Coupled Solvent Dynamics and Protein Dynamics Help Drive Functional Differences in Exon-19 Deletion Mutants in the Epidermal Growth Factor Receptor (EGFR/ErbB1/HER1) Kinase Domain

Deletions in Exon-19 of the epidermal growth factor receptor (EGFR) play a pivotal role in the pathogenesis of non-small cell lung cancer (NSCLC), influencing patient response to tyrosine kinase inhibitors (TKIs). Although these mutations are known to affect treatment efficacy, the precise molecular mechanisms have been unclear. Building upon recent insights from the study [DOI: 10.1038/s41467-022-34398-z], which identified two distinct mutation profiles associated with differential drug sensitivity and clinical outcomes, our research delves into the molecular dynamics that drive these variances.

We employed molecular dynamics simulations, enhanced sampling methods, and machine learning to classify Exon-19 deletion mutations into two profiles based on their conformational dynamics. Profile 1 mutations display only localized motions in key subdomains in their fluctuations about the equilibrium state, and a high affinity for ATP and consequent resistance to TKIs, while profile 2 mutations show reduced ATP binding affinity due to delocalized motion characterized by an increased flexibility between the N-and C-lobes of the EGFR kinase domain. This structural flexibility perturbs the ATP binding site, leading to decreased affinity and, heightened sensitivity to TKIs.

Our use of the INDUS technique has shed light on the collective solvent dynamics, further elucidating the coupling between long timescale solvent fluctuations and protein conformational dynamics, that likely contributes to the observations in HDX-MS studies. Our free energy analysis, covering timescales relevant to both HDX-MS and ligand interaction, provides a deeper understanding of the relationship between protein and solvent dynamics and their collective impact on drug efficacy in NSCLC with EGFR Exon-19 deletions.