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 critical role in the pathogenesis of non-small cell lung cancer (NSCLC) and influence patient response to tyrosine kinase inhibitors (TKIs). Although these mutations are known to influence treatment efficacy, the precise molecular mechanisms are unclear. Building on recent insights from the study (DOI: 10.1038/s41467-022-34398-z), which identified two distinct mutation profiles associated with different drug sensitivity and clinical outcomes, our research delves deeper into the molecular dynamics driving these variances . We used molecular dynamics simulations, improved sampling methods, and machine learning to classify Exon-19 deletion mutations into two profiles based on their conformational dynamics. Profile 1 mutations show localized movements only in major subdomains in their fluctuations around 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 movement characterized by increased flexibility between the N and C lobes of the EGFR kinase domain. This structural flexibility disrupts the ATP binding site, leading to reduced affinity and increased sensitivity to TKIs. Our use of the INDUS technique has shed light on collective solvent dynamics, further elucidating the coupling between long-timescale solvent fluctuations and protein conformational dynamics, which likely contributes to the observations in HDX-MS studies. Our free energy analysis, which spans timescales relevant to both HDX-MS and ligand interaction, provides deeper insight into the relationship between protein and solvent dynamics and their collective impact on drug efficacy in NSCLC with EGFR Exon-19 deletions.