1
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Moianos D, Prifti GM, Makri M, Zoidis G. Targeting Metalloenzymes: The "Achilles' Heel" of Viruses and Parasites. Pharmaceuticals (Basel) 2023; 16:901. [PMID: 37375848 DOI: 10.3390/ph16060901] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Metalloenzymes are central to the regulation of a wide range of essential viral and parasitic functions, including protein degradation, nucleic acid modification, and many others. Given the impact of infectious diseases on human health, inhibiting metalloenzymes offers an attractive approach to disease therapy. Metal-chelating agents have been expansively studied as antivirals and antiparasitics, resulting in important classes of metal-dependent enzyme inhibitors. This review provides the recent advances in targeting the metalloenzymes of viruses and parasites that impose a significant burden on global public health, including influenza A and B, hepatitis B and C, and human immunodeficiency viruses as well as Trypanosoma brucei and Trypanosoma cruzi.
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Affiliation(s)
- Dimitrios Moianos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Georgia-Myrto Prifti
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Maria Makri
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
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2
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Bivacqua R, Barreca M, Spanò V, Raimondi MV, Romeo I, Alcaro S, Andrei G, Barraja P, Montalbano A. Insight into non-nucleoside triazole-based systems as viral polymerases inhibitors. Eur J Med Chem 2023; 249:115136. [PMID: 36708678 DOI: 10.1016/j.ejmech.2023.115136] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Viruses have been recognized as the etiological agents responsible for many pathological conditions ranging from asymptomatic infections to serious diseases, even leading to death. For this reason, many efforts have been made to identify selective viral targets with the aim of developing efficient therapeutic strategies, devoid of drug-resistance issues. Considering their crucial role in the viral life cycle, polymerases are very attractive targets. Among the classes of compounds explored as viral polymerases inhibitors, here we present an overview of non-nucleoside triazole-based compounds identified in the last fifteen years. Furthermore, the structure-activity relationships (SAR) of the different chemical entities are described in order to highlight the key chemical features required for the development of effective antiviral agents.
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Affiliation(s)
- Roberta Bivacqua
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Marilia Barreca
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Maria Valeria Raimondi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy.
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, 88100, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Università Magna Græcia, Viale Europa, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università Magna Græcia, Viale Europa, 88100, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Università Magna Græcia, Viale Europa, 88100, Catanzaro, Italy
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Belgium
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123, Palermo, Italy
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3
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Miropolskaya N, Kozlov M, Petushkov I, Prostova M, Pupov D, Esyunina D, Kochetkov S, Kulbachinskiy A. Effects of natural polymorphisms in SARS-CoV-2 RNA-dependent RNA polymerase on its activity and sensitivity to inhibitors in vitro. Biochimie 2023; 206:81-88. [PMID: 36252889 PMCID: PMC9568283 DOI: 10.1016/j.biochi.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is the key enzyme required for viral replication and mRNA synthesis. RdRp is one of the most conserved viral proteins and a promising target for antiviral drugs and inhibitors. At the same time, analysis of public databases reveals multiple variants of SARS-CoV-2 genomes with substitutions in the catalytic RdRp subunit nsp12. Structural mapping of these mutations suggests that some of them may affect the interactions of nsp12 with its cofactors nsp7/nsp8 as well as with RNA substrates. We have obtained several mutations of these types and demonstrated that some of them decrease specific activity of RdRp in vitro, possibly by changing RdRp assembly and/or its interactions with RNA. Therefore, natural polymorphisms in RdRp may potentially affect viral replication. Furthermore, we have synthesized a series of polyphenol and diketoacid derivatives based on previously studied inhibitors of hepatitis C virus RdRp and found that several of them can inhibit SARS-CoV-2 RdRp. Tested mutations in RdRp do not have strong effects on the efficiency of inhibition. Further development of more efficient non-nucleoside inhibitors of SARS-CoV-2 RdRp should take into account the existence of multiple polymorphic variants of RdRp.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maxim Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maria Prostova
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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4
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Cao Y, Aimaiti A, Zhu Z, Zhou L, Ye D. Discovery of Novel 3-Hydroxyquinazoline-2,4(1 H,3 H)-Dione Derivatives: A Series of Metal Ion Chelators with Potent Anti-HCV Activities. Int J Mol Sci 2022; 23:ijms23115930. [PMID: 35682608 PMCID: PMC9180926 DOI: 10.3390/ijms23115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Millions of people worldwide suffer from acute or chronic liver inflammation caused by the hepatitis C virus (HCV). Metal ion chelators have achieved widespread success in the development of antiviral drugs. Some inhibitors with metal ion chelating structures have been proven to have good inhibitory activities on non-structural protein 5B (NS5B) polymerase. However, most of the reported metal ion chelators showed poor anti-HCV potency at the cellular level. Hence, we designed and synthesized a series of 3-hydroxyquinazoline-2,4(1H,3H)-dione derivatives with novel metal ion chelating structures. Typical compounds such as 21h, 21k, and 21t showed better anti-HCV activities than ribavirin with EC50 values less than 10 μM. 21t is currently known as one of the metal ion chelators with the best anti-HCV potency (EC50 = 2.0 μM) at the cellular level and has a better therapeutic index (TI > 25) as compared to ribavirin and the reported compound 6. In the thermal shift assay, the representative compounds 21e and 21k increased the melting temperature (Tm) of NS5B protein solution by 1.6 °C and 2.1 °C, respectively, at the test concentration, indicating that these compounds may exert an anti-HCV effect by targeting NS5B. This speculation was also supported by our molecular docking studies and ultraviolet-visible (UV-Vis) spectrophotometry assay, in which the possibility of binding of 3-hydroxyquinazoline-2,4(1H,3H)-diones with Mg2+ in the NS5B catalytic center was observed.
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Affiliation(s)
- Yang Cao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Abudumijiti Aimaiti
- Shanghai Medical College, Fudan University, 130 Dongan Rd, Shanghai 200032, China;
| | - Zeyun Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
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5
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Maarifi G, Lagisquet J, Hertel Q, Bonaventure B, Chamontin C, Fuchs K, Moncorgé O, Tauziet M, Mombled M, Papin L, Molès JP, Bodet C, Lévèque N, Gross A, Arhel N, Nisole S, Van de Perre P, Goujon C, Blanchet FP. Alarmin S100A9 restricts retroviral infection by limiting reverse transcription in human dendritic cells. EMBO J 2021; 40:e106540. [PMID: 34121210 DOI: 10.15252/embj.2020106540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
Dendritic cells (DC) subsets, like Langerhans cells (LC), are immune cells involved in pathogen sensing. They express specific antimicrobial cellular factors that are able to restrict infection and limit further pathogen transmission. Here, we identify the alarmin S100A9 as a novel intracellular antiretroviral factor expressed in human monocyte-derived and skin-derived LC. The intracellular expression of S100A9 is decreased upon LC maturation and inversely correlates with enhanced susceptibility to HIV-1 infection of LC. Furthermore, silencing of S100A9 in primary human LC relieves HIV-1 restriction while ectopic expression of S100A9 in various cell lines promotes intrinsic resistance to both HIV-1 and MLV infection by acting on reverse transcription. Mechanistically, the intracellular expression of S100A9 alters viral capsid uncoating and reverse transcription. S100A9 also shows potent inhibitory effect against HIV-1 and MMLV reverse transcriptase (RTase) activity in vitro in a divalent cation-dependent manner. Our findings uncover an unexpected intracellular function of the human alarmin S100A9 in regulating antiretroviral immunity in Langerhans cells.
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Affiliation(s)
- Ghizlane Maarifi
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Justine Lagisquet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Quentin Hertel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Boris Bonaventure
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Célia Chamontin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Kyra Fuchs
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marine Tauziet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Margaux Mombled
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Laure Papin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Charles Bodet
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Nicolas Lévèque
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Antoine Gross
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Nathalie Arhel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
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6
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Metal binding 6-arylthio-3-hydroxypyrimidine-2,4-diones inhibited human cytomegalovirus by targeting the pUL89 endonuclease of the terminase complex. Eur J Med Chem 2021; 222:113640. [PMID: 34147908 DOI: 10.1016/j.ejmech.2021.113640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022]
Abstract
The genome packaging of human cytomegalovirus (HCMV) requires a divalent metal-dependent endonuclease activity localized to the C-terminus of pUL89 (pUL89-C), which is reminiscent of RNase H-like enzymes in active site structure and catalytic mechanism. Our previous work has shown that metal-binding small molecules can effectively inhibit pUL89-C while conferring significant antiviral activities. In this report we generated a collection of 43 metal-binding small molecules by repurposing analogs of the 6-arylthio-3-hydroxypyrimidine-2,4-dione chemotype previously synthesized for targeting HIV-1 RNase H, and by chemically synthesizing new N-1 analogs. The analogs were subjected to two parallel screening assays: the pUL89-C biochemical assay and the HCMV antiviral assay. Compounds with significant inhibition from each assay were further tested in a dose-response fashion. Single dose cell viability and PAMPA cell permeability were also conducted and considered in selecting compounds for the dose-response antiviral testing. These assays identified a few analogs displaying low μM inhibition against pUL89-C in the biochemical assay and HCMV replication in the antiviral assay. The target engagement was further evaluated via a thermal shift assay using recombinant pUL89-C and molecular docking. Overall, our current work identified novel inhibitors of pUL89-C with significant antiviral activities and further supports targeting pUL89-C with metal-binding small molecules as an antiviral approach against HCMV.
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Elghoneimy LK, Ismail MI, Boeckler FM, Azzazy HME, Ibrahim TM. Facilitating SARS CoV-2 RNA-Dependent RNA polymerase (RdRp) drug discovery by the aid of HCV NS5B palm subdomain binders: In silico approaches and benchmarking. Comput Biol Med 2021; 134:104468. [PMID: 34015671 PMCID: PMC8111889 DOI: 10.1016/j.compbiomed.2021.104468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/25/2021] [Accepted: 04/30/2021] [Indexed: 01/18/2023]
Abstract
Corona Virus 2019 Disease (COVID-19) is a rapidly emerging pandemic caused by a newly discovered beta coronavirus, called Sever Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). SARS CoV-2 is an enveloped, single stranded RNA virus that depends on RNA-dependent RNA polymerase (RdRp) to replicate. Therefore, SARS CoV-2 RdRp is considered as a promising target to cease virus replication. SARS CoV-2 polymerase shows high structural similarity to Hepatitis C Virus-1b genotype (HCV-1b) polymerase. Arising from the high similarity between SARS CoV-2 RdRp and HCV NS5B, we utilized the reported small-molecule binders to the palm subdomain of HCV NS5B (genotype 1b) to generate a high-quality DEKOIS 2.0 benchmark set and conducted a benchmarking analysis against HCV NS5B. The three highly cited and publicly available docking tools AutoDock Vina, FRED and PLANTS were benchmarked. Based on the benchmarking results and analysis via pROC-Chemotype plot, PLANTS showed the best screening performance and can recognize potent binders at the early enrichment. Accordingly, we used PLANTS in a prospective virtual screening to repurpose both the FDA-approved drugs (DrugBank) and the HCV-NS5B palm subdomain binders (BindingDB) for SARS CoV-2 RdRp palm subdomain. Further assessment by molecular dynamics simulations for 50 ns recommended diosmin (from DrugBank) and compound 3 (from BindingDB) to be the best potential binders to SARS CoV-2 RdRp palm subdomain. The best predicted compounds are recommended to be biologically investigated against COVID-19. In conclusion, this work provides in-silico analysis to propose possible SARS CoV-2 RdRp palm subdomain binders recommended as a remedy for COVID-19. Up-to-our knowledge, this study is the first to propose binders at the palm subdomain of SARS CoV2 RdRp. Furthermore, this study delivers an example of how to make use of a high quality custom-made DEKOIS 2.0 benchmark set as a procedure to elevate the virtual screening success rate against a vital target of the rapidly emerging pandemic.
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Affiliation(s)
- Laila K Elghoneimy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Muhammad I Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, 11837, Cairo, Egypt
| | - Frank M Boeckler
- Department of Pharmacy, Eberhard-Karls University, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Hassan M E Azzazy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
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8
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Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses 2021; 13:v13020205. [PMID: 33572956 PMCID: PMC7912079 DOI: 10.3390/v13020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are currently recommended for the first line treatment of human immunodeficiency virus type one (HIV-1) infection. The first-generation INSTIs are effective but can select for resistant viruses. Recent advances have led to several potent second-generation INSTIs that are effective against both wild-type (WT) HIV-1 integrase and many of the first-generation INSTI-resistant mutants. The emergence of resistance to these new second-generation INSTIs has been minimal, which has resulted in alternative treatment strategies for HIV-1 patients. Moreover, because of their high antiviral potencies and, in some cases, their bioavailability profiles, INSTIs will probably have prominent roles in pre-exposure prophylaxis (PrEP). Herein, we review the current state of the clinically relevant INSTIs and discuss the future outlook for this class of antiretrovirals.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
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10
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Wei Y, Li W, Du T, Hong Z, Lin J. Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method. Int J Mol Sci 2019; 20:ijms20143572. [PMID: 31336592 PMCID: PMC6678913 DOI: 10.3390/ijms20143572] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/13/2019] [Accepted: 07/21/2019] [Indexed: 12/11/2022] Open
Abstract
Human immunodeficiency virus type-1 and hepatitis C virus (HIV/HCV) coinfection occurs when a patient is simultaneously infected with both human immunodeficiency virus type-1 (HIV-1) and hepatitis C virus (HCV), which is common today in certain populations. However, the treatment of coinfection is a challenge because of the special considerations needed to ensure hepatic safety and avoid drug–drug interactions. Multitarget inhibitors with less toxicity may provide a promising therapeutic strategy for HIV/HCV coinfection. However, the identification of one molecule that acts on multiple targets simultaneously by experimental evaluation is costly and time-consuming. In silico target prediction tools provide more opportunities for the development of multitarget inhibitors. In this study, by combining Naïve Bayes (NB) and support vector machine (SVM) algorithms with two types of molecular fingerprints, MACCS and extended connectivity fingerprints 6 (ECFP6), 60 classification models were constructed to predict compounds that were active against 11 HIV-1 targets and four HCV targets based on a multiple quantitative structure–activity relationships (multiple QSAR) method. Five-fold cross-validation and test set validation were performed to measure the performance of the 60 classification models. Our results show that the 60 multiple QSAR models appeared to have high classification accuracy in terms of the area under the ROC curve (AUC) values, which ranged from 0.83 to 1 with a mean value of 0.97 for the HIV-1 models and from 0.84 to 1 with a mean value of 0.96 for the HCV models. Furthermore, the 60 models were used to comprehensively predict the potential targets of an additional 46 compounds, including 27 approved HIV-1 drugs, 10 approved HCV drugs and nine selected compounds known to be active against one or more targets of HIV-1 or HCV. Finally, 20 hits, including seven approved HIV-1 drugs, four approved HCV drugs, and nine other compounds, were predicted to be HIV/HCV coinfection multitarget inhibitors. The reported bioactivity data confirmed that seven out of nine compounds actually interacted with HIV-1 and HCV targets simultaneously with diverse binding affinities. The remaining predicted hits and chemical-protein interaction pairs with the potential ability to suppress HIV/HCV coinfection are worthy of further experimental investigation. This investigation shows that the multiple QSAR method is useful in predicting chemical-protein interactions for the discovery of multitarget inhibitors and provides a unique strategy for the treatment of HIV/HCV coinfection.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300000, China
| | - Tengfei Du
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China.
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300000, China.
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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11
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Wang Z, Chen Z, Li J, Huang J, Zheng C, Liu JP. Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase. J Biomol Struct Dyn 2019; 38:1071-1082. [PMID: 30915896 DOI: 10.1080/07391102.2019.1593244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q2 of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q2 of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhenming Chen
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jing Huang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Chenni Zheng
- Laboratory of Biocatalysis, College of Life & Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Immunology, Central Eastern Clinical School, Monash University, Melbourne, Vitoria, Australia.,Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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12
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Ganta NM, Gedda G, Rathnakar B, Satyanarayana M, Yamajala B, Ahsan MJ, Jadav SS, Balaraju T. A review on HCV inhibitors: Significance of non-structural polyproteins. Eur J Med Chem 2018; 164:576-601. [PMID: 30639895 PMCID: PMC7185800 DOI: 10.1016/j.ejmech.2018.12.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) mortality and morbidity is a world health misery with an approximate 130–150 million chronically HCV tainted and suffering individuals and it initiate critical liver malfunction like cirrhosis, hepatocellular carcinoma or liver HCV cancer. HCV NS5B protein one of the best studied therapeutic target for the identification of new drug candidates to be added to the combination or multiple combination medication recently approved. During the past few years, NS5B has thus been an important object of attractive medicinal chemistry endeavors, which induced to the surfacing of betrothal preclinical drug molecules. In this scenario, the current review set limit to discuss research published on NS5B and few other therapeutic functional inhibitors concentrating on hit investigation, hit to lead optimization, ADME parameters evaluation, and the SAR data which was out for each compound type and similarity taken into consideration. The discussion outlined in this specific review will surly helpful and vital tool for those medicinal chemists investigators working with HCV research programs mainly pointing on NS5B and set broad spectrum identification of creative anti HCV compounds. This mini review also tells each and every individual compound ability related how much they are active against NS5B and few other targets. Hepatitis C infection causes severe liver cirrhosis and carcinoma. The new acute HCV infections are raising every year and mortality rate become serious concern. The plausible list of anti-HCV drugs and clinical agents were listed in this review. The divergent medicinal scaffolds as anti-HCV agents were presented as per their targets.
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Affiliation(s)
- Narayana Murthy Ganta
- Department of Pharmaceutical Chemistry, Vishnu Institute of Pharmaceutical Education and Research, Narsapur, Medak, Telangana, 502313, India
| | - Gangaraju Gedda
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Bethi Rathnakar
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Mavurapu Satyanarayana
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Bhaskar Yamajala
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Surender Singh Jadav
- CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India.
| | - Tuniki Balaraju
- Deapartment of Chemistry, Material Science Centre, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, WB, 741 246, India.
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13
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Hasan P, Pillalamarri VK, Aneja B, Irfan M, Azam M, Perwez A, Maguire R, Yadava U, Kavanagh K, Daniliuc CG, Ahmad MB, Rizvi MMA, Rizwanul Haq QM, Addlagatta A, Abid M. Synthesis and mechanistic studies of diketo acids and their bioisosteres as potential antibacterial agents. Eur J Med Chem 2018; 163:67-82. [PMID: 30503944 DOI: 10.1016/j.ejmech.2018.11.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/13/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022]
Abstract
A series of diketo esters and their pertinent bioisosteres were designed and synthesized as potent antibacterial agents by targeting methionine amino peptidases (MetAPs). In the biochemical assay against purified MetAPs from Streptococcus pneumoniae (SpMetAP1a), Mycobacterium tuberculosis (MtMetAP1c), Enterococcus faecalis (EfMetAP1a) and human (HsMetAP1b), compounds 3a, 4a and 5a showed more than 85% inhibition of all the tested MetAPs at 100 μM concentration. Compounds 4a and 5a also exhibited antibacterial potential with MIC values 62.5 μg/mL (S. pneumoniae), 31.25 μg/mL (E. faecalis), 62.5 μg/mL (Escherichia coli) and 62.5 μg/mL (S. pneumoniae), 62.5 μg/mL (E. coli), respectively. Moreover, 5a also significantly inhibited the growth of multidrug resistant E. coli strains at 512 μg/mL conc., while showing no cytotoxic effect towards healthy CHO cells and thus being selected. Growth kinetics study showed significant inhibition of bacterial growth when treated with different conc. of 5a. TEM analysis also displayed vital damage to bacterial cells by 5a at MIC conc. Moreover, significant inhibition of biofilm formation was observed in bacterial cells treated with MIC conc. of 5a as visualized by SEM micrographs. Interestingly, 5a did not cause an alteration in the hemocyte density in Galleria mellonella larvae which is considered in vivo model for antimicrobial studies and was non-toxic up to a conc. of 2.5 mg/mL.
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Affiliation(s)
- Phool Hasan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - Vijay K Pillalamarri
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Babita Aneja
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohammad Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mudsser Azam
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ronan Maguire
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | | | - Md Belal Ahmad
- Department of Chemistry, TNB College, TM Bhagalpur University, Bhagalpur, 812007, India
| | - M Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Qazi Mohd Rizwanul Haq
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anthony Addlagatta
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500607, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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14
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Bongarzone S, Nadal M, Kaczmarska Z, Machón C, Álvarez M, Albericio F, Coll M. Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. ACS OMEGA 2018; 3:8497-8505. [PMID: 31458978 PMCID: PMC6645139 DOI: 10.1021/acsomega.8b01472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/19/2018] [Indexed: 05/27/2023]
Abstract
Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.
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Affiliation(s)
- Salvatore Bongarzone
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Marta Nadal
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Zuzanna Kaczmarska
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Cristina Machón
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Mercedes Álvarez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Miquel Coll
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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15
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Lacbay CM, Menni M, Bernatchez JA, Götte M, Tsantrizos YS. Pharmacophore requirements for HIV-1 reverse transcriptase inhibitors that selectively "Freeze" the pre-translocated complex during the polymerization catalytic cycle. Bioorg Med Chem 2018; 26:1713-1726. [PMID: 29478802 DOI: 10.1016/j.bmc.2018.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 12/20/2022]
Abstract
Reverse transcriptase (RT) is responsible for replicating the HIV-1 genome and is a validated therapeutic target for the treatment of HIV infections. During each cycle of the RT-catalyzed DNA polymerization process, inorganic pyrophosphate is released as the by-product of nucleotide incorporation. Small molecules were identified that act as bioisosteres of pyrophosphate and can selectively freeze the catalytic cycle of HIV-1 RT at the pre-translocated stage of the DNA- or RNA-template-primer-enzyme complex.
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Affiliation(s)
- Cyrus M Lacbay
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Michael Menni
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Jean A Bernatchez
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada; Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada.
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16
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Tomei L, Altamura S, Paonessa G, De Francesco R, Migliaccio G. Review HCV Antiviral Resistance: The Impact of in vitro Studies on the Development of Antiviral Agents Targeting the Viral NS5B Polymerase. ACTA ACUST UNITED AC 2016; 16:225-45. [PMID: 16130521 DOI: 10.1177/095632020501600403] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The high prevalence of the disease caused by hepatitis C virus (HCV) and the limited efficacy of interferon-based therapies have stimulated the search for safer and more effective drugs. The development of inhibitors of the HCV NS5B RNA polymerase represents a promising strategy for identifying novel anti-HCV therapeutics. However, the high genetic diversity, mutation rate and turnover of HCV are expected to favour the emergence of drug resistance, limiting the clinical usefulness of polymerase inhibitors. Thus, the characterization of the drug-resistance profile of these antiviral agents is considered crucial for identifying the inhibitors with a higher probability of clinical success. In the absence of an efficient in vitro infection system, HCV sub-genomic replicons have been used to study viral resistance to both nucleoside and non-nucleoside NS5B inhibitors. While these studies suggest that drug-resistant viruses are likely to evolve in vivo, they provide a wealth of information that should help in the identification of inhibitors with improved and distinct resistance profiles that might be used for combination therapy.
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Affiliation(s)
- Licia Tomei
- Istituto di Ricerche di Biologia Molecolare P Angeletti, Pomezia-Roma, Italy
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17
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Li W, Si H, Li Y, Ge C, Song F, Ma X, Duan Y, Zhai H. 3D-QSAR and molecular docking studies on designing inhibitors of the hepatitis C virus NS5B polymerase. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.03.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Identification of a Pyridoxine-Derived Small-Molecule Inhibitor Targeting Dengue Virus RNA-Dependent RNA Polymerase. Antimicrob Agents Chemother 2015; 60:600-8. [PMID: 26574011 DOI: 10.1128/aac.02203-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/10/2015] [Indexed: 01/14/2023] Open
Abstract
The viral RNA-dependent RNA polymerase (RdRp) activity of the dengue virus (DENV) NS5 protein is an attractive target for drug design. Here, we report the identification of a novel class of inhibitor (i.e., an active-site metal ion chelator) that acts against DENV RdRp activity. DENV RdRp utilizes a two-metal-ion mechanism of catalysis; therefore, we constructed a small library of compounds, through mechanism-based drug design, aimed at chelating divalent metal ions in the catalytic site of DENV RdRp. We now describe a pyridoxine-derived small-molecule inhibitor that targets DENV RdRp and show that 5-benzenesulfonylmethyl-3-hydroxy-4-hydroxymethyl-pyridine-2-carboxylic acid hydroxyamide (termed DMB220) inhibited the RdRp activity of DENV serotypes 1 to 4 at low micromolar 50% inhibitory concentrations (IC50s of 5 to 6.7 μM) in an enzymatic assay. The antiviral activity of DMB220 against DENV infection was also verified in a cell-based assay and showed a 50% effective concentration (EC50) of <3 μM. Enzyme assays proved that DMB220 was competitive with nucleotide incorporation. DMB220 did not inhibit the enzymatic activity of recombinant HIV-1 reverse transcriptase and showed only weak inhibition of HIV-1 integrase strand transfer activity, indicating high specificity for DENV RdRp. S600T substitution in the DENV RdRp, which was previously shown to confer resistance to nucleoside analogue inhibitors (NI), conferred 3-fold hypersusceptibility to DMB220, and enzymatic analyses showed that this hypersusceptibility may arise from the decreased binding/incorporation efficiency of the natural NTP substrate without significantly impacting inhibitor binding. Thus, metal ion chelation at the active site of DENV RdRp represents a viable anti-DENV strategy, and DMB220 is the first of a new class of DENV inhibitor.
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19
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Zhong D, Liu M, Cao Y, Zhu Y, Bian S, Zhou J, Wu F, Ryu KC, Zhou L, Ye D. Discovery of Metal Ions Chelator Quercetin Derivatives with Potent Anti-HCV Activities. Molecules 2015; 20:6978-99. [PMID: 25913935 PMCID: PMC6272327 DOI: 10.3390/molecules20046978] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022] Open
Abstract
Analogues or isosteres of α,γ-diketoacid (DKA) 1a show potent inhibition of hepatitis C virus (HCV) NS5B polymerase through chelation of the two magnesium ions at the active site. The anti-HCV activity of the flavonoid quercetin (2) could partly be attributed to it being a structural mimic of DKAs. In order to delineate the structural features required for the inhibitory effect and improve the anti-HCV potency, two novel types of quercetin analogues, 7-O-arylmethylquercetins and quercetin-3-O-benzoic acid esters, were designed, synthesized and evaluated for their anti-HCV properties in cell-based assays. Among the 38 newly synthesized compounds, 7-O-substituted derivative 3i and 3-O-substituted derivative 4f were found to be the most active in the corresponding series (EC50 = 3.8 μM and 9.0 μΜ, respectively). Docking studies suggested that the quercetin analogues are capable of establishing key coordination with the two magnesium ions as well as interactions with residues at the active site of HCV NS5B.
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Affiliation(s)
- Dongwei Zhong
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Mingming Liu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Yang Cao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Yelin Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Shihui Bian
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Jiayi Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Fengjie Wu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Kum-Chol Ryu
- Institute of Pharmacy, HamHung Pharmaceutical University, HamHung 999093, Democratic People's Republic of Korea.
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhang-Heng Rd, Shanghai 201203, China.
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20
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Lacbay CM, Mancuso J, Lin YS, Bennett N, Götte M, Tsantrizos YS. Modular Assembly of Purine-like Bisphosphonates as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2014; 57:7435-49. [DOI: 10.1021/jm501010f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Cyrus M. Lacbay
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - John Mancuso
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Yih-Shyan Lin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Nicholas Bennett
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
- Department
of Medicine, Division of Experimental Medicine, McGill University, 1110
Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Youla S. Tsantrizos
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
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21
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Hepatitis C Virus Polymerase as a Target for Antiviral Drug Intervention: Non-Nucleoside Inhibitors. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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22
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Kozlov MV, Kleymenova AA, Romanova LI, Konduktorov KA, Smirnova OA, Prasolov VS, Kochetkov SN. Benzohydroxamic acids as potent and selective anti-HCV agents. Bioorg Med Chem Lett 2013; 23:5936-40. [PMID: 24035094 DOI: 10.1016/j.bmcl.2013.08.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/14/2013] [Accepted: 08/18/2013] [Indexed: 01/30/2023]
Abstract
A diverse collection of 40 derivatives of benzohydroxamic acid (BHAs) of various structural groups were synthesized and tested against hepatitis C virus (HCV) in full-genome replicon assay. Some of these compounds demonstrated an exceptional activity, suppressing viral replication at sub-micromolar concentrations. The compounds were inactive against key viral enzymes NS3, and NS5B in vitro assays, suggesting host cell inhibition target(s). The testing results were consistent with metal coordination by the BHAs hydroxamic group in complex with a target(s). Remarkably, this class of compounds did not suppress poliomyelitis virus (PV) propagation in RD cells indicating a specific antiviral activity of BHAs against HCV.
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Affiliation(s)
- Maxim V Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia.
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23
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Song WH, Liu MM, Zhong DW, Zhu YL, Bosscher M, Zhou L, Ye DY, Yuan ZH. Tetrazole and triazole as bioisosteres of carboxylic acid: Discovery of diketo tetrazoles and diketo triazoles as anti-HCV agents. Bioorg Med Chem Lett 2013; 23:4528-31. [DOI: 10.1016/j.bmcl.2013.06.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/12/2013] [Accepted: 06/15/2013] [Indexed: 02/02/2023]
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24
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Krieger IV, Freundlich JS, Gawandi VB, Roberts JP, Gawandi VB, Sun Q, Owen JL, Fraile MT, Huss SI, Lavandera JL, Ioerger TR, Sacchettini JC. Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase. ACTA ACUST UNITED AC 2013; 19:1556-67. [PMID: 23261599 DOI: 10.1016/j.chembiol.2012.09.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/14/2012] [Accepted: 09/19/2012] [Indexed: 11/16/2022]
Abstract
The glyoxylate shunt plays an important role in fatty acid metabolism and has been shown to be critical to survival of several pathogens involved in chronic infections. For Mycobacterium tuberculosis (Mtb), a strain with a defective glyoxylate shunt was previously shown to be unable to establish infection in a mouse model. We report the development of phenyl-diketo acid (PDKA) inhibitors of malate synthase (GlcB), one of two glyoxylate shunt enzymes, using structure-based methods. PDKA inhibitors were active against Mtb grown on acetate, and overexpression of GlcB ameliorated this inhibition. Crystal structures of complexes of GlcB with PDKA inhibitors guided optimization of potency. A selected PDKA compound demonstrated efficacy in a mouse model of tuberculosis. The discovery of these PDKA derivatives provides chemical validation of GlcB as an attractive target for tuberculosis therapeutics.
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Affiliation(s)
- Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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25
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Weidlich IE, Filippov IV, Brown J, Kaushik-Basu N, Krishnan R, Nicklaus MC, Thorpe IF. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorg Med Chem 2013; 21:3127-37. [PMID: 23608107 DOI: 10.1016/j.bmc.2013.03.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/10/2013] [Accepted: 03/18/2013] [Indexed: 12/30/2022]
Abstract
Hepatitis C virus (HCV) is a global health challenge, affecting approximately 200 million people worldwide. In this study we developed SAR models with advanced machine learning classifiers Random Forest and k Nearest Neighbor Simulated Annealing for 679 small molecules with measured inhibition activity for NS5B genotype 1b. The activity was expressed as a binary value (active/inactive), where actives were considered molecules with IC50 ≤0.95 μM. We applied our SAR models to various drug-like databases and identified novel chemical scaffolds for NS5B inhibitors. Subsequent in vitro antiviral assays suggested a new activity for an existing prodrug, Candesartan cilexetil, which is currently used to treat hypertension and heart failure but has not been previously tested for anti-HCV activity. We also identified NS5B inhibitors with two novel non-nucleoside chemical motifs.
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Affiliation(s)
- Iwona E Weidlich
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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26
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Viral enzymes containing magnesium: Metal binding as a successful strategy in drug design. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Progress in the development of anti-hepatitis C virus nucleoside and nucleotide prodrugs. Future Med Chem 2012; 4:625-50. [PMID: 22458682 DOI: 10.4155/fmc.12.10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The search for new anti-hepatitis C virus (HCV) therapeutics continues as the current treatment, consisting of PEGylated IFN-α and ribavirin, is of limited efficacy, nonspecific and can cause significant side effects. Modified nucleoside analogues with improved efficacy and selectivity, may become the backbone of the future standard of care for anti-HCV therapies. Several families of modified nucleoside are known to inhibit HCV RNA-dependent RNA polymerase, a vital enzyme for viral replication. Ongoing efforts are focused on improvement of potency, selectivity and delivery of antiviral nucleoside analogues, with several recent promising advances into clinical trials. This review summarizes the current progress in the development of new anti-HCV nucleoside and nucleotide prodrugs.
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28
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Sandmann L, Wilson M, Back D, Wedemeyer H, Manns MP, Steinmann E, Pietschmann T, von Hahn T, Ciesek S. Anti-retroviral drugs do not facilitate hepatitis C virus (HCV) infection in vitro. Antiviral Res 2012; 96:51-8. [PMID: 22842003 DOI: 10.1016/j.antiviral.2012.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 07/03/2012] [Accepted: 07/12/2012] [Indexed: 12/16/2022]
Abstract
An estimated 4 to 5 million people are co-infected with HIV/HCV worldwide. Recently observed outbreaks of acute HCV infection among HIV-positive men who have sex with men (MSM) have been linked to behavioral factors such as high risk sexual practices and recreational drug use. However, at the molecular level, many drugs such as glucocorticoids or cyclosporine A have been found to modulate viral replication. Thus, it is conceivable that drugs used in highly active antiretroviral therapy (HAART) may heighten susceptibility to HCV infection and contribute to the recent outbreaks. We therefore performed a comprehensive screen of antiretroviral drugs covering all available drug classes both individually and in typical combinations used during HAART to probe for direct effects on HCV cell entry, replication, new particle assembly and release. Importantly, no significant enhancement or inhibition of HCV cell entry, replication or new particle production was detected. While raltegravir and ritonavir boosted atazanavir reduce HCV replication, a tenfold reduction of HCVcc entry by the CCR5 antagonist maraviroc was observed. In conclusion, commonly used HAART agents do not specifically enhance HCV replication. Thus recent epidemic outbreaks of acute HCV in HIV-infected MSM are unlikely to be related to enhancing effects of HAART drugs.
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Affiliation(s)
- Lisa Sandmann
- Klinik für Gastroenterologie, Hepatologie und Endokrinologie, Medizinische Hochschule Hannover, Hannover, Germany
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29
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C-6 aryl substituted 4-quinolone-3-carboxylic acids as inhibitors of hepatitis C virus. Bioorg Med Chem 2012; 20:4790-800. [PMID: 22748708 DOI: 10.1016/j.bmc.2012.05.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/21/2012] [Accepted: 05/29/2012] [Indexed: 12/20/2022]
Abstract
Quinolone-3-carboxylic acid represents a highly privileged chemotype in medicinal chemistry and has been extensively explored as antibiotics and antivirals targeting human immunodeficiency virus (HIV) integrase (IN). Herein we describe the synthesis and anti-hepatitis C virus (HCV) profile of a series of C-6 aryl substituted 4-quinlone-3-carboxylic acid analogues. Significant inhibition was observed with a few analogues at low micromolar range against HCV replicon in cell culture and a reduction in replicon RNA was confirmed through an RT-qPCR assay. Interestingly, evaluation of analogues as inhibitors of NS5B in a biochemical assay yielded only modest inhibitory activities, suggesting that a different mechanism of action could operate in cell culture.
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30
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Liu Y, Lim BH, Jiang WW, Flentge CA, Hutchinson DK, Madigan DL, Randolph JT, Wagner R, Maring CJ, Kati WM, Molla A. Identification of aryl dihydrouracil derivatives as palm initiation site inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2012; 22:3747-50. [PMID: 22542020 DOI: 10.1016/j.bmcl.2012.04.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/26/2012] [Accepted: 04/03/2012] [Indexed: 12/01/2022]
Abstract
Aryl dihydrouracil derivatives were identified from high throughput screening as potent inhibitors of HCV NS5B polymerase. The aryl dihydrouracil derivatives were shown to be non-competitive with respect to template RNA and elongation nucleotide substrates. They demonstrated genotype 1 specific activity towards HCV NS5B polymerases. Structure activity relationships and genotype specific activities of aryl dihydrouracil derivatives suggested that they bind to the palm initiation nucleotide pocket, a hypothesis which was confirmed by studies with polymerases containing mutations in various inhibitor binding sites. Therefore, aryl dihydrouracil derivatives represent a novel class of palm initiation site inhibitors of HCV NS5B polymerase.
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Affiliation(s)
- Yaya Liu
- Antiviral Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
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31
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Liu MM, Zhou L, He PL, Zhang YN, Zhou JY, Shen Q, Chen XW, Zuo JP, Li W, Ye DY. Discovery of flavonoid derivatives as anti-HCV agents via pharmacophore search combining molecular docking strategy. Eur J Med Chem 2012; 52:33-43. [PMID: 22445328 DOI: 10.1016/j.ejmech.2012.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
Common feature based pharmacophore and structure-based docking approaches have been employed in the identification of novel anti-HCV candidates from our in-house database. A total of 31 hits identified in silico were screened in vitro assay. 20 Compounds demonstrated anti-HCV activities (EC(50)<50 μM), including two naturally occurring flavones apigenin (21) and luteolin (22) with low micromole EC(50) values and three compounds (23, 24 and 25) of novel scaffolds with moderate potencies. In addition, pharmacophore refinement was also conducted based on the current knowledge of flavone-derived anti-HCV candidates and the results of combined in silico and in vitro assays.
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Affiliation(s)
- Ming-Ming Liu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China
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32
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Deore RR, Chen GS, Chang PT, Chern TR, Lai SY, Chuang MH, Lin JH, Kung FL, Chen CS, Chiou CT, Chern JW. Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide Derivatives as HCV NS5B Polymerase Inhibitors. ChemMedChem 2012; 7:850-60. [DOI: 10.1002/cmdc.201200058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 11/06/2022]
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33
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Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS. Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. J Med Chem 2012; 55:2481-531. [PMID: 22185586 DOI: 10.1021/jm201384j] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael J Sofia
- Pharmasset, Inc., 303A College Road East, Princeton, New Jersey 08540, United States.
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34
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Chen YL, Tang J, Kesler MJ, Sham YY, Vince R, Geraghty RJ, Wang Z. The design, synthesis and biological evaluations of C-6 or C-7 substituted 2-hydroxyisoquinoline-1,3-diones as inhibitors of hepatitis C virus. Bioorg Med Chem 2011; 20:467-79. [PMID: 22100256 DOI: 10.1016/j.bmc.2011.10.058] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/13/2011] [Accepted: 10/18/2011] [Indexed: 12/14/2022]
Abstract
C7-Substituted 2-hydroxyisoquinoline-1,3-diones inhibit the strand transfer of HIV integrase (IN) and the reverse-transcriptase-associated ribonuclease H (RNH). Hepatitis C virus (HCV) NS5B polymerase shares a similar active site fold to RNH and IN, suggesting that N-hydroxyimides could be useful inhibitor scaffolds of HCV via targeting the NS5B. Herein we describe the design, chemical synthesis, replicon and biochemical assays, and molecular docking of C-6 or C-7 aryl substituted 2-hydroxyisoquinoline-1,3-diones as novel HCV inhibitors. The synthesis involved an improved and clean cyclization method, which allowed the convenient preparation of various analogs. Biological studies revealed that the C-6 analogs, a previously unknown chemotype, consistently inhibit both HCV replicon and recombinant NS5B at low micromolar range. Molecular modeling studies suggest that these inhibitors may bind to the NS5B active site.
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Affiliation(s)
- Yue-Lei Chen
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, MMC 204, Minneapolis, MN 55455, USA
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35
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Kim MK, Yu MS, Park HR, Kim KB, Lee C, Cho SY, Kang J, Yoon H, Kim DE, Choo H, Jeong YJ, Chong Y. 2,6-Bis-arylmethyloxy-5-hydroxychromones with antiviral activity against both hepatitis C virus (HCV) and SARS-associated coronavirus (SCV). Eur J Med Chem 2011; 46:5698-704. [PMID: 21925774 PMCID: PMC7115508 DOI: 10.1016/j.ejmech.2011.09.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/08/2011] [Accepted: 09/03/2011] [Indexed: 12/22/2022]
Abstract
In this study, as a bioisosteric alternative scaffold of the antiviral aryl diketoacids (ADKs), we used 5-hydroxychromone on which two arylmethyloxy substituents were installed. The 5-hydroxychromones (5b–5g) thus prepared showed anti-HCV activity and, depending on the aromatic substituents on the 2-arylmethyloxy moiety, some of the derivatives (5b–5f) were also active against SCV. In addition, unlike the ADKs which showed selective inhibition against the helicase activity of the SCV NTPase/helicase, the 5-hydroxychromones (5b–5f) were active against both NTPase and helicase activities of the target enzyme. Among those, 3-iodobenzyloxy-substituted derivative 5e showed the most potent activity against HCV (EC50 = 4 μM) as well as SCV (IC50 = 4 μM for ATPase activity, 11 μM for helicase activity) and this might be used as a platform structure for future development of the multi-target or broad-spectrum antivirals.
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Affiliation(s)
- Mi Kyoung Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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36
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Bhatt A, Gurukumar KR, Basu A, Patel MR, Kaushik-Basu N, Talele TT. Synthesis and SAR optimization of diketo acid pharmacophore for HCV NS5B polymerase inhibition. Eur J Med Chem 2011; 46:5138-45. [PMID: 21893371 DOI: 10.1016/j.ejmech.2011.08.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
Abstract
Hepatitis C virus (HCV) NS5B polymerase is a key target for anti-HCV therapeutics development. Here we report the synthesis and biological evaluation of a new series of α,γ-diketo acids (DKAs) as NS5B polymerase inhibitors. We initiated structure-activity relationship (SAR) optimization around the furan moiety of compound 1a [IC(50) = 21.8 μM] to achieve more active NS5B inhibitors. This yielded compound 3a [IC(50) = 8.2 μM] bearing the 5-bromobenzofuran-2-yl moiety, the first promising lead compound of the series. Varying the furan moiety with thiophene, thiazole and indazole moieties resulted in compound 11a [IC(50) = 7.5 μM] bearing 3-methylthiophen-2-yl moiety. Finally replacement of the thiophene ring with a bioisosteric phenyl ring further improved the inhibitory activity as seen in compounds 21a [IC(50) = 5.2 μM] and 24a [IC(50) = 2.4 μM]. Binding mode of compound 24a using glide docking within the active site of NS5B polymerase will form the basis for future SAR optimization.
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Affiliation(s)
- Aaditya Bhatt
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, St. John's University, Queens, NY 11439, USA
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37
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2-Arylmethylaminomethyl-5,6-dihydroxychromone derivatives with selective anti-HCV activity. Bioorg Med Chem Lett 2011; 21:3202-5. [DOI: 10.1016/j.bmcl.2011.04.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/08/2011] [Accepted: 04/13/2011] [Indexed: 11/20/2022]
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38
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Komissarov VV, Panova NG, Kritzyn AM. Polymethylene derivatives of nucleic bases with ω-functional groups: VI. [8-(2-oxocyclohexyl)-9-oxooctyl]pyrimidines as potential inhibitors of pyrimidine phosphorylases. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 34:75-82. [DOI: 10.1134/s1068162008010093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Mukovnya AV, Komissarov VV, Kritsyn AM, Mitkevich VA, Tunitskaya VL, Kochetkov SN. Interactions between the hepatitis C virus protein NS3 and polymethylene derivatives of nucleic bases. Mol Biol 2010. [DOI: 10.1134/s0026893310060105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Lee CW, Park KS, Park HR, Park JC, Lee BH, Kim DE, Chong YH. 5-Hydroxychromone, An Alternative Scaffold for Anti-HCV 1,3-Diketo Acid (DKA). B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.11.3471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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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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42
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Lee HS, Park KS, Lee B, Kim DE, Chong Y. 3-O-arylmethylgalangin, a novel isostere for anti-HCV 1,3-diketoacids (DKAs). Bioorg Med Chem 2010; 18:7331-7. [PMID: 20888241 DOI: 10.1016/j.bmc.2010.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 09/07/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
Abstract
Through chelation of the metal ions at the enzyme active site, 1,3-diketoacids (DKAs) show potent inhibition of viral enzymes such as HIV integrase and HCV NS5B. In order to optimize the antiviral activity of the DKAs, structural modification of their metal-binding units, keto-enol acids or monoketo acids, have been actively performed. In this study, we proposed 3-O-arylmethylgalangin 3 as an alternative to ortho-substituted aromatic DKA, a potent inhibitor of HCV NS5B. As a proof-of-concept study, a series of 3-O-arylmethylgalangin derivatives (3a-3r) were prepared and their inhibitory activity against HCV NS5B was estimated. Structure-activity relationship of the 3-O-arylmethylgalangin derivatives was in good accordance with that of the ortho-substituted aromatic DKA series. In particular, two galangin ethers (3g and 3i) completely superimposable with the most potent ortho-substituted aromatic DKA analogue (2) in atom-by-atom fashion showed equipotent inhibitory activity to that of 2. Taken together, this result provides convincing evidence that the 3-O-arylmethylgalangin can successfully mimic the chelating function of the DKA pharmacophore to show potent inhibitory activity against the target enzyme, HCV NS5B.
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Affiliation(s)
- Hyo Seon Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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43
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Lee HS, Park KS, Lee C, Lee B, Kim DE, Chong Y. 7-O-Arylmethylgalangin as a novel scaffold for anti-HCV agents. Bioorg Med Chem Lett 2010; 20:5709-12. [PMID: 20797857 DOI: 10.1016/j.bmcl.2010.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 12/17/2022]
Abstract
In spite of potent antiviral activity, suboptimal physicochemical properties of aryl diketo acids (ADKs) necessitates modification of the core 1,3-diketo acid functionality into a novel scaffold. As the metal-binding affinity of the diketo acid is the key to the antiviral activity of ADKs, we anticipated 3,5-dihydroxy-4-oxo arrangement of galangin scaffold would serve as an excellent mimic for the diketo acid functionality. In this study, through synthesis and biological evaluation of various galangin derivatives, we have shown that the diketo acid functionality can be successfully replaced with the galangin scaffold by specific combination of the substituents to result in identification of a novel galangin derivative (3s) with anti-HCV activity (EC(50)=0.9 μM) comparable to the ADK counterpart.
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Affiliation(s)
- Hyo Seon Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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Banville J, Bouthillier G, Plamondon S, Remillard R, Meanwell NA, Martel A, Walker MA. (Z)-2,2-Dimethyl-5-carboxymethylene-1,3-dioxolan-4-one: a new synthon for the synthesis of α,γ-diketoacid derivatives. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Ryu K, Kim KH, Yoo SY, Lee EY, Lim KH, Min MK, Kim H, Choi SI, Seong BL. Production and characterization of active hepatitis C virus RNA-dependent RNA polymerase. Protein Expr Purif 2010; 71:147-52. [DOI: 10.1016/j.pep.2010.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/28/2009] [Accepted: 01/04/2010] [Indexed: 01/24/2023]
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46
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Mechanism of hepatitis C virus RNA polymerase inhibition with dihydroxypyrimidines. Antimicrob Agents Chemother 2009; 54:977-83. [PMID: 20028820 DOI: 10.1128/aac.01216-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the biochemical mechanisms associated with inhibition and resistance to a 4,5-dihydroxypyrimidine carboxylate that inhibits the hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B. On the basis of the structure of the pharmacophore, it has been suggested that these compounds may act as pyrophosphate (PP(i)) mimics. We monitored nucleotide incorporation events during the elongation phase and showed that the polymerase activity of wild-type NS5B was inhibited by the dihydroxypyrimidine at a 50% inhibitory concentration (IC(50)) of 0.73 muM. Enzymes with the G152E or P156L mutation, either of which confers resistance to this compound, showed four- to fivefold increases in IC(50)s. The inhibitor was competitive with respect to nucleotide incorporation. It was likewise effective at preventing the PP(i)-mediated excision of an incorporated chain terminator in a competitive fashion. In the absence of the dihydroxypyrimidine, the reaction was not significantly affected by the G152E or P156L mutation. These data suggest that the resistance associated with these two mutations is unlikely due to an altered interaction with the pyrophosphate-mimicking domain of the compound but, rather, is due to altered interactions with its specificity domain at a region distant from the active site. Together, our findings provide strong experimental evidence that supports the notion that the members of this class of compounds can act as PP(i) mimics that have the potential to mechanistically complement established nucleoside and nonnucleoside analogue inhibitors.
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47
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2-(3-Thienyl)-5,6-dihydroxypyrimidine-4-carboxylic acids as inhibitors of HCV NS5B RdRp. Bioorg Med Chem Lett 2009; 19:6245-9. [DOI: 10.1016/j.bmcl.2009.06.106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/23/2022]
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Chen Y, Bopda-Waffo A, Basu A, Krishnan R, Silberstein E, Taylor DR, Talele TT, Arora P, Kaushik-Basu N. Characterization of aurintricarboxylic acid as a potent hepatitis C virus replicase inhibitor. Antivir Chem Chemother 2009; 20:19-36. [PMID: 19794229 DOI: 10.3851/imp1286] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) NS5B is an essential component of the viral replication machinery and an important target for antiviral intervention. Aurintricarboxylic acid (ATA), a broad-spectrum antiviral agent, was evaluated and characterized for its anti-NS5B activity in vitro and in HCV replicon cells. METHODS Recombinant NS5B, HCV replicase and Huh-7 cells harbouring the subgenomic HCV replicon of genotype 1b were employed for biochemical and mechanistic investigations. RESULTS Analysis of ATA activity in vitro yielded equipotent inhibition of recombinant NS5B and HCV replicase in the submicromolar range (50% inhibition concentration [IC(50)] approximately 150 nM). Biochemical and mechanistic studies revealed a bimodal mechanism of ATA inhibition with characteristics of pyrophosphate mimics and non-nucleoside inhibitors. Molecular modelling and competition displacement studies were consistent with these parameters, suggesting that ATA might bind to the benzothiadiazine allosteric pocket 3 of NS5B or at its catalytic centre. Kinetic studies revealed a mixed mode of ATA inhibition with respect to both RNA and UTP substrates. Under single-cycle assay conditions, ATA inhibited HCV NS5B initiation and elongation from pre-bound RNA, but with > or =fivefold decreased potency compared with continuous polymerization conditions. The IC(50) value of ATA for the native replicase complex was 145 nM. In HCV replicon cells, ATA treatment ablated HCV RNA replication (50% effective concentration =75 nM) with concomitant decrease in NS5B expression and no apparent cytotoxic effects. CONCLUSIONS This study identified ATA as a potent anti-NS5B inhibitor and suggests that its unique mode of action might be exploited for structural refinement and development of novel anti-NS5B agents.
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Affiliation(s)
- Ye Chen
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, USA
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Kozlov MV, Polyakov KM, Filippova SE, Evstifeev VV, Lyudva GS, Kochetkov SN. RNA-dependent RNA polymerase of hepatitis C virus: Study on inhibition by α,γ-diketo acid derivatives. BIOCHEMISTRY (MOSCOW) 2009; 74:834-41. [DOI: 10.1134/s0006297909080033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee C, Lee JM, Lee NR, Jin BS, Jang KJ, Kim DE, Jeong YJ, Chong Y. Aryl diketoacids (ADK) selectively inhibit duplex DNA-unwinding activity of SARS coronavirus NTPase/helicase. Bioorg Med Chem Lett 2009; 19:1636-8. [PMID: 19233643 PMCID: PMC7127030 DOI: 10.1016/j.bmcl.2009.02.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/02/2009] [Accepted: 02/02/2009] [Indexed: 11/18/2022]
Abstract
As anti-HCV aryl diketoacids (ADK) are good metal chelators, we anticipated that ADKs might serve as potential inhibitors of SARS CoV (SCV) NTPase/helicase (Hel) by mimicking the binding modes of the bismuth complexes which effectively competes for the Zn(2+) ion binding sites in SCV Hel thereby disrupting and inhibiting both the NTPase and helicase activities. Phosphate release assay and FRET-based assay of the ADK analogues showed that the ADKs selectively inhibit the duplex DNA-unwinding activity without significant impact on the helicase ATPase activity. Also, antiviral activities of the ADKs were shown dependent upon the substituent. Taken together, these results suggest that there might be ADK-specific binding site in the SCV Hel, which warrants further investigations with diverse ADKs to provide valuable insights into rational design of specific SCV Hel inhibitors.
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Affiliation(s)
- Chaewoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Jin Moo Lee
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Na-Ra Lee
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Bong-Suk Jin
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Kyoung Jin Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yong-Joo Jeong
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Youhoon Chong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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