An analogue of a kinase inhibitor exhibits subjective characteristics that contribute to its inhibitory activities as a potential anti-cancer candidate: insights through computational biomolecular modelling of UM-164 binding with lyn protein

Abstract

The recent emergence of lyn kinase as a driver of aggressive behaviour in triple-negative breast cancer (TNBC) remains a major concern posing a burden for people living with breast cancer and drug development. The binding of UM-164 to lyn protein has been noted to impact the conformational dynamics required for drug fitness. Herein, we provide the first account of the molecular impact of an experimental drug, UM-164 binding on lyn protein using various computational approaches including molecular docking and molecular dynamics simulation. These computational modelling methods enabled us to analyse parameters, for example principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, hydrogen bond occupancy, thermodynamics calculation and ligand–residue interaction. Findings from these analyses revealed that UM-164 exhibited a higher binding affinity of −9.9 kcal mol⁻¹ with lyn protein than Dasatinib, with a binding affinity of −8.3 kcal mol⁻¹ on docking. It was observed that the binding of UM-164 to lyn protein decreases the capacity of its loop to fluctuate, influences the ligand optimum orientation on the conformational space of lyn protein, and increases the hydrogen bond formation in the lyn-UM-164 system. Also, an increase in drug binding energy of UM-164 was recorded with increasing residue correlation in the lyn-UM-164 system. It is quite informative to note that Met85 was a key stabilising factor in the binding of UM-164 to lyn protein. These findings can provide important insights that will potentially serve as a baseline in the design of novel lyn inhibitors. It could also stimulate further research into multidimensional approaches required to curb the influence of lyn protein in TNBC.