2GIR

Hepatitis C virus RNA-dependent RNA polymerase NS5B with NNI-1 inhibitor

Summary for 2GIR

• Entry DOI: 10.2210/pdb2gir/pdb
• Related: 2GIQ
• Descriptor: RNA-directed RNA polymerase, 3-{ISOPROPYL[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL]AMINO}-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID (3 entities in total)
• Functional Keywords: hcv, hepatitis, ns5b, transferase rna-dependent rna polymerase, transferase
• Biological source: Hepatitis C virus (isolate BK)
• Cellular location: Core protein p21: Host endoplasmic reticulum membrane; Single-pass membrane protein. Core protein p19: Virion . Envelope glycoprotein E1: Virion membrane ; Single-pass type I membrane protein . Envelope glycoprotein E2: Virion membrane ; Single-pass type I membrane protein . p7: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Protease NS2-3: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Serine protease NS3: Host endoplasmic reticulum membrane ; Peripheral membrane protein . Non-structural protein 4A: Host endoplasmic reticulum membrane ; Single-pass type I membrane protein . Non-structural protein 4B: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Non-structural protein 5A: Host endoplasmic reticulum membrane ; Peripheral membrane protein . RNA-directed RNA polymerase: Host endoplasmic reticulum membrane ; Single-pass type I membrane protein : P26663
• Total number of polymer chains: 2
• Total formula weight: 127270.15

Authors

Harris, S.F. (deposition date: 2006-03-29, release date: 2007-04-03, Last modification date: 2024-02-14)

Primary citation

Le Pogam, S.,Kang, H.,Harris, S.F.,Leveque, V.,Giannetti, A.M.,Ali, S.,Jiang, W.R.,Rajyaguru, S.,Tavares, G.,Oshiro, C.,Hendricks, T.,Klumpp, K.,Symons, J.,Browner, M.F.,Cammack, N.,Najera, I.
Selection and characterization of replicon variants dually resistant to thumb- and palm-binding nonnucleoside polymerase inhibitors of the hepatitis C virus.
J.Virol., 80:6146-6154, 2006

PubMed Abstract: Multiple nonnucleoside inhibitor binding sites have been identified within the hepatitis C virus (HCV) polymerase, including in the palm and thumb domains. After a single treatment with a thumb site inhibitor (thiophene-2-carboxylic acid NNI-1), resistant HCV replicon variants emerged that contained mutations at residues Leu419, Met423, and Ile482 in the polymerase thumb domain. Binding studies using wild-type (WT) and mutant enzymes and structure-based modeling showed that the mechanism of resistance is through the reduced binding of the inhibitor to the mutant enzymes. Combined treatment with a thumb- and a palm-binding polymerase inhibitor had a dramatic impact on the number of replicon colonies able to replicate in the presence of both inhibitors. A more exact characterization through molecular cloning showed that 97.7% of replicons contained amino acid substitutions that conferred resistance to either of the inhibitors. Of those, 65% contained simultaneously multiple amino acid substitutions that conferred resistance to both inhibitors. Double-mutant replicons Met414Leu and Met423Thr were predominantly selected, which showed reduced replication capacity compared to the WT replicon. These findings demonstrate the selection of replicon variants dually resistant to two NS5B polymerase inhibitors binding to different sites of the enzyme. Additionally, these findings provide initial insights into the in vitro mutational threshold of the HCV NS5B polymerase and the potential impact of viral fitness on the selection of multiple-resistant mutants.

PubMed: 16731953
DOI: 10.1128/JVI.02628-05

Experimental method

X-RAY DIFFRACTION (1.9 Å)