Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus

LaPlante, Steven R.; Padyana, Anil K.; Abeywardane, Asitha; Bonneau, Pierre; Cartier, Mireille; Coulombe, René; Jakalian, Araz; Wildeson-Jones, Jessi; Li, Xiang; Liang, Shuang; White, Peter W.; Zhang, Qiang; Taylor, Steven J.

doi:10.1021/jm401432c

Cited by 18 publications

(22 citation statements)

References 42 publications

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“…The allosteric tunnel site discussed in the Introduction is shown (gray ligand) as well as fragments bound to the ATP site (green) and two distinct regions of the nucleic acid binding groove (cyan and yellow). Compound 12, originally reported by workers at Schering Plough (35), also binds within the nucleic acid binding groove, as confirmed by a recent X-ray structure published by researchers at Boehringer Ingelheim (14). Our compound 11 is very similar to compound 12 and adopts the same binding mode (PDB 4OJQ; Inset).…”

Section: Resultssupporting

confidence: 78%

“…Furthermore, many computational methods have been developed to predict ligand-binding sites from protein sequence conservation, 3D structure (12), or both (13). These tools have had some success in predicting sites from the apo structure (14), including the presence of cryptic pockets (15). However, identifying ligand-induced pockets remains a largely unsolved problem.…”

Section: Fragment-based Drug Designmentioning

confidence: 99%

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Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

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Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.protein structure | protein function | X-ray crystallography | fragment-based drug design

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Section: Resultssupporting

confidence: 78%

Section: Fragment-based Drug Designmentioning

confidence: 99%

Detection of secondary binding sites in proteins using fragment screening

Ludlow¹,

Verdonk²,

Saini³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

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“…NS5B polymerase and NS3 helicase. These two targets were chosen as first choice because indole derivatives have been reported in literature as both HCV NS5B polymerase and NS3 helicase inhibitors [20,21]. …”

Section: Resultsmentioning

confidence: 99%

Discovery of the 2-phenyl-4,5,6,7-Tetrahydro-1H-indole as a novel anti-hepatitis C virus targeting scaffold

Андреев

Manvar

Barreca

et al. 2015

European Journal of Medicinal Chemistry

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Although all-oral direct-acting antiviral (DAA) therapy for hepatitis C virus (HCV) treatment is now a reality, today's HCV drugs are expensive, and more affordable drugs are still urgently needed. In this work, we report the identification of the 2-phenyl-4,5,6,7-Tetrahydro-1H-indole chemical scaffold that inhibits cellular replication of HCV genotype 1b and 2a subgenomic replicons. The anti-HCV genotype 1b and 2a profiling and effects on cell viability of a selected representative set of derivatives as well as their chemical synthesis are described herein. The most potent compound 39 displayed EC50 values of 7.9 and 2.6 µM in genotype 1b and 2a, respectively. Biochemical assays showed that derivative 39 had no effect on HCV NS5B polymerase, NS3 helicase, IRES mediated translation and selected host factors. Thus, future work will involve both the chemical optimization and target identification of 2-phenyl-4,5,6,7-Tetrahydro-1H-indoles as new anti-HCV agents.

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“…The important residues, His57, Asp81 Gly137, and Ser139, were defined to be in the active site of the protease (Rosenquist et al, 2014). For helicase, [[6‐(3,5‐diaminophenyl)‐1‐(2‐methoxy‐5‐nitrobenzyl)‐1 H ‐indol‐3‐yl]acetic acid] (compound 19; PDB ID: http://4OKS) was selected as the in silico standard (LaPlante et al., 2014) while primuline was chosen as the in vitro standard (due to the unavailability of compound 19). Nevertheless, the 3D structural file of the active component of primuline, primuline_p4 (CID 44251437), was downloaded from PubChem, and its possible interactions with HCV helicase were studied (Li et al., 2012; Ndjomou et al., 2012).…”

Section: Methodsmentioning

confidence: 99%

Rational drug discovery: Ellagic acid as a potent dual‐target inhibitor against hepatitis C virus genotype 3 (HCV G3) NS3 enzymes

et al. 2020

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Structure-based virtual screening (SBVS) has served as a popular strategy for rational drug discovery. In this study, we aimed to discover novel benzopyran-based inhibitors that targeted the NS3 enzymes (NS3/4A protease and NS3 helicase) of HCV G3 using a combination of in silico and in vitro approaches. With the aid of SBVS, six novel compounds were discovered to inhibit HCV G3 NS3/4A protease and two phytochemicals (ellagic acid and myricetin) were identified as dual-target inhibitors that inhibited both NS3/4A protease and NS3 helicase in vitro (IC 50 = 40.37 ± 5.47 nm and 6.58 ± 0.99 µm, respectively). Inhibitory activities against the replication of HCV G3 replicons were further assessed in a cell-based system with four compounds showed dose-dependent inhibition. Compound P8 was determined to be the most potent compound from the cell-based assay with an EC 50 of 19.05 µm. The dual-target inhibitor, ellagic acid, was determined as the second most potent (EC 50 = 32.37 µm) and the most selective in its inhibitory activity against the replication of HCV replicons, without severely affecting the viability of the host cells (selectivity index > 6.18).

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Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus

Cited by 18 publications

References 42 publications

Detection of secondary binding sites in proteins using fragment screening

Detection of secondary binding sites in proteins using fragment screening

Discovery of the 2-phenyl-4,5,6,7-Tetrahydro-1H-indole as a novel anti-hepatitis C virus targeting scaffold

Rational drug discovery: Ellagic acid as a potent dual‐target inhibitor against hepatitis C virus genotype 3 (HCV G3) NS3 enzymes

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