title: In silico and in vitro methods to identify ebola virus VP35-dsRNA inhibitors.
abstract: Ebola virus continues to be problematic as sporadic outbreaks in Africa continue to arise, and as terrorist organizations have considered the virus for bioterrorism use. Several proteins within the virus have been targeted for antiviral chemotherapy, including VP35, a dsRNA binding protein that promotes viral replication, protects dsRNA from degradation, and prevents detection of the viral genome by immune complexes. To augment the scope of our antiviral research, we have now employed molecular modeling techniques to enrich the population of compounds for further testing in vitro. In the initial docking of a static VP35 structure with an 80,000 compound library, 40 compounds were selected, of which four compounds inhibited VP35 with IC50<200μM, with the best compounds having an IC50of 20μM. By superimposing 26 VP35 structures, we determined four aspartic acid residues were highly flexible and the docking was repeated under flexible parameters. Of 14 compounds chosen for testing, five compounds inhibited VP35 with IC50<200μM and one compound with an IC50of 4μM. These studies demonstrate the value of docking in silico for enriching compounds for testing in vitro, and specifically using multiple structures as a guide for detecting flexibility and provide a foundation for further development of small molecule inhibitors directed towards VP35.
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Glanzer
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
authors.forename: Brendan M
authors.initials: BM
authors.lastname: Byrne
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: McCoy
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: James
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Frank
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, United States.
authors.forename: Greg G
authors.initials: GG
authors.lastname: Oakley
mesh_terms: D000998:Antiviral Agents / Q000737:chemistry / Q000494:pharmacology*; D003198:Computer Simulation; D004305:Dose-Response Relationship, Drug; D062105:Molecular Docking Simulation; D015394:Molecular Structure; D019590:Nucleocapsid Proteins; D009698:Nucleoproteins / Q000037:antagonists & inhibitors*; D013329:Structure-Activity Relationship; D014758:Viral Core Proteins / Q000037:antagonists & inhibitors*
chemical_list: D000998:Antiviral Agents; D019590:Nucleocapsid Proteins; D009698:Nucleoproteins; D014758:Viral Core Proteins; C084818:nucleoprotein VP35, Ebola virus
keywords: Ebola; Inhibitor; Innate immune response; Molecular dynamic modeling; VP35