EXECUTIVE AND DIRECTOR COMPENSATION

Donald V. Dougherty, CFA, CPA has served as our senior vice president, chief financial officer since June 2017. Mr. Dougherty founded Compound Capital Growth Investments, LLC, a Boston investment firm focused on biopharmaceutical and other technology sectors, and served as its president from November 1999 to June 2017. Previously, Mr. Dougherty held senior positions at Essex Investment Management, where he was a principal, portfolio manager and lead biotechnology analyst, and Putnam Investments, where he was a senior vice president and analyst in the Specialty Growth Group. Mr. Dougherty received a B.A. from Williams College and a M.B.A. from New York University.

D. Allen Annis, Ph.D. has served as our senior vice president, research since November 2018. From the time Dr. Annis joined our company in November 2007, Dr. Annis served as our senior director biophysical and analytical technology from November 2007 to September 2009, and as our vice president of research from September 2009 to November 2018. Previously, Dr. Annis served as director of technology development at Schering-Plough Research Institute, and as vice president of new technologies at NeoGenesis Pharmaceuticals, Inc. While at NeoGenesis, Dr. Annis co-developed the company’s core drug discovery platform, the affinity selection-mass spectrometry-based Automated Ligand Identification System, or ALIS. Dr. Annis authored several patents and publications that describe the ALIS technology, and also invented many novel techniques that use ALIS to study protein-drug interactions. Dr. Annis received a M.A. and Ph.D. in chemistry from Harvard University, and a B.S. in chemistry from Georgia Institute of Technology.

Kathryn Gregory has served as our senior vice president, chief business officer since February 2019. Previously, from March 2018 to February 2019, Ms. Gregory was President of KG BioPharma Consulting LLC, a strategic advisory company, where she assisted small and mid-size biopharma companies in a range of corporate strategy and business development activities. From September 2017 to February 2018, Ms. Gregory served as chief business officer for Avillion LLP, a biopharmaceutical firm. From April 2009 to December 2017, Ms. Gregory served as co-founder, chief executive officer and chief business officer for Seneb BioSciences, an early-stage, rare disease company. Previously, Ms. Gregory served in senior roles for several pharmaceutical and biotechnology companies, including as executive director, licensing & business development at Purdue Pharma, and as head, transactions at Shire Pharmaceuticals for the Neuroscience and Ophthalmology business units. Ms. Gregory received an M.B.A. from Pepperdine University and a B.A. degree from the University of California, Berkeley.

Vojislav Vukovic, M.D., Ph.D. has served as our senior vice president, chief medical officer since November 2018. Previously, from May 2017 to November 2018, Dr. Vukovic provided consulting and advisory services to biotechnology and pharmaceutical clients, including our company. From February 2016 to May 2017, Dr. Vukovic served as senior vice president and chief medical officer at Taiho Oncology, Inc., a pharmaceutical company. From January 2009 to November 2015, Dr. Vukovic served as senior vice president and chief medical

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officer at Synta Pharmaceuticals, Inc., a company focused on novel oncology medicines. Prior to Synta, Dr. Vukovic served as medical director at Pfizer. He also was a member of the leadership team for Pfizer’s Oncology Radiotherapy Initiative. Dr. Vukovic received a M.Sc. in tumor biology and a Ph.D. in radiation biology from the University of Toronto, and a M.D. from Medicinski Fakultet Sarajevo.

Narrative Disclosure to Summary Compensation Table

We review compensation for our executive officers annually. The material terms of the elements of our executive compensation program for 2018 are described below.

Our compensation committee sets base salaries and bonus targets and grants bonuses and equity incentive awards to our executive officers. In setting base salaries and bonus targets and granting equity incentive awards, our compensation committee considers compensation for comparable positions in the market, the historical compensation levels of our executives, individual and corporate performance as compared to our expectations and objectives, our desire to motivate our employees to achieve short- and long-term results that are in the best interests of our stockholders, and a long-term commitment to our company. In granting bonuses, our compensation committee considers corporate and individual performance.

As part of our annual compensation process, our president and chief executive officer prepares performance evaluations for the other executive officers and recommends annual salary increases, annual stock option awards and cash bonuses to the compensation committee. The compensation committee conducts a performance evaluation of our president and chief executive officer. The compensation committee consults with the board of directors as to the achievement of corporate objectives that drive compensation awards.

During its annual compensation review, our compensation committee also consults with external advisors.

In fiscal 2018, the compensation committee engaged Radford as its independent compensation consultant to provide comparative data on executive compensation practices in our industry and assess our executives’ compensation relative to comparable companies.

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Base Salary

We use base salaries to recognize the experience, skills, knowledge and responsibilities required of all our employees, including our named executive officers. None of our named executive officers is currently party to an employment agreement or other agreement or arrangement that provides for automatic or scheduled increases in base salary.

In January 2017, Dr. Aivado’s base salary was set at $382,130 and in July 2017, following our initial public offering, or IPO, his annual base salary was further increased to $400,000. In February 2018, as part of his annual performance review, Dr. Aivado’s annual base salary was increased to $414,000 effective January 1, 2018. In September 2018, in connection with his appointment as our president and chief executive officer, Dr. Aivado’s annual base salary was increased to $500,000. In February 2019, as part of his annual performance review, Dr. Aivado’s annual base salary was increased to $507,400 effective as of January 1, 2019.

Mr. Dougherty commenced employment with us in June 2017 with an annual base salary of $335,000. In July 2017, following our IPO, Mr. Dougherty’s annual base salary was increased from $335,000 to $345,000. As part of his annual performance reviews, Mr. Dougherty’s base salary was increased in February 2018 to $357,100 effective January 1, 2018 and increased in February 2019 to $367,800 effective as of January 1, 2019.

Dr. Vukovic commenced employment with us in November 2018. Pursuant to the terms of his employment offer letter, Dr. Vukovic’s annual base salary was set at $405,000. Dr. Vukovic also provided consulting services to us for several months prior to commencing employment with us. Dr. Vukovic’s base salary was not adjusted as part of the annual performance review.

From May 2018 to September 2018, we paid Dr. Longenecker a base salary at a rate of $43,558.33 per month, which was based on an annualized base salary of $522,700, for his service as our interim president and chief executive officer. After Dr. Longenecker ceased serving in such capacity in September 2018, we entered into a consulting agreement with Dr. Longenecker, pursuant to which Dr. Longenecker agreed to provide us with certain advisory services for up to 4 days per calendar month, unless otherwise agreed by Dr. Longenecker and us. Pursuant to the terms of the consulting agreement, we agreed to pay Dr. Longenecker a consulting fee of $12,000 per month.

In January 2017, Mr. Yanchik’s annual base salary was set at $437,950 and in July 2017, following our IPO, his annual base salary was increased to $505,000. In February 2018, as part of his annual performance review, Mr. Yanchik’s annual base salary was increased to $522,700 effective January 1, 2018.

Cash Incentives

The compensation committee awarded annual performance-based cash bonuses to our executive officers for 2017 and 2018, for up to a specific percentage of his or her salary as a vehicle to reward achievement of value-driving milestones and recognize individual performance. In 2017, Dr. Aivado and Mr. Dougherty were eligible for a performance-based cash bonus of up to 35% of such named executive officer’s base salary in 2017, subject to the achievement of corporate goals as determined by the compensation committee and subject to the achievement of individual goals as recommended by our chief executive officer and approved by the compensation committee. Mr. Yanchik was eligible for a performance-based cash bonus of up to 50% of his base salary in 2017, subject to achievement of corporate goals as determined by the compensation committee.

In February 2018, we made cash bonus awards of $252,500 to Mr. Yanchik, $162,613 to Dr. Aivado and $80,500 to Mr. Dougherty, based on the compensation committee’s assessment of achievement of corporate and individual goals in calendar year 2017 and, in the case of Mr. Dougherty, the percentage of the year in which he was employed by us. In addition, in 2017 we also paid a transition bonus of $25,000 to Mr. Dougherty upon his commencement of employment with us.

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In connection with Dr. Aivado’s appointment as our president and chief executive officer, we entered into a new employment agreement with Dr. Aivado in September 2018. Under the terms of the new employment agreement, Dr. Aivado is eligible to receive, commencing in 2019 and for each calendar year thereafter that Dr. Aivado is employed by us, a discretionary performance target bonus of up to 50% of his annual base salary based on the achievement of performance milestones set by either our board of directors or the compensation committee of the board. For the 2018 calendar year, Dr. Aivado was eligible to receive a discretionary performance target bonus calculated on the basis of 35% of his base salary as of August 31, 2018, pro-rated for the first eight months of the fiscal year, and 50% of his current base salary under the new employment agreement, pro-rated for the remaining four months of the fiscal year. The amount of such bonus and the achievement of such milestones are determined by our board in its sole discretion.

Pursuant to the terms of Dr. Vukovic’s employment offer letter, Dr. Vukovic is eligible to receive a performance-based cash bonus of up to 35% of his annual base salary, subject to the achievement of performance milestones as determined by our board of directors in its sole discretion.

In February 2019, we made cash bonus awards of $164,549 to Dr. Aivado, $99,988 to Mr. Dougherty, and $20,144 to Dr. Vukovic, based on the compensation committee’s assessment of achievement of corporate and individual goals in calendar year 2018 and, in the case of Dr. Vukovic, the percentage of the year in which he was employed by us.

Target bonuses as a percentage of annual salary for 2019 remain at 50%, 35% and 35% for each of Dr. Aivado, Mr. Dougherty and Dr. Vukovic, respectively.

Pursuant to the terms of the employment agreement we entered into with Dr. Longenecker in May 2018, Dr. Longenecker was eligible to receive a discretionary performance bonus of up to 50% of his annual base salary for the period of time he was employed by us in 2018 based on the achievement of performance milestones set by either our board of directors or the compensation committee of the board. The amount of such bonus and the achievement of such milestones are determined by the board of directors in its sole discretion. Following the conclusion of Dr. Longenecker’s service as our interim president and chief executive officer in September 2018, we paid Dr. Longenecker a cash bonus award in the amount of $122,508.

Pursuant to the terms of the separation and release of claims agreement we entered into with Mr. Yanchik in May 2018, Mr. Yanchik was eligible for a performance-based bonus of up to $87,166 based on our achievement of previously-agreed performance milestones in 2018, as determined by our board of directors in its sole discretion. In March 2019, we paid Mr. Yanchik a cash bonus award for 2018 in the amount of $79,321.

Equity Incentives

Although we do not have a formal policy with respect to the grant of equity incentive awards to our executive officers, or any formal equity ownership guidelines applicable to them, we believe that equity grants provide our executives with a strong link to our long-term performance, create an ownership culture and help to align the interests of our executives and our stockholders. In addition, we believe that equity grants with a time-based vesting feature promote executive retention because this feature incents our executive officers to remain in our employment during the vesting period, and equity grants with a performance-based feature incents our executive officers to focus on what we see as key business goals. Accordingly, the compensation committee periodically reviews the equity incentive compensation of our named executive officers and from time to time may grant equity incentive awards to them in the form of stock options.

In 2017, our board of directors granted options to purchase shares of our common stock to our executive officers, including Mr. Yanchik, Dr. Aivado and Mr. Dougherty.

Our board of directors granted options to Mr. Yanchik to purchase up to 159,001 and 157,449 shares of common stock, on March 2, 2017 and July 25, 2017, respectively. These options were scheduled to vest in equal monthly installments through March 2, 2021 and July 25, 2021, respectively.

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Our board of directors granted Dr. Aivado options to purchase up to 143,906 and 57,388 shares of common stock, on March 2, 2017 and July 25, 2017, respectively. These options vest in equal monthly installments through March 2, 2021 and July 25, 2021, respectively.

Our board of directors granted Mr. Dougherty options to purchase up to 140,887 and 60,331 shares of common stock, on June 28, 2017 and July 25, 2017, respectively. Mr. Dougherty’s first grant vested as to 25% of the shares on June 8, 2018, with the remaining shares vesting in equal monthly installments thereafter through June 8, 2021. Mr. Dougherty’s second grant vests in equal monthly installments through July 25, 2021.

In May 2018, in connection with Dr. Longenecker’s appointment as our interim president and chief executive officer, our board of directors granted Dr. Longenecker options to purchase 30,000 shares of our common stock, which would vest in full on the earlier of September 15, 2018 or the date on which Dr. Longenecker’s employment was terminated in connection with our hiring a new chief executive officer. These options vested in September 2018 in connection with Dr. Aivado’s appointment as our president and chief executive officer.

In September 2018, in connection with Dr. Aivado’s appointment as our president and chief executive officer, our board of directors granted Dr. Aivado options to purchase 232,914 shares of our common stock. The options vest in equal monthly installments over four years from September 6, 2018.

In November 2018, in connection with Dr. Vukovic’s appointment as our senior vice president, chief medical officer, our board of directors granted Dr. Vukovic options to purchase 150,000 shares of our common stock. The options vest as to 25% of the shares on November 5, 2019, with the remaining shares vesting in equal monthly installments thereafter through November 5, 2022.

In April 2019, our board of directors granted options to purchase 500,000, 150,000 and 100,000 shares of our common stock to Dr. Aivado, Mr. Dougherty and Dr. Vukovic, respectively. Each of the options vest in equal monthly installments over four years from April 15, 2019. In addition, in April 2019, our board of directors also granted Dr. Vukovic options to purchase 67,000 shares of common stock that vest upon the achievement of certain performance-based milestones in connection with our clinical trials.

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Employment Agreements

Manuel C. Alves Aivado, M.D., Ph.D.

In September 2018, in connection with our appointment of Dr. Aivado as our president and chief executive officer, we entered into a new employment agreement with Dr. Aivado, which superseded his July 2014 employment agreement with us. Pursuant to the terms of Dr. Aivado’s new employment agreement, we agreed to pay Dr. Aivado a base salary at a rate of $41,666.67 per month, which was based on an annualized base salary of $500,000. Beginning in 2019, following the end of each calendar year that Dr. Aivado is employed by us, Dr. Aivado will be eligible to receive a discretionary performance target bonus of up to 50% of his then annual base salary based on the achievement of performance milestones set by either our board of directors or the compensation committee of the board. The new employment agreement also provided that following the end of the 2018 calendar year, Dr. Aivado was eligible to receive a discretionary performance target bonus calculated on the basis of 35% of his base salary as of August 31, 2018 pro-rated for the first eight months of the fiscal year, and 50% of his current base salary under the new employment agreement pro-rated for the remaining four months of the fiscal year. The amount of such bonus and the achievement of such milestones were determined by our board in its sole discretion. Dr. Aivado is also entitled to receive reimbursement of up to $4,000 per month for travel and living accommodations pursuant to the new employment agreement. Dr. Aivado’s employment is at will.

Pursuant to the new employment agreement, we granted Dr. Aivado options to purchase 232,914 shares of our common stock under our 2017 Stock Incentive Plan. The options have an exercise price of $3.39, which was the closing price of our common stock on September 6, 2018. The options vest in equal monthly installments over four years from September 6, 2018.

We and Dr. Aivado had previously entered into an employment agreement in July 2014 in connection with our appointment of Dr. Aivado as our senior vice president, chief medical officer, which was superseded by the new employment agreement described above. The July 2014 employment agreement established Dr. Aivado’s then title, base salary, eligibility for an annual bonus, and eligibility for benefits made available to employees generally, and also provided for certain benefits upon termination of his employment under specified conditions. Pursuant to the terms of the July 2014 employment agreement, Dr. Aivado was entitled to receive a one-time transition bonus of $50,000, payable within thirty days of his commencement of employment, reimbursement of up to $3,750 per month for travel and living accommodations in order to commute to and live in the Boston area

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and options to purchase 125,792 shares of our common stock. We granted Dr. Aivado additional options to purchase shares of our common stock in March 2017, July 2017 and September 2018, as described in greater detail under “Outstanding Equity Awards at Fiscal Year End 2018” above.

Under the terms of the July 2014 employment agreement, if Dr. Aivado’s employment was terminated by us without cause or by Dr. Aivado for good reason, each as defined in his employment agreement, and subject to Dr. Aivado’s execution of a general release of potential claims against us, we would have continued to pay his then-current base salary for a period of 12 months and premiums for continuation health coverage under COBRA for up to 12 months. In addition, if Dr. Aivado’s employment was terminated by us without cause or by Dr. Aivado for good reason within one year following a change of control, as defined in the stock option agreement evidencing the options granted to Dr. Aivado in March 2015 and March 2017, these options will accelerate in full.

In connection with his appointment as our president and chief executive officer, in September 2018, we entered into a severance agreement with Dr. Aivado. Upon the execution of the severance agreement, Dr. Aivado ceased to be entitled to the severance and post-employment payments and benefits provided for in his July 2014 employment agreement. The terms of Dr. Aivado’s severance agreement are described below under “—Severance and Change in Control Agreements.”

Donald V. Dougherty

In June 2017, in connection with our appointment of Mr. Dougherty as our senior vice president, chief financial officer, we entered into an employment agreement with Mr. Dougherty. The employment agreement establishes Mr. Dougherty’s title, his base salary, his eligibility for an annual bonus, and his eligibility for benefits made available to employees generally and also provides for certain benefits upon termination of his employment under specified conditions. Mr. Dougherty was also entitled to receive a one-time transition bonus of $25,000, payable within 90 days of his commencement of employment. Mr. Dougherty’s employment is at will. We agreed to grant Mr. Dougherty options to purchase 140,887 shares of our common stock, which are subject to service-based vesting at an exercise price equal to the initial public offering price of $15.00 per share.

Mr. Dougherty’s employment agreement also provided that if Mr. Dougherty’s employment was terminated by us without cause or by Mr. Dougherty for good reason, each as defined in the employment agreement, and subject to Mr. Dougherty’s execution of a general release of potential claims against us, (i) we would have continued to pay his then-current base salary for a period of six months and premiums for continuation health coverage under COBRA for up to six months, and (ii) 25% of the shares granted to Mr. Dougherty in June 2017 will vest immediately upon termination of his employment.

In October 2018, we entered into a severance agreement with Mr. Dougherty, which modified and replaced the severance and post-employment payments set forth in his June 2017 employment agreement. The terms of Mr. Dougherty’s severance agreement are described below under “—Severance and Change in Control Agreements.”

Vojislav Vukovic, M.D., Ph.D.

In November 2018, we entered into an employment offer letter with Vojislav Vukovic, M.D., Ph.D. pursuant to which Dr. Vukovic agreed to serve as our senior vice president, chief medical officer. The offer letter establishes Dr. Vukovic’s title, his base salary, his eligibility for an annual bonus, and his eligibility for benefits made available to employees generally. Dr. Vukovic’s employment is at will. We agreed to grant Dr. Vukovic options to purchase 150,000 shares of our common stock, which are subject to service-based vesting, at an exercise price equal to $2.16, which was the fair market value of one share of our common stock on the date of grant. Dr. Vukovic’s employment is at will.

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John P. Longenecker, Ph.D.

In May 2018, following Joseph A. Yanchik III’s resignation as our president and chief executive officer and as a member of our board, we appointed John P. Longenecker, Ph.D., as our interim president and chief executive officer, to serve while we conducted a search for a new chief executive officer. In connection with his appointment, we entered into an employment agreement with Dr. Longenecker in May 2018. Pursuant to the employment agreement, we paid Dr. Longenecker a base salary at a rate of $43,558.33 per month, which is based on an annualized base salary of $522,700. The terms of the employment agreement provided that. following the end of each calendar year that Dr. Longenecker was employed by us or following the termination of his employment upon the hiring of a new chief executive officer, Dr. Longenecker was eligible to receive a discretionary performance bonus of up to 50% of his annual base salary based on the achievement of performance milestones set by either our board or the compensation committee of the board. The amount of such bonus and the achievement of such milestones were determined by the Board in its sole discretion. The employment agreement also provided that Dr. Longenecker would receive reimbursement for reasonable expenses incurred in connection with travel to and working in Massachusetts.

Pursuant to the Employment Agreement, we granted Dr. Longenecker options to purchase 30,000 shares of our common stock. The options have an exercise price equal to $5.50, the closing price of the common stock on May 15, 2018. The options vested in full in September 2018 in accordance with the terms of the employment agreement.

In September 2018, Dr. Aivado was named our new president and chief executive officer, and Dr. Longenecker’s employment with us ended. On September 30, 2018, we entered into a consulting agreement with Dr. Longenecker, pursuant to which Dr. Longenecker agreed to provide us with certain advisory services for up to 4 days per calendar month, unless otherwise agreed by Dr. Longenecker and us. Pursuant to the terms of the consulting agreement, we agreed to pay Dr. Longenecker a consulting fee of $12,000 per month, and to reimburse Dr. Longenecker for any reasonable and necessary documented expenses he incurs in the performance of his consulting services. The initial term of the consulting agreement continued until December 2018. Prior to the expiration of the initial term, we and Dr. Longenecker agreed to extend the term until June 30, 2019. Either we or Dr. Longenecker can terminate the consulting agreement at any time upon not less than fifteen days prior written notice to the other party, or immediately upon mutual written consent of both parties. In addition, if a party materially breaches the consulting agreement, the non-breaching party may terminate the agreement upon 24 hours prior written notice to the breaching party.

Joseph A. Yanchik III

In connection with Mr. Yanchik’s resignation as our president and chief executive officer in May 2018, we entered into a separation and release of claims agreement with Mr. Yanchik. The separation agreement provides for the terms of Mr. Yanchik’s separation from employment with us, including his resignation from his positions as president and chief executive officer and as a member of our board of directors.

Pursuant to the terms of the separation agreement, we agreed to provide Mr. Yanchik with the following separation payments and benefits consistent with his employment agreement: (i) salary continuation payments, in equal installments in accordance with our regular payroll practices, in an aggregate amount equal to one year of Mr. Yanchik’s base salary, for 12 months following the effective date of the separation agreement; (ii) payment on Mr. Yanchik’s behalf of the monthly premiums for group health and/or dental insurance coverage under COBRA until the earlier of the date that is 12 months after the effective date of the separation agreement or the date on which Mr. Yanchik becomes eligible to receive group health insurance coverage through another employer; (iii) accelerated vesting by six months of all stock options held by Mr. Yanchik; (iv) an extension of the exercise period of all of Mr. Yanchik’s outstanding options for 24 months following Mr. Yanchik’s resignation, and (v) eligibility for a performance-based bonus of up to $87,166 based on our achievement of previously-agreed performance milestones for 2018, as determined by our board of directors in its sole

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discretion. In addition, the separation agreement contains mutual releases, subject to customary exceptions, and covenants not to solicit or disparage and to cooperate with us.

We had previously entered into an employment agreement with Mr. Yanchik in March 2008, as subsequently amended in December 2008. The employment agreement established Mr. Yanchik’s title, his base salary, his eligibility for an annual bonus, and his eligibility for benefits made available to employees generally and also provided for certain benefits upon termination of his employment under specified conditions. Prior to Mr. Yanchik’s resignation, our board of directors had determined that Mr. Yanchik was eligible to receive an annual bonus of up to 50% of his base salary. Under the terms of the employment agreement, if Mr. Yanchik’s employment was terminated by us without cause or by Mr. Yanchik for good reason, each as defined in his employment agreement, and subject to Mr. Yanchik’s execution of a general release of potential claims against us, we agreed to continue to pay his then-current base salary for a period of 12 months, premiums for continuation health coverage under COBRA for up to 12 months, and a performance-based bonus pro-rated based on Mr. Yanchik’s target bonus percentage and his achievement of certain milestones agreed upon by him and us for the calendar year in which his employment was terminated, as determined by our board of directors in its sole discretion, and to accelerate vesting by six months of any restricted stock or stock options held by Mr. Yanchik. The employment agreement also provided that if Mr. Yanchik’s employment were terminated by us without cause or by Mr. Yanchik for good reason within one year following a change of control, as defined in the stock option agreement evidencing the options granted to Mr. Yanchik in June 2015 and March 2017, these options would have accelerated in full.

Severance and Change in Control Agreements

We have entered into severance agreements with each of our executive officers, including Dr. Aivado, Mr. Dougherty and Dr. Vukovic. Under the terms of each severance agreement, if we terminate the executive officer’s employment other than for cause or by reason of death or disability, or if such executive officer terminates his employment for good reason and, in each case, not upon or within twelve months of a change in control event, as such terms are defined in the severance agreements, such executive officer will be entitled to receive (A) his then current base salary for nine months, or, in the case of Dr. Aivado, 12 months, following the date of the executive officer’s termination and (B) payments on such executive officer’s behalf of the monthly premiums for medical insurance coverage under COBRA until the earlier of the date that is nine months, or, in the case of Dr. Aivado, 12 months, following the date of such executive officer’s termination or the date on which such executive officer becomes eligible to receive group health insurance coverage through another employer, which we refer to collectively as the standard severance benefits. If we terminate the executive officer’s employment other than for cause or by reason of death or disability, of the executive terminates his employment for good reason, in each case upon or within 12 months after a change in control event, the executive will be entitled to receive the standard severance benefits for a period of twelve months, or, in the case of Dr. Aivado, 18 months, following the date of the executive officer’s termination and a lump sum payment equal to one times, or, in the case of Dr. Aivado, one and one-half times, the executive’s target bonus for the year in which the executive officer is terminated, and the vesting of any unvested equity awards will accelerate in full on the date of the executive officer’s termination. Each executive officer’s receipt of any post-separation benefits under the severance agreement are conditioned upon his execution of a severance and release of claims agreement in a form satisfactory to us. With respect to Dr. Aivado and Mr. Dougherty, upon the execution of their respective severance agreement, each such executive ceased to be entitled to the severance and post-employment payments and benefits provided under any preexisting agreements between us and such executive officer.

Other Agreements

We have also entered into employee confidentiality, inventions, non-solicitation and non-competition agreements with each of our named executive officers. Under the employee confidentiality, inventions, non-solicitation and non-competition agreements, each named executive officer has agreed (1) not to compete with us during his

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employment and for a period of one year after the termination of his employment, (2) not to solicit our employees during his employment and for a period of two years after the termination of his employment, (3) to protect our confidential and proprietary information and (4) to assign to us related intellectual property developed during the course of his employment.

401(k) Retirement Plan

We maintain a 401(k) retirement plan that is intended to be a tax-qualified defined contribution plan under Section 401(k) of the Internal Revenue Code. In general, all of our employees are eligible to participate, beginning on the first day of the month following commencement of their employment. The 401(k) plan includes a salary deferral arrangement pursuant to which participants may elect to reduce their current compensation by up to the statutorily prescribed limit, equal to $18,000 in 2017, and have the amount of the reduction contributed to the 401(k) plan. Participants over the age of 50 are entitled to an additional catch-up contribution up to the statutorily prescribed limit, equal to $6,000 in 2017. Currently, we do not match employee contributions.

Limitations on Liability and Indemnification

As permitted by Delaware law, we adopted provisions in our certificate of incorporation that limit or eliminate the personal liability of our directors. Our certificate of incorporation limits the personal liability of directors for breach of fiduciary duty to the maximum extent permitted by the General Corporation Law of the State of Delaware and provides that no director will have personal liability to us or to our stockholders for monetary damages for breach of fiduciary duty. However, these provisions do not eliminate or limit the liability of any of our directors:

Any amendment to or repeal of these provisions will not eliminate or reduce the effect of these provisions in respect of any act, omission or claim that occurred or arose prior to such amendment or repeal. If the General Corporation Law of the State of Delaware is amended to provide for further limitations on the personal liability of directors of corporations, then the personal liability of our directors will be further limited to the greatest extent permitted by the General Corporation Law of the State of Delaware.

In addition, our certificate of incorporation provides that we must indemnify our directors and officers and we must advance expenses, including attorneys’ fees, to our directors and officers in connection with legal proceedings, subject to very limited exceptions.

We maintain a general liability insurance policy that covers specified liabilities of our directors and officers arising out of claims based on acts or omissions in their capacities as directors or officers. In addition, we entered into indemnification agreements with each of our officers and directors. These indemnification agreements require us, among other things, to indemnify each such director or officer for some expenses, including attorneys’ fees, judgments, fines and settlement amounts, incurred by him or her in any action or proceeding arising out of his or her service as one of our directors or officers.

Some of our non-employee directors may, through their relationships with their employers, be insured or indemnified against specified liabilities incurred in their capacities as members of our board of directors.

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Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors, executive officers or persons controlling us, in the opinion of the SEC, such indemnification is against public policy as expressed in the Securities Act and is therefore unenforceable.

Director Compensation

Our board of directors approved a director compensation program that became effective at the closing of our IPO in July 2017. Under this program, we pay our non-employee directors a cash retainer for service on the board of directors and for service on each committee on which the director is a member. The chair of each committee and the chair of the board of directors receive higher retainers for such service. These fees are payable in arrears in four equal quarterly installments on the last day of each quarter, subject to proration for any portion of such quarter that the director is not serving on our board of directors, on such committee or in such position. The fees paid to non-employee directors for service on the board of directors and for service on each committee of the board of directors on which the director is a member are as follows:

In November 2018, our board of directors modified our director compensation program to provide that Dr. Ambros would receive an additional annual fee of $20,000, effective as of March 21, 2018, for his services as our lead director.

In addition, under this director compensation program, we granted the directors who were in office at the time of the closing of our IPO, and agreed to grant to new non-employee directors upon their initial election to the board, an initial option to purchase 20,000 shares of our common stock, with an exercise price equivalent to fair market value of a share of common stock at the time of grant, which option will vest in equal annual installments over three years from the director’s initial election, subject to continued service, with full acceleration upon a change in control of our company. The option will have a term of 10 years.

Immediately following each annual meeting of our stockholders, we would grant to each director who has served on our board of directors for at least six months an option to purchase 10,000 shares of our common stock, with an exercise price equivalent to fair market value of a share of common stock at the time of grant, which option will vest in full on the earlier of the first anniversary of the date of grant and the date of the next annual meeting of stockholders, subject to continued service, with full acceleration upon a change in control of our company. The option will have a term of 10 years.

In April 2019, we modified the equity awards that non-employee directors are entitled to receive under the director compensation program. Under the director compensation program as modified, we will grant to new non-employee directors upon their initial election to the board, an initial option to purchase 25,000 shares of our common stock and, immediately following each annual meeting of our stockholders, beginning with the 2020 annual meeting of stockholders, we will grant to each director who has served on our board of directors for at least six months an option to purchase 12,500 shares of our common stock, in each case, with an exercise price equivalent to fair market value of a share of common stock at the time of grant. We did not modify the vesting or other terms of any of the equity awards our non-employee directors are entitled to receive under the director compensation program.

In connection with our decision to modify the equity awards under the director compensation program, the board of directors also determined that, immediately following the 2019 annual meeting of stockholders, in lieu of the

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option grants contemplated by the director compensation program, each non-employee director who has served on our board of directors for at least six months will receive an option to purchase 25,000 shares of our common stock, the chair of the board and lead director will receive an additional option to purchase 25,000 shares of our common stock and Dr. Sigal will receive an option to purchase 5,000 shares of our common stock. Each of the options granted immediately following the 2019 annual meeting of stockholders will have an exercise price equivalent to fair market value of a share of common stock at the time of grant and, except for the option that will be granted to Dr. Sigal, will vest in full on the earlier of the first anniversary of the date of grant and the date of the next annual meeting of stockholders, subject to continued service, with full acceleration upon a change in control of our company. The option granted to Dr. Sigal will vest in equal annual installments over three years from April 2, 2019, subject to continued service, with full acceleration upon a change in control of our company. Each option will have a term of 10 years.

We also reimburse our non-employee directors for reasonable travel and out-of-pocket expenses incurred in connection with attending our board of directors and committee meetings.

We do not pay any compensation to our president and chief executive officer in connection with his service on our board of directors. The compensation that we pay to our president and chief executive officer is discussed earlier in this “Executive Compensation” section.

The following table sets forth information regarding compensation earned by our non-employee directors for service during fiscal 2018.

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As of December 31, 2018, our non-employee directors that served in such capacity during fiscal 2018 held the following stock options, all of which were granted under our 2006 Equity Incentive Plan, as amended, or 2006 Plan, and our 2017 Stock Incentive Plan, or 2017 Plan:

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SECURITIES AUTHORIZED FOR ISSUANCE UNDER EQUITY COMPENSATION PLANS

The following table contains information about our equity compensation plans as of December 31, 2018. As of December 31, 2018, we had four equity compensation plans, each of which was approved by our stockholders: our 2006 Plan, our 2016 Plan, our 2017 Plan and our 2017 Employee Stock Purchase Plan, or 2017 ESPP.

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STOCK OWNERSHIP AND REPORTING

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Section 16(a) Beneficial Ownership Reporting Compliance

Section 16(a) of the Exchange Act requires our directors and officers and holders of more than 10% of our common stock to file with the SEC initial reports of ownership of our common stock and other equity securities on a Form 3 and reports of changes in such ownership on a Form 4 or Form 5. Directors and officers and holders of 10% of our common stock are required by SEC regulations to furnish us with copies of all Section 16(a) forms they file. To our knowledge, based solely on a review of our records and representations made by our directors and officers regarding their filing obligations, all Section 16(a) filing requirements were satisfied with respect to fiscal 2018.

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TRANSACTIONS WITH RELATED PERSONS

Since January 1, 2018, we have engaged in the following transactions in which the amount involved exceeded $120,000 and any of our executive officers, directors, director nominees or beneficial holders of more than 5% of any class of voting securities, or any of their affiliates, had a direct or indirect material interest. We believe that all of these transactions were on terms comparable to terms that could have been obtained from unrelated third parties.

Investors’ Rights Agreement

We are a party to an investor rights agreement, dated as of December 23, 2016, with certain stockholders who held our preferred stock prior to our IPO, including some of our directors and 5% stockholders and their affiliates and entities affiliated with our directors. The investor rights agreement provides these holders the right to demand that we file a registration statement or request that their shares be covered by a registration statement that we are otherwise filing.

April 2019 Private Placement

On March 28, 2019, we entered into a definitive agreement with respect to the private placement of (i) 11,838,582 units, consisting of 11,838,582 shares of our common stock and associated warrants, which we refer to as common warrants, to purchase an aggregate of 11,838,582 shares of common stock, which we collectively refer to as the common units, and (ii) 1,096,741 units, consisting of pre-funded warrants to purchase 1,096,741 shares of our common stock and associated common warrants to purchase 1,096,741 shares of our common stock, which we refer to collectively as the pre-funded warrant units, to a group of accredited investors. These investors paid $2.01 per common unit and $2.01 per pre-funded warrant unit. The pre-funded warrants are exercisable at an exercise price of $0.01 per share and have no expiration. The common warrants are exercisable at an exercise price of $2.00 per share and expire five years from the date of issuance. We completed this private placement on April 2, 2019, resulting in approximately $26.0 million in gross proceeds to us. The number of shares that each of our directors, executive officers and holders of more than 5% of our voting securities purchased and the aggregate purchase price paid for such shares is set forth in the table below.

Indemnification Agreements

Our certificate of incorporation provides that we will indemnify our directors and officers to the fullest extent permitted by Delaware law. In addition, we have entered into indemnification agreements with each of our

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officers and directors that may be broader in scope than the specific indemnification provisions contained in the Delaware General Corporation Law. See “Executive Compensation—Limitations on Liability and Indemnification” for additional information regarding these agreements.

Policies and Procedures for Related Person Transactions

Our board of directors has adopted a written related person transaction policy to set forth policies and procedures for the review of any transaction, arrangement or relationship in which we are a participant, the amount involved exceeds $120,000 and one of our executive officers, directors, director nominees or 5% stockholders, or their immediate family members, each of whom we refer to as a “related person,” has a direct or indirect material interest.

If a related person proposes to enter into such a transaction, arrangement or relationship, which we refer to as a “related person transaction,” the related person must report the proposed related person transaction to our chief executive officer or our chief financial officer. The policy calls for the proposed related person transaction to be reviewed and approved by our audit committee. Whenever practicable, the reporting, review and approval will occur prior to entry into the transaction. If advance review and approval is not practicable, the committee will review, and, in its discretion, may ratify the related person transaction. The policy also permits the chair of the audit committee to review and, if deemed appropriate, approve proposed related person transactions that arise between committee meetings, subject to ratification by the committee at its next meeting. Any related person transactions that are ongoing in nature will be reviewed annually.

A related person transaction reviewed under the policy will be considered approved or ratified if it is authorized by the audit committee after full disclosure of the related person’s interest in the transaction. As appropriate for the circumstances, the committee will review and consider:

The audit committee may approve or ratify the transaction only if the committee determines that, under all of the circumstances, the transaction is in our best interests. The committee may impose any conditions on the related person transaction that it deems appropriate.

In addition to the transactions that are excluded by the instructions to the SEC’s related-person transaction disclosure rule, our board of directors has determined that the following transactions do not create a material direct or indirect interest on behalf of related persons and, therefore, are not related-person transactions for purposes of this policy:

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The policy provides that transactions involving compensation of executive officers shall be reviewed and approved by the compensation committee in the manner specified in its charter.

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AILERON VOTE 000004 ENDORSEMENT_LINE SACKPACK MR A SAMPLE DESIGNATION (IF ANY) ADD 1 ADD 2 ADD 3 ADD 4 ADD 5 ADD 6 Using a black ink pen, mark your votes with an X as shown in this example. Please do not write outside the designated areas.    C123456789 000000000.000000 ext 000000000.000000 ext 000000000.000000 ext 000000000.000000 ext 000000000.000000 ext 000000000.000000 ext Your vote matters – here’s how to vote! You may vote online or by phone instead of mailing this card. Votes submitted electronically must be received by 11:59 p.m. , (Eastern Time), on June 18, 2019. Online Go to www.envisionreports.com/ALRN or scan the QR code — login details are located in the shaded bar below. Phone Call toll free 1-800-652-VOTE (8683) within the USA, US territories and Canada Save paper, time and money! Sign up for electronic delivery at www.envisionreports.com/ALRN 2019 Annual Meeting Proxy Card 1234 5678 9012 345 qIF VOTING BY MAIL, SIGN, DETACH AND RETURN THE BOTTOM PORTION IN THE ENCLOSED ENVELOPE. q    A Proposals — The Board of Directors recommend a vote FOR all the nominees listed and FOR Proposal 2. 1. Election of one Class II Director: 01—Nolan Sigal, M.D., Ph.D. Mark here to vote FOR all nominees Mark here to WITHHOLD vote from all nominees 01 For All EXCEPT—To withhold a vote for one or more nominees, mark the box to the left and the corresponding numbered box(es) to the right. For Against Abstain 2. Ratification of the appointment of PricewaterhouseCoopers LLP as Aileron’s independent registered public accounting firm for the fiscal year ending December 31, 2019.    B Authorized Signatures — This section must be completed for your vote to count. Please date and sign below. Please sign exactly as name(s) appears hereon. Joint owners should each sign. When signing as attorney, executor, administrator, corporate officer, trustee, guardian, or custodian, please give full title. Date (mm/dd/yyyy) — Please print date below. Signature 1 — Please keep signature within the box. Signature 2 — Please keep signature within the box.    C 1234567890                J N T MR A SAMPLE (THIS AREA IS SET UP TO ACCOMMODATE 140 CHARACTERS) MR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE AND 1UPX 416950 MR A SAMPLE AND MR A SAMPLE AND MR A SAMPLE AND + 032BTB                

Small steps make an impact. Help the environment by consenting to receive electronic delivery, sign up at www.envisionreports.com/ALRN qIF VOTING BY MAIL, SIGN, DETACH AND RETURN THE BOTTOM PORTION IN THE ENCLOSED ENVELOPE. q Proxy—Aileron Therapeutics, Inc. + Notice of 2019 Annual Meeting of Stockholders Wilmer Cutler Pickering Hale and Dorr LLP, 60 State Street, Boston, MA 02109 Proxy Solicited by Board of Directors for Annual Meeting — June 19, 2019 Manuel C. Aivado, M.D., Ph.D. and Donald V. Dougherty, or any of them, each with the power of substitution, are hereby authorized to represent and vote the shares of the undersigned, with all the powers which the undersigned would possess if personally present, at the Annual Meeting of Stockholders of Aileron Therapeutics, Inc. to be held on June 19, 2019 or at any postponement or adjournment thereof. This Proxy, when properly executed, will be voted as directed. If no direction is given, the Proxies will have authority to vote FOR Proposal 1 “Election of one Class II Director”, and FOR Proposal 2 “Ratification of the appointment of PricewaterhouseCoopers LLP as Aileron’s independent registered public accounting firm for the fiscal year ending December 31, 2019”. In their discretion, the Proxies are authorized to vote upon such other business as may properly come before the Annual Meeting. Attendance of the undersigned at the Annual Meeting or at any adjournment thereof will not be deemed to revoke this Proxy unless the undersigned revokes this Proxy in writing. Unless voting by the internet or telephone, please complete, sign and date this proxy card and return it in the enclosed postage-prepaid envelope. (Items to be voted appear on reverse side) C Non-Voting Items Change of Address — Please print new address below. Comments — Please print your comments below.