Document:

Exhibit 4.36

 

Execution Version

 

October 6, 2016

 

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention: John Melo, President and Chief Executive Officer

 

	RE:		Amendment to Loan and Security Agreement Relating to (i) Maturity Date, (ii) Payments
and (iii) Cash Covenants

 

Dear Mr. Melo:

 

Reference is made to that certain Loan and Security Agreement dated
as of March 29, 2014, as amended on June 12, 2014, March 31, 2015, and November 30, 2015 (as amended, the “LSA”),
by and between Amyris, Inc., a Delaware corporation (the “Parent”), and each of its Subsidiaries that
has delivered a Joinder Agreement (collectively, “Borrower”), the other financial institutions or entities
from time to time parties to the LSA (collectively, referred to as “Lender”) and Stegodon Corporation,
a Delaware corporation, as assignee of Hercules Capital, Inc., a Maryland corporation, in its capacity as administrative agent
for itself and Lender (in such capacity, the “Agent”). Capitalized terms used but not otherwise defined
herein have the meaning set forth in the LSA.

 

Borrower has requested that the Lender amend certain provisions
of the LSA by (i) extending the Term Loan Maturity Date and (ii) amending the definition of “Permitted Transfers” and
Sections 2.2(d) (“Term Loan – Payment”) and 7.14 (“Minimum Cash”) of the LSA, in each case subject
to certain conditions further described below.

 

For good and valuable consideration, the receipt and sufficiency
of which are hereby acknowledged, based upon the mutual covenants contained herein, and subject to the effectiveness of the Collaboration
Agreement dated on or about the date hereof, by and between Parent and Ginkgo Bioworks, Inc. (the “Ginkgo Collaboration
Agreement”), Borrower, the Agent and Lender, in accordance with Section 11.3(b) of the LSA, hereby amend the LSA
(this “Amendment”) as follows:

 

I.       Effective immediately upon the
Agent’s receipt of evidence reasonably satisfactory to it, in its sole discretion, that the maturity date(s) of the existing
indebtedness of Borrower listed on Exhibit A hereto have been extended (the “Extension Condition”),
the “Term Loan Maturity Date” as defined in the LSA shall be the Business Day immediately preceding the earliest maturity
date of the existing indebtedness of Borrower listed on Exhibit B hereto, after giving effect to any extensions thereof
(and subject to the Agent’s receipt of evidence reasonably satisfactory to it, in its sole discretion, of such extensions
thereof) as of the date of satisfaction of the Extension Condition; provided, that the Term Loan Maturity Date shall in
no event be later than April 12, 2019.

 

II.       The following
sentence shall be added to the end of the definition of “Permitted Transfers” in Section 1 of the LSA:

 

“Notwithstanding anything herein
to the contrary, the license or transfer of Borrower’s Intellectual Property rights pursuant to and in connection with the
Ginkgo Collaboration Agreement and all the transactions contemplated thereby shall be deemed, at all times, to be Permitted Transfers.”

 

III.       New definitions
of “Ginkgo Collaboration Agreement” and “Net Profits” are hereby inserted into Section 1 of the LSA in
appropriate alphabetical order:

 

     

     

    

 

“Ginkgo Collaboration Agreement”
means that certain Collaboration Agreement, dated as of September 30, 2016, by and between Parent and Ginkgo Bioworks, Inc.

 

“Net Profits” has the
meaning ascribed to such term in the Ginkgo Collaboration Agreement.

 

IV.       Section 2.2(d)
(“Term Loan – Payment”) of the LSA is hereby deleted in its entirety and the following is substituted therefor:

 

“Payment. Borrower will pay
interest on each Term Loan Advance on the first Business Day of each month, beginning the month after the (i) Closing Date with
respect to the Closing Date Term Loan Advance, (ii) First Amendment Effective Date with respect to the Additional Term Loan Advance
and (iii) the Third Amendment Effective Date for the Third Amendment Term Loan Advance. At its sole discretion, Lender will either
(i) initiate debit entries to the Borrower’s account as authorized on the ACH Authorization on each payment date of all periodic
interest obligations payable to Lender under each Term Loan Advance and any costs and expenses reimbursable to Lender, (ii) submit
a written invoice to Borrower for all amounts due by Borrower on each payment date of all periodic interest obligations payable
to Lender under each Term Loan Advance and any costs and expenses reimbursable to Lender, which invoice must be paid by Borrower
within five days of receipt or (iii) submit other written instructions to Borrower regarding the proper method for payment of such
periodic interest obligations and costs and expenses. In addition, Borrower shall pay to Agent, for the benefit of Lender, promptly
upon Borrower’s receipt thereof, all Net Profits earned by and actually received by Parent under the Ginkgo Collaboration
Agreement, up to a maximum of $1,000,000 in any calendar month, and any such payments shall be applied to the principal balance
outstanding under the LSA on the first Business Day of the month following payment. For the sake of clarification, any such payments
of Net Profits made to the Agent, for the benefit of Lender, in accordance with this paragraph shall not be subject to any Prepayment
Charge under Section 2.5 hereof. The entire Term Loan Advance principal balance outstanding and all accrued but unpaid interest
hereunder shall be due and payable on the Term Loan Maturity Date. Borrower shall make all payments due under this Agreement without
setoff, recoupment or deduction and regardless of any counterclaim or defense.”

 

V.       Section 7.14
(“Minimum Cash”) of the LSA is hereby deleted in its entirety and the following is substituted therefor:

 

“Section 7.14. Minimum Cash. So long as the Secured
Obligations are outstanding, Borrower shall, as of any date, have at least the Threshold Amount of unrestricted, unencumbered Cash
in one or more Deposit Accounts subject to an Account Control Agreement in favor of Agent. Notwithstanding anything herein to the
contrary, through and until the Term Loan Maturity Date, the “Threshold Amount” as defined herein shall be $0.”

 

Within five (5) days following receipt of an invoice, Borrower shall
pay the Agent’s reasonable out-of-pocket costs, including reasonable attorneys’ fees, incurred in connection with the
LSA.

 

Except to the extent of this Amendment, the LSA shall remain unaltered
and in full force and effect. This Amendment shall not be a waiver of any existing default or breach of a covenant unless specified
herein.

 

This Amendment shall be limited precisely as written and shall not
be deemed (a) to be a waiver or modification of any other term or condition of the LSA or of any other instrument or agreement
referred to therein or to prejudice any right or remedy which Lender may now have or may have in the future under or in connection
with the LSA or any instrument or agreement referred to therein; or (b) to be a

 

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consent to any future amendment or modification of any instrument
or agreement the execution and delivery of which is consented to hereby, or to any waiver of any of the provisions thereof.

 

The Borrower acknowledges and agrees that it remains obligated to
pay all principal, interest, reimbursement obligations, fees, and other amounts owing to the Agent and Lender under and in respect
of the Loan Documents when due and payable in accordance with the terms thereof.

 

The Borrower hereby acknowledges and agrees that as of the date
hereof, the Borrower has outstanding Secured Obligations to the Agent and the Lender which include indebtedness to the Agent and
Lender in an aggregate outstanding principal amount equal to $28,565,748.86 plus accrued interest and fees. The Borrower hereby
acknowledges and agrees that, to the best of its knowledge as of the date hereof, the liens and security interests granted in favor
of the Agent and/or the Lender under the terms of the Loan Documents are perfected, effective, enforceable, and valid and such
liens and security interests are, in each case, a first priority lien and security interest subject to Permitted Liens. Notwithstanding
the foregoing, each of the Agent and the Lender acknowledges and agrees that Borrower is not responsible for perfecting or ensuring
such liens are effective and enforceable.

 

The Borrower hereby acknowledges and agrees that as of the date
hereof: (a) it does not have any claim or cause of action related to the LSA, the Loan Documents or any other agreement between
or among Borrower, the Agent and/or the Lender against the Agent or the Lender (or any of their respective directors, officers,
employees, agents, subsidiaries, affiliates, attorneys, attorneys’ consultants, predecessors, successors or assigns); (b)
it does not have any offset right, counterclaim, or defense of any kind against the Secured Obligations or any portion thereof;
and (c) each of the Agent and the Lender has heretofore properly performed and satisfied in a timely manner all of its obligations
and commitments to the Borrower. For and in consideration of the agreements contained in this Amendment and other good and valuable
consideration, the Borrower unconditionally and irrevocably releases, waives, and forever discharges each of the Agent and the
Lender, together with their respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors,
officers, attorneys and attorneys’ consultants (collectively, the “Released Parties”), from the
following, in each case only as related to the LSA, the Loan Documents and any other agreement between or among Borrower, the Agent
and/or the Lender: (x) any and all liabilities, obligations, duties, promises, or indebtedness of any kind (if any) of the Released
Parties to the Borrower or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world
to the date of this Amendment, and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any),
which the Borrower or any of its affiliates might otherwise have against the Released Parties, or any of them, in either case (x)
or (y) on account of any condition, act, omission, event, contract, liability, obligation, indebtedness, claim, cause of action,
defense, circumstance, or matter of any kind, which existed, arose, or occurred at any time from the beginning of the world to
the date of this Amendment. Notwithstanding anything to the contrary herein, the Borrower does not hereby release, waive, or forever
discharge the Released Parties from any claims, offsets, causes of action, suits or defenses of any kind relating to any conduct
or action by the Agent or Lender that is illegal under federal, state or local law.

 

Without limitation, each party hereto acknowledges that it has been
advised by its attorneys concerning, and is familiar with, the California Civil Code Section 1542. Section 1542 of the California
Civil Code provides as follows:

 

A general release does not extend to claims which the creditor
does not know or suspect to exist in his or her favor at the time of the executing of the release, which if known by him or her
must have materially affected his or her settlement with the debtor.

 

    	 	3	 

     

    

 

Each party hereto expressly waives any and all rights under California
Civil Code Section 1542 and under any other federal or state statute or law of similar effect as to all matters released pursuant
to this Amendment.

 

Except as expressly set forth in this Amendment, this Amendment
shall become effective upon the receipt of a fully executed Amendment.

 

This Amendment may be executed in two or more counterparts, each
of which shall constitute an original, but all of which, when taken together, shall constitute but one instrument, and, except
as expressly set forth herein, shall become effective when one or more counterparts have been signed by each party hereto and delivered
to the other party. Facsimile signatures shall be deemed originals for all purposes hereunder. This Amendment shall be governed
by, and construed and enforced in accordance with, the laws of the State of California, excluding conflict of laws principles that
would cause the application of laws of any other jurisdiction.

 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

 

 

 

 

 

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IN WITNESS WHEREOF, Borrower, the Agent and the Lender have
duly executed and delivered this Amendment as of the day and year first above written.

 

	 	AGENT AND LENDER:	 
	 	 	 	 
	 	STEGODON CORPORATION, as Agent and as Lender	 
	 	 	 	 
	 	Signature:	/s/ Austin Che	 
	 	 	 	 
	 	Print Name:	Austin Che	 
	 	 	 	 
	 	Title:	President	 
	 	 	 	 
	 	 	 	 
	 	BORROWER:	 
	 	 	 	 
	 	AMYRIS, INC.	 
	 	 	 	 
	 	Signature:	 	 
	 	 	 	 
	 	Print Name:	 	 
	 	 	 	 
	 	Title:	 	 
	 	 	 	 
	 	 	 	 
	 	AMYRIS FUELS, LLC	 
	 	 	 	 
	 	By: Amyris, Inc., its sole manager	 
	 	 	 	 
	 	Signature:	 	 
	 	 	 	 
	 	Print Name:	 	 
	 	 	 	 
	 	Title:	 	 

 

 

 

 

 

    	 	[Signature Page to LSA Agreement]	 

     

    

 

IN WITNESS WHEREOF, Borrower, the Agent and the Lender have
duly executed and delivered this Amendment as of the day and year first above written.

 

	 	AGENT AND LENDER:	 
	 	 	 	 
	 	STEGODON CORPORATION, as Agent and as Lender	 
	 	 	 	 
	 	Signature:	 	 
	 	 	 	 
	 	Print Name:	 	 
	 	 	 	 
	 	Title:	 	 
	 	 	 	 
	 	BORROWER:	 
	 	 	 	 
	 	AMYRIS, INC.	 
	 	 	 	 
	 	Signature:	/s/ R. Asadorian	 
	 	 	 	 
	 	Print Name:	R. Asadorian	 
	 	 	 	 
	 	Title:	CFO	 
	 	 	 	 
	 	AMYRIS FUELS, LLC	 
	 	 	 	 
	 	By: Amyris, Inc., its sole manager	 
	 	 	 	 
	 	Signature:	/s/ R. Asadorian	 
	 	 	 	 
	 	Print Name:	R. Asadorian	 
	 	 	 	 
	 	Title:	CFO	 

 

 

 

 

 

 

    	 	[Signature Page to LSA Agreement]	 

     

    

 

Exhibit
A

 

	Existing 

Holder(s)	Description	Current Amount 

Outstanding	Current Maturity 

Date
	Entities affiliated with FMR LLC	3% Senior Unsecured Convertible Notes 	$15,309,000	March 1, 2017

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

     

     

    

 

Exhibit
B

 

	Existing 

Holder(s)	Description	Current Amount 

Outstanding	Current Maturity 

Date
	Entities affiliated with FMR LLC	3% Senior Unsecured Convertible Notes 	$15,309,000	March 1, 2017
	Entities affiliated with FMR LLC	Tranche I Senior Convertible Notes	$9,694,724	October 16, 2018
	Entities not party to the Maturity Treatment Agreement, dated July 29, 2015	Tranche II Senior Convertible Notes	$3,639,172	January 15, 2019Exhibit 4.63

 

 

Note pUrchase AGREEMENT

 

This Note Purchase Agreement (this “Agreement”)
is made as of October 5, 2016 (the “Effective Date”) by and among Amyris, Inc., a Delaware corporation (the
“Company”), and the individuals or entities listed on Schedule I hereto (each, a “Purchaser,”
and collectively, the “Purchasers”).

 

Preliminary Statement

 

Subject to the terms and conditions hereof,
each Purchaser desires to purchase, and the Company desires to offer and sell to each Purchaser, that aggregate principal amount
of Secured Promissory Notes with a principal amount set forth opposite each such Purchaser’s name on Schedule I hereto
(which aggregate principal amount for all Purchasers as of the Closing (as defined below) shall be $6,000,000) (each such Secured
Promissory Note, a “Note” and collectively, the “Notes”). If and when issued, each of the
Notes shall be evidenced by a promissory note in the form attached hereto as Exhibit A.

 

Agreement

 

The parties, intending to be legally bound, agree as follows:

 

1.     
Sale of Notes. Subject to the terms and conditions hereof, at the Closing (as defined in Section 2),
the Company shall sell to each Purchaser, and, subject to satisfaction of the conditions set forth in this Agreement, each such
Purchaser will purchase from the Company, (i) a Note in a principal amount as set forth next to such Purchaser’s name on
Schedule I hereto for a purchase price equal to the purchase price set forth next to such Purchaser’s name on Schedule
I hereto under the column “Note Purchase Price” (the “Purchase Price”). The sale and purchase
of the Notes to each Purchaser shall constitute a separate sale and purchase hereunder.

 

2.     
Closing. The closing (“Closing”) of the transactions contemplated hereby shall be
held at the offices of Fenwick & West LLP, 801 California Street, Mountain View, California 94041 within one business day following
the date on which the last of the conditions set forth in Sections 7 and 8 have been satisfied or waived in accordance with this
Agreement but in no event later than October 31, 2016 (such date, the “Closing Date”), or at such other time
and place as the Company and the Purchasers mutually agree upon.

 

3.     
Delivery.

 

(a)      
At the Closing, each Purchaser shall (i) pay the Company the applicable Purchase Price in immediately available funds, or
(ii) (A) initiate irrevocable payment instructions to its paying bank to make the payment (an “Irrevocable Payment Instruction”)
to the Company of the applicable Purchase Price in immediately available funds and (B) deliver to the Company confirmation that
such Purchaser has made an Irrevocable Payment Instruction, such confirmation to be in the form of a federal reference number or
other similar written evidence that a wire has been initiated.

 

     

     

    

 

(b)      
At the Closing, or, if applicable, upon receipt of the applicable amount of the Purchase Price due in respect of the Closing
from any Purchaser who makes an Irrevocable Payment Instruction at the Closing, the Company shall deliver to such Purchaser a Note
with a principal amount as provided in Section 1 above, such Note to be registered in the name of such Purchaser, or in such nominee’s
or nominees’ name(s) as provided by such Purchaser to the Company, against payment of the Purchase Price therefor as provided
in Section 1 above by wire transfer of immediately available funds to such account or accounts as the Company shall designate
in writing to such Purchaser at least two (2) days prior to the date of the Closing.

 

4.     
Company Representations. The Company represents and warrants to the Purchasers as follows:

 

(a)      
Organization and Standing. The Company is duly incorporated, validly existing, and in good standing under the laws
of the State of Delaware. The Company has all requisite power and authority to own and operate its properties and assets and to
carry on its business as presently conducted and as proposed to be conducted. The Company is qualified to do business as a foreign
entity in every jurisdiction in which the failure to be so qualified would have, or would reasonably be expected to have, a material
adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations,
prospects, financial condition or results of operation of the Company or the ability of the Company to perform its obligations
under this Agreement (a “Material Adverse Effect”). For the purposes of clarity, the implementation of any plan
for the significant restructuring of the Company, which has been approved by the Board of Directors of the Company as of the date
hereof, shall not constitute a Material Adverse Effect.

 

(b)     
Power. The Company has all requisite power to execute and deliver this Agreement, to sell and issue the Notes hereunder,
and to carry out and perform its obligations under the terms of this Agreement and the Notes (collectively, the “Transaction
Agreements”).

 

(c)      
Authorization. Subject to any waivers of covenants limiting the Company’s ability to incur further debt under
outstanding debt instruments and loans, each of which would be obtained or waived as required prior to the Closing (the “Pre-Closing
Consents”), the execution, delivery, and performance of the Transaction Agreements by the Company has been duly authorized
by all requisite action on the part of the Company and its officers, directors and stockholders, and this Agreement and the Notes
constitute the legal, valid, and binding obligation of the Company enforceable in accordance with its terms, except (a) as limited
by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of
creditors’ rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive
relief or other equitable remedies (together, the “Enforceability Exceptions”).

 

(d)     
Consents and Approvals. Except for any Current Report on Form 8-K or other document to be filed by the Company with
the U.S. Securities and Exchange Commission (the “SEC”) in connection with the transactions contemplated hereby,
the Company is not required to give any notice to, make any filing with, or obtain any authorization, consent, or approval of any
government or governmental agency in order to consummate the transactions contemplated hereby. Assuming the accuracy of the representations
of the Purchasers in Section 5, no consent,

 

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approval, authorization or other order of, or
registration, qualification or filing with, any court, regulatory body, administrative agency, self-regulatory organization, stock
exchange or market (including The NASDAQ Stock Market LLC (“The NASDAQ Stock Market”), or other governmental
body is required for the execution and delivery of the Transaction Agreements, the valid issuance, sale and delivery of the Notes
to be sold pursuant to this Agreement other than such as have been made or obtained, or for any securities filings required to
be made under federal or state securities laws applicable to the offering of the Notes.

 

(e)      
Non-Contravention. The execution and delivery of this Agreement and, following satisfaction of the Closing conditions
set forth in Sections 7 and 8 hereof as applicable to the Closing, the issuance, sale and delivery of the Notes to be sold by the
Company under this Agreement and the performance by the Company of its obligations under the Transaction Agreements and/or the
consummation of the transactions contemplated thereby, will not (a) conflict with, result in the breach or violation of, or
constitute (with or without the giving of notice or the passage of time or both) a violation of, or default under, (i) subject
to obtaining the Pre-Closing Consents, any bond, debenture, note or other evidence of indebtedness, or under any lease, license,
franchise, permit, indenture, mortgage, deed of trust, loan agreement, joint venture or other agreement or instrument to which
the Company or any subsidiary is a party or by which it or its properties may be bound or affected, (ii) the Company’s
Restated Certificate of Incorporation, as amended and as in effect on the date hereof, the Company’s Bylaws, as amended and
as in effect on the date hereof, or the equivalent document with respect to any subsidiary, as amended and as in effect on the
date hereof, or (iii) any statute or law, judgment, decree, rule, regulation, ordinance or order of any court or governmental
or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration panel or authority applicable to the Company,
any of its subsidiaries or their respective properties, except in the case of clauses (i) and (iii) for such conflicts,
breaches, violations or defaults that would not be likely to have, individually or in the aggregate, a Material Adverse Effect,
or (b) except for any security interests granted pursuant to the Notes, result in the creation or imposition of any lien,
encumbrance, claim, security interest or restriction whatsoever upon any of the material properties or assets of the Company or
any of its subsidiaries or an acceleration of indebtedness pursuant to any obligation, agreement or condition contained in any
material bond, debenture, note or any other evidence of indebtedness or any material indenture, mortgage, deed of trust or any
other agreement or instrument to which the Company or any if its subsidiaries is a party or by which the Company or any of its
subsidiaries is bound or to which any of the property or assets of the Company is subject. For purposes of this Section 4(e), the
term “material” shall apply to agreements, understandings, instruments, contracts or proposed transactions to which
the Company is a party or by which it is bound involving obligations (contingent or otherwise) of, or payments to, the Company
in excess of $100,000 in a 12-month period.

 

(f)      
Notes. The Notes have been duly authorized by the Company and, when duly executed and delivered and paid for as provided
herein, will be duly and validly issued and outstanding and will constitute valid and legally binding obligations of the Company
enforceable against the Company in accordance with their terms, subject to the Enforceability Exceptions. The issuance and delivery
of each of the Notes is not subject to preemptive, co-sale, right of first refusal or any other similar rights of the stockholders
of the Company or any other person, or any liens or encumbrances or result in the triggering of any anti-dilution or other similar
rights under any outstanding securities of the Company.

 

    	 	3	 

     

    

 

(g)      
No Registration. Assuming the accuracy of each of the representations and warranties of the Purchaser herein, the
issuance by the Company of the Notes is exempt from registration under the Securities Act of 1933, as amended (the “Securities
Act”).

 

(h)      
Reporting Status. The Company is subject to the reporting requirements of the Securities Exchange Act of 1934, as
amended (the “Exchange Act”), and, as of the Closing, will have filed all documents and reports that the Company
was required to file pursuant to Section I.A.3.b of the General Instructions to Form S-3 promulgated under the Securities Act in
order for the Company to be eligible to use Form S-3 (the foregoing materials, together with any materials filed by the Company
under the Exchange Act, whether or not required, collectively, the “SEC Documents”). The SEC Documents complied
as to form in all material respects with requirements of the Securities Act and Exchange Act and the rules and regulations of the
SEC promulgated thereunder (collectively, the “SEC Rules”), and none of the SEC Documents and the information
contained therein, as of their respective filing dates, contained any untrue statement of a material fact or omitted to state a
material fact required to be stated therein or necessary in order to make the statements therein, in light of the circumstances
under which they were made, not misleading. As used in this Agreement, “Previously Disclosed” means information
set forth in or incorporated by reference into the SEC Documents filed with the SEC on or after November 9, 2015 but prior to the
date hereof (except for risks and forward-looking information set forth in the “Risk Factors” section of the applicable
SEC Documents or in any forward-looking statement disclaimers or similar statements that are similarly non-specific and are predictive
or forward-looking in nature).

 

(i)       
Legal Proceedings. Except as Previously Disclosed, there is no action, suit or proceeding before any court, governmental
agency or body, domestic or foreign, now pending or, to the knowledge of the Company, threatened against the Company or its subsidiaries
wherein an unfavorable decision, ruling or finding would reasonably be expected to, individually or in the aggregate, (i) materially
adversely affect the validity or enforceability of, or the authority or ability of the Company to perform its obligations under,
the Transaction Agreements or (ii) have a Material Adverse Effect. The Company is not a party to or subject to the provisions
of any injunction, judgment, decree or order of any court, regulatory body, administrative agency or other governmental agency
or body that might have, individually or in the aggregate, a Material Adverse Effect.

 

(j)       
No Violations. Neither the Company nor any of its subsidiaries is in violation of its respective certificate of incorporation,
bylaws or other organizational documents, or to its knowledge, is in violation of any statute or law, judgment, decree, rule, regulation,
ordinance or order of any court or governmental or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration
panel or authority applicable to the Company or any of its subsidiaries, which violation, individually or in the aggregate, would
be reasonably likely to have a Material Adverse Effect. Neither the Company nor any of its subsidiaries is in default (and there
exists no condition which, with or without the passage of time or giving of notice or both, would constitute a default) in the
performance of any bond, debenture, note or any other evidence of indebtedness in any indenture, mortgage, deed of trust or any
other material agreement or instrument to which the Company or any of its subsidiaries is a party or by which the Company or any
of its subsidiaries is bound or by which the properties of the Company are bound, which would be reasonably likely to have a Material
Adverse Effect. There has not been, and to the knowledge of the Company, there is not pending or contemplated, any investigation
by the SEC

 

    	 	4	 

     

    

 

involving the Company or any current or former
director or officer of the Company and the Company is not an “ineligible issuer” pursuant to Rules 164, 405 and 433
under the Securities Act. The Company has not received any comment letter from the SEC relating to any SEC Documents which has
not been resolved. The SEC has not issued any stop order or other order suspending the effectiveness of any registration statement
filed by the Company under the Exchange Act or the Securities Act.

 

(k)      
Listing Compliance. Except as disclosed in its filings with the SEC, the Company is in compliance with the requirements
of The NASDAQ Stock Market for continued listing of the Common Stock thereon and has no knowledge of any facts or circumstances
that could reasonably lead to delisting of its Common Stock from The NASDAQ Stock Market. The Company has taken no action designed
to, or likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act or the listing of
the Common Stock on The NASDAQ Stock Market, nor has the Company received any notification that the SEC or The NASDAQ Stock Market
is contemplating terminating such registration or listing. The transactions contemplated by the Transaction Agreements will not
contravene the rules and regulations of The NASDAQ Stock Market.

 

(l)       
Financial Statements. The consolidated financial statements of the Company and its subsidiaries and the related notes
thereto included in the SEC Documents (the “Financial Statements”) comply in all material respects with applicable
accounting requirements and the rules and regulations of the SEC with respect thereto as in effect at the time of filing and present
fairly, in all material respects, the financial position of the Company and its subsidiaries as of the dates indicated and the
results of its operations and cash flows for the periods therein specified subject, in the case of unaudited statements, to normal
year-end audit adjustments. Except as set forth in such Financial Statements (or the notes thereto), such Financial Statements
(including the related notes) have been prepared in accordance with U.S. generally accepted accounting principles applied on a
consistent basis throughout the periods therein specified (“GAAP”). Except as set forth in the Financial Statements,
neither the Company nor its subsidiaries has any material liabilities other than liabilities and obligations that have arisen in
the ordinary course of business and which would not be required to be reflected in financial statements prepared in accordance
with GAAP.

 

(m)     
Disclosure. The Company understands and confirms that the Purchasers will rely on the foregoing representations in
effecting transactions in the Notes. All disclosure furnished by or on behalf of the Company to the Purchasers in connection with
this Agreement regarding the Company, its business and the transactions contemplated hereby is true and correct in all material
respects and does not contain any untrue statement of a material fact or omit to state any material fact necessary in order to
make the statements made therein, in light of the circumstances under which they were made, not misleading. The Company acknowledges
and agrees that the Purchasers have not made and do not make any representations or warranties with respect to the transactions
contemplated hereby other than those set forth in Section 5 hereto.

 

5.     
Investment Representations. In connection with the receipt of the Notes, each Purchaser represents
and warrants to the Company the following:

 

    	 	5	 

     

    

 

(a)      
Organization. Purchaser is duly organized, validly existing, and in good standing under the laws of the jurisdiction
of its organization.

 

(b)      
Power. Purchaser has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations
under the terms of this Agreement.

 

(c)      
Authorization. The execution, delivery, and performance of this Agreement by Purchaser has been duly authorized by
all requisite action, and this Agreement constitutes the legal, valid, and binding obligation of Purchaser enforceable in accordance
with its terms (subject to the Enforceability Exceptions).

 

(d)      
Consents and Approvals. Purchaser need not give any notice to, make any filing with, or obtain any authorization,
consent, or approval of any government or governmental agency in order to consummate the transactions contemplated by this Agreement.

 

(e)      
Non-Contravention. The execution, delivery and, subject to satisfaction by the Company of the conditions to Closing
set forth in Sections 7 and 8 hereof on or prior to the issuance of the Notes, or performance, by Purchaser of this Agreement do
not and will not contravene or constitute a default under, or violation of, or be subject to penalties under, (i) any agreement
(or require the consent of any party under any such agreement that has not been made or obtained) to which Purchaser is a party,
or (ii) any judgment, injunction, order, decree or other instrument binding upon Purchaser, except where such contravention, default,
violation or failure to obtain a consent, individually or in the aggregate, would not reasonably be expected to impair Purchaser’s
ability to perform fully any obligation which Purchaser has or will have under this Agreement.

 

(f)       
Investor Qualification. Purchaser understands the definition of the term “accredited investor” within
the meaning of Regulation D, Rule 501(a), promulgated by the SEC under the Securities Act, and qualifies as an accredited
investor.

 

(g)      
Information; Purchase for Investment Only. Purchaser is aware of the Company’s business affairs and financial
condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire
the Notes. Purchaser is acquiring the Notes for investment for its own account only and not with a view to, or for resale in connection
with, any “distribution” thereof within the meaning of the Securities Act or under any applicable provision of state
law. Purchaser does not have any present intention to transfer the Notes to any other person or entity in such a “distribution.”

 

(h)      
No Registration. Purchaser understands that the Notes have not been registered under the Securities Act by reason
of a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Purchaser’s
investment intent as expressed herein.

 

(i)       
Restricted Securities. Purchaser understands that the Notes are “restricted securities” under applicable
U.S. federal and state securities laws and that, pursuant to these laws, Purchaser must hold the Notes indefinitely unless they
are registered with the SEC and qualified by state authorities, or an exemption from such registration and qualification requirements
is

 

    	 	6	 

     

    

 

available. Purchaser acknowledges that the Company
has no obligation to register or qualify the Notes for resale.

 

(j)        
Risk of Investment. Purchaser realizes that the purchase of the Notes will be a highly speculative investment and
Purchaser may suffer a complete loss of its investment. Purchaser understands all of the risks related to the purchase of the Notes.
By reason of its business and financial experience, Purchaser has the ability to protect its own interests in connection with the
purchase of the Notes.

 

(k)      
Advisors. Purchaser has reviewed with its own tax advisors the federal, state, and local tax consequences of this
investment and the transactions contemplated by this Agreement. Purchaser acknowledges that it has had the opportunity to review
this Agreement and the transactions contemplated hereby with Purchaser’s own legal counsel.

 

(l)       
Finder. Purchaser is not obligated and will not be obligated to pay any broker commission, finders’ fee, success
fee, or commission in connection with the transactions contemplated by this Agreement.

 

6.     
Restrictive Legends and Stop-Transfer Orders. The Notes shall bear such legends as the Company deems
to be required for the purpose of compliance with applicable federal or state securities laws or as otherwise required by law.

 

7.     
Conditions to Company’s Obligations at the Closing. The Company’s obligation to complete
the sale and issuance of the Notes, and deliver the Notes to the Purchasers at the Closing shall be subject to the following conditions
to the extent not waived by the Company:

 

(a)      
Receipt of Payment. The Company shall have received payment (or confirmation that an Irrevocable Payment Instruction
has been made with respect to such payment), by wire transfer of immediately available funds or by cancellation of indebtedness
of the Company to each applicable Purchaser, in the full amount of the Purchase Price for the Notes being purchased by such Purchaser
at the Closing.

 

(b)      
Representations and Warranties. The representations and warranties made by the Purchasers in Section 5 hereof
shall be true and correct in all material respects as of, and as if made on, the date of such Closing.

 

(c)       
Subordination Agreement. The Purchasers shall have executed and delivered to the Company the Subordination Agreement
(as defined in Section 9(b)(ii) hereof).

 

8.     
Conditions to Purchaser’s Obligations at the Closing. Each Purchaser’s obligation to accept
delivery of the Notes and to pay for such Purchaser’s respective Notes at the Closing shall be subject to the following conditions
to the extent not waived by such Purchaser:

 

(a)      
Representations and Warranties. The representations and warranties made by the Company in Section 4 hereof shall
be true and correct in all material respects (except for any representations and warranties which are qualified as to materiality,
which shall be true and correct in all respects) as of, and as if made on, the date of this Agreement and as of the date of the
Closing as though such representations and warranties were made on and as of such date.

 

    	 	7	 

     

    

 

(b)      
Certificate. The Purchaser shall have received a certificate dated as of the Closing and signed by the Company’s
Chief Executive Officer and Chief Financial Officer to the effect that the representations and warranties of the Company in Section 4
hereof are true and correct in all material respects (except for any representations and warranties which are qualified as to materiality,
which shall be true and correct in all respects) as of, and as if made on, the date of this Agreement and as of the Closing, and
that the Company has satisfied all of the conditions set forth in this Agreement and required to be satisfied as of the Closing.

 

(c)      
Good Standing. The Company shall be validly existing as a corporation in good standing under the laws of Delaware
as evidenced by a certificate of the Secretary of State of the State of Delaware, a copy of which shall be provided to the Purchaser
at the Closing.

 

(d)      
Board Approval. The terms and conditions of the issuance of the Notes and the Transaction Agreements shall have been
duly approved by the Board of Directors of the Company (including the Audit Committee and at least six directors who are disinterested
with respect to the transactions contemplated hereby).

 

(e)      
Other Approvals. The Company shall have obtained all governmental, regulatory or third party consents and approvals
required in connection with the transactions contemplated hereby, if any, including obtaining the Pre-Closing Consents and any
waivers of any other negative covenants and pro rata or similar preemptive rights that may apply to the issuance of the Notes.

 

9.     
Other Agreements

 

(a)      
SEC Filings. Upon execution of this Agreement and the issuances of Notes, the Company will complete any SEC filings
(such as a Current Report on Form 8-K) that are, in the judgment of the Company’s legal counsel, required to be completed.

 

(b)      
Security Interest.

 

(i)       
As security for the prompt, complete and indefeasible payment when due (whether on the payment dates or otherwise) of all
the Company’s obligations under the Notes, including any obligation to pay any amount now owning or later arising under the
Notes (collectively, the “Secured Obligations”), the Company grants to each Purchaser a second priority security interest
in all of the Company’s right, title, and interest in and to the Collateral (as defined in that certain Loan and Security
Agreement dated as of March 29, 2014, as amended on June 12, 2014, March 31, 2015 and November 30, 2015 (as amended, the “LSA”)
by and between the Company, and each of its subsidiaries that has delivered a Joinder Agreement (as defined in the LSA), the other
financial institutions or entities from time to time parties to the LSA (collectively, referred to as “Lender”)
and Stegodon Corporation, a Delaware corporation, as assignee of Hercules Capital, Inc., a Maryland corporation, in its capacity
as administrative agent for itself and the Lender (in such capacity, the “Agent”)), as limited by Section 3.2
of the LSA.

 

(ii)     
The Company hereby agrees to enter into any additional Security Documents (as defined below) with the Purchasers as may
be reasonably required by the Purchasers in connection with the grant of the security interest contemplated by Section 9(b)(i)
hereof, provided, however, that such security interest shall be subject to the Subordination

 

    	 	8	 

     

    

 

Agreement dated as of October 5, 2016, by and
among the Purchasers, the Company and the Agent (the “Subordination Agreement”). As used herein, “Security
Documents” means each security agreement, all other mortgages, deeds of trust, security agreements, pledge agreements,
assignments, control agreements, financing statements and other documents as shall from time to time secure or relate to the Secured
Obligations or any part thereof, in each case, executed by the Company or any subsidiary of the Company.

 

10. 
Miscellaneous.

 

(a)      
Governing Law. This Agreement and all acts and transactions pursuant hereto and the rights and obligations of the
parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of California, without giving
effect to principles of conflicts of law.

 

(b)      
Assignment; Successors and Assigns. This Agreement may not be assigned by the Purchaser without the prior written
consent of the Company; provided, that this Agreement may be assigned by a Purchaser to the valid transferee of any security
purchased hereunder if such security remains a “restricted security” under the Securities Act. This Agreement and all
provisions thereof shall be binding upon, inure to the benefit of, and are enforceable by the parties hereto and their respective
successors and permitted assigns.

 

(c)      
Notices. All notices, requests, and other communications hereunder shall be in writing and will be deemed to have
been duly given and received (i) when personally delivered, (ii) when sent by facsimile upon confirmation of receipt,
(iii) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service,
or (iv) five business days after the deposit in the United States mail, registered or certified, return receipt requested,
postage prepaid, in each case addressed, as to the Company, to Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608,
Attn: General Counsel, facsimile number:                    , with a copy to Fenwick & West LLP, 801 California Street, Mountain View, CA 94041,
Attn: , facsimile number: , and as to each Purchaser at the address and facsimile number set forth opposite such Purchaser’s
name on the Schedule of Purchasers on Schedule I. Any party hereto from time to time may change its address, facsimile number,
or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto.
The Purchasers and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic
communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular
notices or communications.

 

(d)     
Severability. In the event that any provision of this Agreement or the application of any provision hereof is declared
to be illegal, invalid, or otherwise unenforceable by a court of competent jurisdiction, the remainder of this Agreement shall
not be affected except to the extent necessary to delete such illegal, invalid, or unenforceable provision unless that provision
held invalid shall substantially impair the benefits of the remaining portions of this Agreement.

 

    	 	9	 

     

    

 

(e)       
Headings. The headings in this Agreement are for convenience of reference only and shall not constitute a part of
this Agreement, nor shall they affect its meaning, construction, or effect.

 

(f)       
Entire Agreement. This Agreement embodies the entire understanding and agreement between the parties hereto with
respect to the subject matter hereof and supersedes all prior agreements and understandings relating to the subject matter hereof.

 

(g)      
Expenses. Each party will bear its own costs and expenses in connection with this Agreement.

 

(h)      
Further Assurances. The parties agree to execute and deliver all such further documents, agreements and instruments
and take such other and further action as may be necessary or appropriate to carry out the purposes and intent of this Agreement.

 

(i)       
Counterparts. This Agreement may be executed in two or more counterparts, each of which shall constitute an original,
but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts
have been signed by each party hereto and delivered to the other party. Facsimile signatures shall be deemed originals for all
purposes hereunder.

 

(j)       
Amendments and Waivers. This Agreement may not be amended, supplemented or otherwise modified except in a written
instrument executed by the Company and the holders of a majority of the aggregate principal amount of the then outstanding Notes.
No waiver by any of the parties of any default, misrepresentation, or breach of warranty or covenant hereunder, whether intentional
or not, shall be deemed to extend to any prior or subsequent default, misrepresentation, or breach of warranty or covenant hereunder
or affect in any way any rights arising by virtue of any prior or subsequent such occurrence. No waiver by any of the parties of
any of the provisions hereof shall be effective unless explicitly set forth in writing and executed by the party sought to be charged
with such waiver. No action taking pursuant to this Agreement, including any investigation by or on behalf of any party, shall
be deemed to constitute a waiver by the party taking such action of compliance with any representation, warranty, covenant or agreement
contained herein. No failure on the part of any party to exercise, and no delay in exercising, any right, power or remedy hereunder
shall operate as a waiver thereof, nor shall any single or partial exercise of such right, power or remedy by such party preclude
any other or further exercise thereof or the exercise of any other right, power or remedy.

 

[Signature Pages Follow]

 

 

 

 

 

    	 	10	 

     

    

 

The undersigned has executed this Agreement as of the date first
set forth above.

 

	 	the company:	 
	 	 	 	 
	 	AMYRIS, inc.	 
	 	 	 	 
	 	By:	/s/ Raffi Asadorian 	 
	 	 	(Signature)	 
	 	 	 	 
	 	Name: Raffi Asadorian	 
	 	 	 	 
	 	Title: Chief Financial Officer
	 	 	 	 
	 	Address: 	 
	 	5885 Hollis Street, Suite 100
	 	Emeryville, CA 94608
	 	Attention: General Counsel
	 	Facsimile: 
	 	Email:

 

 

 

 

 

 

 

 

    	 	[Note Purchase Agreement Signature Page]	 

     

    

 

The undersigned has executed this Agreement as of the date first
set forth above.

 

	 	PURCHASER:	 
	 	 	 	 
	 	FORIS VENTURES, LLC	 
	 	 	 	 
	 	By:	/s/ B Hager 	 
	 	 	(Signature)	 
	 	 	 	 
	 	Name:	Barbara Hager 	 
	 	 	 	 
	 	Title:	Manager 	 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

    	 	[Note Purchase Agreement Signature Page]	 

     

    

 

Schedule
I

 

Schedule of Purchasers

 

Closing: October 5, 2016

 

	Name of Purchaser	Notes Principal Amount	Note Purchase Price	Address and Facsimile
	Foris Ventures, LLC	$6,000,000	$6,000,000	Foris Ventures, LLC
	 	 	 	Attention: Barbara S. Hager
	 	 	 	JEMA Management LLC
	 	 	 	751 Laurel St. #717
	 	 	 	San Carlos, CA  94070
	 	 	 	Fax: 
	 	 	 	 
	TOTAL	$6,000,000	$6,000,000	 

 

 

 

 

 

 

 

 

     

     

    

 

exhibit
a

 

form
of note

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