Defining and overriding mechanisms of in vitro and clinical resistance to the first highly active allosteric kinase inhibitor

/ABSTRACT Although effective therapeutics that target the dysregulated kinase activity of BCR::ABL1 have been developed for patients with chronic myeloid leukemia (CML), acquired resistance remains an important clinical issue. Additionally, problematic side effects plague a considerable proportion of patients who are expected to require lifelong therapy. The first five approved tyrosine kinase inhibitors (TKIs) for CML target the ATP binding pocket of BCR::ABL1 (“orthosteric” TKIs). Asciminib is the first active “allosteric” TKI for CML and was recently approved as a frontline therapy based on high response rates and excellent tolerability. Asciminib is rapidly being adopted as a preferred treatment in all lines of therapy. We have demonstrated that several mutations that confer resistance to orthosteric TKIs unexpectedly confer in vitro and/or clinical resistance to asciminib. We have further demonstrated that a clinical variant of BCR::ABL1 lacking ABL1 exon 2 is uniquely and highly resistant to asciminib. Notably, these isoforms retain asciminib binding affinity, thereby invoking a novel molecular mechanism of resistance. Our central hypothesis is that asciminib will be vulnerable to multiple resistance- conferring mutations that disrupt its allosteric effect on kinase conformation, in addition to a limited number of mutations that impair its ability to bind BCR::ABL1. Our rationale is that pioneering work on orthosteric TKI resistance mechanisms in CML have informed kinase conformational dynamics, optimal CML patient management, development of next-generation TKIs and successful prediction of TKI resistance mechanisms in several other malignancies. We propose to (i) employ orthogonal approaches to identify and validate single point mutants in BCR::ABL1 that can confer resistance to asciminib, and compound (≥2 on one DNA strand) mutants that arise following subsequent orthosteric TKI therapy, (ii) assess their sensitivities to a novel active investigational allosteric inhibitor, combinations of TKIs, and a novel bitopic TKI, (iii) determine mechanisms of resistance through computational and structural studies, (iv) define residues necessary for adoption of the closed ABL1 kinase conformation, and (v) assess the ability of asciminib-resistant mutants to pathologically activate ABL1 kinase activity. The proposed research is significant due to its potential to rapidly impact clinical investigation and optimize patient management, inform understanding of kinase regulation and other malignancies. The proposed research is innovative because it applies state-of-the-art methodologies to comprehensively define and characterize a novel mechanism of resistance to a first-in-class highly clinically active allosteric TKI and thereby establish a new paradigm. Additionally, it will assess the promise of emerging agents, TKI combinations, and an innovative bitopic TKI with best-in-class features for treating asciminb-resistant single and compound mutants. Project Number: 1R01CA311995-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Neil Shah (+1 co-PI) | Institution: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, SAN FRANCISCO, CA | Award Amount: $700,338 | Activity Code: R01 | Study Section: Mechanisms of Cancer Therapeutics B Study Section[MCTB] View on NIH RePORTER: https://reporter.nih.gov/project-details/11347974