title: Identification of potential hit compounds for Dengue virus NS2B/NS3 protease inhibitors by combining virtual screening and binding free energy calculations.
abstract: Dengue virus (DV) infections are a serious public health problem and there is currently no vaccine or drug treatment. NS2B/NS3 protease, an essential enzyme for viral replication, is one of the promising targets in the search for drugs against DV. In this research work, virtual screening (VS) was carried out on four multi-conformational databases using several criteria. Firstly, molecular dynamics simulations of the NS2B/NS3 protease and four known inhibitors, which reveal an importance of both electrostatic and van der Waals interactions in stabilizing the ligand-enzyme interaction, were used to generate three different pharmacophore models (a structure-based, a static and a dynamic). Subsequently, these three models were employed for pharmacophore search in the VS. Secondly, compounds passing the first criterion were further reduced using the Lipinski's rule of five to keep only compounds with drug-like properties. Thirdly, molecular docking calculations were performed to remove compounds with unsuitable ligand-enzyme interactions. Finally, binding free energy of each compound was calculated. Compounds having better energy than the known inhibitors were selected and thus 20 potential hits were obtained.
authors.affiliation: Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: K
authors.initials: K
authors.lastname: Wichapong
authors.forename: A
authors.initials: A
authors.lastname: Nueangaudom
authors.forename: S
authors.initials: S
authors.lastname: Pianwanit
authors.forename: W
authors.initials: W
authors.lastname: Sippl
authors.forename: S
authors.initials: S
authors.lastname: Kokpol
mesh_terms: D003716:Dengue Virus / Q000187:drug effects* / Q000201:enzymology*; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D056004:Molecular Dynamics Simulation; D011480:Protease Inhibitors / Q000302:isolation & purification*; D011485:Protein Binding; D012697:Serine Endopeptidases / Q000378:metabolism*; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors*; D000085242:Viral Proteases
chemical_list: D011480:Protease Inhibitors; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C080102:NS2B protein, flavivirus; C504449:NS3 protease, dengue virus; D000085242:Viral Proteases