Identification of potential inhibitors of dengue virus ns5 methyltransferase and polymerase domains through virtual screening and molecular dynamics studies

Abstract

Context: The dengue virus continues to pose a serious global health challenge due to the absence of effective antiviral therapies. Non-structural protein 5 (NS5), a multifunctional non-structural protein containing methyltransferase and RNA-dependent RNA polymerase domains, is essential for viral replication and represents a high-priority therapeutic target. In this study, potential inhibitors targeting two functional sites of Dengue virus serotype 3 (DENV-3) NS5 were identified through structure-based virtual screening and structural dynamics analysis. Docking results identified PubChem compound 135,625,223 as the strongest binder at the RNA-binding site with a binding affinity of - 11.8 kcal/mol, forming a hydrogen bond with Arg₄₈₁ and a hydrophobic interaction with Phe₄₈₅. Molecular dynamics simulations showed that the S-adenosylmethionine (SAM)-binding site ligand formed a more stable complex with lower root-mean-square deviation (RMSD) (0.26 nm) and reduced flexibility, indicating a promising lead candidate for further optimization and experimental validation against dengue virus NS5.

Methods: The full-length NS5 structure was constructed using homology modeling with MODELLER, ab initio modeling, and AlphaFold, and the best model was selected based on low RMSD and stereochemical quality. A library of 587 antiviral compounds retrieved from PubChem was docked against the SAM-binding site of the methyltransferase domain and the RNA-binding site of the polymerase domain using AutoDock Vina. The top-ranked ligands were further evaluated through Insilico screening and 300-ns molecular dynamics simulations using GROMACS.

Keywords: Dengue virus NS5; Dual-site inhibitors; Molecular dynamics; Structure-based drug discovery; Virtual screening.