8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of The Securities Exchange Act of 1934

Date of Report (Date of Earliest Event Reported): January 4, 2019

Allena Pharmaceuticals, Inc.

(Exact name of registrant as specified in its charter)

DELAWARE	001-38268	45-2729920
(State or other jurisdiction of incorporation)	(Commission File Number)	(I.R.S. Employer Identification No.)

One Newton Executive Park, Suite 202 Newton, Massachusetts	02462
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code (617) 467-4577

Not Applicable

(Former name or former address, if changed since last report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

☐ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

☐ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

☐ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

☐ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§240.12b-2 of this chapter).

Emerging growth company  ☒

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.  ☒

5.02 Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers.

Margolin Transition to Chairman

On January 4, 2019, Alexey Margolin, Ph.D., the Chief Executive Officer of Allena Pharmaceuticals, Inc. (the “Company”) executed a transition agreement with the Company (the “Transition Agreement”) pursuant to which he will resign as Chief Executive Officer of the Company, effective as of February 1, 2019 (the “CEO Transition Date”). Dr. Margolin will remain on the Board of Directors (the “Board”) following his resignation and will transition to Chairman of the Board as of the CEO Transition Date. As a non-employee member of the Board, Dr. Margolin will be eligible to participate in the Company’s non-employee director compensation policy and, pursuant to the Transition Agreement, shall receive an additional cash retainer in 2019 of $80,000 for his service as Chairman. Subject to his continued service on the Board, all outstanding stock options held by Dr. Margolin shall continue to vest according to their existing vesting schedules.

The foregoing description of the Transition Agreement does not purport to be complete and is qualified in its entirety by reference to the full text thereof, which is attached hereto as Exhibit 10.1 and incorporated by reference herein.

Brenner Transition to Chief Executive Officer

On January 4, 2019, Louis Brenner, M.D., the Company’s President and Chief Operating Officer, executed an amended and restated employment agreement with the Company (the “Employment Agreement”) to become the Company’s President and Chief Executive Officer and a member of the Board effective as the CEO Transition Date.

Pursuant to the Employment Agreement, Dr. Brenner’s initial base salary shall be equal to $500,000, his initial annual target incentive compensation shall be equal to fifty percent of his base salary, and he shall be eligible to participate in the Company’s benefit plans as in effect from time to time. The Employment Agreement also provides that Dr. Brenner will be granted an option to purchase 305,000 shares of the Company’s common stock, which shall vest over four years, with 25% vesting on the one year anniversary of the CEO Transition Date and the remaining shares vesting in equal monthly installments thereafter, in each case subject to Dr. Brenner’s continued employment with the Company. In addition, in the event that his employment is terminated by us without “cause” (as defined in the Employment Agreement) or he terminates his employment for “good reason” (as defined in the Employment Agreement), and subject to the delivery of a fully effective release of claims, he will be entitled to an amount equal to twelve (12) months of his then-current base salary plus twelve (12) months of his target annual incentive compensation for the prior fiscal year, payable in substantially equal installments for a period of twelve (12) months following his termination of employment, plus our continued payment of the employer portion of health insurance premiums for twelve (12) months or, if earlier, until such time as Dr. Brenner’s COBRA period expires or he becomes eligible for group health insurance from another employer. If Dr. Brenner’s employment is terminated by us without cause or he terminates his employment for good reason, in each case within 12 months after a change in control, then in lieu of the foregoing severance, and subject to the delivery of a fully effective release of claims, Dr. Brenner will be entitled to receive (i) a lump sum amount equal to the sum of eighteen (18) months of his then-current base salary plus his target annual incentive compensation for the year in which the termination occurs, (ii) a prorated portion of the target annual incentive compensation for the year in which the date of termination occurs, payable when the annual incentive compensation would otherwise be paid, (iii) any earned, but unpaid annual bonus for the year immediately prior to the year in which the date of termination occurs and (iv) continued payment of the employer portion of health insurance premiums for eighteen (18) months or, if earlier, until such time as Dr. Brenner’s COBRA period expires or he becomes eligible for group health insurance from another employer. In addition, all time-based stock options or other time-based stock awards granted to Dr. Brenner will accelerate and vest in full.

The foregoing description of the Employment Agreement does not purport to be complete and is qualified in its entirety by reference to the full text thereof, which is attached hereto as Exhibit 10.2 and incorporated by reference herein.

Santini Transition to Lead Independent Director

As of the CEO Transition Date, Gino Santini, currently a member of the Board, including service on the Audit Committee and Compensation Committee, will become the Company’s Lead Independent Director.

Item 7.01 Regulation FD Disclosure.

The Company will be conducting meetings with investors attending the 37th Annual J.P. Morgan Healthcare Conference in San Francisco beginning on January 7, 2019. As part of these meetings, the Company will deliver the slide presentation furnished to this report as Exhibit 99.2 and which is incorporated herein by reference.

The information in this report furnished pursuant to Item 7.01 shall not be deemed “filed” for the purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liabilities of that section. It may only be incorporated by reference in another filing under the Exchange Act or the Securities Act of 1933, as amended, if such subsequent filing specifically references the information furnished pursuant to Item 7.01 of this report.

Item 8.01 Other Events.

On January 4, 2019, the Company issued a press release reporting various matters, including plans for 2019 and the leadership transition described above. A copy of the press release is attached hereto as Exhibit 99.1 and is incorporated herein by reference.

Item 9.01 Financial Statements and Exhibits.

(d) Exhibits

Exhibit No.	Description
10.1	Transition Agreement, dated January 4, 2019 by and between Allena Pharmaceuticals, Inc. and Alexey Margolin, Ph.D.
10.2	Amended and Restated Employment Agreement, dated January 4, 2019 by and between Allena Pharmaceuticals, Inc. and Louis Brenner, M.D.
99.1	Press Release by Allena Pharmaceuticals, Inc. dated January 4, 2019
99.2	Investor Presentation furnished by Allena Pharmaceuticals, Inc.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

Date: January 4, 2019	Allena Pharmaceuticals, Inc.
	By:	/s/ Edward Wholihan
		Edward Wholihan
		Chief Financial Officer

EX-10.1

Exhibit 10.1

January 4, 2019

Alexey Margolin, Ph.D.

Re: Transition Agreement

Dear Alexey:

This letter follows our recent discussions about your employment as Chief Executive Officer of Allena Pharmaceuticals, Inc. (the “Company”). As you know, you have informed the Company of your decision to resign your employment with the Company, and the Company has accepted your resignation. The Company sincerely appreciates your contributions and looks forward to continuing to work with you in your new capacity as Chairman of the Company’s Board of Directors (the “Board”). This letter agreement (the “Agreement”) confirms the terms related to the ending of your employment and your transition to serving as Chairman of the Board. With those understandings, you and the Company agree as follows:

1. Resignation from Employment. Your employment with the Company will end on February 1, 2019 (the “Date of Termination”). The ending of your employment is a termination by you other than for “Good Reason” under Section 3(e) of the Employment Agreement entered into by you and the Company dated as of October 18, 2017 (the “Employment Agreement”). You and the Company waive any requirements of a “Notice of Termination” pursuant to Section 3(f) of the Employment Agreement. Pursuant to Section 3(h) of the Employment Agreement, the termination of your employment with the Company shall automatically be deemed a resignation by you of any other position held by you with the Company or any affiliate of the Company. For the avoidance of doubt, and notwithstanding the foregoing, your service as Chairman of the Board shall not be subject to the preceding sentence.

2. Accrued Obligations. Consistent with Section 4(a) of the Employment Agreement, the Company will pay you (i) any earned but unpaid base salary through the Date of Termination, (ii) any earned but unpaid expense reimbursements, and (iii) any accrued but unused vacation days on or before the time required by law but in no event more than 30 days after the Date of Termination. The Company will also pay you any earned 2018 incentive compensation, in accordance with Section 2(b) of the Employment Agreement. By signing below, you acknowledge and agree that you are not entitled now, nor will you be entitled at any time in the future, to any payments or benefits pursuant to Section 4(b) or Section 5(a) of the Employment Agreement.

3. Appointment and Compensation as Chairman. If you enter into this Agreement, the Board shall appoint you as Chairman of the Board effective February 1, 2019, and approve a compensation package for your service as Chairman of the Board. Such compensation package shall include (i) for calendar year 2019 a cash retainer and equity compensation consistent with the Company’s non-employee director compensation policy as currently in effect, with such equity to be granted at the time of the Company’s 2019 annual meeting, and (ii) an additional cash retainer for your service as Chairman, which for 2019 shall be in the amount of $80,000, and for each year thereafter shall be determined by the Board consistent with the Company’s peer market companies, payable on terms consistent with the Company’s non-employee director compensation policy.

4. Treatment of Outstanding Options. Subject to your continued service on the Board (or such other service relationship permitted under the Company’s 2011 Stock Incentive Plan or 2017 Stock Option and Incentive Plan, as applicable), your outstanding stock options shall continue to vest, including without limitation those explicitly referenced in the Employment Agreement. In the event of a Change in Control (as defined in the Employment Agreement), or in the event you are removed or not re-nominated and re-elected to the Board following the completion of your current term (currently expected to expire at the annual meeting of stockholders to be held in 2021), then all your outstanding stock options, including without limitation those explicitly referenced in the Employment Agreement, shall immediately accelerate and become fully exercisable, effective as of the Change in Control or such annual meeting of stockholders, as applicable.

5. Release of Claims. In consideration for, among other terms, the Chairman compensation package described in Section 3, to which you acknowledge you would otherwise not be entitled, you voluntarily release and forever discharge the Company, its affiliated and related entities, its and their respective predecessors, successors and assigns, its and their respective employee benefit plans and fiduciaries of such plans, and the current and former officers, directors, shareholders, employees, attorneys, accountants and agents of each of the foregoing in their official and personal capacities (collectively referred to as the “Releasees”) generally from all claims, demands, debts, damages and liabilities of every name and nature, known or unknown (“Claims”) that, as of the date when you sign this Agreement, you have, ever had, now claim to have or ever claimed to have had against any or all of the Releasees. This release includes, without limitation, all Claims: relating to your employment by and termination of employment with the Company; of wrongful discharge or violation of public policy; of breach of contract; of defamation or other torts; of retaliation or discrimination under federal, state or local law (including, without limitation, Claims of discrimination or retaliation under the Age Discrimination in Employment Act, the Americans with Disabilities Act, Title VII of the Civil Rights Act of 1964, or Chapter 151B of the Massachusetts General Laws); under any other federal or state statute (including, without limitation, the Fair Labor Standards Act); for wages, bonuses, incentive compensation, commissions, stock, stock options, vacation pay or any other compensation or benefits, either under the Massachusetts Wage Act, M.G.L. c. 149, §§148-150C, or otherwise; and for damages or other remedies of any sort, including, without limitation, compensatory damages, punitive damages, injunctive relief and attorney’s fees; provided, however, this release shall not release your rights under this Agreement. You agree not to accept damages of any nature, other equitable or legal remedies for your own benefit or attorney’s fees or costs from any of the Releasees with respect to any Claim released by this Agreement. As a material inducement to the Company to enter into this Agreement, you represent that you have not assigned any Claim to any third party.

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6. Protected Disclosures. Nothing contained in this Agreement limits your ability to file a charge or complaint with any federal, state or local governmental agency or commission (a “Government Agency”). In addition, nothing contained in this Agreement limits your ability to communicate with any Government Agency or otherwise participate in any investigation or proceeding that may be conducted by any Government Agency, nor does anything contained in this Agreement apply to truthful testimony in litigation. If you file any charge or complaint with any Government Agency and if the Government Agency pursues any claim on your behalf, or if any other third party pursues any claim on your behalf, you waive any right to monetary or other individualized relief (either individually or as part of any collective or class action); provided that nothing in this Agreement limits any right you may have to receive a whistleblower award or bounty for information provided to the Securities and Exchange Commission.

7. Absence of Reliance. In signing this Agreement, you are not relying upon any promises or representations made by anyone at or on behalf of the Company.

8. Waiver; Amendment. No waiver of any provision of this Agreement shall be effective unless made in writing and signed by the waiving party. This Agreement may not be modified or amended except in a writing signed by both you and a duly authorized officer of the Company.

9. Governing Law; Interpretation. This Agreement shall be interpreted and enforced under the laws of the Commonwealth of Massachusetts, without regard to conflict of law principles. In the event of any dispute, this Agreement is intended by the parties to be construed as a whole, to be interpreted in accordance with its fair meaning, and not to be construed strictly for or against either you or the Company or the “drafter” of all or any portion of this Agreement.

10. Time for Consideration; Effective Date. You acknowledge that you have had an adequate opportunity to consider this Agreement and that you have knowingly and voluntarily entered into this Agreement. To accept this Agreement, you must return a signed, unmodified original or PDF copy of this Agreement so that it is received by the undersigned no later than ten (10) days after the date of this letter. This Agreement shall become effective on the date when it becomes fully executed (the “Effective Date”).

11. Counterparts. This Agreement may be executed in separate counterparts. When both counterparts are signed, they shall be treated together as one and the same document. PDF copies of signed counterparts shall be equally effective as originals.

[Signature page follows.]

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Please indicate your agreement to the terms of this Agreement by signing and returning to the undersigned the original or a PDF copy of this letter within the time period set forth above.

Sincerely,

ALLENA PHARMACEUTICAL, INC.
By:	/s/ Gino Santini	January 4, 2019
Name: Gino Santini		Date
Title: Director

This is a legal document. Your signature will commit you to its terms. By signing below, you acknowledge that you have carefully read and fully understand all of the provisions of this Agreement and that you are knowingly and voluntarily entering into this Agreement.

/s/ Alexey Margolin, Ph.D.	January 4, 2019
Alexey Margolin, Ph.D.	Date

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EX-10.2

Exhibit 10.2

AMENDED AND RESTATED EMPLOYMENT AGREEMENT

This Amended and Restated Employment Agreement (this “Agreement”) is entered into and effective as of January 4, 2019 (the “Effective Date”), by and between Allena Pharmaceuticals, Inc. (the “Company”) and Louis Brenner, M.D. (the “Executive”).

RECITALS

WHEREAS, the Company and the Executive are parties to an Employment Agreement dated as of October 19, 2017 (the “Prior Agreement”), and both parties desire to amend and restate the Prior Agreement as set forth herein.

WHEREAS, this Agreement supersedes, amends and restates in all respects any other employment agreements and offer letters between the Executive and the Company, including without limitation the Prior Agreement, except for the Restrictive Covenant Obligations, as defined in Section 8, and the agreements governing Executive’s equity awards as well as the equity incentive plans pursuant to which such equity awards were granted, each of which remain in effect.

WHEREAS, the Company desires to continue to employ the Executive and the Executive desires to continue be employed by the Company beginning on the Effective Date pursuant to the terms contained herein.

NOW, THEREFORE, in consideration of the mutual covenants and agreements herein contained and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties agree that the Prior Agreement is hereby amended and restated in its entirety as follows:

1. Position and Duties. Effective as of February 1, 2019 (the “CEO Appointment Date”), Executive shall serve as the President and Chief Executive Officer of the Company and shall have responsibilities and duties as may from time to time be prescribed by the Board of Directors of the Company (including any committee of the Board of Directors, the “Board”), commensurate with the customary scope and authority of the Executive’s position. Prior to the CEO Appointment Date, Executive shall continue to serve as the President and Chief Operating Officer of the Company. In addition, the Company shall cause the Executive to be appointed to the Board effective as of the CEO Appointment Date, provided the Executive shall resign from the Board and from any related positions upon the termination of his employment for any reason. The Executive shall devote the Executive’s full working time and efforts to the business and affairs of the Company. Notwithstanding the foregoing, the Executive may engage in religious, charitable or other community activities, and such other activities as are set forth on Exhibit A attached hereto, as long as such activities are disclosed to the Board and do not interfere with the Executive’s performance of the Executive’s duties to the Company, and the Executive may continue to perform clinical patient-care responsibilities on an occasional basis, as set forth of Schedule B. Notwithstanding the foregoing, the time and schedule commitment associated with such clinical patient-care activities set forth of Schedule B will be evaluated by both parties after June 30, 2019 and from time to time thereafter. The Executive agrees that, if the Board at any

time after June 30, 2019 determines in good faith that such clinical patient-care activities interfere with the performance of the Executive’s duties to the Company, he will wind down such activities upon delivery of written notice by the Company to the Executive. Executive represents that Exhibit A attached hereto is a comprehensive list of all outside professional activities with which Executive is currently involved.

2. Compensation and Related Matters.

(a) Base Salary. The Executive’s initial annual base salary rate shall be increased to $500,000 effective as of the CEO Appointment Date. The Executive’s base salary rate shall be subject to increase by the Board or the Compensation Committee of the Board (the “Compensation Committee”) from time to time and shall not be subject to diminution except as provided in Section 3(e)(i). The annual base salary in effect at any given time is referred to herein as “Base Salary.” The Base Salary shall be payable in a manner that is consistent with the Company’s usual payroll practices for executives.

(b) Incentive Compensation. The Executive shall be eligible to receive annual cash incentive compensation as determined by the Board or the Compensation Committee from time to time based upon achievement of corporate goals and the Executive’s personal goals, in each case as adopted by the Board. Commencing in calendar year 2019, Executive’s initial target annual incentive compensation shall be fifty percent (50%) of the Executive’s annual base salary. The target annual incentive compensation in effect at any given time is referred to herein as “Target Annual Cash Incentive Compensation” and the actual Annual Cash Incentive Compensation with respect to any given time is the “Annual Cash Incentive Compensation.” To avoid doubt, whether incentive compensation is awarded, the criteria governing any incentive compensation, and the amount of any incentive compensation is in the sole discretion of the Board. Except as provided in Section 5(a), to earn incentive compensation, the Executive must be employed by the Company on the last day of the calendar year to which the incentive compensation applies. Annual Cash Incentive Compensation shall be paid on or before March 15th of the calendar year following the year for which the bonus was earned.

(c) Expenses. The Executive shall be entitled to receive reimbursement for all reasonable expenses incurred by the Executive in performing services hereunder, in accordance with the policies and procedures then in effect and established by the Company for its executives.

(d) Other Benefits. The Executive shall be entitled to participate in or receive benefits under any employee benefit plan or arrangement currently maintained or which may, in the future, be made available by the Company generally to its executives, subject to and on a basis consistent with the terms, conditions and overall administration of such plan or arrangement. Notwithstanding the foregoing or anything else to the contrary, Executive shall be entitled to four (4) weeks paid vacation per year. Executive agrees that he will use his best efforts to schedule his absences at times that do not interfere with the operations of the Company. The Executive’s accrual, use and carryover (if any) of vacation is subject in all respects to the standard written policies of the Company in effect at such time.

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(e) Equity Grant. The Company will grant to the Executive an option (the “Option”) under the Company’s 2017 Stock Option and Incentive Plan (the “Plan”) for the purchase of 305,000 shares of the Company’s common stock, at a price per share equal to the closing trading price of the Company’s common stock on January 4, 2018 (“Grant Date”). The Option shall be subject to vesting over a four-year period commencing on the CEO Appointment Date, with 25% vesting on the one-year anniversary of the vesting commencement date and the balance vesting ratably on a monthly basis over the remaining three-year period. Vesting shall be subject to acceleration as set forth in this Agreement. The Option shall be subject to the terms and provisions set forth in the Plan and in a separate option agreement between the Company and the Executive.

3. Termination. The Executive’s employment hereunder is at-will and may be terminated without any breach of this Agreement under the following circumstances:

(a) Death. The Executive’s employment hereunder shall terminate upon the Executive’s death.

(b) Disability. The Company may terminate the Executive’s employment upon the Disability of the Executive. “Disability” shall mean that (1) the Executive is unable to engage in any substantial gainful activity by reason of any medically determinable physical or mental impairment that can be expected to result in death or can be expected to last for a continuous period of not less than 12 months; or (2) the Executive is, by reason of any medically determinable physical or mental impairment that can be expected to result in death or can be expected to last for a continuous period of not less than 12 months, receiving income replacement benefits for a period of not less than three months under an accident and health plan covering employees of his employer. A determination of disability shall be made by a physician satisfactory to both the Executive and the Company, provided that if the Executive and the Company do not agree on a physician, the Executive and the Company shall each select a physician and these two together shall select a third physician, whose determination as to disability shall be binding on all parties.

(c) Termination by the Company for Cause. The Company may terminate the Executive’s employment hereunder for Cause. For purposes of this Agreement, “Cause” shall mean: (i) conduct by the Executive constituting a material act of misconduct in connection with the performance of the Executive’s duties, including, without limitation, unlawful harassment or misappropriation of funds or property of the Company or any of its affiliates other than the occasional, customary and de minimis use of Company property for personal purposes; (ii) the conviction of the Executive of, or the entry of a pleading of guilty or nolo contendere by the Executive to, any crime involving moral turpitude or any felony; (iii) any conduct by the Executive that would reasonably be expected to result in material injury or reputational harm to the Company or its affiliates if the Executive were retained in the Executive’s position; (iv) continued non-performance by the Executive of substantially all of the Executive’s responsibilities hereunder (other than by reason of the Executive’s physical or mental illness, incapacity or disability) that has continued for more than 30 days following written notice of such non-performance from the Board; or (v) a breach by the Executive of Section 8 or of any other Restrictive Covenant Obligation. In the event of a breach or violation of subsections (iv) or (v), if the breach or violation is curable as determined by the Board (which determination shall be conclusive), the Executive shall have no more than 30 days to cure such violation after written notice of such breach or violation by the Board (the “Cause Cure Period,”) provided that Executive shall not be entitled to more than one Cause Cure Period in any 12-month period.

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(d) Termination by the Company without Cause. The Company may terminate the Executive’s employment hereunder at any time without Cause.

(e) Termination by the Executive. The Executive may terminate employment hereunder at any time for any reason, including but not limited to Good Reason. For purposes of this Agreement, “Good Reason” shall mean that the Executive has complied with the “Good Reason Process” (hereinafter defined) following the occurrence of any of the following events: (i) a material diminution in the Executive’s Base Salary except for across-the-board salary reductions based on the Company’s financial performance similarly affecting all or substantially all senior management employees of the Company; (ii) a material breach of this Agreement by the Company; (iii) a change of greater than 50 miles in the geographic location at which the Executive provides services to the Company; or (iv) a material diminution in the Executive’s duties or responsibilities (each a “Good Reason Condition”). Good Reason Process shall mean that (i) the Executive reasonably determines in good faith that a Good Reason Condition has occurred; (ii) the Executive notifies the Company in writing of the occurrence of the Good Reason Condition within 60 days of the occurrence of such condition; (iii) the Executive cooperates in good faith with the Company’s efforts, for a period not less than 30 days following such notice (the “Good Reason Cure Period”), to remedy the Good Reason Condition; (iv) notwithstanding such efforts, the Good Reason condition continues to exist; and (v) the Executive terminates employment within 60 days after the end of the Good Reason Cure Period. If the Company cures the Good Reason Condition during the Good Reason Cure Period, Good Reason shall be deemed not to have occurred.

(f) Notice of Termination. Except for termination due to the Executive’s death, any termination of the Executive’s employment by the Company or any such termination by the Executive shall be communicated by written Notice of Termination to the other party hereto. For purposes of this Agreement, a “Notice of Termination” shall mean a notice which shall indicate the specific termination provision in this Agreement relied upon. If the Executive provides the Executive’s Notice of Termination to the Company in accordance with the notice provisions of this Agreement, such Notice is effective immediately, no manifestation of acceptance or assent by the Company is required, and the Executive may not rescind the Notice without the written consent of the Company.

(g) Date of Termination. “Date of Termination” shall mean: (i) if the Executive’s employment is terminated by death, the date of death; (ii) if the Executive’s employment is terminated by the Company for any reason, including for Cause, without Cause or on account of Disability, the date of the Notice of Termination (accounting for any applicable Cause Cure Period); (iii) if the Executive’s employment is terminated by the Executive without Good Reason, 30 days after the date on which a Notice of Termination is given, or (iv) if the Executive’s employment is terminated by the Executive with Good Reason, the date on which a Notice of Termination is given after the end of the Good Reason Cure Period. Notwithstanding the foregoing, in the event that the Executive gives a Notice of Termination to the Company, the Company may unilaterally accelerate the Date of Termination and such acceleration shall not result in a termination by the Company for purposes of this Agreement.

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(h) Automatic Resignation of Other Positions. The termination of Executive’s employment with the Company for any reason shall automatically be deemed a resignation by the Executive of any other position held by the Executive with the Company or any affiliate of the Company, whether as an officer, director, fiduciary or otherwise.

4. Compensation Upon Termination.

(a) Termination Generally. If the Executive’s employment with the Company is terminated for any reason, the Company shall pay or provide to the Executive any earned but unpaid base salary, earned but unpaid expense reimbursements, accrued but unused vacation (but only if required by state law or the Company’s vacation policy, and in the event of a conflict between this Agreement and the Company’s policy, the policy shall control) on or before the time required by law but in no event more than 30 days after the Executive’s Date of Termination.

(b) Termination by the Company without Cause or by the Executive for Good Reason. If the Executive’s employment is terminated by the Company without Cause or by the Executive for Good Reason, subject to the Executive signing, returning and not revoking a separation agreement to be provided by the Company that includes, among other terms, a general release of claims (which shall include, without limitation, a release of all releasable claims other than to payments under Section 4 or outstanding equity, obligations to cooperate with the Company and reaffirmation of the Executive’s obligations under any noncompetition, non-solicitation, non-disclosure or inventions agreement (the “Release”)) within the time period required by the Release but in no event later than 60 days after the Date of Termination:

(i) the Company shall pay the Executive an amount equal to (A) twelve (12) months of Executive’s annual Base Salary; and (B) an amount equal to twelve (12) months of the Executive’s Target Annual Cash Incentive Compensation for the year preceding the Date of Termination (the “Severance Amount”). The Severance Amount shall be paid out in substantially equal installments in accordance with the Company’s applicable payroll practices over twelve (12) months (the twelve (12) months after the Date of Termination, the “Severance Period”). The Company shall also pay Executive any earned, unpaid annual bonus for the year immediately prior to the year in which the Date of Termination occurs, subject to Section 2(b);

(ii) subject to the Executive’s election of and eligibility for COBRA rights and copayment of premium amounts at the active employees’ rate as of the Date of Termination (the “Active Employee Premiums”), the Company shall pay the remainder of the premiums for the Executive’s participation in the Company’s group health plans pursuant to COBRA; provided that the Company’s payment obligation shall cease upon the earliest of the end of the Severance Period, the Executive’s eligibility for group health insurance from another employer, or the expiration of the Executive’s rights under COBRA. As a condition of eligibility for such payments, the Executive (A) authorizes the deduction of the Active Employee Premiums from the Severance Amount; and (B) shall promptly respond fully to any reasonable inquiries from the Company related to the Executive’s COBRA eligibility; and

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(iii) the amounts payable under this Section 4(b) shall be paid or commence to be paid within 60 days after the Date of Termination; provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar year, such payment shall be paid or commence to be paid in the second calendar year by the last day of such 60-day period; provided, further, that the initial payment shall include a catch-up payment to cover amounts retroactive to the day immediately following the Date of Termination. Each payment pursuant to this Agreement is intended to constitute a separate payment for purposes of Treasury Regulation Section 1.409A-2(b)(2).

5. Change in Control Payment. The provisions of this Section 5 set forth certain terms of an agreement reached between the Executive and the Company regarding the Executive’s rights and obligations upon the occurrence of a Change in Control (as defined below). These provisions shall apply in lieu of, and expressly supersede, the provisions of Section 4(b) regarding severance pay and benefits upon a termination of employment by the Company without Cause or by the Executive for Good Reason, if either such termination of employment occurs within 12 months after the occurrence of the first event constituting a Change in Control. These provisions shall terminate and be of no further force or effect beginning 12 months after the occurrence of a Change in Control.

(a) Change in Control. If within 12 months after a Change in Control, the Executive’s employment is terminated by the Company without Cause or the Executive terminates the Executive’s employment for Good Reason, then, in either case subject to the signing of the Release by the Executive and the Release becoming fully effective, all within the time frame set forth in the Release but in no event later than 60 days following the Date of Termination:

(i) the Company shall pay the Executive a lump sum amount equal to one times the sum of (A) eighteen (18) months of the Executive’s then current Base Salary; and (B) the Executive’s Target Annual Cash Incentive Compensation for the year in which the Date of Termination occurs;

(ii) The Company shall pay the Executive a prorated portion of the Executive’s Target Annual Cash Incentive Compensation under Section 2(b) for the year in which the Date of Termination occurs, payable when such Annual Cash Incentive Compensation would otherwise be paid, which to avoid doubt shall be no later than March 15 of the year following the year in which the Date of Termination occurs;

(iii) The Company shall also pay Executive any earned, unpaid annual bonus for the year immediately prior to the year in which the Date of Termination occurs, subject to Section 2(b);

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(iv) subject to the Executive’s election of and eligibility for COBRA rights and copayment of the Active Employee Premiums, the Company shall pay the remainder of the premiums for the Executive’s participation in the Company’s group health plans pursuant to COBRA; provided that the Company’s payment obligation shall cease upon the earliest of the date that is eighteen (18) months after the Date of Termination; the Executive’s eligibility for group health insurance from another employer; or the expiration of the Executive’s rights under COBRA. As a condition of eligibility for such payments, the Executive shall promptly respond fully to any reasonable inquiries from the Company related to the Executive’s COBRA eligibility;

(v) notwithstanding anything to the contrary in any applicable option agreement or stock-based award agreement, all time-based stock options and other time-based stock-based awards granted to the Executive shall immediately accelerate and become fully exercisable or nonforfeitable as of the Date of Termination provided that, to avoid doubt, nothing in this Section 5 shall limit the Executive’s rights under Section 2 of the Incentive Stock Option Agreements dated (respectively) June 18, 2015 and February 26, 2017, including with respect to the acceleration of the vesting of 100% of the Executive’s Shares in connection with the Executive’s termination by the Company without Cause or by the Executive for Good Reason “as of or at any time following the consummation of a Reorganization Event” (as defined in those Stock Option Agreements); and

(vi) the amounts payable under this Section 5(a) shall be paid or commence to be paid within 60 days after the Date of Termination; provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar year, such payment shall be paid or commence to be paid in the second calendar year by the last day of such 60-day period. Each payment pursuant to this Agreement is intended to constitute a separate payment for purposes of Treasury Regulation Section 1.409A-2(b)(2).

(b) Additional Limitation.

(i) Anything in this Agreement to the contrary notwithstanding, in the event that the amount of any compensation, payment or distribution by the Company to or for the benefit of the Executive, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise, calculated in a manner consistent with Section 280G of the Internal Revenue Code of 1986, as amended (the “Code”), and the applicable regulations thereunder (the “Aggregate Payments”), would be subject to the excise tax imposed by Section 4999 of the Code, then the Aggregate Payments shall be reduced (but not below zero) so that the sum of all of the Aggregate Payments shall be $1.00 less than the amount at which the Executive becomes subject to the excise tax imposed by Section 4999 of the Code; provided that such reduction shall only occur if it would result in the Executive receiving a higher After Tax Amount (as defined below) than the Executive would receive if the Aggregate Payments were not subject to such reduction. In such event, the Aggregate Payments shall be reduced in the following order, in each case, in reverse chronological order beginning with the Aggregate Payments that are to be paid the furthest in time from consummation of the transaction that is subject to Section 280G of the Code: (1) cash payments not subject to Section 409A of the Code; (2) cash payments subject to Section 409A of the Code; (3) equity-based payments and acceleration; and (4) noncash forms of benefits; provided that in the case of all the foregoing Aggregate Payments all amounts or payments that are not subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c) shall be reduced before any amounts that are subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c).

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(ii) For purposes of this Section 5(b), the “After Tax Amount” means the amount of the Aggregate Payments less all federal, state, and local income, excise and employment taxes imposed on the Executive as a result of the Executive’s receipt of the Aggregate Payments. For purposes of determining the After Tax Amount, the Executive shall be deemed to pay federal income taxes at the highest marginal rate of federal income taxation applicable to individuals for the calendar year in which the determination is to be made, and state and local income taxes at the highest marginal rates of individual taxation in each applicable state and locality, net of the maximum reduction in federal income taxes which could be obtained from deduction of such state and local taxes.

(iii) The determination as to whether a reduction in the Aggregate Payments shall be made pursuant to Section 5(b)(i) shall be made by a nationally recognized accounting firm selected by the Company (the “Accounting Firm”), which shall provide detailed supporting calculations both to the Company and the Executive within 15 business days of the Date of Termination, if applicable, or at such earlier time as is reasonably requested by the Company or the Executive. Any determination by the Accounting Firm shall be binding upon the Company and the Executive.

(c) Definitions. For purposes of this Section 5, the following terms shall have the following meanings:

“Change in Control” shall mean any of the following:

(i) any “person,” as such term is used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended (the “Act”), any of its subsidiaries, or any trustee, fiduciary or other person or entity holding securities under any employee benefit plan or trust of the Company or any of its subsidiaries), together with all “affiliates” and “associates” (as such terms are defined in Rule 12b-2 under the Act) of such person, shall become the “beneficial owner” (as such term is defined in Rule 13d-3 under the Act), directly or indirectly, of securities of the Company representing 50 percent or more of the combined voting power of the Company’s then outstanding securities having the right to vote in an election of the Board (“Voting Securities”) (in such case other than as a result of an acquisition of securities directly from the Company); or

(ii) the date a majority of the members of the Board is replaced during any 12-month period by directors whose appointment or election is not endorsed by a majority of the members of the Board before the date of the appointment or election; or

(iii) the consummation of (A) any consolidation or merger of the Company where the stockholders of the Company, immediately prior to the consolidation or merger, would not, immediately after the consolidation or merger, beneficially own (as such term is defined in Rule 13d-3 under the Act), directly or indirectly, shares representing in the aggregate more than 50 percent of the voting shares of the Company issuing cash or securities in the consolidation or merger (or of its ultimate parent corporation, if any), or (B) any sale or other transfer (in one transaction or a series of transactions contemplated or arranged by any party as a single plan) of all or substantially all of the assets of the Company.

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Notwithstanding the foregoing, a “Change in Control” shall not be deemed to have occurred for purposes of the foregoing clause (i) solely as the result of an acquisition of securities by the Company which, by reducing the number of shares of Voting Securities outstanding, increases the proportionate number of Voting Securities beneficially owned by any person to 50 percent or more of the combined voting power of all of the then outstanding Voting Securities; provided, however, that if any person referred to in this sentence shall thereafter become the beneficial owner of any additional shares of Voting Securities (other than pursuant to a stock split, stock dividend, or similar transaction or as a result of an acquisition of securities directly from the Company) and immediately thereafter beneficially owns 50 percent or more of the combined voting power of all of the then outstanding Voting Securities, then a “Change in Control” shall be deemed to have occurred for purposes of the foregoing clause (i).

6. Acknowledgement. To avoid doubt, and notwithstanding anything to the contrary in this Agreement, the Executive shall not be entitled to any severance compensation or benefits in connection with a termination due to the Executive’s Disability or death, by the Company for Cause, or by the Executive without Good Reason.

7. Section 409A.

(a) Anything in this Agreement to the contrary notwithstanding, if at the time of the Executive’s separation from service within the meaning of Section 409A, the Company determines that the Executive is a “specified employee” within the meaning of Section 409A(a)(2)(B)(i), then to the extent any payment or benefit that the Executive becomes entitled to under this Agreement on account of the Executive’s separation from service would be considered deferred compensation subject to the 20 percent additional tax imposed pursuant to Section 409A(a) as a result of the application of Section 409A(a)(2)(B)(i), 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 the Executive’s separation from service, or (B) the Executive’s death. If any such delayed cash payment is otherwise payable on an installment basis, the first payment shall include a catch-up payment covering amounts that would otherwise have been paid during the six-month period but for the application of this provision, and the balance of the installments shall be payable in accordance with their original schedule.

(b) All in-kind benefits provided and expenses eligible for reimbursement under this Agreement shall be provided by the Company or incurred by the Executive during the time periods set forth in this Agreement. All reimbursements shall be paid as soon as administratively practicable, but in no event shall any reimbursement be paid after the last day of the taxable year following the taxable year in which the expense was incurred. The amount of in-kind benefits provided or reimbursable expenses incurred in one taxable year shall not affect the in-kind benefits to be provided or the expenses eligible for reimbursement in any other taxable year. Such right to reimbursement or in-kind benefits is not subject to liquidation or exchange for another benefit.

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(c) To the extent that any payment or benefit described in this Agreement constitutes “non-qualified deferred compensation” under Section 409A, and to the extent that such payment or benefit is payable upon the Executive’s termination of employment, then such payments or benefits shall be payable only upon the Executive’s “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).

(d) The parties intend that this Agreement will be administered in accordance with Section 409A. To the extent that any provision of this Agreement is ambiguous as to its compliance with Section 409A, the provision shall be read in such a manner so that all payments hereunder comply with Section 409A. The parties agree that this Agreement may be amended, as reasonably requested by either party, and as may be necessary to fully comply with Section 409A and all related rules and regulations in order to preserve the payments and benefits provided hereunder without additional cost to either party.

(e) The Company makes no representation or warranty and shall have no liability to the Executive or any other person if any provisions of this Agreement are determined to constitute deferred compensation subject to Section 409A but do not satisfy an exemption from, or the conditions of, such Section.

8. Restrictive Covenants.

(a) For the purposes of this Section 8, all references to the “Company” refer to the Company, its affiliates and its and their successors and assigns. Reference is made to the Invention and Nondisclosure Agreement between the Company and Executive and the Non-Competition and Non-Solicitation Agreement between the Company and Executive dated March 17, 2015 (the “Non-Competition Agreement”) (along with any other restrictive covenant obligations the Executive has to the Company, the “Restrictive Covenant Obligations”). The Executive acknowledges and agrees that the Restrictive Covenant Obligations remain in full force and effect.

(b) Third-Party Agreements and Rights. The Executive hereby confirms that the Executive is not bound by the terms of any agreement with any previous employer or other party that restricts in any way the Executive’s use or disclosure of information or the Executive’s engagement in any business. The Executive represents to the Company that the Executive’s execution of this Agreement, the Executive’s employment with the Company and the performance of the Executive’s proposed duties for the Company will not violate any obligations the Executive may have to any such previous employer or other party. In the Executive’s work for the Company, the Executive shall not disclose or make use of any information in violation of any agreements with or rights of any such previous employer or other party, and the Executive shall not bring to the premises of the Company any copies or other tangible embodiments of non-public information belonging to or obtained from any such previous employment or other party.

(c) Litigation and Regulatory Cooperation. During and after the Executive’s employment, the Executive shall cooperate fully with the Company in the defense or prosecution of any claims or actions now in existence or that may be brought in the future against or on behalf of the Company that relate to events or occurrences that transpired while the Executive was employed by the Company. The Executive’s full cooperation in connection with such claims or actions shall include, but not be limited to, being available to meet with counsel to prepare for

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discovery or trial and to act as a witness on behalf of the Company at mutually convenient times. During and after the Executive’s employment, the Executive also shall cooperate fully and at mutually convenient times with the Company in connection with any investigation or review of any federal, state or local regulatory authority as any such investigation or review relates to events or occurrences that transpired while the Executive was employed by the Company. The Company shall reimburse the Executive for any reasonable out-of-pocket expenses incurred in connection with the Executive’s performance of obligations pursuant to this Section. For any period of time during which Executive performs obligations under this Section and is not receiving payments of the Severance Amount, the Company shall reimburse the Executive at an hourly rate calculated by dividing the Executive’s Base Salary as of the Date of Termination by 2,080.

(d) Protected Disclosures. The Executive understands that nothing contained in this Agreement limits the Executive’s ability to communicate with any federal, state or local governmental agency or commission, including to provide documents or other information, without notice to the Company. The Executive also understands that nothing in this Agreement limits the Executive’s ability to share compensation information concerning the Executive or others, except that this does not permit the Executive to disclose compensation information concerning others that the Executive obtains because the Executive’s job responsibilities require or allow access to such information.

(e) Defend Trade Secrets Act of 2016. The Executive understands that pursuant to the federal Defend Trade Secrets Act of 2016, the Executive shall not be held criminally or civilly liable under any federal or state trade secret law for the disclosure of a trade secret that (a) is made (i) in confidence to a federal, state, or local government official, either directly or indirectly, or to an attorney; and (ii) solely for the purpose of reporting or investigating a suspected violation of law; or (b) is made in a complaint or other document filed in a lawsuit or other proceeding, if such filing is made under seal.

9. Consent to Jurisdiction; Jury Waiver. The parties hereby agree that the state and federal courts of Massachusetts shall be the exclusive jurisdiction and exclusive venue for any such court action. Accordingly, with respect to any such court action, the Executive submits to the exclusive personal jurisdiction of such courts. THE PARTIES HEREBY WAIVE ANY RIGHT TO A JURY TRIAL WITH RESPECT TO ANY SUCH COURT ACTION.

10. Integration. This Agreement constitutes the entire agreement between the parties with respect to the subject matter hereof and supersedes all prior agreements, communications and understandings between the parties concerning such subject matter, including without limitation the Prior Agreement, provided that (and to avoid doubt) the Restrictive Covenant Obligations and the equity documents referenced herein shall remain in full effect and shall supplement, and shall not limit or be limited by, this Agreement.

11. Absence of Reliance. In signing this Agreement, the Executive acknowledges and agrees that the Executive is not relying upon any promise, communication or representation made by anyone at or on behalf of the Company or its affiliates with respect to the subject matter herein, except as expressly contained herein.

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12. Withholding. All payments made by the Company to the Executive under this Agreement shall be net of any tax or other amounts required to be withheld by the Company under applicable law.

13. Reasonable Modification. The Executive and the Company agree and intend that, if any provision of this Agreement, including without limitation Section 8, is found by a court of competent jurisdiction to be unenforceable as written in any respect, such provision shall be deemed to be modified (and shall in fact be so modified) and enforced to its maximum permissible extent. Neither a finding that any provision is unenforceable as written nor any modification of such provision shall affect any other provision of this Agreement, including Section 8, and such other provisions shall remain in full effect.

14. Survival. The provisions of this Agreement shall survive the termination of this Agreement and/or the termination of the Executive’s employment to the extent necessary to effectuate the terms contained herein.

15. Waiver. No waiver of any provision hereof shall be effective unless made in writing and signed by the waiving party. The failure of any party to require the performance of any term or obligation of this Agreement, or the waiver by any party of any breach of this Agreement, shall not prevent any subsequent enforcement of such term or obligation or be deemed a waiver of any subsequent breach.

16. Notices. Any notices, requests, demands and other communications provided for by this Agreement shall be sufficient if in writing and delivered in person or sent by (i) a nationally recognized overnight courier service (ii) by registered or certified mail, postage prepaid, return receipt requested, in each case to the Executive at the last address the Executive has filed in writing with the Company or, in the case of the Company, at its main offices, attention of the Board, or (iii) by email to the Executive at the Executive’s Company email address, or personal email address expressly provided by the Executive to the Company, and to the Company at the Company email address of the Company’s Chairperson of the Board.

17. No Strict Construction. The language used in this Agreement shall be deemed to be the language chosen by the parties to express their mutual intent, and no rule of strict construction shall be applied against any party.

18. Amendment. This Agreement may be amended or modified only by a written instrument signed by the Executive and by a duly authorized representative of the Company (which shall not include the Executive) with Board approval.

19. Governing Law. This is a Massachusetts contract and shall be construed under and be governed in all respects by the laws of Massachusetts, without giving effect to the conflict of laws principles of such State.

20. Counterparts. This Agreement may be executed in any number of counterparts, each of which when so executed and delivered shall be taken to be an original; but such counterparts shall together constitute one and the same document.

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21. Assignment and Transfer by the Company; Successors. The Company shall have the right to assign and/or transfer this Agreement to any person or entity, including without limitation the Company’s affiliates and any purchaser of any portion of the Company’s (or its affiliates’) equity or other assets. The Executive expressly consents to such assignment and/or transfer. This Agreement shall inure to the benefit of and be enforceable by the Company’s successors and assigns.

[Remainder of page intentionally left blank.]

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IN WITNESS WHEREOF, the parties have executed this Agreement effective on the date and year first above written.

COMPANY:
Allena Pharmaceuticals, Inc.
By:	/s/ Gino Santini
	Gino Santini
Its:	Chairman of Compensation Committee
EXECUTIVE:
By:	/s/ Louis Brenner, M.D.
Louis Brenner, M.D.

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Exhibit A

Outside Activities

The Executive serves as a member of the boards of directors of Goldfinch Biopharma, Inc. and the Yale Club of Boston.

Exhibit B

Clinical Activities

The Executive may provide clinical patient care in a manner that requires less of a time commitment than the five hours per week that the Executive previously provided during his prior tenure as President and Chief Operating Officer of the Company.

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EX-99.1

Exhibit 99.1

Allena Pharmaceuticals Announces Appointment of Louis Brenner, M.D. as Chief Executive Officer

and Confirms Key Milestones for 2019

— Alexey Margolin, Ph.D. to Transition to Chairman of the Board –

— URIROX-2™ Initiated; URIROX-1™ Topline Data Expected in Second Half of 2019 —

— Multiple Catalysts Expected Across Pipeline in 2019 —

NEWTON, Mass., January 4, 2019 – Allena Pharmaceuticals, Inc. (NASDAQ:ALNA), a late-stage, biopharmaceutical company dedicated to developing and commercializing first-in-class, oral enzyme therapeutics to treat patients with rare and severe metabolic and kidney disorders, today announced that Louis Brenner, M.D., President and Chief Operating Officer at Allena, will be promoted to Chief Executive Officer and appointed to the Board of Directors effective February 1, 2019. Dr. Brenner will succeed Alexey Margolin, Ph.D. as Chief Executive Officer.    Dr. Margolin, who co-founded Allena in 2011, will transition to Chairman of the Board effective February 1, 2019. He will continue advising the company in this new role.

“I am honored to succeed Alex as the CEO of Allena. Since the company’s founding, Alex has played a key role in shaping our vision and cementing our position as a leader in the development of novel medicines for people living with rare and severe metabolic and kidney disorders. We are grateful for his many contributions,” said Louis Brenner, M.D., Chief Executive Officer designate of Allena Pharmaceuticals. “2019 promises to be a transformational year for Allena, following our recent alignment with the FDA on the design of our Phase 3 program for reloxaliase in patients with enteric hyperoxaluria, including our strategy to seek approval using the accelerated approval regulatory pathway, and we anticipate numerous milestones across our broader pipeline throughout the year. I look forward to working with the entire Allena team as we build on our strong foundation and advance our pipeline of first-in-class non-absorbed, oral enzyme therapeutics.”

Louis Brenner, M.D. has served as Chief Operating Officer of Allena since April 2015 and as President since February 2017. Dr. Brenner has more than a decade of industry leadership experience, including pharmaceutical development strategy, regulatory affairs, business development and commercialization. Prior to joining Allena, Dr. Brenner served as Chief Medical Officer at Idera Pharmaceuticals, Chief Medical Officer at Radius Health, and Senior Vice President at AMAG Pharmaceuticals. He began his industry career at Genzyme Corporation. In these roles, he led successful product development programs for medicines that are currently marketed in the renal and metabolic areas. He holds an M.D. from Duke University, an M.B.A. from Harvard Business School and a B.S. from Yale University. He completed his residency in internal medicine at Brigham and Women’s Hospital and his fellowship in nephrology at Brigham and Women’s Hospital and Massachusetts General Hospital. Dr. Brenner holds a clinical appointment at Brigham and Women’s Hospital.

“I have worked together with Lou for several years, and cannot think of a better candidate to lead Allena through its next stage of growth. Lou’s extensive experience in late-stage clinical development and the pursuit of new regulatory approvals uniquely fits the needs of Allena as we approach our ultimate goal – bringing to patients the first ever drug for enteric hyperoxaluria,” said Alexey Margolin, Ph.D., outgoing Chief Executive Officer of Allena Pharmaceuticals. “I feel privileged to have had the opportunity to help build our Company’s platform, and I am deeply thankful to all of the stakeholders – including patients, clinicians, investors, business partners, and especially Allena employees – who have enabled this progress to-date.”

“I am encouraged by Allena’s progress in developing its pipeline of oral enzyme therapies, including the successful advancement of reloxaliase from preclinical studies into the ongoing Phase 3 program in patients with enteric hyperoxaluria, “ said Gino Santini, who will become Lead Independent Director of Allena Pharmaceuticals in connection with the leadership transition. “I have enjoyed working with Alex since the early days of the Company and look forward to his continued contributions as our new Chairman. I am also eager to work more closely with Lou. Given his expertise in nephrology, his experience in late-stage drug development, and, most importantly, his passion for helping patients, Lou is the ideal choice to lead Allena as it advances its pipeline toward the market.”

2019 Corporate Strategy and Milestones

Reloxaliase: Reloxaliase is a first-in-class, non-absorbed, orally-administered enzyme for the treatment of severe hyperoxaluria. Allena is currently evaluating reloxaliase in two ongoing pivotal Phase 3 trials, URIROX-1 and URIROX-2, which are designed to evaluate the safety and efficacy of reloxaliase in patients with enteric hyperoxaluria. Allena recently announced that it had reached alignment with the FDA on both the design of URIROX-2 and its strategy to pursue a Biologics License Application submission for reloxaliase using the accelerated approval regulatory pathway. URIROX-1 is currently enrolling patients, and Allena initiated URIROX-2 in the fourth quarter of 2018.

Allena is also evaluating reloxaliase in Study 206, a multi-center, open-label, single arm Phase 2 basket study of reloxaliase in adults and adolescents with primary hyperoxaluria or enteric hyperoxaluria with advanced chronic kidney disease (CKD) and elevated plasma oxalate.

Allena expects to achieve the following key milestones for reloxaliase:

• Report interim clinical data from Study 206 in the first half of 2019;

• Report topline data from the URIROX-1 Phase 3 clinical trial in the second half of 2019; and

• Report topline data from Study 206 in the second half of 2019.

ALLN-346: ALLN-346 is a first-in-class, orally administered, novel urate degrading enzyme that has been designed for activity and stability in the gastrointestinal tract. Allena is working to complete its preclinical development of ALLN-346 for the treatment of hyperuricemia in patients with gout in the setting of advanced CKD, and to scale its manufacturing processes to support clinical studies.

Allena expects to achieve the following key milestones for ALLN-346:

• File an Investigational New Drug application with the FDA in 2019; and

• Initiate the first clinical trial in the first half of 2020.

About Allena Pharmaceuticals

Allena Pharmaceuticals, Inc. is a late-stage biopharmaceutical company dedicated to developing and commercializing first-in-class, oral enzyme therapeutics to treat patients with rare and severe metabolic and kidney disorders. Allena’s lead product candidate, reloxaliase, is a first in class, oral enzyme therapeutic for the treatment of hyperoxaluria, a metabolic disorder characterized by markedly elevated urinary oxalate levels and commonly associated with kidney stones, chronic kidney disease and other serious kidney disorders.

Forward-Looking Statements

This release contains “forward-looking statements” within the meaning of the Private Securities Litigation Reform Act of 1995, including statements regarding Allena’s URIROX clinical program and alignment with the FDA, statements regarding Allena’s ability to utilize the accelerated approval regulatory pathway for reloxaliase, statements regarding the timing of announcement of interim clinical data from Study 206 and topline data from the URIROX-1 trial and Study 206, statements regarding the filing of an IND and the initiation of a clinical trial for ALLN-346, and statements regarding the ability of reloxaliase to provide clinical benefit to patients with hyperoxaluria. Any forward- looking statements in this press release are based on management’s current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements. These risks and uncertainties include, but are not limited to: the risk that results of earlier studies may not be predictive of future clinical trial results, and planned and ongoing studies may not establish an adequate safety or efficacy profile for reloxaliase to support regulatory approval or the use of the accelerated approval regulatory pathway; risks related to Allena’s ability to utilize the accelerated approval pathway for reloxaliase, including the risk that

available data at the time of any sample size re-estimation or interim analysis conducted during the URIROX-2 trial may not be sufficient to demonstrate an increased probability of kidney stone events in patients with enteric hyperoxaluria and increasing UOx levels; the risk that the FDA may require that Allena increase the sample size or duration of treatment following the sample size reassessments to be conducted in accordance with the adaptive design element of the trial or otherwise collect additional clinical data from the URIROX-2 or other clinical trials prior to submitting a BLA for reloxaliase; risks associated with Allena’s ability to enroll a sufficient number of patients to adequately power URIROX-2 in order to achieve ultimate statistical success for kidney stone disease progression in the long-term follow-up phase of the trial; risks associated with obtaining, maintaining and protecting intellectual property; risks associated with Allena’s ability to enforce its patents against infringers and defend its patent portfolio against challenges from third parties; the risk of competition from other companies developing products for similar uses; risk associated with Allena’s ability to manage operating expenses and/or obtain additional funding to support its business activities; and risks associated with Allena’s dependence on third parties. For a discussion of other risks and uncertainties, and other important factors, any of which could cause Allena’s actual results to differ from those contained in the forward-looking statements, see the section entitled “Risk Factors” in Item 1A of Part II of Allena’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2018, as well as discussions of potential risks, uncertainties and other important factors in Allena’s subsequent filings with the Securities and Exchange Commission. All information in this press release is as of the date of the release, and Allena undertakes no duty to update this information unless required by law.

Investor Contact

Hannah Deresiewicz

Stern Investor Relations, Inc.

212-362-1200

hannahd@sternir.com

Media Contact

Adam Daley

Berry & Company Public Relations

212-253-8881

adaley@berrypr.com

EX-99.2

Bringing First-in-Class Oral Enzyme Therapeutics to Patients with Rare and Severe Metabolic and Kidney Disorders January 2019 Exhibit 99.2

Allena Pharmaceuticals, Inc. These slides, and any accompanying presentation, contain forward-looking statements and information. The use of words such as “may,” “might,” “will,” “should,” “expect,” “plan,” “anticipate,” “believe,” “estimate,” “project,” “intend,” “future,” “potential,” or “continue,” and other similar expressions are intended to identify forward-looking statements. All forward-looking statements are based on estimates and assumptions by our management that, although we believe them to be reasonable, are inherently uncertain. All forward-looking statements are subject to risks and uncertainties that may cause actual results to differ materially from those that we expected, including those material risks and uncertainties that are described under the heading “Risk Factors” in our Quarterly Report on Form 10-Q for the quarter ended September 30, 2018 filed with the Securities and Exchange Commission on November 7, 2018, as well as discussions of potential risks, uncertainties and other important factors in our subsequent filings with the Securities and Exchange Commission. Any forward-looking statement speaks only as of the date on which it was made. We undertake no obligation to publicly update or revise any forward-looking statement, whether as a result of new information, future events or otherwise, except as required by law.

Highlights – Pioneering Oral Enzyme Therapeutic Platform Significant Unmet Need in Oxalate and Urate Disorders Focused on rare and severe metabolic disorders that can cause kidney stones, damage the kidney, and potentially lead to CKD and ESRD No approved oxalate therapies; potential untapped multi-billion dollar market First-in-class, oral therapy for severe hyperoxaluria Achieved FDA alignment on pivotal Phase 3 program and accelerated approval pathway Enrolling two Phase 3 trials in enteric hyperoxaluria; URIROX-1 topline data expected 2H19 Enrolling Phase 2 basket study (Study 206) in orphan populations Proprietary technological approach designed to enable treatment of metabolic diseases with oral, non-absorbed enzyme therapeutics GI MOA reduces subsequent metabolic burden on the kidney First-in-class, oral therapy designed for gout patients with moderate-to-severe CKD; designed to degrade urate in the GI tract, reducing urate burden on kidney Gout patients with renal impairment are not optimally managed with existing therapies IND submission targeted in 2H19 Late-Stage Development Candidate: Reloxaliase Pioneering Expertise in Oral Enzyme Therapeutics Second Product Candidate: ALLN-346

Post-Approval Clinical Benefit Phase In December 2018, Allena Achieved FDA Alignment on Accelerated Approval Pathway for Reloxaliase and Design of URIROX-2 1° efficacy endpoint: Percent change from baseline in mean UOx excretion during Weeks 1-4 2° efficacy endpoint: Proportion of patients with ≥20% reduction in mean UOx excretion during Weeks 1-4 and percent change from baseline in mean UOx excretion during Weeks 16-24 (URIROX-2) Long-term efficacy endpoints to confirm clinical benefit: Primary: Proportion of subjects with kidney stone disease progression Secondary: Change in eGFR from baseline and ER visits/hospitalizations/ procedures for management of kidney stones Expect to submit an accelerated approval BLA filing to the FDA after ~400 patients have been randomized and followed for six months. URIROX Phase 3 program – a landmark study for patients suffering from enteric hyperoxaluria: Urinary oxalate (UOx) biomarker as surrogate endpoint URIROX-2 has the same primary efficacy endpoint as URIROX-1 with topline data expected in 2H19 Kidney stone disease progression as long-term endpoint for clinical benefit Adaptive design elements to streamline clinical benefit phase of URIROX-2

Product Indication Discovery Pre-Clinical Phase 1 Phase 2 Phase 3 Next Milestone Commercial Rights Reloxaliase Enteric hyperoxaluria 2H19: Topline data URIROX-1 Worldwide Systemic oxalosis* 1H19: Interim data Worldwide Primary hyperoxaluria* (Orphan Designation) 1H19: Interim data Worldwide Pediatric hyperoxaluria* (Orphan Designation) 1H19: Interim data Worldwide ALLN-346 Hyperuricemia and CKD 2H19: IND filing Worldwide Allena’s Pipeline: First-in-Class Therapeutic Strategy for Oxalate and Urate Disorders * Being evaluated in a single Phase 2 clinical trial with a basket design (Study 206) that will enroll subsets of patients suffering from complications of severe hyperoxaluria, including adolescents and adults with primary or enteric hyperoxaluria with advanced CKD, both of which can lead to systemic oxalosis.

First-in-Class Therapeutic Strategy Expertise and Proprietary Technological Approach in Enzyme Therapeutics Enables First-in-Class Therapeutic Strategy for Oxalate and Urate Disorders Pioneering Expertise in Oral Enzyme Therapeutics Design, formulation, and delivery of non-absorbed and stable enzymes orally for activity in GI tract First-in-Class Enzyme Therapeutics Oral enzymes designed to rapidly degrade a specific metabolite within the gut, reducing absorption in blood and urine, and in turn, diminishing disease burden on kidney Proprietary and Scalable Manufacturing Capabilities Proven ability to produce large quantities of oral enzymes COGS anticipated to be comparable to small molecule therapeutics

Hyperoxaluria is Characterized by Markedly Elevated Urinary Oxalate Levels Source: Illustration adapted from Coe, Fred. “Control of Urine Oxalate Excretion.” Kidneystones.uchicago.edu. University of Chicago, kidneystones.uchicago.edu/control-of-urine-oxalate-excretion . March 2017. Fecal Excretion Gastrointestinal Tract Oxalate is absorbed and secreted along the GI tract Urinary Excretion Kidney Damage and Inflammation Crystal deposition in parenchyma Kidney Impairment Kidney is unable to filter (declining eGFR) Oxalate is measured in plasma Kidney Stones Excreted or removed Oxalate is measured in the urine Oxalate Rich Foods Oxalate Absorbed Secreted Filtered Primary Hyperoxaluria: Orphan genetic disorder caused by endogenous excess production of oxalate in the liver Liver blood Secondary Hyperoxaluria: Disorder caused by excess absorption of oxalate in the GI tract Enteric: due to underlying GI disorders Idiopathic: due to an unknown cause Degrades Oxalate along GI tract Reloxaliase

Enteric Hyperoxaluria Patients Are a High Risk Population Who Are Identifiable by Physicians and in Need of Treatment There are no FDA approved pharmacological therapies to treat any form of hyperoxaluria Enteric GI malabsorptive conditions include: gastric bypass surgery, Crohn’s disease, ulcerative colitis, pancreatic insufficiency, celiac disease, and liver disease High unmet need: frequent and more complex stones, fail standard of care (i.e., hydration, dietary modifications) Stones and CKD burden: $66K average annual direct expenditures four years post GI malabsorptive procedure or disease diagnosis EH patients in Allena’s Phase 2 clinical program, presented at ASN Kidney Week 2018: Very high baseline UOx On average, EH subjects had experienced 6 stones prior to enrollment, with an average of 3 kidney stones visible by routine CT scan at time of enrollment Study 713 Patient Examples: Whipple (Pancreatic Insufficiency): 14 stones in last 5 years (16 stones visible by CT) Celiac disease: 3 stones in last 2 years ( 4 stones visible by CT) Gastric Bypass: 8 stones in the last 5 years (3 stones visible by CT) ~5K Primary 200-250K Enteric ~5M Idiopathic and Kidney Stone Disease

Risk of Renal Complications Rises with Higher Urinary Oxalate Levels: Reduction of UOx Improves Renal Outcomes Illustrative Diagram Sources: Robertson and Hughes, Scanning Microsc. 1993; Keddis Curr Opin Nephrol Hypertens. 2013; Robertson and Peacock, Nephron. 1980; Milliner, Kidney Int. 2006; Curhan and Taylor, Kidney Int. 2008; Milliner, Clin J Am Soc Nephrol. 2015. Key Studies: Borghi N Eng J Med. 2002; Taylor and Curhan, J Am Soc Nephrol. 2007; Milliner, N Eng J Med 1994 and Lieske JASN Abstract Supplement 2017 Urinary Oxalate Literature and KOL Input: ~20% reduction in UOx would be clinically meaningful Key Peer Review Studies: Higher baseline UOx predicts future stone events in enteric hyperoxaluria patients (Lieske ASN 2017) 50% reduction in risk of kidney stone recurrence associated with >20% decrease in UOx (Borghi 2002) 25-50% reduction in kidney stone recurrence rate associated with >20% decrease in UOx (Curhan and Taylor 2008) Preservation of renal function associated with ~10% reduction in UOx (Milliner 1994) Urinary Oxalate (UOx) mg/24h Kidney Damage 102030405060708090100>100 Kidney Failure Normal Kidney Function Kidney Stones CaOx Crystal Formation Systemic Crystal Deposition Risk of Kidney Complications* Increasing Severity Reloxaliase Mechanism of Action * The complications noted in the figure represent a general progression of kidney harm and disease associated with increasing urinary oxalate excretion levels. Not all patients experience this progression and there is considerable variability among individuals between urinary oxalate excretion levels and kidney function and disease. Idiopathic Hyperoxaluria Enteric Hyperoxaluria Primary Hyperoxaluria Normal

Allena Initially Targeting Enteric Hyperoxaluria Patients with Underlying Malabsorptive GI Diseases and Kidney Stones 1Truven Health Analytics, part of the IBM Watson Health business longitudinal Claims Analysis, August 2017. 4-year progression of disease 4.4M Estimated Patients with GI Malabsorptive Conditions with No Prior Kidney Stones or CKD Patients potentially at risk for enteric hyperoxaluria1 Kidney stones, often the first clinical manifestation of hyperoxaluria, facilitate patient identification of patients with kidney stone disease developed CKD 80-100K Estimated Patients with Kidney Stones and Chronic Kidney Disease (CKD) ~2% 200-250K Estimated Patients with Enteric Hyperoxaluria and Kidney Stones of patients developed kidney stone disease ~5% In CKD Stages IV-V or transplant in year 4 ~16K In Late Stage (IV-V) or Transplant in Year 4 ~0.2% Analysis tracked patients for whom an enteric disease diagnosis or procedure code was entered between 7/1/10 - 6/30/12 who did not have a claim with an KSD, CKD/ESRD/ Dialysis diagnosis or procedure code from 1/1/10 - 6/30/10. Analysis showed that approximately 5% of patients subsequently developed one or more kidney stones (“Kidney Stone Disease"), of which 40% also developed CKD over the subsequent four years to determine prevalence in 2012. 2017 figures apply 3.6% CAGR to 2012 population figures. Approximately 9% of patients develop CKD without kidney stone disease within 4 years URIROX Program Study 206

The Patient Journey for Severe Hyperoxaluria Patients Can Include Complex Specialty Care with Progressive Disease Strong Patient Advocacy: The Kidney Health Initiative project brings together patients, clinicians, industry and the FDA to evaluate potential endpoints for future clinical trials in enteric and primary hyperoxaluria Waever & Holihan Patient Market Research January 2017, https://www.asn-online.org/khi/mission.aspx. Recurrent Kidney Stones Stone Clinic Kidney Stone Disease Management Nephrologist/Urologist Metabolic Management Complex Specialty Care Monitoring Kidney Function Nephrologist Renal Damage and ESRD Dialysis Center Routine Dialysis URIROX Program Study 206

Reloxaliase for the Treatment of Hyperoxaluria

Clinical and Regulatory Progression of Reloxaliase (ALLN-177) Preclinical Ph 1 Healthy Volunteers Ph 2 Open Label Ph 2 Randomized Controlled Ph 3 Randomized Controlled ✓ ✓ ✓ ✓ Initiated 1Q 2018 and 4Q 2018 Progressive Increase in Enzyme Activity Porcine Rhubarb Model Presented at AUA 2016 Porcine Western Diet Model Presented at ASN 2016 n=30 A Double Blind, Placebo Controlled, Randomized Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme Langman et al, Am. J Nephrol 2016;44:150-158 Presented at ASN 2014 n=16 Multicenter, Open Label, Single Arm Outpatient Study in Enteric and Idiopathic Hyperoxaluria Presented at ASN 2015 n=30 649: Multi-Center, Randomized, Double-Blind, Placebo-Controlled, Crossover in Enteric and Idiopathic Hyperoxaluria n=67 713: Multi-Center, Randomized, Double-Blind, Placebo-Controlled in Enteric and Idiopathic Hyperoxaluria Presented at ASN 2017 n≈124 URIROX-1: Multi-Center, Global, Randomized, Double-Blind, Placebo-Controlled Study in Enteric Hyperoxaluria n≈400 URIROX-2: Multi-Center, Global, Randomized, Double-Blind, Placebo-Controlled Study in Enteric Hyperoxaluria 2° Hyperoxaluria 1° Hyperoxaluria Preclinical Orphan Designation Initiated Ph 2 Study ✓ ✓ ✓ AGTKO Mouse Model Grujic et al, Am. J Nephrol 2009; 29: 86-93 Porcine Dietary Hydroxyproline and Porcine Sodium ox-IV injection model FDA grants Orphan Disease Designation for ALLN-177 in both PH and Pediatric Hyperoxaluria (Primary and Secondary) EC grants Orphan Disease Designation for ALLN-177 in PH Study 206: Clinical Trial in Patients with Primary or Enteric Hyperoxaluria Patients and Hyperoxalemia CT.GOV: NCT03391804

Study 713: Substantially Greater ALLN-177 Treatment Response in Enteric Population 1. Beyond the primary endpoint analysis, all p-values are descriptive. Overall (n=67) Enteric (n=18) Key Endpoints: ALLN-177 vs. placebo ∆ p-value ∆ p-value Change in UOx (mg/24h) from baseline to week 4 -6.35 mg/24h 0.160 -16.45 mg/24h 0.184 Change in UOx (mg/24h) from baseline to TWA across 4 weeks1 -8.13mg/24h 0.016 -25.69 mg/24h 0.018 Percent change in UOx from baseline to TWA across 4 weeks1 -14.23% 0.015 -39.15% 0.010 Responder Analysis: Proportion of Patients with Reduction in TWA UOx Excretion (%) Reduction in TWA UOx (%) -10 -20 -30 -40 -50 Enteric ALLN-177 73 64 36 18 9 Enteric Placebo 29 14 0 0 0

Study 713: Substantially Greater ALLN-177 Treatment Response in Enteric Population *Beyond the primary endpoint analysis, all p-values are descriptive. Enteric ALLN-177 Enteric Placebo Change in TWA Urinary Oxalate (mg/24h) Baseline Urinary Oxalate (mg/24h) Change in TWA UOx Excretion vs. Baseline UOx Excretion Create table ∆ = (8.13) mg/24h *p = 0.016 ∆ = (25.69) mg/24h *p = 0.018 LS Mean UOx Change in TWA (mg/24h) Overall Enteric ALLN-177 Overall ALLN-177 Enteric n Placebo

Reloxaliase Generally Well-Tolerated in Clinical Trials to Date 11,500 u/meal, 3,000 u/meal, and 7,500 u/meal. 2TEAE = Treatment emergent adverse events are defined as AEs with onset at the time of or following the first dose of treatment with study drug through 7 days after their last dose of study medication, or AEs starting before the start of treatment but increasing in severity or relationship at the time of or following the start of treatment through 7 days after their last dose of study medication. 3One subject reported congestive heart failure of moderate severity, considered not related to study drug, but secondary to a recent cardioversion for atrial fibrillation. This resulted in hospitalization and withdrawal from the study; same subject in both rows. 4Two placebo treated subjects withdrew from study drug, one after nearly 4 weeks of treatment due to nausea, considered not related, and another due to hives/dermatitis with onset 3 days after starting placebo, considered possibly related. Study 396 Study 649 Study 713 All (n=16) Reloxaliase1 (n=30) Placebo (n=24) Reloxaliase (n=32) Placebo (n=35) n (%) n (%) n (%) n (%) n (%) TEAE2 9 (56.3%) 13 (43.3%) 6 (25.0%) 16 (50%) 22 (62.9%) Severe TEAE 0 0 0 0 0 Related TEAE 2 (12.5%) 5 (16.7%) 2 (8.3%) 3 (9.4%) 8 (22.9%) Serious AE (SAE) 0 1 (3.3%)3 0 0 0 Related SAEs 0 0 0 0 0 AEs Leading to Study Drug Withdrawal 0 1 (3.3%)3 0 0 2 (5.7%)4 AEs Leading to Death 0 0 0 0 0 Rare disease and demonstrated safety profile of reloxaliase led to reduced requirement for Phase 3 trial size

Phase 3 Program Incorporates Key Learnings from Phase 2 Phase 3 Program Phase 2 Program Identified Proposed Phase 3 Patient Population Identified Proposed Pivotal Endpoint Identified Proposed Phase 3 Trial Design ü Identified Proposed Key Secondary Endpoints Enteric hyperoxaluria is a rare disease without available treatment ü Percent change from baseline in mean 24-hour UOx excretion during Weeks 1 to 4 ü Proportion of subjects with a ≥ 20% reduction from baseline in mean 24-hour UOx during Weeks 1-4 Percent change from baseline in mean 24-hour UOx excretion during Weeks 16 to 24 ü Multicenter, global, parallel, RCT vs placebo with adaptive design strategy Dosing up to 5x per day per meal or snack Six month UOx biomarker phase with minimum of 2 year long-term follow-up phase post approval ü Identified Endpoint to Confirm Clinical Benefit Post Approval Kidney Stone Disease (KSD) progression Change in estimated glomerular filtration rate (eGFR) Emergency room visits, hospitalizations or procedures for the management of KSD

1H 2018 2H 2018 1H 2019 2H 2019 1H 2020 2H 2020 Reloxaliase Pivotal Program in Enteric Hyperoxaluria Incorporates Consistent Biomarker Endpoints in Both Phase 3 Trials Follow subjects for a minimum of 2 years for post approval confirmation URIROX-1 in Enteric HO RCT x 4 weeks n=~124 Topline Data URIROX-2 in Enteric HO RCT ≈ 24 weeks n=~400 Key Features URIROX-1 URIROX-2 Biomarker measurement: UOx as surrogate endpoint Primary efficacy endpoint: percent change from baseline in mean 24h UOx excretion during Weeks 1-4 Secondary efficacy endpoint: proportion of subjects with a ≥ 20% reduction from baseline in mean 24h UOx excretion during Weeks 1-4 Dosing: up to 5x a day with meals and snacks Expect to submit an accelerated approval BLA filing to the FDA after ~400 patients have been randomized and followed for six months. If necessary, adaptive design allows for increases in sample size and duration of treatment to support confirmation of clinical benefit.

URIROX-1: Evaluate the Safety and Efficacy of Reloxaliase in Patients with Enteric Hyperoxaluria Key Features: Tailored dose regimen: dose with each meal/snack 3-5x per day to maximize degradation of oxalate ingested or secreted Primary Endpoint: Percent change from baseline in 24-h UOx excretion averaged during Weeks 1-4, with demonstration of a mean reduction in UOx with reloxaliase vs placebo Secondary Endpoint: Proportion of subjects with a ≥20% reduction from baseline in 24-h UOx excretion averaged during Weeks 1-4 Randomization Reloxaliase (7,500 u) or placebo 2 cap with meal/snack 3 to 5 times per day x 28 days UOx>50mg/24h Normal to Stage 3 CKD (eGFR ≥30) 1:1 n≈124 2X 24h 1X 24h 2X 24h 2X 24h 2X 24h 2X 24h Screening Study Aim: Determine the Safety and Efficacy of Reloxaliase in Reducing UOx in Subjects with Enteric Hyperoxaluria Follow up 4 weeks Reloxaliase Placebo

Randomization UOx>50mg/24h eGFR ≥30 1:1 n≈400 RCT follow-up for minimum of 2 years Patient Population: Patients with enteric hyperoxaluria UOx ≥50 mg/d, history of kidney stones and eGFR >30 prior to screening Randomization stratified by: bariatric surgery vs. other enteric condition Endpoints for UOx Biomarker: Primary: percent change from baseline in mean 24h UOx excretion during Weeks 1-4 Secondary: proportion of subjects with a ≥ 20% reduction from baseline in mean 24h UOx excretion during Weeks 1-4 and percent change from Baseline in mean 24-hour UOx excretion during Weeks 16 to 24 Adaptive Design Strategy: Expect to submit an accelerated approval BLA filing after n=400 have been randomized and followed for six months Incorporates adaptive design elements that will, if necessary, allow for increases in sample size and duration of treatment to support confirmation of clinical benefit Endpoints for Post-Approval Confirmatory Study: Primary: Kidney stone disease progression – composite of either symptomatic kidney stones or finding of new or enlarged kidney stones using imaging Secondary: Change in estimated glomerular filtration rate (eGFR), and ER visits/hospitalizations/procedures for management of kidney stones Reloxaliase Placebo Reloxaliase (7,500 u) or PBO 2 capsules with meal/snack 3 to 5 times per day Study Aim: Determine the Efficacy and Safety of Reloxaliase in Reducing UOx in Subjects with Enteric Hyperoxaluria Weeks 1-4 Weeks 16-24 URIROX-2: Evaluate the Efficacy and Safety of Reloxaliase in Patients with Enteric Hyperoxaluria Follow up 4 weeks Screening

Reloxaliase Additional Indications

Elevated Plasma Oxalate Increases Risk for CaOx Crystal Deposition in the Kidney and Other Organ Systems Time and progression of disease Plasma Oxalate Level CKD 1 CKD 2 CKD 3 CKD 4 ESRD 0 15 30 45 2-5 µmol/L Normal range Systemic Oxalosis Dialysis Hyperoxalemia Study Population: Enteric Hyperoxaluria Primary and Enteric Hyperoxaluria with Hyperoxalemia Source:1. Ermer T 2016 Curr Opin Nephrol Hypertens. 2. Roodnat JI 2017 Transplant Direct 3. Elgstoen KB 2010 Neph Dial Transplant 4.Health Advances interviews and analysis, OPTN 5.Pinheiro HS 2005 Am J Transplant 6. Bagnasco SM 2009 Nephrol Dial Transplant 7. Palsson R J Am Soc Nephrol 28, 2017:356. Oxalate crystals are associated with renal inflammation, fibrosis and progressive renal failure1 Patients with hyperoxalemia or systemic oxalosis can accumulate oxalate in the blood and other tissues, creating “oxalate stores” in the body2,3 Hyperoxalemia or systemic oxalosis can prohibit patients from getting a transplant4 or jeopardize the transplanted kidney2,4,5 Growing awareness of association between oxalate crystal deposition and poor long-term graft survival, declining kidney function and return to dialysis4,5,6,7 Unmet Need: Reduce Risk of Oxalate Damage to the Kidney

Reloxaliase has the Potential to Reduce Oxalate Burden in Patients with Primary Hyperoxaluria and Enteric Hyperoxaluria with Advanced CKD Sources: Grujic et al, Am. J Nephrol 2009; 29: 86-93 and company data *Pigs not colonized with oxalobacter formigenes. Degraded Oxalate in the GI Tract and Reduced Plasma Oxalate in Porcine Model of Secondary Hyperoxaluria In porcine model, reloxaliase reduced plasma 30% and urinary oxalate 35% after 7 days of treatment with reloxaliase. Oral therapy of 22,500 u/day normalized both plasma and urine oxalate.* Urine Oxalate (mg/gCr/24h) Plasma Oxalate (µmol/L) Nephrocalcinosis (% of animals) Prevented Nephrocalcinosis and Increased Survival in the AGXT KO Mouse Model of Primary Hyperoxaluria Control 25 mg 80 mg

Screening and Baseline 28 d Follow up 4 Weeks Study 206: Reloxaliase Treatment of Adult and Pediatric Patients with Primary or Enteric Hyperoxaluria and Advanced CKD ('Basket' Study) Primary Hyperoxaluria (PH) Enteric Hyperoxaluria (EH) Urinary Oxalate (UOx) Plasma Oxalate (POx) Regulatory: Reloxaliase has been granted separate orphan designations for primary hyperoxaluria and pediatric hyperoxaluria Study Initiation: 1Q 18 (CT.GOV: NCT03391804) Hypothesis: By degrading oxalate within the GI tract, reloxaliase is designed to reduce plasma and urinary oxalate levels in patients with PH or EH and hyperoxalemia. Reduction in plasma oxalate levels (POx) should lead to decreased systemic oxalate deposition (systemic oxalosis). Study Design: Uncontrolled, Open-label Enroll subjects ≥12 yrs, body weight ≥ 35 kg, in PH or EH with hyperoxalemia Dose regiment as 5 x/day to maximize the degradation of oxalate ingested or secreted in the GI tract Key Endpoints: Change from baseline in POx and UOx Study Aim: Evaluate effect of reloxaliase in reducing plasma and UOx in patients with primary or enteric hyperoxaluria and hyperoxalemia 1 x POx 2 x 24h n ≈ up to 20 ≥ 12 years PH or EH UOx ≥ 40mg/24hr * Required for EH *POx > 5 µmol/L *eGFR < 45 mL/minute/1.73 m2 2 x POx 2 x 24h 1 x POx 2 x 24h 1 x POx 2 x 24h 1 x POx 2 x 24h Reloxaliase caps per meal/snack up to 5 x/day (max 10/d) Treatment x 12 Weeks Week 8 Week 12 Week 4

ALLN-346: Significant Opportunity in Gout Patients with Moderate-to-Severe CKD The Gout Market is Incompletely Served by Existing Therapies ~375,000 gout patients with moderate to severe CKD who have uncontrolled gout on urate lowering therapy (ULT)* Gout patients with renal impairment are not optimally managed due to limitations of existing therapies Gout patients with kidney and liver problems are contraindicated for allopurinol, Uloric, and Zurampic Current ULT’s may interact with other medications Co-morbidities (e.g. cardiovascular) may also limit ULT options Significant unmet need for safe and effective therapy that can be used in patients with renal impairment Sources: . *Lim JJ, Fu AC, and Reasner D. Prevalence of CKD and Uncontrolled Gout Among US Adults: Results from NHANES 2007-2012. Poster presented at: The National Kidney Foundation Spring Clinical Meetings; April 18-22, 2017; Orlando Florida. Fletcher Spaght Analysis July 2016; Image: Retailleau, P., Colloc'h, N., Vivares, D., Bonnete, F., Castro, B., El Hajji, M., Prange, T. (2005) Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site. Acta Crystallogr.,Sect.D, 61, 218-229; D. Grujic Urol Res 2008, 193. ALLN-346 Therapeutic Strategy: Novel urate degrading enzyme optimized for stability in the GI tract MOA: orally administered, gut restricted enzyme therapeutic Animal POC: demonstrated a robust reduction in urine and plasma uric acid levels in a severe animal model of hyperuricemia with advanced CKD Data presented at American College of Rheumatology meeting October 22, 2018

Execution of Clinical and Regulatory Milestones YEAR TARGET MILESTONE STATUS 2018 1Q18 Initiate URIROX-1 ü 1Q18 Initiate Study 206, Phase 2 Study in PH and EH with Hyperoxalemia ü 2H18 Present ALLN-346 Animal Data New ü 2H18 Initiate URIROX-2 ü 2H18 Study 206 Interim Data Update ü 2019 1H19 File IND ALLN-346 2H19 1H19 Study 206 Additional Interim Data On Track 2H19 URIROX-1 Topline Data On Track 2H19 Study 206 Topline Data On Track

Highlights – Pioneering Oral Enzyme Therapeutic Platform Significant Unmet Need in Oxalate and Urate Disorders Focused on rare and severe metabolic disorders that can cause kidney stones, damage the kidney, and potentially lead to CKD and ESRD No approved oxalate therapies; potential untapped multi-billion dollar market First-in-class, oral therapy for severe hyperoxaluria Achieved FDA alignment on pivotal Phase 3 program and accelerated approval pathway Enrolling two Phase 3 trials in enteric hyperoxaluria; URIROX-1 topline data expected 2H19 Enrolling Phase 2 basket study (Study 206) in orphan populations Proprietary technological approach designed to enable treatment of metabolic diseases with oral, non-absorbed enzyme therapeutics GI MOA reduces subsequent metabolic burden on the kidney First-in-class, oral therapy designed for gout patients with moderate-to-severe CKD; designed to degrade urate in the GI tract, reducing urate burden on kidney Gout patients with renal impairment are not optimally managed with existing therapies IND submission targeted in 2H19 Late-Stage Development Candidate: Reloxaliase Pioneering Expertise in Oral Enzyme Therapeutics Second Product Candidate: ALLN-346