2WCX

Crystal Structure of Hepatitis C Virus NS5B Polymerase in Complex with Thienopyrrole-Based Finger-Loop Inhibitors

Summary for 2WCX

• Entry DOI: 10.2210/pdb2wcx/pdb
• Related: 1A1Q 1C2P 1CSJ 1CU1 1GX5 1GX6 1JXP 1NHU 1NHV 1NS3 1OS5 1QUV 2AWZ 2AX0 2AX1 2BRK 2BRL 2I1R 2JC0 2JC1
• Descriptor: RNA-DIRECTED RNA POLYMERASE, MANGANESE (II) ION, 6-CYCLOHEXYL-4-METHYL-5-PHENYL-4H-THIENO[3,2-B]PYRROLE-2-CARBOXYLIC ACID, ... (4 entities in total)
• Functional Keywords: envelope protein, hepatitis c virus, rna-dependent rna-polymerase, nucleotide-binding, allosteric inhibitor, non nucleoside inhibitor, nni, hcv, ns5b, membrane, helicase, hydrolase, polymerase, atp-binding, rna-binding, genotype 1b, viral protein, transmembrane, rna replication
• Biological source: HEPATITIS C VIRUS
• Cellular location: Core protein p21: Host endoplasmic reticulum membrane; Single-pass membrane protein. Core protein p19: Virion (By similarity). Envelope glycoprotein E1: Virion membrane; Single-pass type I membrane protein (Potential). Envelope glycoprotein E2: Virion membrane; Single-pass type I membrane protein (Potential). p7: Host endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). Protease NS2-3: Host endoplasmic reticulum membrane; Multi-pass membrane protein (Potential). Serine protease NS3: Host endoplasmic reticulum membrane; Peripheral membrane protein (By similarity). Non-structural protein 4A: Host endoplasmic reticulum membrane; Single-pass type I membrane protein (Potential). Non-structural protein 4B: Host endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). Non-structural protein 5A: Host endoplasmic reticulum membrane; Peripheral membrane protein (By similarity). RNA-directed RNA polymerase: Host endoplasmic reticulum membrane; Single-pass type I membrane protein (Potential): P26663
• Total number of polymer chains: 1
• Total formula weight: 60222.04

Authors

Di Marco, S. (deposition date: 2009-03-17, release date: 2009-08-18, Last modification date: 2023-12-13)

Primary citation

Martin Hernando, J.I.,Ontoria, J.M.,Malancona, S.,Attenni, B.,Fiore, F.,Bonelli, F.,Koch, U.,Di Marco, S.,Colarusso, S.,Ponzi, S.,Gennari, N.,Vignetti, S.E.,Del Rosario Rico Ferreira, M.,Habermann, J.,Rowley, M.,Narjes, F.
Optimization of Thienopyrrole-Based Finger-Loop Inhibitors of the Hepatitis C Virus Ns5B Polymerase.
Chemmedchem, 4:1695-, 2009

PubMed Abstract: Infections caused by the hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The NS5B polymerase of HCV is responsible for the replication of viral RNA and has been a prime target in the search for novel treatment options. We had discovered allosteric finger-loop inhibitors based on a thieno[3,2-b]pyrrole scaffold as an alternative to the related indole inhibitors. Optimization of the thienopyrrole series led to several N-acetamides with submicromolar potency in the cell-based replicon assay, but they lacked oral bioavailability in rats. By linking the N4-position to the ortho-position of the C5-aryl group, we were able to identify the tetracyclic thienopyrrole 40, which displayed a favorable pharmacokinetic profile in rats and dogs and is equipotent with recently disclosed finger-loop inhibitors based on an indole scaffold.

PubMed: 19672916
DOI: 10.1002/CMDC.200900184

Experimental method

X-RAY DIFFRACTION (2 Å)