Structural and energetic insights into SARS ‐ CoV ‐2 nucleocapsid protein inhibitors from molecular dynamics and MM ‐ PBSA analyses

Abstract The SARS‐CoV‐2 nucleocapsid (N) protein is a key regulator of viral genome packaging and replication, making it an attractive antiviral target. Here, we provide structural and energetic insights into N‐protein inhibition using molecular docking, pharmacophore screening, molecular dynamics (MD) simulations, and MM‐PBSA analyses. Experimentally known inhibitors Onalespib, JQ‐1, and Zotatifin were used to construct pharmacophores that screened the ZINC database, yielding 927 hits. Three top candidates, ZINC37602048, ZINC06246181, and ZINC12077824, underwent 150 ns MD simulations to assess their long‐term dynamic stability within the N‐protein binding pocket. MM‐PBSA calculations over the 150 ns trajectories revealed strong binding for ZINC37602048 (−27.24 kcal/mol) and ZINC06246181 (−22.81 kcal/mol), driven mainly by van der Waals contributions, whereas ZINC12077824 showed comparatively weaker, though still favorable, affinity (−18.91 kcal/mol) owing to a large unfavorable electrostatic contribution partially offset by polar solvation. These results highlight promising scaffolds for further optimization and underscore the utility of MD and free energy‐based methods in guiding antiviral drug discovery targeting the SARS‐CoV‐2 N protein.