Identification of new dasatinib analogues targeting mutated BCR-ABL1: virtual screening, molecular docking, and dynamics simulations studies.

Abstract

Drug resistance is a major challenge in cancer chemotherapy and accounts for a majority of cancer-related deaths globally. One of the well-identified and characterised mechanisms of drug resistance in chronic myeloid leukaemia (CML) is the presence of BCR-ABL1 mutations, which is responsible for resistance against first-line tyrosine kinase inhibitors (TKIs) such as imatinib, dasatinib, and nilotinib. In the present work, we first performed a three-tier virtual screening against the human tyrosine kinase ABL1 protein (PDB ID: 2GQG). Top-performing compounds were then selected for molecular dynamics (MD) simulation studies at 500 ns to understand their affinity, dynamics, and stability with the target protein. Finally, density functional theory (DFT) studies at the B3LYP/6-31G* level of theory were conducted to elucidate the molecular features of the identified compounds. Based on the docking scores (-14.80 to -13.79 kcal/mol) and ADMET profiles, we identify 45375848, 88575518, and 23589024 as the most promising candidates. All three compounds contained N-(2-chloro-6-methylphenyl)-2-(methylamino) thiazole-5 carboxamide as the common fragment. MD parameters (RMSD, RMSF and SSE) further complemented the docking results, showing stabilisation of the ABL1 protein in the presence of identified compounds. High drug-likeness, acceptable pharmacokinetic profile and other molecular features warrant the drug-like behaviour of the compounds. Overall, this study highlights promising ABL1 inhibitors, laying the ground for further investigations.