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 Abl mutant kinase to combat imatinib resistance in chronic myeloid leukemia.

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, 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 mutation. A natural product library sourced from the ZINC database was screened against the experimental structure of Abl kinase to identify compounds that selectively target the mutated kinase. The top-scoring compound was empirically tested for inhibition of Abl 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 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 inhibitor ponatinib. Cell proliferation assays showed SISB-A1 to have a GI of 164.0 nM against the ABL-T315I stable cell line, whereas imatinib had a GI of 5035 nM. The IC value obtained for SISB-A1 against the Abl kinase was 197.9 nM. The results indicate SISB-A1 to have a notable ability to bind the catalytic domain of the Abl 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.