MDS LSTF II (QGP) Inc.

		
	By:	 	/s/ Stephen Cummings  /s/ Graysanne Bedell
	Name:	 	Stephen Cummings  Graysanne Bedell
	Title:	 	Vice-President Finance       V.P. & Secretary

  

			
	 MLII CO-INVESTMENT FUND NC
 LIMITED
PARTNERSHIP, by its General Partner, MLII (NCGP) Inc.

		
	By:	 	/s/ Stephen Cummings  /s/ Graysanne Bedell
	Name:	 	Stephen Cummings  Graysanne Bedell
	Title:	 	Vice-President Finance       V.P. & Secretary

  

			
	CDIB BIOSCIENCE VENTURES I, INC.
		
	By:	 	/s/ Benny T. Hu
	Name:	 	Benny T. Hu
	Title:	 	Chairman

  

			
	 TVM V LIFE SCIENCE VENTURES
 GMBH & CO. KG

		
	By:	 	/s/ Gert Caspritz
	Name:	 	Gert Caspritz
	Title:	 	Managing Limited Partner
		
	By:	 	/s/ Mark C. Cipriano
	Name:	 	Mark C. Cipriano
	Title:	 	Managing Limited Partner

  

			
	TVM IV GMBH & CO. KG
		
	By:	 	/s/ Gert Caspritz
	Name:	 	Gert Caspritz
	Title:	 	Managing Limited Partner
		
	By:	 	/s/ Mark C. Cipriano
	Name:	 	Mark C. Cipriano
	Title:	 	Authorized Signatory

 SIGNATURE PAGE TO WAIVER
AND AMENDMENT TO 
 SERIES D-1 WARRANTS 

			
	WARRANTHOLDERS (Cont’d):
	
	BAB BIOVENTURES L.P.
		
	By:	 	 BAB BioVentures L.P., its
 General
Partner

		
	By:	 	 BAB BioVentures, N.V., its
 General
Partner

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Manager

  

			
	 MPM BIOVENTURES PARALLEL
 FUND,
L.P.

		
	By:	 	 MPM BioVentures I LP, its
 General
Partner

		
	By:	 	 MPM BioVentures I LLC, its
 General
Partner

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Manager

  

			
	 MPM ASSET MANAGEMENT
 INVESTORS
1999 LLC

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Manager

 SIGNATURE PAGE TO WAIVER
AND AMENDMENT TO 
 SERIES D-1 WARRANTS 

			
	WARRANTHOLDERS (Cont’d):
	
	MPM BIOVENTURES III, L.P.
		
	By:	 	 MPM BioVentures III GP, L.P., its
 General
Partner

		
	By:	 	 MPM BioVentures III LLC, its
 General
Partner

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Series A Member

  

			
	MPM BIOVENTURES III-QP, L.P.
		
	By:	 	 MPM BioVentures III GP, L.P., its
 General
Partner

		
	By:	 	 MPM BioVentures III LLC, its
 General
Partner

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Series A Member

  

			
	 MPM BIOVENTURES III GMBH & CO.
 BETEILIGUNGS KG

		
	By:	 	 MPM BioVentures III GP, L.P., in its
 capacity as the
Managing Limited Partner

		
	By:	 	 MPM BioVentures III LLC, its
 General
Partner

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Series A Member

 SIGNATURE PAGE TO WAIVER
AND AMENDMENT TO 
 SERIES D-1 WARRANTS 

			
	WARRANTHOLDERS (Cont’d):
	
	 MPM BIOVENTURES III PARALLEL
 FUND,
L.P.

		
	By:	  	 MPM BioVentures III GP, L.P., its
 General
Partner

		
	By:	  	 MPM BioVentures III LLC, its
 General
Partner

		
	By:	  	/s/ Ansbert Gadicke
	Name:	  	Ansbert Gadicke
	Title:	  	Series A Member

  

			
	 MPM ASSET MANAGEMENT
 INVESTORS
2004 BVIII LLC

		
	By:	 	/s/ Ansbert Gadicke
	Name:	 	Ansbert Gadicke
	Title:	 	Manager

 SIGNATURE PAGE TO WAIVER
AND AMENDMENT TO 
 SERIES D-1 WARRANTSWaiver and Fourth Amendment to the Second Amended and Restated Stockholders'

 EXHIBIT 4.14 
 WAIVER AND FOURTH AMENDMENT TO THE 
 SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

 THIS WAIVER AND FOURTH AMENDMENT (the “Waiver and Amendment”) TO THE SECOND AMENDED AND RESTATED STOCKHOLDERS’
AGREEMENT dated as of August 4, 2004, as amended (the “Stockholders’ Agreement”), is entered into as of the Effective Date (as defined below) by and among Pharmasset, Inc., a Delaware corporation (the
“Company”), and the undersigned holders of the Company’s capital stock (collectively, the “Stockholders”). Capitalized terms used but not otherwise defined in this Waiver and Amendment shall have the meanings
set forth in the Stockholders’ Agreement. 
 RECITALS 
 WHEREAS, the Company intends to issue and sell shares of common stock of the Company, par value $.001 per share, in an underwritten public offering (the “Offering”) and has filed a Registration
Statement (No. 333-133907) with the Securities and Exchange Commission (the “Commission”) related to the Offering (the “Registration Statement”); and 
 WHEREAS, the Company and the Stockholders desire to amend the definition of “Qualified IPO” contained in Section 1.1 of the
Stockholders’ Agreement; 
 WHEREAS, each Stockholder desires to waive its rights under Section 2.2 of the Stockholders’
Agreement with respect to the Offering; 
 NOW, THEREFORE, in consideration of the mutual promises and covenants hereinafter set forth, the
receipt, sufficiency and adequacy of which are hereby acknowledged, the parties hereto agree as follows: 
 1. Amendment of
Definition of “Qualified IPO”. The definition of the term “Qualified IPO” set forth in Section 1.1 of the Stockholders’ Agreement is hereby amended in its entirety as follows: 
 “Qualified IPO” shall mean a fully underwritten, firm commitment public offering that is consummated pursuant to an effective
registration statement under the Securities Act covering the offer and sale by the Company of Common Stock in which the aggregate offering amount equals or exceeds $30,000,000 and in which the price per share of the Common Stock offered to the
public equals or exceeds $5.00 (such price to be equitably adjusted in the event of any stock dividend, stock split, reverse split, combination, recapitalization or other similar event). 
 2. Waiver. Solely with respect to the Offering, each of the undersigned hereby waives its respective rights pursuant to Section 2.2 of the
Stockholders’ Agreement, including the right to receive notice. 

 3. Governing Law. This Waiver and Amendment shall be governed by and construed under the laws of
the State of Delaware (without giving effect to any conflicts or choice of laws provisions which would cause the application of the domestic substantive laws of any other jurisdiction). 
 4. Effective Date. This Waiver and Amendment shall become effective (the “Effective Date”) upon receipt by the Company of
counterparts of this Waiver and Amendment duly executed by (a) with respect to Section 1 hereof (i) the Majority Investors and (ii) Stockholders holding a majority of the outstanding shares of the Common Stock subject to the
Stockholders’ Agreement and the Preferred Stock (on an as-if-converted basis) voting together as a single class and (b) with respect to Section 2 hereof, (i) the Majority Investors and (ii) Stockholders other than the
Investors holding a majority of the Common Stock and Preferred Stock (on an as-if-converted basis) owned by such stockholders. Each Stockholder shall be bound by this Waiver and Amendment whether or not such Stockholder shall have consented to this
Waiver and Amendment. 
 5. Termination of Waiver and Amendment. This Waiver and Amendment shall terminate and have no further effect
in the event that the Registration Statement has not been declared effective by the Commission and the Company terminates the Offering. 
 6. Miscellaneous. From and after the Effective Date of this Waiver and Amendment, unless otherwise terminated pursuant to Section 5 hereof, each reference in the Stockholders’ Agreement to “this Agreement”,
“hereof”, “hereunder”, or words of like import in any and all agreements, instruments, documents, notes, certificates and other writings of any kind and nature shall be deemed to refer to the Stockholders’ Agreement as
amended by this Waiver and Amendment. This Waiver and Amendment may be executed in any number of counterparts, each of which shall be an original, but all of which together constitute one instrument. The headings in this Waiver and Amendment are for
purposes of reference only and shall not limit or otherwise effect the meaning hereof. 
 [Signatures on Following Pages] 

 

 WAIVER AND FOURTH AMENDMENT
TO 
 SECOND AMENDED AND RESTATED STOCKHOLDERS’
AGREEMENT 
 2 

 IN WITNESS WHEREOF, the parties hereto have executed this Waiver and Fourth Amendment to the Second
Amended and Restated Stockholders’ Agreement as of the Effective Date. 
  

			
	 COMPANY:

	
	 PHARMASSET, INC.

		
	 By:
	 	 /s/ P. Schaefer Price

	 Name:
	 	 P. Schaefer Price

	 Title:
	 	 President and Chief Executive Officer

	
	 STOCKHOLDERS:

	
	 /s/ Raymond F. Schinazi
 Raymond F. Schinazi, Ph.D.

	
	 RFS PARTNERS, L.P.

		
	 By:
	 	 RFS & Associates, LLC

		
	 By:
	 	 /s/ Raymond F. Schinazi

	 Name:
	 	 Raymond F. Schinazi

	 Title:
	 	 Manager

	
	 RAYMOND F. SCHINAZI 2005

	 QUALIFIED ANNUITY TRUST

		
	 By:
	 	 /s/ Raymond F. Schinazi

	 Name:
	 	 Raymond F. Schinazi

	 Title:
	 	 Trustee

	
	 /s/ Chung K. Chu
 Chung K. Chu, Ph.D.

	
	
 Dennis Liotta, Ph.D.

	
	
 Jean-Pierre Sommadossi, Ph.D.

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	 STOCKHOLDERS (Cont’d):

	
	 JEAN-PIERRE SOMMADOSSI 2004

	 QUALIFIED ANNUITY TRUST NO. 2

		
	 By:
	 	  

	 Name:
	 	 Jean-Pierre Sommadossi

	 Title:
	 	 Trustee

	
	 /s/ Carol Lynn Schinazi
 Carol Lynn Schinazi

	
	 /s/ Rebecca Elizabeth Schinazi
 Rebecca Elizabeth Schinazi

	
	 /s/ Jaime L. Rabi
 Jaime L. Rabi

	
	 /s/ Marcela Rabi
 Marcela Rabi

	
	
 Andrea Rabi

	
	
 Jaclyn H. Chu

	
	 /s/ Susan Chu Walley
 Susan Chu Walley

	
	 IDENIX PHARMACEUTICALS, INC.

		
	 By:
	 	  

	 Name:
	 	
	 Title:
	 	

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	 STOCKHOLDERS (Cont’d):

	
	 HOFFMANN-LA ROCHE INC.

		
	 By:
	 	  

	 Name:
	 	
	 Title:
	 	
	
	 BURRILL LIFE SCIENCES

	 CAPITAL FUND, L.P.

		
	By:	 	Burrill & Company (Life Sciences GP), LLC, its General Partner
		
	 By:
	 	  

	 Name:
	 	
	 Title:
	 	
	
	BURRILL INDIANA LIFE SCIENCES CAPITAL FUND, L.P.
		
	 By:
	 	Burrill and Company (Indiana GP), LLC, its General Partner
		
	 By:
	 	  

	 Name:
	 	
	 Title:
	 	
	
	 MPM BIOVENTURES III, L.P.

		
	 By:
	 	 MPM BioVentures III GP, L.P., its
 General Partner

		
	 By:
	 	 MPM BioVentures III LLC, its
 General Partner

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Series A Member

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	 STOCKHOLDERS (Cont’d):

	
	 BB BIOVENTURES L.P.

		
	 By:
	 	 BAB BioVentures L.P., its
 General Partner

		
	 By:
	 	 BAB BioVentures, N.V., its
 General Partner

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Manager

	
	 MPM BIOVENTURES PARALLEL FUND, L.P.

		
	 By:
	 	 MPM BioVentures I LP, its
 General Partner

		
	 By:
	 	 MPM BioVentures I LLC, its
 General Partner

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Manager

	
	 MPM ASSET MANAGEMENT

	 INVESTORS 1999 LLC

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Manager

	
	 MPM BIOVENTURES III-QP, L.P.

		
	 By:
	 	 MPM BioVentures III GP, L.P., its
 General Partner

		
	 By:
	 	 MPM BioVentures III LLC, its
 General Partner

	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Series A Member

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	 STOCKHOLDERS (Cont’d):

	
	 MPM BIOVENTURES III GMBH & CO.

	 BETEILIGUNGS KG

		
	 By:
	 	 MPM BioVentures III GP, L.P., in its
 capacity as the Managing Limited Partner

		
	 By:
	 	 MPM BioVentures III LLC, its
 General Partner

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Series A Member

	
	 MPM BIOVENTURES III PARALLEL

	 FUND, L.P.

		
	 By:
	 	 MPM BioVentures III GP, L.P., its
 General Partner

		
	 By:
	 	 MPM BioVentures III LLC, its
 General Partner

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Series A Member

	
	 MPM ASSET MANAGEMENT

	 INVESTORS 2004 BVIII LLC

		
	 By:
	 	 /s/ Ansbert Gadicke

	 Name:
	 	 Ansbert Gadicke

	 Title:
	 	 Series A Member

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	 STOCKHOLDERS (Cont’d):

	
	 TVM V LIFE SCIENCE VENTURES

	 GMBH & CO. KG

		
	 By:
	 	 /s/ Mark C. Cipriano

	 Name:
	 	Mark C. Cipriano
	 Title:
	 	Managing Limited Partner
		
	 By:
	 	 /s/ John J. Dibello

	 Name:
	 	John J. Dibello
	 Title:
	 	Managing Limited Partner
	
	 TVM IV GMBH & CO. KG

		
	 By:
	 	 /s/ Mark C. Cipriano

	 Name:
	 	 Mark C. Cipriano

	 Title:
	 	Authorized Signatory
		
	 By:
	 	 /s/ John J. Dibello

	 Name:
	 	John J. Dibello
	 Title:
	 	Managing Limited Partner
	
	 MDS LIFE SCIENCES TECHNOLOGY

	 FUND II NC LIMITED PARTNERSHIP,
 with respect to paragraphs 1, 3, 4, 5 and 6 hereof only

		
	 By:
	 	 MDS LSTF II (NCGP) Inc., its
 General Partner

		
	 By:
	 	 /s/ Graysanne Bedell    /s/ Stephen Cummings

	 Name:
	 	Graysanne Bedell    Stephen Cummings
	 Title:
	 	Vice-President Finance    V.P. & Secretary
	
	 MDS LIFE SCIENCES TECHNOLOGY

	 FUND II QUEBEC LIMITED PARTNERSHIP,
 with respect to paragraphs 1, 3, 4, 5 and 6 hereof only

		
	 By:
	 	 MDS LSTF II (QGP) Inc., its
 General Partner

		
	 By:
	 	 /s/ Graysanne Bedell    /s/ Stephen Cummings

	 Name:
	 	Graysanne Bedell    Stephen Cummings
	 Title:
	 	Vice-President Finance    V.P. & Secretary

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT 

			
	
	STOCKHOLDERS (Cont’d):
	MLII CO-INVESTMENT FUND NC
	LIMITED PARTNERSHIP, with respect to paragraphs 1, 3, 4, 5 and 6 hereof only
		
	 By:
	 	MLII (NCGP) Inc., its General Partner
		
	 By:
	 	 /s/ Graysanne Bedell    /s/ Stephen Cummings

	 Name:
	 	Graysanne Bedell    Stephen Cummings
	 Title:
	 	Vice-President Finance    V.P. & Secretary
	
	CDIB BIOSCIENCE VENTURES I, INC.
		
	 By:
	 	 /s/ Benny T. Hu

	 Name:
	 	Benny T. Hu
	 Title:
	 	Chairman

  

 SIGNATURE PAGE TO WAIVER AND
FOURTH AMENDMENT TO 
 SECOND AMENDED AND
RESTATED STOCKHOLDERS’ AGREEMENT

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