APTE BIOS : Aptose Corporate Presentation December 2023

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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Oral Presentation Delivered by Naval Daver, MD To the 65th ASH Annual Meeting & Exposition Saturday 09Dec2023

Tuspetinib Oral Myeloid Kinase Inhibitor Safety and

Efficacy As Monotherapy and Combined with Venetoclax in Phase 1/2 Trial of Patients with Relapsed or Refractory (R/R) Acute Myeloid Leukemia (AML)

Naval Daver1, Kyoo-Hyun Lee2, Yunsuk Choi2, Brian Jonas3, Martha Arellano4, Justin M Watts5, Pau Montesinos6, Uma Borate7, Paul B. Koller8, Chul-Won Jung9, Sang Kyun Sohn10, Pankit Vachhani11, Amir T. Fathi12, Sung-Soo Yoon13, Jeong-Ok Lee14, Ho-Jin Shin15, Gabriel Mannis16, Nikolai A.

Podoltsev17, Tan Shuhying18, Harry P. Erba19, Eric Tam20, Mar Tormo Diaz21, Jia Hu22, Ranjeet Kumar Sinha22, Nawazish Khan22, William Rice22, Rafael Bejar22

1. The University of Texas MD Anderson Cancer Center Houston, TX,2Asan Medical Center, Seoul, SK, 3UC Davis Comprehensive Cancer Center, Davis, CA, 4Emory University, Atlanta, GA, 5University of Miami, FL, 6Hospital Universitari i Politècnic La Fe, Valencia, ESP, 7The James Cancer Hospital and Solove Research Institute, The Ohio State University, OH, 8Department of Hematology/HCT, City of Hope, Duarte,
   CA, 9Samsung Medical Center, Seoul, SK, 10Kyungpook National University Hospital Daegu, SK, 11University of Alabama, AL, 12Massachusetts General Hospital Boston, MA, 13Seoul National University Hospital, Seoul, SK, 14 Seoul National University Bundang Hospital, Seongnam, SK, 15Pusan National University Hospital, Busan, SK, 16 Stanford Cancer Center, Stanford, Palo Alto, 17 Yale School of Medicine, New Haven, CT, 18 St. Vincent's Hospital, Melbourne, AUS, 19Duke Cancer Center, Durham, NC, 20 USC Norris Comprehensive Cancer Center, Los Angeles, CA , 21Hospital Clínico Universitario, Valencia, ESP

1. Aptose Biosciences Inc, San Diego, CA

Investment Highlights

Precision oncology company developing oral targeted agents to treat hematologic malignancies Tuspetinib (TUS) lead agent │Once daily oral kinase inhibitor for R/R acute myeloid leukemia (R/R AML)

• Highly active as a single agent with an excellent safety record
• Targets FLT3WT/MUT, SYK, KITMUT, JAK1/2, RSK2, TAK1-TAB1 kinases and suppresses MCL-1 expression
• CR/CRh=36% All-comers │ CR/CRh=50% FLT3MUT │ CR/CRh=25% FLT3WT at the RP2D 80mg in VEN-naïve R/R AML

AML care shifted to Venetoclax(VEN) based combinations │ Emergenceof difficult-to-treatPrior-VEN failure population

• Prior-Venfailure R/R AML patients have dismal response to salvage therapy: CR/CRh = 4-15% │ mOS = 2.8 months
• Any new drug needs to combine well with VEN and treat Prior-VEN failure AML patients

Opportunities │ Tuspetinib is ideal for combination therapy with VEN-containing regimens and treating Prior-VEN failures

‒ TUS directly targets VEN resistance mechanisms │ Re-sensitizes VEN failures to VEN │ TUS/VEN successfully treats these VEN failures

TUS/VEN doublet planned for registrational trial in R/R Prior-VEN AML → Estimated $400 million market1 TUS/VEN/AZA triplet planned for pilot study in 1L Newly Diagnosed AML → Estimated $1 billion market1 Multiple value-creating milestones ahead

• TUS/VEN further data on duration of response in R/R AML planned: 1Q & 2Q 2024
• TUS/VEN/HMA planned initiation of pilot study in 1L AML: 1H 2024
• Extension into HR-MDS and CMML planned

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1 Companycommercial forecast estimates

Tuspetinib Directly and Indirectly Targets Venetoclax Escape Mechanisms

Tuspetinib targets pathways involved

in resistance to Venetoclax

TUS

FLT3-ITD

KIT-MUT

JAK1/2 RAS/MAPK TP53-MUTMCL-1 ↑

VEN BCL-2i resistance involves mutations in multiple pathways to evade BCL-2 blockade

By shutting down escape pathways, TUS may re-sensitizeprior-VEN failures to venetoclax

• Strong evidence for combination therapy with tuspetinib and venetoclax
• ESH Poster: Tuspetinib oral myeloid kinase inhibitor creates synthetic lethal vulnerability to venetoclax

KITMUT	FLT3MUT

SYK

JAKMUT/STAT TUS

PI3K/AKT

RASMUT/

MAPK

MCL-1

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C O N F I D E N T I A L

TUS/VENMay be Ideal Doublet Therapy in R/R Prior-VEN Failure AML

R/R AML Setting:AML care shifted toward Venetoclax (VEN) containing combination regimens and a new population of difficult-to-treat VEN failures is emerging

After failing venetoclax, AML is highly refractory to salvage

therapy(1,2,3,4)

• Prior-VENfailures have "dismal" response rates to salvage therapy
• Resistance involves alterations in multiple pathways (FLT3, NRAS, KIT, TP53, JAK1/STAT5, MCL-1)

Need Improved Therapy for R/R Prior-VEN Failures TUS/VEN combination is safe & active in Prior-VEN Potential first-to-market in R/R Prior-VEN setting

1Estimated $400 Mn opportunity forecast to treat the majority of R/R AML patients

66%
	15%
4%	6%

1L CR Rate	Salvage 2L CR	Salvage 2L	Salvage 3L
		Targeted CR	Targeted CR

1 Pei, Cancer Discos 2020); 2 DiNardo, Blood 2020); 3 (Maiti et al., Haematologica 2021); 4 (Mannis et al., Leukemia Research 2023); 5 Datamonitor Healthcare AML forecast July 2023; Also, Bewersforf et al., Leukemia Research 2022; 122: 106942.

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1 Companycommercial forecast estimates

TUS/VEN/HMAMay be Ideal Triplet Therapy in 1L Newly Diagnosed AML

1L Newly Diagnosed Setting:Venetoclax (VEN/HMA) in "Unfit"

patients dramatically increased response rates (CRc = 66%) and mOS (14.7 mos)

Problem: Need Improved 1L Therapy

• 1L chemo and VEN/HMA not universally curative
• VEN containing regimens are highly successful and will further revolutionize 1L therapy
• Proof of Concept: Gilt/VEN/HMA triplet delivered high response rates, but Gilt limited to FLT3+ population (~30%) and limited by AEs

Need Improved 1L Triplet Therapy

TUS/VEN/HMA Triplet may expand treatable 1L populations (improved safety; fit and unfit ; FLT3 agnostic)

1Estimated $1Bn opportunity forecasted in front-line AML

66%
	15%
4%	6%

1L CR Rate	Salvage 2L CR	Salvage 2L	Salvage 3L
		Targeted CR	Targeted CR

1 Pei, Cancer Discos 2020); 2 DiNardo, Blood 2020); 3 (Maiti et al., Haematologica 2021); 4 (Mannis et al., Leukemia Research 2023); 5 Datamonitor Healthcare AML forecast July 2023; Also, Bewersforf et al., Leukemia Research 2022; 122: 106942.

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1 Companycommercial forecast estimates

Clinical Path to Support Clinical Development and Registrational Plans

Dose Escalation Ph 1/2	EOP1 Meeting
Trial in R/R AML	with FDA
• Demonstrated	• Successful meeting
tuspetinib single	and outcomes
agent activity

• RP2D = 80mg once

• Favorable safety and daily tolerability

• All approval paths remain available

APTIVATE Expansion Trial in R/R AML

• Tuspetinib or
  TUS/VEN
• TUS/VEN favorable safety profile and is highly active, including prior-VEN failure difficult-to- treat subgroup

TUS/VEN Differentiation from Other Therapies

• TUS/VEN impressive response rate in R/R prior-VEN AML
• ~80% R/R prior-VEN patients entering APTIVATE trial
• May enable accelerated approval development path

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Tuspetinib Single Agent Phase 1/2 Clinical Study

Tuspetinib Single Agent Phase 1/2 Study in R/R AML

• TUS is dosed orally once daily in 28-day cycles without interruption
• Safety and efficacy analyses include all dosed patients1
• CRc = CR + CRh +CRp + CRi (incl MLFS)
• Extensive dose exploration │ 91 patients dosed
• Proportion of Prior-VEN patients increased over time, resulting in lower response rates at 120mg & 160mg
• Therapeutic window 80 mg - 160 mg
• CRs with no DLTs
• CRs in patients with highly adverse genetics
• RP2D = 80 mg once daily

Dose Escalation + Exploration + Expansion

	Total VEN- Prior-
		Naïve	VEN
	n=	n=	n=
Cohort 1: 20 mg QD	2	1	1
Cohort 2: 40 mg QD	17	8	9
Cohort 3: 80 mg QD	20	14	6
Cohort 4: 120 mg QD	32	6	26
Cohort 5: 160 mg QD	16	8	8
Cohort 6: 200 mg QD	4	1	3

71% Prior-

VEN

9	1Data cut Oct 23, 2023

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Tuspetinib Single Agent Patient Baseline Characteristics

Highly treatment experienced and representative of current R/R AML patient population

Patient Characteristics (n=91)	FLT3MUT	FLT3WT
Patient number n (%)1		34	56	Population included FLT3WT & FLT3MUT
Median Age Years (Range)	60	(21-84)	65.5 (18-83)	Older: Median age > 60 years
Female n (%)	14	(41.2%)	24 (42.9%)
Lines prior therapy Mean (Range)	3.3 (1-11)	2.4 (1-6)	• Prior-VEN represented > 50% of patients
				• Percentage increased as trial proceeded
Prior-VEN
19	(55.9%)	33 (58.9%)	• Higher dose levels had higher percentages of
				Prior-VEN patients
Prior FLT3 Inhibitor	17	(50.0%)	3 (5.4%)	Over 50% failed Prior-FLT3i
Prior Cytotoxic chemotherapy	26	(76.5%)	36 (64.3%)
Prior HMAs	22 (64.7%)	37 (66.1%)
				Over 1/3 failed Prior-transplant
Prior HSCT	14	(41.2%)	19 (33.9%)

1 One patient had an indeterminant status for FLT3

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