Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases

Abstract

Understanding how point mutations can render a ligand or a drug ineffective against a given biological target is a problem of immense fundamental and practical relevance. Often the efficacy of such resistance mutations can be explained purely on a thermo-dynamic basis wherein the mutated system displays a reduced binding affinity for the ligand. However, the more perplexing and harder to explain situation is when two protein sequences have the same binding affinity for a drug. In this work, we demonstrate how all-atom molecular dynamics simulations, specifically using recent developments grounded in statistical mechanics and information theory, can provide a detailed mechanistic rationale for such variances. We establish the dissociation mechanism for the popular anti-cancer drug Imatinib (Gleevec) against wild-type and N387S mutant of Abl kinase. We show how this single point mutation triggers a non-local response in the proteins flexibility and eventually leads to pathway differentiation during dissociation. This pathway differentiation explains why Gleevec has a long residence time in the wild-type Abl, but for the mutant, by opening up a backdoor pathway for ligand exit, an order of magnitude shorter residence time is obtained. We thus believe that this work marks an efficient and scalable approach to pinpoint the molecular determinants of resistance mutations in biomolecular receptors of pharmacological relevance that are hard to explain using a simple structural perspective and require mechanistic and kinetic insights. Significance statementRelapse in late-stage cancer patients is often correlated with the onset of drug resistance mutations. Some of these mutations are very far from the binding site and thus hard to explain from a purely structural perspective. Here we employ all-atom molecular dynamics simulations aided by ideas from information theory that can reach timescales of seconds with minimal human bias in how the sampling is enhanced. Through these we explain how a single point mutation triggers a non-local response in the protein kinases flexibility and eventually leads to pathway differentiation during dissociation, thereby significantly reducing the residence time of the drug.