Molecular Dynamics–Based validation of a quinazoline-based KRAS inhibitor (C9) identified through QSAR-guided discovery

Background KRAS remains one of the most challenging oncogenic targets in lung cancer because of its shallow binding surfaces, conformational flexibility, and limited availability of druggable pockets. In a preceding QSAR-guided screening and molecular docking study, compound C9, a quinazoline-based scaffold, was identified as a potential KRAS inhibitor. However, static docking alone is insufficient to fully characterize ligand stability, conformational persistence, and energetic behavior within dynamic solvent environments. Therefore, the present study employed molecular dynamics (MD) simulations and end-point free energy calculations to further investigate the dynamic interaction profile of C9 within the KRAS binding pocket. Methods The four top-ranked docking poses of C9 (Modes 1–4) were subjected to 200 ns explicit-solvent molecular dynamics simulations. Structural stability and conformational behavior were evaluated using root-mean-square deviation root-mean-square fluctuation (RMSF), radius of gyration (Rg), dynamic cross-correlation matrix (DCCM), principal component analysis (PCA), center-of-mass distance analysis, and residue-wise ligand contact frequency profiling. Binding energetics were further assessed using MM-GBSA and MM-PBSA calculations with energy decomposition analyses. Results The four binding modes exhibited distinct dynamic and energetic behaviors during the simulations. Modes one and 3 demonstrated comparatively greater structural persistence and reduced conformational instability relative to Modes 2 and 4. Mode one maintained prolonged ligand contact persistence with key switch-region residues, compact conformational sampling, and relatively stable COM distance profiles throughout most of the trajectory. PCA further revealed a comparatively confined conformational basin for Mode 1, consistent with restricted collective motions and reduced conformational dispersion. However, MM-GBSA and MM-PBSA analyses identified unusually large van der Waals energy fluctuations in Modes 1, 2, and 4, suggesting transient steric instability or nonphysical energetic excursions during portions of the simulations. In contrast, Mode 3 exhibited comparatively more stable and physically interpretable interaction energy profiles with sustained negative interaction energies and reduced fluctuation amplitudes. Across all systems, electrostatic interactions represented the dominant favorable energetic contribution to KRAS–C9 binding. Conclusion The combined structural, dynamic, and energetic analyses indicate that C9 is capable of adopting dynamically persistent binding conformations within the KRAS binding pocket. Among the evaluated docking modes, Modes one and 3 exhibited the most favorable balance between structural persistence and energetic stability. These findings provide computational support for the potential of the quinazoline-based scaffold C9 as a candidate KRAS-targeting compound and establish a mechanistic framework for future structure-guided optimization and experimental validation in KRAS-driven lung cancer systems.