Identification by molecular dynamic simulation and in vitro validation of SISB-A1, N-[1-(4-bromophenyl)-3-methyl-1H-pyrazol-5-yl]-2-[(2-oxo-4-phenyl-2H-chromen-7-yl) oxy], as an inhibitor of the AblT315I mutant kinase to combat imatinib resistance in chronic myeloid leukemia

Abstract

The discovery of imatinib, a specific inhibitor of Abl kinase, revolutionized the therapeutic approach to chronic myeloid leukemia (CML); however, its efficacy can be impeded by the emergence of novel mutations within the kinase domain, particularly Abl^T315I, that lead to the development of drug resistance. It therefore remains necessary to identify specific inhibitors that can effectively target imatinib-resistant CML harboring the Abl^T315I mutation. A natural product library sourced from the ZINC database was screened against the experimental structure of Abl^T315I kinase to identify compounds that selectively target the mutated kinase. The top-scoring compound was empirically tested for inhibition of Abl^T315I kinase using a luminescence-based kit and for impact on cellular proliferation using the BaF3-BCR-ABL-T315I stable cell line. Computational docking and molecular dynamic simulations identified the compound SISB-A1, N-[1-(4-bromophenyl)-3-methyl-1H-pyrazol-5-yl]-2-[(2-oxo-4-phenyl-2H-chromen-7-yl)oxy] acetamide, to effectively bind the catalytic domain of the mutant Abl^T315I kinase. Moreover, SISB-A1 exhibited greater preference than imatinib for amino acid residues of the mutant kinase's active site, including isoleucine 315. MMPBSA-based Gibbs binding free energy estimation predicted SISB-A1 to have a free energy of -51.5 versus -65.0 kcal/mol for the conventional Abl^T315I inhibitor ponatinib. Cell proliferation assays showed SISB-A1 to have a GI₅₀ of 164.0 nM against the ABL-T315I stable cell line, whereas imatinib had a GI₅₀ of 5035 nM. The IC₅₀ value obtained for SISB-A1 against the Abl^T315I kinase was 197.9 nM. The results indicate SISB-A1 to have a notable ability to bind the catalytic domain of the Abl^T315I mutant kinase and effectively suppress its activity, thereby surpassing the associated resistance to imatinib. Continued advancement of this lead compound has the potential to yield innovative therapeutics for imatinib-resistant CML.

Keywords: AblT315I kinase mutation; Chronic myeloid leukemia (CML); Imatinib; Molecular dynamic simulation; Ponatinib.