Using Multiscale Molecular Modeling to Analyze Possible NS2b-NS3 Protease Inhibitors from Philippine Medicinal Plants

Abstract

Within the field of Philippine folkloric medicine, the utilization of indigenous plants like Euphorbia hirta (tawa-tawa), Carica papaya (papaya), and Psidium guajava (guava) as potential dengue remedies has gained attention. Yet, limited research exists on their comprehensive effects, particularly their anti-dengue activity. This study screened 2944 phytochemicals from various Philippine plants for anti-dengue activity. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling provided 1265 compounds demonstrating pharmacokinetic profiles suitable for human use. Molecular docking targeting the dengue virus NS2b-NS3 protease’s catalytic triad (Asp 75, Ser 135, and His 51) identified ten ligands with higher docking scores than reference compounds idelalisib and nintedanib. Molecular dynamics simulations confirmed the stability of eight of these ligand–protease complexes. Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) analysis highlighted six ligands, including veramiline (−80.682 kJ/mol), cyclobranol (−70.943 kJ/mol), chlorogenin (−63.279 kJ/mol), 25beta-Hydroxyverazine (−61.951 kJ/mol), etiolin (−59.923 kJ/mol), and ecliptalbine (−56.932 kJ/mol) with favorable binding energies, high oral bioavailability, and drug-like properties. This integration of traditional medical knowledge with advanced computational drug discovery methods paves new pathways for the development of treatments for dengue.

Keywords

• molecular modeling
• computer-aided drug design
• dengue virus
• NS2b-NS3 protease
• phytochemicals