Allosteric co-binding restores tyrosine kinase inhibitor affinity in T790M-mutant EGFR through conformational reprogramming

Drug resistance in epidermal growth factor receptor (EGFR)–mutant cancers commonly arises from kinase-domain substitutions that remodel the adenosine triphosphate binding pocket and reduce complementarity to orthosteric inhibitors, with the T790M gatekeeper mutation posing a major challenge. This study evaluated whether pre-occupying a proximal allosteric pocket with selected phytochemicals could bias mutant EGFR toward drug-compatible conformations and improve inhibitor binding. A two-phase computational workflow was employed: (i) molecular docking of gefitinib and erlotinib to wild-type and mutant EGFR; and (ii) allosteric pre-docking of phytochemicals followed by redocking of the ATP–site inhibitor. Top-ranked complexes were advanced to 200-nanosecond all-atom molecular dynamics simulations in explicit solvent and end-state binding free-energy estimation using Molecular Mechanics Generalized Born Surface Area (MM/GBSA). Docking predicted stronger binding to wild-type EGFR and reduced affinity for the T790M mutant, whereas co-binding produced compound-dependent improvements. Simulations suggested partial stabilization of the protein–ligand complexes, characterized by reduced root mean square deviation, damped hinge and αC-helix motions, reduced solvent exposure, and radii of gyration approaching wild-type behavior. Binding free energies improved from −12.6 to −17.6 kcal mol−1 (Genistein) and −19.58 kcal mol−1 (Tupichinols C) for gefitinib, and from −13.4 to −18.1 and −20.1 kcal mol−1, respectively, for erlotinib. Absorption, distribution, metabolism, excretion, and toxicity screening supported the developability of the leading candidates. This integrated framework provides structural, dynamic, and energetic criteria for prioritize cooperative allosteric–orthosteric co-binding chemotypes for experimental validation.