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Discovery of Beclabuvir: A Potent Allosteric Inhibitor of the Hepatitis C Virus Polymerase. HCV: THE JOURNEY FROM DISCOVERY TO A CURE 2018; 31. [PMCID: PMC7123187 DOI: 10.1007/7355_2018_38] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of beclabuvir occurred through an iterative series of structure-activity relationship studies directed at the optimization of a novel class of indolobenzazepines. Within this research, a strategic decision to abandon a highly potent but physiochemically problematic series in favor of one of lower molecular weight and potency was key in the realization of the program’s objectives. Subsequent cycles of analog design incorporating progressive conformational constraints successfully addressed off-target liabilities and identified compounds with improved physiochemical profiles. Ultimately, a class of alkyl-bridged piperazine carboxamides was found to be of particular interest, and from this series, beclabuvir was identified as having superior antiviral, safety, and pharmacokinetic properties. The clinical evaluation of beclabuvir in combination with both the NS5A replication complex inhibitor daclatasvir and the NS3 protease inhibitor asunaprevir in a single, fixed-dose formulation (Ximency) resulted in the approval by the Japanese Pharmaceutical and Food Safety Bureau for its use in the treatment of patients infected with genotype 1 HCV.
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Abstract
The persistence of West Nile virus (WNV) infections throughout the USA since its inception in 1999 and its continuous spread throughout the globe calls for an urgent need of effective treatments and prevention measures. Although the licensing of several WNV vaccines for veterinary use provides a proof of concept, similar efforts on the development of an effective vaccine for humans remain still unsuccessful. Increased understanding of biology and pathogenesis of WNV together with recent technological advancements have raised hope that an effective WNV vaccine may be available in the near future. In addition, rapid progress in the structural and functional characterization of WNV and other flaviviral proteins have provided a solid base for the design and development of several classes of inhibitors as potential WNV therapeutics. Moreover, the therapeutic monoclonal antibodies demonstrate an excellent efficacy against WNV in animal models and represent a promising class of WNV therapeutics. However, there are some challenges as to the design and development of a safe and efficient WNV vaccine or therapeutic. In this chapter, we discuss the current approaches, progress, and challenges toward the development of WNV vaccines, therapeutic antibodies, and antiviral drugs.
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Parcella K, Nickel A, Beno BR, Sheriff S, Wan C, Wang YK, Roberts SB, Meanwell NA, Kadow JF. Discovery and initial optimization of alkoxyanthranilic acid derivatives as inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2016; 27:295-298. [PMID: 27908764 DOI: 10.1016/j.bmcl.2016.11.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 10/20/2022]
Abstract
Alkoxyanthranilic acid derivatives have been identified to inhibit HCV NS5B polymerase, binding in an allosteric site located at the convergence of the palm and thumb regions. Information from co-crystal structures guided the structural design strategy. Ultimately, two independent structural modifications led to a similar shift in binding mode that when combined led to a synergistic improvement in potency and the identification of inhibitors with sub-micromolar HCV NS5B binding potency.
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Affiliation(s)
- Kyle Parcella
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA.
| | - Andrew Nickel
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brett R Beno
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Steven Sheriff
- Bristol-Myers Squibb, Research and Development, PO Box 4000, Princeton, NJ 08540, USA
| | - Changhong Wan
- Bristol-Myers Squibb, Research and Development, PO Box 4000, Princeton, NJ 08540, USA
| | - Ying-Kai Wang
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Susan B Roberts
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Nicholas A Meanwell
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - John F Kadow
- Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
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Rigat KL, Lu H, Wang YK, Argyrou A, Fanslau C, Beno B, Wang Y, Marcinkeviciene J, Ding M, Gentles RG, Gao M, Abell LM, Roberts SB. Mechanism of inhibition for BMS-791325, a novel non-nucleoside inhibitor of hepatitis C virus NS5B polymerase. J Biol Chem 2014; 289:33456-68. [PMID: 25301950 DOI: 10.1074/jbc.m114.613653] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
HCV infection is an urgent global health problem that has triggered a drive to discover therapies that specifically target the virus. BMS-791325 is a novel direct antiviral agent specifically targeting HCV NS5B, an RNA-dependent RNA polymerase. Robust viral clearance of HCV was observed in infected patients treated with BMS-791325 in combination with other anti-HCV agents in Phase 2 clinical studies. Biochemical and biophysical studies revealed that BMS-791325 is a time-dependent, non-competitive inhibitor of the polymerase. Binding studies with NS5B genetic variants (WT, L30S, and P495L) exposed a two-step, slow binding mechanism, but details of the binding mechanism differed for each of the polymerase variants. For the clinically relevant resistance variant (P495L), the rate of initial complex formation and dissociation is similar to WT, but the kinetics of the second step is significantly faster, showing that this variant impacts the final tight complex. The resulting shortened residence time translates into the observed decrease in inhibitor potency. The L30S variant has a significantly different profile. The rate of initial complex formation and dissociation is 7-10 times faster for the L30S variant compared with WT; however, the forward and reverse rates to form the final complex are not significantly different. The impact of the L30S variant on the inhibition profile and binding kinetics of BMS-791325 provides experimental evidence for the dynamic interaction of fingers and thumb domains in an environment that supports the formation of active replication complexes and the initiation of RNA synthesis.
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Affiliation(s)
| | - Hao Lu
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | | | - Argyrides Argyrou
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | - Caroline Fanslau
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | | | - Yi Wang
- From the Departments of Virology
| | - Jovita Marcinkeviciene
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
| | - Min Ding
- Early Discovery Chemistry, Research and Development, Bristol Myers Squibb Co., Wallingford, Connecticut 06492 and
| | - Robert G Gentles
- Early Discovery Chemistry, Research and Development, Bristol Myers Squibb Co., Wallingford, Connecticut 06492 and
| | - Min Gao
- From the Departments of Virology
| | - Lynn M Abell
- the Department of Mechanistic Biochemistry, Research and Development, Bristol Myers Squibb Co., Pennington, New Jersey 08534
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Preclinical characterization of BMS-791325, an allosteric inhibitor of hepatitis C Virus NS5B polymerase. Antimicrob Agents Chemother 2014; 58:3485-95. [PMID: 24733465 DOI: 10.1128/aac.02495-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BMS-791325 is an allosteric inhibitor that binds to thumb site 1 of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase. BMS-791325 inhibits recombinant NS5B proteins from HCV genotypes 1, 3, 4, and 5 at 50% inhibitory concentrations (IC50) below 28 nM. In cell culture, BMS-791325 inhibited replication of HCV subgenomic replicons representing genotypes 1a and 1b at 50% effective concentrations (EC50s) of 3 nM and 6 nM, respectively, with similar (3 to 18 nM) values for genotypes 3a, 4a, and 5a. Potency against genotype 6a showed more variability (9 to 125 nM), and activity was weaker against genotype 2 (EC50, 87 to 925 nM). Specificity was demonstrated by the absence of activity (EC50s of >4 μM) against a panel of mammalian viruses, and cytotoxic concentrations (50%) were >3,000-fold above the HCV EC50. Resistance substitutions selected by BMS-791325 in genotype 1 replicons mostly mapped to a single site, NS5B amino acid 495 (P495A/S/L/T). Additive or synergistic activity was observed in combination studies using BMS-791325 with alfa interferon plus ribavirin, inhibitors of NS3 protease or NS5A, and other classes of NS5B inhibitor (palm site 2-binding or nucleoside analogs). Plasma and liver exposures in vivo in several animal species indicated that BMS-791325 has a hepatotropic disposition (liver-to-plasma ratios ranging from 1.6- to 60-fold across species). Twenty-four hours postdose, liver exposures across all species tested were ≥ 10-fold above the inhibitor EC50s observed with HCV genotype 1 replicons. These findings support the evaluation of BMS-791325 in combination regimens for the treatment of HCV. Phase 3 studies are ongoing.
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Gentles RG, Ding M, Bender JA, Bergstrom CP, Grant-Young K, Hewawasam P, Hudyma T, Martin S, Nickel A, Regueiro-Ren A, Tu Y, Yang Z, Yeung KS, Zheng X, Chao S, Sun JH, Beno BR, Camac DM, Chang CH, Gao M, Morin PE, Sheriff S, Tredup J, Wan J, Witmer MR, Xie D, Hanumegowda U, Knipe J, Mosure K, Santone KS, Parker DD, Zhuo X, Lemm J, Liu M, Pelosi L, Rigat K, Voss S, Wang Y, Wang YK, Colonno RJ, Gao M, Roberts SB, Gao Q, Ng A, Meanwell NA, Kadow JF. Discovery and preclinical characterization of the cyclopropylindolobenzazepine BMS-791325, a potent allosteric inhibitor of the hepatitis C virus NS5B polymerase. J Med Chem 2014; 57:1855-79. [PMID: 24397558 DOI: 10.1021/jm4016894] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Described herein are structure-activity relationship studies that resulted in the optimization of the activity of members of a class of cyclopropyl-fused indolobenzazepine HCV NS5B polymerase inhibitors. Subsequent iterations of analogue design and syntheses successfully addressed off-target activities, most notably human pregnane X receptor (hPXR) transactivation, and led to significant improvements in the physicochemical properties of lead compounds. Those analogues exhibiting improved solubility and membrane permeability were shown to have notably enhanced pharmacokinetic profiles. Additionally, a series of alkyl bridged piperazine carboxamides was identified as being of particular interest, and from which the compound BMS-791325 (2) was found to have distinguishing antiviral, safety, and pharmacokinetic properties that resulted in its selection for clinical evaluation.
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Affiliation(s)
- Robert G Gentles
- Discovery Chemistry, ‡Molecular Discovery Technologies, Molecular Structure & Design, §Molecular Discovery Technologies, Protein Science, ∥Pharmaceutical Candidate Optimization, ⊥Discovery Virology, Disease Sciences and Biologics, #Leads Discovery and Optimization, ▽Materials Science, Drug Product Science and Technology, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
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Hovestädt M, Kuckelkorn U, Niewienda A, Keller C, Goede A, Ay B, Günther S, Janek K, Volkmer R, Holzhütter HG. Rapid degradation of solid-phase bound peptides by the 20S proteasome. J Pept Sci 2013; 19:588-97. [DOI: 10.1002/psc.2536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Marc Hovestädt
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Ulrike Kuckelkorn
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Agathe Niewienda
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Christin Keller
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Andrean Goede
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Bernhard Ay
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics Group, Institute of Pharmaceutical Sciences; Albert-Ludwigs-University Freiburg; Freiburg Germany
| | - Katharina Janek
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Rudolf Volkmer
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Hermann-Georg Holzhütter
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
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Holler TP, Parkinson T, Pryde DC. Targeting the non-structural proteins of hepatitis C virus: beyond hepatitis C virus protease and polymerase. Expert Opin Drug Discov 2013; 4:293-314. [PMID: 23489127 DOI: 10.1517/17460440902762802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection is a main cause of cirrhosis of the liver and hepatocellular carcinoma. The standard of care is a combination of pegylated interferon with ribavirin, a regimen that has undesirable side effects and is frequently ineffective. Compounds targeting HCV protease and polymerase are in late-stage clinical trials and have been extensively reviewed elsewhere. OBJECTIVE To review and evaluate the progress towards finding novel HCV antivirals targeting HCV proteins beyond the already precedented NS3 protease and NS5B polymerase. METHODS Searches of CAplus and Medline databases were combined with information from key conferences. This review focuses on NS2/3 serine protease, NS3 helicase activity and the non-structural proteins 4A, 4B and 5A. CONCLUSIONS Use of the replicon model of HCV replication and biochemical assays of specific targets has allowed screening of vast libraries of compounds, but resulted in clinical candidates from only NS4A and NS5A. The field is hindered by a lack of good chemical matter that inhibits the remaining enzymes from HCV, and a lack of understanding of the functions of non-structural proteins 4A, 4B and 5A in the replication of HCV.
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Affiliation(s)
- Tod P Holler
- Associate Research Fellow Pfizer Global Research and Development, Antiviral Biology, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK +44 130 464 6387 ; +44 130 465 1819 ;
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Ding M, He F, Hudyma TW, Zheng X, Poss MA, Kadow JF, Beno BR, Rigat KL, Wang YK, Fridell RA, Lemm JA, Qiu D, Liu M, Voss S, Pelosi LA, Roberts SB, Gao M, Knipe J, Gentles RG. Synthesis and SAR studies of novel heteroaryl fused tetracyclic indole-diamide compounds: Potent allosteric inhibitors of the hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2012; 22:2866-71. [DOI: 10.1016/j.bmcl.2012.02.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 02/21/2012] [Indexed: 11/15/2022]
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Tseng CK, Chen KJ, Lin CK, Hsu SH, Lee JC. An in vitro coupled transcription/translation reporter system for hepatitis C virus RNA-dependent RNA polymerase. Anal Biochem 2011; 418:50-7. [PMID: 21782784 DOI: 10.1016/j.ab.2011.06.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 06/20/2011] [Accepted: 06/29/2011] [Indexed: 10/18/2022]
Abstract
Hepatitis C virus (HCV) NS5B, an RNA-dependent RNA polymerase (RdRp), is an attractive target for antiviral agents. The in vitro RNA synthesis system based on radioisotopic readout is commonly used for polymerase inhibitor screening; however, this system generates large amounts of radioactive waste and is not amenable to high-throughput applications. To overcome this limitation, we generated pFLuc-(-)UTRΔC-RLuc, a bicistronic reporter vector, which allows effective and sensitive distinction of RdRp activity by using a cell-free coupled transcription/translation system. This reporter construct comprises the firefly luciferase (FLuc) and the Renilla luciferase (RLuc) genes in reverse orientation flanked by the two negative strands of the HCV 5'- and 3'-untranslated regions in which FLuc and RLuc reporter proteins are regulated by bacteriophage T7 polymerase and NS5B polymerase, respectively. The increase in RLuc activity was proportional to the amount of active RdRp. This cell-free dual reporter system was further validated using specific RdRp inhibitors. Hence, linear dose-response curves between RLuc activity and specific inhibitors were obtained, as was faster drug screening through real-time measurement of chemiluminescence. Moreover, this reporter system is suitable for robust in vitro screening because of a statistically acceptable Z' factor value of 0.79 under the antiviral screening condition in the 96-well format.
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Affiliation(s)
- Chin-kai Tseng
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung City 807, Taiwan, ROC
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Preannealing of poly(A) template and oligo(dT) primer is not required for hepatitis C virus RNA-dependent RNA polymerase activity. Anal Biochem 2011; 416:132-4. [PMID: 21565152 DOI: 10.1016/j.ab.2011.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 11/21/2022]
Abstract
Preannealed homopolymeric DNAs or RNAs are often used as templates and/or primers to characterize activities of DNA or RNA-dependent RNA polymerases. Based on the calculated melting temperatures (T(m) values), however, poly(A)/oligo(dT(12-18)) is not expected to form stable duplexes. To determine this, we compared the enzymatic activity of hepatitis C virus polymerase using poly(A)/oligo(dT(12)) that were or were not preannealed. No significant differences were observed. These results suggest that it is not necessary to perform preannealing reactions for poly(A) and oligo(dT(12)), making it possible to characterize mechanism of inhibition of NS5B inhibitors against either template RNA poly(A) or primer oligo(dT(12)) independently.
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Gentles RG, Sheriff S, Beno BR, Wan C, Kish K, Ding M, Zheng X, Chupak L, Poss MA, Witmer MR, Morin P, Wang YK, Rigat K, Lemm J, Voss S, Liu M, Pelosi L, Roberts SB, Gao M, Kadow JF. Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase. Bioorg Med Chem Lett 2011; 21:2212-5. [DOI: 10.1016/j.bmcl.2011.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 02/26/2011] [Accepted: 03/02/2011] [Indexed: 12/17/2022]
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Syntheses and initial evaluation of a series of indolo-fused heterocyclic inhibitors of the polymerase enzyme (NS5B) of the hepatitis C virus. Bioorg Med Chem Lett 2011; 21:2925-9. [PMID: 21486696 DOI: 10.1016/j.bmcl.2011.03.067] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 02/02/2023]
Abstract
Herein, we present initial SAR studies on a series of bridged 2-arylindole-based NS5B inhibitors. The introduction of bridging elements between the indole N1 and the ortho-position of the 2-aryl moiety resulted in conformationally constrained heterocycles that possess multiple additional vectors for further exploration. The binding mode and pharmacokinetic (PK) properties of select examples, including: 13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[2,1-d][1,4]benzodiazepine-10-carboxylic acid (7) (IC(50)=0.07 μM, %F=18), are reported.
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Niyomrattanakit P, Abas SN, Lim CC, Beer D, Shi PY, Chen YL. A fluorescence-based alkaline phosphatase-coupled polymerase assay for identification of inhibitors of dengue virus RNA-dependent RNA polymerase. ACTA ACUST UNITED AC 2011; 16:201-10. [PMID: 21220550 DOI: 10.1177/1087057110389323] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The flaviviral RNA-dependent RNA polymerase (RdRp) is an attractive drug target. To discover new inhibitors of dengue virus RdRp, the authors have developed a fluorescence-based alkaline phosphatase-coupled polymerase assay (FAPA) for high-throughput screening (HTS). A modified nucleotide analogue (2'-[2-benzothiazoyl]-6'-hydroxybenzothiazole) conjugated adenosine triphosphate (BBT-ATP) and 3'UTR-U(30) RNA were used as substrates. After the polymerase reaction, treatment with alkaline phosphatase liberates the BBT fluorophore from the polymerase reaction by-product, BBT(PPi), which can be detected at excitation and emission wavelengths of 422 and 566 nm, respectively. The assay was evaluated by examining the time dependency, assay reagent effects, reaction kinetics, and signal stability and was validated with 3'dATP and an adenosine-nucleotide triphosphate inhibitor, giving IC(50) values of 0.13 µM and 0.01 µM, respectively. A pilot screen of a diverse compound library of 40,572 compounds at 20 µM demonstrated good performance with an average Z factor of 0.81. The versatility and robustness of FAPA were evaluated with another substrate system, BBT-GTP paired with 3'UTR-C(30) RNA. The FAPA method presented here can be readily adapted for other nucleotide-dependent enzymes that generate PPi.
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Ding M, He F, Poss MA, Rigat KL, Wang YK, Roberts SB, Qiu D, Fridell RA, Gao M, Gentles RG. The synthesis of novel heteroaryl-fused 7,8,9,10-tetrahydro-6H-azepino[1,2-a]indoles, 4-oxo-2,3-dihydro-1H-[1,4]diazepino[1,7-a]indoles and 1,2,4,5-tetrahydro-[1,4]oxazepino[4,5-a]indoles. Effective inhibitors of HCV NS5B polymerase. Org Biomol Chem 2011; 9:6654-62. [DOI: 10.1039/c1ob05525a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Rigat K, Wang Y, Hudyma TW, Ding M, Zheng X, Gentles RG, Beno BR, Gao M, Roberts SB. Ligand-induced changes in hepatitis C virus NS5B polymerase structure. Antiviral Res 2010; 88:197-206. [PMID: 20813137 DOI: 10.1016/j.antiviral.2010.08.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/20/2010] [Accepted: 08/26/2010] [Indexed: 12/28/2022]
Abstract
Hepatitis C virus (HCV) RNA-dependent RNA polymerase (NS5B) is required for viral replication. Crystal structures of the NS5B apoprotein show that the finger and thumb domains interact to encircle the active site, and that inhibitors defined by P495 resistance that bind to the thumb-finger interface displace the Δ1 finger loop and disrupt this structure. Since crystal structures may not reveal all of the conformations of a protein in solution we have developed an alternative method, using limited trypsin protease digestion, to investigate the impact of inhibitors as well as substrates on the movement of the Δ1 loop. This assay can be used to study NS5B under conditions that support enzymatic activity. In the absence of inhibitors, no specific region of NS5B was hypersensitive to trypsin, and no specific intermediate cleavage products were formed. Binding of P495-site inhibitors to NS5B induced specific trypsin hypersensitivity at lysine residues 50 and 51. Previously characterized inhibitors and mutant polymerases were used to link this specific trypsin hypersensitivity to movement of the Δ1 loop. Trypsin hypersensitivity identical to the inhibitor pattern was also induced by the binding of the RNA template. The addition of primer to the NS5B-template complex eliminated the hypersensitivity. The data are consistent with displacement of the Δ1 finger loop from the thumb by the binding of template, and reversal by the addition of primer or NTP. Our results complement inhibitor-enzyme co-crystal studies, and the assay provides a rapid and sensitive method to study dynamic changes in HCV NS5B polymerase conformation under conditions that support functional activity.
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Affiliation(s)
- Karen Rigat
- Department of Virology, Bristol-Myers Squibb Co., Research & Development, Wallingford, CT 06492, USA.
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Lee JC, Tseng CK, Chen KJ, Huang KJ, Lin CK, Lin YT. A cell-based reporter assay for inhibitor screening of hepatitis C virus RNA-dependent RNA polymerase. Anal Biochem 2010; 403:52-62. [DOI: 10.1016/j.ab.2010.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 04/03/2010] [Accepted: 04/05/2010] [Indexed: 12/20/2022]
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18
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Glickman JF, Schmid A, Ferrand S. Scintillation Proximity Assays in High-Throughput Screening. Assay Drug Dev Technol 2008; 6:433-55. [DOI: 10.1089/adt.2008.135] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Andres Schmid
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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Wang YK, Rigat KL, Sun JH, Gao M, Roberts SB. RNA template-mediated inhibition of hepatitis C virus RNA-dependent RNA polymerase activity. Arch Biochem Biophys 2007; 470:146-52. [PMID: 18062913 DOI: 10.1016/j.abb.2007.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/18/2007] [Indexed: 01/15/2023]
Abstract
The enzymatic activity of hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is modulated by the molar ratio of NS5B enzyme and RNA template. Depending on the ratio, either template or enzyme can inhibit activity. Inhibition of NS5B activity by RNA template exhibited characteristics of substrate inhibition, suggesting the template binds to a secondary site on the enzyme forming an inactive complex. Template inhibition was modulated by primer. Increasing concentrations of primer restored NS5B activity and decreased the affinity of template for the secondary site. Conversely, increasing template concentration reduced the affinity of primer binding. The kinetic profiles suggest template inhibition results from the binding of template to a site that interferes with primer binding and the formation of productive replication complexes.
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Affiliation(s)
- Ying-Kai Wang
- Department of Virology, Bristol Myers Squibb Co., Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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