title: Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins.
abstract: The chikungunya virus (CHIKV) envelope glycoproteins are considered important potential targets for anti-CHIKV drug discovery due to their crucial roles in virus attachment and virus entry. In this study, using two available crystal structures of the immature and mature forms of envelope glycoproteins, virtual screenings based on blind dockings and focused dockings were carried out to identify potential binding pockets and hit compounds for the virus. The chemical library database of compounds, NCI Diversity Set II, was used in these docking studies. In addition to reproducing previously reported examples, new binding pockets were identified, e.g., Pocket 2 in the 3N40, and Pocket 2 and Pocket 3 in the 3N42. Convergences in conformational sampling in docking using AutoDock Vina were evaluated. An analysis of docking results was carried out to understand interactions of the envelope glycoproteins complexes. Some key residues for interactions, for example Gly91 and His230, are identified as possessing important roles in the fusion process.
authors.affiliation: School of Chemistry, University of Wollongong, Wollongong, 2522, Australia.|Faculty of Pharmacy, University of Medicine and Pharmacy at Hochiminh City, 41 Dinh Tien Hoang, District 1, Hochiminh, Vietnam.
authors.forename: Phuong T V
authors.initials: PTV
authors.lastname: Nguyen
authors.affiliation: School of Chemistry, University of Wollongong, Wollongong, 2522, Australia. hyu@uow.edu.au.
authors.forename: Haibo
authors.initials: H
authors.lastname: Yu
authors.affiliation: School of Chemistry, University of Wollongong, Wollongong, 2522, Australia. keller@uow.edu.au.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Keller
mesh_terms: D000998:Antiviral Agents / Q000494:pharmacology*; D001665:Binding Sites; D002646:Chikungunya virus / Q000187:drug effects*; D006023:Glycoproteins / Q000037:antagonists & inhibitors* / Q000737:chemistry; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D014759:Viral Envelope Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry
chemical_list: D000998:Antiviral Agents; D006023:Glycoproteins; D014759:Viral Envelope Proteins
keywords: Binding pockets; Chikungunya virus; Envelope glycoproteins; Hit compounds; Molecular docking; Virtual screening