Document:

EX-10.12

 Exhibit 10.12 
  

					
	

	 	www.akebia.com	 	 Akebia Therapeutics, Inc.

245 First Street
 Suite
1100
 Cambridge, MA 02142

	 	 	 
		 	February 7, 2014	 	

 William Daly 
 13 Via Abrazar

 San Clemente, CA 92673 
 Dear Bill: 

This letter agreement (“Agreement”) will confirm the agreement between you and Akebia Therapeutics, Inc. (the
“Company”) concerning your engagement to provide certain consulting services. 
 1. Services. You agree to provide
services as requested by the Company. The services to be provided hereunder shall include advising the Company with respect to its business development activities, intellectual property portfolio, and such other assistance as specifically requested
by your designated Company contact (in the aggregate, the “Services”). Your designated Company contact for this engagement is John P. Butler, Chief Executive Officer. You agree to devote as much business time as is necessary to
properly perform the Services, but no more than five (5) hours each week unless otherwise agreed upon by the parties. The term of this Agreement shall commence on February 7, 2014 (the “Effective Date”) and continue for a
period of twelve (12) months, unless earlier terminated as provided herein (the “Consulting Period”). 
 2.
Relationship of Parties. It is expressly agreed that, in providing the Services to the Company under this Agreement, you will be an independent contractor and that you will not be an employee or agent of the Company and that nothing herein is
intended to create an employment relationship between you and the Company. It is also agreed that you shall have no right to make any commitments on behalf of the Company without the express written consent of your designated contact or a properly
authorized Company officer. You are free to accept engagements from others during the Consulting Period, so long as those engagements do not prevent you from performing the Services or otherwise violate your obligations under this Agreement,
including those obligations set forth in Sections 6, 7 and 8. In addition to your obligations under this Agreement, you acknowledge your additional obligations set forth in the Separation Agreement between you and the Company dated as of
February 7, 2014 (the “Separation Agreement”). For the avoidance of doubt, this Agreement shall be void ab initio if you fail to execute or revoke the Separation Agreement. 

3. Consideration. Consideration for the Services provided hereunder will be in the form of a restricted stock award granted to you on
the Effective Date pursuant to the Company’s 2008 Equity Incentive Plan in the amount of 32,000 restricted shares (the “February 2014 

 Award”). The terms and conditions of the February 2014 Award shall be set forth in a restricted stock award
agreement between you and the Company which shall provide for vesting as follows, subject to Section 11 below: (i) 50% of the restricted stock shall vest on the date that is six (6) months after the Effective Date and (ii) the
remaining 50% of the restricted stock shall vest on the last day of the Consulting Period. In addition, if you provide written evidence to the Company that you have timely made a valid 83(b) election with respect to at least 14,500 shares, the
Company shall pay you One Hundred Fifty Thousand Dollars ($150,000) to partially offset your costs associated with the 83(b) election. The Company shall pay you within five (5) days of you providing the Company with documentation of your 83(b)
election. 
 4. Expenses. The Company will reimburse your reasonable and necessary business expenses directly incurred by you in the
performance of the Services under this Agreement during the Consulting Period, subject to prior approval of such expenses and timely submission of such documentation and substantiation as the Company may require. You agree to submit monthly requests
for reimbursement of expenses. The Company will pay properly documented expenses within thirty (30) days after receipt of properly documented requests. Any reimbursements provided hereunder that would constitute nonqualified deferred
compensation subject to Section 409A of the Internal Revenue Code of 1986, as amended from time to time, and guidance issued thereunder, including exemptive and transition relief provisions, shall be subject to the following additional rules:
(i) no reimbursement of any such expense shall affect your right to reimbursement of any other such expense in any other taxable year; (ii) reimbursement of the expense shall be made not later than the end of your taxable year following
the taxable year in which the expense was incurred; and (iii) the right to reimbursement shall not be subject to liquidation or exchange for any other benefit. 

5. Taxes, Insurance and Benefits. As an independent contractor, you shall be solely responsible for all insurance including, but not
limited to, workers’ compensation insurance and unemployment insurance, if required, and for the withholding and payment of all federal, state and local income taxes, social security and Medicare taxes and other
legally-required payments on sums received from the Company under this Agreement. As applicable, the Company will provide you with an IRS Form 1099 evidencing all consideration paid by it to you in connection
with this engagement. You will also be solely responsible for any comprehensive general liability, automobile or other insurance which you decide to obtain and keep in effect. 

Because you are an independent contractor, neither you nor any dependent or other individual claiming through you will be eligible to
participate in, or receive benefits under, any of the employee benefit plans, programs, agreements or arrangements maintained by the Company, other than as set forth in the Separation Agreement. 

6. Confidentiality and Related Matters. 

(a) Confidential Information. You acknowledge that you have learned of, and during the course of the Consulting Period you will learn
of, Confidential Information, as defined below, and have developed and may develop Confidential Information on behalf of the Company and its Affiliates. You agree that, except as otherwise permitted by the Company in writing signed by an expressly
authorized agent, you will not use or disclose to any Person 

  
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(except as required by applicable law or for the proper performance of the Services for the Company) any Confidential Information obtained by you incident to your engagement under this Agreement
or any other past, present or future association with the Company or any of its Affiliates, and that you will comply with the policies and procedures of the Company and its Affiliates for protecting Confidential Information. You agree that this
restriction shall continue to apply after the Consulting Period terminates, regardless of the reason for such termination. Further, you agree to furnish prompt notice to the Company of any required disclosure of Confidential Information sought
pursuant to subpoena, court order or any other legal process or requirement, and agree to provide the Company a reasonable opportunity to seek protection of the Confidential Information prior to any such disclosure. 

(b) Protection of Documents. All documents, records and files, in any media of whatever kind and description, relating to the business,
present or otherwise, of the Company or any of its Affiliates, and any copies, in whole or in part, thereof (the “Documents”), whether or not prepared by you, shall be the sole and exclusive property of the Company. You agree to
safeguard all Documents and to surrender to the Company, at the time the Consulting Period terminates or at such earlier time or times as the Company may specify, all Documents then in your possession or control. You also agree to disclose to the
Company, at the time the Consulting Period terminates or at such earlier time or times as the Company may specify, alt passwords necessary or desirable to obtain access to, or that would assist in obtaining access to, any information which you have
password-protected on any computer equipment, network or system of the Company or any of its Affiliates. 
 (c) No Public Comment.
During the Consulting Period and thereafter, you shall not give any statement or make any announcement, directly or indirectly, orally or in writing, publicly or to the media (electronic, print or otherwise), about the Company or any of its
Affiliates without the prior written consent of the Chief Executive Officer of the Company or his expressly authorized representative. 
 7.
Assignment of Rights to Intellectual Properly. You shall promptly and fully disclose all Intellectual Property to the Company. You hereby assign and agree to assign to the Company (or as otherwise directed by the Company) your full right,
title and interest in and to all Intellectual Property. You agree to execute any and all applications for domestic and foreign patents, copyrights or other proprietary rights and to do such other acts (including without limitation the execution and
delivery of instruments of further assurance or confirmation) requested by the Company to assign the Intellectual Property to the Company and to permit the Company to enforce any patents, copyrights or other proprietary rights to Intellectual
Property. You will not charge the Company for time spent in complying with these obligations. All copyrightable works that you create shall be considered “work made for hire” and shall, upon creation, be owned exclusively by the Company.
This Agreement does not apply to any invention or development that qualifies fully as a nonassignable invention under Section 2870 of the California Labor Code. By signing this Agreement, you acknowledge that you have received and reviewed the
notification contained in Exhibit A attached hereto. 
 8. Restricted Activities. In consideration of (i) the Company
granting you access to goodwill, Confidential Information and trade secrets, and (ii) the severance, equity and other benefits provided to you pursuant to the Separation Agreement, and (iii) the February 2014 

  
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Award, you acknowledge and agree that the following restrictions on your activities during and after the Consulting Period are necessary to protect the goodwill, Confidential Information, trade
secrets and other legitimate interests of the Company and its Affiliates: 
 (a) Conflicts of Interest Prohibited. You agree that,
during the Consulting Period, you will not undertake any outside activity, whether or not competitive with the business of the Company or its Affiliates that could reasonably give rise to a conflict of interest or otherwise interfere with yow
performance of the Services. 
 (b) Non-Competition. During the Consulting Period, you shall not, directly or indirectly, in any
capacity, whether as owner, partner, investor, consultant, agent, independent contractor, employee, co-venturer or otherwise, work or provide services, whether with or without compensation, to any of the following companies, their affiliates or any
Persons associated therewith: FibroGen, Inc., GlaxoSmithKline plc, Keryx Biopharrnaceuticals, Inc., Japan Tobacco Inc. or Regeneron Pharmaceuticals, Inc. The foregoing shall not prevent (i) your passive ownership of 3% percent or less of the
equity securities of any publicly traded company or (ii) your provision of services to Aerpio Therapeutics, Inc., but only to the extent your provision of such services does not otherwise violate the provisions of this Agreement. 

(c) Non-Solicitation of Investors, Business Partners or Vendors. During the Consulting Period, you agree that you will not directly or
indirectly solicit or encourage any investor, business partner or vendor of the Company or any of its Affiliates to terminate or diminish its relationship with them. 

(d) Non-Solicitation of Employees and Contractors. During the Consulting Period and for a period of twelve (12) months thereafter,
excluding any activities undertaken on behalf of the Company or any of its Affiliates in the course of your duties, you will not, and will not assist any other Person to, (i) solicit for hiring any employee of the Company or any of its
Affiliates or seek to persuade any employee of the Company or any of its Affiliates to discontinue employment or (ii) solicit or encourage any independent contractor providing services to the Company or any of its Affiliates to terminate or
diminish its relationship with them. 
 9. Enforcement. In signing this Agreement, you give the Company assurance that you have
carefully read and considered all the terms and conditions of this Agreement, including the restraints imposed on you under Sections 6, 7 and 8 hereof. You agree without reservation that these restraints are necessary for the reasonable and proper
protection of the Company and its Affiliates, and that each and every one of the restraints is reasonable in respect to subject matter, length of time and geographic area. You further agree that, were you to breach any of the covenants contained in
Sections 6, 7 and 8, the damage to the Company and its Affiliates would be irreparable. You therefore agree that if you breach any of the covenants contained in Sections 6, 7 or 8 hereof, the Company, in addition to any other remedies available to
it including those set forth in Section 11 hereof, shall be entitled to (i) immediately cease all consideration provided under this Agreement (including, without limitation, the February 2014 Award) and all compensation and benefits
provided under the Separation Agreement (including, without limitation, any severance payments, benefits and equity) and (ii) preliminary and permanent injunctive relief against any breach or threatened breach by you of any of those covenants,

  
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without having to post bond, together with an award of its reasonable attorney’s fees incurred in enforcing its rights hereunder. So that the Company may enjoy the full benefit of the
covenants contained in Sections 6, 7 and 8, you further agree that the restricted period shall be tolled, and shall not run, during the period of any breach by you of any of the covenants contained in Sections 6, 7 and 8. You and the Company further
agree that, in the event that any provision of Sections 6, 7 and 8 are determined by any court of competent jurisdiction to be unenforceable by reason of its being extended over too great a time, too large a geographic area or too great a range of
activities, that provision shall be deemed to be modified to permit its enforcement to the maximum extent permitted by law. It is also agreed that each of the Company’s Affiliates shall have the right to enforce all of your obligations to that
Affiliate under this Agreement including, without limitation, pursuant to Sections 6, 7 and 8. Finally, no claimed breach of this Agreement or other violation of law attributed to the Company, or change in the nature or scope of your relationship
with the Company, shall operate to excuse you from the performance of your obligations under Section 6, 7 and 8. 
 10.
[INTENTIONALLY LEFT BLANK] 
 11. Termination. This Agreement and your Services may be terminated by you or the Company upon
thirty (30) days’ written notice to the other, except that the Company may terminate this Agreement immediately for cause in the event that it determines, in its sole discretion, (i) that you are in breach of any provision of this
Agreement or the Separation Agreement; or (ii) that you have acted or failed to act in a manner that is actually or potentially harmful to the business interests or reputation of the Company or that you have committed an act or omission that
could expose the Company to liability to a third party (hereinafter referred to as termination for “Cause”). Upon termination of this Agreement by you for convenience or by the Company for Cause, the unvested portion of the February 2014
Award shall immediately terminate without payment of consideration therefor and any and all other consideration provided under this Agreement and all compensation and benefits provided under the Separation Agreement (including, without limitation,
any severance payments, benefits and equity) shall immediately cease. Upon termination of this Agreement by the Company (or any successor-in interest or assignee) other than for Cause or upon a Change of Control (as defined below), vesting of the
February 2012 Award and the February 2014 Award shall accelerate in full. Upon termination of this Agreement, the Consulting Period shall end and the Company shall have no further obligation to you, other than for payment of un-reimbursed expenses
that are satisfactorily documented. 
 12. Survival. Provisions of this Agreement shall survive any termination if so provided herein
or if necessary or desirable to accomplish the purposes of other surviving provisions. 
 13. Governing Law. This Agreement shall be
governed and construed, and the rights and obligations of the parties hereto shall be determined, in accordance with the laws of the Commonwealth of Massachusetts, without regard to its conflicts of law principles. 

  
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 14. Notices. Any and all notices, requests, demands and other communications provided for
by this Agreement shall be in writing and shall be effective when delivered in person, consigned to a reputable national courier service or deposited in the United States mail, postage prepaid, registered or certified, and addressed as follows: 

Consultant: 

Mr. William Daly 
 13 Via
Abrazar 
 San Clemente, CA 92673 

Company: 
 Akebia
Therapeutics, Inc. 
 Attention: Chief Executive Officer 

245 First Street, Suite 1100 

Cambridge, MA 02142 
 with a copy
to: 
 Akebia Therapeutics, Inc. 

Attention: General Counsel 
 245
First Street, Suite 1100 
 Cambridge, MA 02142 

15. Definitions. Words or phrases which are initially capitalized or are within quotation marks shall have the meanings provided in
this Section and as provided elsewhere herein. For purposes of this Agreement, the following definitions apply: 
 (a)
“Affiliates” means all persons and entities directly or indirectly controlling, controlled by or under common control with the Company, where control may be by management authority, equity interest or otherwise. 

(b) “Confidential Information” includes any information considered confidential and proprietary by the Company including,
without limitation, such information relating to (i) the development, research, testing, manufacturing, marketing and financial activities of the Company and its Affiliates, (ii) the Products, (iii) the costs, sources of supply,
financial performance and strategic plans of the Company and its Affiliates, (iv) the identity and special needs of the customers of the Company and its Affiliates and (v) the people and organizations with whom the Company and its
Affiliates have business relationships and those relationships. Confidential Information also includes information that the Company or any of its Affiliates have received, or may receive hereafter, belonging to others or which was received by the
Company or any of its Affiliates with any understanding, express or implied, that it would not be disclosed. 
 (c) “Intellectual
Property” means inventions, discoveries, developments, methods, processes, compositions, works, concepts and ideas (whether or not patentable or copyrightable or constituting trade secrets) conceived, made, created, developed or reduced to
practice by you (whether alone or with others, whether or not during normal business hours or on 

  
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or off the Company premises) during the Consulting Period that relate either to the business of the Company or to any prospective activity of the Company or any of its Affiliates, that result
from any work performed by you for the Company or any of its Affiliates or that make use of Confidential Information or any of the equipment or facilities of the Company or any of its Affiliates. 

(d) “Person” means an individual, a corporation, a limited liability company, an association, a partnership, an estate, a
trust and any other entity or organization, other than the Company or any of its Affiliates. 
 (e) “Products” means all
products and product candidates planned, researched, developed, tested, sold, licensed, or distributed by the Company or any of its Affiliates, together with all services provided or otherwise planned by the Company or any of its Affiliates, during
the Consulting Period. 
 (f) “Change of Control” means (i) the date any “person” (as such term is used in
Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended) is or becomes the “ beneficial owner” (as defined in Rule l3d-3 under said Act), directly or indirectly, of securities of the Company representing more than 50%
of the total voting power represented by the Company’s then outstanding voting securities; (ii) the date of the consummation of a merger or consolidation of the Company with any other corporation that has been approved by the stockholders
of the Company, other than a merger or consolidation which would result in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting
securities of the surviving entity or its parent) at least fifty percent (50%) of the total voting power represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately after such merger or
consolidation; or (iii) the date of the consummation of the sale or disposition by the Company of all or substantially all the Company’s assets. Notwithstanding the foregoing provisions of this definition, a transaction will not be deemed
a Change of Control unless the transaction qualifies as a “change in control event” within the meaning of Section 409A of the Internal Revenue Codes. 

16. Severability. If any portion or provision of this Agreement shall to any extent be declared illegal or unenforceable by a court of
competent jurisdiction, then the remainder of this Agreement, or the application of such portion or provision in circumstances other than those as to which it is so declared illegal or unenforceable, shall not be affected thereby, and each portion
and provision of this Agreement shall be valid and enforceable to the fullest extent permitted by law. 
 17. Miscellaneous. This
Agreement contains the entire agreement between you and the Company, and replaces all prior agreements between you and the Company, whether written or oral, other than the Separation Agreement and, except as otherwise explicitly modified herein or
in the Separation Agreement, the award agreements evidencing the February 2012 Award and the February 2014 Award, with respect to the Services to be provided by you to the Company pursuant to this Agreement. This Agreement may not be amended and no
breach will be waived unless agreed in a signed writing by you and an authorized officer of the Company. 

  
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 If the terms of this Agreement are acceptable to you, please sign, date and return it to me. The
Agreement will take effect as a legally-binding agreement between you and the Company as of the Effective Date. 
  

	
	Very truly yours,
	
	/s/ John P. Butler
	
	 John P. Butler
 President and Chief Executive
Officer

 Accepted and agreed: 
  

			
	/s/ William Daly
	William Daly
		
	Date:	 	2/7/2014

  
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 Exhibit 10.12 

EXHIBIT A 

LIMITED EXCLUSION NOTIFICATION 

This Is To Notify you in accordance with Section 2872 of the California Labor Code that the foregoing Agreement between you and
Akebia Therapeutics, Inc. (the “Company”) does not require you to assign or offer to assign to the Company any invention that you developed entirely on your own time without using the Company’s equipment, supplies, facilities or trade
secret information except for those inventions that either: 
 (1) Relate at the time of conception or reduction to practice of the
invention to the Company’s business, or actual or demonstrably anticipated research or development of the Company; 
 (2) Result from
any work performed by you for the Company. 
 To the extent a provision in the foregoing Agreement purports to require you to assign an
invention otherwise excluded from the preceding paragraph, the provision is against the public policy of this state and is unenforceable. 

This limited exclusion does not apply to any patent or invention covered by a contract between the Company and the United States or any of its
agencies requiring full title to such patent or invention to be in the United States. 

  
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 Exhibit 10.13 

SEPARATION AGREEMENT 

This Separation Agreement (“Agreement”) is made as of February 7, 2014, by and between Akebia Therapeutics, Inc. (the
“Company”) and William Daly (“Employee”) under the following circumstances (Employee and the Company collectively referred to as the “Parties” or individually referred to as a “Party”). This Agreement shall
become effective on the eighth day after its execution by Employee (the “Effective Date”), provided that Employee has not revoked this Agreement as set forth in Paragraph 4 of the below Acknowledgment. 

A. The Company and Employee have mutually agreed to sever their employment relationship as of February 7, 2014 (the “Termination
Date”). 
 B. The Company has proposed, and Employee has agreed to, certain individualized severance benefits in connection with his
termination from employment, as further set forth below (the “Severance Benefits”). 
 NOW, THEREFORE, the parties agree, in
consideration of the provisions and payments described below, as follows: 
 1. The Company shall pay Employee the gross amount of Three
Hundred Ten Thousand Dollars ($310,000) as severance pay, which shall be paid during the Severance Period (as defined below) in equal installments in accordance with the normal pay practices of the Company (the “Severance Payments”). The
Severance Payments shall commence with the first payroll period following the Effective Date and continue for twelve (12) months (the “Severance Period”), with the first payment to be retroactive to the Termination Date. Any
applicable deductions and required withholdings shall be made from the Severance Payments. In addition, Company shall reimburse Employee up to Five Thousand Dollars ($5,000), upon receipt of appropriate documentation (which shall be provided within
thirty (30) days after the Effective Date) for Employee’s attorney’s fees incurred in reviewing and negotiating this Agreement, the Consulting Agreement (defined below), and any other agreement relating to Employee’s employment
by the Company and termination from employment. 
 2. Regardless of whether Employee executes this Agreement, and provided he timely
completes the required election forms, Employee will be eligible to continue receiving group medical and/or dental insurance pursuant to the Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”). If Employee executes and does
not rescind this Agreement, then during the Severance Period the Company shall pay Employee’s COBRA premiums and Employee shall only pay the amount equivalent to the health and dental insurance premiums it would have paid on his behalf had he
remained employed by the Company. After the Severance Period, Employee may, at his own expense, continue participation in COBRA for the balance of time provided under COBRA (provided, however, the “qualifying event” under COBRA shall be
deemed to have occurred on the Termination Date). Company shall deduct Employee’s contributions to COBRA premiums from his Severance Payments unless otherwise directed by Employee in writing. The Company’s obligation to provide premium
payments under this Section 2, however, shall cease upon the earlier to occur of (a) expiration or earlier termination of the Severance Period as set forth herein or pursuant to Section 11 of the Consulting Agreement (defined below);
(b) Employee’s loss of eligibility for COBRA; and/or (c) Employee becoming eligible to obtain substantially equivalent health benefits from an alternative source through future employment or otherwise, in which case Employee agrees to
promptly notify the Company. 

 3. As of the Separation Date, you held a stock option to purchase 51,698 shares of stock of the
Company granted pursuant to an Equity Award Agreement dated December 23, 2013 (the “December 2013 Option”), an award of 30,763 shares of restricted stock of the Company granted pursuant to an Equity Award Agreement dated April 1,
2013 (the “April 2013 Award”), and an award of 30,047 shares of restricted stock of the Company granted pursuant to an Equity Award Agreement dated February 21, 2012 (the “February 2012 Award”), each of which were granted
pursuant to the Company’s 2008 Equity Incentive Plan (the “2008 Equity Incentive Plan”). With respect to the February 2012 Award, these restricted shares will continue vesting in accordance with their terms during the Severance
Period; provided, that, subject to Section 4 below, the remainder of the restricted shares granted to Employee pursuant to that award shall vest in full on the last day of the Severance Period. Employee hereby acknowledges and agrees
that, as of the Termination Date: (i) after giving effect to this Section 3, other than the February 2012 and the February 2014 Award (as defined in the Consulting Agreement), Employee holds no other equity or equity-based awards with
respect to the Company’s stock, whether granted pursuant to the 2008 Equity Incentive Plan or other equity incentive plan; (ii) no portion of the December 2013 Option or the April 2013 Award is currently vested; and
(iii) notwithstanding any other provision in the 2008 Equity Incentive Plan or the applicable Equity Award Agreement to the contrary, the December 2013 Option and the April 2013 Award shall be cancelled as of the Termination Date without
payment of any consideration therefor and that Employee has and shall have no further rights under the applicable Equity Award Agreement or the 2008 Equity Incentive Plan. Prior to the Effective Date, Employee shall execute a lock-up agreement in
connection with a potential public offering of the Company’s stock. 
 4. Employee and Company entered into a separate Consulting
Agreement dated as of February 7, 2014 (the “Consulting Agreement”). The Consulting Agreement contains certain restrictive covenants, including those relating to non-competition, non-solicitation, and confidentiality. If
Employee’s consulting relationship under the Consulting Agreement is terminated by the Company for Cause (as defined in the Consulting Agreement) or if Employee breaches any term of the Consulting Agreement or this Separation Agreement, Company
shall so notify Employee and (i) the Severance Period shall terminate and all Severance Benefits provided hereunder and all consideration provided under the Consulting Agreement shall immediately cease, including any vesting of equity under the
February 2012 Award and the February 2014 Award (as defined in the Consulting Agreement); (ii) any unvested portion of the February 2012 Award and the February 2014 Award shall immediately terminate without payment of any consideration
therefor; and (iii) all of Company’s other obligations under the Separation Agreement and the Consulting Agreement shall cease. Company shall also be entitled to pursue any other remedies available to the Company, including injunctive or
other equitable relief. Employee acknowledges that the Company cannot necessarily be reasonably or adequately compensated in monetary damages in an action at law in the event Employee breaches his obligations under this Agreement, because such
obligations are of a unique, special and personal character and of peculiar value to the Company. 

  
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 5. Employee agrees that the Severance Benefits provided by this Agreement are in lieu of, and
replace, any severance benefits for which he might have been eligible, or entitled to, under any Company policy or practice, or any agreement with the Company (written or otherwise). Employee further acknowledges and agrees that (a) this
Agreement and the Severance Benefits are neither intended to nor shall constitute a severance plan and shall confer no benefit on anyone other than the Company and him; (b) the Severance Benefits provided for herein are not otherwise due or
owing to him under any employment or other agreement between him and the Company (written or otherwise); and (c) except for unpaid regular wages, unpaid Company bonus amount (which shall be paid by the Company on or about the Termination Date),
unpaid expense reimbursements submitted by Employee (which shall be paid by the Company within ten (10) business days after the Termination Date), vacation time accrued through the Termination Date (which shall be paid by the Company on or
about the Termination Date), any vested account balance under the Company’s 401(k) savings plan, and his rights with respect to the February 2012 Award and the February 2014 Award, Employee has been paid and provided all wages, vacation pay,
holiday pay, commissions, bonuses and any other form of compensation or benefit that may be due to him now or which would have become due in the future in connection with his employment with or termination of employment from the Company. 

6. For and in consideration of the Severance Benefits provided by this Agreement, Employee on behalf of himself or anyone claiming by, through,
or under him (including without limitation his heirs, executors, administrators, attorneys, representatives, successors, assigns, and agents), fully settles, releases, and forever discharges the Company, and its present and former Affiliates (which
term, for the purposes of this Agreement shall include, without limitation, Aerpio Therapeutics, Inc.), and all of their related persons, associations, corporations, entities, parents, subsidiaries, predecessors, partners, principals, officers,
directors, employees, employee benefit plans, shareholders, agents, attorneys, insurers, successors and assigns, of and from any and all past, present, or future liability, claims, rights, demands, obligations, controversies, damages, costs,
expenses (including reasonable attorneys’ fees), actions, causes of actions, or compensation of any nature whatsoever, known or unknown (collectively, “Claims”), arising directly or indirectly, up to and including the day of this
Agreement, out of or related to his employment or his termination from employment with the Company, including, but not limited to, any Claims which have been or could have been brought for discrimination under federal, state, or local law including,
without limitation, Title VII of the Civil Rights Act, the Americans with Disabilities Act, the Age Discrimination in Employment Act and the fair employment practices statutes of the state or states in which the Employee has provided services to the
Company, as well as any Claims under any law dealing with employment torts, intentional torts, employee benefits, wrongful discharge, retaliation, breach of contract, implied contract, promissory estoppel, wage and hour violations (including,
without limitation, the Massachusetts Payment of Wages Law (Massachusetts General Laws Chapter 149, §§ 148, 150), Massachusetts General Laws Chapter 149 in its entirety, and Massachusetts General Laws Chapter 151 in its entirety (including
but not limited to the minimum wage and overtime provisions)), federal, state, local or other taxes, violation of public policy, workers’ compensation or personal injury, as well as Claims for or in any way related to wages, overtime pay,
vacation pay, commissions, bonuses, profit sharing, expenses, benefits, termination pay, severance pay, reasonable notice or pay in lieu of such notice, equity awards or other compensation arrangements, and including all Claims that are or may be
available to Employee under his Employment Offer Letter by and between Employee and the Company dated January 7, 

  
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2012 (the “Employment Offer Letter”), as well as any and all Claims under the California Fair Employment and Housing Act, the California Family Leave Acts, the California Labor Code,
the California Code Section 12940, et seq., and Section 1542 of the Civil Code of the State of California and under any statute, rule or principle of common law or equity of any jurisdiction that is similar to Section 1542
(“Similar Provision”). 
 Employee acknowledges that this release extends to all Claims that he has or may have, even Claims that
Employee does not know or expect to exist at this time, and is an express waiver by Employee of the protection of Section 1542 of the California Civil Code. This provision reads as follows: 

A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS FAVOR AT THE TIME OF EXECUTING THE
RELEASE, WHICH IF KNOWN BY HIM MUST HAVE MATERIALLY AFFECTED HIS SETTLEMENT WITH THE DEBTOR. 
 This Agreement, including the release of claims set forth in
this Section 6, creates legally binding obligations, and the Company hereby advises Employee to seek the advice of an attorney prior to signing this Agreement. 

As of the Effective Date, Company has no actual knowledge of any claims or actions against Employee arising from or related to his employment
with the Company. 
 7. Employee covenants not to sue Company, its Affiliates or any other party released herein with respect to any Claim
released pursuant to this Agreement. Further, Employee agrees not to assist any third party in pursuing a lawsuit, administrative charge, or complaint, or any other action against Company or its Affiliates. Moreover, Employee agrees that in the
event he violates this covenant, he will pay all expenses and costs incurred by Company in defending against such lawsuit, administrative charge, or complaint. 

Nothing in this paragraph or in this Agreement is intended or shall be deemed to prohibit Employee from filing a charge of discrimination or
otherwise participating in, or cooperating with, the Equal Employment Opportunity Commission (the “EEOC”) in any action brought by the EEOC, or other similar state agency. Employee agrees and acknowledges, however, that he is not entitled
to and will not seek or permit anyone to seek on his behalf any personal, equitable or monetary relief in any such action. 
 8. Employee
shall return all Company property (including, but not limited to, laptops and peripherals, iPads or other tablets, cell phones, files (hard copies and electronic), documents, keyless entry cards, keys, and identification badges) on or before his
Termination Date, in accordance with any directions provided by the Company. 
 9. Employee shall not, at any time, directly or indirectly,
use any trade secrets or confidential information of Employer for Employee’s benefit or the benefit of any other person or, directly or indirectly, disclose any such trade secrets or confidential information of the Employer to any other person.
Nothing in this Agreement shall be construed to terminate, 

  
 -4- 

 
limit or otherwise modify the obligations of Employee not to disclose or use any confidential information of the Company, its Affiliates and its affiliated entities and persons, which obligations
Employee expressly acknowledges. Due to the unique nature of the confidential information, Employee understands, agrees and acknowledges that the Company will suffer irreparable harm in the event that Employee fails to comply with his duty of
confidentiality. In the event of such breach, Employee agrees that the Company shall be entitled to injunctive relief to protect its confidential information. Nothing in this Agreement shall be construed as prohibiting the Company from pursuing any
other remedies available, including the recovery of damages, against Employee. 
 10. Employee shall not express (in writing or otherwise)
any disparaging, negative or unfavorable remarks, comments, statements or criticisms with regard to: (a) the Company, or its affiliates, directors, officers or employees, (b) their respective partners, shareholders, agents, attorneys,
insurers, or investors; and (c) their respective products or potential products. He further agrees that he will refrain from engaging in any publicity or any other activity that damages or impairs, or could damage or impair, the business,
goodwill or reputation of individuals, entities, and products referred to in this Section above in subparagraphs (a)-(c). Employee acknowledges and agrees that this prohibition extends to statements written or verbal, made to anyone including, but
not limited to, the news media, investors, potential investors, any board of directors (or its members), any advisory board (or its members), industry analysts, competitors, strategic partners, vendors, employees (past and present), key opinion
leaders and customers. Company agrees that its Chief Executive Officer and members of its Board of Directors will not express (in writing or otherwise) any disparaging, negative or unfavorable remarks, comments, statements, or criticisms with regard
to Employee or his employment with the Company. 
 11. Employee covenants that, as of the date of execution of this Agreement, he has not
reviewed, discussed or disclosed, in writing or otherwise, the termination of his Employment with the Company or any of the terms or conditions of this Agreement with any person other than his spouse, attorneys and tax advisors and certain employees
and directors of the Company. From the date of signing this Agreement onward, Employee shall keep the existence of this Agreement, the underlying disputes, the negotiations and discussions leading to this Agreement, and the terms and conditions of
this Agreement strictly confidential and, except as may be required by law, will not review, discuss or disclose, in writing or otherwise, the existence of this Agreement, the underlying disputes, the negotiations leading to this Agreement, or any
of its terms or conditions with any persons, organization, or entity, other than his spouse, attorney, or tax consultant, on the condition that disclosure by such persons shall be deemed a breach of this Agreement. If inquiries arise regarding
Employee’s separation from employment from Company, or any related dispute, or the terms of this Agreement by anyone other than those listed above, the Parties mutually agree to state the following: “When John Butler became CEO of the
Company, the decision was made to move the Company’s corporate headquarters to Cambridge, Massachusetts. As the Chief Business Officer of the Company, this required that William Daly commute from Southern California to Cambridge, Massachusetts
and spend a great deal of time away from his home and his family. Although William Daly is ending his employment relationship with the Company, he will have the opportunity to consult for the Company for the next 12 months.” If Employee is
required by law through subpoena or otherwise to disclose information described in this paragraph, he will immediately contact the Company’s General Counsel to inform the General Counsel of that fact and to provide the Company an opportunity to
challenge the legal process which Employee believes would result in the disclosure of such information. 

  
 -5- 

 12. This Agreement does not constitute an admission by the Company that it has violated any
contract, law, or regulation, or in any way infringed Employee’s rights or privileges. 
 13. The provisions of this Agreement are
divisible. If any provisions shall be deemed invalid or unenforceable, it shall not affect the applicability or validity of any other provision of this Agreement, but rather such provision shall be amended to the extent necessary to render it valid
and enforceable. 
 14. The terms of this Agreement, as well as the terms of the Consulting Agreement, represent the entire agreement between
the parties and the only consideration for signing this Agreement. No other promises or agreements of any kind have been made to or with the parties to cause them to execute this Agreement. The parties state that they have carefully read this
Agreement, that its contents have been fully explained to them; that they have been given adequate time to consider the Agreement; that they have had full opportunity to review its contents with their own legal counsel; and that they know and
understand its contents and its legal effect, including, but not limited to, its binding effect, and that they sign this Agreement as their own free act and deed. 

15. This Agreement shall be governed by and construed in accordance with the laws of the Commonwealth of Massachusetts, without regard to the
conflicts of laws principles thereof. 

  
 -6- 

 Exhibit 10.13 

ACKNOWLEDGMENT 

Employee, in connection with his execution of this Agreement, acknowledges the following: 

1. that he is waiving rights or claims arising under the Age Discrimination in Employment Act, including (without limitation) any claims of
discrimination or harassment on the basis of age; 
 2. that he has been advised by the Company to consult with an attorney prior to
executing this Agreement; 
 3. that he has had a period of up to 21 days in which to consider this Agreement; 

4. that for a period of 7 days following execution of this Agreement, he may revoke the Agreement, and that the Agreement shall not become
effective or enforceable until the 7-day revocation period has expired. To be effective, such notice of rescission must be postmarked and sent by certified mail, return receipt requested, or delivered within the seven-day period to Akebia
Therapeutics, Inc., Attention: General Counsel, 245 First Street, Suite 1000, Cambridge, MA 02142. 

 NOT VALID IF SIGNED BEFORE FEBRUARY 7, 2014 

 

							
	 Date:
	 	 2/7/2014
	 		 	William Daly
				
		 		 		 	/s/ William Daly

  

							
		 		 		 	Akebia Therapeutics, Inc.
				
	 Date:
	 	 February 7, 2014
	 		 	/s/ John P. Butler
		 		 		 	John P. Butler
		 		 		 	President and Chief Executive Officer

 RECEIPT OF SEPARATION AGREEMENT 

I acknowledge that I received today a copy of the Separation Agreement (“Agreement”). I have been advised of the following: 

1. I have the opportunity to discuss with a representative of Akebia Therapeutics, Inc. any questions or concerns I may have
over the terms or language of the Agreement. 
 2. I have been advised to see an attorney of my choosing to review the
Agreement. 
 3. I should not sign the Agreement unless I fully understand its terms and enter into the Agreement of my own
free will. 
 4. No other promises have been made to me beyond the terms of the Agreement. 

 

					
	 Date:
	 	 2/7/2014
	 	/s/ William Daly
		 		 	William Daly

 (Signature only acknowledges receipt of this entire agreement.)

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