Discovery of thiophene-2-carboxylic acids as potent inhibitors of HCV NS5B polymerase and HCV subgenomic RNA replication. Part 1: Sulfonamides

Chan, Laval; Das, Sanjoy K.; Reddy, T. Jagadeeswar; Poisson, Carl; Proulx, Melanie; Pereira, Oswy Z.; Courchesne, Marc; Roy, Caroline; Wang, Wuyi; Siddiqui, A. M.; Yannopoulos, Constantin G.; Nguyen-Ba, Nghe; Labrecque, Denis; Bethell, Richard C.; Hamel, Martine; Courtemanche-Asselin, Philippe; L’Heureux, Lucille; David, Maud; Nicolas, Olivier; Brunette, Stéphanie; Bilimoria, Darius; Bédard, Jean

doi:10.1016/j.bmcl.2003.10.067

Cited by 79 publications

(23 citation statements)

References 20 publications

(4 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As controls (Fig. 1D), compounds with known activities against HCV RdRp (LCY967) (8), polymerases ␣ (aphidicolin) (17), and polymerases ␤ (lithocholic) (31) showed expected anti-polymerase results, with IC 50 s of 50 nM, 40 M, and 40 M, respectively. These results indicate that NITD-2 selectively inhibits DENV-2 polymerase.…”

Section: Resultsmentioning

confidence: 96%

Inhibition of Dengue Virus Polymerase by Blocking of the RNA Tunnel

Niyomrattanakit

Chen

Dong

et al. 2010

J Virol

108

116

View full text Add to dashboard Cite

Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen in humans. Neither vaccine nor antiviral therapy is currently available for DENV. We report here that N-sulfonylanthranilic acid derivatives are allosteric inhibitors of DENV RNA-dependent RNA polymerase (RdRp). The inhibitor was identified through high-throughput screening of one million compounds using a primer extension-based RdRp assay [substrate poly(C)/oligo(G) 20 ]. Chemical modification of the initial "hit" improved the compound potency to an IC 50 (that is, a concentration that inhibits 50% RdRp activity) of 0.7 M. In addition to suppressing the primer extension-based RNA elongation, the compound also inhibited de novo RNA synthesis using a DENV subgenomic RNA, but at a lower potency (IC 50 of 5 M). Remarkably, the observed anti-polymerase activity is specific to DENV RdRp; the compound did not inhibit WNV RdRp and exhibited IC 50 s of >100 M against hepatitis C virus RdRp and human DNA polymerase ␣ and ␤. UV cross-linking and mass spectrometric analysis showed that a photoreactive inhibitor could be cross-linked to Met343 within the RdRp domain of DENV NS5. On the crystal structure of DENV RdRp, Met343 is located at the entrance of RNA template tunnel. Biochemical experiments showed that the order of addition of RNA template and inhibitor during the assembly of RdRp reaction affected compound potency. Collectively, the results indicate that the compound inhibits RdRp through blocking the RNA tunnel. This study has provided direct evidence to support the hypothesis that allosteric pockets from flavivirus RdRp could be targeted for antiviral development.

show abstract

Section: Resultsmentioning

confidence: 96%

Inhibition of Dengue Virus Polymerase by Blocking of the RNA Tunnel

Niyomrattanakit

Chen

Dong

et al. 2010

J Virol

108

116

View full text Add to dashboard Cite

show abstract

“…[11][12][13][14][15][16][17] Recently, many non-nucleoside inhibitors (NNIs) of HCV NS5B RNA polymerase have been discovered. [18][19][20][21][22][23][24][25][26][27][28][29] Structural studies of HCV NS5B polymerase genotypes 1b and 2a in complex with phenylalanine, dihydropyranone, thiophene, and indole-based non-nucleoside analogue inhibitors bound non-covalently have also been carried out. [30][31][32][33][34] These studies revealed that phenylalanine, dihydropyranone and thiophene-based non-nucleoside inhibitors bind to a common predominantly hydrophobic depression in the thumb domain, that is located approximately 35 Å from the polymerase active site.…”

Section: Introductionmentioning

confidence: 99%

Non-nucleoside Inhibitors Binding to Hepatitis C Virus NS5B Polymerase Reveal a Novel Mechanism of Inhibition

Biswal

Wang

Cherney

et al. 2006

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

“…1). These inhibitors were synthesized as part of ongoing structure-activity relationship optimization efforts that have been described elsewhere (21)(22)(23). The details of the inhibitor binding site, protein-inhibitor interactions, and plausible mechanisms of inhibition will be discussed in the second part of the paper.…”

Section: Hepatitis C Virus (Hcv)mentioning

confidence: 99%

Crystal Structures of the RNA-dependent RNA Polymerase Genotype 2a of Hepatitis C Virus Reveal Two Conformations and Suggest Mechanisms of Inhibition by Non-nucleoside Inhibitors

Biswal

Cherney

Wang

et al. 2005

Journal of Biological Chemistry

Self Cite

188

198

View full text Add to dashboard Cite

Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus (HCV) from two crystal forms have been determined. Similar to the three-dimensional structures of HCV polymerase genotype 1b and other known polymerases, the structures of the HCV polymerase genotype 2a in both crystal forms can be depicted in the classical right-hand arrangement with fingers, palm, and thumb domains. The main structural differences between the molecules in the two crystal forms lie at the interface of the fingers and thumb domains. The relative orientation of the thumb domain with respect to the fingers and palm domains and the ␤-flap region is altered. Structural analysis reveals that the NS5B polymerase in crystal form I adopts a "closed" conformation that is believed to be the active form, whereas NS5B in crystal form II adopts an "open" conformation and is thus in the inactive form. In addition, we have determined the structures of two NS5B polymerase/non-nucleoside inhibitor complexes. Both inhibitors bind at a common binding site, which is nearly 35 Å away from the polymerase active site and is located in the thumb domain. The binding pocket is predominantly hydrophobic in nature, and the enzyme inhibitor complexes are stabilized by hydrogen bonding and van der Waals interactions. Inhibitors can only be soaked in crystal form I and not in form II; examination of the enzyme-inhibitor complex reveals that the enzyme has undergone a dramatic conformational change from the form I (active) complex to the form II (inactive).

show abstract

Discovery of thiophene-2-carboxylic acids as potent inhibitors of HCV NS5B polymerase and HCV subgenomic RNA replication. Part 1: Sulfonamides

Abstract: The discovery of a novel class of HCV NS5B polymerase inhibitors, 3-arylsulfonylamino-5-phenyl-thiophene-2-carboxylic acids is described. SAR studies have yielded several potent inhibitors of HCV polymerase as well as of HCV subgenomic RNA replication in Huh-7 cells.

Cited by 79 publications

References 20 publications

Inhibition of Dengue Virus Polymerase by Blocking of the RNA Tunnel

Inhibition of Dengue Virus Polymerase by Blocking of the RNA Tunnel

Non-nucleoside Inhibitors Binding to Hepatitis C Virus NS5B Polymerase Reveal a Novel Mechanism of Inhibition

Crystal Structures of the RNA-dependent RNA Polymerase Genotype 2a of Hepatitis C Virus Reveal Two Conformations and Suggest Mechanisms of Inhibition by Non-nucleoside Inhibitors

Contact Info

Product

Resources

About