Elucidating structure-activity relationships of benzopyran derivatives as inhibitors of Chikungunya virus nsP2 and nsP4 via integrated docking, molecular dynamics, and DFT studies.

Chikungunya virus (CHIKV) poses a significant public health threat with no approved antivirals. The viral non-structural proteins nsP2 (a cysteine protease) and nsP4 (an RNA-dependent RNA polymerase) are essential for viral replication and represent attractive drug targets. We evaluated fifteen benzopyran derivatives as dual-targeting inhibitors using integrated computational approaches, including molecular docking, 100 ns all-atom molecular dynamics simulations, MM-GBSA binding free energy calculations, and DFT quantum chemical analysis. Four compounds emerged as lead candidates: 3b and 3e for nsP2 targeting (docking scores -7.0 and -6.4 kcal/mol; MM-GBSA ΔG = -19.02 and -16.10 kcal/mol), and 3d and 3o for nsP4 targeting (docking scores -7.2 and -7.4 kcal/mol; MM-GBSA ΔG = -22.89 and -17.63 kcal/mol). All four compounds outperformed the reference inhibitors in terms of molecular dynamics stability. RMSD, RMSF, and radius of gyration profiles demonstrated that ligand binding attenuated conformational fluctuations and preserved protein structural integrity. DFT analysis revealed distinct electronic properties: compounds 3b and 3d possess favorable electrophilicity indices (18.679 and 14.172 eV) facilitating charge-assisted interactions with catalytic residues, while compounds 3e and 3o exhibit larger HOMO-LUMO gaps (2.476 and 2.503 eV) indicating greater thermodynamic stability compatible with hydrophobic binding environments. The binding selectivity arises from integration of electronic properties, geometric complementarity to active sites, and dynamic stabilization during molecular dynamics simulations. Benzopyran derivatives 3b, 3e, 3d, and 3o represent promising candidates for experimental antiviral validation, with distinct selectivity profiles enabling targeted inhibition of specific viral enzymes. These findings provide a computational foundation for lead optimization toward CHIKV therapeutics.