Molecular Docking Study for Screening Inhibitors for Nipah Virus Glycoprotein G
Nipah virus (NiV) is a highly pathogenic zoonotic virus from the Paramyxoviridae family that causes high mortality rates during outbreaks. NiV is an 18.2 kb negative-sense single-stranded RNA genome composed of 6 genes that encode 9 proteins including a glycoprotein G. The NiV-G protein interacts with the host cell surface receptors ephrin B2 or B3. This study used the computational structure-based screening system for screening the list of FDA approved library for compounds that might interact with NiV-G protein. The Schrodinger LLC Maestro suite software was used to prepare NiV-G protein (PDB ID: 3D11) ligand-binding site. The selected site was implemented for grid generation and a grid box generated at the centroid of the active site. Then the structure based virtual screening of FDA approved library of Selleckchem databse containing 1587 compounds was implemented and filtered by Extra Precision (XP) filtration protocol implemented in the Glide program. The ligand was docked with the active site and the final docking score, glide energy, and glide emodel values were recorded. A total of 93 FDA approved compounds were narrowed down by the Glide XP and the six lead molecules were sorted: Rutin (Rutoside), Iopromide, Fidaxomicin, Amikacin disulfate, Citicoline sodium and Digoxin with docking scores (kcal/mol) -6.298, -5.946, -5.41, -5.303, -5.165 and -4.959, respectively. The Glide energy (kcal/mol) for the six molecules was -39.02, -39.975, -44.637, -43.986, -38.041 and -51.023, respectively. The Glide Emodel (kcal/mol) for the six molecules was -41.842, -37.731, -45.419, -46.586, -41.678 and -54.319, respectively. These compounds exhibit potential to interact with the NiV-G binding site that might block its attachment to the ephrinB3 receptor and may inhibit viral entry. Among the screened compounds, rutin and digoxin have shown antiviral potential against certain viruses, which can be implicated in repurposing these molecules for developing antiviral agents against NiV.
Keywords: nipah virus, glycoprotein G, molecular docking, small molecule inhibitors, antiviral