title: Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme.
abstract: The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has become an attractive target for anti-HCV therapy. Using a high-throughput screen, we discovered a novel NS5B inhibitor that binds to the enzyme noncompetitively with respect to nucleotide substrates. Here we report the crystal structure of NS5B complexed with this small molecule inhibitor. Unexpectedly, the inhibitor is bound within a narrow cleft on the protein's surface in the "thumb" domain, about 30 A from the enzyme's catalytic center. The interaction between this inhibitor and NS5B occurs without dramatic changes to the structure of the protein, and sequence analysis suggests that the binding site is conserved across known HCV genotypes. Possible mechanisms of inhibition include perturbation of protein dynamics, interference with RNA binding, and disruption of enzyme oligomerization.
authors.affiliation: Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. robert.love@pfizer.com
authors.forename: Robert A
authors.initials: RA
authors.lastname: Love
authors.forename: Hans E
authors.initials: HE
authors.lastname: Parge
authors.forename: Xiu
authors.initials: X
authors.lastname: Yu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hickey
authors.forename: Wade
authors.initials: W
authors.lastname: Diehl
authors.forename: Jingjin
authors.initials: J
authors.lastname: Gao
authors.forename: Hilary
authors.initials: H
authors.lastname: Wriggers
authors.forename: Anne
authors.initials: A
authors.lastname: Ekker
authors.forename: Liann
authors.initials: L
authors.lastname: Wang
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.forename: Peter S
authors.initials: PS
authors.lastname: Dragovich
authors.forename: Shella A
authors.initials: SA
authors.lastname: Fuhrman
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D011994:Recombinant Proteins; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase