Document:

EX-10.1

 Exhibit 10.1 

October 3, 2017 
 Thomas E. Hughes 

Dear Tom: 
 I am pleased to set forth the terms of your continued
employment with Zafgen, Inc. (the “Company”) from and following October 9, 2017 (the “Effective Date”). 
 Commencing on the
Effective Date the following terms shall apply: 
  

	 	1.	Position and Duties: You will serve as President and Chief Scientific Officer (“CSO”) and will no longer serve as the Company’s Chief Executive Officer (“CEO”). You will continue to serve
as a member of the Company’s Board of Directors (the “Board”), subject to election and other governance procedures. 

  

	 	2.	Compensation and Benefits: Your base salary, benefits and target bonus opportunity shall remain as you had immediately prior to the Effective Date. 

 

	 	3.	Equity: You will continue to vest in your outstanding equity awards subject to the terms of the Company’s 2014 Stock Option and Incentive Plan and related stock option and/or restricted stock agreements (the
“‘Equity Documents”). In addition, subject to your execution of this letter agreement, on the Effective Date, the Company will grant you an option to purchase 275,000 shares of the Company’s common stock at the then fair market
value which equals approximately 1% of the Company’s issued and outstanding capital stock as of the date of this Agreement (the “Option”), such option to vest subject to meeting certain defined stock price performance objectives that
are summarized in Appendix 1, the terms of which are incorporated as material terms to this Agreement by reference herein. 

  

	 	4.	Severance and Change in Control: Your employment with the Company will continue to be governed by the Severance and Change in Control Agreement between you and the Company dated June 30, 2016 (the
“Severance Agreement”), provided you agree to waive your option to resign for Good Reason in connection with any changes associated with transitioning from CEO to CSO, except you may elect to resign for Good Reason on the third (3rd) anniversary of the Effective Date (the “Third Anniversary”) by written notice served by you at least 15 days prior to the Third Anniversary (the “Good Reason Option”)
subject to the following: 

  

	 	a.	If you elect the Good Reason Option, subject to the terms and conditions of the Severance Agreement you will be entitled to: (i) 12 months of severance and benefits as set forth in Section 5 of the Severance
Agreement; (ii) a pro-rated bonus for the time period between January 1, 2020 and the Third Anniversary, as determined by the Compensation Committee; and (iii) 12 months of accelerated vesting of your then outstanding time-based
equity awards. 

	 	b.	If you do not elect the Good Reason Option, the Severance Agreement as revised by this letter agreement will remain in effect for the remainder of the term set forth in Section 8 of the Severance Agreement.

 This letter agreement, together with the Severance Agreement as revised by this letter agreement and the Equity Documents shall govern the
relationship between you and the Company from and after the Effective Date and, except as provided herein, shall supersede and negate all previous agreements and understandings with respect to the subject matter herein. For purposes of clarity, this
letter agreement is not intended to, and does not, supersede or negate or otherwise affect the Company’s rights under any pre-existing proprietary inventions assignment agreement or non-competition agreement that you had entered into prior to
the Effective Date including the Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement by and between the Company and yourself, dated July 29, 2008, which you hereby reaffirm. Neither party has made any
representation to the other regarding any of the subject matters hereof except as expressly set forth in this letter. 
 Anything in this letter agreement
to the contrary notwithstanding, if at the time of your separation from service within the meaning of Section 409A of the Internal Revenue Code of 1986, as amended (the “Code”), the Company determines that you are a “specified
employee” within the meaning of Section 409A(a)(2)(B)(i) of the Code, then to the extent any payment or benefit that you become entitled to under this letter agreement on account of your separation from service would be considered deferred
compensation subject to the 20 percent additional tax imposed pursuant to Section 409A(a) of the Code as a result of the application of Section 409A(a)(2)(B)(i) of the Code, such payment shall not be payable and such benefit shall not be
provided until the date that is the earlier of (A) six months and one day after your separation from service, or (B) your death. To the extent that any payment or benefit described in this letter agreement constitutes “non-qualified
deferred compensation” under Section 409A of the Code, and to the extent that such payment or benefit is payable upon your termination of employment, then such payments or benefits shall be payable only upon your “separation from
service.” The determination of whether and when a separation from service has occurred shall be made in accordance with the presumptions set forth in Treasury Regulation Section 1.409A 1(h). The Company and you intend that this letter
agreement will be administered in accordance with Section 409A of the Code. To the extent that any provision of this letter agreement is ambiguous as to its compliance with Section 409A of the Code, the provision shall be read in such a
manner so that all payments hereunder comply with Section 409A of the Code. Each payment hereunder shall be considered a separate payment for purposes of Section 409A of the Code. 

To accept the terms of this offer of continued employment, please sign below and return it to me. 

 

	
	Very truly yours,
	
	/s/ Peter Barrett
	 Peter Barrett
 Chairman, Board of
Directors

  
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 I agree to the terms and conditions as set forth in this letter and, subject to those terms and conditions, I
accept the employment opportunity set forth herein as of the Effective Date. 
  

					
	/s/ Thomas E. Hughes	 		 	October 3, 2017
	Thomas E. Hughes	 		 	Date

  
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 Appendix 1 

[Omitted] 

  
 4EX-10.2

 Exhibit 10.2 

October 3, 2017 
 Jeffrey Hatfield 

727 Saint James Drive 
 Langhorne, PA 19047 

 

	Re:	Employment Offer 

 Dear Jeff: 

On behalf of Zafgen, Inc., a Delaware corporation (the “Company”), I am pleased to offer you the position of the Company’s Chief Executive
Officer (“CEO”). If accepted, this letter agreement sets forth the terms and conditions of your employment (the “Agreement”). 

1. Position. As the Company’s CEO, you will report directly to the Company’s Board of Directors (the “Board”). You
shall have supervision and control over and responsibility for the day-to-day business and affairs of the Company and shall have such other powers and duties as may from
time to time be prescribed by the Board. You shall devote your full working time and efforts to the business and affairs of the Company. Notwithstanding the foregoing, you may serve on up to three (3) other boards of directors, with the prior
written approval of the Board, or engage in religious, charitable or other community activities as long as such services and activities are disclosed to the Board and do not interfere with the performance of your duties to the Company. During your
employment as CEO, you also shall serve as a member of the Board. Upon the ending of your employment as CEO for any reason, you shall immediately resign from the Board as well as from any other position(s) to which you were elected or appointed in
connection with your position as CEO. 
 2. Work Location. You will report to the Company’s headquarters, currently in Boston,
Massachusetts, and will reside within commuting distance of such headquarters. You agree to travel as reasonably necessary to accomplish your job duties. 

3. Start Date. Your employment with the Company will begin on October 9, 2017 (the “Start Date”). 

4. Salary. Effective on the Start Date, the Company will pay you a base salary at the rate of $500,000 per year, payable in accordance
with the Company’s standard payroll schedule and subject to applicable deductions and withholdings. Your Base Salary will be subject to periodic review and adjustments at the discretion of the Board or the Board’s Compensation Committee
(the “Compensation Committee”). Your base salary in effective at any given time shall be referred to herein as the “Base Salary”. 

5. Signing Bonus. The Company shall pay you a one-time lump sum signing bonus of $100,000 (the “Signing Bonus”) within thirty
(30) days after your employment commences. The Signing Bonus shall be subject to tax-related deductions and withholdings. If prior to the 

 
one year anniversary of the Start Date, you resign without Good Reason (as defined in the Severance Agreement (as defined below)) from your employment or if you are terminated by the Company for
Cause (as defined in the Severance Agreement), then you shall repay the Signing Bonus to the Company within ten (10) days of the Date of Termination (as defined below). In the event that you are obligated to repay the Signing Bonus, the Company
may, at its option, withhold such amount from any other payments due to you, to the fullest extent permitted by law. 
 6. Annual
Bonus. You will be eligible to receive an annual performance bonus (the “Bonus”). The Bonus shall be targeted at 50% of the Base Salary (the “Target Bonus”), and will be prorated for 2017 based on the Start Date. The actual
Bonus is discretionary and will be subject to the assessment of your performance, as well as business conditions at the Company as determined by the Board or the Compensation Committee. To earn any part of the Bonus, except as otherwise provided in
Section 10, you must be employed by the Company on the date that the Bonus is paid, which will be on or before March 15 of the calendar year following the applicable performance year. In addition, the Bonus will be subject to the terms of
any applicable bonus plan as may be adopted and amended from time to time. 
 7. Expenses.  

 

	 	a.	The Company will provide a relocation package in 2018 whereby the Company will reimburse you up to a certain amount to cover your relocation costs to Massachusetts. 

 

	 	b.	The Company will pay the reasonable legal fees incurred in the review and completion of this letter. 

8. Equity. Subject to final Board approval, upon or promptly following commencement of your employment, the Company shall grant you
(i) an option to purchase 550,000 shares of the Company’s common stock at the then fair market value (“FMV”), which equals approximately 2% of the Company’s issued and outstanding capital stock as of the date of this
Agreement (“Option Grant 1”) such option to vest monthly over a four year period with a one year cliff, and (ii) an option to purchase 1,100,000 shares of the Company’s common stock at the then FMV which equals approximately 4%
of the Company’s issued and outstanding capital stock as of the date of this Agreement (“Option Grant 2”), such option to vest subject to meeting certain defined stock price performance objectives that are summarized in Appendix
1, the terms of which are incorporated as material terms to this Agreement by reference herein. Option Grant 1 and Option Grant 2 are collectively referred to herein as the “Initial Equity Award.” The Initial Equity Award equals
approximately 6% of the Company’s issued and outstanding capital stock as of the date of this Agreement. The Initial Equity Award will be subject to the Company’s Stock Option Plan and any associated stock option agreement(s) required to
be entered into by you and the Company (the “Equity Documents”). 
 9. Benefits/Vacation. As a regular, full time employee
you will be eligible to participate in or receive benefits under the Company’s employee benefit plans in effect from time to time, subject to the terms of such plans. These plans may be amended or terminated with or without prior notice. You
will be entitled to accrue up to four (4) weeks paid vacation days in each full year of employment, which shall be accrued ratably. You shall also be entitled to all paid holidays given by the Company to its executives. 

  
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 10. At-will Employment; Accrued Obligations. Your employment relationship with the Company
is “at will,” meaning either you or the Company may terminate it at any time for any or no reason. In the event of the ending of your employment for any reason, the Company shall pay you (i) your Base Salary plus any accrued but
unused vacation through your last day of employment (the “Date of Termination”), (ii) any vested benefits you may have under any employee benefit or incentive plans of the Company through the Date of Termination, which vested benefits
shall be paid and/or provided in accordance with the terms of such employee benefit plans, and (iii) the amount of any documented expenses properly incurred by you on behalf of the Company prior to any such termination and not yet reimbursed
(collectively, the “Accrued Payments”). In addition, if your employment ceases due to your death or Disability (as defined in the Severance Agreement), the Company will pay to you any otherwise earned but unpaid Bonus with respect to the
year ending prior to the date of such cessation. 
 11. Severance. In the event the Date of Termination is as a result of a
Terminating Event as defined in the Severance and Change in Control Agreement (the “Severance Agreement”) attached as Appendix 2, in addition to the Accrued Payments, you shall be entitled to severance pay and benefits subject to
and in accordance with the Severance Agreement. The Severance Agreement is incorporated by reference herein. 
 12. Confidential
Information and Restricted Activities. As a material condition of your employment, you agree to enter into the Company’s Employee Non-Disclosure, Non-Competition, and Assignment of Intellectual Property Agreement (the “Restrictive
Covenant Agreement”). The Restrictive Covenant Agreement is incorporated by reference herein. 
 13. Taxes. All forms of
compensation referred to in this Agreement are subject to reduction to reflect applicable withholding and payroll taxes and other deductions required by law. You hereby acknowledge that the Company does not have a duty to design its compensation
policies in a manner that minimizes your tax liabilities, and you will not make any claim against the Company or its board of directors related to tax liabilities arising from your compensation. 

14. Interpretation and Enforcement. This Agreement, including the Severance Agreement and the Equity Documents, constitutes the
complete agreement between you and the Company, contains all of the terms of your employment with the Company and supersedes any prior agreements, representations or understandings (whether written, oral or implied) between you and the Company. The
terms of this Agreement and the resolution of any disputes as to the meaning, effect, performance or validity of this Agreement or arising out of, related to, or in any way connected with this Agreement, your employment with the Company or any other
relationship between you and the Company (the “Disputes”) will be governed by the laws of the Commonwealth of Massachusetts, excluding laws relating to conflicts or choice of law. You and the Company submit to the exclusive personal
jurisdiction of the federal and state courts located in the Commonwealth of Massachusetts in connection with any Dispute or any claim related to any Dispute. 

  
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 15. Assignment. Neither you nor the Company may make any assignment of this Agreement or
any interest in it, by operation of law or otherwise, without the prior written consent of the other; provided, however, that the Company may assign its rights and obligations under this Agreement (including the Severance Agreement) without your
consent to any affiliate or to any person or entity with whom the Company shall hereafter effect a reorganization, consolidate with, or merge into or to whom it transfers all or substantially all of its properties or assets. This Agreement shall
inure to the benefit of and be binding upon you and the Company, and each of your and its respective successors, executors, administrators, heirs and permitted assigns. 

16. Miscellaneous. This Agreement may not be modified or amended, and no breach shall be deemed to be waived, unless agreed to in
writing by you and a Board member of the Company. The headings and captions in this Agreement are for convenience only and in no way define or describe the scope or content of any provision of this Agreement. The words “include,”
“includes” and “including” when used herein shall be deemed in each case to be followed by the words “without limitation.” This Agreement may be executed in two or more counterparts, each of which shall be
an original and all of which together shall constitute one and the same instrument. 
 17. Other Terms. By signing this Agreement,
you represent to the Company that you have no contractual commitments or other legal obligations that would or may prohibit you from performing your duties for the Company. As with any employee, you must submit satisfactory proof of your identity
and your legal authorization to work in the United States. 
 18. Indemnification. Both during and following your employment, the
Company will (a) indemnify and defend you for acts performed in your capacity as an employee, officer and/or director of the Company as specified in the Company’s by-laws, Certificate of Incorporation, and standard form of indemnification
agreement to be entered into by you, and (b) provide you with directors’ and officers’ insurance at least equal to the coverage applicable to the then current officers and directors of the Company. 

We are excited about you becoming Zafgen’s next CEO. If you have any questions about this offer, please do not hesitate to contact me. Otherwise, please
confirm your acceptance of this offer of employment by signing below and returning an unmodified copy to me no later than October 5, 2017. 

  
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 Please acknowledge, by signing below, that you have accepted this Agreement. 

 

			
	Very truly yours,
	
	Zafgen, Inc.
		
	By:	 	/s/ Peter Barrett
	Name: Peter Barrett
	Title:   Chairman, Board of Directors

 I have read and accept this employment offer: 

	
	
	/s/ Jeffrey Hatfield
	Jeffrey Hatfield
	Dated: October 3, 2017

  
 5 

 Appendix 1 

[Omitted] 

  
 6 

 Appendix 2 

[See Exhibit 10.3 of this Form 8-K] 

  
 7

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