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Palazzotti D, Sguilla M, Manfroni G, Cecchetti V, Astolfi A, Barreca ML. Small Molecule Drugs Targeting Viral Polymerases. Pharmaceuticals (Basel) 2024; 17:661. [PMID: 38794231 PMCID: PMC11124969 DOI: 10.3390/ph17050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Small molecules that specifically target viral polymerases-crucial enzymes governing viral genome transcription and replication-play a pivotal role in combating viral infections. Presently, approved polymerase inhibitors cover nine human viruses, spanning both DNA and RNA viruses. This review provides a comprehensive analysis of these licensed drugs, encompassing nucleoside/nucleotide inhibitors (NIs), non-nucleoside inhibitors (NNIs), and mutagenic agents. For each compound, we describe the specific targeted virus and related polymerase enzyme, the mechanism of action, and the relevant bioactivity data. This wealth of information serves as a valuable resource for researchers actively engaged in antiviral drug discovery efforts, offering a complete overview of established strategies as well as insights for shaping the development of next-generation antiviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; (D.P.); (M.S.); (G.M.); (V.C.); (A.A.)
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2
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Perovic V, Stevanovic K, Bukreyeva N, Paessler S, Maruyama J, López-Serrano S, Darji A, Sencanski M, Radosevic D, Berardozzi S, Botta B, Mori M, Glisic S. Exploring the Antiviral Potential of Natural Compounds against Influenza: A Combined Computational and Experimental Approach. Int J Mol Sci 2024; 25:4911. [PMID: 38732151 PMCID: PMC11084791 DOI: 10.3390/ijms25094911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The influenza A virus nonstructural protein 1 (NS1), which is crucial for viral replication and immune evasion, has been identified as a significant drug target with substantial potential to contribute to the fight against influenza. The emergence of drug-resistant influenza A virus strains highlights the urgent need for novel therapeutics. This study proposes a combined theoretical criterion for the virtual screening of molecular libraries to identify candidate NS1 inhibitors. By applying the criterion to the ZINC Natural Product database, followed by ligand-based virtual screening and molecular docking, we proposed the most promising candidate as a potential NS1 inhibitor. Subsequently, the selected natural compound was experimentally evaluated, revealing measurable virus replication inhibition activity in cell culture. This approach offers a promising avenue for developing novel anti-influenza agents targeting the NS1 protein.
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Affiliation(s)
- Vladimir Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Kristina Stevanovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Natalya Bukreyeva
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Junki Maruyama
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Sergi López-Serrano
- Infection Biology Laboratory, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
- Institut de Recerca en Tecnologies Agroalimentaries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ayub Darji
- Institut de Recerca en Tecnologies Agroalimentaries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Milan Sencanski
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Draginja Radosevic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Simone Berardozzi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Roma, 00185 Roma, Italy
- CLNS—Center for Life Nano Sciences@Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
| | - Bruno Botta
- Department of Chemistry and Technologies of Drugs, Sapienza University of Roma, 00185 Roma, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
| | - Sanja Glisic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
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3
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Sake SM, Zhang X, Rajak MK, Urbanek-Quaing M, Carpentier A, Gunesch AP, Grethe C, Matthaei A, Rückert J, Galloux M, Larcher T, Le Goffic R, Hontonnou F, Chatterjee AK, Johnson K, Morwood K, Rox K, Elgaher WAM, Huang J, Wetzke M, Hansen G, Fischer N, Eléouët JF, Rameix-Welti MA, Hirsch AKH, Herold E, Empting M, Lauber C, Schulz TF, Krey T, Haid S, Pietschmann T. Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor. Nat Commun 2024; 15:1173. [PMID: 38332002 PMCID: PMC10853176 DOI: 10.1038/s41467-024-45241-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a common cause of acute lower respiratory tract infection in infants, older adults and the immunocompromised. Effective directly acting antivirals are not yet available for clinical use. To address this, we screen the ReFRAME drug-repurposing library consisting of 12,000 small molecules against RSV. We identify 21 primary candidates including RSV F and N protein inhibitors, five HSP90 and four IMPDH inhibitors. We select lonafarnib, a licensed farnesyltransferase inhibitor, and phase III candidate for hepatitis delta virus (HDV) therapy, for further follow-up. Dose-response analyses and plaque assays confirm the antiviral activity (IC50: 10-118 nM). Passaging of RSV with lonafarnib selects for phenotypic resistance and fixation of mutations in the RSV fusion protein (T335I and T400A). Lentiviral pseudotypes programmed with variant RSV fusion proteins confirm that lonafarnib inhibits RSV cell entry and that these mutations confer lonafarnib resistance. Surface plasmon resonance reveals RSV fusion protein binding of lonafarnib and co-crystallography identifies the lonafarnib binding site within RSV F. Oral administration of lonafarnib dose-dependently reduces RSV virus load in a murine infection model using female mice. Collectively, this work provides an overview of RSV drug repurposing candidates and establishes lonafarnib as a bona fide fusion protein inhibitor.
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Affiliation(s)
- Svenja M Sake
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Manoj Kumar Rajak
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Melanie Urbanek-Quaing
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Arnaud Carpentier
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Antonia P Gunesch
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Christina Grethe
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Alina Matthaei
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Jessica Rückert
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Ronan Le Goffic
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | | | | | - Katharina Rox
- Department of Chemical Biology, Helmholtz Center of Infection Research, Braunschweig, Germany
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
| | - Walid A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Jiabin Huang
- Insitute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Wetzke
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Partner Site Hannover, BREATH, Hannover, Germany
| | - Gesine Hansen
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Partner Site Hannover, BREATH, Hannover, Germany
| | - Nicole Fischer
- Insitute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, Université de Versailles St. Quentin; UMR 1173 (2I), INSERM; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15, Versailles, France
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Helmholtz International Lab for Anti-infectives, HZI, Braunschweig, Germany
| | - Elisabeth Herold
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Martin Empting
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Luebeck-Borstel-Riems, Luebeck, Germany
| | - Sibylle Haid
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- Helmholtz International Lab for Anti-infectives, HZI, Braunschweig, Germany.
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4
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He Y, Zhou J, Gao H, Liu C, Zhan P, Liu X. Broad-spectrum antiviral strategy: Host-targeting antivirals against emerging and re-emerging viruses. Eur J Med Chem 2024; 265:116069. [PMID: 38160620 DOI: 10.1016/j.ejmech.2023.116069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Viral infections are amongst the most prevalent diseases that pose a significant threat to human health. Targeting viral proteins or host factors represents two primary strategies for the development of antiviral drugs. In contrast to virus-targeting antivirals (VTAs), host-targeting antivirals (HTAs) offer advantages in terms of overcoming drug resistance and effectively combating a wide range of viruses, including newly emerging ones. Therefore, targeting host factors emerges as an extremely promising strategy with the potential to address critical challenges faced by VTAs. In recent years, extensive research has been conducted on the discovery and development of HTAs, leading to the approval of maraviroc, a chemokine receptor type 5 (CCR5) antagonist used for the treatment of HIV-1 infected individuals, with several other potential treatments in various stages of development for different viral infections. This review systematically summarizes advancements made in medicinal chemistry regarding various host targets and classifies them into four distinct catagories based on their involvement in the viral life cycle: virus attachment and entry, biosynthesis, nuclear import and export, and viral release.
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Affiliation(s)
- Yong He
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Jiahui Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Huizhan Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
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5
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Qin C, Xie T, Yeh WW, Savas AC, Feng P. Metabolic Enzymes in Viral Infection and Host Innate Immunity. Viruses 2023; 16:35. [PMID: 38257735 PMCID: PMC10820379 DOI: 10.3390/v16010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Metabolic enzymes are central players for cell metabolism and cell proliferation. These enzymes perform distinct functions in various cellular processes, such as cell metabolism and immune defense. Because viral infections inevitably trigger host immune activation, viruses have evolved diverse strategies to blunt or exploit the host immune response to enable viral replication. Meanwhile, viruses hijack key cellular metabolic enzymes to reprogram metabolism, which generates the necessary biomolecules for viral replication. An emerging theme arising from the metabolic studies of viral infection is that metabolic enzymes are key players of immune response and, conversely, immune components regulate cellular metabolism, revealing unexpected communication between these two fundamental processes that are otherwise disjointed. This review aims to summarize our present comprehension of the involvement of metabolic enzymes in viral infections and host immunity and to provide insights for potential antiviral therapy targeting metabolic enzymes.
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Affiliation(s)
- Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
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6
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Onodera T, Sakudo A, Sugiura K, Haritani M, Furusaki K, Kirisawa R. Antiviral agents and disinfectants for foot‑and‑mouth disease (Review). Biomed Rep 2023; 19:57. [PMID: 37614986 PMCID: PMC10442741 DOI: 10.3892/br.2023.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 08/25/2023] Open
Abstract
Fluorouracil, 5-azacytidine, 6-azauridine, ribavirin, favipiravir (T-705) and its derivative (T-1105) exhibit anti-foot-and-mouth disease virus (FMDV) effects. In particular, T-1105 exhibits promising results when administered to guinea pigs orally, and pigs in their feed. FMDV is excreted in the early stages of infection in aerosols and oral or nasal droplets from animals. T-1105 along with the FMDV vaccine can be used to combat foot-and-mouth disease (FMD) epidemics. Several studies have shown that sodium hypochlorous solutions are widely used to inactivate viruses, including FMDV. However, these solutions must be stored under cool and dark conditions to maintain their virucidal effects. Interestingly, a study indicated that the virucidal activity of a calcium bicarbonate solution with a mesoscopic structure (CAC-717) did not decrease after storage at room temperature for at least four years outside direct sunlight. Numerous lessons acquired from the 2010 FMD outbreak in Japan are relevant for the control of COVID-19. However, the widespread use of chlorite can cause environmental issues. Chlorite can be combined with nitrogen to produce chloramine or N-nitrosodimethylamine, which plays a role in carcinogenesis. Therefore, risk assessments should be conducted in aquatic environments. Moreover, there is a need to develop nonchlorine disinfectants that can be used during epidemics, including FMD. The approach of 'One Health' should be shared between the public health and veterinary fields to improve the management of viral outbreaks, including those due to FMD.
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Affiliation(s)
- Takashi Onodera
- Laboratory of Environmental Science for Sustainable Development, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Research Center for Food Safety, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akikazu Sakudo
- Department of Food Safety, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime 794-8555, Japan
| | - Katsuaki Sugiura
- Laboratory of Environmental Science for Sustainable Development, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Haritani
- Laboratory of Environmental Science for Sustainable Development, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koichi Furusaki
- Mineral Activation Research Institute, Kumamoto 865-0023, Japan
| | - Rikio Kirisawa
- Laboratory of Environmental Science for Sustainable Development, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Department of Pathobiology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
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7
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Skidmore AM, Bradfute SB. The life cycle of the alphaviruses: From an antiviral perspective. Antiviral Res 2023; 209:105476. [PMID: 36436722 PMCID: PMC9840710 DOI: 10.1016/j.antiviral.2022.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
The alphaviruses are a widely distributed group of positive-sense, single stranded, RNA viruses. These viruses are largely arthropod-borne and can be found on all populated continents. These viruses cause significant human disease, and recently have begun to spread into new populations, such as the expansion of Chikungunya virus into southern Europe and the Caribbean, where it has established itself as endemic. The study of alphaviruses is an active and expanding field, due to their impacts on human health, their effects on agriculture, and the threat that some pose as potential agents of biological warfare and terrorism. In this systematic review we will summarize both historic knowledge in the field as well as recently published data that has potential to shift current theories in how alphaviruses are able to function. This review is comprehensive, covering all parts of the alphaviral life cycle as well as a brief overview of their pathology and the current state of research in regards to vaccines and therapeutics for alphaviral disease.
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Affiliation(s)
- Andrew M Skidmore
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3245, Albuquerque, NM, 87131, USA.
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3330A, Albuquerque, NM, 87131, USA.
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8
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Russell T, Gangotia D, Barry G. Assessing the potential of repurposing ion channel inhibitors to treat emerging viral diseases and the role of this host factor in virus replication. Biomed Pharmacother 2022; 156:113850. [DOI: 10.1016/j.biopha.2022.113850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/25/2022] [Accepted: 10/06/2022] [Indexed: 12/03/2022] Open
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9
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Diaz O, Vidalain PO, Ramière C, Lotteau V, Perrin-Cocon L. What role for cellular metabolism in the control of hepatitis viruses? Front Immunol 2022; 13:1033314. [PMID: 36466918 PMCID: PMC9713817 DOI: 10.3389/fimmu.2022.1033314] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2023] Open
Abstract
Hepatitis B, C and D viruses (HBV, HCV, HDV, respectively) specifically infect human hepatocytes and often establish chronic viral infections of the liver, thus escaping antiviral immunity for years. Like other viruses, hepatitis viruses rely on the cellular machinery to meet their energy and metabolite requirements for replication. Although this was initially considered passive parasitism, studies have shown that hepatitis viruses actively rewire cellular metabolism through molecular interactions with specific enzymes such as glucokinase, the first rate-limiting enzyme of glycolysis. As part of research efforts in the field of immunometabolism, it has also been shown that metabolic changes induced by viruses could have a direct impact on the innate antiviral response. Conversely, detection of viral components by innate immunity receptors not only triggers the activation of the antiviral defense but also induces in-depth metabolic reprogramming that is essential to support immunological functions. Altogether, these complex triangular interactions between viral components, innate immunity and hepatocyte metabolism may explain why chronic hepatitis infections progressively lead to liver inflammation and progression to cirrhosis, fibrosis and hepatocellular carcinoma (HCC). In this manuscript, we first present a global overview of known connections between the innate antiviral response and cellular metabolism. We then report known molecular mechanisms by which hepatitis viruses interfere with cellular metabolism in hepatocytes and discuss potential consequences on the innate immune response. Finally, we present evidence that drugs targeting hepatocyte metabolism could be used as an innovative strategy not only to deprive viruses of key metabolites, but also to restore the innate antiviral response that is necessary to clear infection.
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Affiliation(s)
- Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, Team VIRal Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Team VIRal Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Christophe Ramière
- CIRI, Centre International de Recherche en Infectiologie, Team VIRal Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Team VIRal Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, Team VIRal Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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10
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Peng S, Wang H, Wang Z, Wang Q. Progression of Antiviral Agents Targeting Viral Polymerases. Molecules 2022; 27:7370. [PMID: 36364196 PMCID: PMC9654062 DOI: 10.3390/molecules27217370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/08/2023] Open
Abstract
Viral DNA and RNA polymerases are two kinds of very important enzymes that synthesize the genetic materials of the virus itself, and they have become extremely favorable targets for the development of antiviral drugs because of their relatively conserved characteristics. There are many similarities in the structure and function of different viral polymerases, so inhibitors designed for a certain viral polymerase have acted as effective universal inhibitors on other types of viruses. The present review describes the development of classical antiviral drugs targeting polymerases, summarizes a variety of viral polymerase inhibitors from the perspective of chemically synthesized drugs and natural product drugs, describes novel approaches, and proposes promising development strategies for antiviral drugs.
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11
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Xu Q, Dunbrack R. The protein common assembly database (ProtCAD)-a comprehensive structural resource of protein complexes. Nucleic Acids Res 2022; 51:D466-D478. [PMID: 36300618 PMCID: PMC9825537 DOI: 10.1093/nar/gkac937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 01/29/2023] Open
Abstract
Proteins often act through oligomeric interactions with other proteins. X-ray crystallography and cryo-electron microscopy provide detailed information on the structures of biological assemblies, defined as the most likely biologically relevant structures derived from experimental data. In crystal structures, the most relevant assembly may be ambiguously determined, since multiple assemblies observed in the crystal lattice may be plausible. It is estimated that 10-15% of PDB entries may have incorrect or ambiguous assembly annotations. Accurate assemblies are required for understanding functional data and training of deep learning methods for predicting assembly structures. As with any other kind of biological data, replication via multiple independent experiments provides important validation for the determination of biological assembly structures. Here we present the Protein Common Assembly Database (ProtCAD), which presents clusters of protein assembly structures observed in independent structure determinations of homologous proteins in the Protein Data Bank (PDB). ProtCAD is searchable by PDB entry, UniProt identifiers, or Pfam domain designations and provides downloads of coordinate files, PyMol scripts, and publicly available assembly annotations for each cluster of assemblies. About 60% of PDB entries contain assemblies in clusters of at least 2 independent experiments. All clusters and coordinates are available on ProtCAD web site (http://dunbrack2.fccc.edu/protcad).
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- To whom correspondence should be addressed. Tel: +1 215 728 2434; Fax: +1 215 728 2412;
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12
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Morenikeji OB, Adegbaju MS, Okoh OS, Babalola AE, Grytsay A, Braimah OA, Akinyemi MO, Thomas BN. Deciphering inhibitory mechanism of coronavirus replication through host miRNAs-RNA-dependent RNA polymerase interactome. Front Genet 2022; 13:973252. [PMID: 36092931 PMCID: PMC9459146 DOI: 10.3389/fgene.2022.973252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Despite what we know so far, Covid-19, caused by SARS-CoV-2 virus, remains a pandemic that still require urgent healthcare intervention. The frequent mutations of the SARS-CoV-2 virus has rendered disease control with vaccines and antiviral drugs quite challenging, with newer variants surfacing constantly. There is therefore the need for newer, effective and efficacious drugs against coronaviruses. Considering the central role of RNA dependent, RNA polymerase (RdRp) as an enzyme necessary for the virus life cycle and its conservation among coronaviruses, we investigated potential host miRNAs that can be employed as broad-range antiviral drugs averse to coronaviruses, with particular emphasis on BCoV, MERS-CoV, SARS-CoV and SARS-CoV-2. miRNAs are small molecules capable of binding mRNA and regulate expression at transcriptional or translational levels. Our hypothesis is that host miRNAs have the potential of blocking coronavirus replication through miRNA-RdRp mRNA interaction. To investigate this, we retrieved the open reading frame (ORF1ab) nucleotide sequences and used them to interrogate miRNA databases for miRNAs that can bind them. We employed various bioinformatics tools to predict and identify the most effective host miRNAs. In all, we found 27 miRNAs that target RdRp mRNA sequence of multiple coronaviruses, of which three - hsa-miR-1283, hsa-miR-579-3p, and hsa-miR-664b-3p target BCoV, SARS-CoV and SARS-CoV-2. Additionally, hsa-miR-374a-5p has three bovine miRNA homologs viz bta-miR-374a, bta-miR-374b, and bta-miR-374c. Inhibiting the expression of RdRp enzyme via non-coding RNA is novel and of great therapeutic importance in the control of coronavirus replication, and could serve as a broad-spectrum antiviral, with hsa-miR-1283, hsa-miR-579-3p, and hsa-miR-664b-3p as highly promising.
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Affiliation(s)
- Olanrewaju B. Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
- *Correspondence: Olanrewaju B. Morenikeji,
| | - Muyiwa S. Adegbaju
- Institute for Plant Biotechnology, Stellenbosch University, Stellenbosch, South Africa
| | - Olayinka S. Okoh
- Department of Chemical Sciences, Anchor University, Lagos, Nigeria
| | | | - Anastasia Grytsay
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
| | - Olubumi A. Braimah
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
| | - Mabel O. Akinyemi
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, United States
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
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13
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Inhibitors of Nucleotide Biosynthesis as Candidates for a Wide Spectrum of Antiviral Chemotherapy. Microorganisms 2022; 10:microorganisms10081631. [PMID: 36014049 PMCID: PMC9413629 DOI: 10.3390/microorganisms10081631] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Emerging and re-emerging viruses have been a challenge in public health in recent decades. Host-targeted antivirals (HTA) directed at cellular molecules or pathways involved in virus multiplication represent an interesting strategy to combat viruses presently lacking effective chemotherapy. HTA could provide a wide range of agents with inhibitory activity against current and future viruses that share similar host requirements and reduce the possible selection of antiviral-resistant variants. Nucleotide metabolism is one of the more exploited host metabolic pathways as a potential antiviral target for several human viruses. This review focuses on the antiviral properties of the inhibitors of pyrimidine and purine nucleotide biosynthesis, with an emphasis on the rate-limiting enzymes dihydroorotate dehydrogenase (DHODH) and inosine monophosphate dehydrogenase (IMPDH) for which there are old and new drugs active against a broad spectrum of pathogenic viruses.
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14
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Bergant V, Yamada S, Grass V, Tsukamoto Y, Lavacca T, Krey K, Mühlhofer MT, Wittmann S, Ensser A, Herrmann A, Vom Hemdt A, Tomita Y, Matsuyama S, Hirokawa T, Huang Y, Piras A, Jakwerth CA, Oelsner M, Thieme S, Graf A, Krebs S, Blum H, Kümmerer BM, Stukalov A, Schmidt-Weber CB, Igarashi M, Gramberg T, Pichlmair A, Kato H. Attenuation of SARS-CoV-2 replication and associated inflammation by concomitant targeting of viral and host cap 2'-O-ribose methyltransferases. EMBO J 2022; 41:e111608. [PMID: 35833542 PMCID: PMC9350232 DOI: 10.15252/embj.2022111608] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
The SARS‐CoV‐2 infection cycle is a multistage process that relies on functional interactions between the host and the pathogen. Here, we repurposed antiviral drugs against both viral and host enzymes to pharmaceutically block methylation of the viral RNA 2'‐O‐ribose cap needed for viral immune escape. We find that the host cap 2'‐O‐ribose methyltransferase MTr1 can compensate for loss of viral NSP16 methyltransferase in facilitating virus replication. Concomitant inhibition of MTr1 and NSP16 efficiently suppresses SARS‐CoV‐2 replication. Using in silico target‐based drug screening, we identify a bispecific MTr1/NSP16 inhibitor with anti‐SARS‐CoV‐2 activity in vitro and in vivo but with unfavorable side effects. We further show antiviral activity of inhibitors that target independent stages of the host SAM cycle providing the methyltransferase co‐substrate. In particular, the adenosylhomocysteinase (AHCY) inhibitor DZNep is antiviral in in vitro, in ex vivo, and in a mouse infection model and synergizes with existing COVID‐19 treatments. Moreover, DZNep exhibits a strong immunomodulatory effect curbing infection‐induced hyperinflammation and reduces lung fibrosis markers ex vivo. Thus, multispecific and metabolic MTase inhibitors constitute yet unexplored treatment options against COVID‐19.
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Affiliation(s)
- Valter Bergant
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Shintaro Yamada
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Yuta Tsukamoto
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Teresa Lavacca
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Maria-Teresa Mühlhofer
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Anja Vom Hemdt
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yuriko Tomita
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Shutoku Matsuyama
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,Division of Biomedical Science, University of Tsukuba, Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Yiqi Huang
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Antonio Piras
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Constanze A Jakwerth
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Madlen Oelsner
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Susanne Thieme
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Alexander Graf
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Stefan Krebs
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Helmut Blum
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany.,German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Alexey Stukalov
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Carsten B Schmidt-Weber
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Manabu Igarashi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
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15
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Ibba R, Riu F, Delogu I, Lupinu I, Carboni G, Loddo R, Piras S, Carta A. Benzimidazole-2-Phenyl-Carboxamides as Dual-Target Inhibitors of BVDV Entry and Replication. Viruses 2022; 14:v14061300. [PMID: 35746771 PMCID: PMC9231222 DOI: 10.3390/v14061300] [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: 03/31/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV), also known as Pestivirus A, causes severe infection mostly in cattle, but also in pigs, sheep and goats, causing huge economical losses on agricultural farms every year. The infections are actually controlled by isolation of persistently infected animals and vaccination, but no antivirals are currently available to control the spread of BVDV on farms. BVDV binds the host cell using envelope protein E2, which has only recently been targeted in the research of a potent and efficient antiviral. In contrast, RdRp has been successfully inhibited by several classes of compounds in the last few decades. As a part of an enduring antiviral research agenda, we designed a new series of derivatives that emerged from an isosteric substitution of the main scaffold in previously reported anti-BVDV compounds. Here, the new compounds were characterized and tested, where several turned out to be potent and selectively active against BVDV. The mechanism of action was thoroughly studied using a time-of-drug-addition assay and the results were validated using docking simulations.
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Affiliation(s)
- Roberta Ibba
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy; (R.I.); (F.R.); (I.L.); (A.C.)
| | - Federico Riu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy; (R.I.); (F.R.); (I.L.); (A.C.)
| | - Ilenia Delogu
- Department of Biomedical Sciences, Cittadella Universitaria Monserrato, University of Cagliari, 09042 Monserrato, Italy;
| | - Ilenia Lupinu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy; (R.I.); (F.R.); (I.L.); (A.C.)
| | - Gavino Carboni
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Roberta Loddo
- Department of Biomedical Sciences, Cittadella Universitaria Monserrato, University of Cagliari, 09042 Monserrato, Italy;
- Correspondence: (R.L.); (S.P.)
| | - Sandra Piras
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy; (R.I.); (F.R.); (I.L.); (A.C.)
- Correspondence: (R.L.); (S.P.)
| | - Antonio Carta
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy; (R.I.); (F.R.); (I.L.); (A.C.)
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16
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Chen K, Krischuns T, Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Delpal A, Courtney D, O'Brien A, Baker S, Decroly E, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. Antiviral Res 2022; 201:105272. [PMID: 35278581 PMCID: PMC8906008 DOI: 10.1016/j.antiviral.2022.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for the screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified two molecules which show anti-nsp5 activity, both in our cell-based assay and in vitro on purified nsp5 protein, and inhibit SARS-CoV-2 replication in A549-ACE2 cells with EC50 values in the 4–8 μM range. The here described high-throughput-compatible assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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17
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Favipiravir Inhibits Hepatitis A Virus Infection in Human Hepatocytes. Int J Mol Sci 2022; 23:ijms23052631. [PMID: 35269774 PMCID: PMC8910232 DOI: 10.3390/ijms23052631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis A virus (HAV) is a causative agent of acute hepatitis and can occasionally induce acute liver failure. However, specific potent anti-HAV drug is not available on the market currently. Thus, we investigated several novel therapeutic drugs through a drug repositioning approach, targeting ribonucleic acid (RNA)-dependent RNA polymerase and RNA-dependent deoxyribonucleic acid polymerase. In the present study, we examined the anti-HAV activity of 18 drugs by measuring the HAV subgenomic replicon and HAV HA11-1299 genotype IIIA replication in human hepatoma cell lines, using a reporter assay and real-time reverse transcription polymerase chain reaction, respectively. Mutagenesis of the HAV 5’ untranslated region was also examined by next-generation sequencing. These specific parameters were explored because lethal mutagenesis has emerged as a novel potential therapeutic approach to treat RNA virus infections. Favipiravir inhibited HAV replication in both Huh7 and PLC/PRF/5 cells, although ribavirin inhibited HAV replication in only Huh7 cells. Next-generation sequencing demonstrated that favipiravir could introduce nucleotide mutations into the HAV genome more than ribavirin. In conclusion, favipiravir could introduce nucleotide mutations into the HAV genome and work as an antiviral against HAV infection. Provided that further in vivo experiments confirm its efficacy, favipiravir would be useful for the treatment of severe HAV infection.
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18
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Cho WK, Ma JY. Antiviral activity of Epimedium koreanum Nakai water extract against influenza viruses. Biomed Pharmacother 2022; 146:112581. [PMID: 34965505 DOI: 10.1016/j.biopha.2021.112581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/15/2022] Open
Abstract
Epimedium koreanum Nakai (EKN) is a popular plant in Korean and Chinese medicine for treating a variety of ailments. The aqueous extract of EKN has a significant inhibitory impact on influenza A virus (IAV) infection by directly blocking viral attachment and having a virucidal effect, according to this study. Using fluorescent microscopy and fluorescence-activated cell sorting (FACS) with a green fluorescent protein (GFP)-tagged Influenza A/PR/8/34 virus, we examined the effect of EKN on viral infection. By viral infection, EKN strongly suppresses GFP expression, and at a dosage of 100 µg/mL, EKN decreased GFP expression by up to 90% of the untreated infected control. Immunofluorescence and Western blot analyses against influenza viral proteins revealed that EKN decreased influenza viral protein expression in a dose-dependent manner. EKN inhibited the H1N1 influenza virus's hemagglutinin (HA) and neuraminidase (NA), preventing viral attachment to cells. Furthermore, EKN had a virucidal impact and inhibited the cytopathic effects of H1N1, H3N2 and influenza B virus infection. Finally, our findings show that EKN has the potential to be developed as a natural viral inhibitor against influenza virus infection.
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Affiliation(s)
- Won-Kyung Cho
- KM Application Center, Korea Institute of Oriental Medicine, 70 Chemdanro, Dong-gu, Daegu 41062, Republic of Korea
| | - Jin Yeul Ma
- KM Application Center, Korea Institute of Oriental Medicine, 70 Chemdanro, Dong-gu, Daegu 41062, Republic of Korea.
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19
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Asrani P, Tiwari K, Eapen MS, McAlinden KD, Haug G, Johansen MD, Hansbro PM, Flanagan KL, Hassan MI, Sohal SS. Clinical features and mechanistic insights into drug repurposing for combating COVID-19. Int J Biochem Cell Biol 2022; 142:106114. [PMID: 34748991 PMCID: PMC8570392 DOI: 10.1016/j.biocel.2021.106114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/24/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged from Wuhan in China before it spread to the entire globe. It causes coronavirus disease of 2019 (COVID-19) where mostly individuals present mild symptoms, some remain asymptomatic and some show severe lung inflammation and pneumonia in the host through the induction of a marked inflammatory 'cytokine storm'. New and efficacious vaccines have been developed and put into clinical practice in record time, however, there is a still a need for effective treatments for those who are not vaccinated or remain susceptible to emerging SARS-CoV-2 variant strains. Despite this, effective therapeutic interventions against COVID-19 remain elusive. Here, we have reviewed potential drugs for COVID-19 classified on the basis of their mode of action. The mechanisms of action of each are discussed in detail to highlight the therapeutic targets that may help in reducing the global pandemic. The review was done up to July 2021 and the data was assessed through the official websites of WHO and CDC for collecting the information on the clinical trials. Moreover, the recent research papers were also assessed for the relevant data. The search was mainly based on keywords like Coronavirus, SARS-CoV-2, drugs (specific name of the drugs), COVID-19, clinical efficiency, safety profile, side-effects etc.This review outlines potential areas for future research into COVID-19 treatment strategies.
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Affiliation(s)
- Purva Asrani
- Department of Microbiology, University of Delhi, South Campus, New Delhi, India
| | - Keshav Tiwari
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - Mathew Suji Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | - Kielan Darcy McAlinden
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | - Greg Haug
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia; Department of Respiratory Medicine, Launceston General Hospital, Launceston 7250, Australia
| | - Matt D Johansen
- Centre for Inflammation, Centenary Institute, Sydney, NSW 2050, Australia; University of Technology Sydney, Faculty of Science, School of Life Sciences, Ultimo, NSW 2007, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW 2050, Australia; University of Technology Sydney, Faculty of Science, School of Life Sciences, Ultimo, NSW 2007, Australia
| | - Katie L Flanagan
- Clinical School, College of Health and Medicine, University of Tasmania, Launceston, Tasmania 7250, Australia; School of Health and Biomedical Science, RMIT University, Melbourne, Victoria, Australia; Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia; Tasmania Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, Tasmania 7250, Australia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sukhwinder Singh Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia.
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20
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Elfiky AA, Mahran HA, Ibrahim IM, Ibrahim MN, Elshemey WM. Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase. RSC Adv 2022; 12:2741-2750. [PMID: 35425333 PMCID: PMC8979119 DOI: 10.1039/d1ra07447d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/06/2021] [Indexed: 01/18/2023] Open
Abstract
According to the World Health Organization (WHO), SARS-CoV-2 is responsible for more than 5 M deaths and is reported in 223 countries infecting +250 M people.
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Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Hanan A. Mahran
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed N. Ibrahim
- Clinical Laboratories Department, College of Applied Medical Sciences, Jouf University, Sakakah, Kingdom of Saudi Arabia
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Wael M. Elshemey
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Physics Department, Faculty of Science, Islamic University in Madinah, KSA
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21
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IMTIAZ F, PASHA MK. A systematic review of RdRp of SARS-CoV-2 through artificial intelligence and machine learning utilizing structure-based drug design strategy. Turk J Chem 2021; 46:583-594. [PMID: 37720604 PMCID: PMC10503974 DOI: 10.55730/1300-0527.3355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 06/16/2022] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Since the coronavirus disease has been declared a global pandemic, it had posed a challenge among researchers and raised common awareness and collaborative efforts towards finding the solution. Caused by severe acute respiratory coronavirus syndrome-2 (SARS-CoV-2), coronavirus drug design strategy needs to be optimized. It is understandable that cognizance of the pathobiology of COVID-19 can help scientists in the development and discovery of therapeutically effective antiviral drugs by elucidating the unknown viral pathways and structures. Considering the role of artificial intelligence and machine learning with its advancements in the field of science, it is rational to use these methods which can aid in the discovery of new potent candidates in silico. Our review utilizes similar methodologies and focuses on RNA-dependent RNA polymerase (RdRp), based on its importance as an essential element for virus replication and also a promising target for COVID-19 therapeutics. Artificial neural network technique was used to shortlist articles with the support of PRISMA, from different research platforms including Scopus, PubMed, PubChem, and Web of Science, through a combination of keywords. "English language", from the year "2000" and "published articles in journals" were selected to carry out this research. We summarized that structural details of the RdRp reviewed in this analysis will have the potential to be taken into consideration when developing therapeutic solutions and if further multidisciplinary efforts are taken in this domain then potential clinical candidates for RdRp of SARS-CoV-2 could be successfully delivered for experimental validations.
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Affiliation(s)
- Fariha IMTIAZ
- Punjab University College of Pharmacy, University of the Punjab, Lahore,
Pakistan
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22
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Chen KY, Krischuns T, Ortega Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Courtney D, O’Brien A, Baker SC, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.18.473303. [PMID: 34981051 PMCID: PMC8722588 DOI: 10.1101/2021.12.18.473303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC 50 values in the 4-21 µM range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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Affiliation(s)
- KY Chen
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - T Krischuns
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - L Ortega Varga
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - E Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - S Paisant
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Zettor
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - J Chiaravalli
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - D Courtney
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A O’Brien
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - SC Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - C Isel
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - F Agou
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - Y Jacob
- Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Blondel
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - N Naffakh
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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23
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Dhankhar P, Dalal V, Kumar V. Screening of Severe Acute Respiratory Syndrome Coronavirus 2 RNA-Dependent RNA Polymerase Inhibitors Using Computational Approach. J Comput Biol 2021; 28:1228-1247. [PMID: 34847746 PMCID: PMC8819516 DOI: 10.1089/cmb.2020.0639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The detrimental effect of coronavirus disease 2019 (COVID-19) pandemic has manifested itself as a global crisis. Currently, no specific treatment options are available for COVID-19, so therapeutic interventions to tackle the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection must be urgently established. Therefore, cohesive and multidimensional efforts are required to identify new therapies or investigate the efficacy of small molecules and existing drugs against SARS-CoV-2. Since the RNA-dependent RNA Polymerase (RdRP) of SARS-CoV-2 is a promising therapeutic target, this study addresses the identification of antiviral molecules that can specifically target SARS-CoV-2 RdRP. The computational approach of drug development was used to screen the antiviral molecules from two antiviral libraries (Life Chemicals [LC] and ASINEX) against RdRP. Here, we report six antiviral molecules (F3407-4105, F6523-2250, F6559-0746 from LC and BDG 33693278, BDG 33693315, LAS 34156196 from ASINEX), which show substantial interactions with key amino acid residues of the active site of SARS-CoV-2 RdRP and exhibit higher binding affinity (>7.5 kcalmol-1) than Galidesivir, an Food and Drug Administration-approved inhibitor of the same. Further, molecular dynamics simulation and Molecular Mechanics Poisson-Boltzmann Surface Area results confirmed that identified molecules with RdRP formed higher stable RdRP-inhibitor(s) complex than RdRP-Galidesvir complex. Our findings suggest that these molecules could be potential inhibitors of SARS-CoV-2 RdRP. However, further in vitro and preclinical experiments would be required to validate these potential inhibitors of SARS-CoV-2 protein.
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Affiliation(s)
- Poonam Dhankhar
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Viney Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
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24
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Arwansyah A, Arif AR, Ramli I, Kurniawan I, Sukarti S, Nur Alam M, Illing I, Farid Lewa A, Manguntungi B. Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:699-718. [PMID: 34392751 DOI: 10.1080/1062936x.2021.1960601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
SARS-CoV-2 PLpro was investigated as a therapeutic target for potent antiviral drugs due to its essential role in not only viral replication but also in regulating the inborn immune response. Several computational approaches, including homology modelling, molecular docking, and molecular dynamics (MD) studies, were employed to search for promising drugs in treating SARS-CoV-2. Eighty-one compounds, sub-structurally similar to the antiviral drug, were used as potential inhibitors of PLpro. From our results, three complexes containing the ligands with Pubchem IDs: 153012995, 12149203, and 123608715 showed lower binding energies than the control (Ritonavir), indicating that they may become promising inhibitors for PLpro. MD was performed in a water solvent to validate the stability of the three complexes. All complexes achieved stable structure during the simulation as no significant fluctuations were observed in the validation parameters. Moreover, the binding energy for each complex was estimated using the MM-GBSA method. Complex 1 was the most stable structure based on the lowest binding energy score and its structure remained in a similar cavity with the docket snapshot. Based on our studies, three ligands were assumed to be potential inhibitors. The ligand of complex 1 may become the most promising antiviral drug against SARS-CoV-2 targeting PLpro.
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Affiliation(s)
- A Arwansyah
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A R Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - I Ramli
- Department of Physics, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Kurniawan
- School of Computing, Telkom University, Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University, Bandung, Indonesia
| | - S Sukarti
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - M Nur Alam
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Illing
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A Farid Lewa
- Department of Nutrition, Poltekkes Kemenkes Palu, Palu, Indonesia
| | - B Manguntungi
- Department of Biotechnology, Faculty of Biotechnology, Sumbawa University of Technology, Sumbawa, Indonesia
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25
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Kataev VE, Garifullin BF. Antiviral nucleoside analogs. Chem Heterocycl Compd (N Y) 2021; 57:326-341. [PMID: 34007086 PMCID: PMC8118684 DOI: 10.1007/s10593-021-02912-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
The minireview surveys the modification of native nucleosides as a result of which huge libraries of nucleoside analogs of various structures were synthesized. Particular attention is paid to the synthesis of the so-called prodrug forms of nucleoside analogs which ensure their penetration into the cell and metabolism to active 5'-triphosphate derivatives. All the best known antiviral cyclic nucleoside analogs approved for the treatment of HIV infections, hepatitis B, C, and influenza since the 1960s, as well as those in various stages of clinical trials in recent years, are listed. Nucleoside analogs that have shown the ability to inhibit the replication of SARS-CoV and MERS-CoV are discussed, including remdesivir, approved by the FDA for emergency use in the fight against COVID-19.
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Affiliation(s)
- Vladimir E. Kataev
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Akademika Arbuzova St., Kazan, 420088 Tatarstan Russia
| | - Bulat F. Garifullin
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Akademika Arbuzova St., Kazan, 420088 Tatarstan Russia
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26
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Xu J, Xue Y, Zhou R, Shi PY, Li H, Zhou J. Drug repurposing approach to combating coronavirus: Potential drugs and drug targets. Med Res Rev 2021; 41:1375-1426. [PMID: 33277927 PMCID: PMC8044022 DOI: 10.1002/med.21763] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/03/2020] [Accepted: 11/20/2020] [Indexed: 01/18/2023]
Abstract
In the past two decades, three highly pathogenic human coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus, and, recently, SARS-CoV-2, have caused pandemics of severe acute respiratory diseases with alarming morbidity and mortality. Due to the lack of specific anti-CoV therapies, the ongoing pandemic of coronavirus disease 2019 (COVID-19) poses a great challenge to clinical management and highlights an urgent need for effective interventions. Drug repurposing is a rapid and feasible strategy to identify effective drugs for combating this deadly infection. In this review, we summarize the therapeutic CoV targets, focus on the existing small molecule drugs that have the potential to be repurposed for existing and emerging CoV infections of the future, and discuss the clinical progress of developing small molecule drugs for COVID-19.
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Affiliation(s)
- Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yu Xue
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Richard Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
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27
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Maddipati VC, Mittal L, Mantipally M, Asthana S, Bhattacharyya S, Gundla R. A Review on the Progress and Prospects of Dengue Drug Discovery Targeting NS5 RNA- Dependent RNA Polymerase. Curr Pharm Des 2021; 26:4386-4409. [PMID: 32445444 DOI: 10.2174/1381612826666200523174753] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023]
Abstract
Dengue virus (DENV) infection threatens the health and wellbeing of almost 100 million people in the world. Vectored by mosquitoes, DENV may cause a severe disease in human hosts called Dengue hemorrhagic fever (DHF)/Dengue shock syndrome (DSS), which is not preventable by any known drug. In the absence of a universally-accepted vaccine, a drug capable of inhibiting DENV multiplication is an urgent and unmet clinical need. Here we summarize inhibitory strategies by targeting either host biochemical pathways or virus-encoded proteins. A variety of approaches have been generated to design Directly-acting anti-virals or DAAs targeting different DENV proteins, with diverse success. Among them, DAAs targeting genome replicating viral enzymes have proven effective against many viruses including, Human Immuno-deficiency Virus and Hepatitis C Virus. DAAs may be derived either from existing compound libraries of novel molecules and plant secondary metabolites or devised through Computer-aided Drug design (CADD) methods. Here, we focus on compounds with reported DAA-activity against the DENV RNA-dependent RNA polymerase (RdRp), which replicate the viral RNA genome. The structure-activity relationship (SAR) and toxicity of the natural compounds, including secondary plant metabolites, have been discussed in detail. We have also tabulated novel compounds with known anti-RdRp activity. We concluded with a list of DAAs for which a co-crystal structure with RdRp is reported. Promising hit compounds are often discarded due to poor selectivity or unsuitable pharmacokinetics. We hope this review will provide a useful reference for further studies on the development of an anti-DENV drug.
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Affiliation(s)
- Venkatanarayana C Maddipati
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Manohar Mantipally
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
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28
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Abstract
Wolbachia is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The Wolbachia strain colonizing Drosophila melanogaster creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using Wolbachia-transfected mosquitoes for dengue control, knowledge of how Wolbachia and viruses jointly affect insect biology remains limited. Using the Drosophila melanogaster model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to Wolbachia colonization and virus infection. Included are metabolic pathways previously unknown to be important for Wolbachia-host interactions. Additionally, Wolbachia-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using Drosophila genetics, we show that Wolbachia and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of Wolbachia-mediated vector control programs.IMPORTANCE Recently developed arbovirus control strategies leverage the symbiotic bacterium Wolbachia, which spreads in insect populations and blocks viruses from replicating. While this strategy has been successful, details of how this "pathogen blocking" works are limited. Here, we use a combination of virus infections, fly genetics, and transcriptomics to show that Wolbachia and virus interact at host nucleotide metabolism pathways.
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29
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Nguyen S, Truong JQ, Bruning JB. Targeting Unconventional Pathways in Pursuit of Novel Antifungals. Front Mol Biosci 2021; 7:621366. [PMID: 33511160 PMCID: PMC7835888 DOI: 10.3389/fmolb.2020.621366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 01/31/2023] Open
Abstract
The impact of invasive fungal infections on human health is a serious, but largely overlooked, public health issue. Commonly affecting the immunocompromised community, fungal infections are predominantly caused by species of Candida, Cryptococcus, and Aspergillus. Treatments are reliant on the aggressive use of pre-existing antifungal drug classes that target the fungal cell wall and membrane. Despite their frequent use, these drugs are subject to unfavorable drug-drug interactions, can cause undesirable side-effects and have compromised efficacy due to the emergence of antifungal resistance. Hence, there is a clear need to develop novel classes of antifungal drugs. A promising approach involves exploiting the metabolic needs of fungi by targeted interruption of essential metabolic pathways. This review highlights potential antifungal targets including enolase, a component of the enolase-plasminogen complex, and enzymes from the mannitol biosynthesis and purine nucleotide biosynthesis pathways. There has been increased interest in the enzymes that comprise these particular pathways and further investigation into their merits as antifungal targets and roles in fungal survival and virulence are warranted. Disruption of these vital processes by targeting unconventional pathways with small molecules or antibodies may serve as a promising approach to discovering novel classes of antifungals.
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jia Q Truong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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30
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Laha JK, Singh N, Hunjan MK. Synthesis of unsymmetrical urea from aryl- or pyridyl carboxamides and aminopyridines using PhI(OAc) 2via in situ formation of aryl- or pyridyl isocyanates. NEW J CHEM 2021. [DOI: 10.1039/d1nj03160k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of unsymmetrical ureas (N-aryl-N′-pyridylurea and N,N′-bipyridylurea) from aryl- or pyridyl carboxamides and aminopyridines in the presence of PhI(OAc)2 has been reported. The formation of pyridylisocyanates from their corresponding carboxamides via Hofmann rearrangement is confirmed.
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Affiliation(s)
- Joydev K. Laha
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Punjab 160062, India
| | - Neha Singh
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Punjab 160062, India
| | - Mandeep Kaur Hunjan
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Punjab 160062, India
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31
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Xiao Y, Xu H, Guo W, Zhao Y, Luo Y, Wang M, He Z, Ding Z, Liu J, Deng L, Sha F, Ma X. Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines. MOLECULAR BIOMEDICINE 2020; 1:16. [PMID: 34765999 PMCID: PMC7711057 DOI: 10.1186/s43556-020-00017-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) triggered by the new member of the coronaviridae family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented challenge for global health. In addition to mild to moderate clinical manifestations such as fever, cough, and fatigue, severe cases often developed lethal complications including acute respiratory distress syndrome (ARDS) and acute lung injury. Given the alarming rate of infection and increasing trend of mortality, the development of underlying therapeutic and preventive treatment, as well as the verification of its effectiveness, are the top priorities. Current research mainly referred to and evaluated the application of the empirical treatment based on two precedents, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), including antiviral drugs targeting different stages of virus replication, immunotherapy modulating the overactivated inflammation response, and other therapies such as herbal medicine and mesenchymal stem cells. Besides, the ongoing development of inventing prophylactic interventions such as various vaccines by companies and institutions worldwide is crucial to decline morbidity and mortality. This review mainly focused on promising candidates for the treatment of COVID-19 and collected recently updated evidence relevant to its feasibility in clinical practice in the near future.
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Affiliation(s)
- Yinan Xiao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Hanyue Xu
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Wen Guo
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yunuo Zhao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yuling Luo
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Ming Wang
- Infectious Diseases Center, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Zhiyao He
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Zhenyu Ding
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Jiyan Liu
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Lei Deng
- Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, New York, 10465 USA
| | - Fushen Sha
- Department of Internal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York, 11203 USA
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
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32
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Kongmanas K, Punyadee N, Wasuworawong K, Songjaeng A, Prommool T, Pewkliang Y, Manocheewa S, Thiemmeca S, Sa-ngiamsuntorn K, Puttikhunt C, Faull KF, Hongeng S, Avirutnan P. Immortalized stem cell-derived hepatocyte-like cells: An alternative model for studying dengue pathogenesis and therapy. PLoS Negl Trop Dis 2020; 14:e0008835. [PMID: 33216752 PMCID: PMC7717553 DOI: 10.1371/journal.pntd.0008835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 12/04/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Suitable cell models are essential to advance our understanding of the pathogenesis of liver diseases and the development of therapeutic strategies. Primary human hepatocytes (PHHs), the most ideal hepatic model, are commercially available, but they are expensive and vary from lot-to-lot which confounds their utility. We have recently developed an immortalized hepatocyte-like cell line (imHC) from human mesenchymal stem cells, and tested it for use as a substitute model for hepatotropic infectious diseases. With a special interest in liver pathogenesis of viral infection, herein we determined the suitability of imHC as a host cell target for dengue virus (DENV) and as a model for anti-viral drug testing. We characterized the kinetics of DENV production, cellular responses to DENV infection (apoptosis, cytokine production and lipid droplet metabolism), and examined anti-viral drug effects in imHC cells with comparisons to the commonly used hepatoma cell lines (HepG2 and Huh-7) and PHHs. Our results showed that imHC cells had higher efficiencies in DENV replication and NS1 secretion as compared to HepG2 and Huh-7 cells. The kinetics of DENV infection in imHC cells showed a slower rate of apoptosis than the hepatoma cell lines and a certain similarity of cytokine profiles to PHHs. In imHC, DENV-induced alterations in levels of lipid droplets and triacylglycerols, a major component of lipid droplets, were more apparent than in hepatoma cell lines, suggesting active lipid metabolism in imHC. Significantly, responses to drugs with DENV inhibitory effects were greater in imHC cells than in HepG2 and Huh-7 cells. In conclusion, our findings suggest superior suitability of imHC as a new hepatocyte model for studying mechanisms underlying viral pathogenesis, liver diseases and drug effects. A model system resembling normal human liver cells is needed for advancement of hepatotropic infectious disease research. Here we show that immortalized cells (imHC) derived from human stem cells have a higher efficiency of DENV replication and a lower rate of cell death in response to DENV infection than the cancer cell-derived model systems currently used. The imHC also have active fat metabolism and respond well to anti-viral drug treatment, making them an attractive model for the initial stage of drug discovery and testing.
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Affiliation(s)
- Kessiri Kongmanas
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nuntaya Punyadee
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kasima Wasuworawong
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Adisak Songjaeng
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tanapan Prommool
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
| | - Yongyut Pewkliang
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Siriphan Manocheewa
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Somchai Thiemmeca
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Chunya Puttikhunt
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
| | - Kym Francis Faull
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, California, United States of America
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Panisadee Avirutnan
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
- * E-mail:
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Mohapatra S, Nath P, Chatterjee M, Das N, Kalita D, Roy P, Satapathi S. Repurposing therapeutics for COVID-19: Rapid prediction of commercially available drugs through machine learning and docking. PLoS One 2020; 15:e0241543. [PMID: 33180803 PMCID: PMC7660547 DOI: 10.1371/journal.pone.0241543] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/16/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The outbreak of the novel coronavirus disease COVID-19, caused by the SARS-CoV-2 virus has spread rapidly around the globe during the past 3 months. As the virus infected cases and mortality rate of this disease is increasing exponentially, scientists and researchers all over the world are relentlessly working to understand this new virus along with possible treatment regimens by discovering active therapeutic agents and vaccines. So, there is an urgent requirement of new and effective medications that can treat the disease caused by SARS-CoV-2. METHODS AND FINDINGS We perform the study of drugs that are already available in the market and being used for other diseases to accelerate clinical recovery, in other words repurposing of existing drugs. The vast complexity in drug design and protocols regarding clinical trials often prohibit developing various new drug combinations for this epidemic disease in a limited time. Recently, remarkable improvements in computational power coupled with advancements in Machine Learning (ML) technology have been utilized to revolutionize the drug development process. Consequently, a detailed study using ML for the repurposing of therapeutic agents is urgently required. Here, we report the ML model based on the Naive Bayes algorithm, which has an accuracy of around 73% to predict the drugs that could be used for the treatment of COVID-19. Our study predicts around ten FDA approved commercial drugs that can be used for repurposing. Among all, we found that 3 of the drugs fulfils the criterions well among which the antiretroviral drug Amprenavir (DrugBank ID-DB00701) would probably be the most effective drug based on the selected criterions. CONCLUSIONS Our study can help clinical scientists in being more selective in identifying and testing the therapeutic agents for COVID-19 treatment. The ML based approach for drug discovery as reported here can be a futuristic smart drug designing strategy for community applications.
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Affiliation(s)
- Sovesh Mohapatra
- Department of Physics, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, India
| | - Prathul Nath
- Department of Physics, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, India
| | - Manisha Chatterjee
- Department of Pharmacology, Subharti Medical College, Meerut, Uttar Pradesh, India
| | - Neeladrisingha Das
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Deepjyoti Kalita
- Department of Microbiology, All India Institute of Medical Science, Rishikesh, Uttarakhand, India
| | - Partha Roy
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Soumitra Satapathi
- Department of Physics, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, India
- Centre of Nanotechnology, Indian Institute of Technology, Roorkee, Haridwar, Uttarakhand, India
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Felicetti T, Manfroni G, Cecchetti V, Cannalire R. Broad-Spectrum Flavivirus Inhibitors: a Medicinal Chemistry Point of View. ChemMedChem 2020; 15:2391-2419. [PMID: 32961008 DOI: 10.1002/cmdc.202000464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Infections by flaviviruses, such as Dengue, West Nile, Yellow Fever and Zika viruses, represent a growing risk for global health. There are vaccines only for few flaviviruses while no effective treatments are available. Flaviviruses share epidemiological, structural, and ecologic features and often different viruses can co-infect the same host. Therefore, the identification of broad-spectrum inhibitors is highly desirable either for known flaviviruses or for viruses that likely will emerge in the future. Strategies targeting both virus and host factors have been pursued to identify broad-spectrum antiflaviviral agents. In this review, we describe the most promising and best characterized targets and their relative broad-spectrum inhibitors, identified by drug repurposing/libraries screenings and by focused medicinal chemistry campaigns. Finally, we discuss about future strategies to identify new broad-spectrum antiflavivirus agents.
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Affiliation(s)
- Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy
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Chitalia VC, Munawar AH. A painful lesson from the COVID-19 pandemic: the need for broad-spectrum, host-directed antivirals. J Transl Med 2020; 18:390. [PMID: 33059719 PMCID: PMC7558548 DOI: 10.1186/s12967-020-02476-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/02/2020] [Indexed: 02/06/2023] Open
Abstract
While the COVID-19 pandemic has spurred intense research and collaborative discovery worldwide, the development of a safe, effective, and targeted antiviral from the ground up is time intensive. Therefore, most antiviral discovery efforts are focused on the re-purposing of clinical stage or approved drugs. While emerging data on drugs undergoing COVID-19 repurpose are intriguing, there is an undeniable need to develop broad-spectrum antivirals to prevent future viral pandemics of unknown origin. The ideal drug to curtail rapid viral spread would be a broad-acting agent with activity against a wide range of viruses. Such a drug would work by modulating host-proteins that are often shared by multiple virus families thereby enabling preemptive drug development and therefore rapid deployment at the onset of an outbreak. Targeting host-pathways and cellular proteins that are hijacked by viruses can potentially offer broad-spectrum targets for the development of future antiviral drugs. Such host-directed antivirals are also likely to offer a higher barrier to the development and selection of drug resistant mutations. Given that most approved antivirals do not target host-proteins, we reinforce the need for the development of such antivirals that can be used in pre- and post-exposure populations.
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Affiliation(s)
- Vipul C Chitalia
- Boston University Medical Center, 625 Albany Street, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ali H Munawar
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.
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Mutations on VEEV nsP1 relate RNA capping efficiency to ribavirin susceptibility. Antiviral Res 2020; 182:104883. [PMID: 32750467 DOI: 10.1016/j.antiviral.2020.104883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 11/22/2022]
Abstract
Alphaviruses are arthropod-borne viruses of public health concern. To date no efficient vaccine nor antivirals are available for safe human use. During viral replication the nonstructural protein 1 (nsP1) catalyzes capping of genomic and subgenomic RNAs. The capping reaction is unique to the Alphavirus genus. The whole three-step process follows a particular order: (i) transfer of a methyl group from S-adenosyl methionine (SAM) onto a GTP forming m7GTP; (ii) guanylylation of the enzyme to form a m7GMP-nsP1adduct; (iii) transfer of m7GMP onto 5'-diphosphate RNA to yield capped RNA. Specificities of these reactions designate nsP1 as a promising target for antiviral drug development. In the current study we performed a mutational analysis on two nsP1 positions associated with Sindbis virus (SINV) ribavirin resistance in the Venezuelan equine encephalitis virus (VEEV) context through reverse genetics correlated to enzyme assays using purified recombinant VEEV nsP1 proteins. The results demonstrate that the targeted positions are strongly associated to the regulation of the capping reaction by increasing the affinity between GTP and nsP1. Data also show that in VEEV the S21A substitution, naturally occurring in Chikungunya virus (CHIKV), is a hallmark of ribavirin susceptibility. These findings uncover the specific mechanistic contributions of these residues to nsp1-mediated methyl-transfer and guanylylation reactions.
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Barati F, Pouresmaieli M, Ekrami E, Asghari S, Ziarani FR, Mamoudifard M. Potential Drugs and Remedies for the Treatment of COVID-19: a Critical Review. Biol Proced Online 2020; 22:15. [PMID: 32754003 PMCID: PMC7377207 DOI: 10.1186/s12575-020-00129-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
ABSTRACT COVID-19 disease with a high rate of contagious and highly nonspecific symptoms, is an infectious disease caused by a newly discovered coronavirus. Most people who fall sick with COVID-19 will experience mild to moderate symptoms such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia and recover without any special cure. However, some others need special and emergency treatment to get rid of this widespread disease. Till now, there are numbers of proposed novel compounds as well as standards therapeutics agent existed for other conditions seems to have efficacy against the 2019-nCoV. Some which are being tested for MERS-CoV and SARS-CoV are validated that could be also efficient against this new coronavirus. However, there are currently no effective specific antivirals or drug combinations introduced for 2019-nCoV specifically that be supported by high-level evidence. The main purpose of this paper is to review typical and ongoing treatments for coronavirus disease including home remedies, herbal medicine, chemical drugs, plasma therapy, and also vaccinies. In this regards, famous herbal medicines and common chemical drugs which are routinely to be prescribed for patients are introduced. Moreover, a section is assigned to the drug interactions and some outdated drugs which have been proved to be inefficient. We hope that this work could pave the way for researchers to develop faster and more reliable methods for earlier treatment of patients and rescue more people. GRAPHICAL ABSTRACT
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Affiliation(s)
- Fatemeh Barati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahdi Pouresmaieli
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Elena Ekrami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sahar Asghari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Farzad Ramezani Ziarani
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Matin Mamoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Vellingiri B, Jayaramayya K, Iyer M, Narayanasamy A, Govindasamy V, Giridharan B, Ganesan S, Venugopal A, Venkatesan D, Ganesan H, Rajagopalan K, Rahman PKSM, Cho SG, Kumar NS, Subramaniam MD. COVID-19: A promising cure for the global panic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138277. [PMID: 32278175 PMCID: PMC7128376 DOI: 10.1016/j.scitotenv.2020.138277] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 04/13/2023]
Abstract
The novel Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, which is the causative agent of a potentially fatal disease that is of great global public health concern. The outbreak of COVID-19 is wreaking havoc worldwide due to inadequate risk assessment regarding the urgency of the situation. The COVID-19 pandemic has entered a dangerous new phase. When compared with SARS and MERS, COVID-19 has spread more rapidly, due to increased globalization and adaptation of the virus in every environment. Slowing the spread of the COVID-19 cases will significantly reduce the strain on the healthcare system of the country by limiting the number of people who are severely sick by COVID-19 and need hospital care. Hence, the recent outburst of COVID-19 highlights an urgent need for therapeutics targeting SARS-CoV-2. Here, we have discussed the structure of virus; varying symptoms among COVID-19, SARS, MERS and common flu; the probable mechanism behind the infection and its immune response. Further, the current treatment options, drugs available, ongoing trials and recent diagnostics for COVID-19 have been discussed. We suggest traditional Indian medicinal plants as possible novel therapeutic approaches, exclusively targeting SARS-CoV-2 and its pathways.
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Affiliation(s)
- Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India.
| | - Kaavya Jayaramayya
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641 043, Tamil Nadu, India
| | - Mahalaxmi Iyer
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641 043, Tamil Nadu, India
| | - Arul Narayanasamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | | | - Bupesh Giridharan
- Virology Laboratory, Central Research and Development Wing, Sree Balaji Medical College and Hospital (SBMCH), Bharath University, (BIHER), Chromepet, Chennai 600044, Tamil Nadu, India; Department of Forest Science, Central University of Nagaland, Lumami, Zunhebeto, India
| | | | - Anila Venugopal
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Dhivya Venkatesan
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Harsha Ganesan
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Kamarajan Rajagopalan
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Pattanathu K S M Rahman
- Deploy Lead - Centre for Enzyme Innovation, Office No: 6.06, King Henry Building School of Biological Science, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Nachimuthu Senthil Kumar
- Department of Biotechnology, Mizoram University (A Central University), Aizawl 796 004, Mizoram, India
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai 600 006, India
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Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, Ahmad A, Munawar N. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med 2020; 18:275. [PMID: 32635935 PMCID: PMC7339606 DOI: 10.1186/s12967-020-02439-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/25/2020] [Indexed: 02/13/2023] Open
Abstract
Background The Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) outbreak originating in Wuhan, China, has raised global health concerns and the pandemic has now been reported on all inhabited continents. Hitherto, no antiviral drug is available to combat this viral outbreak. Methods Keeping in mind the urgency of the situation, the current study was designed to devise new strategies for drug discovery and/or repositioning against SARS-CoV-2. In the current study, RNA-dependent RNA polymerase (RdRp), which regulates viral replication, is proposed as a potential therapeutic target to inhibit viral infection. Results Evolutionary studies of whole-genome sequences of SARS-CoV-2 represent high similarity (> 90%) with other SARS viruses. Targeting the RdRp active sites, ASP760 and ASP761, by antiviral drugs could be a potential therapeutic option for inhibition of coronavirus RdRp, and thus viral replication. Target-based virtual screening and molecular docking results show that the antiviral Galidesivir and its structurally similar compounds have shown promise against SARS-CoV-2. Conclusions The anti-polymerase drugs predicted here—CID123624208 and CID11687749—may be considered for in vitro and in vivo clinical trials.
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Affiliation(s)
- Syed Ovais Aftab
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan.,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zubair Ghouri
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan. .,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Umer Masood
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zeshan Haider
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan. .,Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nayla Munawar
- Department of Chemistry, United Arab Emirates University, Al-Ain, UAE
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40
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Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, Ahmad A, Munawar N. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med 2020. [DOI: https://doi.org/10.1186/s12967-020-02439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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41
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Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, Ahmad A, Munawar N. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med 2020. [PMID: 32635935 DOI: 10.1186/s12967-020-02439-0/figures/9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND The Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) outbreak originating in Wuhan, China, has raised global health concerns and the pandemic has now been reported on all inhabited continents. Hitherto, no antiviral drug is available to combat this viral outbreak. METHODS Keeping in mind the urgency of the situation, the current study was designed to devise new strategies for drug discovery and/or repositioning against SARS-CoV-2. In the current study, RNA-dependent RNA polymerase (RdRp), which regulates viral replication, is proposed as a potential therapeutic target to inhibit viral infection. RESULTS Evolutionary studies of whole-genome sequences of SARS-CoV-2 represent high similarity (> 90%) with other SARS viruses. Targeting the RdRp active sites, ASP760 and ASP761, by antiviral drugs could be a potential therapeutic option for inhibition of coronavirus RdRp, and thus viral replication. Target-based virtual screening and molecular docking results show that the antiviral Galidesivir and its structurally similar compounds have shown promise against SARS-CoV-2. CONCLUSIONS The anti-polymerase drugs predicted here-CID123624208 and CID11687749-may be considered for in vitro and in vivo clinical trials.
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Affiliation(s)
- Syed Ovais Aftab
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zubair Ghouri
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan.
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Umer Masood
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zeshan Haider
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nayla Munawar
- Department of Chemistry, United Arab Emirates University, Al-Ain, UAE
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Abstract
Antiviral drugs have traditionally been developed by directly targeting essential viral components. However, this strategy often fails due to the rapid generation of drug-resistant viruses. Recent genome-wide approaches, such as those employing small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeats (CRISPR) or those using small molecule chemical inhibitors targeting the cellular "kinome," have been used successfully to identify cellular factors that can support virus replication. Since some of these cellular factors are critical for virus replication, but are dispensable for the host, they can serve as novel targets for antiviral drug development. In addition, potentiation of immune responses, regulation of cytokine storms, and modulation of epigenetic changes upon virus infections are also feasible approaches to control infections. Because it is less likely that viruses will mutate to replace missing cellular functions, the chance of generating drug-resistant mutants with host-targeted inhibitor approaches is minimized. However, drug resistance against some host-directed agents can, in fact, occur under certain circumstances, such as long-term selection pressure of a host-directed antiviral agent that can allow the virus the opportunity to adapt to use an alternate host factor or to alter its affinity toward the target that confers resistance. This review describes novel approaches for antiviral drug development with a focus on host-directed therapies and the potential mechanisms that may account for the acquisition of antiviral drug resistance against host-directed agents.
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Yousefi B, Valizadeh S, Ghaffari H, Vahedi A, Karbalaei M, Eslami M. A global treatments for coronaviruses including COVID-19. J Cell Physiol 2020; 235:9133-9142. [PMID: 32394467 PMCID: PMC7273044 DOI: 10.1002/jcp.29785] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023]
Abstract
In late December 2019 in Wuhan, China, several patients with viral pneumonia were identified as 2019 novel coronavirus (2019‐nCoV). So far, there are no specific treatments for patients with coronavirus disease‐19 (COVID‐19), and the treatments available today are based on previous experience with similar viruses such as severe acute respiratory syndrome‐related coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), and Influenza virus. In this article, we have tried to reach a therapeutic window of drugs available to patients with COVID‐19. Cathepsin L is required for entry of the 2019‐nCoV virus into the cell as target teicoplanin inhibits virus replication. Angiotensin‐converting‐enzyme 2 (ACE2) in soluble form as a recombinant protein can prevent the spread of coronavirus by restricting binding and entry. In patients with COVID‐19, hydroxychloroquine decreases the inflammatory response and cytokine storm, but overdose causes toxicity and mortality. Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Ribavirin reduces hemoglobin concentrations in respiratory patients, and remdesivir improves respiratory symptoms. Use of ribavirin in combination with LPV/r in patients with SARS‐CoV reduces acute respiratory distress syndrome and mortality, which has a significant protective effect with the addition of corticosteroids. Favipiravir increases clinical recovery and reduces respiratory problems and has a stronger antiviral effect than LPV/r. currently, appropriate treatment for patients with COVID‐19 is an ACE2 inhibitor and a clinical problem reducing agent such as favipiravir in addition to hydroxychloroquine and corticosteroids.
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Affiliation(s)
- Bahman Yousefi
- Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Saeid Valizadeh
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Hadi Ghaffari
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Azadeh Vahedi
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Majid Eslami
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran.,Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 67 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Huettenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Jose Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Phillip P Sharp
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin A Cavero
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Oren S Rosenberg
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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Wei Y, Wang H, Xi C, Li N, Li D, Yao C, Sun G, Ge H, Hu K, Zhang Q. Antiviral Effects of Novel 2-Benzoxyl-Phenylpyridine Derivatives. Molecules 2020; 25:E1409. [PMID: 32204528 PMCID: PMC7144376 DOI: 10.3390/molecules25061409] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/06/2020] [Indexed: 01/19/2023] Open
Abstract
Coxsackievirus B3 (CVB3) is the most common cause of acute and chronic viral myocarditis, primarily in children, while human adenovirus infections represent a significant cause of morbidity and mortality worldwide, in people of all ages. A series of novel 2-benzoxyl-phenylpyridine derivatives were evaluated for their potential antiviral activities against CVB3 and adenovirus type 7 (ADV7). Preliminary assays indicated that some of these compounds exhibited excellent antiviral effects on both CVB3 and ADV7 viruses; they could effectively inhibit virus-induced cytopathic effects, reduce viral progeny yields, and had similar or superior antiviral activities compared with the control drug, ribavirin. Further, these compounds targeted the early stages of CVB3 replication in cells, including viral RNA replication and protein synthesis, rather than inactivating the virus directly, inhibiting virus adsorption/entry, or affecting viral release from cells. Our data demonstrate that the tested 2-benzoxyl-phenylpyridine derivatives are effective inhibitors of CVB3 and ADV7, raising the possibility that these compounds might be feasible candidates for anti-viral agents.
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Affiliation(s)
- Yanhong Wei
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Haijie Wang
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Caili Xi
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Ni Li
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Dong Li
- School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Chenguang Yao
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Ge Sun
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Hongmei Ge
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Kanghong Hu
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Sino-German Biomedical Center, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (Y.W.); (H.W.); (C.X.); (N.L.); (C.Y.); (G.S.); (H.G.)
| | - Qian Zhang
- School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China;
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Identification and Characterization of Novel Compounds with Broad-Spectrum Antiviral Activity against Influenza A and B Viruses. J Virol 2020; 94:JVI.02149-19. [PMID: 31941776 DOI: 10.1128/jvi.02149-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022] Open
Abstract
Influenza A (IAV) and influenza B (IBV) viruses are highly contagious pathogens that cause fatal respiratory disease every year, with high economic impact. In addition, IAV can cause pandemic infections with great consequences when new viruses are introduced into humans. In this study, we evaluated 10 previously described compounds with antiviral activity against mammarenaviruses for their ability to inhibit IAV infection using our recently described bireporter influenza A/Puerto Rico/8/34 (PR8) H1N1 (BIRFLU). Among the 10 tested compounds, eight (antimycin A [AmA], brequinar [BRQ], 6-azauridine, azaribine, pyrazofurin [PF], AVN-944, mycophenolate mofetil [MMF], and mycophenolic acid [MPA]), but not obatoclax or Osu-03012, showed potent anti-influenza virus activity under posttreatment conditions [median 50% effective concentration (EC50) = 3.80 nM to 1.73 μM; selective index SI for 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, >28.90 to 13,157.89]. AmA, 6-azauridine, azaribine, and PF also showed potent inhibitory effect in pretreatment (EC50 = 0.14 μM to 0.55 μM; SI-MTT = 70.12 to >357.14) or cotreatment (EC50 = 34.69 nM to 7.52 μM; SI-MTT = 5.24 to > 1,441.33) settings. All of the compounds tested inhibited viral genome replication and gene transcription, and none of them affected host cellular RNA polymerase II activities. The antiviral activity of the eight identified compounds against BIRFLU was further confirmed with seasonal IAVs (A/California/04/2009 H1N1 and A/Wyoming/3/2003 H3N2) and an IBV (B/Brisbane/60/2008, Victoria lineage), demonstrating their broad-spectrum prophylactic and therapeutic activity against currently circulating influenza viruses in humans. Together, our results identified a new set of antiviral compounds for the potential treatment of influenza viral infections.IMPORTANCE Influenza viruses are highly contagious pathogens and are a major threat to human health. Vaccination remains the most effective tool to protect humans against influenza infection. However, vaccination does not always guarantee complete protection against drifted or, more noticeably, shifted influenza viruses. Although U.S. Food and Drug Administration (FDA) drugs are approved for the treatment of influenza infections, influenza viruses resistant to current FDA antivirals have been reported and continue to emerge. Therefore, there is an urgent need to find novel antivirals for the treatment of influenza viral infections in humans, a search that could be expedited by repurposing currently approved drugs. In this study, we assessed the influenza antiviral activity of 10 compounds previously shown to inhibit mammarenavirus infection. Among them, eight drugs showed antiviral activities, providing a new battery of drugs that could be used for the treatment of influenza infections.
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Prutkov AN, Chudinov MV, Matveev AV, Grebenkina LE, Akimov MG, Berezovskaya YV. 5-alkylvinyl-1,2,4-triazole nucleosides: Synthesis and biological evaluation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:943-963. [PMID: 32126895 DOI: 10.1080/15257770.2020.1723624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Some 5-substituted ribavirin analogues have a high antiviral and anticancer activity, but their mechanisms of action are obviously not the same as their parent compound. The SAR studies performed on 3 (5)-substituted 1,2,4-triazole nucleosides have shown a high dependency between the structure of the 3 (5)-substituent and the level of antiviral/anticancer activity. The most active substances of the row contain coplanar with the 1,2,4-triazole ring aromatic substituent which is connected by a rigid ethynyl bond. However, the compounds with the trans-vinyl linker also had antiviral activity. We decided to study the antitumor activity of ribavirin analogues with alkyl/aryl vinyl substituents in the 5th position of the 1,2,4-triazole ring. Protected nucleoside analogues with various 5-alkylvinyl substituents were obtained by Horner-Wadsworth-Emmons reaction from the common precursor and converted to the nucleosides. Arylvinyl nucleosides were synthesised according the reported procedures. All compounds did not show significant antiproliferative activity on several tumour cell lines. Coplanar aromatic motif in the 5-substituent for the anticancer activity manifestation was confirmed.
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Affiliation(s)
- Alexander N Prutkov
- Biotechnology & Industrial Pharmacy Department, Lomonosov Institute of Fine Chemical Tehnologies, MIREA - Russian Technological University, Moscow, Russia
| | - Mikhail V Chudinov
- Biotechnology & Industrial Pharmacy Department, Lomonosov Institute of Fine Chemical Tehnologies, MIREA - Russian Technological University, Moscow, Russia
| | - Andrey V Matveev
- Biotechnology & Industrial Pharmacy Department, Lomonosov Institute of Fine Chemical Tehnologies, MIREA - Russian Technological University, Moscow, Russia
| | - Lyubov E Grebenkina
- Biotechnology & Industrial Pharmacy Department, Lomonosov Institute of Fine Chemical Tehnologies, MIREA - Russian Technological University, Moscow, Russia
| | - Mikhail G Akimov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yulia V Berezovskaya
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
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48
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Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sci 2020; 248:117477. [PMID: 32119961 PMCID: PMC7089605 DOI: 10.1016/j.lfs.2020.117477] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 02/07/2023]
Abstract
Aims A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan, China (COVID-19). Until today >2700 deaths from the 80,000 confirmed cases reported mainly in China and 40 other countries. Human to human transmission is confirmed for COVID-19 by China a month ago. Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for >8000 cases with confirmed 774 deaths. Additionally, MERS HCoV is responsible for 858 deaths out of about 2500 reported cases. The current study aims to test anti-HCV drugs against COVID-19 RNA dependent RNA polymerase (RdRp). Materials and methods In this study, sequence analysis, modeling, and docking are used to build a model for Wuhan COVID-19 RdRp. Additionally, the newly emerged Wuhan HCoV RdRp model is targeted by anti-polymerase drugs, including the approved drugs Sofosbuvir and Ribavirin. Key findings The results suggest the effectiveness of Sofosbuvir, IDX-184, Ribavirin, and Remidisvir as potent drugs against the newly emerged HCoV disease. Significance The present study presents a perfect model for COVID-19 RdRp enabling its testing in silico against anti-polymerase drugs. Besides, the study presents some drugs that previously proved its efficiency against the newly emerged viral infection. COVID-19 RdRp shares 97% sequence identity to SARS. COVID-19 RdRp model is built to study inhibitors. Sofosbuvir, Ribavirin, and Remdesivir can bind to COVID-19 RdRp. IDX-184 may be used as a seed to obtain a potent inhibitor specific against COVID-19 RdRp.
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49
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Ji X, Li Z. Medicinal chemistry strategies toward host targeting antiviral agents. Med Res Rev 2020; 40:1519-1557. [PMID: 32060956 PMCID: PMC7228277 DOI: 10.1002/med.21664] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022]
Abstract
Direct‐acting antiviral agents (DAAs) represent a class of drugs targeting viral proteins and have been demonstrated to be very successful in combating viral infections in clinic. However, DAAs suffer from several inherent limitations, including narrow‐spectrum antiviral profiles and liability to drug resistance, and hence there are still unmet needs in the treatment of viral infections. In comparison, host targeting antivirals (HTAs) target host factors for antiviral treatment. Since host proteins are probably broadly required for various viral infections, HTAs are not only perceived, but also demonstrated to exhibit broad‐spectrum antiviral activities. In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. In this review, we summarize various host proteins as antiviral targets from a medicinal chemistry prospective. Challenges and issues associated with HTAs are also discussed.
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Affiliation(s)
- Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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50
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Skidmore AM, Adcock RS, Jonsson CB, Golden JE, Chung DH. Benzamidine ML336 inhibits plus and minus strand RNA synthesis of Venezuelan equine encephalitis virus without affecting host RNA production. Antiviral Res 2020; 174:104674. [PMID: 31816348 PMCID: PMC6935354 DOI: 10.1016/j.antiviral.2019.104674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an alphavirus that is endemic to the Americas. VEEV outbreaks occur periodically and cause encephalitis in both humans and equids. There are currently no therapeutics or vaccines for treatment of VEEV in humans. Our group has previously reported on the development of a benzamidine VEEV inhibitor, ML336, which shows potent antiviral activity in both in vitro and in vivo models of infection. In cell culture experiments, ML336 inhibits viral RNA synthesis when added 2-4 h post-infection, and mutations conferring resistance occur within the viral nonstructural proteins (nsP2 and nsP4). We hypothesized that ML336 targets an activity of the viral replicase complex and inhibits viral RNA synthesis. To test this hypothesis, we employed various biochemical and cellular assays. Using structural analogues of ML336, we demonstrate that the cellular antiviral activity of these compounds correlates with their inhibition of viral RNA synthesis. For instance, the IC50 of ML336 for VEEV RNA synthesis inhibition was determined as 1.1 nM, indicating potent anti-RNA synthesis activity in the low nanomolar range. While ML336 efficiently inhibited VEEV RNA synthesis, a much weaker effect was observed against the Old World alphavirus Chikungunya virus (IC50 > 4 μM), agreeing with previous data from a cell based assay. Using a tritium incorporation assay, we demonstrated that there was no significant inhibition of cellular transcription. With a combination of fluorography, strand-specific qRT-PCR, and tritium incorporation, we demonstrated that ML336 inhibits the synthesis of the positive sense genomic, negative sense template, and subgenomic RNAs of VEEV. Based on these results, we propose that the mechanism of action for this class of antiviral compounds is inhibition of viral RNA synthesis through interaction with the viral replicase complex.
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Affiliation(s)
- Andrew M Skidmore
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA.
| | - Robert S Adcock
- Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave, Room 810 B, Memphis, TN, USA.
| | - Jennifer E Golden
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Dr, Room 7123, Madison, WI, USA.
| | - Dong-Hoon Chung
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA; Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
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