1
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Gidi Y, Robert A, Tordo A, Lovell TC, Ramos-Sanchez J, Sakaya A, Götte M, Cosa G. Binding and Sliding Dynamics of the Hepatitis C Virus Polymerase: Hunting the 3' Terminus. ACS Infect Dis 2023; 9:1488-1498. [PMID: 37436367 DOI: 10.1021/acsinfecdis.3c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
The hepatitis C virus (HCV) nonstructural protein 5B (NS5B) polymerase catalyzes the replication of the (+) single-stranded RNA genome of HCV. In vitro studies have shown that replication can be performed in the absence of a primer. However, the dynamics and mechanism by which NS5B locates the 3'-terminus of the RNA template to initiate de novo synthesis remain elusive. Here, we performed single-molecule fluorescence studies based on protein-induced fluorescence enhancement reporting on NS5B dynamics on a short model RNA substrate. Our results suggest that NS5B exists in a fully open conformation in solution wherefrom it accesses its binding site along RNA and then closes. Our results revealed two NS5B binding modes: an unstable one resulting in rapid dissociation, and a stable one characterized by a larger residence time on the substrate. We associate these bindings to an unproductive and productive orientation, respectively. Addition of extra mono (Na+)- and divalent (Mg2+) ions increases the mobility of NS5B along its RNA substrate. However, only Mg2+ ions induce a decrease in NS5B residence time. Dwell times of residence increase with the length of the single-stranded template, suggesting that NS5B unbinds its substrate by unthreading the template rather than by spontaneous opening.
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Affiliation(s)
- Yasser Gidi
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Anaïs Robert
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Alix Tordo
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Terri C Lovell
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Jorge Ramos-Sanchez
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Aya Sakaya
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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2
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Habashy NH, Abu-Serie MM. Major royal-jelly protein 2 and its isoform X1 are two novel safe inhibitors for hepatitis C and B viral entry and replication. Int J Biol Macromol 2019; 141:1072-1087. [DOI: 10.1016/j.ijbiomac.2019.09.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
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3
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Evidence for Internal Initiation of RNA Synthesis by the Hepatitis C Virus RNA-Dependent RNA Polymerase NS5B In Cellulo. J Virol 2019; 93:JVI.00525-19. [PMID: 31315989 DOI: 10.1128/jvi.00525-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/07/2019] [Indexed: 12/11/2022] Open
Abstract
Initiation of RNA synthesis by the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) NS5B has been extensively studied in vitro and in cellulo Intracellular replication is thought to rely exclusively on terminal de novo initiation, as it conserves all genetic information of the genome. In vitro, however, additional modes of initiation have been observed. In this study, we aimed to clarify whether the intracellular environment allows for internal initiation of RNA replication by the HCV replicase. We used a dual luciferase replicon harboring a terminal and an internal copy of the viral genomic 5' untranslated region, which was anticipated to support noncanonical initiation. Indeed, a shorter RNA species was detected by Northern blotting with low frequency, depending on the length and sequence composition upstream of the internal initiation site. By introducing mutations at either site, we furthermore established that internal and terminal initiation shared identical sequence requirements. Importantly, lethal point mutations at the terminal site resulted exclusively in truncated replicons. In contrast, the same mutations at the internal site abrogated internal initiation, suggesting a competitive selection of initiation sites, rather than recombination or template-switching events. In conclusion, our data indicate that the HCV replicase is capable of internal initiation in its natural environment, although functional replication likely requires only terminal initiation. Since many other positive-strand RNA viruses generate subgenomic messenger RNAs during their replication cycle, we surmise that their capability for internal initiation is a common and conserved feature of viral RdRps.IMPORTANCE Many aspects of viral RNA replication of hepatitis C virus (HCV) are still poorly understood. The process of RNA synthesis is driven by the RNA-dependent RNA polymerase (RdRp) NS5B. Most mechanistic studies on NS5B so far were performed with in vitro systems using isolated recombinant polymerase. In this study, we present a replicon model, which allows the intracellular assessment of noncanonical modes of initiation by the full HCV replicase. Our results add to the understanding of the biochemical processes underlying initiation of RNA synthesis by NS5B by the discovery of internal initiation in cellulo Moreover, they validate observations made in vitro, showing that the viral polymerase acts very similarly in isolation and in complex with other viral and host proteins. Finally, these observations provide clues about the evolution of RdRps of positive-strand RNA viruses, which might contain the intrinsic ability to initiate internally.
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4
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Jordan PC, Liu C, Raynaud P, Lo MK, Spiropoulou CF, Symons JA, Beigelman L, Deval J. Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase. PLoS Pathog 2018; 14:e1006889. [PMID: 29425244 PMCID: PMC5823471 DOI: 10.1371/journal.ppat.1006889] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/22/2018] [Accepted: 01/21/2018] [Indexed: 01/27/2023] Open
Abstract
Paramyxoviruses represent a family of RNA viruses causing significant human diseases. These include measles virus, the most infectious virus ever reported, in addition to parainfluenza virus, and other emerging viruses. Paramyxoviruses likely share common replication machinery but their mechanisms of RNA biosynthesis activities and details of their complex polymerase structures are unknown. Mechanistic and functional details of a paramyxovirus polymerase would have sweeping implications for understanding RNA virus replication and for the development of new antiviral medicines. To study paramyxovirus polymerase structure and function, we expressed an active recombinant Nipah virus (NiV) polymerase complex assembled from the multifunctional NiV L protein bound to its phosphoprotein cofactor. NiV is an emerging highly pathogenic virus that causes severe encephalitis and has been declared a global public health concern due to its high mortality rate. Using negative-stain electron microscopy, we demonstrated NiV polymerase forms ring-like particles resembling related RNA polymerases. We identified conserved sequence elements driving recognition of the 3′-terminal genomic promoter by NiV polymerase, and leading to initiation of RNA synthesis, primer extension, and transition to elongation mode. Polyadenylation resulting from NiV polymerase stuttering provides a mechanistic basis for transcription termination. It also suggests a divergent adaptation in promoter recognition between pneumo- and paramyxoviruses. The lack of available antiviral therapy for NiV prompted us to identify the triphosphate forms of R1479 and GS-5734, two clinically relevant nucleotide analogs, as substrates and inhibitors of NiV polymerase activity by delayed chain termination. Overall, these findings provide low-resolution structural details and the mechanism of an RNA polymerase from a previously uncharacterized virus family. This work illustrates important functional differences yet remarkable similarities between the polymerases of nonsegmented negative-strand RNA viruses. RNA viruses replicate and transcribe their genomes using complex enzymatic machines known as RNA-dependent RNA polymerases. The chemical reactions driving nucleotide addition are shared among nucleic acid polymerases but the underlying mechanisms of RNA biosynthesis and the complex polymerase structures are diverse. Of these RNA viruses is the paramyxovirus family, which includes major human pathogens. Paramyxoviruses have common biological and genetic properties but little is known about their replication machinery. Insights into the structure, function, and mechanisms of RNA synthesis of one paramyxovirus polymerase will likely extend to the entire virus family. An emerging, highly pathogenic paramyxovirus is Nipah virus (NiV), which causes encephalitis in humans. We have purified NiV polymerase, probed its enzymatic and biophysical properties and developed it as a model paramyxovirus polymerase. We investigated template strand sequence elements driving RNA biosynthesis for NiV polymerase and obtained a snapshot of NiV polymerase molecular organization using electron microscopy to provide the first structural information on a paramyxovirus polymerase. This work extends previous knowledge by producing the first recombinant paramyxovirus polymerase and using this protein in enzymatic assays to highlight key functional and structural characteristics for the design of new medicines.
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Affiliation(s)
- Paul C. Jordan
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Cheng Liu
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Pauline Raynaud
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Michael K. Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Julian A. Symons
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Jerome Deval
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
- * E-mail:
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5
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Biophysical Mode-of-Action and Selectivity Analysis of Allosteric Inhibitors of Hepatitis C Virus (HCV) Polymerase. Viruses 2017. [PMID: 28621755 PMCID: PMC5490826 DOI: 10.3390/v9060151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Allosteric inhibitors of hepatitis C virus (HCV) non-structural protein 5B (NS5B) polymerase are effective for treatment of genotype 1, although their mode of action and potential to inhibit other isolates and genotypes are not well established. We have used biophysical techniques and a novel biosensor-based real-time polymerase assay to investigate the mode-of-action and selectivity of four inhibitors against enzyme from genotypes 1b (BK and Con1) and 3a. Two thumb inhibitors (lomibuvir and filibuvir) interacted with all three NS5B variants, although the affinities for the 3a enzyme were low. Of the two tested palm inhibitors (dasabuvir and nesbuvir), only dasabuvir interacted with the 1b variant, and nesbuvir interacted with NS5B 3a. Lomibuvir, filibuvir and dasabuvir stabilized the structure of the two 1b variants, but not the 3a enzyme. The thumb compounds interfered with the interaction between the enzyme and RNA and blocked the transition from initiation to elongation. The two allosteric inhibitor types have different inhibition mechanisms. Sequence and structure analysis revealed differences in the binding sites for 1b and 3a variants, explaining the poor effect against genotype 3a NS5B. The indirect mode-of-action needs to be considered when designing allosteric compounds. The current approach provides an efficient strategy for identifying and optimizing allosteric inhibitors targeting HCV genotype 3a.
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6
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Miyamura T, Lemon SM, Walker CM, Wakita T. The HCV Replicase Complex and Viral RNA Synthesis. HEPATITIS C VIRUS I 2016. [PMCID: PMC7122888 DOI: 10.1007/978-4-431-56098-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Replication of hepatitis C virus (HCV) is tightly linked to membrane alterations designated the membranous web, harboring the viral replicase complex. In this chapter we describe the morphology and 3D architecture of the HCV-induced replication organelles, mainly consisting of double membrane vesicles, which are generated by a concerted action of the nonstructural proteins NS3 to NS5B. Recent studies have furthermore identified a number of host cell proteins and lipids contributing to the biogenesis of the membranous web, which are discussed in this chapter. Viral RNA synthesis is tightly associated with these membrane alterations and mainly driven by the viral RNA dependent RNA polymerase NS5B. We summarize our current knowledge of the structure and function of NS5B, the role of cis-acting replication elements at the termini of the genome in regulating RNA synthesis and the contribution of additional viral and host factors to viral RNA synthesis, which is still ill defined.
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Affiliation(s)
- Tatsuo Miyamura
- National Institute of Infectious Diseases, Tokyo, Tokyo Japan
| | - Stanley M. Lemon
- Departments of Medicine and Microbiology & Immunology , The University of North Carolina, Chapel Hill, North Carolina USA
| | - Christopher M. Walker
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio USA
| | - Takaji Wakita
- National Institute of Infectious Diseases, Tokyo, Tokyo Japan
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7
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Devert A, Fabre N, Floris M, Canard B, Robaglia C, Crété P. Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified Arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6. PLoS One 2015; 10:e0120100. [PMID: 25793874 PMCID: PMC4368572 DOI: 10.1371/journal.pone.0120100] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/19/2015] [Indexed: 12/05/2022] Open
Abstract
Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer-independent and primer-dependent RNA polymerase activities with different efficiencies. We further show that RDR2 and RDR6 can initiate dsRNA synthesis either by elongation of 21- to 24- nucleotides RNAs hybridized to complementary RNA template or by elongation of self-primed RNA template. These findings provide new insights into our understanding of the molecular mechanisms of RNA silencing in plants.
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Affiliation(s)
- Anthony Devert
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Nicolas Fabre
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Maïna Floris
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université, AFMB UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Christophe Robaglia
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
| | - Patrice Crété
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, France
- Centre National de la Recherche Scientifique, UMR 7265, Biologie Végétale et Microbiologie Environnementale, Marseille, France
- Commissariat à l’Énergie Atomique, Département des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologies, Marseille, France
- * E-mail:
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8
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Abstract
Hepatitis C virus (HCV) is a major global health burden accounting for around 170 million chronic infections worldwide. Although highly potent direct-acting antiviral drugs to treat chronic hepatitis C have been approved recently, owing to their high costs and limited availability and a large number of undiagnosed infections, the burden of disease is expected to rise in the next few years. In addition, HCV is an excellent paradigm for understanding the tight link between a pathogen and host cell pathways, most notably lipid metabolism. HCV extensively remodels intracellular membranes to establish its cytoplasmic replication factory and also usurps components of the intercellular lipid transport system for production of infectious virus particles. Here, we review the molecular mechanisms of viral replicase function, cellular pathways employed during HCV replication factory biogenesis, and viral, as well as cellular, determinants of progeny virus production.
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9
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Reich S, Kovermann M, Lilie H, Knick P, Geissler R, Golbik RP, Balbach J, Behrens SE. Initiation of RNA synthesis by the hepatitis C virus RNA-dependent RNA polymerase is affected by the structure of the RNA template. Biochemistry 2014; 53:7002-12. [PMID: 25310724 PMCID: PMC4230328 DOI: 10.1021/bi5006656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is
a central enzyme of the intracellular replication of the viral (+)RNA
genome. Here, we studied the individual steps of NS5B-catalyzed RNA
synthesis by a combination of biophysical methods, including real-time
1D 1H NMR spectroscopy. NS5B was found to bind to a nonstructured
and a structured RNA template in different modes. Following NTP binding
and conversion to the catalysis-competent ternary complex, the polymerase
revealed an improved affinity for the template. By monitoring the
folding/unfolding of 3′(−)SL by 1H NMR, the
base pair at the stem’s edge was identified as the most stable
component of the structure. 1H NMR real-time analysis of
NS5B-catalyzed RNA synthesis on 3′(−)SL showed that
a pronounced lag phase preceded the processive polymerization reaction.
The presence of the double-stranded stem with the edge base pair acting
as the main energy barrier impaired RNA synthesis catalyzed by NS5B.
Our observations suggest a crucial role of RNA-modulating factors
in the HCV replication process.
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Affiliation(s)
- Stefan Reich
- Institute of Biochemistry and Biotechnology, Section of Microbial Biotechnology, ‡Institute of Physics, Section of Biophysics, §Institute of Biochemistry and Biotechnology, Section of Technical Biochemistry, Martin Luther University Halle-Wittenberg , D-06120 Halle/Saale, Germany
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10
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Cross-genotypic examination of hepatitis C virus polymerase inhibitors reveals a novel mechanism of action for thumb binders. Antimicrob Agents Chemother 2014; 58:7215-24. [PMID: 25246395 DOI: 10.1128/aac.03699-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Direct-acting antivirals (DAAs) targeting proteins encoded by the hepatitis C virus (HCV) genome have great potential for the treatment of HCV infections. However, the efficacy of DAAs designed to target genotype 1 (G1) HCV against non-G1 viruses has not been characterized fully. In this study, we investigated the inhibitory activities of nonnucleoside inhibitors (NNIs) against the HCV RNA-dependent RNA polymerase (RdRp). We examined the ability of six NNIs to inhibit G1b, G2a, and G3a subgenomic replicons in cell culture, as well as in vitro transcription by G1b and G3a recombinant RdRps. Of the six G1 NNIs, only the palm II binder nesbuvir demonstrated activity against G1, G2, and G3 HCV, in both replicon and recombinant enzyme models. The thumb I binder JTK-109 also inhibited G1b and G3a replicons and recombinant enzymes but was 41-fold less active against the G2a replicon. The four other NNIs, which included a palm I binder (setrobuvir), two thumb II binders (lomibuvir and filibuvir), and a palm β-hairpin binder (tegobuvir), all showed at least 40-fold decreases in potency against G2a and G3a replicons and the G3a enzyme. This antiviral resistance was largely conferred by naturally occurring amino acid residues in the G2a and G3a RdRps that are associated with G1 resistance. Lomibuvir and filibuvir (thumb II binders) inhibited primer-dependent but not de novo activity of the G1b polymerase. Surprisingly, these compounds instead specifically enhanced the de novo activity at concentrations of ≥ 100 nM. These findings highlight a potential differential mode of RdRp inhibition for HCV NNIs, depending on their prospective binding pockets, and also demonstrate a surprising enhancement of de novo activity for thumb RdRp binders. These results also provide a better understanding of the antiviral coverage for these polymerase inhibitors, which will likely be used in future combinational interferon-free therapies.
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11
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Karam P, Powdrill MH, Liu HW, Vasquez C, Mah W, Bernatchez J, Götte M, Cosa G. Dynamics of hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B in complex with RNA. J Biol Chem 2014; 289:14399-411. [PMID: 24692556 DOI: 10.1074/jbc.m113.529743] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis C virus (HCV) non-structural protein 5B (NS5B) is an RNA-dependent RNA polymerase that is essentially required for viral replication. Although previous studies revealed important properties of static NS5B-RNA complexes, the nature and relevance of dynamic interactions have yet to be elucidated. Here, we devised a single molecule Förster Resonance Energy Transfer (SM-FRET) assay to monitor temporal changes upon binding of NS5B to surface immobilized RNA templates. The data show enzyme association-dissociation events that occur within the time resolution of our setup as well as FRET-fluctuations in association with stable binary complexes that extend over prolonged periods of time. Fluctuations are shown to be dependent on the length of the RNA substrate, and enzyme concentration. Mutations in close proximity to the template entrance (K98E, K100E), and in the center of the RNA binding channel (R394E), reduce both the population of RNA-bound enzyme and the fluctuations associated to the binary complex. Similar observations are reported with an allosteric nonnucleoside NS5B inhibitor. Our assay enables for the first time the visualization of association-dissociation events of HCV-NS5B with RNA, and also the direct monitoring of the interaction between HCV NS5B, its RNA template, and finger loop inhibitors. We observe both a remarkably low dissociation rate for wild type HCV NS5B, and a highly dynamic enzyme-RNA binary complex. These results provide a plausible mechanism for formation of a productive binary NS5B-RNA complex, here NS5B slides along the RNA template facilitating positioning of its 3' terminus at the enzyme active site.
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Affiliation(s)
| | - Megan H Powdrill
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | | | - Colins Vasquez
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Wayne Mah
- From the Department of Chemistry and
| | - Jean Bernatchez
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Matthias Götte
- From the Department of Chemistry and the Department of Biochemistry, McGill University, Montréal, Quebec H3G 1Y6, Canada and the Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Quebec H3A 1A3, Canada
| | - Gonzalo Cosa
- From the Department of Chemistry and the Centre for Self-Assembled Chemical Structures (CSACS/CRMAA), McGill University, Montréal, Quebec H3A 2K6, Canada,
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12
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Chen KX, Venkatraman S, Anilkumar GN, Zeng Q, Lesburg CA, Vibulbhan B, Velazquez F, Chan TY, Bennet F, Jiang Y, Pinto P, Huang Y, Selyutin O, Agrawal S, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. Discovery of SCH 900188: A Potent Hepatitis C Virus NS5B Polymerase Inhibitor Prodrug As a Development Candidate. ACS Med Chem Lett 2014; 5:244-8. [PMID: 24900812 DOI: 10.1021/ml400192w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/12/2013] [Indexed: 01/28/2023] Open
Abstract
Starting from indole-based hepatitis C virus (HCV) NS5B polymerase inhibitor lead compound 1, structure modifications were performed at multiple indole substituents to improve potency and pharmacokinetic (PK) properties. Bicyclic quinazolinone was found to be the best substituent at indole nitrogen, while 4,5-furanylindole was identified as the best core. Compound 11 demonstrated excellent potency. Its C2 N,N-dimethylaminoethyl ester prodrug 12 (SCH 900188) demonstrated significant improvement in PK and was selected as the development candidate.
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Affiliation(s)
- Kevin X. Chen
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Srikanth Venkatraman
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Gopinadhan N. Anilkumar
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Qingbei Zeng
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Charles A. Lesburg
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Bancha Vibulbhan
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Francisco Velazquez
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Tin-Yau Chan
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Frank Bennet
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Yueheng Jiang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Patrick Pinto
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Yuhua Huang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Oleg Selyutin
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Sony Agrawal
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Hsueh-Cheng Huang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Cheng Li
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Kuo-Chi Cheng
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Neng-Yang Shih
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Joseph A. Kozlowski
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Stuart B. Rosenblum
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - F. George Njoroge
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
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13
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Kim DW, Lee SA, Kim H, Won YS, Kim BJ. Naturally occurring mutations in the nonstructural region 5B of hepatitis C virus (HCV) from treatment-naïve Korean patients chronically infected with HCV genotype 1b. PLoS One 2014; 9:e87773. [PMID: 24489961 PMCID: PMC3906201 DOI: 10.1371/journal.pone.0087773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 12/30/2013] [Indexed: 12/29/2022] Open
Abstract
The nonstructural 5B (NS5B) protein of the hepatitis C virus (HCV) with RNA-dependent RNA polymerase (RdRp) activity plays a pivotal role in viral replication. Therefore, monitoring of its naturally occurring mutations is very important for the development of antiviral therapies and vaccines. In the present study, mutations in the partial NS5B gene (492 bp) from 166 quasispecies of 15 genotype-1b (GT) treatment-naïve Korean chronic patients were determined and mutation patterns and frequencies mainly focusing on the T cell epitope regions were evaluated. The mutation frequency within the CD8+ T cell epitopes was significantly higher than those outside the CD8+ T cell epitopes. Of note, the mutation frequency within predicted CD4+ T cell epitopes, a particular mutational hotspot in Korean patients was significantly higher than it was in patients from other areas, suggesting distinctive CD4+ T cell-mediated immune pressure against HCV infection in the Korean population. The mutation frequency in the NS5B region was positively correlated with patients with carrier-stage rather than progressive liver disease (chronic hepatitis, liver cirrhosis and hepatocellular carcinoma). Furthermore, the mutation frequency in four codons (Q309, A333, V338 and Q355) known to be related to the sustained virological response (SVR) and end-of treatment response (ETR) was also significantly higher in Korean patients than in patients from other areas. In conclusion, a high degree of mutation frequency in the HCV GT-1b NS5B region, particularly in the predicted CD4+ T cell epitopes, was found in Korean patients, suggesting the presence of distinctive CD4+ T cell pressure in the Korean population. This provides a likely explanation of why relatively high levels of SVR after a combined therapy of pegylated interferon (PEG-IFN) and ribavirin (RBV) in Korean chronic patients with GT-1b infections are observed.
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Affiliation(s)
- Dong-Won Kim
- Department of Biomedical Sciences, Microbiology and Immunology, and Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Seoung-Ae Lee
- Department of Biomedical Sciences, Microbiology and Immunology, and Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Hong Kim
- Department of Biomedical Sciences, Microbiology and Immunology, and Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - You-Sub Won
- Department of Biomedical Sciences, Microbiology and Immunology, and Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, and Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
- * E-mail:
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14
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Kim H, Kim BJ. Naturally Occurring Mutations of Hepatitis B virus and Hepatitis C Virus in Korean Chronic Patients by Distinct CD4 T Cell Responses. JOURNAL OF BACTERIOLOGY AND VIROLOGY 2014; 44:37. [DOI: 10.4167/jbv.2014.44.1.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Affiliation(s)
- Hong Kim
- Department of Microbiology and Immunology, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
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15
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Abstract
Genome replication is a crucial step in the life cycle of any virus. HCV is a positive strand RNA virus and requires a set of nonstructural proteins (NS3, 4A, 4B, 5A, and 5B) as well as cis-acting replication elements at the genome termini for amplification of the viral RNA. All nonstructural proteins are tightly associated with membranes derived from the endoplasmic reticulum and induce vesicular membrane alterations designated the membranous web, harboring the viral replication sites. The viral RNA-dependent RNA polymerase NS5B is the key enzyme of RNA synthesis. Structural, biochemical, and reverse genetic studies have revealed important insights into the mode of action of NS5B and the mechanism governing RNA replication. Although a comprehensive understanding of the regulation of RNA synthesis is still missing, a number of important viral and host determinants have been defined. This chapter summarizes our current knowledge on the role of viral and host cell proteins as well as cis-acting replication elements involved in the biogenesis of the membranous web and in viral RNA synthesis.
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Affiliation(s)
- Volker Lohmann
- Department of Infectious Diseases, University of Heidelberg, Heidelberg, Germany.
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16
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Venkatraman S, Velazquez F, Gavalas S, Wu W, Chen KX, Nair AG, Bennett F, Huang Y, Pinto P, Jiang Y, Selyutin O, Vibulbhan B, Zeng Q, Lesburg C, Duca J, Huang HC, Agrawal S, Jiang CK, Ferrari E, Li C, Kozlowski J, Rosenblum S, Shih NY, Njoroge FG. Discovery of novel tricyclic indole derived inhibitors of HCV NS5B RNA dependent RNA polymerase. Bioorg Med Chem 2013; 21:2007-17. [DOI: 10.1016/j.bmc.2013.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/03/2013] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
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17
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Ferrari E, Huang HC. A novel hepatitis C virus NS5B polymerase assay of de novo initiated RNA synthesis directed from a heteropolymeric RNA template. Methods Mol Biol 2013; 1030:81-92. [PMID: 23821261 DOI: 10.1007/978-1-62703-484-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase is essential for viral replication and a clinically validated antiviral target. Discovery of HCV polymerase inhibitors is greatly facilitated by the availability of a suitable biochemical assay using purified NS5B. We describe here a novel NS5B polymerase assay of de novo initiated RNA synthesis directed from a synthetic heteropolymeric RNA template modified with dideoxycytidine at its 3'-end. This assay has been successfully used for screening and characterization of both initiation and elongation inhibitors of the HCV NS5B polymerase.
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Affiliation(s)
- Eric Ferrari
- Department of Infectious Diseases, Merck Research Laboratories, Kenilworth, NJ, USA
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18
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Golub AG, Gurukumar KR, Basu A, Bdzhola VG, Bilokin Y, Yarmoluk SM, Lee JC, Talele TT, Nichols DB, Kaushik-Basu N. Discovery of new scaffolds for rational design of HCV NS5B polymerase inhibitors. Eur J Med Chem 2012; 58:258-64. [PMID: 23127989 DOI: 10.1016/j.ejmech.2012.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 02/02/2023]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is a key target for the development of anti-HCV drugs. Here we report on the identification of novel allosteric inhibitors of HCV NS5B through a combination of structure-based virtual screening and in vitro NS5B inhibition assays. One hundred and sixty thousand compounds from the Otava database were virtually screened against the thiazolone inhibitor binding site on NS5B (thumb pocket-2, TP-2), resulting in a sequential down-sizing of the library by 2.7 orders of magnitude to yield 59 NS5B non-nucleoside inhibitor (NNI) candidates. In vitro evaluation of the NS5B inhibitory activity of the 59 selected compounds resulted in a 14% hit rate, yielding 8 novel structural scaffolds. Of these, compound 1 bearing a 4-hydrazinoquinazoline scaffold was the most active (IC(50) = 16.0 μM). The binding site of all 8 NNIs was mapped to TP-2 of NS5B as inferred by a decrease in their inhibition potency against the M423T NS5B mutant, employed as a screen for TP-2 site binders. At 100 μM concentration, none of the eight compounds exhibited any cytotoxicity, and all except compound 8 exhibited between 40 and 60% inhibition of intracellular NS5B polymerase activity in BHK-NS5B-FRLuc reporter cells. These inhibitor scaffolds will form the basis for future optimization and development of more potent NS5B inhibitors.
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Affiliation(s)
- Andriy G Golub
- Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, 03143 Kyiv, Ukraine
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19
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Two crucial early steps in RNA synthesis by the hepatitis C virus polymerase involve a dual role of residue 405. J Virol 2012; 86:7107-17. [PMID: 22532694 DOI: 10.1128/jvi.00459-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) NS5B protein is an RNA-dependent RNA polymerase essential for replication of the viral RNA genome. In vitro and presumably in vivo, NS5B initiates RNA synthesis by a de novo mechanism and then processively copies the whole RNA template. Dissections of de novo RNA synthesis by genotype 1 NS5B proteins previously established that there are two successive crucial steps in de novo initiation. The first is dinucleotide formation, which requires a closed conformation, and the second is the transition to elongation, which requires an opening of NS5B. We also recently published a combined structural and functional analysis of genotype 2 HCV-NS5B proteins (of strains JFH1 and J6) that established residue 405 as a key element in de novo RNA synthesis (P. Simister et al., J. Virol. 83:11926-11939, 2009; M. Schmitt et al., J. Virol 85:2565-2581, 2011). We hypothesized that this residue stabilizes a particularly closed conformation conducive to dinucleotide formation. Here we report similar in vitro dissections of de novo synthesis for J6 and JFH1 NS5B proteins, as well as for mutants at position 405 of several genotype 1 and 2 strains. Our results show that an isoleucine at position 405 can promote both dinucleotide formation and the transition to elongation. New structural results highlight a molecular switch of position 405 with long-range effects, resolving the implied paradox of how the same residue can successively favor both the closed conformation of the dinucleotide formation step and the opening necessary to the transition step.
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20
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Chen KX, Lesburg CA, Vibulbhan B, Yang W, Chan TY, Venkatraman S, Velazquez F, Zeng Q, Bennett F, Anilkumar GN, Duca J, Jiang Y, Pinto P, Wang L, Huang Y, Selyutin O, Gavalas S, Pu H, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. A novel class of highly potent irreversible hepatitis C virus NS5B polymerase inhibitors. J Med Chem 2012; 55:2089-101. [PMID: 22247956 DOI: 10.1021/jm201322r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Starting from indole-based C-3 pyridone HCV NS5B polymerase inhibitor 2, structure-activity relationship (SAR) investigations of the indole N-1 benzyl moiety were performed. This study led to the discovery of irreversible inhibitors with p-fluoro-sulfone- or p-fluoro-nitro-substituted N-1 benzyl groups which achieved breakthrough replicon assay potency (EC(50) = 1 nM). The formation of a covalent bond with adjacent cysteine-366 thiol was was proved by mass spectroscopy and X-ray crystal structure studies. The C-5 ethyl C-2 carboxylic acid derivative 47 had an excellent oral area-under-the-curve (AUC) of 18 μM·h (10 mg/kg). Its oral exposure in monkeys and dogs was also very good. The NMR ALARM assay, mass spectroscopy experiments, in vitro counter screening, and toxicology assays demonstrated that the covalent bond formation between compound 47 and the protein was highly selective and specific. The overall excellent profile of 47 made it an interesting candidate for further investigation.
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Affiliation(s)
- Kevin X Chen
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
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21
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Chen KX, Vibulbhan B, Yang W, Sannigrahi M, Velazquez F, Chan TY, Venkatraman S, Anilkumar GN, Zeng Q, Bennet F, Jiang Y, Lesburg CA, Duca J, Pinto P, Gavalas S, Huang Y, Wu W, Selyutin O, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. Structure-activity relationship (SAR) development and discovery of potent indole-based inhibitors of the hepatitis C virus (HCV) NS5B polymerase. J Med Chem 2012; 55:754-65. [PMID: 22148957 DOI: 10.1021/jm201258k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Starting with the indole-based C-3 pyridone lead HCV polymerase inhibitor 2, extensive SAR studies were performed at different positions of the indole core. The best C-5 groups were found to be compact and nonpolar moieties and that the C-6 attachments were not affecting potency. Limited N-1 benzyl-type substituent studies indicated that the best substitutions were fluoro or methyl groups at 2' or 5' positions of the benzyl group. To improve pharmacokinetic (PK) properties, acylsulfonamides were incorporated as acid isosteres at the C-2 position. Further optimization of the combination at N-1, C-2, C-5, and C-6 resulted in the identification of compound 56, which had an excellent potency in both NS5B enzyme (IC(50) = 0.008 μM) and cell-based replicon (EC(50) = 0.02 μM) assays and a good oral PK profile with area-under-the curve (AUC) of 14 and 8 μM·h in rats and dogs, respectively. X-ray structure of inhibitor 56 bound to the enzyme was also reported.
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Affiliation(s)
- Kevin X Chen
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.
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22
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Velázquez F, Venkatraman S, Lesburg CA, Duca J, Rosenblum SB, Kozlowski JA, Njoroge FG. Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors. Org Lett 2012; 14:556-9. [DOI: 10.1021/ol203177g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francisco Velázquez
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Srikanth Venkatraman
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Charles A. Lesburg
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - José Duca
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Stuart B. Rosenblum
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Joseph A. Kozlowski
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - F. George Njoroge
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
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23
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Anilkumar GN, Lesburg CA, Selyutin O, Rosenblum SB, Zeng Q, Jiang Y, Chan TY, Pu H, Vaccaro H, Wang L, Bennett F, Chen KX, Duca J, Gavalas S, Huang Y, Pinto P, Sannigrahi M, Velazquez F, Venkatraman S, Vibulbhan B, Agrawal S, Butkiewicz N, Feld B, Ferrari E, He Z, Jiang CK, Palermo RE, Mcmonagle P, Huang HC, Shih NY, Njoroge G, Kozlowski JA. I. Novel HCV NS5B polymerase inhibitors: Discovery of indole 2-carboxylic acids with C3-heterocycles. Bioorg Med Chem Lett 2011; 21:5336-41. [DOI: 10.1016/j.bmcl.2011.07.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 11/25/2022]
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24
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Clemente-Casares P, López-Jiménez AJ, Bellón-Echeverría I, Encinar JA, Martínez-Alfaro E, Pérez-Flores R, Mas A. De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5. PLoS One 2011; 6:e18515. [PMID: 21490973 PMCID: PMC3072391 DOI: 10.1371/journal.pone.0018515] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/04/2011] [Indexed: 01/20/2023] Open
Abstract
Hepatitis C virus (HCV) shows a great geographical diversity reflected in the high number of circulating genotypes and subtypes. The response to HCV treatment is genotype specific, with the predominant genotype 1 showing the lowest rate of sustained virological response. Virally encoded enzymes are candidate targets for intervention. In particular, promising antiviral molecules are being developed to target the viral NS3/4A protease and NS5B polymerase. Most of the studies with the NS5B polymerase have been done with genotypes 1b and 2a, whilst information about other genotypes is scarce. Here, we have characterized the de novo activity of NS5B from genotypes 1 to 5, with emphasis on conditions for optimum activity and kinetic constants. Polymerase cooperativity was determined by calculating the Hill coefficient and oligomerization through a new FRET-based method. The Vmax/Km ratios were statistically different between genotype 1 and the other genotypes (p<0.001), mainly due to differences in Vmax values, but differences in the Hill coefficient and NS5B oligomerization were noted. Analysis of sequence changes among the studied polymerases and crystal structures show the αF helix as a structural component probably involved in NS5B-NS5B interactions. The viability of the interaction of αF and αT helixes was confirmed by docking studies and calculation of electrostatic surface potentials for genotype 1 and point mutants corresponding to mutations from different genotypes. Results presented in this study reveal the existence of genotypic differences in NS5B de novo activity and oligomerization. Furthermore, these results allow us to define two regions, one consisting of residues Glu128, Asp129, and Glu248, and the other consisting of residues of αT helix possibly involved in NS5B-NS5B interactions.
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Affiliation(s)
- Pilar Clemente-Casares
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - Alberto J. López-Jiménez
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Itxaso Bellón-Echeverría
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
| | - José Antonio Encinar
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Elisa Martínez-Alfaro
- Infectious Disease Unit, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Ricardo Pérez-Flores
- Digestive Department, Complejo Hospitalario Universitario de Albacete, Albacete, Spain
| | - Antonio Mas
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha, Albacete, Spain
- * E-mail:
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25
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Cheng CC, Huang X, Shipps GW, Wang YS, Wyss DF, Soucy KA, Jiang CK, Agrawal S, Ferrari E, He Z, Huang HC. Pyridine Carboxamides: Potent Palm Site Inhibitors of HCV NS5B Polymerase. ACS Med Chem Lett 2010; 1:466-71. [PMID: 24900232 DOI: 10.1021/ml100128h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 07/28/2010] [Indexed: 01/17/2023] Open
Abstract
Pyridine carboxamide-based inhibitors of the hepatitis C virus (HCV) NS5B polymerase were diversified and optimized to a variety of topologically related scaffolds. In particular, the 2-methyl nicotinic acid scaffold was developed into inhibitors with improved biochemical (IC50-GT1b = 0.014 μM) and cell-based HCV replicon potency (EC50-GT1b = 0.7 μM). Biophysical and biochemical characterization identified this novel series of compounds as palm site binders to HCV polymerase.
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Affiliation(s)
- Cliff C. Cheng
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Xiaohua Huang
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Gerald W. Shipps
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Yu-Sen Wang
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Daniel F. Wyss
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Kyle A. Soucy
- Department of Lead Discovery Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Chuan-kui Jiang
- Department of Infectious Diseases, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Sony Agrawal
- Department of Infectious Diseases, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Eric Ferrari
- Department of Infectious Diseases, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Zhiqing He
- Department of Infectious Diseases, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - H.-C. Huang
- Department of Infectious Diseases, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
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26
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Powdrill MH, Bernatchez JA, Götte M. Inhibitors of the Hepatitis C Virus RNA-Dependent RNA Polymerase NS5B. Viruses 2010; 2:2169-2195. [PMID: 21994615 PMCID: PMC3185568 DOI: 10.3390/v2102169] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 12/26/2022] Open
Abstract
More than 20 years after the identification of the hepatitis C virus (HCV) as a novel human pathogen, the only approved treatment remains a combination of pegylated interferon-α and ribavirin. This rather non-specific therapy is associated with severe side effects and by far not everyone benefits from treatment. Recently, progress has been made in the development of specifically targeted antiviral therapy for HCV (STAT-C). A major target for such direct acting antivirals (DAAs) is the HCV RNA-dependent RNA polymerase or non-structural protein 5B (NS5B), which is essential for viral replication. This review will examine the current state of development of inhibitors targeting the polymerase and issues such as the emergence of antiviral resistance during treatment, as well as strategies to address this problem.
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Affiliation(s)
- Megan H. Powdrill
- McGill University, Department of Microbiology and Immunology, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
| | - Jean A. Bernatchez
- McGill University, Department of Biochemistry, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
| | - Matthias Götte
- McGill University, Department of Microbiology and Immunology, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
- McGill University, Department of Biochemistry, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
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27
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Harrus D, Ahmed-El-Sayed N, Simister PC, Miller S, Triconnet M, Hagedorn CH, Mahias K, Rey FA, Astier-Gin T, Bressanelli S. Further insights into the roles of GTP and the C terminus of the hepatitis C virus polymerase in the initiation of RNA synthesis. J Biol Chem 2010; 285:32906-32918. [PMID: 20729191 DOI: 10.1074/jbc.m110.151316] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The hepatitis C virus (HCV) NS5b protein is an RNA-dependent RNA polymerase essential for replication of the viral RNA genome. In vitro and presumably in vivo, NS5b initiates RNA synthesis by a de novo mechanism. Different structural elements of NS5b have been reported to participate in RNA synthesis, especially a so-called "β-flap" and a C-terminal segment (designated "linker") that connects the catalytic core of NS5b to a transmembrane anchor. High concentrations of GTP have also been shown to stimulate de novo RNA synthesis by HCV NS5b. Here we describe a combined structural and functional analysis of genotype 1 HCV-NS5b of strains H77 (subtype 1a), for which no structure has been previously reported, and J4 (subtype 1b). Our results highlight the linker as directly involved in lifting the first boundary to processive RNA synthesis, the formation of the first dinucleotide primer. The transition from this first dinucleotide primer state to processive RNA synthesis requires removal of the linker and of the β-flap with which it is shown to strongly interact in crystal structures of HCV NS5b. We find that GTP specifically stimulates this transition irrespective of its incorporation in neosynthesized RNA.
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Affiliation(s)
- Déborah Harrus
- From the Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Neveen Ahmed-El-Sayed
- CNRS UMR 52342, IFR66, Université Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Philip C Simister
- From the Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Steve Miller
- University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Martine Triconnet
- From the Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Curt H Hagedorn
- University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Kathleen Mahias
- CNRS UMR 52342, IFR66, Université Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Félix A Rey
- From the Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Thérèse Astier-Gin
- CNRS UMR 52342, IFR66, Université Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Stéphane Bressanelli
- From the Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.
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Regulation of de novo-initiated RNA synthesis in hepatitis C virus RNA-dependent RNA polymerase by intermolecular interactions. J Virol 2010; 84:5923-35. [PMID: 20375156 DOI: 10.1128/jvi.02446-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) has been proposed to change conformations in association with RNA synthesis and to interact with cellular proteins. In vitro, the RdRp can initiate de novo from the ends of single-stranded RNA or extend a primed RNA template. The interactions between the Delta1 loop and thumb domain in NS5B are required for de novo initiation, although it is unclear whether these interactions are within an NS5B monomer or are part of a higher-order NS5B oligomeric complex. This work seeks to address how polymerase conformation and/or oligomerization affects de novo initiation. We have shown that an increasing enzyme concentration increases de novo initiation by the genotype 1b and 2a RdRps while primer extension reactions are not affected or inhibited under similar conditions. Initiation-defective mutants of the HCV polymerase can increase de novo initiation by the wild-type (WT) polymerase. GTP was also found to stimulate de novo initiation. Our results support a model in which the de novo initiation-competent conformation of the RdRp is stimulated by oligomeric contacts between individual subunits. Using electron microscopy and single-molecule reconstruction, we attempted to visualize the low-resolution conformations of a dimer of a de novo initiation-competent HCV RdRp.
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Structural and functional analysis of hepatitis C virus strain JFH1 polymerase. J Virol 2009; 83:11926-39. [PMID: 19740982 DOI: 10.1128/jvi.01008-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hepatitis C virus (HCV) isolate JFH1 represents the only cloned wild-type sequence capable of efficient replication in cell culture, as well as in chimpanzees. Previous reports have pointed to the viral polymerase NS5B as a major determinant for efficient replication of this isolate. To understand the underlying mechanisms, we expressed and purified NS5B of JFH1 and of the closely related isolate J6, which replicates below the limit of detection in cell culture. The JFH1 enzyme exhibited a 5- to 10-fold-higher specific activity in vitro, consistent with the polymerase activity itself contributing to efficient replication of JFH1. The higher in vitro activity of the JFH1 enzyme was not due to increased RNA binding, elongation rate, or processivity of the polymerase but to higher initiation efficiency. By using homopolymeric and heteropolymeric templates, we found that purified JFH1 NS5B was significantly more efficient in de novo initiation of RNA synthesis than the J6 counterpart, particularly at low GTP concentrations, probably representing an important prerequisite for the rapid replication kinetics of JFH1. Furthermore, we solved the crystal structure of JFH1 NS5B, which displays a very closed conformation that is expected to facilitate de novo initiation. Structural analysis shows that this closed conformation is stabilized by a sprinkle of substitutions that together promote extra hydrophobic interactions between the subdomains "thumb" and "fingers." These analyses provide deeper insights into the initiation of HCV RNA synthesis and might help to establish more efficient cell culture models for HCV using alternative isolates.
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