Intellectual Property Security Agreement



 Exhibit 10.48 
 ***Text Omitted and Filed Separately 
 with the Securities and Exchange
Commission. 
 Confidential Treatment Requested 
 Under 17 C.F.R. Sections 200.80(b)(4) 
 and 240.24b-2. 

 
 



 
 INTELLECTUAL PROPERTY SECURITY AGREEMENT 

This Intellectual Property Security Agreement (the “Agreement”) is made as of October 19, 2011, by and between
VERENIUM CORPORATION, a Delaware corporation (“Grantor”), and COMERICA BANK, a Texas banking association (“Secured Party”). 
 RECITALS 
 A. Secured Party has agreed to lend to Grantor certain funds
(the “Loan”), and Grantor desires to borrow such funds from Secured Party pursuant to the terms of that certain Loan and Security Agreement, dated as of October 19, 2011, (the “Loan Agreement”), the Loan
Documents and the Ex-Im Facility Documents. All initially capitalized terms used herein without definition shall have the meanings ascribed to them in the Loan Agreement. 
 B. In order to induce Secured Party to enter into the Loan Agreement, the Loan Documents and the Ex-Im Facility Documents, Grantor has agreed to grant a security interest in certain intangible property to
Secured Party for purposes of securing the obligations of Grantor to Secured Party. 
 NOW, THEREFORE, THE PARTIES HERETO AGREE
AS FOLLOWS: 
 1. Grant of Security Interest. As collateral security for the prompt repayment of any and all Obligations
and to secure prompt performance by Grantor of each of its covenants and duties to Secured Party under the Loan Documents (other than the Warrant) and the Ex-Im Facility Documents, Grantor hereby grants a security interest and mortgage to Secured
Party, as security, in and to Grantor’s entire right, title and interest in, to and under the following (all of which shall collectively be called the “Intellectual Property Collateral”), it being understood that security
interests in the Intellectual Property Collateral shall not be perfected in any jurisdiction outside of the United States: 

(a) Any and all copyright rights, copyright applications, copyright registrations and like protections in each work or authorship and
derivative work thereof, whether published or unpublished and whether or not the same also constitutes a trade secret, now or hereafter existing, created, acquired or held, including without limitation those set forth on Exhibit A attached
hereto (collectively, the “Copyrights”); 
 (b) Any and all trade secrets, and any and all intellectual
property rights in computer software and computer software products now or hereafter existing, created, acquired or held; 
 (c)
Any and all design rights which may be available to Grantor now or hereafter existing, created, acquired or held; 
 (d) All
patents, patent applications and like protections including without limitation improvements, divisions, continuations, renewals, reissues, extensions and continuations-in-part of the same, including without limitation the patents and patent
applications set forth on Exhibit B attached hereto (other than the BP Patents) (collectively, the “Patents”); 
 (e) Any trademark and servicemark rights, whether registered or not, applications to register and registrations of the same and like protections, and the entire goodwill of the business of Grantor
connected with and symbolized by such trademarks, including without limitation those set forth on Exhibit C attached hereto (collectively, the “Trademarks”); 







 (f) Any and all claims for damages by way of past, present and future infringement of any of
the rights included above, with the right, but not the obligation, to sue for and collect such damages for said use or infringement of the intellectual property rights identified above; 

(g) All licenses (other than the [...***...] License), including, but not limited to the BP License and all other rights to use any
of the Copyrights, Patents or Trademarks, and all license fees and royalties arising from such use to the extent permitted by such license or rights; and 
 (h) All amendments, renewals and extensions of any of the Copyrights, Trademarks or Patents; and 
 (i) All proceeds and products of the foregoing, including without limitation all payments under insurance or any indemnity or warranty payable in respect of any of the foregoing. 

The Secured Party’s security interest in the Intellectual Property Collateral shall remain in effect until Payment-in-Full.

 2. Authorization and Request. Grantor authorizes and requests that the Register of Copyrights and the Commissioner of
Patents and Trademarks record this security agreement. 
 3. Covenants and Warranties. All covenants, representations and
warranties contained in the Loan Agreement are hereby incorporated by referenced. Grantor further represents, warrants, covenants and agrees as follows: 
 (a) Performance of this Agreement does not conflict with or result in a breach of any agreement to which Grantor is party or by which Grantor is bound, except to the extent that certain intellectual
property agreements prohibit the assignment of the rights thereunder to a third party without the licensor’s or other party’s consent and this Agreement constitutes an assignment, or except to the extent such default could not reasonably
be expected to cause a Material Adverse Effect; 
 (b) Grantor shall register or cause to be registered (to the extent not
already registered) with the United States Patent and Trademark Office or the United States Copyright Office, as applicable, those registerable intellectual property rights listed on Exhibits A, B and C hereto within thirty (30) days of the
date of this Agreement; 
 (c) This Agreement creates in favor of Secured Party, and in the case of after acquired Intellectual
Property Collateral, at the time Grantor first has rights in such after acquired Intellectual Property Collateral this Agreement will create in favor of Secured Party, a valid and perfected first priority security interest in the Intellectual
Property Collateral in the United States securing the payment and performance of the obligations evidenced by the Loan Agreement upon making the filings referred to in clause (i) below, subject to any Permitted Liens; 

(d) Except for, and upon, the filing with the United States Patent and Trademark office with respect to the Patents and Trademarks and
the Register of Copyrights with respect to the Copyrights such documents as are necessary to perfect the security interests created hereunder, and except as has been already made or obtained, no authorization, approval or other action by, and no
notice to or filing with, any U.S. governmental authority or U.S. regulatory body is required either (i) for the grant by Grantor of the security interest granted hereby or for the execution, delivery or performance of this Agreement by Grantor
in the U.S. or (ii) for the perfection in the United States or the exercise by Secured Party of its rights and remedies hereunder; 
 (e) No representation, warranty or other statement made by Grantor or other information provided in any certificate or written statement furnished, whether now or later, to Secured Party with respect to


  

***Confidential Treatment Requested 


  
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the Intellectual Property Collateral taken together with all such certificates and written statements furnished to Secured Party contains any untrue statement of a material fact or omits to state
a material fact necessary in order to make the statements contained in such certificates or statements not misleading; 
 (f)
Grantor shall not enter into any agreement that would materially impair or conflict with Grantor’s obligations hereunder without Secured Party’s prior written consent, which consent shall not be unreasonably withheld. Grantor shall not
permit the inclusion in any material contract to which it becomes a party of any provisions that could or might in any way prevent the creation of a security interest in Grantor’s rights and interests in any property included within the
definition of the Intellectual Property Collateral acquired under such contracts, except that certain contracts may contain anti-assignment provisions that could in effect prohibit the creation of a security interest in such contracts if Grantor is
required, in its commercially reasonable judgment, to accept such provisions; and 
 (g) Upon any executive officer of Grantor
obtaining actual knowledge thereof, Grantor will promptly notify Secured Party in writing of any event that materially adversely affects the value of any Intellectual Property Collateral, the ability of Grantor to dispose of any Intellectual
Property Collateral or the rights and remedies of Secured Party in relation thereto, including the levy of any legal process against any of the Intellectual Property Collateral. 

4. Secured Party’s Rights. Secured Party shall have the right, but not the obligation, to take, at Grantor’s sole
expense, any actions that Grantor is required under this Agreement to take but which Grantor fails to take, after fifteen (15) days’ notice to Grantor. Grantor shall reimburse and indemnify Secured Party for all reasonable costs and
reasonable expenses incurred in the reasonable exercise of its rights under this Section 4, provided that Grantor’s liability for expenses incurred in connection with any audits (including any under Section 6.9 of the Loan
Agreement) shall be limited to the extent provided for in Section 6.2 of the Loan Agreement. 
 5. Inspection
Rights. Grantor hereby grants to Secured Party and its employees, representatives and agents the right to visit, during reasonable hours upon prior reasonable written notice to Grantor, any of Grantor’s plants and facilities that
manufacture, install or store products (or that have done so during the prior six month period) that are sold utilizing any of the Intellectual Property Collateral, and to inspect the products and quality control records relating thereto upon
reasonable written notice to Grantor and as often as may be reasonably requested, in each case, subject to the limitations on inspections set forth in the Loan Agreement. 
 6. Further Assurances; Attorney-in-Fact. 
 (a) On a continuing basis,
Grantor will make, execute, acknowledge and deliver, and file and record in the proper filing and recording places in the United States, all such instruments, including appropriate financing and continuation statements and collateral agreements and
filings with the United States Patent and Trademark Office and the Register of Copyrights, and take all such action as may reasonably be deemed necessary or advisable, or as reasonably requested by Secured Party, to perfect Secured Party’s
security interest in all Copyrights, Patents and Trademarks and otherwise to carry out the intent and purposes of this Agreement, or for assuring and confirming to Secured Party the grant or perfection of a security interest in all Intellectual
Property Collateral. 
 (b) Grantor hereby irrevocably appoints Secured Party as Grantor’s attorney-in-fact, with full
authority in the place and stead of Grantor and in the name of Grantor, from time to time in Secured Party’s discretion, to take any action and to execute any instrument which Secured Party may deem necessary or advisable to accomplish the
purposes of this Agreement, including (i) to modify, in its sole discretion, this Agreement without first obtaining Grantor’s approval of or signature to such modification by amending Exhibit A, Exhibit B and Exhibit C, thereof, as
appropriate, to include reference to any right, title or interest in any Copyrights, Patents or Trademarks acquired by Grantor after the execution hereof or to delete any reference to any right, title or interest in any Copyrights, Patents or
Trademarks in which Grantor no longer has or claims 

  
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any right, title or interest, (ii) to file, in its sole discretion, one or more financing or continuation statements and amendments thereto, relative to any of the Intellectual Property
Collateral without the signature of Grantor where permitted by law, and (iii) after the occurrence of an Event of Default under this Agreement, to transfer the Intellectual Property Collateral into the name of Secured Party or a third party to
the extent permitted under the California Uniform Commercial Code. 
 7. Events of Default. The occurrence of any default
or Event of Default under the Loan Agreement, the Loan Documents or the Ex-Im Facility Documents shall constitute an Event of Default under this Agreement. 
 8. Remedies. Upon the occurrence and continuance of an Event of Default under this Agreement, Secured Party shall have the right to exercise all the remedies of a secured party under the California
Uniform Commercial Code or as otherwise provided for in the Loan Documents, including without limitation the right to require Grantor to assemble the Intellectual Property Collateral and to make it available to Secured Party as Secured Party may
designate. Secured Party shall have a nonexclusive, royalty free license to use the Copyrights, Patents and Trademarks to the extent reasonably necessary to permit Secured Party to exercise its rights and remedies upon the occurrence of an Event of
Default under this Agreement. Grantor will pay any expenses (including reasonable attorneys’ fees) incurred by Secured Party in connection with the exercise of any of Secured Party’s rights hereunder, including without limitation any
expense incurred in disposing of the Intellectual Property Collateral. All of Secured Party’s rights and remedies with respect to the Intellectual Property Collateral shall be cumulative. 

9. Indemnity. Grantor agrees to defend, indemnify and hold harmless Secured Party and its officers, employees, and agents against:
(a) all obligations, demands, claims, and liabilities claimed or asserted by any other party in connection with the transactions contemplated by this Agreement; and (b) all losses or expenses in any way suffered, incurred, or paid by
Secured Party as a result of or in any way arising out of, following or consequential to transactions between Secured Party and Grantor, whether under this Agreement or otherwise (including without limitation reasonable attorneys’ fees and
reasonable expenses), except for obligations, demands, claims, liabilities, losses or expenses arising from or out of Secured Party’s or its officers’, employees’, or agents’ gross negligence or willful misconduct. 

10. Course of Dealing. No course of dealing, nor any failure to exercise, nor any delay in exercising any right, power or
privilege hereunder shall operate as a waiver thereof. 
 11. Attorneys’ Fees. If any action relating to this
Agreement is brought by either party hereto against the other party, the prevailing party shall be entitled to recover reasonable attorneys’ fees, costs and disbursements. 

12. Amendments. This Agreement may be amended only by a written instrument signed by both parties hereto. 

13. Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original but all of
which together shall constitute the same instrument. 
 14. California Law and Jurisdiction; Jury Waiver. This Agreement
shall be governed by the laws of the State of California, without regard for choice of law provisions. Grantor and Secured Party consent to the exclusive jurisdiction of any state or federal court located in Santa Clara County, California. GRANTOR
AND SECURED PARTY EACH WAIVE THEIR RESPECTIVE RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THE LOAN DOCUMENTS, THIS AGREEMENT, OR ANY OF THE TRANSACTIONS CONTEMPLATED HEREIN, INCLUDING CONTRACT CLAIMS, TORT
CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW OR STATUTORY CLAIMS. 

  
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 IN WITNESS WHEREOF, the parties hereto have executed this Agreement on the day and year
first above written. 
  

					
		 	GRANTOR:
		
	Address of Grantor:	 	VERENIUM CORPORATION,
		 	a Delaware corporation
		
	4955 Directors Place	 	
	San Diego, CA 92121	 	By:	 	 /s/ Jeffrey G. Black

		
		 	Its: Chief Financial Officer
	Attn:	 	
		
		 	SECURED PARTY:
		
	Address of Secured Party:	 	COMERICA BANK
			
	39200 Six Mile Road, MC 7578	 	By:	 	 /s/ Lake T. McGuire

	Livonia, MI 48152	 	
		
		 	Its: Vice President








 EXHIBIT A 
 Copyrights 
 None. 

  
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 EXHIBIT B 
 Patents 
  

			
	 Patent/Serial
No.
	  	 Title

		
	10547956	  	Hydrolases, Nucleic Acids Encoding Them And Methods For Making And Using Them
		
	11575066	  	Compositions and Methods for Making and Modifying Oils
		
	11817865	  	Hydrolases, Nucleic Acids Encoding Them and Methods for Improving Paper Strength
		
	11817997	  	Lyase Enzymes, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	11868909	  	Nitrilases and Methods for Making and Using Them
		
	12032337	  	Chemoenzymatic Methods for the Synthesis of Statins and Statin Intermediates
		
	12202119	  	Hydrolases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12278108	  	Esterases and Related Nucleic Acids and Methods
		
	12281052	  	Aldolases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12303088	  	Lyase Enzymes, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12439459	  	Laccases for Bio-Bleaching
		
	12442207	  	Phytases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12442255	  	Phospholipases, Nucleic Acids Encoding Them and Methods for Making and Using Them


  
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	12499698	  	Pectate Lyases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12520523	  	Amylases and Glucoamylases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12529340	  	Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12567550	  	Enzymes Having Alpha Amylase Activity and Methods of Making and Using Them
		
	12683906	  	Dehalogenases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12697907	  	Amylases, And Methods for used in Starch Processing
		
	12742643	  	Compositions and Methods for Making Androstenediones
		
	12756079	  	Amylases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12763198	  	Methods for Making Simvastatin and Intermediates
		
	12764844	  	Laccases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12773317	  	Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	12810057	  	Transferases and Oxidoreductases, Nucleic Acids Encoding them and methods for making and using them
		
	12810067	  	Isomerases, Nucleic Acids Encoding them and methods for making and using them
		
	12822413	  	Amylases, Nucleic Acids Encoding them and methods for making and using them


  
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	12830157	  	Polymerase
		
	5356801	  	Recombinant DNA Encoding a Desulfurization Biocatalyst
		
	5496729	  	Process for the Desulfurization and the Desalting of a Fossil Fuel
		
	5510265	  	Multistage Process for Deep Desulfurization of a Fossil Fuel
		
	5772901	  	Oil/Water/Biocatalyst Three Phase Separation Process
		
	5814473	  	Transaminases and Aminotransferases
		
	5846813	  	DSZD Utilization in Desulfurization of DBT by Rhodococcus SP. IGTS8
		
	5876997	  	Novel Phytase
		
	5877001	  	Amidase
		
	5879914	  	Recombinant DNA Encoding a Desulfurization Biocatalyst
		
	5925749	  	Carboxymethyl Cellulase from Thermotoga Maritima
		
	5939300	  	Catalases
		
	5948666	  	Isolation and Identification of Polymerases
		
	5952208	  	N DSZ Gene Expression in Pseudomonas
		
	5962258	  	Carboxymethyl Cellulase from Thermotoga Maritima
		
	5962283	  	Transminases and Aminotransferases
		
	5985646	  	Amidase
		
	6004796	  	Amidase
		
	6008032	  	Carboxymethyl Cellulase from Thermotoga Maritima
		
	6013509	  	Transaminases and Aminotransferases
		
	6071738	  	 CONVERSION OF ORGANOSULFUR COMPOUNDS TO OXYORGANOSULFUR COMPOUNDS FOR
 DESULFURIZATION OF FOSSIL FUELS



  
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	6074860	  	Catalases
		
	6110719	  	Novel Phytase
		
	6133016	  	Sphingomonas Biodesulfurization Catalyst
		
	6136583	  	Amidase
		
	6183740	  	Recombinant Bacterial Phytases and Uses Thereof
		
	6190897	  	Novel Phytase
		
	6245547	  	Carboxymethyl Cellulase from Thermotoga Maritima
		
	6303562	  	Compositions comprising 2-(2-hydroxyphenyl)benzenesulfinate and alkyl-substituted derivatives thereof
		
	6410290	  	Catalases
		
	6465204	  	Amidase
		
	6492511	  	Isolation and Identification of Novel Polymerases
		
	6500659	  	Amidase
		
	6632937	  	Nucleic Acids and Proteins From Cenarchaeum Symbiosum
		
	6673552	  	METHODS FOR PURIFYING ANNEALED DOUBLE-STRANDED OLIGONUCLEOTIDES LACKING BASE PAIR MISMATCHES OR NUCLEOTIDE GAPS
		
	6720014	  	Recombinant Bacterial Phytases and Uses Thereof
		
	6855365	  	Recombinant Bacterial Phytases and Uses Thereof
		
	6943001	  	Epoxide Hydrolases, Nucleic Acids Encoding Them and Methods for Making and Using Them


  
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	6979733	  	Epoxide Hydrolases, Nucleic Acids Encoding Them and Methods of Making and Using Them
		
	7049101	  	Enzymes Having High Temperature Polymerase Activity and Methods of Use Thereof
		
	7056703	  	Polypeptides having Polymerase Activity and Methods of Use Thereof
		
	7078035	  	Phytases, Nucleic Acids Encoding Them and Methods for Making and Using them
		
	7078504	  	Enzymes Having Dehgalogenase Activity and Methods of Use Thereof
		
	7226771	  	Phospholipases, Nucleic Acids Encoding Them and Methods for Making and Using them
		
	7232672	  	P450 Enzymes, Nucleic Acids Encoding Them and Methods for Making and Using them
		
	7232677	  	Phytase Expression Systems and Methods of Making and Using Them
		
	7273740	  	Enzymes Having Alpha Amylase Activity and Methods of Use Thereof
		
	7288400	  	Nucleic Acids Encoding Esterases and Methods of Making and Using Them
		
	7300775	  	Methods for Producing Alpha-Substituted Carboxylic Acids Using Nitrilases and Strecker Reagents
		
	7323336	  	Enzymes Having Alpha Amylase Activity and Methods of Use Thereof
		
	7407677	  	Enzymes Having Alpha Amylase Activity and Methods of Use Thereof
		
	7414119	  	Aldolases, Nucleic Acids Encoding Them and Methods for Making and Using them
		
	7416874	  	Recombinant Bacterial Phytases and Uses Thereof
		
	7422876	  	Methods for Generating Cellulases


  
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	7432097	  	Phytases, Nucleic Acids Encoding Them and Methods of Making and Using Them
		
	7432098	  	Phytases and Methods for Making and Using Them
		
	7452706	  	Recombinant Bacterial Phytases and Uses Thereof
		
	7521216	  	Nitrilases and Methods for Making and Using Them
		
	7560126	  	Amylases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7592434	  	Pectate Lyases, Nucleic Encoding Them and Methods for Making and Using Them
		
	7608445	  	Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7642079	  	Proteases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7651849	  	Nitrilases
		
	7659102	  	Amylases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7666633	  	Enzymes Having Alpha Amylase Activity and Methods of Making and Using Them
		
	7671189	  	Enzymes Having Dehalogenase Activity and Methods of Use Thereof
		
	7700329	  	Methods for Making Simvastatin and Intermediates
		
	7741089	  	Laccases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7741092	  	Amylases, Nucleic Acids Encoding Them and Methods for Making and Using Them


  
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	7759093	  	Amylases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7781198	  	Polymerase – Encoding Nucleic Acids and Methods of Making and Using Them
		
	7811804	  	Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7824895	  	Phytases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7863031	  	Phytases and Methods of Making and Using Them
		
	7932064	  	Processes for Making ®-Ethyl 4-Cyano-3-Hydroxybutyric Acid
		
	7943360	  	Phospholipases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7977080	  	Phospholipases, Nucleic Acids Encoding Them and Methods for Making and Using Them
		
	7981844	  	Methods for the Manufacture of Pure Single Enantiomer Compounds and for Selecting Enantioselective Enzymes
		
	7993901	  	Nitrilases and Methods for Making and Using Them
		
	13058584	  	Hydrolases, Nucleic Acids Encoding Them and Methods For Making and Using Them


  
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 EXHIBIT C 
 Trademarks 
  

					
	 Trademark
	  	 Serial/Reg. No.
	  	 
			
	 DIVERSA
	  	2396696	  	
			
	 PYROLASE
	  	2474025	  	
			
	 LUMINASE
	  	3142892	  	
			
	 COTTONASE
	  	2993233	  	
			
	 ACCENTUASE
	  	3490178	  	
			
	 PURIFINE
	  	3308380	  	
			
	 FUELZYME
	  	3373534	  	
			
	 THE NATURE OF ENERGY
	  	3562414	  	
			
	 VERETASE
	  	3815450	  	
			
	 VERENIUM
	  	3773475	  	
			
	 XYLATHIN
	  	3935089	  	
			
	 VERENIUM AND DESIGN
	  	3706903	  	
			
	 THE ENERGY OF NATURE
	  	85086994	  	


  
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