Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid

Pfefferkorn, Jeffrey A.; Nugent, Richard A.; Gross, R.J.; Greene, Meredith; Mitchell, Mark A.; Reding, Matthew T.; Funk, Lee; Anderson, Rebecca M.; Wells, Peter A.; Shelly, John A.; Anstadt, Robert; Finzel, B.C.; Harris, Melissa S.; Kilkuskie, Robert E.; Kopta, Laurice A.; Schwende, Francis J.

doi:10.1016/j.bmcl.2005.03.066

Cited by 67 publications

(51 citation statements)

References 27 publications

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“…More importantly, besides the site previously characterized in the suramin/NF023 complexes (here identified as the A-site), such reverse fragment screening experiments unraveled a novel, unexpected, binding site for NAF2, located in the RdRp thumb domain (B-site). Interestingly, the B-site is located in a position that is roughly structurally equivalent to the benzothiadiazine inhibitor binding site in the Hepatitis C Virus RdRp (Koch and Narjes, 2006;Pfefferkorn et al, 2005). NAF2 binding to two distinct sites is also suggested by analysis of the inhibition mechanism which shows a Hill coefficient higher than 1.…”

Section: Discussionmentioning

confidence: 99%

Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase

et al. 2014

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a b s t r a c tNoroviruses are members of the Caliciviridae family of positive sense RNA viruses. In humans Noroviruses cause rapid onset diarrhea and vomiting. Currently Norovirus infection is responsible for 21 million gastroenteritis yearly cases in the USA. Nevertheless, despite the obvious public health and socio-economic relevance, no effective vaccines/antivirals are yet available to treat Norovirus infection.Since the activity of RNA-dependent RNA polymerase (RdRp) plays a key role in genome replication and in the synthesis/amplification of subgenomic RNA, the enzyme is considered a promising target for antiviral drug development. In this context, following the identification of suramin and NF023 as Norovirus RdRp inhibitors, we analyzed the potential inhibitory role of naphthalene di-sulfonate (NAF2), a fragment derived from these two molecules. Although NAF2, tested in enzymatic polymerase inhibition assays, displayed low activity against RdRp (IC 50 = 14 lM), the crystal structure of human Norovirus RdRp revealed a thumb domain NAF2 binding site that differs from that characterized for NF023/suramin. To further map the new potential inhibitory site, we focused on the structurally related molecule pyridoxal-5 0 -phosphate-6-(2 0 -naphthylazo-6 0 -nitro-4 0 ,8 0 -disulfonate) tetrasodium salt (PPNDS). PPNDS displayed belowmicromolar inhibitory activity versus human Norovirus RdRp (IC 50 = 0.45 lM), similarly to suramin and NF023. Inspection of the crystal structure of the RdRp/PPNDS complex showed that the inhibitor bound to the NAF2 thumb domain site, highlighting the relevance of such new binding site for exploiting Norovirus RdRp inhibitors.

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Section: Discussionmentioning

confidence: 99%

Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase

et al. 2014

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“…They were selected with three criteria: the protein is HCV NS5B polymerase genotype 1b; their NNIs all bind to the same palm binding site and these five NNIs represent five different scaffolds including acrylic acid derivative [13] (Fig. 2, NNI-1) , proline sulfonamide derivative [14] (Fig.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

“…6) affords substantial hydrophobic interactions. For example, the bromobenzene group of NNI-1 extends into this deep, lipophilic pocket affording substantial hydrophobic interactions [13]. The aryl group of the sulfonamide region in compound NNI-2 packs between the hydrophobic side-chains of Tyr448 and Tyr415…”

Section: Binding Free Energy Calculation and Free Energy Decompositionmentioning

confidence: 99%

Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking

Froeyen

Herdewijn

2009

J Mol Model

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Modeling studies were performed on HCV NS5B Polymerase in an effort to design new inhibitors. The binding models of five different scaffold inhibitors were investigated and compared by using molecular dynamics simulations, free energy calculation and decomposition. Our results show Tyr448 plays the most critical role in the binding of most inhibitors. In addition, favorable contributions of residues Pro197, Arg200, Cys366, Met414 and Tyr448 in a deep hydrophobic pocket prove to be important for the selectivity of inhibitors. Furthermore, an optimized docking protocol was presented based on cross-docking the five inhibitors in the palm binding site of this enzyme using the Autodock program. This protocol was used later to virtually screen NCI and Maybridge diversity set libraries. The binding site was profiled via the statistics and analysis of the hydrogen bond networks formed between the receptor and the top-ranked diversity set compounds. Based on our detailed binding site analysis two useful rules were proposed to guide the selection of promising hits.Response to Reviewers: Question1: It is a pity that nothing in detail is discussed about found structures resulting from the virtual screening. Did the authors find new promising ligands with high (higher than the template ligands?) affinity and are they structurally diverse or similar to the used ones?Answer: We have found some promising compounds after the virtual screening. They are structurally diverse. Most of them form hydrogen bonds with the critical residues such as Tyr448 and have strong hydrophobic interaction with the residues in the deep hydrophobic pocket mentioned in our article. These compounds are under biological test.Question2: Additionally to figure 5 at least one figure should be added, showing the amino acid residues of the active site with the discussed most important interactions with one (the best?) ligand. This would considerably help to understand the discussion without looking in the original pdb-files. AbstractModeling studies were performed on HCV NS5B Polymerase in an effort to design new inhibitors. The binding models of five different scaffold inhibitors were investigated and compared by using molecular dynamics simulations, free energy calculation and decomposition. Our results show Tyr448 plays the most critical role in the binding of most inhibitors. In addition, favorable contributions of residues Pro197, Arg200, Cys366, Met414 and Tyr448 in a deep hydrophobic pocket prove to be important for the selectivity of inhibitors.Furthermore, an optimized docking protocol was presented based on cross-docking the five inhibitors in the palm binding site of this enzyme using the Autodock program. This protocol was used later to virtually screen NCI and Maybridge diversity set libraries. The binding site was profiled via the statistics and analysis of the hydrogen bond networks formed between the receptor and the top-ranked diversity set compounds. Based on our detailed binding site analysis two useful rules were proposed to ...

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“…The NNI-3 site is located adjacent to the active site. Reported NNI-3 ligands include benzothiadiazine (11,47), proline sulfonamide (18), benzylidene (24,42), and acrylic acid (40,41) derivatives. In drug discovery, knowledge of the inhibitor site of action is crucial to guiding medicinal chemistry efforts.…”

mentioning

confidence: 99%

“…Structural activity relationships are further complicated by the variation observed for each of the NNI binding sites between genotype and subtypes. These issues can be addressed using X-ray crystallography, as demonstrated by others (2,13,18,24,29,40,41,42,47,55). However, this is a considerable undertaking and requires both time and abundant purified enzyme.…”

mentioning

confidence: 99%

Binding-Site Identification and Genotypic Profiling of Hepatitis C Virus Polymerase Inhibitors

Pauwels¹,

Mostmans²,

Quirynen³

et al. 2007

J Virol

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The search for hepatitis C virus polymerase inhibitors has resulted in the identification of several nonnucleoside binding pockets. The shape and nature of these binding sites differ across and even within diverse hepatitis C virus genotypes. These differences confront antiviral drug discovery with the challenge of finding compounds that are capable of inhibition in variable binding pockets. To address this, we have established a hepatitis C virus mutant and genotypic recombinant polymerase panel as a means of guiding medicinal chemistry through the elucidation of the site of action of novel inhibitors and profiling against genotypes. Using a genotype 1b backbone, we demonstrate that the recombinant P495L, M423T, M414T, and S282T mutant enzymes can be used to identify the binding site of an acyl pyrrolidine analog. We assess the inhibitory activity of this analog and other nonnucleoside inhibitors with our panel of enzyme isolates generated from clinical sera representing genotypes 1a, 1b, 2a, 2b, 3a, 4a, 5a, and 6a.Hepatitis C is estimated to affect 3% of the global population. In a number of individuals, it can lead to liver fibrosis, cirrhosis, and death. Although virus can be cleared by a combination of pegylated interferon and ribavirin, the treatment is successful in only around 50% of treated patients and has considerable liabilities. These weaknesses highlight the need for new drugs to treat hepatitis C virus (HCV) in patients who have failed current therapy, as well as in untreated patients (12,56).HCV is an enveloped virus with an RNA genome of ϳ9.6 kb. Its single-stranded RNA has a positive polarity and encodes a polyprotein of ϳ3,300 amino acids comprising 4 structural proteins (Core, E1, E2, and p7) and 6 nonstructural proteins (NS2, -3, -4A, -4B, -5A, and -5B) (43). These proteins, as well as the viral translation process using the internal ribosomal entry site and a range of host factors, are candidate targets for therapeutic intervention (3, 46). The remarkable clinical success of human immunodeficiency virus reverse transcriptase and protease inhibitors, as well as the availability of several crystal structures, has motivated HCV drug discovery efforts to focus mainly on the development of protease and polymerase inhibitors. HCV NS5B is an RNA-dependent RNA polymerase that is responsible for the replication of the viral genome, which is thought to occur through a primer-independent de novo mechanism (6, 31). Due to the lack of proofreading capacity, this replication process is subject to a high error rate (36). As a result, the virus has evolved into multiple variant strains, classified into six different genotypes (1 to 6) and several subtypes (a, b, c, etc.) (45). To add to this complexity, HCV-infected individuals also harbor different variants or quasispecies of the virus, together representing a pool of genomes on which selective pressure can act (16). It has been speculated that drug resistance will rapidly emerge upon administration of specific HCV antivirals and that together with viral ...

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Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid

Cited by 67 publications

References 27 publications

Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase

Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase

Insight into ligand selectivity in HCV NS5B polymerase: molecular dynamics simulations, free energy decomposition and docking

Binding-Site Identification and Genotypic Profiling of Hepatitis C Virus Polymerase Inhibitors

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