title: Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence.
abstract: The dengue virus (DENV) has four well-known serotypes, namely DENV1 to DENV4, which together cause 50-100 million infections worldwide each year. DENV NS2B/NS3pro is a protease recognized as a valid target for DENV antiviral drug discovery. However, NS2B/NS3pro conformational flexibility, involving in particular the NS2B region, is not yet completely understood and, hence, a big challenge for any virtual screening (VS) campaign. Molecular dynamics (MD) simulations were performed in this study to explore the DENV3 NS2B/NS3pro binding-site flexibility and obtain guidelines for further VS studies. MD simulations were done with and without the Bz-nKRR-H inhibitor, showing that the NS2B region stays close to the NS3pro core even in the ligand-free structure. Binding-site conformational states obtained from the simulations were clustered and further analysed using GRID/PCA, identifying four conformations of potential importance for VS studies. A virtual screening applied to a set of 31 peptide-based DENV NS2B/NS3pro inhibitors, taken from literature, illustrated that selective alternative pharmacophore models can be constructed based on conformations derived from MD simulations. For the first time, the NS2B/NS3pro binding-site flexibility was evaluated for all DENV serotypes using homology models followed by MD simulations. Interestingly, the number of NS2B/NS3pro conformational states differed depending on the serotype. Binding-site differences could be identified that may be crucial to subsequent VS studies.
authors.affiliation: Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Erika
authors.initials: E
authors.lastname: Piccirillo
authors.affiliation: Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Merget
authors.affiliation: Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
authors.forename: Christoph A
authors.initials: CA
authors.lastname: Sotriffer
authors.affiliation: Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil. atdamara@iq.usp.br.
authors.forename: Antonia T
authors.identifier: http://orcid.org/0000-0003-2937-5255
authors.initials: AT
authors.lastname: do Amaral
mesh_terms: D001665:Binding Sites; D003715:Dengue / Q000188:drug therapy / Q000821:virology; D003716:Dengue Virus / Q000187:drug effects* / Q000201:enzymology* / Q000235:genetics; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry / Q000494:pharmacology*; D011487:Protein Conformation; D065288:Serogroup; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism
chemical_list: D004791:Enzyme Inhibitors; C080102:NS2B protein, flavivirus; D010455:Peptides; D017361:Viral Nonstructural Proteins
keywords: Conformational flexibility; Dengue virus; Molecular dynamics simulations; NS2B/NS3 protease