1
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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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Powers A, Yu HH, Suriana P, Koodli RV, Lu T, Paggi JM, Dror RO. Geometric Deep Learning for Structure-Based Ligand Design. ACS CENTRAL SCIENCE 2023; 9:2257-2267. [PMID: 38161364 PMCID: PMC10755842 DOI: 10.1021/acscentsci.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024]
Abstract
A pervasive challenge in drug design is determining how to expand a ligand-a small molecule that binds to a target biomolecule-in order to improve various properties of the ligand. Adding single chemical groups, known as fragments, is important for lead optimization tasks, and adding multiple fragments is critical for fragment-based drug design. We have developed a comprehensive framework that uses machine learning and three-dimensional protein-ligand structures to address this challenge. Our method, FRAME, iteratively determines where on a ligand to add fragments, selects fragments to add, and predicts the geometry of the added fragments. On a comprehensive benchmark, FRAME consistently improves predicted affinity and selectivity relative to the initial ligand, while generating molecules with more drug-like chemical properties than docking-based methods currently in widespread use. FRAME learns to accurately describe molecular interactions despite being given no prior information on such interactions. The resulting framework for quality molecular hypothesis generation can be easily incorporated into the workflows of medicinal chemists for diverse tasks, including lead optimization, fragment-based drug discovery, and de novo drug design.
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Affiliation(s)
- Alexander
S. Powers
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Helen H. Yu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Patricia Suriana
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Rohan V. Koodli
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Biomedical
Informatics Program, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Tianyu Lu
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Joseph M. Paggi
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department
of Computer Science, Stanford University, Stanford, California 94305, United States
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Institute
for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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3
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Hazra M, Dubey RC. Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV. J Biomol Struct Dyn 2022:1-20. [PMID: 35993498 DOI: 10.1080/07391102.2022.2113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.
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Affiliation(s)
- Mousumi Hazra
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
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4
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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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5
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Bamborough P, Chung CW, Demont EH, Bridges AM, Craggs PD, Dixon DP, Francis P, Furze RC, Grandi P, Jones EJ, Karamshi B, Locke K, Lucas SCC, Michon AM, Mitchell DJ, Pogány P, Prinjha RK, Rau C, Roa AM, Roberts AD, Sheppard RJ, Watson RJ. A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification. J Med Chem 2019; 62:7506-7525. [PMID: 31398032 DOI: 10.1021/acs.jmedchem.9b00673] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bromodomain of ATAD2 has proved to be one of the least-tractable proteins within this target class. Here, we describe the discovery of a new class of inhibitors by high-throughput screening and show how the difficulties encountered in establishing a screening triage capable of finding progressible hits were overcome by data-driven optimization. Despite the prevalence of nonspecific hits and an exceptionally low progressible hit rate (0.001%), our optimized hit qualification strategy employing orthogonal biophysical methods enabled us to identify a single active series. The compounds have a novel ATAD2 binding mode with noncanonical features including the displacement of all conserved water molecules within the active site and a halogen-bonding interaction. In addition to reporting this new series and preliminary structure-activity relationship, we demonstrate the value of diversity screening to complement the knowledge-based approach used in our previous ATAD2 work. We also exemplify tactics that can increase the chance of success when seeking new chemical starting points for novel and less-tractable targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paola Grandi
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | | | | | | | | | | | | | | | | | - Christina Rau
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | - Ana Maria Roa
- GlaxoSmithKline Tres Cantos , 28760 Tres Cantos , Madrid , Spain
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6
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Özen A, Prachanronarong K, Matthew AN, Soumana DI, Schiffer CA. Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors. Crit Rev Biochem Mol Biol 2019; 54:11-26. [PMID: 30821513 DOI: 10.1080/10409238.2019.1568962] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Direct acting antivirals have dramatically increased the efficacy and tolerability of hepatitis C treatment, but drug resistance has emerged with some of these inhibitors, including nonstructural protein 3/4 A protease inhibitors (PIs). Although many co-crystal structures of PIs with the NS3/4A protease have been reported, a systematic review of these crystal structures in the context of the rapidly emerging drug resistance especially for early PIs has not been performed. To provide a framework for designing better inhibitors with higher barriers to resistance, we performed a quantitative structural analysis using co-crystal structures and models of HCV NS3/4A protease in complex with natural substrates and inhibitors. By comparing substrate structural motifs and active site interactions with inhibitor recognition, we observed that the selection of drug resistance mutations correlates with how inhibitors deviate from viral substrates in molecular recognition. Based on this observation, we conclude that guiding the design process with native substrate recognition features is likely to lead to more robust small molecule inhibitors with decreased susceptibility to resistance.
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Affiliation(s)
- Ayşegül Özen
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Kristina Prachanronarong
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Ashley N Matthew
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Djade I Soumana
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Celia A Schiffer
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
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7
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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8
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Meeprasert A, Hannongbua S, Kungwan N, Rungrotmongkol T. Effect of D168V mutation in NS3/4A HCV protease on susceptibilities of faldaprevir and danoprevir. MOLECULAR BIOSYSTEMS 2017; 12:3666-3673. [PMID: 27731877 DOI: 10.1039/c6mb00610h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency. The D168V mutation was shown to interrupt the hydrogen bonding network of Q80R155D168R123 embedded in the extended S2 and partial S4 subsites of the NS3 protein and as a result the R123 side chain was displaced and moved out from the binding pocket. By means of MM/PBSA and MM/GBSA binding free energy calculations, the FDV and DNV binding affinities were shown to be significantly reduced by ∼10-15 kcal mol-1 and ∼4-9 kcal mol-1 relative to the wild-type complexes, respectively, which somewhat agrees with the experimental resistance folds.
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Affiliation(s)
- Arthitaya Meeprasert
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand and PhD Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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10
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Parsy CC, Alexandre FR, Bidau V, Bonnaterre F, Brandt G, Caillet C, Cappelle S, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos LB, Leroy F, Liuzzi M, Loi AG, Moulat L, Chiara M, Rahali H, Roques V, Rosinovsky E, Savin S, Seifer M, Standring D, Surleraux D. Discovery and structural diversity of the hepatitis C virus NS3/4A serine protease inhibitor series leading to clinical candidate IDX320. Bioorg Med Chem Lett 2015; 25:5427-36. [DOI: 10.1016/j.bmcl.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
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12
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Berger KL, Scherer J, Ranga M, Sha N, Stern JO, Quinson AM, Kukolj G. Baseline Polymorphisms and Emergence of Drug Resistance in the NS3/4A Protease of Hepatitis C Virus Genotype 1 following Treatment with Faldaprevir and Pegylated Interferon Alpha 2a/Ribavirin in Phase 2 and Phase 3 Studies. Antimicrob Agents Chemother 2015; 59:6017-25. [PMID: 26195509 PMCID: PMC4576130 DOI: 10.1128/aac.00932-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/10/2015] [Indexed: 02/08/2023] Open
Abstract
Analysis of data pooled from multiple phase 2 (SILEN-C1 to 3) and phase 3 studies (STARTVerso1 to 4) of the hepatitis C virus (HCV) nonstructural protein 3/4A (NS3/4A) protease inhibitor faldaprevir plus pegylated interferon alpha/ribavirin (PR) provides a comprehensive evaluation of baseline and treatment-emergent NS3/4A amino acid variants among HCV genotype-1 (GT-1)-infected patients. Pooled analyses of GT-1a and GT-1b NS3 population-based pretreatment sequences (n = 3,124) showed that faldaprevir resistance-associated variants (RAVs) at NS3 R155 and D168 were rare (<1%). No single, noncanonical NS3 protease or NS4A cofactor baseline polymorphism was associated with a reduced sustained virologic response (SVR) to faldaprevir plus PR, including Q80K. The GT-1b NS3 helicase polymorphism T344I was associated with reduced SVR to faldaprevir plus PR (P < 0.0001) but was not faldaprevir specific, as reduced SVR was also observed with placebo plus PR. Among patients who did not achieve SVR and had available NS3 population sequences (n = 507 GT-1a; n = 349 GT-1b), 94% of GT-1a and 83% of GT-1b encoded faldaprevir treatment-emergent RAVs. The predominant GT-1a RAV was R155K (88%), whereas GT-1b encoded D168 substitutions (78%) in which D168V was predominant (67%). The novel GT-1b NS3 S61L substitution emerged in 7% of virologic failures as a covariant with D168V, most often among the faldaprevir breakthroughs; S61L in combination with D168V had a minimal impact on faldaprevir susceptibility compared with that for D168V alone (1.5-fold difference in vitro). The median time to loss of D168 RAVs among GT-1b-infected patients who did not have a sustained virologic response at 12 weeks posttreatment (non-SVR12) after virologic failure was 5 months, which was shorter than the 14 months for R155 RAVs among GT-1a-infected non-SVR12 patients, suggesting that D168V is less fit than R155K in the absence of faldaprevir selective pressure.
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Affiliation(s)
- K L Berger
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - J Scherer
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - M Ranga
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - N Sha
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - J O Stern
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - A-M Quinson
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - G Kukolj
- Boehringer Ingelheim Ltd./Ltée, Burlington, Ontario, Canada
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13
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Rossotti R, Travi G, Pazzi A, Baiguera C, Morra E, Puoti M. Rapid clearance of HCV-related splenic marginal zone lymphoma under an interferon-free, NS3/NS4A inhibitor-based treatment. A case report. J Hepatol 2015; 62:234-7. [PMID: 25285757 DOI: 10.1016/j.jhep.2014.09.031] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 09/25/2014] [Accepted: 09/28/2014] [Indexed: 02/06/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) may lead to B cell activation and transformation into non-Hodgkin lymphoma (NHL). Molecular mechanisms of B cell transformation by HCV are poorly understood. One of the most common lymphoproliferative disorders in HCV-infected patients is splenic marginal zone lymphoma (SMZL). A case of a 42-years old man, affected by HCV-related SMZL, effectively treated with an IFN-free, NS3-NS4A inhibitor-based regimen, is hereby described. The patient was treated for 16 weeks with faldaprevir, deleobuvir, and ribavirin, achieving a very rapid viral eradication without relevant toxicities. A rapid haematologic response was noted as well, with a statistically significant correlation between viral decay and lymphocyte improvement (coefficient r = 0.55, p = 0.042). The viral clearance led to SMZL cure, even without the use of IFN. Thus, the causative role, played by HCV in SMZL development, is once again reinforced, whereby the antiviral, rather than the anti-proliferative activity of IFN is indirectly proven. A regimen including DAAs should be considered when treating a HCV-related extra-hepatic disease.
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Affiliation(s)
- Roberto Rossotti
- Infectious Diseases Department, "Niguarda Cà Granda" Hospital, Milan, Italy.
| | - Giovanna Travi
- Infectious Diseases Department, "Niguarda Cà Granda" Hospital, Milan, Italy
| | - Annamaria Pazzi
- Infectious Diseases Department, "Niguarda Cà Granda" Hospital, Milan, Italy
| | - Chiara Baiguera
- Infectious Diseases Department, "Niguarda Cà Granda" Hospital, Milan, Italy
| | - Enrica Morra
- Oncology/Hematology Department, Niguarda Cancer Center, "Niguarda Cà Granda" Hospital, Milan, Italy
| | - Massimo Puoti
- Infectious Diseases Department, "Niguarda Cà Granda" Hospital, Milan, Italy
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14
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Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
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15
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Barauskas O, Corsa AC, Wang R, Hluhanich S, Jin D, Hung M, Yang H, Delaney WE, Schultz BE. Binding kinetics, potency, and selectivity of the hepatitis C virus NS3 protease inhibitors GS-9256 and vedroprevir. Biochim Biophys Acta Gen Subj 2014; 1840:3292-8. [DOI: 10.1016/j.bbagen.2014.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/08/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
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16
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de Carvalho IMVG, Alves R, de Souza PAVM, da Silva EF, Mazo D, Carrilho FJ, Queiroz ATL, Pessoa MG. Protease inhibitor resistance mutations in untreated Brazilian patients infected with HCV: novel insights about targeted genotyping approaches. J Med Virol 2014; 86:1714-21. [PMID: 25042789 DOI: 10.1002/jmv.24015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2014] [Indexed: 12/11/2022]
Abstract
Several new direct-acting antiviral (DAA) drugs are being developed or are already approved for the treatment of chronic hepatitis C virus (HCV) infection. HCV variants presenting drug-resistant phenotypes were observed both in vitro and during clinical trials. The aim of this study was to characterize amino acid changes at positions previously associated with resistance in the NS3 protease in untreated Brazilian patients infected with HCV genotypes 1a and 1b. Plasma samples from 171 untreated Brazilian patients infected with HCV were obtained from the Department of Gastroenterology of Clinics Hospital (HCFMUSP) in São Paulo, Brazil. Nested PCR and Sanger sequencing were used to obtain genetic information on the NS3 protein. Bioinformatics was used to confirm subtype information and analyze frequencies of resistance mutations. The results from the genotype analysis using non-NS3 targeted methods were at variance with those obtained from the NS3 protease phylogenetic analyses. It was found that 7.4% of patients infected with HCV genotype 1a showed the resistance-associated mutations V36L, T54S, Q80K, and R155K, while 5.1% of patients infected with HCV genotype 1b had the resistance-associated mutations V36L, Q41R, T54S, and D168S. Notably, codons at positions 80 and 155 differed between samples from Brazilian patient used in this study and global isolates. The present study demonstrates that genotyping methods targeting the NS3 protein showed a difference of results when compared to mainstream methodologies (INNO-LiPA and polymerase sequencing). The resistance mutations present in untreated patients infected with HCV and codon composition bias by geographical location warrant closer examination.
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Affiliation(s)
- Isabel M V G de Carvalho
- Viral Imunology, Butantan Institute, Avenida Doutor Vital Brasil, São Paulo, Brazil; Applied Molecular Hepatology Laboratory (LHeMA), Hepatitis Sector, Gastroenterology Division, São Paulo Federal University, São Paulo, Brazil
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17
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Fu J, Wei J. Molecular dynamics study on drug resistance mechanism of HCV NS3/4A protease inhibitor: BI201335. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.917298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Viger-Gravel J, Leclerc S, Korobkov I, Bryce DL. Direct Investigation of Halogen Bonds by Solid-State Multinuclear Magnetic Resonance Spectroscopy and Molecular Orbital Analysis. J Am Chem Soc 2014; 136:6929-42. [DOI: 10.1021/ja5013239] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jasmine Viger-Gravel
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Sophie Leclerc
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Ilia Korobkov
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - David L. Bryce
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
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19
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Ren J, He Y, Chen W, Chen T, Wang G, Wang Z, Xu Z, Luo X, Zhu W, Jiang H, Shen J, Xu Y. Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors. J Med Chem 2014; 57:3588-93. [PMID: 24702184 DOI: 10.1021/jm5002315] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.
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Affiliation(s)
- Jing Ren
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS) , 555 Zuchongzhi Road, Shanghai 201203, China
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20
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Meeprasert A, Hannongbua S, Rungrotmongkol T. Key binding and susceptibility of NS3/4A serine protease inhibitors against hepatitis C virus. J Chem Inf Model 2014; 54:1208-17. [PMID: 24689657 DOI: 10.1021/ci400605a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) causes an infectious disease that manifests itself as liver inflammation, cirrhosis, and can lead to the development of liver cancer. Its NS3/4A serine protease is a potent target for drug design and development since it is responsible for cleavage of the scissile peptide bonds in the polyprotein important for the HCV life cycle. Herein, the ligand-target interactions and the binding free energy of the four current NS3/4A inhibitors (boceprevir, telaprevir, danoprevir, and BI201335) were investigated by all-atom molecular dynamics simulations with three different initial atomic velocities. The per-residue free energy decomposition suggests that the key residues involved in inhibitor binding were residues 41-43, 57, 81, 136-139, 155-159, and 168 in the NS3 domain. The van der Waals interactions yielded the main driving force for inhibitor binding at the protease active site for the cleavage reaction. In addition, the highest number of hydrogen bonds was formed at the reactive P1 site of the four studied inhibitors. Although the hydrogen bond patterns of these inhibitors were different, their P3 site was most likely to be recognized by the A157 backbone. Both molecular mechanic (MM)/Poisson-Boltzmann surface area and MM/generalized Born surface area approaches predicted the relative binding affinities of the four inhibitors in a somewhat similar trend to their experimentally derived biological activities.
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Affiliation(s)
- Arthitaya Meeprasert
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University , 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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21
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The competitive binding between inhibitors and substrates of HCV NS3/4A protease: A general mechanism of drug resistance. Antiviral Res 2014; 103:60-70. [DOI: 10.1016/j.antiviral.2014.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/05/2014] [Accepted: 01/13/2014] [Indexed: 11/19/2022]
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22
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Rosenquist Å, Samuelsson B, Johansson PO, Cummings MD, Lenz O, Raboisson P, Simmen K, Vendeville S, de Kock H, Nilsson M, Horvath A, Kalmeijer R, de la Rosa G, Beumont-Mauviel M. Discovery and Development of Simeprevir (TMC435), a HCV NS3/4A Protease Inhibitor. J Med Chem 2014; 57:1673-93. [DOI: 10.1021/jm401507s] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Maxwell D. Cummings
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19002, United States
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Kenny Simmen
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Herman de Kock
- Galapagos NV Generaal De Wittelaan, L11A3-2800, Mechelen, Belgium
| | | | | | | | - Guy de la Rosa
- Janssen Global Services, LLC, Titusville, New Jersey 08560, United States
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23
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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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24
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Abstract
INTRODUCTION Boceprevir was the first direct acting agent developed for the treatment of hepatitis C virus infection. Boceprevir functions by targeting NS3 protease, a viral enzyme essential for replication. This peptidomimetic molecule was optimized from a peptide lead to provide a potent, selective and orally bioavailable drug that can be combined with ribavirin and peg interferon to achieve sustained viral response (undetectable HCV RNA levels for 24 weeks after completion of therapy) in patients infected with Genotype 1 of the virus. AREAS COVERED This article provides a review of the pre-clinical and clinical discovery of boceprevir. This review includes the role and function of its molecular target, NS3 protease, as well as the assays used to measure in vitro efficacy, compound optimization and clinical studies to demonstrate safety and efficacy. EXPERT OPINION As the first direct acting anti-HCV agent, boceprevir represents an important advance in therapy of this widespread chronic disease. Yet, while this therapy is a valuable approach, it does have limitations. Studies have suggested that 30% of patients do not achieve sustained viral response and 11% of patients have developed anemia and/or neutropenia. Current drug discovery and development efforts are underway to develop novel therapeutic options that address these issues.
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Affiliation(s)
- David P Rotella
- Montclair State University, Department of Chemistry and Biochemistry , 1 Normal Avenue Montclair NJ 07043 , USA +1 973 655 7204 ; +1 973 655 7772 ;
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25
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Bailey MD, Bordeleau J, Garneau M, Leblanc M, Lemke CT, O’Meara J, White PW, Llinàs-Brunet M. Peptide backbone replacement of hepatitis C virus NS3 serine protease C-terminal cleavage product analogs: Discovery of potent succinamide inhibitors. Bioorg Med Chem Lett 2013; 23:4447-52. [DOI: 10.1016/j.bmcl.2013.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/03/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
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26
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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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27
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Hucke O, Coulombe R, Bonneau P, Bertrand-Laperle M, Brochu C, Gillard J, Joly MA, Landry S, Lepage O, Llinàs-Brunet M, Pesant M, Poirier M, Poirier M, McKercher G, Marquis M, Kukolj G, Beaulieu PL, Stammers TA. Molecular Dynamics Simulations and Structure-Based Rational Design Lead to Allosteric HCV NS5B Polymerase Thumb Pocket 2 Inhibitor with Picomolar Cellular Replicon Potency. J Med Chem 2013; 57:1932-43. [DOI: 10.1021/jm4004522] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Oliver Hucke
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - René Coulombe
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Pierre Bonneau
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Mégan Bertrand-Laperle
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Christian Brochu
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - James Gillard
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Marc-André Joly
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Serge Landry
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Olivier Lepage
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Montse Llinàs-Brunet
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Marc Pesant
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Martin Poirier
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Maude Poirier
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Ginette McKercher
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Martin Marquis
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - George Kukolj
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Pierre L. Beaulieu
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
| | - Timothy A. Stammers
- Research
and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Quebec H7S
2G5, Canada
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28
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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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29
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Alves R, Queiroz ATL, Pessoa MG, da Silva EF, Mazo DFC, Carrilho FJ, Carvalho-Filho RJ, de Carvalho IMVG. The presence of resistance mutations to protease and polymerase inhibitors in Hepatitis C virus sequences from the Los Alamos databank. J Viral Hepat 2013; 20:414-21. [PMID: 23647958 DOI: 10.1111/jvh.12051] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/15/2012] [Indexed: 12/14/2022]
Abstract
Several new direct-acting antiviral (DAA) drugs are in development for chronic hepatitis C viral (HCV) infection, and NS3-NS4A serine protease and the NS5B RNA-dependent RNA polymerase have been the major targets. HCV variants displaying drug-resistant phenotypes have been observed both in vitro and during clinical trials. Our aim was to characterize amino acid changes at positions previously associated with resistance in protease (NS3) and polymerase (NS5B) regions from treatment-naïve HCV patients infected with genotypes 1a, 1b and 3a. All 1383 NS3 protease sequences (genotype 1a = 680, 1b = 498 and 3a = 205) and 806 NS5B polymerase sequences (genotypes 1a = 471, 1b = 329, 3a = 6) were collected from Los Alamos databank. Genotype 3a protease sequences showed the typical low-level resistance mutation V36L. NS3 sequences from other genotypes presented mutations on positions 36, 39, 41, 43, 54, 80, 109, 155 and 168 in a frequency lower than 2%, except for the mutation Q80R found in 35% of genotype 1a isolates. Polymerase sequences from genotype 3a patients showed five typical mutations: L419I, I424V, I482L, V499A and S556G. Two positions presented high polymorphism in the NS5B region from genotype 1a (V499A) and genotype 1b (C316N) subjects. Our results demonstrated a natural profile of genotype 3a that can be associated with the pre-existence of HCV variants resistant to first-generation protease inhibitors and to non-nucleoside polymerase inhibitors. Likewise, genotype 1b isolates and genotype 1a sequences exhibited pre-existing mutations associated with resistance to Palm II and Thumb I polymerase inhibitors, respectively.
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Affiliation(s)
- R Alves
- Laboratório de Hepatologia Molecular Aplicada, Setor de Hepatites, Divisão de Gastroenterologia, Universidade Federal de São Paulo, Sao Paulo, Brazil
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30
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Stammers TA, Coulombe R, Rancourt J, Thavonekham B, Fazal G, Goulet S, Jakalian A, Wernic D, Tsantrizos Y, Poupart MA, Bös M, McKercher G, Thauvette L, Kukolj G, Beaulieu PL. Discovery of a novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors. Bioorg Med Chem Lett 2013; 23:2585-9. [DOI: 10.1016/j.bmcl.2013.02.110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/25/2013] [Indexed: 11/26/2022]
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31
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Moreau B, O’Meara JA, Bordeleau J, Garneau M, Godbout C, Gorys V, Leblanc M, Villemure E, White PW, Llinàs-Brunet M. Discovery of Hepatitis C Virus NS3-4A Protease Inhibitors with Improved Barrier to Resistance and Favorable Liver Distribution. J Med Chem 2013; 57:1770-6. [DOI: 10.1021/jm400121t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Benoît Moreau
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Jeff A. O’Meara
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Josée Bordeleau
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Michel Garneau
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Cedrickx Godbout
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Vida Gorys
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Mélissa Leblanc
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Elisia Villemure
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Peter W. White
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
| | - Montse Llinàs-Brunet
- Department of Medicinal Chemistry and ‡Department of Biological
Sciences, Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval,
Quebec H7S 2G5, Canada
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32
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Hotiana HA, Haider MK. Structural modeling of HCV NS3/4A serine protease drug-resistance mutations using end-point continuum solvation and side-chain flexibility calculations. J Chem Inf Model 2013; 53:435-51. [PMID: 23305404 DOI: 10.1021/ci3004754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational methods of modeling protein-ligand interactions have gained widespread application in modern drug discovery. In continuum solvation-based methods of binding affinity estimation, limited description of solvent environment and protein flexibility is traded for a time scale that fits medicinal chemistry test cycles. The results of this speed-accuracy trade-off have been promising in terms of modeling structure-activity relationships of ligand series against protein targets. The potential of these approaches in recapitulating structural and energetic effects of resistance mutations, which involve large changes in binding affinity, remains relatively unexplored. We used continuum solvation binding affinity predictions and graph theory-based flexibility calculations to model thirteen drug resistance mutations in HCV NS3/4A serine protease, against three small-molecule inhibitors, with a 2-fold objective: quantitative assessment of binding energy predictions against experimental data and elucidation of structural/energetic determinants of resistance. The results show statistically significant correlation between predicted and experimental binding affinities, with R(2) and predictive index of up to 0.83 and 0.91, respectively. The level of accuracy was consistent with what has been reported for the inverse problem of binding affinity estimation of congeneric ligands against the same target. The quality of predictions was poor for mutations involving induced-fit effects, primarily, because of the lack of entropy terms. Flexibility analysis explained this discrepancy by indicating characteristic changes in side-chain mobility of a key binding site residue. The combined results from two approaches provide novel insights regarding the molecular mechanism of resistance. NS3/4A inhibitors, with large P2 substituents, derive high affinity with optimal van der Waals interactions in the S2 subsite, in order to overcome unfavorable desolvation and entropic cost of induced-fit effects. High-level resistance mutations tend to increase the desolvation and/or entropic barrier to ligand binding. The lead optimization strategies should, therefore, address the balance of these opposing energetic contributions in both the wild-type and mutant target.
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Affiliation(s)
- Hajira Ahmed Hotiana
- Undergraduate Program in Science, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
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33
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Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology. J Med Chem 2013; 56:1363-88. [DOI: 10.1021/jm3012068] [Citation(s) in RCA: 839] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rainer Wilcken
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Markus O. Zimmermann
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas Lange
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Frank M. Boeckler
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
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34
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Sarwar MG, Dragisić B, Dimitrijević E, Taylor MS. Halogen Bonding between Anions and Iodoperfluoroorganics: Solution-Phase Thermodynamics and Multidentate-Receptor Design. Chemistry 2012; 19:2050-8. [DOI: 10.1002/chem.201202689] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Indexed: 01/04/2023]
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35
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O'Meara JA, Lemke CT, Godbout C, Kukolj G, Lagacé L, Moreau B, Thibeault D, White PW, Llinàs-Brunet M. Molecular mechanism by which a potent hepatitis C virus NS3-NS4A protease inhibitor overcomes emergence of resistance. J Biol Chem 2012; 288:5673-81. [PMID: 23271737 DOI: 10.1074/jbc.m112.439455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although optimizing the resistance profile of an inhibitor can be challenging, it is potentially important for improving the long term effectiveness of antiviral therapy. This work describes our rational approach toward the identification of a macrocyclic acylsulfonamide that is a potent inhibitor of the NS3-NS4A proteases of all hepatitis C virus genotypes and of a panel of genotype 1-resistant variants. The enhanced potency of this compound versus variants D168V and R155K facilitated x-ray determination of the inhibitor-variant complexes. In turn, these structural studies revealed a complex molecular basis of resistance and rationalized how such compounds are able to circumvent these mechanisms.
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Affiliation(s)
- Jeff A O'Meara
- Boehringer Ingelheim (Canada) Limited, Research and Development, Laval, Quebec H7S 2G5, Canada.
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The race for interferon-free HCV therapies: a snapshot by the spring of 2012. Rev Med Virol 2012; 22:392-411. [DOI: 10.1002/rmv.1727] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/05/2012] [Accepted: 07/13/2012] [Indexed: 12/16/2022]
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Beale TM, Chudzinski MG, Sarwar MG, Taylor MS. Halogen bonding in solution: thermodynamics and applications. Chem Soc Rev 2012; 42:1667-80. [PMID: 22858664 DOI: 10.1039/c2cs35213c] [Citation(s) in RCA: 436] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Halogen bonds are noncovalent interactions in which covalently bound halogens act as electrophilic species. The utility of halogen bonding for controlling self-assembly in the solid state is evident from a broad spectrum of applications in crystal engineering and materials science. Until recently, it has been less clear whether, and to what extent, halogen bonding could be employed to influence conformation, binding or reactivity in the solution phase. This tutorial review summarizes and interprets solution-phase thermodynamic data for halogen bonding interactions obtained over the past six decades and highlights emerging applications in molecular recognition, medicinal chemistry and catalysis.
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Affiliation(s)
- Thomas M Beale
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H8, Canada
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Cento V, Mirabelli C, Salpini R, Dimonte S, Artese A, Costa G, Mercurio F, Svicher V, Parrotta L, Bertoli A, Ciotti M, Di Paolo D, Sarrecchia C, Andreoni M, Alcaro S, Angelico M, Perno CF, Ceccherini-Silberstein F. HCV genotypes are differently prone to the development of resistance to linear and macrocyclic protease inhibitors. PLoS One 2012; 7:e39652. [PMID: 22792183 PMCID: PMC3391197 DOI: 10.1371/journal.pone.0039652] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/24/2012] [Indexed: 01/01/2023] Open
Abstract
Background Because of the extreme genetic variability of hepatitis C virus (HCV), we analyzed whether specific HCV-genotypes are differently prone to develop resistance to linear and macrocyclic protease-inhibitors (PIs). Methods The study includes 1568 NS3-protease sequences, isolated from PI-naive patients infected with HCV-genotypes 1a (N = 621), 1b (N = 474), 2 (N = 72), 3 (N = 268), 4 (N = 54) 5 (N = 6), and 6 (N = 73). Genetic-barrier was calculated as the sum of nucleotide-transitions (score = 1) and/or nucleotide-transversions (score = 2.5) required for drug-resistance-mutations emergence. Forty-three mutations associated with PIs-resistance were analyzed (36A/M/L/G-41R-43S/V-54A/S/V-55A-Q80K/R/L/H/G-109K-138T-155K/Q/T/I/M/S/G/L-156T/V/G/S-158I-168A/H/T/V/E/I/G/N/Y-170A/T-175L). Structural analyses on NS3-protease and on putative RNA-models have been also performed. Results Overall, NS3-protease was moderately conserved, with 85/181 (47.0%) amino-acids showing <1% variability. The catalytic-triad (H57-D81-S139) and 6/13 resistance-associated positions (Q41-F43-R109-R155-A156-V158) were fully conserved (variability <1%). Structural-analysis highlighted that most of the NS3-residues involved in drug-stabilization were highly conserved, while 7 PI-resistance residues, together with selected residues located in proximity of the PI-binding pocket, were highly variable among HCV-genotypes. Four resistance-mutations (80K/G-36L-175L) were found as natural polymorphisms in selected genotypes (80K present in 41.6% HCV-1a, 100% of HCV-5 and 20.6% HCV-6; 80G present in 94.4% HCV-2; 36L present in 100% HCV-3-5 and >94% HCV-2-4; 175L present in 100% HCV-1a-3-5 and >97% HCV-2-4). Furthermore, HCV-3 specifically showed non-conservative polymorphisms (R123T-D168Q) at two drug-interacting positions. Regardless of HCV-genotype, 13 PIs resistance-mutations were associated with low genetic-barrier, requiring only 1 nucleotide-substitution (41R-43S/V-54A-55A-80R-156V/T: score = 1; 54S-138T-156S/G-168E/H: score = 2.5). By contrast, by using HCV-1b as reference genotype, nucleotide-heterogeneity led to a lower genetic-barrier for the development of some drug-resistance-mutations in HCV-1a (36M-155G/I/K/M/S/T-170T), HCV-2 (36M-80K-155G/I/K/S/T-170T), HCV-3 (155G/I/K/M/S/T-170T), HCV-4-6 (155I/S/L), and HCV-5 (80G-155G/I/K/M/S/T). Conclusions The high degree of HCV genetic variability makes HCV-genotypes, and even subtypes, differently prone to the development of PIs resistance-mutations. Overall, this can account for different responsiveness of HCV-genotypes to PIs, with important clinical implications in tailoring individualized and appropriate regimens.
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Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Carmen Mirabelli
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Salvatore Dimonte
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Anna Artese
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Giosuè Costa
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Fabio Mercurio
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Lucia Parrotta
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Ada Bertoli
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
| | - Marco Ciotti
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
| | - Daniele Di Paolo
- Department of Internal Medicine, Tor Vergata University Hospital, Rome, Italy
| | - Cesare Sarrecchia
- Department of Public Health, Tor Vergata University Hospital, Rome, Italy
| | - Massimo Andreoni
- Department of Public Health, Tor Vergata University Hospital, Rome, Italy
| | - Stefano Alcaro
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Mario Angelico
- Department of Internal Medicine, Tor Vergata University Hospital, Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
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In vitro resistance profile of the hepatitis C virus NS3 protease inhibitor BI 201335. Antimicrob Agents Chemother 2011; 56:569-72. [PMID: 22024816 DOI: 10.1128/aac.05166-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The in vitro resistance profile of BI 201335 was evaluated through selection and characterization of variants in genotype 1a (GT 1a) and genotype 1b (GT 1b) replicons. NS3 R155K and D168V were the most frequently observed resistant variants. Phenotypic characterization of the mutants revealed shifts in sensitivity specific to BI 201335 that did not alter susceptibility to alpha interferon. In contrast to macrocyclic and covalent protease inhibitors, changes at V36, T54, F43, and Q80 did not confer resistance to BI 201335.
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