title: Discovery of new scaffolds for rational design of HCV NS5B polymerase inhibitors.
abstract: Hepatitis C virus (HCV) NS5B polymerase is a key target for the development of anti-HCV drugs. Here we report on the identification of novel allosteric inhibitors of HCV NS5B through a combination of structure-based virtual screening and in vitro NS5B inhibition assays. One hundred and sixty thousand compounds from the Otava database were virtually screened against the thiazolone inhibitor binding site on NS5B (thumb pocket-2, TP-2), resulting in a sequential down-sizing of the library by 2.7 orders of magnitude to yield 59 NS5B non-nucleoside inhibitor (NNI) candidates. In vitro evaluation of the NS5B inhibitory activity of the 59 selected compounds resulted in a 14% hit rate, yielding 8 novel structural scaffolds. Of these, compound 1 bearing a 4-hydrazinoquinazoline scaffold was the most active (IC(50) = 16.0 μM). The binding site of all 8 NNIs was mapped to TP-2 of NS5B as inferred by a decrease in their inhibition potency against the M423T NS5B mutant, employed as a screen for TP-2 site binders. At 100 μM concentration, none of the eight compounds exhibited any cytotoxicity, and all except compound 8 exhibited between 40 and 60% inhibition of intracellular NS5B polymerase activity in BHK-NS5B-FRLuc reporter cells. These inhibitor scaffolds will form the basis for future optimization and development of more potent NS5B inhibitors.
authors.affiliation: Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, 03143 Kyiv, Ukraine.
authors.forename: Andriy G
authors.initials: AG
authors.lastname: Golub
authors.forename: K R
authors.initials: KR
authors.lastname: Gurukumar
authors.forename: Amartya
authors.initials: A
authors.lastname: Basu
authors.forename: Volodymyr G
authors.initials: VG
authors.lastname: Bdzhola
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Bilokin
authors.forename: Sergiy M
authors.initials: SM
authors.lastname: Yarmoluk
authors.forename: Jin-Ching
authors.initials: JC
authors.lastname: Lee
authors.forename: Tanaji T
authors.initials: TT
authors.lastname: Talele
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Nichols
authors.forename: Neerja
authors.initials: N
authors.lastname: Kaushik-Basu
mesh_terms: D004305:Dose-Response Relationship, Drug; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D057166:High-Throughput Screening Assays; D006834:Hydrazines / Q000737:chemistry / Q000494:pharmacology*; D008958:Models, Molecular; D015394:Molecular Structure; D052999:Quinazolinones / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase
chemical_list: D004791:Enzyme Inhibitors; D006834:Hydrazines; D052999:Quinazolinones; D017361:Viral Nonstructural Proteins; C085354:4-hydrazinoquinazoline; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase