Document:

EX-10.1

 Exhibit 10.1 

CONFIDENTIAL TREATMENT REQUESTED 

CONFIDENTIAL PORTIONS OF THIS DOCUMENT HAVE BEEN REDACTED AND HAVE BEEN SEPARATELY FILED WITH THE SECURITIES AND EXCHANGE COMMISSION.
INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS DOCUMENT WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[***]”. 
  

																	
	AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT	 	 1. CONTRACT ID CODE
	 	 PAGE OF PAGES

1        |        2

	 2. AMENDMENT/MODIFICATION NO.

0002
	 	  3. EFFECTIVE DATE    

 02/17/2016
	 	 4. REQUISITION/PURCHASE REQ. NO.

 
	 	 5 PROJECT NO, (If applicable)

 
  

	6. ISSUED BY	 	CODE 	 	  ASPR-BARDA
	 	7. ADMINISTERED BY (If other than Item 6)	 	CODE    	 	ASPR-BARDA01
	  
 ASPR -
BARDA
 200 Independence Ave., S.W.
 Room
640-G
 Washington DC 20201
  
	 	  

ASPR—BARDA
 330 Independence Ave, SW, Rm G644

Washington DC 20201

															
	 8. NAME AND ADDRESS OF CONTRACTOR (No., street, county, State and ZIP code

 
 PFENEX, INC

10790 ROSELLE ST
 SAN DIEGO CA 921211718
	 	(x)  	 	9A. AMENDMENT OF SOLICITATION NO.
	 	 	 	
	 	 	 	 9B. DATED (SEE ITEM 11)

 

	 	x  	 	 10A. MODIFICATION OF CONTRACT/ORDER NO.

HHSO100201500011C
  

	 	 	 	10B. DATED (SEE ITEM 13)
	CODE 1358378	 	 FACILITY CODE

 
	 	 	 	 08/14/2015

 

 11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS 

 

	 ̈	The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offers  ̈ is extended.  ̈ is not extended. Offers must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended, by one of the following methods: (a) By completing Items
8 and 15, and returning              copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted; or (c) By separate letter
or telegram which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGEMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR
OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by telegram or letter, provided each telegram or letter makes reference to the solicitation and this amendment, and is received prior to
the opening hour and date specified. 

			
	 12. ACCOUNTING AND APPROPRIATION DATA (if
required) 
 See Schedule

	13. THIS ITEM ONLY APPLIES TO MODIFICATION OF CONTRACTS/ORDERS. IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.
	    	 	
	    	 	 
	 	 	 
	 	 	 
	 	 	 
	E. IMPORTANT: Contractor  ̈ is not x
is required to sign this document and return   1   copies to the issuing office.
	14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)
	 Tax ID Number: 27-1356759
 DUNS
Number: 013603710
 Pfenex — RPA563 and Px563L Advanced Development

LIST OF CHANGES:
 Reason for Modification: Other Administrative
Action

  
 1. Update key personnel in Article G.3 Key Personnel

 
 2. ARTICLE 6.5. INVOICE/FINANCING REQUEST AND CONTRACT FINANCIAL REPORTING

Discount Terms: NET 30P
 Period of Performance: 08/14/2015 to
08/09/2020

	Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and
effect.

							
	 15A. NAME AND TITLE OF SIGNER (Type or
print)
 PATRICK LUCY CBO
	 	 16A. NAME AND TITLE OF CONTRACTING OFFICER
(Type or print)
 WENDELL CONYERS

	15B. CONTRACTOR/OFFEROR	 	15C. DATE SIGNED	 	 16B. UNITED STATES OF AMERICA
  
	 	16C. DATE SIGNED
	/s/ Patrick Lucy	 	2/19/16	 	/s/ Wendell Conyers	 	
	(Signature of person authorized to sign)	 	 	 	(Signature of Contracting Officer)	 	2-20-2016

  

			
	NSN 7540-01-152-8070	  	STANDARD FORM 30 (REV. 10-83)
	Previous edition unusable
	  	Prescribed by GSA
		  	FAR (48 CFR) 53.243

  

	[***]	Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 

 CONFIDENTIAL TREATMENT REQUESTED 

CONFIDENTIAL PORTIONS OF THIS DOCUMENT HAVE BEEN REDACTED AND HAVE BEEN SEPARATELY FILED WITH THE SECURITIES AND EXCHANGE COMMISSION.
INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS DOCUMENT WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[***]”. 
  

					
	 Contract No.

HHS0100201500011C
 Modification #02
	  	 Continuation Sheet

Block 14
	  	 Page
 2
 of 2

  

 SUMMARY OF CHANGES 
  

	1.	Update key personnel in Article G.3 Key Personnel: 

 Change PI: 

From: [***] 
 To: [***] 

ARTICLE G.3. KEY PERSONNEL 
 The key personnel specified
in this contract are considered to be essential to work performance. At least 30 days prior to diverting any of the specified individuals to other programs or contracts (or as soon as possible, if an individual must be replaced, for example, as a
result of leaving the employ of the Contractor), the Contractor shall notify the Contracting Officer and shall submit comprehensive justification for the diversion or replacement request (including proposed substitutions for key personnel) to permit
evaluation by the USG of the impact on performance under this contract. The Contractor shall not divert or otherwise replace any key personnel without the written consent of the Contracting Officer. The USG may modify the contract to add or delete
key personnel at the request of the Contractor or USG. 
 The following individuals are considered to be essential to the work being performed hereunder:

  

			
	Name	  	Title
	[***]	  	PI and Project Leader
	[***]	  	Chief Medical Officer
	[***]	  	Project Management

  

	2.	ARTICLE G.5. INVOICE/FINANCING REQUEST AND CONTRACT FINANCIAL REPORTING 

 Include PSC in Receipt of
Invoices: 
 Documents should be delivered electronically to the Contracting Officer (CO), the Contracting Officer’s Representative (COR), PSC, and
e-Room electronically. Unless otherwise specified by the Contracting Officer all deliverables and reports furnished to the Government under the resultant contract (including invoices) shall be addressed as follows: 

 

					
	 Wendell Conyers

Contracting Officer
 HHS/ASPR/AMCG

330 Independence Avenue, S.W.,
 Room G640

Washington, DC 20201
 Email:
wendell.conyers@hhs.gov
	  	 Daniel Wolfe

Contracting Officer
 Representative

HHS/ASPR/BARDA
 330 Independence Avenue, S.W.,

Room G640
 Washington, DC 20201

Email: daniel.wolfe@hhs.gov
  
	  	 Email invoices
to:
  
 PSC_Invoices@psc.hhs.gov

 
 e-Room (Invoice and supporting documentation)

  

	[***]	Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.EX-10.2

 Exhibit 10.2 

THIRD AMENDMENT TO 

MULTI-TENANT INDUSTRIAL/COMMERCIAL LEASE (NET) 

(Roselle Technology Park) 

THIS THIRD AMENDMENT TO MULTI-TENANT INDUSTRIAL/ COMMERCIAL LEASE (NET) dated February 24, 2016 (this “Third Amendment”)
is entered into by and between BRS-TUSTIN SAFEGUARD ASSOCIATES II, LLC, a Delaware limited liability company (“Lessor”), and PFENEX INC., a Delaware corporation (“Lessee”), with reference to the following: 

R E C I T A L S 

WHEREAS, Lessor and Lessee entered into that certain Multi-Tenant Industrial/Commercial Lease (Net) dated June 22, 2010, as
amended by that certain First Amendment to Multi-Tenant Industrial/Commercial Lease (Net) dated September 4, 2014 by and between Lessor and Lessee, and that certain Second Amendment to Multi-Tenant Industrial/Commercial Lease (Net) dated
November 19, 2015 (the “Second Amendment”) by and between Lessor and Lessee (collectively, the “Lease”), for the lease of certain premises (the “Existing Premises”), consisting of approximately 30,148 rentable
square feet comprised of (a) approximately 22,833 rentable square feet located at 10790 Roselle Street, San Diego, California (the “10790 Building”), and (b) approximately 7,315 rentable square feet, commonly known as Suite 102
located at 10788 Roselle Street, San Diego, California (the “10788 Building”). All capitalized terms used herein and not otherwise defined herein shall have the meanings ascribed to such terms in the Lease; and 

WHEREAS, pursuant to the Second Amendment, the Premises shall be expanded to include Suite 101 and Suite 103 and, thereafter, the
Premises shall consist of approximately 46,959 rentable square feet. 
 WHEREAS, Lessor and Lessee desire by this Third Amendment to
amend the Lease in order to provide that the Suite 103 Allowance may be used by Lessee to pay Suite 101 Improvement Costs. 
 NOW,
THEREFORE, in consideration of the Premises and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Lessor and Lessee hereby agree as follows: 

1. Recitals. The Recitals set forth above are incorporated herein as though set forth in full herein. 

2. Use of Suite 103 Allowance to Pay Suite 101 Improvement Costs. Notwithstanding anything to the contrary contained
in the Second Amendment, Lessee shall be entitled to use any unused portion of the Suite 103 Allowance to pay Suite 101 Improvement Costs. 

3. Ratification. Except as otherwise specifically herein amended, the Lease is and shall remain in full force and
effect according to the terms thereof. In the event of any conflict between the Lease and this Third Amendment, this Third Amendment shall control. 
  

Lessor’s Initials: MB  

Lessee’s Initials: BL   

  
 1 

 4. Submission. Submission of this Third Amendment by Lessor to Lessee
for examination and/or execution shall not in any manner bind Lessor and no obligations on Lessor shall arise under this Third Amendment unless and until this Third Amendment is fully signed and delivered by Lessor and Lessee. 

5. Counterparts. This Third Amendment may be executed in several counterparts, each of which shall be deemed an
original, but all of which together shall constitute one and the same agreement. 
 IN WITNESS WHEREOF, this Third Amendment has been
executed by the parties as of the date first referenced above. 
  

							
	“Lessor”
	
	BRS-TUSTIN SAFEGUARD ASSOCIATES II, LLC,
	a Delaware limited liability company
		
	By:	 	Westcore Investments I, LLC
		 	a Delaware limited liability company
		 	its Sole Member
			
		 	By:	 	Westcore Properties, LLC
		 		 	a Delaware limited liability company
		 		 	its Sole Member
				
		 		 	By:	 	 /s/ Matthew Bateman

		 		 	Name:	 	 Matthew Bateman

		 		 	Title:	 	Authorized Signatory
		
	“Lessee”	 	
	
	PFENEX INC.,
	a Delaware corporation
		
	By:	 	 /s/ Bertrand C. Liang

	Name:	 	 Bertrand C. Liang

	Title:	 	 CEO

  
 Lessor’s Initials:
MB  
 Lessee’s Initials: BL   

  
 2

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