Exhibit 10.1

MUTUAL SEPARATION AGREEMENT AND MUTUAL RELEASE

This Mutual Separation Agreement and Mutual Release (“Agreement”) is made by and
between Paul Wagner, Ph.D. (“Executive”) and Pfenex Inc. (the “Company”)
(jointly referred to as the “Parties” or individually referred to as a “Party”)
entered into on September 7, 2017 (the “Execution Date”) and effective as of the
Effective Date (as defined in Section 26 below).

RECITALS

WHEREAS, Executive is currently employed as the Company’s Chief Financial
Officer;

WHEREAS, Executive signed an Executive Employment Agreement with the Company on
June 20, 2014 (the “Employment Agreement”);

WHEREAS, Executive signed the Confidential Information and Invention Assignment
Agreement with the Company on June 20, 2014 (the “CIIA”);

WHEREAS, Executive signed an Indemnification Agreement with the Company, dated
June 24, 2014 (the “Indemnification Agreement”);

WHEREAS, Executive previously was granted options to purchase shares of the
Company’s common stock (each, an “Option”) pursuant to the terms of the
Company’s 2009 Equity Incentive Plan (the “2009 Plan”) or the Company’s 2014
Equity Incentive Plan (the 2014 Plan, and together with the 2009 Plan, the
“Plans”) and individual award agreements thereunder (each, a “Stock Option
Agreement” and together with the Plans, the “Equity Agreements”);

WHEREAS, Executive is resigning his employment with the Company without “Good
Reason” (as defined in the Employment Agreement), which resignation shall be
effective October 13, 2017, though Employee remains an at-will Employee through
October 13, 2017 (the last day of Employee’s employment is the “Separation
Date”); and

WHEREAS, the Parties wish to resolve any and all disputes, claims, complaints,
grievances, charges, actions, petitions, and demands that the Executive may have
against the Company and any of the Releasees as defined below, and that the
Company may have against the Executive, including in each case, but not limited
to, any and all claims arising out of or in any way related to Executive’s
employment with or separation from the Company.

NOW, THEREFORE, in consideration of the mutual promises made herein, the Company
and Executive hereby agree as follows:

COVENANTS

1.    Consideration. In exchange for Executive entering into this Agreement and
executing the resignation letter appended as Exhibit B prior to or
contemporaneously with this Agreement:

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a.    Bonus Severance. If Executive remains employed by the Company through
October 13, 2017, the Company agrees to pay to Executive an award under the
Pfenex Inc. Incentive Compensation Plan and the 2017 Participation and
Performance Goals under the Incentive Compensation Plan (together, the “Bonus
Plan”) for the 2017 Performance Period (as defined in the Bonus Plan) (the
“Bonus Severance”). Pursuant to the Bonus Plan, Executive’s Target Award (as
defined in the Bonus Plan) for the 2017 Performance Period is thirty-five
percent (35%) of his current base salary, or $120,400. The Bonus Severance
amount will be determined by (i) the actual achievement of the corporate
performance goals during the 2017 Performance Period as determined by
Compensation Committee of the Board of Directors, and (ii) the Executive’s
individual performance goals during the 2017 Performance Period, which are
hereby determined to have been achieved at one hundred percent (100%). The Bonus
Severance will be paid in accordance with the terms and conditions of the Bonus
Plan, and no later than March 15, 2018. Executive acknowledges and agrees that
unless he signs this Agreement, he would not otherwise be entitled to the awards
described in this paragraph unless he remained employed through the date bonuses
are paid in 2018.

b.    Consulting Agreement. If Executive remains employed with the Company
through October 13, 2017, then, commencing on the Separation Date, Executive
agrees to provide consulting services to the Company pursuant to the terms of
the Consulting Agreement attached hereto as Exhibit A (the “Consulting
Agreement”) for the period of time specified therein (the “Consulting Period”
and the date on which Executive ceases to provide consulting services to the
Company, the “Consulting End Date”). During the Consulting Period, Executive
agrees to reasonably assist the Company in connection with the transitioning of
Executive’s duties, and to provide such other services as are set forth in the
Consulting Agreement. Nothing in this Agreement or the Consulting Agreement
pertaining to Executive’s subsequent role as a Consultant shall in any way be
construed to constitute Executive continuing as an agent, employee, officer, or
representative of the Company. Executive shall perform the services under the
Consulting Agreement solely as an independent contractor. During the Consulting
Period, Executive shall receive only that compensation set forth in Schedule 1
to Exhibit A for his consulting services. All other aspects of the consulting
arrangement shall be governed by the terms of Exhibit A.

c.    Extension of Option Post-Service Exercisability Period. If Executive
remains employed with the Company through October 13, 2017, and continues to
provide consulting services through the Consulting Period the post-service
exercisability period of the Options shall be extended such that each Option, to
the extent vested and exercisable as of the Consulting End Date, will be
exercisable until the earlier of (i) December 31, 2019 or (ii) the applicable
Option’s expiration date, as set forth in the applicable Stock Option Agreement,
unless otherwise earlier terminated in accordance with Section 13 of the 2009
Plan or Section 14 of the 2014 Plan, as applicable. Executive acknowledges and
agrees that this extension of the Options’ post-service exercisability periods
is a “modification” of the Option under the Internal Revenue Code of 1986, as
amended (the “Code”) and, to the extent any Option or portion thereof is treated
as an incentive stock option, the extension of the post-service exercisability
period with respect to such Options will result in a re-setting of the
applicable holding periods for the incentive stock options; and further, that in
any event, any incentive stock options will convert into nonstatutory stock
options to the extent that the Option remains outstanding three months

 

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and one day after Executive ceases to be an employee of the Company. Executive
acknowledges and agrees that Executive remains solely responsible for all tax
obligations associated with any exercise of the Options.

d.    No Further Severance. Except as explicitly set forth in this Agreement,
Executive acknowledges and agrees that he is not entitled to receive any
severance compensation or post-termination benefits from the Company, including,
but not limited to, the payments described in Section 6 of the Employment
Agreement. Executive hereby acknowledges that without this Agreement, he is not
otherwise entitled to the consideration listed in this section 1 or any other
severance or separation benefits from the Company.

2.    Termination. Effective as of the Separation Date, Executive’s employment
with the Company is terminated, and Executive will no longer serve in any
positions Executive occupied with the Company or any subsidiary or affiliate of
the Company. No earlier than the Separation Date and no later than the date that
is ten (10) days after the Separation Date, Executive and Company shall execute
and deliver the Supplement to this Agreement set forth on Exhibit C hereto with
respect to activities that occur during the period from the Execution Date
through the Separation Date, as set forth in more detail in this Agreement.

3.    Stock. Except as amended by Section 1 of this Agreement, each Option that
is outstanding and unexercised as of the Separation Date shall continue to be
subject to the terms of the Equity Agreements, including that each Option shall
continue to vest during the Consulting Period in accordance with the vesting
schedule under the applicable Equity Agreement.

4.    Benefits. Executive’s health insurance benefits shall cease on the last
day of the month in which Executive’s employment terminates, subject to
Executive’s right to continue Executive’s health insurance under the
Consolidated Omnibus Budget Reconciliation Act of 1985. Executive’s
participation in all benefits and incidents of employment, including, but not
limited to, the accrual of bonuses, vacation, and paid time off, cease as of the
Separation Date.

5.    Payment of Salary and Receipt of All Benefits. Executive acknowledges and
represents that, other than the consideration set forth in this Agreement, the
Company has paid or provided all salary, wages, bonuses, accrued vacation/paid
time off, premiums, leaves, housing allowances, relocation costs, interest,
severance, outplacement costs, fees, reimbursable expenses, commissions, stock,
stock options, vesting, and any and all other benefits and compensation due to
Executive as of the Execution Date. On or before the Separation Date, Company
shall pay or provide Executive all additional salary, wages, bonuses, accrued
vacation/paid time off, premiums, leaves, housing allowances, relocation costs,
interest, severance, outplacement costs, fees, reimbursable expenses,
commissions, stock, stock options, vesting, and any and all other benefits and
compensation due to Executive as of the Separation Date.

6.    Executive’s Release of Claims. Executive agrees that the foregoing
consideration represents settlement in full of all outstanding obligations, as
of the Execution Date, owed to Executive by the Company and its current and
former officers, directors, employees, agents, investors, attorneys,
shareholders, administrators, affiliates, benefit plans, plan administrators,

 

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professional employer organization or co-employer, insurers, trustees,
divisions, and subsidiaries, and predecessor and successor corporations and
assigns (collectively, the “Releasees”). Executive, on Executive’s own behalf
and on behalf of Executive’s respective heirs, family members, executors,
agents, and assigns, hereby and forever releases the Releasees from, and agrees
not to sue concerning, or in any manner to institute, prosecute, or pursue, any
claim, complaint, charge, duty, obligation, demand, or cause of action relating
to any matters of any kind, whether presently known or unknown, suspected or
unsuspected, that Executive may possess against any of the Releasees arising
from any omissions, acts, facts, or damages that have occurred up until and
including the Execution Date of this Agreement in connection with Executive’s
employment by the Company, including, without limitation:

a.    any and all such claims relating to or arising from Executive’s employment
relationship with the Company and the termination of that relationship;

b.    any and all such claims relating to, or arising from, Executive’s right to
purchase, or actual purchase of shares of stock of the Company, including,
without limitation, any claims for fraud, misrepresentation, breach of fiduciary
duty, breach of duty under applicable state corporate law, and securities fraud
under any state or federal law;

c.    any and all such claims for wrongful discharge of employment, termination
in violation of public policy, discrimination, harassment, retaliation, breach
of contract (both express and implied), breach of covenant of good faith and
fair dealing (both express and implied), promissory estoppel, negligent or
intentional infliction of emotional distress, fraud, negligent or intentional
misrepresentation, negligent or intentional interference with contract or
prospective economic advantage, unfair business practices, defamation, libel,
slander, negligence, personal injury, assault, battery, invasion of privacy,
false imprisonment, conversion, and disability benefits;

d.    any and all such claims for violation of any federal, state, or municipal
statute, including, but not limited to, Title VII of the Civil Rights Act of
1964, the Civil Rights Act of 1991, the Rehabilitation Act of 1973, the
Americans with Disabilities Act of 1990, the Equal Pay Act, the Fair Labor
Standards Act, the Fair Credit Reporting Act, the Age Discrimination in
Employment Act of 1967, the Older Workers Benefit Protection Act, the Employee
Retirement Income Security Act of 1974, the Worker Adjustment and Retraining
Notification Act, the Family and Medical Leave Act, the Immigration Reform and
Control Act, the California Family Rights Act, the California Labor Code, the
California Workers’ Compensation Act, and the California Fair Employment and
Housing Act;

e.    any and all such claims for violation of the federal or any state
constitution;

f.    any and all such claims arising out of any other laws and regulations
relating to employment or employment discrimination;

 

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g.    any such claim for any loss, cost, damage, or expense arising out of any
dispute over the nonwithholding or other tax treatment of any of the proceeds
received by Executive as a result of this Agreement; and

h.    any and all claims for attorneys’ fees and costs to the extent related to
claims described in subsections (a) through (g) above.

Executive agrees that the release set forth in this section shall be and remain
in effect in all respects as a complete general release as to the matters
released. This release does not extend to any obligations incurred under this
Agreement. This release does not release (i) claims that cannot be released as a
matter of law, including, but not necessarily limited to, any Protected Activity
(as defined below), nor (ii) any defense or indemnification rights available
under Executive’s Indemnification Agreement, Company Bylaws, insurance policy,
or under applicable law. Any and all disputed wage claims that are released
herein shall be subject to binding arbitration in accordance with section 17,
except as required by applicable law. This release does not extend to any right
Executive may have to unemployment compensation benefits.

7.    Acknowledgment of Waiver of Claims under ADEA. Executive acknowledges that
he is waiving and releasing any rights he may have under the Age Discrimination
in Employment Act of 1967 (“ADEA”), and that this waiver and release is knowing
and voluntary. Executive agrees that this waiver and release does not apply to
any rights or claims that may arise under the ADEA after the Effective Date.
Executive acknowledges that the consideration given for this waiver and release
is in addition to anything of value to which Executive was already entitled.
Executive further acknowledges that he has been advised by this writing that:
(a) he should consult with an attorney prior to executing this Agreement, (b) he
has 21 days within which to consider this Agreement, (c) he has 7 days following
his execution of this Agreement to revoke this Agreement, (d) this Agreement
shall not be effective until after the revocation period has expired, and
(e) nothing in this Agreement prevents or precludes Executive from challenging
or seeking a determination in good faith of the validity of this waiver under
the ADEA, nor does it impose any condition precedent, penalties, or costs for
doing so, unless specifically authorized by federal law. In the event Executive
signs this Agreement and returns it to the Company in less than the 21day period
identified above, Executive hereby acknowledges that he has freely and
voluntarily chosen to waive the time period allotted for considering this
Agreement. Executive acknowledges and understands that revocation must be
accomplished by a written notification to the person executing this Agreement on
the Company’s behalf that is received prior to the Effective Date. The Parties
agree that changes, whether material or immaterial, do not restart the running
of the 21-day period.

8.    Company’s Release of Claims Against Executive. Company hereby waives its
right to any claims, causes of action, rights, and/or remedies it might have
against Executive as of the Execution Date.

9.    California Civil Code Section 1542. The Parties acknowledge that they have
been advised to consult with legal counsel and are familiar with the provisions
of California Civil Code Section 1542, a statute that otherwise prohibits the
release of unknown claims, which provides as follows:

 

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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 EXECUTING THE RELEASE, WHICH
IF KNOWN BY HIM OR HER MUST HAVE MATERIALLY AFFECTED HIS OR HER SETTLEMENT WITH
THE DEBTOR.

The Parties, being aware of said code section, agrees to expressly waive any
rights they may have thereunder, as well as under any other statute or common
law principles of similar effect.

10.    No Pending or Future Lawsuits. Each of Executive and Company represents
that there are no lawsuits, claims, or actions pending in Executive’s or
Company’s name, as applicable, or on behalf of any other person or entity,
against the Company or any of the other Releasees, or against the Executive, as
applicable.

11.    Trade Secrets and Confidential Information/Company Property; Insider
Trading Policy. Executive reaffirms and agrees to observe and abide by the terms
of the restrictions set forth in the CIIA, specifically including the provisions
therein regarding nondisclosure of the Company’s trade secrets and confidential
and proprietary information. Notwithstanding anything in the CIIA, Executive and
Company acknowledge that “Confidential Information” (as defined in the CIIA)
does not include any of the foregoing items that have become publicly known and
made generally available through no wrongful act of Executive’s or of others who
were under confidentiality obligations as to the item or items involved or
improvements or new versions thereof. Executive hereby grants consent to
notification by the Company to any new employer about Executive’s obligations
under this section. Executive represents that Executive has not to date misused
or disclosed Confidential Information to any unauthorized party in breach of the
CIIA. Executive acknowledges and agrees to continue to abide by the terms and
conditions of the Company’s Insider Trading Policy in accordance with its terms.

12.    No Cooperation. Subject to Section 13 governing Protected Activity,
Executive agrees that Executive will not knowingly encourage, counsel, or assist
any attorneys or their clients in the presentation or prosecution of any
disputes, differences, grievances, claims, charges, or complaints by any third
party against any of the Releasees, unless under a subpoena or other court order
to do so or as related directly to the ADEA waiver. Executive agrees both to
immediately notify the Company upon receipt of any such subpoena or court order,
and to furnish, within three (3) business days of its receipt, a copy of such
subpoena or other court order, in each case unless prohibited by applicable law.
Subject to Section 13 governing Protected Activity, if approached by anyone for
counsel or assistance in the presentation or prosecution of any disputes,
differences, grievances, claims, charges, or complaints against any of the
Releasees, Executive shall state no more than that Executive cannot provide
counsel or assistance unless and solely to the extent compelled to do so by
applicable law.

13.    Protected Activity Not Prohibited. Executive understands that nothing in
this Agreement shall in any way limit or prohibit Executive from engaging in any
Protected Activity as defined in this paragraph. “Protected Activity” includes
filing a charge, complaint, or report with, or otherwise communicating,
cooperating, or participating, voluntarily or as compelled, in

 

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any inquiry, examination, investigation or proceeding that may be conducted by,
any federal, state or local government agency or commission, including the
Securities and Exchange Commission, the Department of Justice, the Equal
Employment Opportunity Commission, the Occupational Safety and Health
Administration, and the National Labor Relations Board (“Government Entitites”).
Executive understands that in connection with such Protected Activity, Executive
is permitted to disclose documents or other information as permitted by law,
without giving notice to, or receiving authorization from, the Company.
Notwithstanding the foregoing, Executive agrees to take all reasonable
precautions to prevent any unauthorized use or disclosure of any information
that may constitute Company confidential information to any parties other than
the Government Entitites. Executive further understands that “Protected
Activity” does not include the intentional and knowing disclosure of any Company
attorney-client privileged communications or attorney work product. Any language
in the Employment Agreement regarding Executive’s right to engage in Protected
Activity that conflicts with, or is contrary to, this section is superseded by
this Agreement. In addition, pursuant to the Defend Trade Secrets Act of 2016,
Executive is notified that an individual will not be held criminally or civilly
liable under any federal or state trade secret law for the disclosure of a trade
secret that (i) is made in confidence to a federal, state, or local government
official (directly or indirectly) or to an attorney solely for the purpose of
reporting or investigating a suspected violation of law, or (ii) is made in a
complaint or other document filed in a lawsuit or other proceeding, if (and only
if) such filing is made under seal. In addition, an individual who files a
lawsuit for retaliation by an employer for reporting a suspected violation of
law may disclose the trade secret to the individual’s attorney and use the trade
secret information in the court proceeding, if the individual files any document
containing the trade secret under seal and does not disclose the trade secret,
except pursuant to court order.

14.    Mutual Nondisparagement. Executive agrees to refrain from any
disparagement, defamation, libel, or slander of any of the Company (including
the executive management team and the members of the Board of Directors) and
agrees to refrain from any tortious interference with the contracts and
relationships of the Company. Executive shall direct any inquiries by potential
future employers to the Company’s human resources department, which shall
provide only the Executive’s last position and dates of employment. The Company
agrees to refrain from any disparagement, defamation, libel or slander of
Executive. Executive understands that the Company’s obligations under this
paragraph extend only to the Company’s current executive officers and members of
its Board of Directors and only for so long as each officer or member is an
employee or Director of the Company. Protected Activity is expressly excluded
from this paragraph.

15.    No Admission of Liability. Executive and Company understand and
acknowledge that this Agreement constitutes a compromise and settlement of any
and all actual or potential disputed claims to the extent released hereunder. No
action taken by the Company or Executive, either previously or in connection
with this Agreement, shall be deemed or construed to be (a) an admission of the
truth or falsity of any actual or potential claims or (b) an acknowledgment or
admission by the Company or Executive, as applicable, of any fault or liability
whatsoever to Executive or Company, as applicable, or to any third party.

 

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16.    Costs. The Parties shall each bear their own costs, attorneys’ fees, and
other fees incurred in connection with the preparation of this Agreement.

17.    ARBITRATION. EXCEPT AS PROHIBITED BY LAW, THE PARTIES AGREE THAT ANY AND
ALL DISPUTES ARISING OUT OF THE TERMS OF THIS AGREEMENT, THEIR INTERPRETATION,
EXECUTIVE’S EMPLOYMENT WITH THE COMPANY OR THE TERMS THEREOF, OR ANY OF THE
MATTERS HEREIN RELEASED, SHALL BE SUBJECT TO ARBITRATION IN SAN DIEGO, CA,
BEFORE JUDICIAL ARBITRATION & MEDIATION SERVICES (“JAMS”), PURSUANT TO ITS
EMPLOYMENT ARBITRATION RULES & PROCEDURES (“JAMS RULES”). THE ARBITRATOR MAY
GRANT INJUNCTIONS AND OTHER RELIEF IN SUCH DISPUTES. THE ARBITRATOR SHALL
ADMINISTER AND CONDUCT ANY ARBITRATION IN ACCORDANCE WITH CALIFORNIA LAW,
INCLUDING THE CALIFORNIA CODE OF CIVIL PROCEDURE, AND THE ARBITRATOR SHALL APPLY
SUBSTANTIVE AND PROCEDURAL CALIFORNIA LAW TO ANY DISPUTE OR CLAIM, WITHOUT
REFERENCE TO ANY CONFLICT-OF-LAW PROVISIONS OF ANY JURISDICTION. TO THE EXTENT
THAT THE JAMS RULES CONFLICT WITH CALIFORNIA LAW, CALIFORNIA LAW SHALL TAKE
PRECEDENCE. THE DECISION OF THE ARBITRATOR SHALL BE FINAL, CONCLUSIVE, AND
BINDING ON THE PARTIES TO THE ARBITRATION. THE PARTIES AGREE THAT THE PREVAILING
PARTY IN ANY ARBITRATION SHALL BE ENTITLED TO INJUNCTIVE RELIEF IN ANY COURT OF
COMPETENT JURISDICTION TO ENFORCE THE ARBITRATION AWARD. THE PARTIES TO THE
ARBITRATION SHALL EACH PAY AN EQUAL SHARE OF THE COSTS AND EXPENSES OF SUCH
ARBITRATION, AND EACH PARTY SHALL SEPARATELY PAY FOR ITS RESPECTIVE COUNSEL FEES
AND EXPENSES; PROVIDED, HOWEVER, THAT THE ARBITRATOR MAY AWARD ATTORNEYS’ FEES
AND COSTS TO THE PREVAILING PARTY, WHERE PERMITTED BY LAW. THE PARTIES HEREBY
AGREE TO WAIVE THEIR RIGHT TO HAVE ANY SUCH DISPUTE BETWEEN THEM RESOLVED IN A
COURT OF LAW BY A JUDGE OR JURY. NOTWITHSTANDING THE FOREGOING, THIS SECTION
WILL NOT PREVENT EITHER PARTY FROM SEEKING INJUNCTIVE RELIEF (OR ANY OTHER
PROVISIONAL REMEDY) FROM ANY COURT HAVING JURISDICTION OVER THE PARTIES AND THE
SUBJECT MATTER OF THEIR DISPUTE RELATING TO THIS AGREEMENT AND THE AGREEMENTS
INCORPORATED HEREIN BY REFERENCE. SHOULD ANY PART OF THE ARBITRATION AGREEMENT
CONTAINED IN THIS SECTION CONFLICT WITH ANY OTHER ARBITRATION AGREEMENT BETWEEN
THE PARTIES, THE PARTIES AGREE THAT THIS ARBITRATION AGREEMENT SHALL GOVERN.

18.    Tax Consequences. The Company makes no representations or warranties with
respect to the tax consequences of the payments and any other consideration
provided to Executive or made on Executive’s behalf under the terms of this
Agreement. Executive agrees and understands that Executive is responsible for
payment, if any, of local, state, and/or federal taxes on the payments and any
other consideration provided hereunder by the Company and any penalties or
assessments thereon. Executive further agrees to indemnify and hold the
Releasees harmless from any claims, demands, deficiencies, penalties, interest,
assessments, executions, judgments, or recoveries by any government agency
against the Company for any amounts

 

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claimed due on account of (a) Executive’s failure to pay or delayed payment of
federal or state taxes, or (b) damages sustained by the Company by reason of any
such claims, including attorneys’ fees and costs.

19.    Section 409A. It is intended that this Agreement comply with, or be
exempt from, Code Section 409A and the final regulations and official guidance
thereunder (“Section 409A”) and any ambiguities herein will be interpreted to so
comply and/or be exempt from Section 409A. The Parties reasonably anticipate
that any consulting services during the Consulting Period shall be at a level
equal to twenty percent (20%) or less of the average level of services performed
by Executive during the immediately preceding thirty-six (36)-month period and,
accordingly, the Separation Date will be a “separation from service” within the
meaning of Section 409A (as defined above). Each payment and benefit to be paid
or provided under this Agreement is intended to constitute a series of separate
payments for purposes of Section 1.409A-2(b)(2) of the Treasury Regulations. The
Company and Executive will work together in good faith to consider either
(i) amendments to this Agreement; or (ii) revisions to this Agreement with
respect to the payment of any awards, which are necessary or appropriate to
avoid imposition of any additional tax or income recognition prior to the actual
payment to Executive under Section 409A. In no event will the Releasees
reimburse Executive for any taxes that may be imposed on Executive as a result
of Section 409A.

20.    Authority. The Company represents and warrants that the undersigned has
the authority to act on behalf of the Company and to bind the Company and all
who may claim through it to the terms and conditions of this Agreement.
Executive represents and warrants that Executive has the capacity to act on
Executive’s own behalf and on behalf of all who might claim through Executive to
bind them to the terms and conditions of this Agreement. Each Party warrants and
represents that there are no liens or claims of lien or assignments in law or
equity or otherwise of or against any of the claims or causes of action released
herein.

21.    Severability. In the event that any provision or any portion of any
provision hereof or any surviving agreement made a part hereof becomes or is
declared by a court of competent jurisdiction or arbitrator to be illegal,
unenforceable, or void, this Agreement shall continue in full force and effect
without said provision or portion of provision.

22.    Attorneys’ Fees. Except with regard to a legal action challenging or
seeking a determination in good faith of the validity of the ADEA waiver in this
Agreement, in the event that either Party brings an action to enforce or effect
its rights under this Agreement, the prevailing Party shall be entitled to
recover its costs and expenses, including the costs of mediation, arbitration,
litigation, court fees, and reasonable attorneys’ fees incurred in connection
with such an action.

23.    Entire Agreement. This Agreement represents the entire agreement and
understanding between the Company and Executive concerning the subject matter of
this Agreement and Executive’s employment with and separation from the Company
and the events leading thereto and associated therewith, and supersedes and
replaces any and all prior agreements and understandings concerning the subject
matter of this Agreement and Executive’s relationship with the Company, with the
exception of the confidentiality and inventions

 

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assignment provisions incorporated by reference in the CIIA, the Indemnification
Agreement, the Company’s Insider Trading Policy, and the Equity Agreements.
Nothing in this Agreement shall alter Executive’s indemnification and
advancement rights granted by the Indemnification Agreement, Company Bylaws, or
by applicable law.

24.    No Oral Modification. This Agreement may only be amended in a writing
signed by Executive and the Chief Executive Officer of the Company.

25.    Governing Law. This Agreement shall be governed by the laws of the State
of California, without regard for choice-of-law provisions.

26.    Effective Date. Executive understands that this Agreement shall be null
and void if not executed by Executive within twenty-one (21) days. Each Party
has seven (7) days after that Party signs this Agreement to revoke it. This
Agreement will become effective on the eighth (8th) day after Executive signed
this Agreement, so long as it has been signed by the Parties and has not been
revoked by either Party before that date (the “Effective Date”).

27.    Counterparts. This Agreement may be executed in counterparts and each
counterpart shall be deemed an original and all of which counterparts taken
together shall have the same force and effect as an original and shall
constitute an effective, binding agreement on the part of each of the
undersigned. The counterparts of this Agreement may be executed and delivered by
facsimile, photo, email PDF, or other electronic transmission or signature.

28.    Voluntary Execution of Agreement. Executive understands and agrees that
Executive executed this Agreement voluntarily, without any duress or undue
influence on the part or behalf of the Company or any third party, with the full
intent of releasing all of Executive’s claims against the Company and any of the
other Releasees. Executive acknowledges that:

 

  (a) Executive has read this Agreement;

 

  (b) Executive has been represented in the preparation, negotiation, and
execution of this Agreement by legal counsel of Executive’s own choice or has
elected not to retain legal counsel;

 

  (c) Executive understands the terms and consequences of this Agreement and of
the releases it contains;

 

  (d) Executive is fully aware of the legal and binding effect of this
Agreement; and

 

  (e) Executive has not relied upon any representations or statements made by
the Company that are not specifically set forth in this Agreement.

 

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IN WITNESS WHEREOF, the Parties have executed this Agreement on the respective
dates set forth below.

 

    PAUL WAGNER, Ph.D., an individual Dated: September 7, 2017    

/s/ Paul Wagner

    Paul Wagner, Ph.D.     PFENEX INC. Dated: September 7, 2017     By  

/s/ Evert B. Schimmelpennink

      Evert B. Schimmelpennink       Chief Executive Officer

 

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EXHIBIT A

PFENEX INC.

CONSULTING AGREEMENT

This Consulting Agreement (this “Consulting Agreement”) is made and entered into
as of October 13, 2017 by and between Pfenex Inc. (the “Company”), and Paul
Wagner, Ph.D. (“Consultant”) (each herein referred to individually as a “Party,”
or collectively as the “Parties”).

The Company desires to retain Consultant as an independent contractor to perform
consulting services for the Company, and Consultant is willing to perform such
services, on the terms described below. In consideration of the mutual promises
contained herein, the Parties agree as follows:

 

  1. Services and Compensation

Consultant shall perform the services described in Schedule 1 (the “Services”)
for the Company (or its designee), and the Company agrees to pay Consultant the
compensation described in Schedule 1 for Consultant’s performance of the
Services.

 

  2. Confidentiality

A.    Definition of Confidential Information. “Confidential Information” means
any information (including any and all combinations of individual items of
information) that Consultant learns as a result of performing the Services and
relates to the actual or anticipated business and/or products, research or
development of the Company, its affiliates or subsidiaries, or to the Company’s,
its affiliates’ or subsidiaries’ technical data, trade secrets, or know-how,
including, but not limited to, research, product plans, or other information
regarding the Company’s, its affiliates’ or subsidiaries’ products or services
and markets therefor, customer lists and customers (including, but not limited
to, customers of the Company on whom Consultant called or with whom Consultant
became acquainted during the term of this Consulting Agreement), software,
developments, inventions, discoveries, ideas, processes, formulas, technology,
designs, drawings, engineering, hardware configuration information, marketing,
finances, and other business information disclosed by the Company, its
affiliates or subsidiaries, either directly or indirectly, in writing, orally or
by drawings or inspection of premises, parts, equipment, or other property of
Company, its affiliates or subsidiaries. Notwithstanding the foregoing,
Confidential Information shall not include any such information which Consultant
can establish (i) was publicly known or made generally available prior to the
time of disclosure to Consultant; (ii) becomes publicly known or made generally
available after disclosure to Consultant through no wrongful action or inaction
of Consultant; or (iii) is in the rightful possession of Consultant, without
confidentiality obligations, at the time of disclosure as shown by Consultant’s
then-contemporaneous written records; provided that any combination of
individual items of information shall not be deemed to be within any of the
foregoing exceptions

 

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merely because one or more of the individual items are within such exception,
unless the combination as a whole is within such exception.

B.    Nonuse and Nondisclosure. During and after the term of this Consulting
Agreement, Consultant will hold in the strictest confidence, and take all
reasonable precautions to prevent any unauthorized use or disclosure of
Confidential Information, and Consultant will not (i) use the Confidential
Information for any purpose whatsoever other than as necessary for the
performance of the Services on behalf of the Company, or (ii) subject to
Consultant’s right to engage in Protected Activity (as defined below), disclose
the Confidential Information to any third party without the prior written
consent of an authorized representative of the Company, except that Consultant
may disclose Confidential Information to the extent compelled by applicable law;
provided however, prior to such disclosure, Consultant shall, unless prohibited
by applicable law, provide prior written notice to Company and seek a protective
order or such similar confidential protection as may be available under
applicable law. Consultant agrees that no ownership of Confidential Information
is conveyed to the Consultant. Without limiting the foregoing, Consultant shall
not use or disclose any Company property, intellectual property rights, trade
secrets or other proprietary know-how of the Company to invent, author, make,
develop, design, or otherwise enable others to invent, author, make, develop, or
design identical or substantially similar designs as those developed under this
Consulting Agreement for any third party. Consultant agrees that Consultant’s
obligations under this Section 2.B shall continue after the termination of this
Consulting Agreement.

C.    Other Client Confidential Information. Consultant agrees that Consultant
will not, in connection with the Services, improperly use, disclose, or induce
the Company to use any proprietary information or trade secrets of any former or
current employer of Consultant or other person or entity with which Consultant
has an obligation to keep in confidence. Consultant also agrees that Consultant
will not bring onto the Company’s premises or transfer onto the Company’s
technology systems any unpublished document, proprietary information, or trade
secrets belonging to any third party unless disclosure to, and use by, the
Company has been consented to in writing by such third party.

D.    Third Party Confidential Information. Consultant recognizes that the
Company has received and in the future will receive from third parties their
confidential or proprietary information subject to a duty on the Company’s part
to maintain the confidentiality of such information and to use it only for
certain limited purposes. Consultant agrees that at all times during the term of
this Consulting Agreement and thereafter, Consultant owes the Company and such
third parties a duty to hold all such confidential or proprietary information in
the strictest confidence and not to use it or to disclose it to any person,
firm, corporation, or other third party except as necessary in carrying out the
Services for the Company consistent with the Company’s agreement with such third
party.

 

  3.    Ownership

A.    Assignment of Inventions. Consultant agrees that all right, title, and
interest in and to any copyrightable material, notes, records, drawings,
designs, inventions, improvements, developments, discoveries, ideas and trade
secrets conceived, discovered, authored, invented, developed or reduced to
practice by Consultant, solely or in collaboration

 

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with others, during the term of this Consulting Agreement and arising out of, or
in connection with, performing the Services under this Consulting Agreement and
any copyrights, patents, trade secrets, mask work rights or other intellectual
property rights relating to the foregoing (collectively, “Inventions”), are the
sole property of the Company. Consultant also agrees to promptly make full
written disclosure to the Company of any Inventions and to deliver and assign
(or cause to be assigned) and hereby irrevocably assigns fully to the Company
all right, title and interest in and to the Inventions.

B.    Pre-Existing Materials. Subject to Section 3.A, Consultant will provide
the Company with prior written notice if, in the course of performing the
Services, Consultant incorporates into any Invention or utilizes in the
performance of the Services any invention, discovery, idea, original works of
authorship, development, improvements, trade secret, concept, or other
proprietary information or intellectual property right owned by Consultant or in
which Consultant has an interest, prior to, or separate from, performing the
Services under this Consulting Agreement (“Prior Inventions”), and the Company
is hereby granted a nonexclusive, royalty-free, perpetual, irrevocable,
transferable, worldwide license (with the right to grant and authorize
sublicenses) to make, have made, use, import, offer for sale, sell, reproduce,
distribute, modify, adapt, prepare derivative works of, display, perform, and
otherwise exploit such Prior Inventions, without restriction, including, without
limitation, as part of or in connection with such Invention, and to practice any
method related thereto. Consultant will not incorporate any invention,
discovery, idea, original works of authorship, development, improvements, trade
secret, concept, or other proprietary information or intellectual property right
owned by any third party into any Invention without the Company’s prior written
permission.

C.    Moral Rights. Any assignment to the Company of Inventions includes all
rights of attribution, paternity, integrity, modification, disclosure and
withdrawal, and any other rights throughout the world that may be known as or
referred to as “moral rights,” “artist’s rights,” “droit moral,” or the like
(collectively, “Moral Rights”). To the extent that Moral Rights cannot be
assigned under applicable law, Consultant hereby waives and agrees not to
enforce any and all Moral Rights, including, without limitation, any limitation
on subsequent modification, to the extent permitted under applicable law.

D.    Further Assurances. Consultant agrees to assist the Company, or its
designee, at the Company’s expense, in every proper way to secure the Company’s
rights in Inventions in any and all countries, including the disclosure to the
Company of all pertinent information and data with respect thereto, the
execution of all applications, specifications, oaths, assignments and all other
instruments that the Company may deem necessary in order to apply for, register,
obtain, maintain, defend, and enforce such rights, and in order to deliver,
assign and convey to the Company, its successors, assigns and nominees the sole
and exclusive right, title, and interest in and to all Inventions and testifying
in a suit or other proceeding relating to such Inventions. Consultant further
agrees that Consultant’s obligations under this Section 3.D shall continue after
the termination of this Consulting Agreement.

E.     Attorney-in-Fact. Consultant agrees that, if the Company is unable
because of Consultant’s unavailability, dissolution, mental or physical
incapacity, or for any other reason, to secure Consultant’s signature with
respect to any Inventions, including, without limitation, for the purpose of
applying for or pursuing any application for any United States or

 

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foreign patents or mask work or copyright registrations covering the Inventions
assigned to the Company in Section 3.A, then Consultant hereby irrevocably
designates and appoints the Company and its duly authorized officers and agents
as Consultant’s agent and attorney-in-fact, to act for and on Consultant’s
behalf to execute and file any papers and oaths and to do all other lawfully
permitted acts with respect to such Inventions to further the prosecution and
issuance of patents, copyright and mask work registrations with the same legal
force and effect as if executed by Consultant. This power of attorney shall be
deemed coupled with an interest, and shall be irrevocable.

 

  4. Conflicting Obligations

Consultant represents and warrants that, as of the Effective Date, Consultant
has no agreements, relationships, or commitments to any other person or entity
that conflict with the provisions of this Consulting Agreement, Consultant’s
obligations to the Company under this Consulting Agreement, and/or Consultant’s
ability to perform the Services. Consultant will not enter into any such
conflicting agreement during the Term (as defined in Section 6.A).

 

  5. Return of Company Materials

Upon the termination of this Consulting Agreement, or upon the Company’s earlier
request, Consultant will immediately deliver to the Company, and will not keep
in Consultant’s possession, recreate, or deliver to anyone else, any and all
Company property, including, but not limited to, Confidential Information,
tangible embodiments of the Inventions, all devices and equipment belonging to
the Company, all electronically-stored information and passwords to access such
property, and any reproductions of any of the foregoing items that Consultant
may have in Consultant’s possession or control.

 

  6. Term and Termination

A.    Term. The term of this Consulting Agreement will begin on October 13, 2017
(the “Effective Date”) and will continue for six (6) months (the “Term”) or
until the Consulting Agreement is terminated as provided in Section 6.B.

B.    Termination. The Company may terminate this Consulting Agreement
immediately and without prior notice if for “Cause.” For purposes of this
Consulting Agreement, “Cause” is defined as (i) the willful failure, disregard,
or refusal by Consultant to perform the services hereunder or follow the
reasonable instructions of the Company’s board of directors (the “Board”);
provided, however, that any willful failure, disregard, or refusal by Consultant
to perform the services hereunder that can reasonably be cured shall not
constitute Cause unless cure is not effected, as determined in good faith by the
Board, within thirty (30) days after notice thereof is received by Consultant
from the Company; (ii) any willful or grossly negligent act by Consultant having
the effect of injuring, in a material way (whether financial or otherwise) as
determined in good faith by the Board, the business or reputation of the Company
or any of its subsidiaries or affiliates; (iii) Consultant’s conviction of,
guilty plea to, or plea of nolo contendere to any felony or misdemeanor
involving moral turpitude; (iv) the determination by the Company, after a
reasonable good faith investigation by the Company following a written
allegation by an employee of the Company, that Consultant engaged in some form
of harassment

 

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prohibited by law (including, without limitation, age, sex, disability, or race
discrimination) unless Consultant’s actions were specifically directed by the
Board; or (v) material breach by Consultant of any provision of this Consulting
Agreement.

C.    Survival. Upon any termination, all rights and duties of the Company and
Consultant toward each other shall cease except:

(1)    The Company will pay, within thirty (30) days after the effective date of
termination, all amounts owing to Consultant for Services completed and accepted
by the Company prior to the termination date, in accordance with the Company’s
policies and in accordance with the provisions of Section 1 of this Consulting
Agreement; and

(2)    Section 2 (Confidentiality), Section 3 (Ownership), Section 4
(Conflicting Obligations), Section 5 (Return of Company Materials), Section 6
(Term and Termination), Section 7 (Independent Contractor; Benefits), Section 8
(Indemnification), Section 9 (Nonsolicitation), Section 10 (Limitation of
Liability), and Section 11 (Miscellaneous) will survive termination or
expiration of this Consulting Agreement in accordance with their terms.

 

  7. Independent Contractor; Benefits

A.    Independent Contractor. It is the express intention of the Company and
Consultant that Consultant perform the Services as an independent contractor to
the Company. Nothing in this Consulting Agreement shall in any way be construed
to constitute Consultant as an agent, employee, or representative of the
Company. Without limiting the generality of the foregoing, Consultant is not
authorized to bind the Company to any liability or obligation or to represent
that Consultant has any such authority. Consultant agrees to furnish (or
reimburse the Company for) all tools and materials necessary to accomplish this
Consulting Agreement and shall incur all expenses associated with performance.
Consultant acknowledges and agrees that Consultant is obligated to report as
income all compensation received by Consultant pursuant to this Consulting
Agreement. Consultant agrees to and acknowledges the obligation to pay all
self-employment and other taxes on such income.

B.    Benefits. The Company and Consultant agree that Consultant will receive no
Company-sponsored benefits from the Company where benefits include, but are not
limited to, paid vacation, sick leave, medical insurance and 401(k)
participation. If Consultant is reclassified by a state or federal agency or
court as the Company’s employee, Consultant will become a reclassified employee
and will receive no benefits from the Company, except those mandated by state or
federal law, even if by the terms of the Company’s benefit plans or programs of
the Company in effect at the time of such reclassification, Consultant would
otherwise be eligible for such benefits.

 

  8. Indemnification

Nothing in this Consulting Agreement shall alter or modify Executive’s
indemnification and advancement rights granted by the Indemnification Agreement,
Company Bylaws, or by applicable law.

 

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  9. Nonsolicitation

To the fullest extent permitted under applicable law, from the date of this
Consulting Agreement until twelve (12) months after the termination of this
Consulting Agreement for any reason, Consultant will not, without the Company’s
prior written consent, directly or indirectly, solicit any of the Company’s
employees to leave their employment, or attempt to solicit employees of the
Company, either for Consultant or for any other person or entity. Consultant
agrees that nothing in this Section 9 shall affect Consultant’s continuing
obligations under this Consulting Agreement during and after this twelve
(12) month period, including, without limitation, Consultant’s obligations under
Section 2.

 

  10. Limitation of Liability

IN NO EVENT SHALL A PARTY BE LIABLE TO THE OTHER PARTY OR TO ANY OTHER PARTY FOR
ANY INDIRECT, INCIDENTAL, SPECIAL OR CONSEQUENTIAL DAMAGES, OR DAMAGES FOR LOST
PROFITS OR LOSS OF BUSINESS, HOWEVER CAUSED AND UNDER ANY THEORY OF LIABILITY,
WHETHER BASED IN CONTRACT, TORT (INCLUDING NEGLIGENCE) OR OTHER THEORY OF
LIABILITY, REGARDLESS OF WHETHER THE PARTY WAS ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES AND NOTWITHSTANDING THE FAILURE OF ESSENTIAL PURPOSE OF ANY LIMITED
REMEDY. IN NO EVENT SHALL A PARTY’S LIABILITY ARISING OUT OF OR IN CONNECTION
WITH THIS CONSULTING AGREEMENT EXCEED THE AMOUNTS PAID BY THE COMPANY TO
CONSULTANT UNDER THIS CONSULTING AGREEMENT FOR THE SERVICES, DELIVERABLES OR
INVENTION GIVING RISE TO SUCH LIABILITY.

 

  11. Miscellaneous

A.    Governing Law; Consent to Personal Jurisdiction. This Consulting Agreement
shall be governed by the laws of the State of California, without regard to the
conflicts of law provisions of any jurisdiction. To the extent that any lawsuit
is permitted under this Consulting Agreement, the Parties hereby expressly
consent to the personal and exclusive jurisdiction and venue of the state and
federal courts located in California.

B.    Assignability. This Consulting Agreement will be binding upon Consultant’s
heirs, executors, assigns, administrators, and other legal representatives, and
will be for the benefit of the Company, its successors, and its assigns. There
are no intended third-party beneficiaries to this Consulting Agreement, except
as expressly stated. Except as may otherwise be provided in this Consulting
Agreement, Consultant may not sell, assign or delegate any rights or obligations
under this Consulting Agreement. Notwithstanding anything to the contrary
herein, the Company may assign this Consulting Agreement and its rights and
obligations under this Consulting Agreement to any successor to all or
substantially all of Company’s relevant assets, whether by merger,
consolidation, reorganization, reincorporation, sale of assets or stock, change
of control or otherwise.

C.    Headings. Headings are used in this Consulting Agreement for reference
only and shall not be considered when interpreting this Consulting Agreement.

 

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D.    Severability. If a court or other body of competent jurisdiction finds, or
the Parties mutually believe, any provision of this Consulting Agreement, or
portion thereof, to be invalid or unenforceable, such provision will be enforced
to the maximum extent permissible so as to effect the intent of the Parties, and
the remainder of this Consulting Agreement will continue in full force and
effect.

E.    Modification, Waiver. No modification of or amendment to this Consulting
Agreement, nor any waiver of any rights under this Consulting Agreement, will be
effective unless in a writing signed by the Parties. Waiver by the Company of a
breach of any provision of this Consulting Agreement will not operate as a
waiver of any other or subsequent breach.

F.    Notices. Any notice or other communication required or permitted by this
Consulting Agreement to be given to a Party shall be in writing and shall be
deemed given (i) if delivered personally or by commercial messenger or courier
service, (ii) when sent by confirmed facsimile, or (iii) if mailed by U.S.
registered or certified mail (return receipt requested), to the Party at the
Party’s address written below or at such other address as the Party may have
previously specified by like notice. If by mail, delivery shall be deemed
effective three business days after mailing in accordance with this
Section 11.F.

 

  (1) If to the Company, to:

 

    10790 Roselle Street

    San Diego, CA 92121

(2)    If to Consultant, to the address for notice on the signature page to this
Consulting Agreement or, if no such address is provided, to the last address of
Consultant provided by Consultant to the Company.

G.    Attorneys’ Fees. In any court action at law or equity that is brought by
one of the Parties to this Consulting Agreement to enforce or interpret the
provisions of this Consulting Agreement, the prevailing Party will be entitled
to reasonable attorneys’ fees, in addition to any other relief to which that
Party may be entitled.

H.    Signatures. This Consulting Agreement may be signed in two counterparts,
each of which shall be deemed an original, with the same force and effectiveness
as though executed in a single document.

I.    Protected Activity Not Prohibited. Consultant understands that nothing in
this Consulting Agreement shall in any way limit or prohibit Consultant from
engaging in any Protected Activity. For purposes of this Consulting Agreement,
“Protected Activity” shall mean filing a charge, complaint, or report with, or
otherwise communicating, cooperating, or participating, voluntarily or as
compelled, in any inquiry, examination, investigation or proceeding that may be
conducted by, any federal, state or local government agency or commission,
including the Securities and Exchange Commission, the Department of Justice, the
Equal Employment Opportunity Commission, the Occupational Safety and Health
Administration and the National Labor Relations Board (“Government Entities”).
Consultant understands that in connection with such Protected Activity,
Consultant is permitted to disclose

 

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documents or other information as permitted by law, and without giving notice
to, or receiving authorization from, the Company. Notwithstanding the foregoing,
Consultant agrees to take all reasonable precautions to prevent any unauthorized
use or disclosure of any information that may constitute Company confidential
information to any parties other than the Government Entities. Consultant
further understands that “Protected Activity” does not include the intentional
and knowing disclosure of any Company attorney-client privileged communications.
Pursuant to the Defend Trade Secrets Act of 2016, Consultant is notified that an
individual will not be held criminally or civilly liable under any federal or
state trade secret law for the disclosure of a trade secret that (i) is made in
confidence to a federal, state, or local government official (directly or
indirectly) or to an attorney solely for the purpose of reporting or
investigating a suspected violation of law, or (ii) is made in a complaint or
other document filed in a lawsuit or other proceeding, if (and only if) such
filing is made under seal. In addition, an individual who files a lawsuit for
retaliation by an employer for reporting a suspected violation of law may
disclose the trade secret to the individual’s attorney and use the trade secret
information in the court proceeding, if the individual files any document
containing the trade secret under seal and does not disclose the trade secret,
except pursuant to court order.

IN WITNESS WHEREOF, the Parties hereto have executed this Consulting Agreement
as of the date first written above.

 

CONSULTANT       PFENEX INC. By:  

/s/ Paul Wagner

      By:  

/s/ Evert B. Schimmelpennink

  Paul Wagner, Ph.D. an individual         Evert B. Schimmelpennink          
Chief Executive Officer Address for Notice:        

 

       

 

       

 

       

 

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SCHEDULE 1

SERVICES AND COMPENSATION

1.    Contact. Consultant’s principal Company contact: Eef Schimmelpennink.

2.    Services. The Services will include, but will not be limited to, the
following: Consultant’s reasonable assistance with the transition of duties of
the Company’s Chief Financial Officer, assisting the Company with stockholder
relations, answering discrete questions for the Company, and assisting the
Company with discrete projects. Services will only be provided by teleconference
or email communication, unless Consultant is provided with 20 days advanced
notice that Services will be required in-person. Any request for in-person
Services may only be made up to two times during the Term. Any reasonably
documented travel expenses incurred accordance with the Company’s expense
reimbursement policies shall be reimbursed by the Company and travel time shall
be included as time performing Services. Consultant will perform Services for no
more than five (5) hours per week, unless agreed to in writing, which may be by
email.

3.    Compensation.

A.    The Company will pay Consultant a monthly fee of five thousand dollars
($5,000.00) per month for Services performed during the Term.

B.    Consultant previously was granted options to purchase shares of the
Company’s common stock (each, an “Option”) pursuant to the terms of the
Company’s 2009 Equity Incentive Plan or the Company’s 2014 Equity Incentive Plan
(each, a “Plan”) and individual award agreements thereunder (each, a “Stock
Option Agreement”). During the Term, Consultant will continue to vest in each
Option according to the schedule set forth in the applicable Plan and Stock
Option Agreement, and will include the vesting of twenty-one thousand
two-hundred and fifty (21,250) options, representing twenty five percent (25%)
vesting, of the eighty-five thousand (85,000) options granted to Consultant on
3/1/2017 under grant numbers N2014-255 and I2014-255.

C.    All payments and benefits provided for under this Consulting Agreement are
intended to be exempt from or otherwise comply with the requirements of
Section 409A of the Internal Revenue Code of 1986, as amended, and the
regulations and guidance thereunder (together, “Section 409A”), so that none of
the payments and benefits to be provided hereunder will be subject to the
additional tax imposed under Section 409A, and any ambiguities or ambiguous
terms herein will be interpreted to be exempt or so comply. Each payment and
benefit payable under this Consulting Agreement is intended to constitute a
separate payment for purposes of Section 1.409A-2(b)(2) of the Treasury
Regulations. In no event will the Company reimburse Consultant for any taxes
that may be imposed on Consultant as a result of Section 409A.

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This Schedule 1 is accepted and agreed upon as of October 13, 2017.

 

CONSULTANT       PFENEX INC. By:  

/s/ Paul Wagner

      By:  

/s/ Evert B. Schimmelpennink

  Paul Wagner, Ph.D.         Evert B. Schimmelpennink           Chief Executive
Officer

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EXHIBIT B

LETTER OF RESIGNATION

September 7, 2017

To the Board of Directors of Pfenex:

I hereby resign as the Chief Financial Officer of Pfenex Inc. (the “Company”)
and as an officer of any subsidiaries of the Company effective as of October 13,
2017 (the “Effective Date”). Following the Effective Date, I will cease to
represent myself as an officer or executive of the Company, will not perform any
managerial duties on behalf of the Company, and will cease to be a signatory
for, and to otherwise obligate, the Company.

I also agree to execute any necessary documents or other forms necessary to
effectuate or document my resignation as a matter of local, state, federal or
international law.

Yours Truly,

Paul Wagner, Ph.D.

/s/ Paul Wagner, Ph.D.

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EXHIBIT C

SUPPLEMENT TO AGREEMENT

This Supplement to the Mutual Separation Agreement and Mutual Release is made by
and between Executive and Company and is effective as of the Separation Date.

NOW, THEREFORE, in consideration of the mutual promises made herein, the Company
and Executive hereby agree as follows:

 

  1. Payment of Salary and Receipt of All Benefits. Executive acknowledges and
represents that, other than the consideration set forth in this Agreement, the
Company has paid or provided all salary, wages, bonuses, accrued vacation/paid
time off, premiums, leaves, housing allowances, relocation costs, interest,
severance, outplacement costs, fees, reimbursable expenses, commissions, stock,
stock options, vesting, and any and all other benefits and compensation due to
Executive as of the Separation Date.

 

  2. Executive’s Release of Claims. The Executive’s release of claims set forth
in Section 6 of the Agreement is hereby amended to include all such claims that
have occurred up until and including the Separation Date.

 

  3. Company’s Release of Claims Against Executive. The Company’s release of
claims set forth in Section 8 of the Agreement is hereby amended to include all
such claims that have occurred up until and including the Separation Date.

 

  4. The Parties again acknowledge that they have been advised to consult with
legal counsel and are familiar with the provisions of California Civil Code
Section 1542, a statute that otherwise prohibits the release of unknown claims,
which 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 EXECUTING THE RELEASE, WHICH
IF KNOWN BY HIM OR HER MUST HAVE MATERIALLY AFFECTED HIS OR HER SETTLEMENT WITH
THE DEBTOR.

The Parties, being aware of said code section, agrees to expressly waive any
rights they may have thereunder, as well as under any other statute or common
law principles of similar effect. The Parties acknowledge that the signing of
this Supplement to the Mutual Separation Agreement and Mutual Release is a
condition of the Parties entering into the Mutual Separation Agreement and
Mutual Release.

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IN WITNESS WHEREOF, the Parties have executed this Supplement to the Agreement
on the respective dates set forth below.

 

   

PAUL WAGNER, Ph.D., an individual

Dated:    

 

    Paul Wagner, Ph.D.     PFENEX INC. Dated:     By  

 

      Evert B. Schimmelpennink       Chief Executive Officer