Metadynamics reveals luteolin-mediated conformational stabilization against avapritinib-resistant PDGFRα D842V/G680R GIST.

Gastrointestinal stromal tumors (GISTs) driven by PDGFRα D842V mutations respond robustly to avapritinib, but acquired resistance through secondary mutations such as G680R creates steric hindrance that compromises drug binding. Current therapeutic options for compound-resistant PDGFRα mutations remain limited. We employed integrated computational simulations including molecular docking, classical molecular dynamics (300 ns), and well-tempered metadynamics to evaluate luteolin as an allosteric conformational stabilizer for avapritinib, binding against the PDGFRα D842V/G680R double mutant. Luteolin demonstrated a binding affinity comparable to avapritinib (− 10.0 vs. − 9.9 kcal/mol), binding to an adjacent site distinct from the ATP-binding pocket. The 300 ns MD simulations revealed complete dissociation of avapritinib (> 30 Å RMSD) in the absence of luteolin, whereas stable binding (4–10 Å RMSD) was maintained in its presence. Metadynamics simulation showed that luteolin restricts Arg680 to a gauche conformation, creating energy barriers of approximately 14 kcal/mol that prevent dissociative transitions, increasing the overall dissociation barriers by ~ 4 kcal/mol. Luteolin functions as an allosteric conformational stabilizer that enhances avapritinib retention against resistant PDGFRα mutations. This mechanism-based approach offers a novel strategy to overcome compound resistance while preserving established therapeutic pathways, warranting experimental validation in cellular and preclinical models.