51
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Tran TD, Wakenhut F, Pickford C, Shaw S, Westby M, Smith-Burchnell C, Watson L, Paradowski M, Milbank J, Brimage RA, Halstead R, Glen R, Wilson CP, Adam F, Hay D, Chiva JY, Nichols C, Blakemore DC, Gardner I, Dayal S, Pike A, Webster R, Pryde DC. The Discovery of Potent Nonstructural Protein 5A (NS5A) Inhibitors with a Unique Resistance Profile-Part 1. ChemMedChem 2014; 9:1378-86. [DOI: 10.1002/cmdc.201400045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Indexed: 11/06/2022]
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52
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Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Remenyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin CY, Zhong W, Lloyd-Smith JO, Sun R. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity. PLoS Pathog 2014; 10:e1004064. [PMID: 24722365 PMCID: PMC3983061 DOI: 10.1371/journal.ppat.1004064] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/17/2014] [Indexed: 12/17/2022] Open
Abstract
Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients. The emergence of drug resistance during antiviral treatment limits treatment options and poses challenges to pharmaceutical development. Meanwhile, the search for novel antiviral compounds with chemical genetic screens has led to the identification of antiviral agents with undefined drug mechanisms. Daclatasvir, an effective NS5A inhibitor, is one such example. In traditional methods to identify critical residues governing drug-protein interactions, wild type virus is passaged under drug treatment pressure, enabling the identification of resistant mutations evolved after multiple viral passages. However, this method only characterizes a fraction of the positively selected variants. Here we have simultaneously quantified the relative change in replication fitness as well as the relative sensitivity to Daclatasvir for all possible single amino acid mutations in the NS5A domain IA, thereby identifying the entire panel of positions that interact with the drug. Using mathematical models, we predicted which mutations pose the greatest risk of causing emergence of resistance under different scenarios of treatment compliance. The mutant fitness and drug-sensitivity profiles obtained can also inform the patient-specific use of Daclatasvir and may facilitate the development of second-generation drugs with a higher genetic barrier to resistance.
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Affiliation(s)
- Hangfei Qi
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - C Anders Olson
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Nicholas C Wu
- The Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ruian Ke
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Claude Loverdo
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Virginia Chu
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shawna Truong
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Roland Remenyi
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Zugen Chen
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sheng-Yao Su
- Institute of Information Science, Academia Sinica, Taipei, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Laith Q Al-Mawsawi
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shu-Hua Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Weidong Zhong
- Department of Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America; Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America; The Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America; School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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53
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Lambert SM, Langley DR, Garnett JA, Angell R, Hedgethorne K, Meanwell NA, Matthews SJ. The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors. Protein Sci 2014; 23:723-34. [PMID: 24639329 PMCID: PMC4093949 DOI: 10.1002/pro.2456] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/14/2014] [Indexed: 12/31/2022]
Abstract
New direct acting antivirals (DAAs) such as daclatasvir (DCV; BMS-790052), which target NS5A function with picomolar potency, are showing promise in clinical trials. The exact nature of how these compounds have an inhibitory effect on HCV is unknown; however, major resistance mutations appear in the N-terminal region of NS5A that include the amphipathic helix and domain 1. The dimeric symmetry of these compounds suggests that they act on a dimer of NS5A, which is also consistent with the presence of dimers in crystals of NS5A domain 1 from genotype 1b. Genotype 1a HCV is less potently affected by these compounds and resistance mutations have a greater effect than in the 1b genotypes. We have obtained crystals of domain 1 of the important 1a NS5A homologue and intriguingly, our X-ray crystal structure reveals two new dimeric forms of this domain. Furthermore, the high solvent content (75%) makes it ideal for ligand-soaking. Daclatasvir (DCV) shows twofold symmetry suggesting NS5A dimers may be of physiological importance and serve as potential binding sites for DCV. These dimers also allow for new conformations of a NS5A expansive network which could explain its operation on the membranous web. Additionally, sulfates bound in the crystal structure may provide evidence for the previously proposed RNA binding groove, or explain regulation of NS5A domain 2 and 3 function and phosphorylation, by domain 1.
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Affiliation(s)
- Sebastian M Lambert
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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54
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Abdel-Magid AF. Halting HCV Replication with NS5A Inhibitors and NS5B Polymerase Inhibitors: Effective New Treatments of HCV Infection. ACS Med Chem Lett 2014; 5:234-7. [PMID: 24900810 DOI: 10.1021/ml400456r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 12/22/2022] Open
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55
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McCormick AL, Wang L, Garcia-Diaz A, Macartney MJ, Webster DP, Haque T. Prevalence of baseline polymorphisms for potential resistance to NS5A inhibitors in drug-naive individuals infected with hepatitis C genotypes 1-4. Antivir Ther 2014; 20:81-5. [PMID: 24621453 DOI: 10.3851/imp2763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND The non-structural 5A (NS5A) protein of HCV is a multifunctional phosphoprotein involved in regulation of viral replication and virion assembly. NS5A inhibitors targeting domain I of NS5A protein have demonstrated high potency and pan-genotypic antiviral activity, however they possess a low genetic barrier to resistance. At present, only genotype 1, the most prevalent HCV genotype has been studied in detail for resistant variants. METHODS Utilizing a panel of genotypic-specific resistance assays, population sequencing was performed on plasma-derived viral RNA isolated from 138 patients infected with HCV genotypes 1-4 and not treated with direct-acting antiviral agents. Amino acid changes in HCV NS5A domain I at codon positions 28, 30, 31, 32 and 93, reported to confer reduced susceptibility to certain NS5A inhibitors were examined. Additionally, genotypic outcome based on NS5A sequences were compared with VERSANT HCV Genotype Assay (LiPA) 1.0 (Siemens Healthcare Diagnostics, Surrey, UK) and Abbott m2000 RealTime HCV genotype II assay (Abbott Molecular, Maidenhead, Berkshire, UK). RESULTS Amino acid substitutions associated with moderate to high level resistance to NS5A inhibitors were detected in 2/42 (4.76%) HCV-1a, 3/23 (13.04%) HCV-1b, 4/26 (15.38%) HCV-2, 1/24 (4.17%) HCV-3 and 1/23 (4.35%) HCV-4 infected patients who had not been treated with NS5A inhibitors. Genotype prediction based on NS5A sequences were concordant with LiPA and/or Abbott RealTime for 97.10% of cases. CONCLUSIONS Primary resistance mutations associated with resistance to first-generation NS5A inhibitors such as daclatasvir were observed in all genotypes, albeit at low frequencies. An excellent correlation based on NS5A genotyping and LiPA or Abbott RealTime was achieved.
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Affiliation(s)
- Adele L McCormick
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK.
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56
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Belema M, Lopez OD, Bender JA, Romine JL, St Laurent DR, Langley DR, Lemm JA, O'Boyle DR, Sun JH, Wang C, Fridell RA, Meanwell NA. Discovery and development of hepatitis C virus NS5A replication complex inhibitors. J Med Chem 2014; 57:1643-72. [PMID: 24621191 DOI: 10.1021/jm401793m] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lead inhibitors that target the function of the hepatitis C virus (HCV) nonstructural 5A (NS5A) protein have been identified by phenotypic screening campaigns using HCV subgenomic replicons. The demonstration of antiviral activity in HCV-infected subjects by the HCV NS5A replication complex inhibitor (RCI) daclatasvir (1) spawned considerable interest in this mechanistic approach. In this Perspective, we summarize the medicinal chemistry studies that led to the discovery of 1 and other chemotypes for which resistance maps to the NS5A protein and provide synopses of the profiles of many of the compounds currently in clinical trials. We also summarize what is currently known about the NS5A protein and the studies using NS5A RCIs and labeled analogues that are helping to illuminate aspects of both protein function and inhibitor interaction. We conclude with a synopsis of the results of notable clinical trials with HCV NS5A RCIs.
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Affiliation(s)
- Makonen Belema
- Department of Discovery Chemistry, ‡Department of Virology Discovery, and §Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
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57
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Hundt J, Li Z, Liu Q. Post-translational modifications of hepatitis C viral proteins and their biological significance. World J Gastroenterol 2013; 19:8929-8939. [PMID: 24379618 PMCID: PMC3870546 DOI: 10.3748/wjg.v19.i47.8929] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023] Open
Abstract
Replication of hepatitis C virus (HCV) depends on the interaction of viral proteins with various host cellular proteins and signalling pathways. Similar to cellular proteins, post-translational modifications (PTMs) of HCV proteins are essential for proper protein function and regulation, thus, directly affecting viral life cycle and the generation of infectious virus particles. Cleavage of the HCV polyprotein by cellular and viral proteases into more than 10 proteins represents an early protein modification step after translation of the HCV positive-stranded RNA genome. The key modifications include the regulated intramembranous proteolytic cleavage of core protein, disulfide bond formation of core, glycosylation of HCV envelope proteins E1 and E2, methylation of nonstructural protein 3 (NS3), biotinylation of NS4A, ubiquitination of NS5B and phosphorylation of core and NS5B. Other modifications like ubiquitination of core and palmitoylation of core and NS4B proteins have been reported as well. For some modifications such as phosphorylation of NS3 and NS5A and acetylation of NS3, we have limited understanding of their effects on HCV replication and pathogenesis while the impact of other modifications is far from clear. In this review, we summarize the available information on PTMs of HCV proteins and discuss their relevance to HCV replication and pathogenesis.
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58
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Zhang N, Zhang X, Zhu J, Turpoff A, Chen G, Morrill C, Huang S, Lennox W, Kakarla R, Liu R, Li C, Ren H, Almstead N, Venkatraman S, Njoroge FG, Gu Z, Clausen V, Graci J, Jung SP, Zheng Y, Colacino JM, Lahser F, Sheedy J, Mollin A, Weetall M, Nomeir A, Karp GM. Structure-activity relationship (SAR) optimization of 6-(indol-2-yl)pyridine-3-sulfonamides: identification of potent, selective, and orally bioavailable small molecules targeting hepatitis C (HCV) NS4B. J Med Chem 2013; 57:2121-35. [PMID: 24266880 DOI: 10.1021/jm401621g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel, potent, and orally bioavailable inhibitor of hepatitis C RNA replication targeting NS4B, compound 4t (PTC725), has been identified through chemical optimization of the 6-(indol-2-yl)pyridine-3-sulfonamide 2 to improve DMPK and safety properties. The focus of the SAR investigations has been to identify the optimal combination of substituents at the indole N-1, C-5, and C-6 positions and the sulfonamide group to limit the potential for in vivo oxidative metabolism and to achieve an acceptable pharmacokinetic profile. Compound 4t has excellent potency against the HCV 1b replicon, with an EC50 = 2 nM and a selectivity index of >5000 with respect to cellular GAPDH. Compound 4t has an overall favorable pharmacokinetic profile with oral bioavailability values of 62%, 78%, and 18% in rats, dogs, and monkeys, respectively, as well as favorable tissue distribution properties with a liver to plasma exposure ratio of 25 in rats.
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Affiliation(s)
- Nanjing Zhang
- PTC Therapeutics, Inc. , 100 Corporate Court, South Plainfield, New Jersey 07080, United States
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59
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Coburn CA, Meinke PT, Chang W, Fandozzi CM, Graham DJ, Hu B, Huang Q, Kargman S, Kozlowski J, Liu R, McCauley JA, Nomeir AA, Soll RM, Vacca JP, Wang D, Wu H, Zhong B, Olsen DB, Ludmerer SW. Discovery of MK-8742: an HCV NS5A inhibitor with broad genotype activity. ChemMedChem 2013; 8:1930-40. [PMID: 24127258 DOI: 10.1002/cmdc.201300343] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Indexed: 11/10/2022]
Abstract
The NS5A protein plays a critical role in the replication of HCV and has been the focus of numerous research efforts over the past few years. NS5A inhibitors have shown impressive in vitro potency profiles in HCV replicon assays, making them attractive components for inclusion in all oral combination regimens. Early work in the NS5A arena led to the discovery of our first clinical candidate, MK-4882 [2-((S)-pyrrolidin-2-yl)-5-(2-(4-(5-((S)-pyrrolidin-2-yl)-1H-imidazol-2-yl)phenyl)benzofuran-5-yl)-1H-imidazole]. While preclinical proof-of-concept studies in HCV-infected chimpanzees harboring chronic genotype 1 infections resulted in significant decreases in viral load after both single- and multiple-dose treatments, viral breakthrough proved to be a concern, thus necessitating the development of compounds with increased potency against a number of genotypes and NS5A resistance mutations. Modification of the MK-4882 core scaffold by introduction of a cyclic constraint afforded a series of tetracyclic inhibitors, which showed improved virologic profiles. Herein we describe the research efforts that led to the discovery of MK-8742, a tetracyclic indole-based NS5A inhibitor, which is currently in phase 2b clinical trials as part of an all-oral, interferon-free regimen for the treatment of HCV infection.
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Affiliation(s)
- Craig A Coburn
- Department of Medicinal Chemistry, Merck and Company, Inc. West Point, PA 19486 (USA).
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Transient replication of a hepatitis C virus genotype 1b replicon chimera encoding NS5A-5B from genotype 3a. J Virol Methods 2013; 195:156-63. [PMID: 24120570 DOI: 10.1016/j.jviromet.2013.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/12/2013] [Accepted: 09/24/2013] [Indexed: 01/22/2023]
Abstract
Although hepatitis C virus (HCV) is a pathogen of global significance, experimental therapies in current clinical development include highly efficacious all-oral combinations of HCV direct-acting antivirals (DAAs). If approved for use, these new treatment regimens will impact dramatically upon our capacity to eradicate HCV in the majority of virus-infected patients. However, recent data from late-stage clinical evaluations demonstrated that individuals infected with HCV genotype (GT) 3 responded less well to all-oral DAA combinations than patients infected with other HCV GTs. In light of these observations, the present study sought to expand the number of molecular tools available to investigate small molecule-mediated inhibition of HCV GT3 NS5A and NS5B proteins in preclinical tissue-culture systems. Accordingly, a novel subgenomic HCV replicon chimera was created by utilizing a GT1b backbone modified to produce NS5A and NS5B proteins from a consensus sequence generated from HCV GT3a genomic sequences deposited online at the European Hepatitis C Virus database. This approach avoided the need to isolate and amplify HCV genomes from sera derived from HCV-infected patients. The replicon chimera, together with a version engineered to express NS5A encoding a Y93H mutation, demonstrated levels of replication in transient assays robust enough to assess accurate antiviral activities of inhibitors representing different HCV DAA classes. Thus, the replicon chimera represents a new simple molecular tool suitable for drug discovery programmes aimed at investigating, understanding, and improving GT3a activities of HCV DAAs targeting NS5A or NS5B.
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61
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Lee JA, Berg EL. Neoclassic drug discovery: the case for lead generation using phenotypic and functional approaches. ACTA ACUST UNITED AC 2013; 18:1143-55. [PMID: 24080259 DOI: 10.1177/1087057113506118] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Innovation and new molecular entity production by the pharmaceutical industry has been below expectations. Surprisingly, more first-in-class small-molecule drugs approved by the U.S. Food and Drug Administration (FDA) between 1999 and 2008 were identified by functional phenotypic lead generation strategies reminiscent of pre-genomics pharmacology than contemporary molecular targeted strategies that encompass the vast majority of lead generation efforts. This observation, in conjunction with the difficulty in validating molecular targets for drug discovery, has diminished the impact of the "genomics revolution" and has led to a growing grassroots movement and now broader trend in pharma to reconsider the use of modern physiology-based or phenotypic drug discovery (PDD) strategies. This "From the Guest Editors" column provides an introduction and overview of the two-part special issues of Journal of Biomolecular Screening on PDD. Terminology and the business case for use of PDD are defined. Key issues such as assay performance, chemical optimization, target identification, and challenges to the organization and implementation of PDD are discussed. Possible solutions for these challenges and a new neoclassic vision for PDD that combines phenotypic and functional approaches with technology innovations resulting from the genomics-driven era of target-based drug discovery (TDD) are also described. Finally, an overview of the manuscripts in this special edition is provided.
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Affiliation(s)
- Jonathan A Lee
- 1Quantitative and Structural Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
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62
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A translational study of resistance emergence using sequential direct-acting antiviral agents for hepatitis C using ultra-deep sequencing. Am J Gastroenterol 2013; 108:1464-72. [PMID: 23896953 DOI: 10.1038/ajg.2013.205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/02/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Direct-acting antiviral agents (DAAs) against hepatitis C virus (HCV) have recently been developed and are ultimately hoped to replace interferon-based therapy. However, DAA monotherapy results in rapid emergence of resistant strains and DAAs must be used in combinations that present a high genetic barrier to resistance, although viral kinetics of multidrug-resistant strains remain poorly characterized. The aim of this study is to track the emergence and fitness of resistance using combinations of telaprevir and NS5A or NS5B inhibitors with genotype 1b clones. METHODS HCV-infected chimeric mice were treated with DAAs, and resistance was monitored using direct and ultra-deep sequencing. RESULTS Combination therapy with telaprevir and BMS-788329 (NS5A inhibitor) reduced serum HCV RNA to undetectable levels. The presence of an NS3-V36A telaprevir resistance mutation resulted in poor response to telaprevir monotherapy but showed significant HCV reduction when telaprevir was combined with BMS-788329. However, a BMS-788329-resistant strain emerged at low frequency. Infection with a BMS-788329-resistant NS5A-L31V mutation rapidly resulted in gain of an additional NS5A-Y93A mutation that conferred telaprevir resistance during combination therapy. Infection with dual NS5AL31V/NS5AY93H mutations resulted in poor response to combination therapy and development of telaprevir resistance. Although HCV RNA became undetectable soon after the beginning of combination therapy with BMS-788329 and BMS-821095 (NS5B inhibitor), rebound with emergence of resistance against all three drugs occurred. Triple resistance also occurred following infection with the NS3V36A/NS5AL31V/NS5AY93H triple mutation. CONCLUSIONS Resistant strains easily develop from cloned virus strains. Sequential use of DAAs should be avoided to prevent emergence of multidrug-resistant strains.
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63
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O'Boyle Ii DR, Sun JH, Nower PT, Lemm JA, Fridell RA, Wang C, Romine JL, Belema M, Nguyen VN, Laurent DRS, Serrano-Wu M, Snyder LB, Meanwell NA, Langley DR, Gao M. Characterizations of HCV NS5A replication complex inhibitors. Virology 2013; 444:343-54. [PMID: 23896639 DOI: 10.1016/j.virol.2013.06.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/02/2013] [Accepted: 06/28/2013] [Indexed: 01/28/2023]
Abstract
The hepatitis C virus NS5A protein is an established and clinically validated target for antiviral intervention by small molecules. Characterizations are presented of compounds identified as potent inhibitors of HCV replication to provide insight into structural elements that interact with the NS5A protein. UV-activated cross linking and affinity isolation was performed with one series to probe the physical interaction between the inhibitors and the NS5A protein expressed in HCV replicon cells. Resistance mapping with the second series was used to determine the functional impact of specific inhibitor subdomains on the interaction with NS5A. The data provide evidence for a direct high-affinity interaction between these inhibitors and the NS5A protein, with the interaction dependent on inhibitor stereochemistry. The functional data supports a model of inhibition that implicates inhibitor binding by covalently combining distinct pharmacophores across an NS5A dimer interface to achieve maximal inhibition of HCV replication.
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Affiliation(s)
- Donald R O'Boyle Ii
- Bristol-Myers Squibb Research and Development, Department of Virology Discovery, 5 Research Parkway, Wallingford, CT 06492, USA.
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64
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Gao M. Antiviral activity and resistance of HCV NS5A replication complex inhibitors. Curr Opin Virol 2013; 3:514-20. [PMID: 23896281 DOI: 10.1016/j.coviro.2013.06.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/24/2013] [Accepted: 06/26/2013] [Indexed: 12/13/2022]
Abstract
Treatment of Hepatitis C Virus (HCV) infection is rapidly evolving with the introduction of direct acting antiviral agents (DAA). HCV NS5A replication complex inhibitors, exemplified by Daclatasvir (BMS-790052), represent a new class of DAA. The exceptional in vitro potency (EC50 values at pM to low nM range) and broad genotype coverage of NS5A inhibitors have translated to robust anti-HCV effects in infected patients, making NS5A inhibitors an essential component of effective HCV DAA combination therapies. On the basis of drug-induced resistance substitutions and computer modeling, NS5A inhibitors most likely act at the N-terminus of NS5A (domain I). Mechanism of inhibition studies to elucidate the exquisite potency of these inhibitors have generated several working models.
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Affiliation(s)
- Min Gao
- Bristol Myer Squibb Company, Wallingford, CT 06492, United States.
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65
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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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66
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Aghemo A, De Francesco R. New horizons in hepatitis C antiviral therapy with direct-acting antivirals. Hepatology 2013; 58:428-38. [PMID: 23467911 DOI: 10.1002/hep.26371] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 12/19/2022]
Abstract
Most direct-acting antivirals (DAAs) that are being developed as therapy against hepatitis C virus target the NS3/4A protease, the NS5A protein, and the NS5B polymerase. The latter enzyme offers different target sites: the catalytic domain for nucleos(t)ide analogues as well as a number of allosteric sites for nonnucleos(t)ide inhibitors. Two NS3/4A protease inhibitors have been approved recently, and more than 40 new NS3/4A, NS5A, or NS5B inhibitors are in development. These agents can achieve very high cure rates when combined with pegylated interferon-β and ribavirin and show promising clinical results when administered in all-oral combinations. In addition to the more canonical drug targets, new alternative viral targets for small-molecule drug development are emerging, such as p7 or NS4B and viral entry. Future research will need to define well-tolerated and cost-effective DAA combinations that provide the highest rates of viral eradication in all patients (including those with advanced liver disease), the broadest spectrum of action on viral genotypes showing minimal or no clinical resistance, and the shortest treatment duration.
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Affiliation(s)
- Alessio Aghemo
- A.M. e A. Migliavacca Center for the Study of Liver Disease 1st Division of Gastroenterology, Fondazione IRCCS Cá Granda Ospedale Maggiore Policlinico Milan Italy
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67
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St. Laurent DR, Serrano-Wu MH, Belema M, Ding M, Fang H, Gao M, Goodrich JT, Krause RG, Lemm JA, Liu M, Lopez OD, Nguyen VN, Nower PT, O’Boyle DR, Pearce BC, Romine JL, Valera L, Sun JH, Wang YK, Yang F, Yang X, Meanwell NA, Snyder LB. HCV NS5A Replication Complex Inhibitors. Part 4.1 Optimization for Genotype 1a Replicon Inhibitory Activity. J Med Chem 2013; 57:1976-94. [DOI: 10.1021/jm301796k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Denis R. St. Laurent
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Michael H. Serrano-Wu
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Makonen Belema
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Min Ding
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Hua Fang
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Min Gao
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Jason T. Goodrich
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Rudolph G. Krause
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Julie A. Lemm
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Mengping Liu
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Omar D. Lopez
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Van N. Nguyen
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Peter T. Nower
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Donald R. O’Boyle
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Bradley C. Pearce
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Jeffrey L. Romine
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Lourdes Valera
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Jin-Hua Sun
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Ying-Kai Wang
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Fukang Yang
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Xuejie Yang
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Lawrence B. Snyder
- Departments of †Medicinal Chemistry, ‡Virology, and §Computer-Aided Drug Design, Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
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68
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Delang L, Neyts J, Vliegen I, Abrignani S, Neddermann P, De Francesco R. Hepatitis C Virus-Specific Directly Acting Antiviral Drugs. Curr Top Microbiol Immunol 2013; 369:289-320. [DOI: 10.1007/978-3-642-27340-7_12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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