Computational Insights into the Resistance of the Gatekeeper Mutation V564F of FGFR2 Against Pemigatinib

Abstract

The fibroblast growth factor receptor 2 (FGFR2), a transmembrane receptor tyrosine kinase, is implicated in a plethora of human cancers, including intrahepatic cholangiocarcinomas. The clinically relevant V564F gatekeeper mutation conferred resistance to the current FGFR2 drug−Pemigatinib. Here, we conducted integrated computational methods to compare the protein−ligand interactions between the FGFR2 kinase domain in the wild-type and V564F mutant states and Pemigatinib. Based on molecular docking, molecular dynamic simulations and hydrogen bond analysis, we revealed that the reduced hydrogen bonding interactions in the V564F mutant were the key factor to decrease the binding affinity of Pemigatinib to the FGFR2. The per-residue free energy decomposition analysis implemented by the molecular mechanics/generalized born surface area method revealed the reduced contributions from the key residues G488, F564 and A567 located at the kinase hinge domain were responsible for the decreased binding affinity in the V564F mutant. This study elucidated the molecular mechanism for the resistance of Pemigatinib in FGFR2 triggered by the V564F mutation and may provide insights for future drug development and optimization.