Molecular Mechanisms of Quizartinib Resistance in FLT3 Mutants

Abstract

Quizartinib, a type II FLT3 inhibitor approved for FLT3-ITD-positive acute myeloid leukemia (AML), is frequently limited by acquired resistance, which arises in up to 40% of patients with disease progression and is driven largely by the D835Y and F691L kinase-domain mutations. To define the underlying mechanisms, we performed triplicate 200-ns all-atom molecular dynamics simulations of wild-type FLT3, FLT3-D835Y, and FLT3-F691L in complex with Quizartinib, combining conformational analysis, MM-GBSA binding free-energy calculations, and binding-pocket characterization. Both mutations destabilized the inactive DFG-out conformation required for type II inhibitor binding, with mean binding free-energy reductions of 5 kcal/mol for D835Y and 10 kcal/mol for F691L relative to wild-type. D835Y disrupted the activation-loop electrostatic network and reduced Cys694 hydrogen-bond occupancy from 85% to 45%, whereas F691L abolished key van der Waals contacts and opened a 120 cubic Angstrom hydrophobic void at the gatekeeper position. Both mutants sampled a wider range of conformations and lost 14-17% of binding-pocket volume. These predictions were corroborated by CCK-8 viability assays and Western blotting of p-FLT3 (Y591) in Ba/F3 cells, which reproduced the predicted resistance hierarchy (F691L > D835Y > WT) at the cellular level. Together, these results indicate that D835Y and F691L confer resistance through distinct electrostatic and hydrophobic mechanisms that converge on destabilization of the inactive kinase conformation, providing a structural basis for the design of next-generation FLT3 inhibitors.