3CSO

HCV Polymerase in complex with a 1,5 Benzodiazepine inhibitor

Summary for 3CSO

• Entry DOI: 10.2210/pdb3cso/pdb
• Related: 1nb4
• Descriptor: RNA-directed RNA polymerase, (11S)-10-acetyl-11-[4-(benzyloxy)-3-chlorophenyl]-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one (3 entities in total)
• Functional Keywords: 1, 5-benzodiazepines, hepatitis c virus, ns5b, polymerase, transferase
• Biological source: Hepatitis C virus isolate
• 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 : O92972
• Total number of polymer chains: 2
• Total formula weight: 130636.56

Authors

Nyanguile, O. (deposition date: 2008-04-10, release date: 2009-04-14, Last modification date: 2024-02-21)

Primary citation

Nyanguile, O.,Pauwels, F.,Van den Broeck, W.,Boutton, C.W.,Quirynen, L.,Ivens, T.,van der Helm, L.,Vandercruyssen, G.,Mostmans, W.,Delouvroy, F.,Dehertogh, P.,Cummings, M.D.,Bonfanti, J.F.,Simmen, K.A.,Raboisson, P.
1,5-benzodiazepines, a novel class of hepatitis C virus polymerase nonnucleoside inhibitors.
Antimicrob.Agents Chemother., 52:4420-4431, 2008

PubMed Abstract: The exogenous control of hepatitis C virus (HCV) replication can be mediated through the inhibition of the RNA-dependent RNA polymerase (RdRp) activity of NS5B. Small-molecule inhibitors of NS5B include nucleoside and nonnucleoside analogs. Here, we report the discovery of a novel class of HCV polymerase nonnucleoside inhibitors, 1,5-benzodiazepines (1,5-BZDs), identified by high-throughput screening of a library of small molecules. A fluorescence-quenching assay and X-ray crystallography revealed that 1,5-BZD 4a bound stereospecifically to NS5B next to the catalytic site. When introduced into replicons, mutations known to confer resistance against chemotypes that bind at this site were detrimental to inhibition by 1,5-BZD 7a. Using a panel of enzyme isolates that covered genotypes 1 to 6, we showed that compound 4a inhibited genotype 1 only. In mechanistic studies, 4a was found to inhibit the RdRp activity of NS5B noncompetitively with GTP and to inhibit the formation of the first phosphodiester bond during the polymerization cycle. The specificity for the HCV target was evaluated by profiling the 1,5-BZDs against other viral and human polymerases, as well as BZD receptors.

PubMed: 18852280
DOI: 10.1128/AAC.00669-08

Experimental method

X-RAY DIFFRACTION (2.71 Å)