You should read the following management's discussion and analysis of financial condition and results of operations in conjunction with our unaudited condensed consolidated financial statements and notes thereto included in Part I, Item 1 of this report and with our audited financial statements and related notes thereto and Management's Discussion and Analysis of Financial Condition and Results of Operations included in our Annual Report on Form 10-K, filed with the Securities and Exchange Commission, or the SEC, on March 28, 2022.

Special Note Regarding Forward-Looking Statements

This report contains forward-looking statements that are based on our management's beliefs and assumptions and on information currently available to our management. This section should be read in conjunction with our unaudited condensed consolidated financial statements and related notes included in Part I, Item 1 of this report. The statements contained in this report that are not purely historical are forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended.

In some cases, you can identify forward-looking statements by the following words: "anticipate," "believe," "continue," "could," "estimate," "expect," "intend," "may," "ongoing," "plan," "potential," "predict," "project," "should," "target", "will," "would" or the negative of these terms or other comparable terminology, although not all forward-looking statements contain these words. You should read these statements carefully because they discuss future expectations, contain projections of future results of operations or financial condition, or state other "forward-looking" information. These statements relate to our future plans, objectives, expectations, intentions and financial performance and the assumptions that underlie these statements. These forward-looking statements include, but are not limited to, statements about:

our financial performance;

the sufficiency of our existing cash, cash equivalents and investments to fund our future operating expenses and capital expenditure requirements;

our ability to obtain funding for our operations, including funding necessary to develop and commercialize our product candidates;

the ability of our nonclinical studies and clinical trials to demonstrate safety and efficacy of our product candidates;

the success, cost and timing of our development activities, nonclinical studies and clinical trials;

the rate and degree of market acceptance of our product candidates;

the timing or likelihood of regulatory filings and approvals;

the potential learnings from our ACT-AD trial and LIFT-AD unblinded interim efficacy and futility analysis and their ability to inform and improve future clinical development plans;

the potential of LIFT-AD to show clinical benefits of fosgonimeton following the October 2022 protocol amendment;

the timing and focus of our future clinical trials, and the reporting of data from those trials;

our plans relating to commercializing our product candidates, if approved;

our plans and ability to establish sales, marketing and distribution infrastructure to commercialize any product candidates for which we obtain approval;

our ability to attract and retain key managerial, scientific and clinical personnel;

our ability to contract with third-party suppliers and manufacturers and their ability to perform adequately;

the accuracy of our estimates regarding expenses, future revenue, capital requirements and needs for additional financing;

the pricing and reimbursement of our product candidates, if approved;

our reliance on third parties to conduct clinical trials of our product candidates, and for the manufacture of our product candidates for nonclinical studies and clinical trials;



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our ability to expand our product candidates into additional indications and patient populations;

the success of competing therapies that are or may become available;

the beneficial characteristics, safety and efficacy of our product candidates;

regulatory developments in the United States and other jurisdictions;

our ability to obtain and maintain regulatory approval of our product candidates in the United States and other jurisdictions, and any related restrictions, limitations and/or warnings in the label of any approved product candidate;

future agreements with third parties in connection with the commercialization of our product candidates;

our plans relating to the further development and manufacturing of our product candidates, including additional indications for which we may pursue regulatory approval;

our plans and ability to obtain or protect intellectual property rights, including extensions of existing patent terms where available;

the scope of protection we are able to establish and maintain for intellectual property rights covering our product candidates and technology;

the outcome of legal proceedings which have been or may in the future be instituted against us and certain of our directors and officers, including the legal proceedings discussed in Part II, Item 1 - "Legal Proceedings," and elsewhere in this report;

the actions by activist stockholders, which have in the past been, and may in the future be, disruptive and could cause uncertainty about the strategic direction of our business;

our expectations regarding the continuing impact of COVID-19 on our business;

the size and growth potential of the markets for our product candidates, if approved for commercial use, and our ability to serve those markets;

the potential benefits of any strategic collaboration agreements we may enter into; and

our expectations regarding the time during which we will be an emerging growth company under the JOBS Act.

These forward-looking statements are subject to certain risks and uncertainties that could cause actual results to differ materially from those anticipated in the forward-looking statements. Factors that might cause such a difference include, but are not limited to, those discussed in this report in "Part II, Item 1A-Risk Factors," and elsewhere in this report. These statements, like all statements in this report, speak only as of their date, and we undertake no obligation to update or revise these statements in light of future developments. Our Risk Factors are not guarantees that no such conditions exist as of the date of this report and should not be interpreted as an affirmative statement that such risks or conditions have not materialized, in whole or in part.

In addition, statements that "we believe" and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this report, and although we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted a thorough inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and you are cautioned not to unduly rely upon these statements.

This report includes our trademarks and registered trademarks, including Athira, Athira Pharma, the Athira logo, and other trademarks or service marks of Athira. Each other trademark, trade name or service mark appearing in this report belongs to its holder.

In this report, "we," "our," "us," "Athira," and "the Company" refer to Athira Pharma, Inc.

Overview

We are a late clinical-stage biopharmaceutical company focused on developing small molecules to restore neuronal health and slow neurodegeneration. With our product candidates, we aim to provide rapid cognitive improvement and alter



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the course of neurological diseases, leveraging our novel mechanism of action. Our approach is designed to augment neuronal growth factor signaling through the hepatocyte growth factor/MET, or HGF/MET, a naturally occurring, repair and regenerative system. We believe enhancing HGF/MET signaling has the potential to protect existing neurons from damage, reduce inflammation, promote regeneration, and benefit brain physiology. We anticipate that all of these characteristics may improve neuronal health and translate into clinical benefits. Our pipeline is built from our proprietary drug discovery platform, or ATH platform, and consists of a series of small molecules that are designed to target either (1) the central nervous system, or CNS, by crossing the blood brain barrier, or BBB, or (2) the peripheral nervous system.

Our lead candidate, fosgonimeton ("ATH-1017"), is a subcutaneously administered, BBB-penetrating, small molecule HGF/MET positive modulator. The effects of fosgonimeton in its primary target indication, Alzheimer's disease ("AD"), are being evaluated in two clinical trials:

ACT-AD, a randomized, double-blind, placebo-controlled, parallel-group 26-week proof-of-concept Phase 2 clinical trial in mild-to-moderate AD, with ERP P300 latency as the primary endpoint. Initiated in November 2020, the trial was designed to better characterize the overall effects of fosgonimeton on working memory processing speed and cognitive measures and inform the Phase 2/3 LIFT-AD trial. Topline results for this proof-of-concept Phase 2 ACT-AD trial were announced in June 2022, and the primary endpoint was not met by protocoled analysis. However, a pre-specified subgroup analysis indicated a potential diminished effect of fosgonimeton when given in combination with add-on standard-of-care acetylcholinesterase inhibitors (AChEIs, e.g., donepezil). A subsequent post hoc analysis of the data from patients on fosgonimeton without background therapy (AChEIs) showed a meaningful, but not statistically significant, improvement in both ERP P300 latency (-28 milliseconds) and cognitive performance (ADAS-Cog11: -3.3 points) compared to placebo at 26 weeks. Although post-hoc analyses cannot be used to establish efficacy, these analyses can be helpful in informing the design of current and future clinical studies. In addition, while also not statistically significant, the data from the protocoled study population and analysis method showed a numerical improvement in the functional measure of ADCS-ADL23, a protocoled secondary endpoint which evaluates improvements in patients' activities of daily living as assessed by their caregivers compared to placebo at 26 weeks (+2.12 points). A pre-specified subgroup analysis of plasma biomarker data showed a statistically significant reduction in neurofilament light chain (NfL), a validated biomarker of neurodegeneration, in subjects treated with fosgonimeton without background therapy compared to placebo at 26 weeks (difference of 6.89 pg/ml (p=0.018)). Fosgonimeton was generally well tolerated in the ACT-AD study, with a favorable safety profile, and there were no treatment related serious adverse events or deaths observed.

LIFT-AD, a randomized, double-blind, placebo-controlled, parallel-group 26-week Phase 2/3 clinical trial with fosgonimeton for the treatment of mild-to-moderate AD. In September 2020, we began site initiation and patient screening for LIFT-AD. The primary endpoint for the Phase 2/3 LIFT-AD trial will be measured by the Global Statistical Test, which is a mathematical algorithm that combines the scores from cognition (Alzheimer's Disease Assessment Scale-Cognitive Subscale or ADAS-Cog11), and function (Alzheimer's Disease Cooperative Study-Activities of Daily Living or ADCS-ADL23). Guided by the results from the completed exploratory ACT-AD Phase 2 study, in September 2022, we proactively amended LIFT-AD to focus on patients not on background therapy. In October 2022, we announced that following an unblinded interim efficacy and futility analysis, an independent data monitoring committee recommended continuation of the LIFT-AD study. The committee also determined that, with the additional enrollment of fewer than 150 patients for a total enrollment of less than 300 patients without background therapy (AChEIs), the amended study will be well powered for the primary endpoint given the preliminary effect size observed. We are targeting to complete enrollment in mid-2023 and report topline data in early 2024.

In July 2021, we announced that we are enrolling patients into a 26-week open-label extension study for our LIFT-AD and ACT-AD clinical trials, which will allow us to collect up to a total of one year of safety data with fosgonimeton. In May 2022, we announced that we are extending the 26-week open-label extension study for our LIFT-AD and ACT-AD clinical



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trials for an additional 12 months, enabling eligible patients who have completed either trial, and elect to participate in the ongoing open label extension, to now receive up to 18 months of open-label treatment with fosgonimeton.

The following figure illustrates the current development stage of our ATH compounds and discovery and development programs. In addition, we are expanding our ATH platform to additional indications in the CNS and peripheral nervous system as we aim to improve neuronal health in multiple disorders. Our drug discovery efforts are focused on exploring the potential of ATH technology, which is designed to promote HGF/MET activity for a variety of clinical applications.



                     [[Image Removed: img104323173_0.jpg]]

We constantly strive to grow and optimize our portfolio through in-house discovery and plan on additional external business development activities enabled by our innovative internal research and development capabilities.

We were incorporated in March 2011 and since our inception, we have devoted substantially all of our resources to our research and development efforts such as small molecule compound discovery, nonclinical studies and clinical trials, as well as manufacturing activities, establishing and maintaining our intellectual property portfolio, hiring personnel, raising capital, and providing general and administrative support for these operations. We do not have any products approved for commercial sale, and we have not generated any revenues related to our products since inception. Our ability to generate product revenue sufficient to achieve profitability, if ever, will depend on the successful development of one or more of our product candidates which we expect will take a number of years.

We are focused on the development of small molecule therapeutics which enables us to use well-established and widely available manufacturing processes and infrastructure, formulation compositions and drug administration technologies or devices. We do not currently operate our own facilities for manufacturing, storing, or distributing our product candidates. We utilize third-party contract manufacturing organizations, or CMOs, to manufacture and supply our preclinical and clinical materials during the development of our product candidates. We believe the synthesis of fosgonimeton is reliable and reproducible and the synthetic methods can be further optimized to enable large-scale production that continues to avoid use of toxic materials or specialized equipment or handling during the manufacturing process. We plan to continue to optimize the manufacturing process to support future large-scale and commercial supply. Our goal is to identify and develop small molecule product candidates that are cost-effective to manufacture and easily transferable to third party CMOs. We expect to use similar contract resources for commercialization of our products, at least until our resources and operations are at a scale that justifies investment in internal manufacturing capabilities.

Given our stage of development, we have not yet established a commercial organization or distribution capabilities. We intend to build a commercial infrastructure to support sales of our product candidates. We expect to manage sales, marketing and distribution through internal resources and third-party relationships. While we may commit significant financial and management resources to commercial activities, we will also consider collaborating with one or more pharmaceutical companies to enhance our commercial capabilities.



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To date, we have funded our operations primarily through proceeds from the sale of equity securities, including proceeds from the sale and issuance of common stock in our IPO and in a subsequent follow-on public offering, the sale and issuance of convertible preferred stock, common stock warrants, and convertible notes, and to a lesser extent from grant income and stock option exercises. From inception to September 30, 2022, we have raised aggregate net cash proceeds of approximately $407.4 million primarily from the issuance of our common stock, convertible preferred stock, common stock warrants, and convertible notes. We have incurred significant operating losses to date. Our net losses were $65.5 million and $38.5 million for the nine months ended September 30, 2022 and 2021, respectively. As of September 30, 2022, we had an accumulated deficit of $161.4 million and cash, cash equivalents and investments of $260.0 million.

We expect to continue to incur increasing operating losses for the foreseeable future as we:

continue to advance fosgonimeton and our other product candidates through preclinical studies and clinical trials, and further extend the open label extension of the ACT-AD and LIFT-AD trials;

expand our pipeline of product candidates;

continue to grow our discovery organization and invest in the ATH platform;

ramp up manufacturing activities;

attract, hire and retain additional personnel;

obtain, maintain, expand and protect our intellectual property portfolio;

operate as a public company;

expand our laboratory and office facilities;

implement operational, financial and management information systems;

seek regulatory approval for any product candidates that successfully complete clinical trials;

establish a sales, marketing and distribution infrastructure to commercialize any product candidate for which we may obtain marketing approval; and

incur legal expenses associated with ongoing litigation, as further described in "Part II, Item 1-Legal Proceedings," and elsewhere in this report.

Our net losses may fluctuate significantly from quarter-to-quarter and year-to-year, depending on the timing of our clinical trials and our expenditures on other research and development activities.

We will require substantial additional funding to support our continuing operations and further the development of our product candidates. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through the sale of equity, debt financings, or other capital sources, which could include income from collaboration, licensing or similar arrangements, for the foreseeable future. Adequate funding may not be available when needed or on terms acceptable to us, or at all. If we are unable to raise additional capital as needed, we may have to significantly delay, scale back or discontinue development of our product candidates. Our ability to raise additional funds may be adversely impacted by potential worsening global economic conditions and the recent disruptions to, and volatility in, the credit and financial markets in the United States and worldwide resulting from the COVID-19 pandemic and otherwise. If we fail to obtain necessary capital when needed on acceptable terms, or at all, it could force us to delay, limit, reduce or terminate our product development programs, commercialization efforts or other operations. Insufficient liquidity may also require us to relinquish rights to product candidates at an earlier stage of development or on less favorable terms than we would otherwise choose. We cannot assure you that we will ever be profitable or generate positive cash flow from operating activities. Based upon our current operating plan, we estimate that our existing cash, cash equivalents and investments will be sufficient to fund our operating expenses and capital expenditure requirements through at least the next 12 months following the date of this report.

The global COVID-19 pandemic continues to evolve, and we will continue to monitor the COVID-19 situation closely. While COVID-19 related restrictions have been eased in many locations around the globe, including in Bothell, Washington, where our principal offices are located, a resurgence in cases of COVID-19, including new and highly contagious variants of COVID-19, or similar health epidemic could occur at any time, and the ultimate impact of the COVID-19 pandemic or a similar health epidemic is highly uncertain and subject to change. We will continue to monitor the ongoing impacts of COVID-19 on our clinical trial enrollment, trial sites, contract research organizations, or CROs, third-party manufacturers, and other



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third parties with whom we do business, as well as on regulatory authorities and our key scientific and management personnel. As the situation evolves, we may take further actions that alter our operations, including those that may be required by federal, state or local authorities, or that we determine are in the best interests of our employees and other third parties with whom we do business. At this point, the ultimate extent to which the COVID-19 pandemic, any potential resurgence of a variant thereof, or similar health epidemic, may affect our business, operations and clinical development timelines and plans, including the resulting impact on our expenditures and capital needs, remains uncertain.

Our Collaboration and Grant Agreements

We are party to certain collaboration and grant agreements, as described in the section titled "Part I, Item 1 - Business-Our Collaboration and Grant Agreements" in our Annual Report on Form 10-K filed with the SEC on March 28, 2022.

Components of Operating Results

Operating Expenses

Research and Development

Research and development expenses consist primarily of direct and indirect costs incurred for our research activities, including development of the ATH platform, our drug discovery efforts and the development of our product candidates. Direct costs include laboratory materials and supplies, contracted research and manufacturing, clinical trial costs, consulting fees, and other expenses incurred to sustain our research and development program. Indirect costs include personnel-related expenses, consisting of employee salaries, related benefits, and stock-based compensation expense for employees engaged in research and development activities, and facilities, including expenses associated with relocating to and building out our new lab space, and other expenses consisting of direct and allocated expenses for rent and depreciation, and lab consumables.

We expense research and development costs as incurred. Non-refundable advance payments for goods and services that will be used over time for research and development are capitalized and recognized as goods are delivered or as the related services are performed. In-licensing fees and other costs to acquire technologies used in research and development that have not yet received regulatory approval and that are not expected to have an alternative future use are expensed when incurred. We track direct costs by stage of program, clinical or preclinical. However, we do not track indirect costs on a program specific basis because these costs are deployed across multiple programs and, as such, are not separately classified.

As of the date of this report, we cannot reasonably determine the nature, timing, and estimated costs of the efforts that will be necessary to complete the development of, and obtain regulatory approval for, any of our product candidates. Product candidates in later stages of development generally have higher development costs than those in earlier stages. We expect that our research and development expenses will increase substantially for the foreseeable future as we continue to invest in research and development activities related to developing our product candidates, as our product candidates advance into later stages of development, as we begin to conduct larger clinical trials, as we seek regulatory approvals for any product candidates that successfully complete clinical trials, as we expand our product pipeline, as we maintain, expand, protect and enforce our intellectual property portfolio, and as we incur expenses associated with hiring additional personnel to support our research and development efforts. In particular, we have seen, and expect to continue to see, our research and development expenses increase substantially as we conduct our clinical trials for fosgonimeton, including open-label extensions for those trials. Additionally, we may experience an overall increase in research and development expenses as a result of inflation.

The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain. Our research and development expenses may vary significantly based on factors such as:

the number and scope of preclinical and IND-enabling studies;

the phases of development of our product candidates;

the progress and results of our research and development activities;



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•
per subject trial costs;

•

the number of trials required for regulatory approval, in particular with respect to fosgonimeton for the treatment of mild-to-moderate AD;

the further extension of the open label extension of the ACT-AD and LIFT-AD trials;

the number of sites included in the trials;

the countries in which the trials are conducted;

the length of time required to enroll eligible subjects and initiate clinical trials;

the number of subjects that participate in the trials;

the drop-out and discontinuation rate of subjects;

potential additional safety monitoring requested by regulatory agencies;

the duration of subject participation in the trials and follow-up;

the cost and timing of manufacturing of our product candidates;

the receipt of regulatory approvals from applicable regulatory authorities;

the timing, receipt and terms of any marketing approvals from applicable regulatory authorities;

the hiring and retention of research and development personnel;

the degree to which we obtain, maintain, defend and enforce our intellectual property rights;

the impact of COVID-19 on timelines and clinical operations, which may lead to increased costs; and

the extent to which we establish collaboration, licensing or similar arrangements and the performance of any related third parties.

A change in the outcome of any of these variables with respect to the development of any of our product candidates could significantly change the costs and timing associated with the development of that product candidate.

General and Administrative

General and administrative expenses consist primarily of personnel-related costs, consisting of employee salaries, related benefits, and stock-based compensation expense for our employees in the executive, legal, finance and accounting, human resources, and other administrative functions. General and administrative expenses also include third-party costs such as legal costs, insurance costs, accounting, auditing and tax related fees, consulting fees and facilities and other expenses not otherwise included as research and development expenses. We expense general and administrative costs as incurred.

We expect that our general and administrative expenses will increase substantially for the foreseeable future as we increase our headcount to support our continued research activities and development of our programs. We also anticipate that we will incur substantially increased expenses as a result of operating as a public company, including expenses related to compliance with the rules and regulations of the SEC, and those of any national securities exchange on which our securities are traded, legal, auditing, additional insurance expenses, investor relations activities, and other administrative and professional services. We expect continued legal expenses related to our ongoing litigation. We also expect to continue to increase the size of our administrative function to support the growth of our business. Additionally, we may experience an overall increase in general and administrative expenses as a result of inflation.

Grant Income

Grant income consists of income related to the NIH grants and is recognized as qualifying expenses under the grant agreements are incurred. Under the terms of the agreements and approvals received from the NIH, the Company may receive up to an aggregate of $15.2 million. As of September 30, 2022, we recognized aggregate grant income of $13.8 million in connection with the NIH grants. During the three months ended September 30, 2022, we recognized $3.0 million



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of grant income, which included recognizing $1.3 million of grant income for qualifying expenses incurred between January and May 2022, upon the Company receiving approval from the NIH to carry over previously unused budgets.

Other Income, Net

Other income, net consists primarily of interest earned on our cash, cash equivalents and investments. Absent further fundraising, we expect interest earned on our cash, cash equivalents and investments to decrease over the long term as we continue to expend our cash balances to fund our ongoing operations.

Results of Operations

Comparison of the Three Months Ended September 30, 2022 and 2021



The following table summarizes our results of operations for the periods
presented:

                                     Three Months Ended September 30,
                                                          Dollar         %
                               2022          2021         Change      Change
                                        (in thousands)
Operating expenses:
Research and development     $  16,965     $  10,707     $  6,258          58 %
General and administrative       7,168         7,119           49           1
Total operating expenses        24,133        17,826        6,307          35
Loss from operations           (24,133 )     (17,826 )     (6,307 )        35
Grant income                     2,959         2,079          880          42
Other income, net                  985            73          912       1,249
Net loss                     $ (20,189 )   $ (15,674 )   $ (4,515 )        29

Research and Development Expenses

The following table shows the primary components of our research and development expenses for the periods presented:



                                                   Three Months Ended September 30,
                                                                       Dollar             %
                                         2022           2021           Change          Change
                                                    (in thousands)
Direct costs:
Fosgonimeton (ATH-1017)               $   10,892     $     8,359     $     2,533              30 %
ATH-1020                                     592               -             592               *
Preclinical programs and other
direct costs                               2,078           1,089             989              91
Total direct costs                        13,562           9,448           4,114              44
Indirect costs:
Personnel-related costs, including
stock-
  based compensation                       3,027           1,006           2,021             201
Facilities and other costs                   376             253             123              49
Total research and development
expenses                              $   16,965     $    10,707     $     6,258              58


* Not meaningful

Research and development expenses increased by $6.3 million, from $10.7 million for the three months ended September 30, 2021 to $17.0 million for the three months ended September 30, 2022. The increase was driven primarily by an increase in expenses for fosgonimeton of $2.5 million related to continued patient enrollment and clinical site activity for our Phase 2/3 clinical trial and the corresponding open-label extension for our Phase 2 and Phase 2/3 clinical trials, an increase in personnel-related costs of $2.0 million due to an increase in headcount and stock-based compensation expense in connection with current period equity grants to new hires, an increase in preclinical research and development expenses of $1.0 million, and $0.6 million of expense associated with our ATH-1020 Phase 1 clinical trial, which commenced in the first quarter of 2022.



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General and Administrative Expenses

General and administrative expenses increased by $0.1 million, from $7.1 million for the three months ended September 30, 2021 to $7.2 million for the three months ended September 30, 2022. The increase was primarily due to an increase in personnel-related costs of $1.3 million, due primarily to increases in headcount to support our continued growth and in stock-based compensation expense in connection with current period equity grants to new hires, and an increase in facilities, travel, and other general corporate expenses of $0.4 million, partially offset by a decrease in legal costs of $1.3 million, and a decrease in professional services expenses of $0.3 million.

Grant Income

Grant income increased by $0.9 million, from $2.1 million for the three months ended September 30, 2021 to $3.0 million for the three months ended September 30, 2022. Grant income for the three months ended September 30, 2022 included recognizing $1.3 million of grant income for qualifying expenses incurred between January and May 2022, upon the Company receiving approval from the NIH to carry over previously unused budgets.

Other Income, Net

Other income, net increased by $0.9 million, from $0.1 million for the three months ended September 30, 2021 to $1.0 million for the three months ended September 30, 2022 due to higher interest income earned on our available-for-sale securities resulting from rising interest rates on debt securities, in addition to accretion of discounts on debt securities purchased below par value and held to maturity.

Comparison of the Nine Months Ended September 30, 2022 and 2021



The following table summarizes our results of operations for the periods
presented:

                                      Nine Months Ended September 30,
                                                          Dollar          %
                               2022          2021         Change        Change
                                        (in thousands)
Operating expenses:
Research and development     $  46,228     $  30,176     $  16,052           53 %
General and administrative      24,861        15,068         9,793           65
Total operating expenses        71,089        45,244        25,845           57
Loss from operations           (71,089 )     (45,244 )     (25,845 )         57
Grant income                     3,934         6,499        (2,565 )        (39 )
Other income, net                1,651           231         1,420          615
Net loss                     $ (65,504 )   $ (38,514 )   $ (26,990 )         70




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Research and Development Expenses

The following table shows the primary components of our research and development expenses for the periods presented:



                                                      Nine Months Ended September 30,
                                                                         Dollar         %
                                                2022         2021        Change       Change
                                                        (in thousands)
Direct costs:
Fosgonimeton (ATH-1017)                       $ 30,484     $ 24,697     $  5,787           23 %
ATH-1020                                         1,611            -        1,611            *

Preclinical programs and other direct costs 4,202 1,973 2,229 113 Total direct costs

                              36,297       26,670        9,627           36
Indirect costs:
Personnel-related costs, including stock-
  based compensation                             8,827        2,972        5,855          197
Facilities and other costs                       1,104          534          570          107
Total research and development expenses       $ 46,228     $ 30,176     $ 16,052           53


* Not meaningful

Research and development expenses increased by $16.1 million, from $30.2 million for the nine months ended September 30, 2021 to $46.2 million for the nine months ended September 30, 2022. The increase was driven primarily by an increase in personnel-related costs of $5.9 million due to an increase in headcount and stock-based compensation expense in connection with current period equity grants to new hires and existing employees, an increase in expenses for fosgonimeton of $5.8 million related to continued patient enrollment and clinical site visit activity for our Phase 2 and Phase 2/3 clinical trials and the corresponding open-label extension for our Phase 2 and Phase 2/3 clinical trials, an increase in preclinical research and development expenses of $2.2 million, and $1.6 million of expense associated with our ATH-1020 Phase 1 clinical trial, which commenced in the first quarter of 2022.

General and Administrative Expenses

General and administrative expenses increased by $9.8 million, from $15.1 million for the nine months ended September 30, 2021 to $24.9 million for the nine months ended September 30, 2022. The increase was primarily due to an increase in personnel-related costs of $5.5 million, due primarily to increases in headcount to support our continued growth and in stock-based compensation expense in connection with current period equity grants to new hires and existing employees, an increase in legal costs of $1.6 million, which includes costs related to our ongoing legal proceedings and the proxy contest in connection with our 2022 annual stockholders meeting, an increase in business development expenses of $0.9 million, an increase in insurance and other general corporate expenses of $0.8 million, an increase in professional services expenses of $0.5 million, and to a lesser extent, an increase in facilities costs.

Grant Income

Grant income decreased by $2.6 million, from $6.5 million for the nine months ended September 30, 2021 to $3.9 million for the nine months ended September 30, 2022. The decrease was driven by a decrease in expenses qualifying for reimbursement under the terms of the NIH grants upon the public readout of topline data of our Phase 2 ACT-AD clinical trial in the second quarter of 2022.

Other Income, Net

Other income, net, increased by $1.4 million, from $0.2 million for the nine months ended September 30, 2021 to $1.7 million for the nine months ended September 30, 2022 due to higher interest income earned on our available-for-sale securities resulting from rising interest rates on debt securities, in addition to accretion of discounts on debt securities purchased below par value and held to maturity.



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Liquidity and Capital Resources

Sources of Liquidity

Since our inception, we have funded our operations primarily with proceeds from the sale and issuance of common stock, convertible preferred stock, common stock warrants, and convertible notes, and to a lesser extent from grant income and stock option exercises. From our inception through September 30, 2022, we have raised aggregate net cash proceeds of $407.4 million primarily from the issuance of our common stock, convertible preferred stock, common stock warrants, and convertible notes.

Recent sales of our common stock were as follows.



                                            Common                              Net
                                            Shares           Price           Proceeds
                                            Issued         Per Share       (in millions)
September 2020 IPO                         12,000,000     $     17.00     $         186.4
October 2020 overallotment exercise         1,397,712           17.00                22.1
January 2021 follow-on public offering      4,000,000           22.50                84.1
February 2021 overallotment exercise          600,000           22.50                12.7
Total                                      17,997,712                     $         305.3



As of September 30, 2022, we had $260.0 million in cash, cash equivalents and investments and have not generated positive cash flows from operations. Since our inception, we have devoted substantially all of our resources to our research and development efforts such as small molecule compound discovery, nonclinical studies and clinical trials, as well as manufacturing activities, establishing and maintaining our intellectual property portfolio, hiring personnel, raising capital, and providing general and administrative support for these operations.

Material Cash and Future Funding Requirements

Our material cash requirements include our operating leases for laboratory and office facilities. As of September 30, 2022, we had lease payment obligations of $2.4 million, with $0.5 million payable within 12 months. For additional information regarding our lease commitments, see Note 8 to our unaudited condensed consolidated financial statements included elsewhere in this report. We are contingently committed to $0.9 million of potential future research and development milestone payments, in addition to sales-based payments and royalties, under our license agreement with WSU. Payments generally are due and payable only upon achievement of certain developmental, regulatory, and sales milestones for which the specific timing cannot be predicted. Refer to Note 7 to our unaudited condensed consolidated financial statements for additional information regarding the WSU license agreement. Additionally, we have purchase obligations and open purchase orders that support normal operations and are primarily due in the next 12 months. These purchase obligations and open purchase orders are generally cancellable in full or in part through the contractual provisions. We also anticipate that our research and development expenses and our general and administrative expenses will increase over at least the near-term as we advance our clinical development and our product candidates through clinical trials, increase our headcount to support our operations, and incur legal and other professional expenses related to our ongoing litigation. We cannot predict with certainty the amount and timing of these increased expenses.

Based upon our current operating plan, we estimate that our $260.0 million of cash, cash equivalents and investments at September 30, 2022 will be sufficient to fund our operating expenses and capital expenditure requirements through at least the next 12 months following the date of this report. We will need to raise substantial additional capital to fund the development of our product candidates. Until such time as we can generate significant revenue from product sales, we expect to finance our operations through the sale of equity securities, debt financings, or other capital, which could include income from collaboration, licensing or similar arrangements with third parties, or receiving research contributions, or grants. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of our stockholders will be or could be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing and preferred equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. If we raise funds through collaborations, licenses and other similar arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to us and/or may reduce the value of our common stock. Adequate funding may not be available when needed or on terms acceptable to us,



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or at all. Our ability to raise additional funds may be adversely impacted by potential worsening global economic conditions and the recent disruptions to, and volatility in, the credit and financial markets in the United States and worldwide resulting from the ongoing COVID-19 pandemic and otherwise. If we fail to obtain necessary capital when needed on acceptable terms, or at all, it could force us to delay, limit, reduce or terminate our product development programs, commercialization efforts or other operations. Insufficient liquidity may also require us to relinquish rights to product candidates at an earlier stage of development or on less favorable terms than we would otherwise choose. We cannot assure you that we will ever be profitable or generate positive cash flows from operating activities.

We have based our projections of operating capital requirements on assumptions that may prove to be incorrect and we may use all our available capital resources sooner than we expect. Because of the numerous risks and uncertainties associated with research, development and commercialization of biotechnology products, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

the scope, timing, progress and results of our ongoing preclinical studies and clinical trials of our product candidates;

the number of trials required for regulatory approval, in particular with respect to fosgonimeton for the treatment of mild-to-moderate AD;

the scope, progress, results and costs of preclinical development, laboratory testing and clinical trials of other product candidates that we may pursue;

our ability to establish and maintain collaboration, licensing or other similar arrangements, and the financial terms of any such arrangements, including the timing and amount of any future milestone, royalty or other payments due thereunder;

the costs, timing and outcome of regulatory review of our product candidates;

the costs and timing of future commercialization activities, including product manufacturing, marketing, sales and distribution, for any of our product candidates for which we receive marketing approval;

the revenue, if any, received from commercial sales of our product candidates for which we receive marketing approval;

the costs and timing of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending any intellectual property-related claims;

the costs related to ongoing legal proceedings;

any expenses needed to attract, hire and retain skilled personnel;

the costs of operating as a public company;

the costs associated with expanding our laboratory and office facilities; and

the extent to which we acquire or in-license other companies' product candidates and technologies or engage in other strategic transactions.

A change in the outcome of any of these or other factors with respect to the development of any of our product candidates could significantly change the costs and timing associated with the development of that product candidate. Furthermore, our operating plan may change in the future, and we may need additional funds to meet operational needs and capital requirements associated with such operating plan.



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Cash Flows

The following table summarizes our cash flows for the periods indicated:



                                                            Nine Months Ended September 30,
                                                              2022                   2021
                                                                    (in thousands)
Net cash (used in) provided by:
Operating activities                                    $        (56,802 )     $        (24,921 )
Investing activities                                              33,017                (25,452 )
Financing activities                                                 507                 97,076
Net (decrease) increase in cash, cash equivalents and
restricted cash                                         $        (23,278 )     $         46,703




Operating Activities

During the nine months ended September 30, 2022, net cash used in operating activities was $56.8 million. This consisted primarily of a net loss of $65.5 million, partially offset by non-cash charges of $8.9 million and an increase in our net operating assets of $0.2 million. The non-cash charges primarily consisted of stock-based compensation expense, depreciation expense, and non-cash lease expense. The increase in our net operating assets was primarily due to an increase in prepaid expenses and other current assets, offset by a decrease in unbilled grant receivable, and an increase in accounts payable and accrued expenses.

During the nine months ended September 30, 2021, net cash used in operating activities was $24.9 million. This consisted primarily of a net loss of $38.5 million, partially offset by non-cash charges of $3.9 million and a decrease in our net operating assets of $9.7 million. The non-cash charges primarily consisted of stock-based compensation expense, depreciation expense, and amortization of premiums and accretion of discounts on available-for-sale securities. The decrease in our net operating assets was due to a decrease in prepaid expenses and other current assets and an increase in accounts payable and accrued expenses, partially offset by an increase in unbilled grant receivable.

Investing Activities

During the nine months ended September 30, 2022, net cash provided by investing was $33.0 million. This consisted of maturities of available-for-sale securities, partially offset by purchases of available-for-sale securities and property and equipment.

During the nine months ended September 30, 2021, net cash used in investing was $25.5 million. This consisted of purchases of available-for-sale securities and purchases of property and equipment, partially offset by maturities and proceeds from sales of available-for-sale securities.

Financing Activities

During the nine months ended September 30, 2022, net cash provided by financing activities was $0.5 million, consisting of proceeds received from exercises of stock options.

During the nine months ended September 30, 2021, net cash provided by financing activities was $97.1 million, primarily driven by proceeds received from our follow-on public offering, and to a lesser extent from exercises of stock options.

Critical Accounting Policies, Significant Judgments and Use of Estimates

Our financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or GAAP. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenue and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of



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which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

Critical accounting policies and significant judgments and estimates are those that we consider the most important to the portrayal of our financial condition and results of operations because they require our most difficult, subjective or complex judgments, often as a result of the need to make estimates about the effect of matters that are inherently uncertain.

During the nine months ended September 30, 2022, there were no material changes to our critical accounting policies. Our critical accounting policies are described under the heading "Management's Discussion and Analysis of Financial Condition and Results of Operations-Critical Accounting Policies, Significant Judgments and Use of Estimates" in our Annual Report on Form 10-K filed with the SEC on March 28, 2022 and Note 2 to our unaudited condensed consolidated financial statements included in "Part I, Item 1-Financial Statements (Unaudited)" of this report. We believe that of our critical accounting policies, the following accounting policies involve the most judgment and complexity:

research and development costs;



•
stock-based compensation;

•
income taxes;

•
grant income.

Recent Accounting Pronouncements

See Note 2 to our unaudited interim condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for additional information.

Emerging Growth Company Status

We are an emerging growth company, as defined in the JOBS Act. Under the JOBS Act, emerging growth companies can delay adopting new or revised accounting standards issued subsequent to the enactment of the JOBS Act until such time as those standards apply to private companies. We elected to use this extended transition period for complying with new or revised accounting standards that have different effective dates for public and private companies until the earlier of the date that we (1) are no longer an emerging growth company or (2) affirmatively and irrevocably opt out of the extended transition period provided in the JOBS Act. As a result, our financial statements may not be comparable to companies that comply with the new or revised accounting pronouncements as of public company effective dates.

We will remain an emerging growth company until the earliest to occur of: (1) the last day of the fiscal year in which we have at least $1.235 billion in annual revenue; (2) the last day of the fiscal year in which we are deemed to be a "large accelerated filer," as defined in Rule 12b-2 under the Securities Exchange Act of 1934, as amended, which would occur if the market value of our common stock held by non-affiliates exceeded $700.0 million as of the last business day of the second fiscal quarter of such year; (3) the date on which we have issued more than $1.0 billion in non-convertible debt securities during the prior three-year period; and (4) the last day of the fiscal year in which the fifth anniversary of our initial public offering occurred.

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