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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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2
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Abstract
The need for antiviral drugs is growing rapidly as more viral diseases are recognized. The methods used to discover these drugs have evolved considerably over the past 40 years and the overall process of discovery can be broken down into sub-processes which include lead generation, lead optimization and lead development. Various methods are now employed to ensure these processes are carried out efficiently. For lead generation, screening methodologies have developed to the extent where hundreds of thousands of compounds can be screened against a particular target. An alternative approach is to use the structures of enzyme substrates as a starting point for drug discovery. Much use is now made of X-ray crystallographic data of target–inhibitor complexes for the optimization of lead structures, and methods for preparing libraries of compounds to assist both generation and optimization of leads are welldeveloped. The methods used to predict and improve the pharmacokinetic properties of compounds are also changing rapidly. Finally, novel approaches to antiviral therapy using oligonucleotide-based compounds or modulating the host immune response are also being explored. This review discusses these approaches, provides examples of where their application has been successful and sets them against a historical background.
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Affiliation(s)
- PS Jones
- Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, UK
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3
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Jackson RW, LaPorte MG, Herbertz T, Draper TL, Gaboury JA, Rippin SR, Patel R, Chunduru SK, Benetatos CA, Young DC, Burns CJ, Condon SM. The discovery and structure–activity relationships of pyrano[3,4-b]indole-based inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2011; 21:3227-31. [DOI: 10.1016/j.bmcl.2011.04.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/21/2022]
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4
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Kang IJ, Wang LW, Yeh TK, Lee CC, Lee YC, Hsu SJ, Wu YS, Wang JC, Chao YS, Yueh A, Chern JH. Synthesis, activity, and pharmacokinetic properties of a series of conformationally-restricted thiourea analogs as novel hepatitis C virus inhibitors. Bioorg Med Chem 2010; 18:6414-21. [PMID: 20675142 DOI: 10.1016/j.bmc.2010.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 06/30/2010] [Accepted: 07/01/2010] [Indexed: 01/06/2023]
Abstract
A series of novel conformationally-restricted thiourea analogs were designed, synthesized, and evaluated for their anti-HCV activity. Herein we report the synthesis, structure-activity relationships (SARs), and pharmacokinetic properties of this new class of thiourea compounds that showed potent inhibitory activities against HCV in the cell-based subgenomic HCV replicon assay. Among compounds tested, the fluorene compound 4b was found to possess the most potent activity (EC(50)=0.3 microM), lower cytotoxicity (CC(50)>50 microM), and significantly better pharmacokinetic properties compared to its corresponding fluorenone compound 4c.
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Affiliation(s)
- Iou-Jiun Kang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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5
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LaPorte MG, Draper TL, Miller LE, Blackledge CW, Leister LK, Amparo E, Hussey AR, Young DC, Chunduru SK, Benetatos CA, Rhodes G, Gopalsamy A, Herbertz T, Burns CJ, Condon SM. The discovery and structure–activity relationships of pyrano[3,4-b]indole based inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2010; 20:2968-73. [DOI: 10.1016/j.bmcl.2010.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 03/01/2010] [Indexed: 10/21/2022]
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6
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Kang IJ, Wang LW, Hsu SJ, Lee CC, Lee YC, Wu YS, Yueh A, Wang JC, Hsu TA, Chao YS, Chern JH. Design and efficient synthesis of novel arylthiourea derivatives as potent hepatitis C virus inhibitors. Bioorg Med Chem Lett 2009; 19:6063-8. [DOI: 10.1016/j.bmcl.2009.09.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/10/2009] [Accepted: 09/11/2009] [Indexed: 02/07/2023]
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7
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Kang IJ, Wang LW, Hsu SJ, Lee CC, Lee YC, Wu YS, Hsu TA, Yueh A, Chao YS, Chern JH. Design and synthesis of indole, 2,3-dihydro-indole, and 3,4-dihydro-2H-quinoline-1-carbothioic acid amide derivatives as novel HCV inhibitors. Bioorg Med Chem Lett 2009; 19:4134-8. [PMID: 19539472 DOI: 10.1016/j.bmcl.2009.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 05/19/2009] [Accepted: 06/01/2009] [Indexed: 02/05/2023]
Abstract
An efficient synthetic methodology to provide indole, 2,3-dihydro-indole, and 3,4-dihydro-2H-quinoline-1-carbothioic acid amide derivatives is described. These conformationally restricted heterobicyclic scaffolds were evaluated as a novel class of HCV inhibitors. Introduction of an acyl group at the NH(2) of the thiourea moiety has been found to enhance inhibitory activity. The chain length and the position of the alkyl group on the indoline aromatic ring markedly influenced anti-HCV activity. The indoline scaffold was more potent than the corresponding indole and tetrahydroquinoline scaffolds and analogue 31 displayed excellent activity (EC(50)=510nM) against HCV without significant cytotoxicity (CC(50) >50microM).
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Affiliation(s)
- Iou-Jiun Kang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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8
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Kang IJ, Wang LW, Lee CC, Lee YC, Chao YS, Hsu TA, Chern JH. Design, synthesis, and anti-HCV activity of thiourea compounds. Bioorg Med Chem Lett 2009; 19:1950-5. [PMID: 19251415 DOI: 10.1016/j.bmcl.2009.02.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/09/2009] [Accepted: 02/12/2009] [Indexed: 02/02/2023]
Abstract
A series of thiourea derivatives were synthesized and their antiviral activity was evaluated in a cell-based HCV subgenomic replicon assay. SAR studies revealed that the chain length and the position of the alkyl linker largely influenced the in vitro anti-HCV activity of this class of potent antiviral agents. Among this series of compounds synthesized, the thiourea derivative with a six-carbon alkyl linker at the meta-position of the central phenyl ring (10) was identified as the most potent anti-HCV inhibitor (EC(50) = 0.047 microM) with a selectivity index of 596.
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Affiliation(s)
- Iou-Jiun Kang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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9
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LaPorte M, Jackson R, Draper T, Gaboury J, Galie K, Herbertz T, Hussey A, Rippin S, Benetatos C, Chunduru S, Christensen J, Coburn GA, Rizzo C, Rhodes G, O'Connell J, Howe A, Mansour T, Collett M, Pevear D, Young D, Gao T, Tyrrell D, Kneteman N, Burns C, Condon S. The Discovery of Pyrano[3,4-b]indole-Based Allosteric Inhibitors of HCV NS5B Polymerase with In Vivo Activity. ChemMedChem 2008; 3:1508-15. [DOI: 10.1002/cmdc.200800168] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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10
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Venkatraman S, Njoroge FG, Wu W, Girijavallabhan V, Prongay AJ, Butkiewicz N, Pichardo J. Novel inhibitors of hepatitis C NS3-NS4A serine protease derived from 2-aza-bicyclo[2.2.1]heptane-3-carboxylic acid. Bioorg Med Chem Lett 2006; 16:1628-32. [PMID: 16413182 DOI: 10.1016/j.bmcl.2005.12.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/10/2005] [Accepted: 12/07/2005] [Indexed: 11/23/2022]
Abstract
Prolonged hepatitis C infection is the leading cause for cirrhosis of the liver and hepatocellular carcinoma. The etiological agent HCV virus codes a single polyprotein of approximately 3000 amino acids that is processed with the help of a serine protease NS3A to produce structural and non-structural proteins required for viral replication. Inhibition of NS3 protease can potentially be used to develop drugs for treatment of HCV infections. Herein, we report the development of a series of novel NS3 serine protease inhibitors derived from 2-aza-bicyclo[2.2.1]-heptane carboxylic acid with potential therapeutic use for treatment of HCV infections.
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Affiliation(s)
- Srikanth Venkatraman
- Schering Plough Research Institute, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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11
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Laporte MG, Lessen TA, Leister L, Cebzanov D, Amparo E, Faust C, Ortlip D, Bailey TR, Nitz TJ, Chunduru SK, Young DC, Burns CJ. Tetrahydrobenzothiophene inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2006; 16:100-3. [PMID: 16260131 DOI: 10.1016/j.bmcl.2005.09.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 09/15/2005] [Accepted: 09/16/2005] [Indexed: 12/09/2022]
Abstract
A novel series of selective HCV NS5B RNA dependent RNA polymerase inhibitors has been disclosed. These compounds contain an appropriately substituted tetrahydrobenzothiophene scaffold. This communication will detail the SAR and activities of this series.
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Affiliation(s)
- M G Laporte
- ViroPharma Incorporated, 397 Eagleview Boulevard, Exton, PA 19341, USA.
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12
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Han W, Jiang X, Hu Z, Wasserman ZR, Decicco CP. Investigation of glycine α-ketoamide HCV NS3 protease inhibitors: Effect of carboxylic acid isosteres. Bioorg Med Chem Lett 2005; 15:3487-90. [PMID: 15982872 DOI: 10.1016/j.bmcl.2005.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 05/27/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022]
Abstract
The design and synthesis of tetrapeptide-based alpha-ketoamides containing prime side acid isosteres HCV NS3 protease inhibitors are described. Tetrazole, sulfonic acid, and N-sulfonylcarboxamids were demonstrated to be efficient carboxylic acid replacements. Further optimization yielded a series of potent HCV NS3 protease inhibitors with IC(50) of 0.020-0.060 microM.
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Affiliation(s)
- Wei Han
- Discovery Chemistry, Pharmaceutical Research Institute, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, NJ 08543, USA.
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13
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Venkatraman S, Njoroge FG, Girijavallabhan VM, Madison VS, Yao NH, Prongay AJ, Butkiewicz N, Pichardo J. Design and Synthesis of Depeptidized Macrocyclic Inhibitors of Hepatitis C NS3-4A Protease Using Structure-Based Drug Design. J Med Chem 2005; 48:5088-91. [PMID: 16078825 DOI: 10.1021/jm0489556] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hepatitis C virus (HCV) NS3, when bound to NS-4A cofactor, facilitates development of mature virons by catalyzing cleavage of a polyprotein to form functional and structural proteins of HCV. The enzyme has a shallow binding pocket at the catalytic site, making development of inhibitors difficult. We have designed, preorganized, and depeptidized macrocyclic inhibitors from P(4) to P(2)' and optimized binding to 0.1 microM. The structure of an inhibitor bound to the enzyme was also solved.
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Affiliation(s)
- Srikanth Venkatraman
- Schering Plough Research Institute, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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14
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Watanabe K, Yoshioka K, Yano M, Ishigami M, Ukai K, Ito H, Miyata F, Mizutani T, Goto H. Mutations in the nonstructural region 5B of hepatitis C virus genotype 1b: their relation to viral load, response to interferon, and the nonstructural region 5A. J Med Virol 2005; 75:504-12. [PMID: 15714488 DOI: 10.1002/jmv.20301] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The nonstructural 5B (NS5B) protein of hepatitis C virus possesses RNA-dependent RNA polymerase activity and plays an essential role in viral replication. The mutations in NS5B were determined and the correlation with viral load and response to interferon (IFN) were assessed. The entire NS5B region in 33 patients and its thumb domain in 62 patients was sequenced. The number of amino acid substitutions in the NS5B protein, that in thumb domain and the substitution at aa 389 was correlated with viral load and the response to IFN. Multivariate analysis selected only mutation in IFN sensitivity determining region (ISDR) as a factor associated with the viral load and response to IFN. The number of substitutions in the thumb domain and the substitution at aa 389 correlated with the number of substitutions in the ISDR. These results suggest that mutations in NS5B, especially in the thumb domain and at aa 389, have an important effect on viral load and the response to IFN, although they were dependent on mutations in ISDR. Further studies on the relationship between NS5B and NS5A (ISDR) are necessary to elucidate the mechanism of the correlation with viral load and the response to IFN.
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Affiliation(s)
- Kazumasa Watanabe
- Department of Internal Medicine, Division of Gastroenterology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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15
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Wang QM, Johnson RB, Chen D, Lévêque VJP, Ren J, Hockman MA, Abe K, Hachisu T, Kondo Y, Isaka Y, Sato A, Fujiwara T. Expression and purification of untagged full-length HCV NS5B RNA-dependent RNA polymerase. Protein Expr Purif 2005; 35:304-12. [PMID: 15135407 DOI: 10.1016/j.pep.2004.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 01/21/2004] [Indexed: 10/26/2022]
Abstract
The NS5B encoded by the hepatitis C virus genome is a RNA-dependent RNA polymerase essential to viral replication. The entire NS5B protein contains a catalytic domain followed by a regulatory motif and a membrane-anchor domain at its C-terminus. Reported here is the molecular cloning and expression of the full-length NS5B polymerase (NS5B-FL) in bacterial cells as a non-fusion protein. The non-tagged NS5B-FL was purified to homogeneity using sequential chromatographic columns and its identity was confirmed using anti-NS5B peptide antibodies and amino acid sequencing. Purified NS5B-FL demonstrated RNA-dependent RNA polymerase activity and was able to replicate a HCV RNA genome fragment through both copy-back and de novo mechanisms. Its biochemical properties were further characterized in comparison with a truncated form of NS5B polymerase with a deletion of 51 residues from its C-terminus.
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Affiliation(s)
- Q May Wang
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA.
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16
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Yip Y, Victor F, Lamar J, Johnson R, Wang QM, Glass JI, Yumibe N, Wakulchik M, Munroe J, Chen SH. P4 and P1' optimization of bicycloproline P2 bearing tetrapeptidyl alpha-ketoamides as HCV protease inhibitors. Bioorg Med Chem Lett 2005; 14:5007-11. [PMID: 15341970 DOI: 10.1016/j.bmcl.2004.07.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Accepted: 07/02/2004] [Indexed: 11/30/2022]
Abstract
With the aim of improving HCV protease inhibitors reported in our previous manuscripts, we synthesized and evaluated a series of 1a-based tetrapeptidyl alpha-ketoamides with additional P4 modification. The promising analog discovered through this SAR, 5a, was further derivatized at P1' or P1 position. As a result of these efforts, we found that replacement of the P4 valine as seen in 1a with cyclohexylglycine (Chg) resulted in the discovery of 5a, 5c, and 5e endowed with improved cellular activity in comparison to 1a.
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Affiliation(s)
- Yvonne Yip
- Lilly Research Laboratory, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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17
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Abstract
Hepatitis C virus (HCV) is a human hepatotropic virus with an estimated worldwide prevalence of 170 million cases, including approximately 4 million cases in the US. It is a major cause of liver disease and is the most common indication for liver transplantation in the US. The majority of infected individuals are eligible for therapy. Since it is difficult to predict who will have progressive disease, those with significant inflammation or fibrosis on histologic examination of liver biopsy are generally offered treatment. The following chapter is an overview of the patent literature during 2000-mid-2002, and discusses the potential of various treatment modalities for HCV.
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Affiliation(s)
- F Fred Poordad
- Department of Hepatology and Liver Transplantation, Cedars-Sinai Medical Center, 8635 W. Third St, #590W, Los Angeles, CA 90048, USA
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19
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Abstract
Hepatitis C virus (HCV) has infected millions of people worldwide and has emerged as a global health crisis. The currently available therapy is interferon (IFN) either alone or in combination with ribavirin. However, the disappointing efficacy of IFN has led to the considerable need for improved treatments and a number of new therapies are under evaluation in clinical trials. These include pegylated IFNs, which have altered physiochemical characteristics allowing once-weekly dosing. Combination of pegylated IFN with ribavirin should further improve sustained response rates. However, not all patients are successfully treated with IFNs, particularly those infected with genotype 1 of the virus, and it is likely that potent, specific drugs will be required. The majority of new approaches currently trying to combat this viral disease are aimed at inhibition of viral targets. Most effort has been directed towards inhibition of the NS3 serine protease, and potent inhibitors have now been described. However, a clinical candidate is yet to emerge against this difficult target. Considerable work by leading researchers has provided crystal structures of the key replicative enzymes, NS3 protease, NS3 helicase, NS5B polymerase and full-length NS3 protease-helicase, and there is much hope that such structural information will bear fruit. More recently, inhibition of host targets, particularly inosine monophosphate dehydrogenase (IMPDH), has become of interest and there are on-going clinical trials with such inhibitors. Research aimed at novel treatments for HCV disease is gathering pace and very recent developments in cell-based assay systems can only hasten the discovery of improved therapies.
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Affiliation(s)
- B W Dymock
- Roche Discovery Welwyn, Broadwater Road, Welwyn Garden City, Herts, AL7 3AY, UK.
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21
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Yip Y, Victor F, Lamar J, Johnson R, Wang QM, Barket D, Glass J, Jin L, Liu L, Venable D, Wakulchik M, Xie C, Heinz B, Villarreal E, Colacino J, Yumibe N, Tebbe M, Munroe J, Chen SH. Discovery of a novel bicycloproline P2 bearing peptidyl alpha-ketoamide LY514962 as HCV protease inhibitor. Bioorg Med Chem Lett 2004; 14:251-6. [PMID: 14684337 DOI: 10.1016/j.bmcl.2003.09.074] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We describe herein the design, syntheses and evaluation of a number of bicycloproline P2 bearing HCV protease inhibitors endowed with impressive enzyme potency, enzyme selectivity, cellular activity and favorable ADME profiles.
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Affiliation(s)
- Yvonne Yip
- Lilly Research Laboratory, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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22
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Sun DX, Liu L, Heinz B, Kolykhalov A, Lamar J, Johnson RB, Wang QM, Yip Y, Chen SH. P4 cap modified tetrapeptidyl α-ketoamides as potent HCV NS3 protease inhibitors. Bioorg Med Chem Lett 2004; 14:4333-8. [PMID: 15261297 DOI: 10.1016/j.bmcl.2004.05.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 05/26/2004] [Indexed: 11/17/2022]
Abstract
We describe herein the design, syntheses, and biological evaluation of new series of P4 tetrazole and adipic acid, ester, amide capped tetrapeptidyl alpha-ketoamide based HCV protease inhibitors.
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Affiliation(s)
- David X Sun
- Lilly Research Laboratory, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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23
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Victor F, Lamar J, Snyder N, Yip Y, Guo D, Yumibe N, Johnson RB, Wang QM, Glass JI, Chen SH. P1 and P3 optimization of novel bicycloproline P2 bearing tetrapeptidyl α-ketoamide based HCV protease inhibitors. Bioorg Med Chem Lett 2004; 14:257-61. [PMID: 14684338 DOI: 10.1016/j.bmcl.2003.09.075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
With the aim of discovering potent and selective HCV protease inhibitors, we synthesized and evaluated a series of 1a based tetrapeptidyl ketoamides with additional modification(s) at P1', P1, and P3 positions. As a result of this effort, we found that replacement of the P3 valine with tert-leucine resulted in the discovery of a series of inhibitors (e.g., 3a, 3c, and 4c) endowed with improved enzyme and/or cellular activity relative to 1a. When dosed to F-344 rats orally at 50mg/kg, 3a achieved 2.5x higher liver and plasma exposure in comparison to that detected with 1a.
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Affiliation(s)
- Frantz Victor
- Lilly Research Laboratory, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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24
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Han W, Hu Z, Jiang X, Wasserman ZR, Decicco CP. Glycine alpha-ketoamides as HCV NS3 protease inhibitors. Bioorg Med Chem Lett 2003; 13:1111-4. [PMID: 12643923 DOI: 10.1016/s0960-894x(03)00031-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Using a tetrapeptide-based alpha-ketoamide template, various amines and amino acids were incorporated to explore the prime side of the HCV NS3 protease catalytic site. Glycine carboxylic acid was found to be the most effective prime group. Further optimization yielded an inhibitor with IC(50) of 0.060 microM.
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Affiliation(s)
- Wei Han
- Department of Discovery Chemistry, Pharmaceutical Research Institute, Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543, USA.
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25
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Bougie I, Charpentier S, Bisaillon M. Characterization of the metal ion binding properties of the hepatitis C virus RNA polymerase. J Biol Chem 2003; 278:3868-75. [PMID: 12458224 DOI: 10.1074/jbc.m209785200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis C virus nonstructural 5B protein (NS5B) protein has been shown to require either magnesium or manganese for its RNA-dependent RNA polymerase activity. As a first step toward elucidating the nature and the role(s) of the metal ions in the reaction chemistry, we have utilized endogenous tryptophan fluorescence to quantitate the interactions of magnesium and manganese ions with this protein. The association of either Mg(2+) or Mn(2+) ions with the enzyme resulted in a decrease in the intensity of the tryptophan emission spectrum. This decrease was used to determine the apparent dissociation constants for both ions. The apparent K(d) values for the binding of Mg(2+) and Mn(2+) ions to the free enzyme were 3.1 and 0.3 mm, respectively. Dual ligand titration experiments demonstrated that both ions bind to a single common site, for which they compete. The kinetics of real time metal ion binding to the NS5B protein were also investigated. Based on the results of our fluorescence and near-UV circular dichroism experiments, we show that NS5B undergoes conformational changes upon the binding of metal ions. However, this process does not significantly stimulate the binding to the RNA or NTP substrates. We envisage that the ion-induced conformational change is a prerequisite for catalytic activity by both correctly positioning the side chains of the residues located in the active site of the enzyme and also contributing to the stabilization of the intermediate transition state.
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Affiliation(s)
- Isabelle Bougie
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Québec J1H 5N4, Canada
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26
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Abstract
In recent years, significant advances have been achieved both in the development of animal- and tissue-culture models for HCV. Among all the new systems, the small animal model based on transgenic mice with chimeric mouse-human livers and the replicon system will presumably have the most profound impact on future HCV research. Yet, in spite of this progress, much more work will be required to optimizse both systems. In case of the mouse model, breeding homozygous Alb-uPa animals is difficult because of the toxicity of the transgene, and the transplantation of primary human hepatocytes into mice a few days after birth is technically challenging. These are immunodeficient, and, therefore, it will be desirable to furnish them with components of the human immune system in order to expand the applicability of this in vivo model to questions related to pathogenesis. Advances in cryopreservation techniques are urgently needed, moreover, as this would improve the availability of primary hepatocytes and in turn also the accessibility of this small animal model. As regards the replicon system, a number of open questions remain that will hopefully be answered by future research. Why, for instance, has replication in cell culture so far been achieved only with genotype 1b isolates, whereas an isolate with proven infectivity derived from genotype 1a failed to replicate in Huh-7 cells? And why can replicons so far be propagated only in this particular cell line? Is this attributable to the lack of certain inhibitory factors, or the presence of specific activators? What are the mechanisms underlying cell-culture adaptation. and what determines whether a certain Huh-7 cell replicates HCV RNA more efficiently? Finally, the replicon system may also lead the way to the development of systems for efficient virus production in cell culture, and ultimately also a permissive cell line. These developments would at last allow us to model the complete viral life cycle, something researchers have been struggling with ever since the first identification of HCV.
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Affiliation(s)
- Thomas Pietschmann
- Department of Molecular Virology, University of Heidelberg, 350 Otto-Meyerhof-Zentrum Im Neuenheimer Feld, Heidelberg 69120, Germany
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27
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Labonté P, Axelrod V, Agarwal A, Aulabaugh A, Amin A, Mak P. Modulation of hepatitis C virus RNA-dependent RNA polymerase activity by structure-based site-directed mutagenesis. J Biol Chem 2002; 277:38838-46. [PMID: 12145289 DOI: 10.1074/jbc.m204657200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis C virus (HCV) encodes an RNA-dependent RNA polymerase (NS5B), which is indispensable for the viral genome replication. Although structural comparison among HCV NS5B, poliovirus 3D-pol, and human immunodeficiency virus-reverse transcriptase RNA-dependent polymerase reveals the canonical palm, fingers, and thumb domains, the crystal structure of HCV NS5B highlights the presence of a unique A1-loop, which extends from the fingers to the thumb domain (amino acids 12-46), providing many contact points for the proposed "closed" conformation of the enzyme. The polymerase also possesses a tunnel, which starts at the active site and terminates on the back surface of the enzyme. This tunnel of 19 A contains five basic amino acids, which may be engaged in NTP trafficking. In the present study, we exploited the crystal structure of the enzyme to elucidate the involvement of these two structural motifs in enzyme activity by site-directed mutagenesis. As predicted, the replacement of leucine 30 located in the Lambda 1-loop is detrimental to the NS5B activity. Heparin-Sepharose column chromatography and analytical ultracentrifugation experiments strongly suggest a local alteration in the structure of the Leu-30 mutant. An analysis of amino acid substitutions in Arg-222 and Lys-151 within the putative NTP tunnel indicates that Arg-222 was critical in delivering NTPs to the active site, whereas Lys-151 was dispensable. Interestingly, the substitution of lysine 151 for a glutamic acid resulted in an enzyme that was consistently more active in de novo synthesis as well as by "copy-back" mechanism of a self-primed substrate when compared with the wild type NS5B enzyme. Burst kinetic analyses indicate that the gain in function of K151E enzyme was primarily the result of the formation of more productive pre-initiation complexes that were used for the elongation reaction. In contrast to the recent observations, both the wild type and mutant enzymes were monomeric in solution, whereas molecules of higher order were apparent in the presence of RNA template.
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Affiliation(s)
- Patrick Labonté
- Department of Infectious Disease, Wyeth, Pearl River, New York 10965, USA
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28
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Kashiwagi T, Hara K, Kohara M, Iwahashi J, Hamada N, Honda-Yoshino H, Toyoda T. Promoter/origin structure of the complementary strand of hepatitis C virus genome. J Biol Chem 2002; 277:28700-5. [PMID: 12039953 DOI: 10.1074/jbc.m201251200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hepatitis C virus (HCV) NS5B protein encodes an RNA-dependent RNA polymerase (RdRp). Sequences in the 3' termini of both the plus and minus strand of HCV genomic RNA harbor the activity of a replication origin and a transcription promoter. There are unique stem-loop structures in both termini of the viral RNA. We found that the complementary strand of the internal ribosome-binding site (IRES) showed strong template activity in vitro. The complementary strand RNA of the HCV genome works as a template for mRNA and viral genomic RNA. We analyzed the promoter/origin structure of the complementary sequence of IRES and found that the first and second stem-loops worked as negative and positive elements in RNA synthesis, respectively. The complementary strand of the second stem-loop of IRES was an important element also for binding to HCV RdRp.
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Affiliation(s)
- Takahito Kashiwagi
- Department of Virology, Kurume University, School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
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29
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Peng XX, Wang SY, Zhang JY, Zhu H. Analysis of HCV-immunoglobulin isotype complexes provide new insights into antibody response to HCV. Scand J Immunol 2002; 56:94-100. [PMID: 12100476 DOI: 10.1046/j.1365-3083.2002.01112.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hepatitis C virus (HCV) is known for its ability to establish persistent infection and cause chronic hepatitis in most infected individuals. The antibody response to HCV in HCV-circulating immune complexes (CIC) is unknown. In the present study, we have characterized distinct changes in patterns of HCV-immunoglobulin (Ig) constituents with disease category, viral mutation and clinical markers. The number of samples positive for single HCV-Ig, HCV-IgG and HCV-IgA, HCV-IgM and HCV-IgA, HCV-IgM and HCV-IgG, HCV-IgM, HCV-IgG and HCV-IgA in 47 samples tested were 8 (17%), 1 (2.1%), 9 (19.1%), 4 (8.5%) and 17 (36.2%), respectively. The occurrence of HCV-IgM and HCV-IgA in combination of two isotypes of HCV-Ig became predominant. These results show that defective IgG in HCV-CIC may contribute to long-term viremia. Further analysis indicated that the frequency of HCV RNA/IgA-CIC in the abnormal aspartic aminotransferase (AST) group was significantly higher than that of the normal AST group, and HCV RNA/IgA-CIC frequency in the abnormal alanine aminotransferase (ALT) group was slightly higher than that in the normal ALT group. IgA complexes may reflect the damage degree of liver function during the course of HCV infection. We also found that there were more mutations in supernatant than in other constituents from single-strand conformation polymorphism (SSCP) analysis. Our results suggest that Ig-complexed virions and free virions may have different biological consequences, with the latter being elusive to immunological elimination. The findings in this study may provide some new insights into antibody response to HCV.
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Affiliation(s)
- X X Peng
- The Key Laboratory of Education Ministry for Cell Biology and Tumor Cell Engineering, Department of Biology, School of Life Sciences, Xiamen University, Fujian, P. R. China.
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30
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Zhang R, Durkin JP, Windsor WT. Azapeptides as inhibitors of the hepatitis C virus NS3 serine protease. Bioorg Med Chem Lett 2002; 12:1005-8. [PMID: 11909704 DOI: 10.1016/s0960-894x(02)00102-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Truncation and substitution SAR studies of azapeptide-based inhibitors of the Hepatitis C virus (HCV) NS3 serine protease have been performed. These azapeptides were designed from the HCV polyprotein's NS5A-NS5B trans cleavage junction and contained an azaamino acid residue at the P1 position. These azapeptides exhibited predominantly non-acylating, competitive inhibition, contrary to classical azapeptides.
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Affiliation(s)
- Rumin Zhang
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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31
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Abstract
The RNA-dependent RNA polymerase of hepatitis C virus (HCV) is responsible for replication of genomic RNA. A novel nonisotopic assay method is described for detecting its enzymatic activity. The 5' end of the in vitro-transcribed template RNA was attached covalently to the surface of a Covalink module using carbodiimide condensation. The RNA strand containing the 3' untranslated region (3' UTR) of HCV at its 3' end was free in the solution. A purified NS5B polymerase and NTPs along with biotin-labeled UTP were added to this module and the polymerization activity could be detected colorimetrically with streptavidin-conjugated alkaline phosphatase.
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Affiliation(s)
- Chanhee Park
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Kyung-Gi Do, South Korea
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32
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Beevers R, Carr MG, Jones PS, Jordan S, Kay PB, Lazell RC, Raynham TM. Solution and solid-phase synthesis of potent inhibitors of hepatitis C virus NS3 proteinase. Bioorg Med Chem Lett 2002; 12:641-3. [PMID: 11844690 DOI: 10.1016/s0960-894x(01)00816-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A versatile route for the synthesis of homochiral alpha-ketoamide analogues of amino acids is described. Incorporation of this functionality into peptide sequences using either solution or solid-phase chemistry resulted in potent inhibitors of the Hepatitis C Virus NS3 proteinase.
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Affiliation(s)
- Rebekah Beevers
- Department of Chemistry, Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, Hertfordshire, UK
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33
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Kashiwagi T, Hara K, Kohara M, Kohara K, Iwahashi J, Hamada N, Yoshino H, Toyoda T. Kinetic analysis of C-terminally truncated RNA-dependent RNA polymerase of hepatitis C virus. Biochem Biophys Res Commun 2002; 290:1188-94. [PMID: 11811988 DOI: 10.1006/bbrc.2001.6333] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biochemical properties of hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) truncated with C-terminal 21 amino acids and expressed in insect cells were analyzed. The enzyme carried copy-back and de novo RNA synthesis activity but not terminal nucleotidyl transferase activity. k(pol) and K(m) for de novo RNA synthesis were calculated as 10.0 pmol/microg/h and 2.5 microM under 0.5 mM GTP and 2.0 pmol/microg/h and 3.5 microM under 50 microM GTP, respectively. Those for copy-back RNA synthesis were similar under both conditions (k(pol), 1.8 pmol/microg/h; K(m), 3.0 microM). De novo RNA synthesis was activated by 0.5 mM GTP. However, the ratio of GTP to three other NTPs was important for activation. Our HCV RdRp showed high activity for the complementary sequence of the HCV internal ribosomal entry site and a synergistic effect of Mg(2+) to Mn(2+).
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Affiliation(s)
- Takahito Kashiwagi
- Department of Virology, Kurume University, School of Medicine, 67 Asahimachi, Kurume, Fukuoka, 830-0011, Japan
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34
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Bennett JM, Campbell AD, Campbell AJ, Carr MG, Dunsdon RM, Greening JR, Hurst DN, Jennings NS, Jones PS, Jordan S, Kay PB, O'Brien MA, King-Underwood J, Raynham TM, Wilkinson CS, Wilkinson TC, Wilson FX. The identification of alpha-ketoamides as potent inhibitors of hepatitis C virus NS3-4A proteinase. Bioorg Med Chem Lett 2001; 11:355-7. [PMID: 11212109 DOI: 10.1016/s0960-894x(00)00654-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Peptides based upon the non-prime side residues of the NS4A-4B cleavage site of hepatitis C virus (HCV) NS3-4A proteinase containing an alpha-ketoamide moiety in place of the scissile amide bond are potent inhibitors of this enzyme.
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Affiliation(s)
- J M Bennett
- Department of Chemistry, Roche Discover Welwyn, Welwyn Garden City, Hertfordshire, UK
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35
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LaPlante SR, Aubry N, Déziel R, Ni F, Xu P. Transferred 13C T1 Relaxation at Natural Isotopic Abundance: A Practical Method for Determining Site-Specific Changes in Ligand Flexibility upon Binding to a Macromolecule. J Am Chem Soc 2000. [DOI: 10.1021/ja0017817] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven R. LaPlante
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Norman Aubry
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Robert Déziel
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Feng Ni
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Ping Xu
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
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36
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Hussein G, Miyashiro H, Nakamura N, Hattori M, Kakiuchi N, Shimotohno K. Inhibitory effects of sudanese medicinal plant extracts on hepatitis C virus (HCV) protease. Phytother Res 2000; 14:510-6. [PMID: 11054840 DOI: 10.1002/1099-1573(200011)14:7<510::aid-ptr646>3.0.co;2-b] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
One hundred fifty-two methanol and water extracts of different parts of 71 plants commonly used in Sudanese traditional medicine were screened for their inhibitory effects on hepatitis C virus (HCV) protease (PR) using in vitro assay methods. Thirty-four extracts showed significant inhibitory activity (>/=60% inhibition at 100 microg/mL). Of these, eight extracts, methanol extracts of Acacia nilotica, Boswellia carterii, Embelia schimperi, Quercus infectoria, Trachyspermum ammi and water extracts of Piper cubeba, Q. infectoria and Syzygium aromaticum, were the most active (>/=90% inhibition at 100 microg/mL). From the E. schimperi extract, two benzoquinones, embelin (I) and 5-O-methylembelin (II), were isolated and found as potent HCV-PR inhibitors with IC(50) values of 21 and 46 microM, respectively. Inhibitory activities of derivatives of I against HCV-PR as well as their effects on other serine proteases were also investigated.
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Affiliation(s)
- G Hussein
- Institute of Natural Medicine, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama 930-0194, Japan
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37
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LaPlante SR, Aubry N, Bonneau PR, Kukolj G, Lamarre D, Lefebvre S, Li H, Llinàs-Brunet M, Plouffe C, Cameron DR. NMR line-broadening and transferred NOESY as a medicinal chemistry tool for studying inhibitors of the hepatitis C virus NS3 protease domain. Bioorg Med Chem Lett 2000; 10:2271-4. [PMID: 11055336 DOI: 10.1016/s0960-894x(00)00466-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work describes the use of NMR as a medicinal chemistry tool for better understanding the binding characteristics of inhibitors of the HCV NS3 protease. The protease-bound structure of a tetrapeptide-like inhibitor that has an acid C-terminus, a norvaline at P1 and a naphthylmethoxy proline at P2 is described. Conformational comparisons are made with a similar compound having a 1-amino-cyclopropylcarboxylic acid at P1 and with a hexapeptide inhibitor. Differences between the free and bound states are identified. 19F NMR also helped in determining that a single complex is observed when an inhibitor is added to the protease at a 1:1 ratio.
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Affiliation(s)
- S R LaPlante
- Department of Chemistry, Boehringer Ingelheim, Laval, Québec, Canada.
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38
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Tautz N, Kaiser A, Thiel HJ. NS3 serine protease of bovine viral diarrhea virus: characterization of active site residues, NS4A cofactor domain, and protease-cofactor interactions. Virology 2000; 273:351-63. [PMID: 10915606 DOI: 10.1006/viro.2000.0425] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gene expression of bovine viral diarrhea virus (BVDV), a pestivirus, occurs via translation of a hypothetical polyprotein that is processed cotranslationally and posttranslationally by viral and cellular enzymes. A protease located in the N-terminal region of nonstructural (NS) protein NS3 catalyzes the cleavages, leading to the release of NS4A, NS4B, NS5A, and NS5B. Our study provides experimental evidence that histidine at position 1658 and aspartic acid at position 1686 constitute together with the previously identified serine at position 1752 (S1752) the catalytic triad of the pestiviral NS3 serine protease. Interestingly, a mutant protease encompassing an exchange of the active site S1752 to threonine still showed residual activity. This finding links the NS3 protease of pestiviruses to the capsid protease of Sindbis virus. Furthermore, we observed that the minimal protease domain of NS3 encompasses about 209 amino acids. The NS3 protease was found to be sensitive to N-terminal truncation because a deletion of 6 amino acids significantly reduced the cleavage efficiency at the NS4A/4B site. Larger N-terminal deletions also impaired the activity of the enzyme with respect to the other cleavage sites but to a different degree at each site. The NS3 protease of BVDV has previously been shown to depend on NS4A as cofactor. We demonstrate here that the central region of NS4A represents the cofactor domain. Furthermore, coprecipitation studies strongly suggest an interaction between NS4A and the N-terminal region of NS3. Besides the remarkable similarities observed between the pestiviral NS3 protease and the corresponding enzyme of hepatitis C virus (HCV), our results suggest a common ancestry between these enzymes and the capsid protease of Sindbis virus.
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Affiliation(s)
- N Tautz
- Institut für Virologie (FB Veterinärmedizin), Justus-Liebig-Universität Giebetaen, Giebetaen, D-35392, Germany.
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39
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Ueno T, Misawa S, Ohba Y, Matsumoto M, Mizunuma M, Kasai N, Tsumoto K, Kumagai I, Hayashi H. Isolation and characterization of monoclonal antibodies that inhibit hepatitis C virus NS3 protease. J Virol 2000; 74:6300-8. [PMID: 10864639 PMCID: PMC112135 DOI: 10.1128/jvi.74.14.6300-6308.2000] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A series of mouse monoclonal antibodies (MAbs) to the nonstructural protein 3 (NS3) of hepatitis C virus was prepared. One of these MAbs, designated 8D4, was found to inhibit NS3 protease activity. This inhibition was competitive with respect to the substrate peptide (K(i) = 39 nM) but was significantly decreased by the addition of the NS4A peptide, a coactivator of the NS3 protease. 8D4 also showed marked inhibition of the NS3-dependent cis processing of the NS3/4A polyprotein but had virtually no effect on the succeeding NS3/4A-dependent trans processing of the NS5A/5B polyprotein in vitro. Epitope mapping of 8D4 with a random peptide library revealed a consensus sequence, DxDLV, that matched residues 79 to 83 (DQDLV) of NS3, a region containing the catalytic residue Asp-81. Furthermore, synthetic peptides including this sequence were shown to block the ability of 8D4 to bind to NS3, indicating that 8D4 interacts with the catalytic region of NS3. The data showing decreased inhibition potency of 8D4 against the NS3/4A complex suggest that 8D4 recognizes the conformational state of the protease active site caused by the association of NS4A with the protease.
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Affiliation(s)
- T Ueno
- Pharmaceuticals & Biotechnology Laboratory, Japan Energy Corporation, Toda-shi, Saitama, 335-8502, Japan.
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40
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Hicham Alaoui-Ismaili M, Gervais C, Brunette S, Gouin G, Hamel M, Rando RF, Bedard J. A novel high throughput screening assay for HCV NS3 helicase activity. Antiviral Res 2000; 46:181-93. [PMID: 10867156 DOI: 10.1016/s0166-3542(00)00085-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A novel assay for measurement of Hepatitis C virus (HCV) NS3 helicase activity was developed using Flashplate technology. This assay involves the use of a DNA duplex substrate and recombinant HCV NS3 produced in Escherichia coli. The DNA duplex consisted of a pair of oligonucleotides, one biotinylated, the other radiolabeled at their respective 5' termini. This DNA duplex was immobilized, via the biotin molecule, on the surface of a neutravidin-coated SMP103 Flashplate (NEN Life Science Products). Helicase activity results in the release of the radiolabeled oligonucleotide, which translates in signal reduction with respect to control wells. Biochemical characterization of the HCV NS3 helicase activity was performed using this assay. We demonstrated that the NS3-mediated unwinding is proportional to both the amount of DNA substrate in the well, and to the NS3 concentration in the reaction. Most of the NS3-mediated unwinding was achieved in the initial 60 min of incubation. As expected the reactions were ATP-dependent and found to be affected by the concentration of MgCl(2), MnCl(2), KCl, EDTA, and by pH. We found this assay to be highly reproducible since only slight variation was observed when a total of 68 helicase reactions were performed on one plate. Therefore, this Flashplate helicase assay is fast, convenient and reproducible. These criteria make it suitable for high throughput screening of potential NS3 helicase inhibitors.
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41
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Fattori D, Urbani A, Brunetti M, Ingenito R, Pessi A, Prendergast K, Narjes F, Matassa VG, De Francesco R, Steinkühler C. Probing the active site of the hepatitis C virus serine protease by fluorescence resonance energy transfer. J Biol Chem 2000; 275:15106-13. [PMID: 10809747 DOI: 10.1074/jbc.275.20.15106] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A serine protease domain contained within the viral NS3 protein is a key player in the maturational processing of the hepatitis C virus polyprotein and a prime target for the development of antiviral drugs. In the present work, we describe a dansylated hexapeptide inhibitor of this enzyme. Active site occupancy by this compound could be monitored following fluorescence resonance energy transfer between the dansyl fluorophore and protein tryptophan residues and could be used to 1) unambiguously assess active site binding of NS3 protease inhibitors, 2) directly determine equilibrium and pre-steady-state parameters of enzyme-inhibitor complex formation, and 3) dissect, using site-directed mutagenesis, the contribution of single residues of NS3 to inhibitor binding in direct binding assays. The assay was also used to characterize the inhibition of the NS3 protease by its cleavage products. We show that enzyme-product inhibitor complex formation depends on the presence of an NS4A cofactor peptide. Equilibrium and pre-steady-state data support an ordered mechanism of ternary (enzyme-inhibitor-cofactor) complex formation, requiring cofactor complexation prior to inhibitor binding.
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Affiliation(s)
- D Fattori
- Istituto di Ricerche di Biologia Molecolare "P. Angeletti" Via Pontina Km 30,600, Pomezia, 00040 Rome, Italy
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42
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Han W, Hu Z, Jiang X, Decicco CP. Alpha-ketoamides, alpha-ketoesters and alpha-diketones as HCV NS3 protease inhibitors. Bioorg Med Chem Lett 2000; 10:711-3. [PMID: 10782670 DOI: 10.1016/s0960-894x(00)00074-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Peptide-based alpha-ketoamides, alpha-ketoesters and alpha-diketones were designed, synthesized and evaluated against HCV NS3 protease. Alpha-ketoamides have the highest affinity among the three classes, with 8 being the most potent inhibitor with an IC50 of 340 nM.
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Affiliation(s)
- W Han
- Department of Chemical and Physical Sciences, DuPont Pharmaceuticals Company, Wilmington, DE 19880, USA.
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Zhong W, Uss AS, Ferrari E, Lau JY, Hong Z. De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase. J Virol 2000; 74:2017-22. [PMID: 10644375 PMCID: PMC111680 DOI: 10.1128/jvi.74.4.2017-2022.2000] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRp) encoded by positive-strand RNA viruses is critical to the replication of viral RNA genome. Like other positive-strand RNA viruses, replication of hepatitis C virus (HCV) RNA is mediated through a negative-strand intermediate, which is generated through copying the positive-strand genomic RNA. Although it has been demonstrated that HCV NS5B alone can direct RNA replication through a copy-back primer at the 3' end, de novo initiation of RNA synthesis is likely to be the mode of RNA replication in infected cells. In this study, we demonstrate that a recombinant HCV NS5B protein has the ability to initiate de novo RNA synthesis in vitro. The NS5B used HCV 3' X-tail RNA (98 nucleotides) as the template to synthesize an RNA product of monomer size, which can be labeled by ¿gamma-(32)Pnucleoside triphosphate. The de novo initiation activity was further confirmed by using small synthetic RNAs ending with dideoxynucleotides at the 3' termini. In addition, HCV NS5B preferred GTP as the initiation nucleotide. The optimal conditions for the de novo initiation activity have been determined. Identification and characterization of the de novo priming or initiation activity by HCV NS5B provides an opportunity to screen for inhibitors that specifically target the initiation step.
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Affiliation(s)
- W Zhong
- Department of Antiviral Therapy, Schering-Plough Research Institute, Kenilworth, New Jersey 07033-0539, USA.
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Leyssen P, De Clercq E, Neyts J. Perspectives for the treatment of infections with Flaviviridae. Clin Microbiol Rev 2000; 13:67-82, table of contents. [PMID: 10627492 PMCID: PMC88934 DOI: 10.1128/cmr.13.1.67] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The family Flaviviridae contains three genera: Hepacivirus, Flavivirus, and Pestivirus. Worldwide, more than 170 million people are chronically infected with Hepatitis C virus and are at risk of developing cirrhosis and/or liver cancer. In addition, infections with arthropod-borne flaviviruses (such as dengue fever, Japanese encephalitis, tick-borne encephalitis, St. Louis encephalitis, Murray Valley encephalitis, West Nile, and yellow fever viruses) are emerging throughout the world. The pestiviruses have a serious impact on livestock. Unfortunately, no specific antiviral therapy is available for the treatment or the prevention of infections with members of the Flaviviridae. Ongoing research has identified possible targets for inhibition, including binding of the virus to the cell, uptake of the virus into the cell, the internal ribosome entry site of hepaciviruses and pestiviruses, the capping mechanism of flaviviruses, the viral proteases, the viral RNA-dependent RNA polymerase, and the viral helicase. In light of recent developments, the prevalence of infections caused by these viruses, the disease spectrum, and the impact of infections, different strategies that could be pursued to specifically inhibit viral targets and animal models that are available to study the pathogenesis and antiviral strategies are reviewed.
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Affiliation(s)
- P Leyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Luo G, Hamatake RK, Mathis DM, Racela J, Rigat KL, Lemm J, Colonno RJ. De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J Virol 2000; 74:851-63. [PMID: 10623748 PMCID: PMC111606 DOI: 10.1128/jvi.74.2.851-863.2000] [Citation(s) in RCA: 235] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hepatitis C virus (HCV) NS5B protein possesses an RNA-dependent RNA polymerase (RdRp) activity, a major function responsible for replication of the viral RNA genome. To further characterize the RdRp activity, NS5B proteins were expressed from recombinant baculoviruses, purified to near homogeneity, and examined for their ability to synthesize RNA in vitro. As a result, a highly active NS5B RdRp (1b-42), which contains an 18-amino acid C-terminal truncation resulting from a newly created stop codon, was identified among a number of independent isolates. The RdRp activity of the truncated NS5B is comparable to the activity of the full-length protein and is 20 times higher in the presence of Mn(2+) than in the presence of Mg(2+). When a 384-nucleotide RNA was used as the template, two major RNA products were synthesized by 1b-42. One is a complementary RNA identical in size to the input RNA template (monomer), while the other is a hairpin dimer RNA synthesized by a "copy-back" mechanism. Substantial evidence derived from several experiments demonstrated that the RNA monomer was synthesized through de novo initiation by NS5B rather than by a terminal transferase activity. Synthesis of the RNA monomer requires all four ribonucleotides. The RNA monomer product was verified to be the result of de novo RNA synthesis, as two expected RNA products were generated from monomer RNA by RNase H digestion. In addition, modification of the RNA template by the addition of the chain terminator cordycepin at the 3' end did not affect synthesis of the RNA monomer but eliminated synthesis of the self-priming hairpin dimer RNA. Moreover, synthesis of RNA on poly(C) and poly(U) homopolymer templates by 1b-42 NS5B did not require the oligonucleotide primer at high concentrations (>/=50 microM) of GTP and ATP, further supporting a de novo initiation mechanism. These findings suggest that HCV NS5B is able to initiate RNA synthesis de novo.
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Affiliation(s)
- G Luo
- Department of Virology, Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492-7660, USA.
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46
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De Francesco R, Steinkühler C. Structure and function of the hepatitis C virus NS3-NS4A serine proteinase. Curr Top Microbiol Immunol 1999; 242:149-69. [PMID: 10592660 DOI: 10.1007/978-3-642-59605-6_8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- R De Francesco
- Istituto di Ricerche di Biologia Molecolare (IRBM) P. Angeletti, Pomezia, Rome, Italy
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47
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Attwood MR, Bennett JM, Campbell AD, Canning GG, Carr MG, Conway E, Dunsdon RM, Greening JR, Jones PS, Kay PB, Handa BK, Hurst DN, Jennings NS, Jordan S, Keech E, O'Brien MA, Overton HA, King-Underwood J, Raynham TM, Stenson KP, Wilkinson CS, Wilkinson TC, Wilson FX. The design and synthesis of potent inhibitors of hepatitis C virus NS3-4A proteinase. Antivir Chem Chemother 1999; 10:259-73. [PMID: 10574181 DOI: 10.1177/095632029901000505] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Hepatitis C virus (HCV) is the cause of the majority of transfusion-associated hepatitis and a significant proportion of community-acquired hepatitis worldwide. Infection by HCV frequently leads to persistent infections that result in a range of clinical conditions including an asymptomatic carrier state, severe chronic active hepatitis, cirrhosis and, in some cases, hepatocellular carcinoma. The HCV genome consists of a single-stranded, positive sense RNA containing an open reading frame of approximately 9060 nucleotides. This is translated into a single polyprotein of approximately 3020 amino acids (C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B), which in turn is processed by a series of host and viral proteinases into at least 10 cleavage products. The N-terminal portion of the NS3 protein encodes a serine proteinase that is responsible for the cleavage at the NS3-4A, NS4A-4B, NS4B-5A and NS5A-5B junctions. The 54 amino acid NS4A protein is a cofactor that binds to the NS3 protein and enhances its proteolytic activity. This report describes the expression of a recombinant NS3-4A proteinase fusion protein in Escherichia coli and the in vitro characterization of the enzyme activity using synthetic peptide substrates. It then demonstrates how these results were employed to guide the design of potent inhibitors of this enzyme.
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Affiliation(s)
- M R Attwood
- Department of Chemistry, Roche Discovery Welwyn, Welwyn Garden City, Hertfordshire, UK
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48
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Rosen HR, Gretch DR. Hepatitis C virus: current understanding and prospects for future therapies. MOLECULAR MEDICINE TODAY 1999; 5:393-9. [PMID: 10462751 DOI: 10.1016/s1357-4310(99)01523-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hepatitis C virus (HCV) is the leading cause of chronic liver disease worldwide and the leading indication for liver transplantation. The hallmark of the disease is its propensity to evolve into chronicity, probably because viral heterogeneity allows the virus to escape immune-mediated neutralization. Treatment with interferon alpha (IFN-alpha) has been disappointing, but higher and more frequent doses, and combination therapies, including nucleoside analogs, might lead to improved suppression of HCV RNA levels. Molecular analysis of HCV before and during treatment has indicated that high viral RNA levels and the presence of HCV genotype 1 are independent predictors of poor treatment outcome. New antiviral agents in development include inhibitors of HCV replicative enzymes, such as protease, helicase and polymerase, as well as several genetic approaches, such as ribozymes and antisense oligonucleotides. The main hindrance to drug development for hepatitis C is the lack of a small animal model or a productive tissue culture system for assessing drug action.
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Affiliation(s)
- H R Rosen
- Division of Gastroenterology and Hepatology, Portland VA Medical Center, Portland, OR 97207, USA.
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49
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Abstract
Sequence motifs within the non-structural protein NS5 or NS5B of the members of the family Flaviviridae suggest that this protein is the RNA-dependent RNA polymerase. This protein has now been expressed in various in vitro systems and used in polymerase assays. To understand the role of the RNA polymerase in RNA replication, this review will examine not only the polymerase protein but also the other proteins in the RNA replication complex. To date, several groups have investigated the interaction of these proteins both in vitro and in vivo and also the interaction of these proteins with the RNA signals at the 3' terminus of the RNA. Infectious clones and replicons containing the non-structural proteins have now been generated and these will be useful tools in understanding the processes of initiation and elongation of both positive and negative RNA synthesis.
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Affiliation(s)
- A Bartholomeusz
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
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50
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LaPlante SR, Cameron DR, Aubry N, Lefebvre S, Kukolj G, Maurice R, Thibeault D, Lamarre D, Llinàs-Brunet M. Solution structure of substrate-based ligands when bound to hepatitis C virus NS3 protease domain. J Biol Chem 1999; 274:18618-24. [PMID: 10373473 DOI: 10.1074/jbc.274.26.18618] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interactions of the NS3 protease domain with inhibitors that are based on N-terminal cleavage products of peptide substrates were studied by NMR methods. Transferred nuclear Overhauser effect experiments showed that these inhibitors bind the protease in a well defined, extended conformation. Protease-induced line-broadening studies helped identify the segments of inhibitors which come into contact with the protease. A comparison of the NMR data of the free and protease-bound states suggests that these ligands undergo rigidification upon complexation. This work provides the first structure of an inhibitor when bound to NS3 protease and should be valuable for designing more potent inhibitors.
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Affiliation(s)
- S R LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Québec H7S 2G5, Canada.
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