Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms and Relative State Populations

TL;DR

This study uses advanced simulations to explore how compound mutations in Abl1 kinase alter its conformational dynamics, leading to inhibitor resistance by stabilizing specific inactive states and revealing potential drug targets.

Contribution

It provides the first comprehensive simulation-based analysis of DFG flip pathways in Abl1 and its resistant variants, identifying molecular mechanisms and intermediate states involved in inhibitor resistance.

Findings

Mutations increase the free energy barrier of DFG flip, stabilizing resistant conformations.

Multiple DFG flip pathways and intermediate states were identified.

Resistant variants show altered state populations affecting inhibitor binding.

Abstract

The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate their activity in response to different stimuli. These conformational changes constitute a conserved mechanism for self-regulation that dramatically impacts kinases' affinities for inhibitors. Few studies have attempted to extensively sample the pathways and elucidate the mechanisms that underlie kinase inactivation. Seeking to bridge this knowledge gap, we present a thorough analysis of the ``DFG flip'' inactivation pathway in Abl1 kinase. By leveraging the power of the Weighted Ensemble methodology, which accelerates sampling without the use of biasing forces, we have comprehensively simulated DFG flip events in Abl1 and its inhibitor-resistant variants, revealing a rugged landscape punctuated by potentially druggable intermediate states. Through our strategy, we successfully simulated dozens of uncorrelated DFG flip events distributed along two principal pathways, identified the molecular mechanisms that govern them, and measured their relative probabilities. Further, we show that the compound Glu255Lys/Val Thr315Ile Abl1 variants owe their inhibitor resistance phenotype to an increase in the free energy barrier associated with completing the DFG flip. This barrier stabilizes Abl1 variants in conformations that can lead to loss of binding for Type-II inhibitors such as Imatinib or Ponatinib. Finally, we contrast our Abl1 observations with the relative state distributions and propensity for undergoing a DFG flip of evolutionarily-related protein tyrosine kinases with diverging Type-II inhibitor binding affinities. Altogether, we expect that our work will be of significant importance for protein tyrosine kinase inhibitor discovery.