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Martino SD, Petri GL, De Rosa M. Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn? J Med Chem 2024; 67:885-921. [PMID: 38179950 DOI: 10.1021/acs.jmedchem.3c01971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.
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Affiliation(s)
- Simona Di Martino
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Giovanna Li Petri
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Maria De Rosa
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
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2
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Ghiasi T, Ahmadi S, Ahmadi E, Talei Bavil Olyai MR, Khodadadi Z. The index of ideality of correlation: QSAR studies of hepatitis C virus NS3/4A protease inhibitors using SMILES descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:495-520. [PMID: 34074200 DOI: 10.1080/1062936x.2021.1925344] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Robust and reliable QSAR models were developed to predict half-maximal inhibitory concentration (IC50) values of hepatitis C virus NS3/4A protease inhibitors from the Monte Carlo technique. 524 HCV NS3/4A protease inhibitors were extracted from the scientific literature to create a reasonably large set. The models were developed using CORAL software by using two target functions namely target function 1 (TF1) without applying the index of ideality of correlation (IIC) and target function 2 (TF2) that uses IIC. The constructed models based on TF2 were statistically more significant and robust than the models based on TF1. The determination coefficients (r2) of training and test sets were 0.86 and 0.88 for the best split based on TF2. The promoters of the increase/decrease of activity were also extracted and interpreted in detail. The model interpretation results explain the role of different structural attributes in predicting the pIC50 values of hepatitis C virus NS3/4A protease inhibitors. Based on the mechanistic model interpretation results, eight new compounds were designed and their pIC50 values were predicted based on the average prediction of ten models.
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Affiliation(s)
- T Ghiasi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - S Ahmadi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - E Ahmadi
- Department of Chemistry, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - M R Talei Bavil Olyai
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - Z Khodadadi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
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3
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Wypych RM, LaPlante SR, White PW, Martin SF. Structure-thermodynamics-relationships of hepatitis C viral NS3 protease inhibitors. Eur J Med Chem 2020; 192:112195. [PMID: 32151833 DOI: 10.1016/j.ejmech.2020.112195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
Thermodynamic parameters were determined for structurally-related inhibitors of HCV NS3 protease to assess how binding entropies and enthalpies vary with incremental changes at the P2 and P3 inhibitor subsites. Changing the heterocyclic substituent at P2 from a pyridyl to a 7-methoxy-2-phenyl-4-quinolyl group leads to a 710-fold increase in affinity. Annelating a benzene ring onto a pyridine ring leads to quinoline-derived inhibitors having higher affinities, but the individual enthalpy and entropy contributions are markedly different for each ligand pair. Introducing a phenyl group at C2 of the heterocyclic ring at P2 uniformly leads to higher affinity analogs with more favorable binding entropies, while adding a methoxy group at C7 of the quinoline ring at P2 provides derivatives with more favorable binding enthalpies. Significant enthalpy/entropy compensation is observed for structural changes made to inhibitors lacking a 2-phenyl substituent, whereas favorable changes in both binding enthalpies and entropies accompany structural modifications when a 2-phenyl group is present. Overall, binding energetics of inhibitors having a 2-phenyl-4-quinolyl group at P2 are dominated by entropic effects, whereas binding of the corresponding norphenyl analogs are primarily enthalpy driven. Notably, the reversal from an entropy driven association to an enthalpy driven one for this set of inhibitors also correlates with alternate binding modes. When the steric bulk of the side chain at P3 is increased from a hydrogen atom to a tert-butyl group, there is a 770-fold improvement in affinity. The 30-fold increase resulting from the first methyl group is solely the consequence of a more favorable change in entropy, whereas subsequent additions of methyl groups leads to modest increases in affinity that arise primarily from incremental improvements in binding enthalpies accompanied with smaller favorable entropic contributions.
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Affiliation(s)
- Rachel M Wypych
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA
| | - Steven R LaPlante
- Université du Québec, INRS-Centre Armand Frappier Santé et Biotechnologie, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
| | - Peter W White
- Boehringer Ingelheim (Canada) Limited, Research and Development, 2100 rue Cunard, Laval, Quebec, H7S 2G5, Canada
| | - Stephen F Martin
- The University of Texas at Austin, Department of Chemistry, 105 E 24th St Station A5300, Austin, TX, 78712-1224, USA.
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4
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Liverton NJ. Evolution of HCV NS3/4a Protease Inhibitors. TOPICS IN MEDICINAL CHEMISTRY 2019. [DOI: 10.1007/7355_2018_39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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5
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QSAR studies of the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by multiple linear regression (MLR) and support vector machine (SVM). Bioorg Med Chem Lett 2017; 27:2931-2938. [PMID: 28501513 DOI: 10.1016/j.bmcl.2017.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
In this study, quantitative structure-activity relationship (QSAR) models using various descriptor sets and training/test set selection methods were explored to predict the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by using a multiple linear regression (MLR) and a support vector machine (SVM) method. 512 HCV NS3/4A protease inhibitors and their IC50 values which were determined by the same FRET assay were collected from the reported literature to build a dataset. All the inhibitors were represented with selected nine global and 12 2D property-weighted autocorrelation descriptors calculated from the program CORINA Symphony. The dataset was divided into a training set and a test set by a random and a Kohonen's self-organizing map (SOM) method. The correlation coefficients (r2) of training sets and test sets were 0.75 and 0.72 for the best MLR model, 0.87 and 0.85 for the best SVM model, respectively. In addition, a series of sub-dataset models were also developed. The performances of all the best sub-dataset models were better than those of the whole dataset models. We believe that the combination of the best sub- and whole dataset SVM models can be used as reliable lead designing tools for new NS3/4A protease inhibitors scaffolds in a drug discovery pipeline.
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6
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Ozdemir Isik G, Ozer AN. Prediction of substrate specificity in NS3/4A serine protease by biased sequence search threading. J Biomol Struct Dyn 2016; 35:1102-1114. [DOI: 10.1080/07391102.2016.1171801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gonca Ozdemir Isik
- Department of Bioengineering, Marmara University , Goztepe, Kadikoy, 34722 Istanbul, Turkey
| | - A. Nevra Ozer
- Department of Bioengineering, Marmara University , Goztepe, Kadikoy, 34722 Istanbul, Turkey
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7
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Parsy C, Alexandre FR, Brandt G, Caillet C, Cappelle S, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos L, Leroy F, Liuzzi M, Loi AG, Moulat L, Musiu C, Rahali H, Roques V, Seifer M, Standring D, Surleraux D. Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease. Bioorg Med Chem Lett 2014; 24:4444-4449. [DOI: 10.1016/j.bmcl.2014.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 10/24/2022]
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8
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LaPlante SR, Nar H, Lemke CT, Jakalian A, Aubry N, Kawai SH. Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. J Med Chem 2013; 57:1777-89. [PMID: 24144444 DOI: 10.1021/jm401338c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds. All adopt similar bioactive conformations for the common core derived from the hit peptide DDIVPC. A carefully designed SAR analysis, based on the advanced inhibitor 1 in which the P1 to P3 side chains and the N-terminal Boc were sequentially truncated, revealed a correlation between affinity and the relative predominance of the bioactive conformation in the free state. Interestingly, synergistic conformation effects on potency were also noted. Comparisons with clinical and recently marketed drugs from the pharmaceutical industry showed that all have the same core and similar bioactive conformations. This suggested that the variety of appendages discovered for these compounds also properly satisfy the bioactive conformation requirements and allowed for a large variety of HCV protease drug candidates to be designed.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer-Ingelheim (Canada) Ltd., Research and Development , Laval, Québec H7S 2G5, Canada
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9
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Bailey MD, Halmos T, Lemke CT. Discovery of novel P2 substituted 4-biaryl proline inhibitors of hepatitis C virus NS3 serine protease. Bioorg Med Chem Lett 2013; 23:4436-40. [DOI: 10.1016/j.bmcl.2013.05.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
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10
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Bilodeau F, Bailey MD, Bhardwaj PK, Bordeleau J, Forgione P, Garneau M, Ghiro E, Gorys V, Halmos T, Jolicoeur ES, Leblanc M, Lemke CT, Naud J, O’Meara J, White PW, Llinàs-Brunet M. Synthesis and optimization of a novel series of HCV NS3 protease inhibitors: 4-Arylproline analogs. Bioorg Med Chem Lett 2013; 23:4267-71. [DOI: 10.1016/j.bmcl.2013.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
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11
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Dach R, Song JJ, Roschangar F, Samstag W, Senanayake CH. The Eight Criteria Defining a Good Chemical Manufacturing Process. Org Process Res Dev 2012. [DOI: 10.1021/op300144g] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rolf Dach
- Department of Process Development Chemicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Binger Straße 173, 55216 Ingelheim am Rhein, Germany
| | - Jinhua J. Song
- Department of Chemical
Development
US, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road/P.O. Box 368, Ridgefield, Connecticut 06877,
United States
| | - Frank Roschangar
- Department of Chemical
Development
US, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road/P.O. Box 368, Ridgefield, Connecticut 06877,
United States
| | - Wendelin Samstag
- Department of Process Development Chemicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Binger Straße 173, 55216 Ingelheim am Rhein, Germany
| | - Chris H. Senanayake
- Department of Chemical
Development
US, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road/P.O. Box 368, Ridgefield, Connecticut 06877,
United States
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13
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Busacca CA, Fandrick DR, Song JJ, Senanayake CH. The Growing Impact of Catalysis in the Pharmaceutical Industry. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100488] [Citation(s) in RCA: 369] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Small molecule inhibitors of the human papillomavirus E1-E2 interaction. Curr Top Microbiol Immunol 2011; 348:61-88. [PMID: 20676971 DOI: 10.1007/82_2010_92] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Human papillomaviruses are responsible for multiple human diseases, including cervical cancer caused by multiple high-risk types and genital warts caused by the low-risk types 6 and 11. Based on the research indicating that low-risk HPV could be successfully targeted by inhibitors of viral DNA replication, we carried out several high-throughput screens for inhibitors of DNA replication activities. Two series were identified in screens for inhibitors of the interaction between the viral proteins E1 and E2. The two series were demonstrated to bind to overlapping sites on the transactivation domain of E2, at the E1-binding interface, by a series of biochemical and biophysical experiments. A member of the first series was also cocrystallized with the E2 transactivation domain. For both series, structure-activity investigations are described, which resulted in several hundred fold improvements in activity. The best compounds in each series had low nanomolar activity against the HPV11 E1-E2 interaction, and EC(50) values in cellular DNA replication assays of approximately 1 μM. Binding modes for the two series are compared, and some general conclusions about the discovery of protein-protein interaction inhibitors are drawn from the work described.
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15
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Lemke CT, Goudreau N, Zhao S, Hucke O, Thibeault D, Llinàs-Brunet M, White PW. Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335. J Biol Chem 2011; 286:11434-43. [PMID: 21270126 PMCID: PMC3064199 DOI: 10.1074/jbc.m110.211417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/17/2011] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.
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Affiliation(s)
- Christopher T Lemke
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada.
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16
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The effect of the P1 side chain on the binding of optimized carboxylate and activated carbonyl inhibitors of the hepatitis C virus NS3 protease. Future Med Chem 2010; 2:1073-81. [DOI: 10.4155/fmc.10.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Peptidyl inhibitors of the hepatitis C virus NS3 protease hold much promise as direct-acting antiviral agents against hepatitis C infection. The optimization of N-terminal cleavage products, found to exhibit activity (product inhibition) against the enzyme, has led to potent tripeptide inhibitors that bear free C-terminal carboxylate groups. An analogous activated carbonyl compound (pentafluoroethyl ketone) bearing a P1 norvaline (Nva) was found to possess comparable activity against hepatitis C virus protease. However, an analogue bearing an aminocyclopropylcarboxylic acid (Acca) P1 residue exhibited very poor activity. 19F-NMR studies indicate that the propensity of the Acca-derived activated carbonyl to form hemiketals is only slightly reduced compared with that of a P1 Nva equivalent. These results, as well as molecular modeling studies, argue against steric hindrance of the nucleophilic attack of Ser-139 accounting for the poor mechanism-based inhibition by the former. We hypothesize that the conformational properties of the respective C-termini in the context of an adaptable active site account for the divergent P1 structure–activity relationships.
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17
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Cummings MD, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist A, Samuelsson B, Raboisson P, Simmen K. Induced-fit binding of the macrocyclic noncovalent inhibitor TMC435 to its HCV NS3/NS4A protease target. Angew Chem Int Ed Engl 2010; 49:1652-5. [PMID: 20166108 DOI: 10.1002/anie.200906696] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Cummings M, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist Å, Samuelsson B, Raboisson P, Simmen K. Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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19
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Di Francesco ME, Dessole G, Nizi E, Pace P, Koch U, Fiore F, Pesci S, Di Muzio J, Monteagudo E, Rowley M, Summa V. Novel Macrocyclic Inhibitors of Hepatitis C NS3/4A Protease Featuring a 2-Amino-1,3-thiazole as a P4 Carbamate Replacement. J Med Chem 2009; 52:7014-28. [DOI: 10.1021/jm900524b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Emilia Di Francesco
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Gabriella Dessole
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Emanuela Nizi
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Paola Pace
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Uwe Koch
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Fabrizio Fiore
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Silvia Pesci
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Jillian Di Muzio
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania
| | - Edith Monteagudo
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Michael Rowley
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Vincenzo Summa
- Istituto Di Ricerche Di Biologia Molecolare P. Angeletti S.p.A., Merck Research Laboratories Rome, Via Pontina Km 30,600, 00040 Pomezia, Italy
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Schinazi RF, Coats SJ, Bassit LC, Lennerstrand J, Nettles JH, Hurwitz SJ. Approaches for the development of antiviral compounds: the case of hepatitis C virus. Handb Exp Pharmacol 2009:25-51. [PMID: 19048196 DOI: 10.1007/978-3-540-79086-0_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Traditional methods for general drug discovery typically include evaluating random compound libraries for activity in relevant cell-free or cell-based assays. Success in antiviral development has emerged from the discovery of more focused libraries that provide clues about structure activity relationships. Combining these with more recent approaches including structural biology and computational modeling can work efficiently to hasten discovery of active molecules, but that is not enough. There are issues related to biology, toxicology, pharmacology, and metabolism that have to be addressed before a hit compound becomes nominated for clinical development. The objective of gaining early preclinical knowledge is to reduce the risk of failure in Phases 1, 2, and 3, leading to the goal of approved drugs that benefit the infected individual. This review uses hepatitis C virus (HCV), for which we still do not have an ideal therapeutic modality, as an example of the multidisciplinary efforts needed to discover new antiviral drugs for the benefit of humanity.
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Affiliation(s)
- Raymond F Schinazi
- Laboratory of Biochemical Pharmacology, VA Medical Center, Emory University School of Medicine, 1670 Clairmont Road, Decatur, GA 30033, USA.
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21
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Kawai S, Bailey M, Halmos T, Forgione P, LaPlante S, Llinàs-Brunet M, Naud J, Goudreau N. The Use of Chemical Double-Mutant Cycles in Biomolecular Recognition Studies: Application to HCV NS3 Protease Inhibitors. ChemMedChem 2008; 3:1654-7. [DOI: 10.1002/cmdc.200800214] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Raboisson P, Lin TI, Kock HD, Vendeville S, Vreken WVD, McGowan D, Tahri A, Hu L, Lenz O, Delouvroy F, Surleraux D, Wigerinck P, Nilsson M, Rosenquist Å, Samuelsson B, Simmen K. Discovery of novel potent and selective dipeptide hepatitis C virus NS3/4A serine protease inhibitors. Bioorg Med Chem Lett 2008; 18:5095-100. [DOI: 10.1016/j.bmcl.2008.07.124] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 07/28/2008] [Accepted: 07/30/2008] [Indexed: 12/20/2022]
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23
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Naud J, Lemke C, Goudreau N, Beaulieu E, White PD, Llinàs-Brunet M, Forgione P. Potent triazolyl-proline-based inhibitors of HCV NS3 protease. Bioorg Med Chem Lett 2008; 18:3400-4. [DOI: 10.1016/j.bmcl.2008.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/03/2008] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
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Bäck M, Johansson PO, Wångsell F, Thorstensson F, Kvarnström I, Ayesa S, Wähling H, Pelcman M, Jansson K, Lindström S, Wallberg H, Classon B, Rydergård C, Vrang L, Hamelink E, Hallberg A, Rosenquist S, Samuelsson B. Novel potent macrocyclic inhibitors of the hepatitis C virus NS3 protease: Use of cyclopentane and cyclopentene P2-motifs. Bioorg Med Chem 2007; 15:7184-202. [PMID: 17845856 DOI: 10.1016/j.bmc.2007.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 07/02/2007] [Accepted: 07/06/2007] [Indexed: 01/23/2023]
Abstract
Several highly potent novel HCV NS3 protease inhibitors have been developed from two inhibitor series containing either a P2 trisubstituted macrocyclic cyclopentane- or a P2 cyclopentene dicarboxylic acid moiety as surrogates for the widely used N-acyl-(4R)-hydroxyproline in the P2 position. These inhibitors were optimized for anti HCV activities through examination of different ring sizes in the macrocyclic systems and further by exploring the effect of P4 substituent removal on potency. The target molecules were synthesized from readily available starting materials, furnishing the inhibitor compounds in good overall yields. It was found that the 14-membered ring system was the most potent in these two series and that the corresponding 13-, 15-, and 16-membered macrocyclic rings delivered less potent inhibitors. Moreover, the corresponding P1 acylsulfonamides had superior potencies over the corresponding P1 carboxylic acids. It is noteworthy that it has been possible to develop highly potent HCV protease inhibitors that altogether lack the P4 substituent. Thus the most potent inhibitor described in this work, inhibitor 20, displays a K(i) value of 0.41 nM and an EC(50) value of 9 nM in the subgenomic HCV replicon cell model on genotype 1b. To the best of our knowledge this is the first example described in the literature of a HCV protease inhibitor displaying high potency in the replicon assay and lacking the P4 substituent, a finding which should facilitate the development of orally active small molecule inhibitors against the HCV protease.
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Affiliation(s)
- Marcus Bäck
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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25
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Brackmann F, de Meijere A. Natural Occurrence, Syntheses, and Applications of Cyclopropyl-Group-Containing α-Amino Acids. 1. 1-Aminocyclopropanecarboxylic Acid and Other 2,3-Methanoamino Acids. Chem Rev 2007; 107:4493-537. [DOI: 10.1021/cr078376j] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farina Brackmann
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Armin de Meijere
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
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26
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De Francesco R, Carfí A. Advances in the development of new therapeutic agents targeting the NS3-4A serine protease or the NS5B RNA-dependent RNA polymerase of the hepatitis C virus. Adv Drug Deliv Rev 2007; 59:1242-62. [PMID: 17869377 DOI: 10.1016/j.addr.2007.04.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 04/13/2007] [Indexed: 01/28/2023]
Abstract
The HCV NS3 protease and NS5B polymerase play essential roles in the replication of the hepatitis C virus (HCV). Following the successful paradigm established for HIV protease and reverse transcriptase inhibitors, these enzymes have been elected as targets for the development of small molecule HCV inhibitors. By combining the power of high-throughput screening with rational, knowledge-based drug discovery, a number of competitive inhibitors of the NS3 protease as well as nucleoside and non-nucleoside inhibitors of the NS5B polymerase have been identified and some have now entered clinical trials. In this article we review recent progress in the discovery and development of small molecule inhibitors of these two essential viral enzymes as they are advancing in the clinic.
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Affiliation(s)
- Raffaele De Francesco
- Istituto di Ricerche di Biologia Molecolare, P. Angeletti, Via Pontina Km 30,600, 00040 Pomezia (Rome), Italy.
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27
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Prongay AJ, Guo Z, Yao N, Pichardo J, Fischmann T, Strickland C, Myers J, Weber PC, Beyer BM, Ingram R, Hong Z, Prosise WW, Ramanathan L, Taremi SS, Yarosh-Tomaine T, Zhang R, Senior M, Yang RS, Malcolm B, Arasappan A, Bennett F, Bogen SL, Chen K, Jao E, Liu YT, Lovey RG, Saksena AK, Venkatraman S, Girijavallabhan V, Njoroge FG, Madison V. Discovery of the HCV NS3/4A Protease Inhibitor (1R,5S)-N-[3-Amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key Steps in Structure-Based Optimization. J Med Chem 2007; 50:2310-8. [PMID: 17444623 DOI: 10.1021/jm060173k] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures of both the native holo-HCV NS3/4A protease domain and the protease domain with a serine 139 to alanine (S139A) mutation were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contribution to the binding energy arises from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets [the numbering of the subsites is as defined in Berger, A.; Schechter, I. Philos. Trans. R. Soc. London, Ser. B 1970, 257, 249-264]. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease that is currently in clinical trials.
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Affiliation(s)
- Andrew J Prongay
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
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28
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Thorstensson F, Wångsell F, Kvarnström I, Vrang L, Hamelink E, Jansson K, Hallberg A, Rosenquist S, Samuelsson B. Synthesis of novel potent hepatitis C virus NS3 protease inhibitors: Discovery of 4-hydroxy-cyclopent-2-ene-1,2-dicarboxylic acid as a N-acyl-l-hydroxyproline bioisostere. Bioorg Med Chem 2007; 15:827-38. [PMID: 17107807 DOI: 10.1016/j.bmc.2006.10.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 10/17/2006] [Accepted: 10/23/2006] [Indexed: 11/22/2022]
Abstract
Potent tetrapeptidic inhibitors of the HCV NS3 protease have been developed incorporating 4-hydroxy-cyclopent-2-ene-1,2-dicarboxylic acid as a new N-acyl-l-hydroxyproline mimic. The hydroxycyclopentene template was synthesized in eight steps from commercially available (syn)-tetrahydrophthalic anhydride. Three different amino acids were explored in the P1-position and in the P2-position the hydroxyl group of the cyclopentene template was substituted with 7-methoxy-2-phenyl-quinolin-4-ol. The P3/P4-positions were then optimized from a set of six amino acid derivatives. All inhibitors were evaluated in an in vitro assay using the full-length NS3 protease. Several potent inhibitors were identified, the most promising exhibiting a K(i) value of 1.1nM.
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29
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Tsantrizos YS, Ferland JM, McClory A, Poirier M, Farina V, Yee NK, Wang XJ, Haddad N, Wei X, Xu J, Zhang L. Olefin ring-closing metathesis as a powerful tool in drug discovery and development – potent macrocyclic inhibitors of the hepatitis C virus NS3 protease. J Organomet Chem 2006. [DOI: 10.1016/j.jorganchem.2006.09.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Exploiting Ligand and Receptor Adaptability in Rational Drug Design Using Dynamics and Structure-Based Strategies. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_2006_087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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31
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Yee NK, Farina V, Houpis IN, Haddad N, Frutos RP, Gallou F, Wang XJ, Wei X, Simpson RD, Feng X, Fuchs V, Xu Y, Tan J, Zhang L, Xu J, Smith-Keenan LL, Vitous J, Ridges MD, Spinelli EM, Johnson M, Donsbach K, Nicola T, Brenner M, Winter E, Kreye P, Samstag W. Efficient Large-Scale Synthesis of BILN 2061, a Potent HCV Protease Inhibitor, by a Convergent Approach Based on Ring-Closing Metathesis. J Org Chem 2006; 71:7133-45. [PMID: 16958506 DOI: 10.1021/jo060285j] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A multistep scalable synthesis of the clinically important hepatitis C virus (HCV) protease inhibitor BILN 2061 (1) is described. The synthesis is highly convergent and consists of two amide bond formations, one etherification, and one ring-closing metathesis (RCM) step, using readily available building blocks 2-5. The optimization of each step is described at length. The main focus of the paper is the study of the RCM step and the description of the main problems faced when scaling up to pilot scale this highly powerful but very challenging synthetic operation. Eventually, the RCM reaction was smoothly scaled up to produce >400 kg of cyclized product.
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Affiliation(s)
- Nathan K Yee
- Department of Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, USA.
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32
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Gallou F, Saim S, Koenig KJ, Bochniak D, Horhota ST, Yee NK, Senanayake CH. A Practical Method for the Removal of Ruthenium Byproducts by Supercritical Fluid Extraction. Org Process Res Dev 2006. [DOI: 10.1021/op0601114] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabrice Gallou
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - Said Saim
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - Kenneth J. Koenig
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - David Bochniak
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - Steve T. Horhota
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - Nathan K. Yee
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
| | - Chris H. Senanayake
- Chemical and Analytical Development, Novartis Pharma, AG, 4002 Basel, Switzerland, and Department of Chemical Development and Department of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, U.S.A
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33
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Johansson PO, Bäck M, Kvarnström I, Jansson K, Vrang L, Hamelink E, Hallberg A, Rosenquist A, Samuelsson B. Potent inhibitors of the hepatitis C virus NS3 protease: Use of a novel P2 cyclopentane-derived template. Bioorg Med Chem 2006; 14:5136-51. [PMID: 16675222 DOI: 10.1016/j.bmc.2006.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/30/2006] [Accepted: 04/04/2006] [Indexed: 11/18/2022]
Abstract
The HCV NS3 protease is essential for replication of the hepatitis C virus (HCV) and therefore constitutes a promising new drug target for anti-HCV therapy. Several potent and promising HCV NS3 protease inhibitors, some of which display low nanomolar activities, were identified from a series of novel inhibitors incorporating a trisubstituted cyclopentane dicarboxylic acid moiety as a surrogate for the widely used N-acyl-(4R)-hydroxyproline in the P2 position.
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Affiliation(s)
- Per-Ola Johansson
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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34
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White PW, Llinas-Brunet M, Bös M. Blunting the Swiss army knife of hepatitis C virus: inhibitors of NS3/4A protease. PROGRESS IN MEDICINAL CHEMISTRY 2006; 44:65-107. [PMID: 16697895 DOI: 10.1016/s0079-6468(05)44402-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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35
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Rönn R, Sabnis YA, Gossas T, Akerblom E, Danielson UH, Hallberg A, Johansson A. Exploration of acyl sulfonamides as carboxylic acid replacements in protease inhibitors of the hepatitis C virus full-length NS3. Bioorg Med Chem 2006; 14:544-59. [PMID: 16213143 DOI: 10.1016/j.bmc.2005.08.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 08/12/2005] [Accepted: 08/19/2005] [Indexed: 11/16/2022]
Abstract
The hepatitis C virus (HCV) NS3 protease has emerged as a promising anti-HCV drug target. Herein, we present an investigation of NS3 inhibitors comprising the acyl sulfonamide functionality. A series of tetra- and tripeptide based acyl sulfonamide inhibitors and their structure-activity relationships from both enzymatic and cell-based in vitro assays are presented. In summary, the acidity of the acyl sulfonamide functionality, the character of the P1 side chain, and the acyl sulfonamide substituent were found to be important for the inhibitory potencies.
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Affiliation(s)
- Robert Rönn
- Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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36
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Vidal P, Timm D, Broughton H, Chen SH, Martín JA, Rivera-Sagredo A, McCarthy JR, Shapiro MJ, Espinosa JF. Preorganization of the Hydroxyethylene Dipeptide Isostere: The Preferred Conformation in Solution Resembles the Conformation Bound to BACE. J Med Chem 2005; 48:7623-7. [PMID: 16302802 DOI: 10.1021/jm050631+] [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] [Indexed: 11/30/2022]
Abstract
Conformational analysis in solution of beta-secretase inhibitors 1 and 2 by NMR spectroscopy reveals that the hydroxyethylene isostere, an apparently flexible fragment widely used as a scissile bond replacement in aspartic protease inhibitors, exists in one predominant conformation in solution. This preferred conformation is similar to that adopted by the hydroxyethylene core of 1 in complex with beta-secretase and that adopted by hydroxyethylene cores of related compounds when bound to aspartic proteases, indicating that this structural unit is preorganized in solution.
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Affiliation(s)
- Paloma Vidal
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
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37
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Faucher AM, Bailey MD, Beaulieu PL, Brochu C, Duceppe JS, Ferland JM, Ghiro E, Gorys V, Halmos T, Kawai SH, Poirier M, Simoneau B, Tsantrizos YS, Llinàs-Brunet M. Synthesis of BILN 2061, an HCV NS3 protease inhibitor with proven antiviral effect in humans. Org Lett 2005; 6:2901-4. [PMID: 15330643 DOI: 10.1021/ol0489907] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of BILN 2061, an NS3 protease inhibitor with proven antiviral effect in humans, was accomplished in a convergent manner from four building blocks. The procedure described here was suitable for the preparation of multigram quantities of BILN 2061 for preclinical pharmacological evaluation.
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Affiliation(s)
- Anne-Marie Faucher
- Chemistry Department, Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5.
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38
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De Francesco R, Migliaccio G. Challenges and successes in developing new therapies for hepatitis C. Nature 2005; 436:953-60. [PMID: 16107835 DOI: 10.1038/nature04080] [Citation(s) in RCA: 316] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) will continue to be a serious global health threat for many years to come because of the chronic nature of the infection, its high prevalence and the significant morbidity of the resulting disease. Recently, a small number of molecules have produced encouraging results in proof-of-concept clinical trials. At the same time, preclinical evidence is accumulating that development of resistance will eventually limit the efficacy of new drugs. Thus, combinations of multiple agents will be required to treat chronic HCV infection.
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Affiliation(s)
- Raffaele De Francesco
- Istituto di Ricerche di Biologia Molecolare P. Angeletti, Via Pontina km 30.600, 00040 Pomezia-Rome, Italy.
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39
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Böcker A, Derksen S, Schmidt E, Teckentrup A, Schneider G. A Hierarchical Clustering Approach for Large Compound Libraries. J Chem Inf Model 2005; 45:807-15. [PMID: 16045274 DOI: 10.1021/ci0500029] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A modified version of the k-means clustering algorithm was developed that is able to analyze large compound libraries. A distance threshold determined by plotting the sum of radii of leaf clusters was used as a termination criterion for the clustering process. Hierarchical trees were constructed that can be used to obtain an overview of the data distribution and inherent cluster structure. The approach is also applicable to ligand-based virtual screening with the aim to generate preferred screening collections or focused compound libraries. Retrospective analysis of two activity classes was performed: inhibitors of caspase 1 [interleukin 1 (IL1) cleaving enzyme, ICE] and glucocorticoid receptor ligands. The MDL Drug Data Report (MDDR) and Collection of Bioactive Reference Analogues (COBRA) databases served as the compound pool, for which binary trees were produced. Molecules were encoded by all Molecular Operating Environment 2D descriptors and topological pharmacophore atom types. Individual clusters were assessed for their purity and enrichment of actives belonging to the two ligand classes. Significant enrichment was observed in individual branches of the cluster tree. After clustering a combined database of MDDR, COBRA, and the SPECS catalog, it was possible to retrieve MDDR ICE inhibitors with new scaffolds using COBRA ICE inhibitors as seeds. A Java implementation of the clustering method is available via the Internet (http://www.modlab.de).
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Affiliation(s)
- Alexander Böcker
- Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Marie-Curie-Str. 11, D-60439 Frankfurt, Germany
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40
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Latli B, Hrapchak M, Gorys V, Busacca CA, Senanayake C. Synthesis of deuterium-, tritium-, and carbon-14-labeled BILN2061, a potent hepatitis C virus protease inhibitor. J Labelled Comp Radiopharm 2005. [DOI: 10.1002/jlcr.940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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42
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Llinàs-Brunet M, Bailey MD, Ghiro E, Gorys V, Halmos T, Poirier M, Rancourt J, Goudreau N. A Systematic Approach to the Optimization of Substrate-Based Inhibitors of the Hepatitis C Virus NS3 Protease: Discovery of Potent and Specific Tripeptide Inhibitors. J Med Chem 2004; 47:6584-94. [PMID: 15588093 DOI: 10.1021/jm0494523] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The inadequate efficacy and tolerability of current therapies for the infectious liver disease caused by the hepatitis C virus have warranted significant efforts in the development of new therapeutics. We have previously reported competitive peptide inhibitors of the NS3 serine protease based on the N-terminal cleavage products of peptide substrates. A detailed study of the interactions of these substrate-based inhibitors with the different subsites of the serine protease active site led to the discovery of novel residues that increased the affinity of the inhibitors. In this paper, we report the combination of the best binding residues in a tetrapeptide series that resulted in extremely potent inhibitors that bind exquisitely well to this enzyme. A substantial increase in potency was obtained with the simultaneous introduction of a 7-methoxy-2-phenyl-4-quinolinoxy moiety at the gamma-position of the P2 proline and a tert-leucine as a P3 residue. The increase in potency allowed for the further truncation and led to the identification of tripeptide inhibitors. Structure activity relationship studies on this inhibitor series led to the identification of carbamate-containing tripeptides that are able to inhibit replication of subgenomic HCV RNA in cell culture with potencies below 1 microM. This inhibitor series has the potential of becoming antiviral agents for the treatment of HCV infections.
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Affiliation(s)
- Montse Llinàs-Brunet
- Department of Chemistry, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada.
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43
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Goudreau N, Brochu C, Cameron DR, Duceppe JS, Faucher AM, Ferland JM, Grand-Maître C, Poirier M, Simoneau B, Tsantrizos YS. Potent Inhibitors of the Hepatitis C Virus NS3 Protease: Design and Synthesis of Macrocyclic Substrate-Based β-Strand Mimics. J Org Chem 2004; 69:6185-201. [PMID: 15357576 DOI: 10.1021/jo049288r] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring beta-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.
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Affiliation(s)
- Nathalie Goudreau
- Department of Chemistry, Boehringer Ingelheim Ltd., Research and Development, 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5
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44
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Bailey MD, Halmos T, Goudreau N, Lescop E, Llinàs-Brunet M. Novel Azapeptide Inhibitors of Hepatitis C Virus Serine Protease. J Med Chem 2004; 47:3788-99. [PMID: 15239657 DOI: 10.1021/jm049864b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Azapeptides are known inhibitors of several serine and cysteine proteases. In seeking different classes of inhibitors for the HCV serine protease, a series of novel azapeptide-based inhibitors were investigated which incorporated noncleavable P1/P1' aza-amino acyl residues. Extensive SAR studies around the P1/P1' aza-amino acyl fragment resulted in the identification of potent and selective inhibitors. Using NMR studies, we have shown that this series of inhibitors bind in a noncovalent competitive fashion to the NS3 protease active site. The bound conformation of one of these new azapeptide-based inhibitors was determined using the transfer NOE technique. Incorporation of these new aza-amino acyl functionalities in the P1 position provided a handle to probe for new interactions in the S' region of the enzyme.
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Affiliation(s)
- Murray D Bailey
- Boehringer Ingelheim (Canada) Ltd. Research and Development, 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5.
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45
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Rancourt J, Cameron DR, Gorys V, Lamarre D, Poirier M, Thibeault D, Llinàs-Brunet M. Peptide-Based Inhibitors of the Hepatitis C Virus NS3 Protease: Structure−Activity Relationship at the C-Terminal Position. J Med Chem 2004; 47:2511-22. [PMID: 15115394 DOI: 10.1021/jm030573x] [Citation(s) in RCA: 49] [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
The structure-activity relationship at the C-terminal position of peptide-based inhibitors of the hepatitis C virus NS3 protease is presented. The observation that the N-terminal cleavage product (DDIVPC-OH) of a substrate derived from the NS5A/5B cleavage site was a competitive inhibitor of the NS3 protease was previously described. The chemically unstable cysteine residue found at the P1 position of these peptide-based inhibitors could be replaced with a norvaline residue, at the expense of a substantial drop in the enzymatic activity. The fact that an aminocyclopropane carboxylic acid (ACCA) residue at the P1 position of a tetrapeptide such as 1 led to a significant gain in the inhibitory enzymatic activity, as compared to the corresponding norvaline derivative 2, prompted a systematic study of substituent effects on the three-membered ring. We report herein that the incorporation of a vinyl group with the proper configuration onto this small cycle produced inhibitors of the protease with much improved in vitro potency. The vinyl-ACCA is the first reported carboxylic acid containing a P1 residue that produced NS3 protease inhibitors that are significantly more active than inhibitors containing a cysteine at the same position.
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Affiliation(s)
- Jean Rancourt
- Research and Development, Boehringer Ingelheim (Canada) Ltd, 2100 Cunard Street, Laval (Québec), Canada H7S 2G5.
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46
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Llinàs-Brunet M, Bailey MD, Bolger G, Brochu C, Faucher AM, Ferland JM, Garneau M, Ghiro E, Gorys V, Grand-Maître C, Halmos T, Lapeyre-Paquette N, Liard F, Poirier M, Rhéaume M, Tsantrizos YS, Lamarre D. Structure−Activity Study on a Novel Series of Macrocyclic Inhibitors of the Hepatitis C Virus NS3 Protease Leading to the Discovery of BILN 2061. J Med Chem 2004; 47:1605-8. [PMID: 15027850 DOI: 10.1021/jm0342414] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From the discovery of competitive hexapeptide inhibitors, potent and selective HCV NS3 protease macrocyclic inhibitors have been identified. Structure-activity relationship studies were performed focusing on optimizing the N-terminal carbamate and the aromatic substituent on the (4R)-hydroxyproline moiety. Inhibitors meeting the potency criteria in the cell-based assay and with improved oral bioavailability in rats were identified. BILN 2061 was selected as the best compound, the first NS3 protease inhibitor reported with antiviral activity in man.
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Affiliation(s)
- Montse Llinàs-Brunet
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada.
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Tsantrizos YS. The design of a potent inhibitor of the hepatitis C virus NS3 protease:BILN 2061?From the NMR tube to the clinic. Biopolymers 2004; 76:309-23. [PMID: 15386268 DOI: 10.1002/bip.20127] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The virally encoded serine protease NS3/NS4A is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. Until very recently, the design of inhibitors for the HCV NS3 protease was limited to large peptidomimetic compounds with poor pharmacokinetic properties, making drug discovery an extremely challenging endeavor. In our quest for the discovery of a small-molecule lead that could block replication of the hepatitis C virus by binding to the HCV NS3 protease, the critical protein-polypeptide interactions between the virally encoded NS3 serine protease and its polyprotein substrate were investigated. Lead optimization of a substrate-based hexapeptide, guided by structural data, led to the understanding of the molecular dynamics and electronic effects that modulate the affinity of peptidomimetic ligands for the active site of this enzyme. Macrocyclic beta-strand scaffolds were designed that allowed the discovery of potent, highly selective, and orally bioavailable compounds. These molecules were the first HCV NS3 protease inhibitors reported that inhibit replication of HCV subgenomic RNA in a cell-based replicon assay at low nanomolar concentrations. Optimization of their biopharmaceutical properties led to the discovery of the clinical candidate BILN 2061. Oral administration of BILN 2061 to patients infected with the hepatitis C genotype 1 virus resulted in an impressive reduction of viral RNA levels, establishing proof-of-concept for HCV NS3 protease inhibitors as therapeutic agents in humans.
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Affiliation(s)
- Youla S Tsantrizos
- Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval (Québec) H7S 2G5, Canada.
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