Allosteric inhibition of EGFR triple-mutant (L858R/T790M/C797S) in non-small cell lung cancer: an integrative conformational dynamics framework

The advent of Epidermal growth factor receptor (EGFR) C797S missense mutation, predominantly in a “triple mutant” conformation with L858R and T790M gatekeeper mutations, confers resistance to all approved Tyrosine kinase inhibitors (TKI) in non-small cell lung cancer (NSCLC). To examine resistance mechanism at the conformational level, fourth-generation TKIs were systematically compared against EGFR L858R/T790M/C797S triple mutant in both active (αC-in) and inactive (αC-out) states. Kinase-domain specific Molecular Dynamics analysis (residues 698–1014, block-averaged 300–400 ns) revealed that the inactive triple mutant (RMSD 0.45 ± 0.03 nm) adopts a more compact conformational ensemble than the active state, reducing ATP-site adaptability but enhancing allosteric retention. The BDTX-1535 inactive complex demonstrated stable ligand retention (ligand RMSD 0.67 ± 0.08 nm) and kinase domain compaction (Rg 2.007 ± 0.004 nm), unlike ATP-competitive TKIs which showed progressive ligand displacement; BDTX-1535 uniquely confined the inactive mutant kinase to a single dominant low-energy basin, while all ATP-competitive inhibitors sampled heterogeneous conformational ensembles. MM/PBSA analysis yielded converged ΔG_bind of − 28.93 ± 2.50, − 41.07 ± 1.24, − 33.53 ± 5.36, and − 17.63 ± 4.08 kcal/mol for BDTX-1535, TQB-3804, JND-3229, and BI-4020, respectively; per-residue decomposition reveals JND-3229’s apparent advantage partly reflects non-kinase contacts outside the catalytic domain, while TQB-3804’s superior energetics are mechanistically inaccessible at C797S-disrupted ATP site. Overall, BDTX-1535 emerges as the computationally most viable candidate through allosteric engagement of a C797S-unaffected pocket, stable ligand retention, and unique conformational confinement of the mutant kinase, collectively establishing an integrative quantum-to-dynamics framework for the rational design of resistance-overcoming inhibitors.