APTE BIOS : Aptose Corporate Presentation May 2024

Tuspetinib to Treat Newly Diagnosed AML

Corporate Presentation

May 2024

P R E C I S I O N O N C O L O G Y F O R T H E R A P I E S O F T O M O R R O W

Aptose Leadership Team: Multifaceted Expertise in Therapeutic Development

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Aptose Disclosure

This presentation does not, and is not intended to, constitute or form part of, and should not be construed as, an offer or invitation for the sale or purchase of, or a solicitation of an offer to purchase, subscribe for or otherwise acquire, any securities, businesses and/or assets of any entity, nor shall it or any part of it be relied upon in connection with or act as any inducement to enter into any contract or commitment or investment decision whatsoever.

This presentation contains forward-lookingstatements, which reflect APTOSE Biosciences Inc.'s (the "Company") current expectations, estimates and projections regarding future events, including statements relating to our business strategy, our clinical development plans, our ability to obtain the substantial capital we require, our plans to secure strategic partnerships and to build our pipeline, our clinical trials and their projected timelines and milestones, the efficacy and toxicity of our product candidates, potential new intellectual property, our plans, objectives, expectations and intentions; and other statements including words such as "anticipate", "contemplate", "continue", "believe", "plan", "estimate", "expect", "intend", "will", "should", "may", and other similar expressions. Such statements constitute forward-looking statements within the meaning of securities laws.

Although the Company believes that the views reflected in these forward-looking statements are reasonable, such statements involve significant risks and uncertainties, and undue reliance should not be placed on such statements. Certain material factors or assumptions are applied in making these forward-looking statements, and actual results may differ materially from those statements. Those factors and risks include, but are not limited to, our ability to raise the funds necessary to continue our operations, changing market conditions, the successful and timely completion of our clinical studies including delays, the demonstration of safety and efficacy of our drug candidates, our ability to recruit patients, the establishment and maintenance of corporate alliances, the market potential of our product candidates, the impact of competitive products and pricing, new product development, changes in laws and regulations, uncertainties related to the regulatory approval process and other risks detailed from time to time in the Company's ongoing quarterly filings and annual reports.

Forward-looking statements contained in this document represent views only as of the date hereof and are presented for the purpose of assisting potential investors in understanding the Company's business and may not be appropriate for other purposes. The Company does not undertake to update any forward-looking statements, whether written or oral, that may be made from time to time by or on its behalf, except as required under applicable securities legislation. Investors

should read the Company's continuous disclosure documents available at www.sedarplus.comand EDGAR at www.sec.gov/edgar.shtml,especially the risk factors detailed therein.

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Tuspetinib Lead Clinical Asset

• TUS+VEN+HMA triplet is being developed as frontline therapy to treat newly diagnosed AML
• Frontline triplet clinical data expected 2H 2024
• Potently targets SYK, FLT3, KITMUT, JAK1/2, RSK2 kinases

4TUS : Tuspetinib ; VEN : Venetoclax ; HMA : Hypomethylating agent

AML : Acute Myeloid Leukemia ; SOC : Standard of Care

Unmet Need for Superior Frontline (1L) Therapy in AML

• Progress made with VEN+HMA (SOC) but unmet needs still exists
• • Response rates too low and survival too short in 1L therapy
  • Resistance to VEN compromises subsequent R/R therapies
• A 3rd agent is needed to boost responses with VEN+HMA SOC
• Current 3rd agents inadequate - those in development only address specific genetic subtypes and are limited by toxicities

Tuspetinib Opportunity ׀ Addressing 1L Unmet Needs

• TUS is the ideal 3rd agent for addition to VEN+HMA
• TUS has excellent safety in combination with VEN and HMA
• TUS increases efficacy in combination with VEN and HMA
• TUS has broad scope of activity across AML genetic subgroups

TUS+VEN+HMA … creating a new SOC addressing safety, scope, and survival needs of newly diagnosed AML patients

Tuspetinib Enhancing Venetoclax Efficacy in Frontline Therapy TUS and VEN mechanistically cooperate to prevent drug resistance

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Greatest Need in AML Therapy Today

"We are making progress but are not curing our patients1."

Frontline therapies are making progress but leave substantial room for improvement

• Younger "Fit" patients achieve >50% CR, but only 30-50% of patients are "Fit" and many relapse3
• Older "Unfit" patients achieve improved efficacy with VEN+HMA doublet but many relapse
• • VEN+HMA(AZA): CR = 37%, CR/CRi = 66%, median OS = 14.7 months4
• Patients with adverse FLT3, N/KRAS, and TP53 mutations correlated with poor response/outcomes

Current triplets can deliver better efficacy, but increased toxicity requires dose reductions

• Studies have shown upper ranges of response at CRc >90%
• Current 3rd agents with VEN+HMA have been more toxic, requiring dose reductions of all agents
• Current 3rd agents with VEN+HMA do not deliver broad activity across AML genotypes

Urgent need for safer and more effective 1L triplet therapies to improve outcomes for AML patients of all genetic subtypes

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AML Patient Journey | 1L Therapy High-Level Overview

Current Standard-of-Care (SOC) treatment options leading to therapeutic failure……

AML Patient Journey | 1L Therapy High-Level Overview

Tuspetinib-containing triplet can become a new 1L SOC to increase survival

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New Paradigm in Frontline Therapy to Treat Newly Diagnosed AML

Deploying Triplet Combinations of Targeted Drugs | Building on VEN + HMA Backbone for 1L Therapy

Proof for Triplets : Addition of a 3rd Targeted Agent Boosts VEN+HMA Responses in 1L AML

Addition of gilteritinib (Gilt) FLT3i to VEN+HMA boosts CR rate 2.4X in newly diagnosed FLT3+ AML patients1

Problem: Current 3rd Agents for Triplets have Limitations

Gilt is not active in FLT3-Wildtype AML (70% of patients) and toxicities of Gilt with VEN+HMA require SOC dose reductions

Solution: TUS Fulfills Ideal Profile as

3rd Agent for 1L Triplet

FDA Requirements for TUS to Enter Frontline Therapy in Newly Diagnosed AML

Tuspetinib has Met the FDA Requirements to Perform the Triplet Pilot Study

Tuspetinib Achieved Orphan Drug Designation and Fast Track Status

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