APTE BIOS : Aptose Corporate Presentation April 2024

Tuspetinib to Treat Newly Diagnosed AML

Corporate Presentation

April 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 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 timeline, 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.sedar.comand EDGAR at www.sec.gov/edgar.shtml,especially the risk factors detailed therein.

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Tuspetinib Lead Clinical Asset

• Developing TUS+VEN+HMA triplet as frontline therapy to treat newly diagnosed AML ׀ Begins Summer of 2024
• Excellent safety profile ׀ Ideal for combination therapy
• Potently targets SYK, FLT3, KITMUT, JAK1/2, RSK2 kinases

3TUS : Tuspetinib ; VEN : Venetoclax ; HMA : Hypomethylating agent

AML : Acute Myeloid Leukemia

The Problem Treating AML

• Response rates too low and survival too short in frontline (1L) therapy
• Progress treating 1L AML with VEN+HMA (SOC) but not curing

The Needs of AML Patients

• Achieve longer survival and treat broader scope of subgroups in 1L
• Add a 3rd agent to VEN+HMA SOC - Current inadequate

Tuspetinib Opportunity ׀ Addressing 1L Unmet Needs

• 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 as a new SOC addresses 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."

Annual Deaths 11,2003 | 5-yr Survival 30% in Adults1 | 5-yr Survival 9% for Age >651. | Avg age a diagnosis 68

• Chemotherapy is not an option for most of the AML patient population
• • Chemotherapy may be beneficial for "Fit" younger patients without co-morbidities
  • Only 30-50% of AML patients are "Fit" for Chemo based therapies
  • Frontline therapies are making progress but leave substantial room for improvement
  • The CR rate of first-line treatment in young and middle-aged adults is 60%-80%,
  • Older patients >65 years of age have CR rates in first-line therapy of 40%-60% with high rates of relapse
• Elderly populations have seen improved efficacy with venetoclax-containing doublet therapy
• • VEN/HMA: CR = 37%, CRc = 66%, median OS = 14.7 months
  • However, patients with adverse mutations in FLT3, NRAS, KRAS, and TP53 have inferior outcomes
• Triplet combination studies have shown better efficacy, but increased toxicity requires dose reductions
• • Studies have shown upper ranges of response at CRc 90% and CR >70%
  • • Combinations have been more toxic, requiring dose reductions of all agents
    • And the targeted agents do not have broad activity across AML genotypes
• Safe and effective therapies to improve outcomes for AML patients of all genotypes represent an urgent need in AML

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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

VEN + HMA + Gilteritinib triplet has superior OS to VEN + HMA doublet in newly diagnosed FLT3+ AML patients

Current Problem

Gilteritinib-basedtriplet not active in FLT3-WildtypeAML (70% of patients) and toxicities require SOC dose reductions

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

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

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TUS+VEN+AZA TRIPLETPilot Study: Design, Patient Populations, Dose Selection, Goals

Patient Populations │ 20-36 Pts Total │ 50% FLT3-MUT │ <20% TP53+/CK

Dose Selection │ Explore 80, 120, 160mg Doses for Optimal Phase 2 Dose of TUS and Avoid SOC Dose Reductions

Trial Goals │ Safety, CR rate, MRD negativity and OS across AML subtypes (FLT3MUT/WT , TP53MUT, RASMUT)