Deciphering the Antagonistic Nature of Phytocompounds Against Chikungunya Virus nsP2 Protease: A Combined Virtual Screening, Docking, Molecular Dynamics, and DFT Investigation

ABSTRACT Chikungunya virus (CHIKV) remains a significant global health threat due to recurrent outbreaks and the lack of approved antiviral therapies. The viral non‐structural protein 2 (nsP2) protease, which is crucial for viral replication and immune evasion, is a promising drug target. In this study, an integrated computational approach combining virtual screening, molecular docking, molecular dynamics (MD) simulations, and quantum chemical analysis (DFT) was employed to identify phytochemical inhibitors of CHIKV nsP2. A library of 5000 antiviral phytochemicals was filtered using drug‐likeness and ADMET criteria, yielding 17 candidates for docking. Protocol validation using known inhibitors (E‐64 and Ribostamycin sulfate) produced RMSD values <2.5 Å. Isorhamnetin (−8.7 kcal/mol) and apigenin (−8.2 kcal/mol) showed strong binding affinity and stable interactions with the catalytic dyad (Cys478–His548). Alanine mutagenesis confirmed the importance of these residues. MD simulations demonstrated structural stability and favorable binding energies, with isorhamnetin exhibiting superior performance. DFT analysis revealed enhanced electronic adaptability of isorhamnetin, supporting its binding efficiency. Overall, isorhamnetin emerges as a promising natural scaffold for nsP2 inhibition, warranting further experimental validation.