Research Article: Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

Date Published: January 13, 2009

Publisher: Public Library of Science

Author(s): Dariusz Ekonomiuk, Xun-Cheng Su, Kiyoshi Ozawa, Christophe Bodenreider, Siew Pheng Lim, Zheng Yin, Thomas H. Keller, David Beer, Viral Patel, Gottfried Otting, Amedeo Caflisch, Danzhi Huang, Diane Joseph-McCarthy

Abstract: BackgroundThe non-structural 3 protease (NS3pro) is an essential flaviviral enzyme and therefore one of the most promising targets for drug development against West Nile virus (WNV) and dengue infections.MethodologyIn this work, a small-molecule inhibitor of the WNV NS3pro has been identified by automatic fragment-based docking of about 12000 compounds and testing by nuclear magnetic resonance (NMR) spectroscopy of only 22 molecules. Specific binding of the inhibitor into the active site of NS3pro and its binding mode are confirmed by 15N-HSQC NMR spectra. The inhibitory activity is further validated by an enzymatic assay and a tryptophan fluorescence quenching assay.ConclusionThe inhibitor [4-(carbamimidoylsulfanylmethyl)-2,5-dimethylphenyl]-methylsulfanylmethanimidamide has a good ratio of binding affinity versus molecular weight (ligand efficiency of 0.33 kcal/mol per non-hydrogen atom), and thus has good potential as lead compound for further development to combat West Nile virus infections.

Partial Text: West Nile virus (WNV) and the closely related dengue virus, members of the family Flaviviridae, are worldwide-spread global threats transmitted by mosquito bites. WNV encephalitis infects mainly birds but also other vertebrates including humans. It has been reported in four continents during the last decade [1] and has been spreading in North America causing several thousand cases per year since 1999 [2]. Despite its growing distribution and epidemic character, there are no specific antiviral treatments that can prevent or cure this infection.

The in silico screening was performed by a fragment-based docking procedure and an efficient evaluation of binding free energy with electrostatic solvation. All of the calculations were performed on the WNV protease from its complex with the tetrapeptide inhibitor Bz-Nle-Lys-Arg-Arg-H (PDB code 2fp7 [10]).



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