Aptose Corporate Presentation NASDAQ: APTO July 2020 TSX: APS - PowerPoint PPT Presentation

Aptose Corporate Presentation NASDAQ: APTO July 2020 TSX: APS www.aptose.com

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-looking statements, 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.com and EDGAR at www.sec.gov/edgar.shtml, especially the risk factors detailed therein. 2

Investment Highlights APTOSE Strong leadership and strong balance sheet to advance clinical programs Clinical stage biotech company developing 1 st -in-class targeted medicines Precision treatment of hematologic malignancies; life-threatening / orphan diseases CG-806 Oral FLT3 / BTK Kinase Inhibitor FDA Orphan Drug Designation in AML Inhibits all forms of FLT3 and BTK : Drivers of AML, CLL / NHL hematologic cancers Precision that suppresses multiple oncogenic pathways, yet spares safety targets Phase 1a/b trial ongoing for CLL & NHL Phase 1a/b trial in start-up phase for AML APTO-253 MYC Inhibitor FDA Orphan Drug Designation in AML Only clinical stage agent directly targeting G-Quadruplex of notable MYC oncogene Phase 1b in dose level 4 for AML & MDS demonstrating safety and MYC inhibition Serving Patients and Market Opportunities Potential to serve broadly CLL and AML patient needs Potential for near-term clinical POC and value creation with hematologic cancers 3

Delivery of 2020 First Half Goals On Track q Following December 2019 financing, delivered goals during first half of 2020 q Maintained clinical development momentum through COVID-19 crisis period q CG-806 Phase 1 in R/R CLL & NHL Proceeding on Track o Completed 150mg, 300mg, 450mg BID lower dose levels o Now completing intermediate dose level 600mg BID o Amendment to allow back filling of patients to boost number of patients o Demonstrated BTK inhibition and induction of lymphocytosis in CLL patients o Plan to move into higher dose levels 750 and 900mg BID during 2H2020 q CG-806 Phase I in R/R AML Proceeding o Identified a dose that should be therapeutically active in AML patients o New IND allowed in R/R AML patients at desired starting dose of 450mg BID q CG-806 positioned for likelihood of CLL and AML responses over next 6-12 months 4

CG-806 1 st -in-Class Oral Kinase Inhibitor • Mutation Agnostic FLT3 Inhibitor • Mutation Agnostic rBTK Inhibitor q Ongoing trial Ph1a/b for CLL / lymphoid malignancies as rBTKi q Initiating trial Ph1a/b for AML / myeloid malignancies as FLT3i q Small molecule “reversible” kinase inhibitor q Cluster-selective agent with highly unique kinome targeting profile q Developing across spectrum of lymphoid and myeloid hematologic malignancies q Retains potency on CLL & AML cells with mutations that render other agents ineffective 5

“Cluster-Selective Kinase Inhibitor”: CG-806 Potently and Selectively Inhibits Clusters of Related Kinases Receptors TRK • Mutation Agnostic FLT3 TRKC TRKB TRKB CSF1R TRKA RET • Inhibits WT and all mutant forms of FLT3 DDR2 FLT3 PDGFR PDGFRa SRC MET LYN B LYN A TIE2 • Inhibits WT and all mutant forms of BTK HCK LCK BLK BMX/ ITK ETK • Simultaneously suppresses multiple oncogenic BTK signaling pathways MTS1 BTK • Robust Safety Profile • NOT a “dirty” kinase inhibitor • Avoids kinases that negatively impact safety • No drug-related AEs seen to date AURA AURB AURC • Inhibits Clusters of Kinases that Drive Lymphoid and Myeloid Hematologic Malignancies • BTK cluster → CLL & NHL • FLT3 cluster → AML & MDS 6

CG-806 Suppresses Key Oncogenic Targets and Pathways in Myeloid & Lymphoid Malignancies CSF1R PDGFRα TRK A/B/C CG-806 CG-806 CG-806 SRC LYN CG-806 CG-806 SYK CG-806 CG-806 PI3K CG-806 BTK TEC FLT3i PLCγ2 CG-806 Ras PKC CG-806 JAK AKT CG-806 BTKi BTK upreg FLT3 mut IKK CLL AML CG-806 mTOR CG-806 CG-806 CG-806 CG-806 CG-806 S6K STAT MAPK ERK NFĸB JAK / STAT MAPK / ERK NFĸB PI3K / AKT / mTOR / S6K pathway pathway pathway pathway CG-806 Inhibited directly CG-806 MYC Inhibited indirectly CG-806 Cell Growth and Proliferation 7

CG-806 Phase 1 Clinical Development Plan for Patients with Lymphoid (CLL/NHL) and Myeloid (AML) Malignancies Phase 1a/b R/R CLL & NHL : Ongoing o Seek to define safety, tolerance, PK, PD and RP2D CLL & NHL o Seek to inhibit P-BTK, induce lymphocytosis and observe responses in CLL/NHL patients Lymphoid o R/R AML patients are acutely ill, and we did not wish to dose sub-therapeutically o During CLL trial, identified a dose of 450mg likely “therapeutically active” for AML patients Phase 1a/b in R/R AML : FDA Allowed New IND AML o Seek to define safety, tolerance, PK, PD and RP2D Myeloid o Initiate dosing in AML patients at 450mg BID as a dose likely to be active o Seek to inhibit P-FLT3, decrease PB blast counts and observe responses in AML patients 8

CG-806 Phase 1a/b Trial for Patients with CLL and NHL B-cell Cancers 9

CG-806 for the Treatment of CLL & Lymphoid Malignancies Overexpressed BTK (Bruton’s Tyrosine Kinase) is Driver Kinase R/R CLL Patients Need BTK and Other Oncogenic Kinases Inhibited Over Half (54%) CLL patients discontinue Ibrutinib by 44 Months (1,2) - Patients resistant (C481S mutant), intolerant or refractory to ibrutinib Patients Failing a Host of Other Agents - Covalent BTKi, Non-covalent BTKi, BCL-2i, PI3Ki, Anti-CD20 Abs CG-806 May Overcome Shortcomings of Ibrutinib & Other Agents • “Non-covalent” : retains activity against WT and C481S-BTK enzyme • Inhibits multiple “oncogenic rescue” pathways to potentially avoid R/R disease (1) Byrd et al. Blood ; 2019: 133(19): 2031-2042 | (2) Woyach et al. J Clin Oncol .; 2017: 35; 1-7 10

CG-806 Non-Covalent Inhibitor Retains Potency Against Wildtype and C481S-BTK CG-806 Binds Non-Covalently to BTK CG-806 X-ray Crystallographic Analysis: • Reversibly binds to WT-BTK and C481S-BTK Active Sites • Atypical Binding Mode Not Reported with Other Drugs • Chemical Structure Distinct from Ibrutinib/Other BTKi’s Kinase CG-806 IC 50 (nM) Retains potency against C481S-BTK BTK-WT 8.4 BTK-C481S 2.5 But, does NOT inhibit TEC, EGFR or ErbB2 kinases linked to ibrutinib related toxicities; IC 50 (nM) TEC EGFR ErbB2 including bleeding disorders, gut and skin Ibrutinib 78 5.6 9.4 toxicity and atrial fibrillation, respectively. CG-806 >1,000 >1,000 >1,000 Expect Superior Safety Profile for CG-806 11