In Silico Screening of 10 Natural Compounds from Oroxylum indicum and Other Medicinal Plants against SARS-CoV-2 Mpro

Abstract

This study conducted structure-based virtual screening using AutoDock Vina to assess the inhibitory potential of ten natural compounds against the main protease (Mpro/3CLpro, PDB: 6LU7) of SARS-CoV-2. The study aimed to identify promising anti-SARS-CoV-2 candidates from Oroxylum indicum and other medicinal plants. Six compounds were sourced from Oroxylum indicum: Oroxin B, Quercetin, Quercitrin, Isoquercitrin, Rutin, and Baicalein; four additional compounds were sourced from other medicinal plants: Artemisinin (Artemisia annua), Naringenin (Citrus spp.), 6-Gingerol (Zingiber officinale), and Andrographolide (Andrographis paniculata). All ten compounds established stable interactions within the Mpro active site, with ΔG values ranging from −5.2 to −7.3 kcal/mol. Artemisinin demonstrated the highest binding affinity (−7.3 kcal/mol) and the highest Ligand Efficiency (LE = 0.365 kcal/mol/HA), surpassing Favipiravir and approaching Remdesivir in per-atom efficiency. Detailed PLIP v2.4.0 interaction analysis identified conserved key residues GLN110 (present in 9/10 complexes), THR111, VAL104, PHE294, LYS5, GLU288/290, and LYS137, with diverse interaction types including H-bonds (1–10 per complex), hydrophobic contacts, salt bridges, π-cation, and π-stacking interactions. Baicalein, Naringenin, Quercetin, and Artemisinin fully satisfied Lipinski and Veber criteria, predicting favorable oral bioavailability. These results provide a multi-level in silico evidence base supporting preclinical research on Oroxylum indicum constituents and Vietnamese medicinal plant-derived compounds as anti-SARS-CoV-2 candidates.