Document:

Document

Exhibit 4.09

Execution Copy 

SECOND AMENDMENT TO SENIOR CONVERTIBLE NOTE DUE 2022 AND WAIVER AND FORBEARANCE AGREEMENT 
This SECOND AMENDMENT TO SENIOR CONVERTIBLE NOTE DUE 2022 AND WAIVER AND FORBEARANCE AGREEMENT (this “Second Amendment”) is made and entered into as of June 4, 2020, by and among Amyris, Inc., a Delaware corporation (the “Company”) and HT Investments MA LLC (the “Holder”). 
RECITALS 
WHEREAS, the Company has issued that certain Senior Convertible Note due 2022 (the “Note”), to the Holder pursuant to exchanges for prior convertible notes of the Company in reliance upon the exemption from registration provided by Section 3(a)(9) of the Securities Act of 1933, as amended (the “Securities Act”), as set forth in (i) that certain Exchange Agreement, dated as of November 8, 2019, by and among the Company and the investors on the Schedule of Buyers attached thereto (the “Original Exchange Agreement”) (as the same may be amended from time to time) and (ii) that certain Exchange Agreement, dated as of December 30, 2019, by and among the Company and the Buyer (the “Subsequent Exchange Agreement”) (as the same may be amended from time to time); 
WHEREAS, the Company and Holder previously entered into that certain Amendment to Senior Convertible Note Due 2022 and Waiver and Forbearance Agreement as of May 1, 2020 (the First Amendment”); and 
WHEREAS, the Company and the Holder desire to further amend certain provisions of the Note; 
WHEREAS, pursuant to Section 18 of the Note, the Note may be amended with the written consent of the Company and the Required Holders (as defined in the Original Exchange Agreement); 
WHEREAS, as of the date hereof, the Holder constitutes the Required Holders (as defined in the Original Exchange Agreement); and 
WHEREAS, the Company and Holder have entered into that certain Waiver and Forbearance Agreement, dated as of February 18, 2020 (the “Forbearance Agreement”) and desire to further amend certain provisions of the Forbearance Agreement. 
NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending to be legally bound, agree as follows: 
ARTICLE I 
AMENDMENT OF NOTES 
1.1. Section 5(G)(iii) of the Note. Section 5(G)(iii) of the Note is hereby amended and restated in its entirety to read as follows: 
(iii)Pre-Delivery Share Reduction. Notwithstanding anything to the contrary contained herein, (A) from and after May 1, 2020, one million seven hundred 

          

thousand (1,700,000) shares of Common Stock that were previously Pre-Delivery Shares hereunder shall no longer constitute Pre-Delivery Shares and, subject to that certain letter agreement between the Company and the Holder dated as of May 1, 2020, shall be Freely Tradable shares of Common Stock owned by the Holder, free from all preemptive or similar rights or Liens with respect thereto and (B) from and after June 4, 2020, an additional seven hundred thousand (700,000) shares of Common Stock that were previously Pre-Delivery Shares hereunder shall no longer constitute Pre-Delivery Shares, subject to that certain letter agreement between the Company and the Holder dated as of June 4, 2020, and shall be Freely Tradable shares of Common Stock owned by the Holder, free from all preemptive or similar rights or Liens with respect thereto. For the avoidance of doubt, as of June 4, 2020, the total number of Pre-Delivery Shares outstanding shall be deemed to be two million six hundred thousand (2,600,000) shares. 
1.2. Section 5(G)(iv) of the Note. Section 5(G)(iv) of the Note is hereby amended and restated in its entirety to read as follows: 
 (ii) Delivery of Pre-Delivery Shares by the Holder. Within ten (10) Business Days following redemption or repayment of this Note in full and the satisfaction or discharge by the Company of all outstanding Company obligations hereunder, the Holder shall deliver two million six hundred thousand (2,600,000) shares (subject to proportionate adjustments for events of the type set forth in Section 8(F)(i)(1)) of the Company’s Common Stock to the Company, free from all preemptive or similar rights or Liens with respect to the delivery thereof; provided, that, to the extent the Company fails to deliver any fully paid and nonassessable Freely Tradable shares of Common Stock to the Holder as required under Section 5(G)(i) or Section 5(G)(ii), the number of shares of the Company’s Common Stock to be delivered under this Section 5(G)(iv) shall be reduced by the number of such shares of Common Stock the Company failed to deliver. For the avoidance of doubt, this Section 5(G)(iv) shall not apply to the transactions contemplated by the Exchange Agreement. 
ARTICLE II 
AMENDMENT OF FORBEARANCE AGREEMENT 
2.1. The definition of “Forbearance Period” as set forth in the Forbearance Agreement is hereby amended and restated in its entirety to read as follows: 
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(a) “Forbearance Period” means the period commencing on the date hereof and ending on the date which is the earliest of (i) with respect to the Specified Existing Defaults, the earlier of (X) the day the Company has received aggregate cash proceeds from any public offerings or private placements of its securities occurring on or after May 1, 2020 of not less than fifty million dollars ($50,000,000) and (Y) June 30, 2020, and with respect to the Specified Anticipated Default, May 29, 2020, (ii) the occurrence or existence of any Event of Default, other than the Specified 

          

Defaults and any Event of Default giving rise to a Termination Event, or (iii) the occurrence of any Termination Event. 
2.2. The definition of “Specified Existing Defaults” as set forth in the Forbearance Agreement is hereby amended and restated in its entirety to read as follows: 
(d) “Specified Existing Defaults” means each of: (1) Company's failure, on or before January 31, 2020, to receive aggregated net cash proceeds of not less than fifty million dollars ($50,000,000) from one or more issuances of Capital Stock or incurrences of Permitted Indebtedness (as defined in the Note) by the Company, or any combination thereof, and before giving effect to transaction expenses; (2) Company’s failure, on or before January 31, 2020, to (i) repay in full or convert into equity all Indebtedness outstanding under its Credit and Security Agreement, dated November 14, 2019 by and among the Company, certain of the Company’s subsidiaries, Schottenfeld Opportunities Fund II, L.P. (“SOP”) and Phase Five Partners, LP (“Phase Five”) (the “November Credit Agreement”), or (ii) amend all such Indebtedness to fit within clause (E) of the definition of Permitted Indebtedness so it does not have a final maturity date, amortization payment, sinking fund, mandatory redemption or other repurchase obligation or put right at the option of the lender or holder of such Indebtedness earlier than ninety one (91) days following the Maturity Date, or any combination of the foregoing with respect to all such Indebtedness; (3) Company’s entry into a secured loan agreement on December 19, 2019 with an initial maturity date of January 31, 2020 with Nikko Chemicals Co., Ltd., in violation of Section 9(D) of the Note; and (4) the occurrence of an Event of Default under clause 11(A)(xi) of the Note, solely to the extent arising from defaults (I) in existence on the date hereof with respect to the notes issued under (A) those certain credit agreements dated September 10, 2019 by and among the Company, certain of the Company’s subsidiaries and each of SOP, Koyote Trading, LLC, and Phase Five (the “September Credit Agreements”) or (B) the November Credit Agreement and (II) for which the holder of such notes has not declared any portion of such indebtedness due and payable or taken any other steps to enforce such indebtedness. 

ARTICLE III 
MISCELLANEOUS 
3.1. Rule 144 Holding Period. The Company and the Holder acknowledge and agree that, as set forth in the Original Exchange Agreement and the Subsequent Exchange 

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Agreement, the Note will continue to have a holding period under Rule 144 promulgated under the Securities Act that will be deemed to have commenced as of December 10, 2018.  

3.2. Material Non-Public Information. The Company represents to Holder that neither this Second Amendment, nor the further amendment of the Note and/or the Warrant pursuant to the terms of this Second Amendment constitutes material, nonpublic information (if any) provided to the Holder by the Company. 

3.3 Captions. The headings contained in this Amendment are for reference purposes only and shall not affect in any way the meaning or interpretation of this Amendment. Except as otherwise indicated, all references in this Amendment to “Sections” are intended to refer to the Sections or Articles of the Note, as applicable. 

3.4. Governing Law. The internal law of the State of New York will govern and be used to construe this Amendment. The Company and the Holder irrevocably waive, to the fullest extent permitted by applicable law, any and all right to trial by jury in any legal proceeding arising out of or relating to this Amendment. 
3.5. Principal Amount; No Other Amendment. The Company and the Holder acknowledge and agree that the Principal Amount outstanding under the Note as of the date hereof is twenty million dollars ($20,000,000). Except for the matters expressly set forth in this Second Amendment, all other terms of the Note and Warrant, as amended by the First Amendment, are hereby ratified and shall remain unchanged and in full force and effect. 
3.6. Counterparts. This Amendment may be executed in counterparts, each of which shall be deemed to be an original, and all of which together shall be deemed to be one and the same instrument. 
3.7. Electronic and Facsimile Signatures. Any signature page delivered electronically or by facsimile (including without limitation transmission by .pdf) shall be binding to the same extent as an original signature page, with regard to any agreement subject to the terms hereof or any amendment thereto. Any party who delivers such a signature page agrees to later deliver an original counterpart to the other party if so requested. 
[Signature Pages Follow] 

          

The parties hereto have executed this Second Amendment to Senior Convertible Note due 2022 and Waiver and Forbearance Agreement as of the date first written above.
COMPANY:

AMYRIS, INC.

By: /s/ Han Kieftenbeld
        Name: Han Kieftenbeld
        Title: Chief Financial Officer

          

The parties hereto have executed this Second Amendment to Senior Convertible Note due 2022 and Waiver and Forbearance Agreement as of the date first written above.
REQUISITE HOLDER:

HT INVESTMENTS MA LLC

By: /s/ Eric Helenek
        Name: Eric Helenek
        Title: Authorized SignatoryDocument

Exhibit 10.01

EXECUTION VERSION

WAIVER AGREEMENT 

This Waiver Agreement (this “Third Waiver Agreement”) is made as of May 6, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and Ginkgo Bioworks, Inc., a Delaware corporation (“Ginkgo”), pursuant to the terms of (i) that certain Promissory Note, dated October 20, 2017 (as amended, the “Note”), issued by the Company to Ginkgo, (ii) that certain Partnership Agreement, dated October 20, 2017 (the “Partnership Agreement”), by and between the Company and Ginkgo, (iii) that certain Waiver Agreement and Amendment to Promissory Note Issued October 20, 2017, dated September 29, 2019 (the “First Waiver Agreement”), by and between the Company and Ginkgo, and (iv) that certain Waiver Agreement and Amendment, dated March 11, 2020 (the “Second Waiver Agreement”), by and between the Company and Ginkgo. Capitalized terms used but not otherwise defined herein shall have the meanings given to such terms in the Note or the Partnership Agreement, as applicable. 

RECITALS

A. Pursuant to Section 2.1(b) of the Note, the Company is required to make monthly interest payments to Ginkgo beginning on November 30, 2017 and continuing on the last day of each month thereafter, through and including the Maturity Date (each, an “Interest Payment”). 

B. Pursuant to Section 4.3(a) of the Partnership Agreement, as amended by the Second Waiver Agreement, the Company is required to pay Ginkgo monthly fees beginning on March 31, 2020 and continuing on the last day of each month thereafter, through and including October 31, 2021 (each, a “Partnership Payment”). 

C. Pursuant to Section 6.3 of the Note, the Company is required to notify Ginkgo in writing in the event that the consolidated cash balance of the Company is less than $10,000,000 at monthly close (the “Reporting Covenant”). 

D. Pursuant to Section 4(d) of the Note, certain cross defaults by the Company are considered an Event of Default (the “Cross Default”). 

E. Pursuant to Section 6 of the Second Waiver Agreement, the Company was required to pay Ginkgo on or before April 30, 2020, an aggregate of $7,153,770 (the “April 2020 Payment”), which represents all the payments due on or before April 30, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, and the Second Waiver Agreement.

F. The Company has requested and Ginkgo has agreed, in consideration of and subject to the terms and conditions contained herein, to (i) waive any failure by the Company to make the April 2020 Payment prior to April 30, 2020, (ii) waive any failure by the Company to comply with the Reporting Covenant prior to the date hereof, and (iii) waive any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. 

G. Pursuant to Section 10.7 of the Note, provisions of the Note may be amended or waived only by written agreement of the Company and Ginkgo. 

H. Pursuant to Section 9.4 of the Partnership Agreement, any modification to the Partnership Agreement shall only be effective if made in a writing signed by the Company and Ginkgo. 

AGREEMENT

For good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and Ginkgo agree as follows: 

1. Reporting Covenant Waiver.  In accordance with Section 10.7 of the Note, Ginkgo hereby waives any failure by the Company to comply with the Reporting Covenant prior to the date hereof, including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement. 

2. Cross Default Waiver.  In accordance with Section 10.7 of the Note, Ginkgo hereby waives any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (inclusive), including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement. 

3. May 2020 Payment.  Ginkgo hereby waives timely payment of the April 2020 Payment until the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (the “Payment Deadline”), and agrees that, notwithstanding anything to the contrary in this Third Waiver Agreement, the Second Waiver Agreement remains in full force and effect with respect to the waivers and amendment set forth therein. Moreover, the Company agrees that in addition to the April 2020 Payment, it will pay to Ginkgo the additional sum of $774,011, for a total payment of $7,927,781 (the “May 2020 Payment”), which represents all the payments due on or before May 31, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, the Second Waiver Agreement, and this Third Waiver Agreement.  The May 2020 Payment will be paid by the Company by wire transfer of immediately available funds in accordance with the wire instructions delivered to the Company by Ginkgo no later than two (2) Business Days prior to the applicable payment date.  Any failure by the Company to make any payment set forth in this Section 3 on or prior to the applicable payment deadline shall (a) constitute an Event of Default under the Note and the Partnership Agreement; and (b) render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

4. Full Force and Effect.  Except as expressly modified by this Third Waiver Agreement, the terms of the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements shall remain in full force and effect. 

5. Release.  In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably releases, waives, and forever discharges Ginkgo, together with its respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors, officers, attorneys, and attorneys’ consultants (collectively, the “Released Parties”), from (x) any and all liabilities, obligations, duties, promises, or 
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indebtedness of any kind (if any) of the Released Parties to the Company or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world to the date of this Third Waiver Agreement; and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any), which the Company or any of its affiliates might otherwise have against the Released Parties, or any of them; in either case of (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 Third Waiver Agreement, whether at law or in equity, whether based upon statute, common law or otherwise, whether matured, contingent or non-contingent, whether direct or indirect, whether known or unknown, whether suspected or unsuspected, which the Company ever had, now has, or may claim to have against, arising out of, based on, asserted in, or in connection with any agreement or event. 

6. Section 1542 Waiver.  In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably waives any rights it has or may have pursuant to California Civil Code Section 1542, which provides as follows:

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

7. Attorneys’ Fees.  The Company promises to pay to Ginkgo immediately upon receipt of an invoice any and all reasonable attorneys’ and other professionals’ fees and expenses incurred by Ginkgo  between March 12, 2020 and the date hereof, inclusive, in connection with the Note, the Partnership Agreement, the First and Second  Waiver Agreements, and/or this Third Waiver Agreement, including, without limitation, with respect to the administration, collection, enforcement, amendment or modification of any of them; and with respect to any waiver, consent, release, termination, litigation, administrative proceeding, arbitration, bankruptcy proceeding, or dispute resolution.  Any failure by the Company to make timely payment as set forth in this Section 7 shall render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

8. Integration.  This Third Waiver Agreement, the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between the parties hereto with respect to the specific subject matter hereof. 

9. Counterparts.  This Third Waiver Agreement may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Third Waiver Agreement may be executed and delivered by facsimile, or by email in portable document format (.pdf) or other electronic format, and delivery of any signature page by any such method will be deemed to have the same effect as if the original signature page had been delivered to the other party. 

[Signature pages follow]
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IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

AMYRIS, INC.

By: /s/ Kathleen Valiasek 
Name: Kathleen Valiasek
Title: Chief Business Officer

[Waiver Signature Page]

IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

GINKGO BIOWORKS, INC.

By: /s/ Jason Kelly
Name: Jason Kelly
Title: CEO

[Waiver Signature Page]

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