Molecular dynamics characterization of marine alkaloid binding to the SARS-CoV-2 KP.2 receptor-binding domain

The KP.2 receptor-binding domain (RBD) contains the F456L substitution within the receptor-binding motif (RBM), where ligand binding was evaluated in this study. Three marine fungal alkaloids, Versiquinazoline A (VQA), Spirobrocazine A (SBA), and Notoamide O (NTO), were selected from the CMNPD library and evaluated by triplicate all-atom molecular dynamics (MD) simulations. The KP.2-L456 Apo and ligand-bound systems were simulated for 400 ns in triplicate, and the corresponding F456 controls on the same KP.2 sequence background were simulated for 300 ns in triplicate. Protein backbone RMSD and radius of gyration analyses showed preservation of the global RBD fold across all systems. In the L456 background, VQA showed the lowest late-stage ensemble-average ligand RMSD, whereas SBA and NTO exhibited greater replicate-dependent pose variability. MM/PBSA calculations yielded overlapping replicate-level energy distributions; NTO had the most negative mean total-energy estimate, while VQA showed more persistent poses and concentrated distance distributions involving residue 456, TYR473, and TYR488. Common-basis PCA and free-energy landscape analysis showed that VQA increased projected RBM conformational dispersion relative to Apo. Overall, these results prioritise VQA as a computational candidate based on pose persistence and residue-contact distributions, although experimental validation is required to determine binding affinity and antiviral activity.