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Geedkar D, Kumar A, Sharma P. Synthesis and in silico inhibitory action studies of azo-anchored imidazo[4,5-b]indole scaffolds against the COVID-19 main protease (M pro). Sci Rep 2024; 14:10419. [PMID: 38710746 PMCID: PMC11074333 DOI: 10.1038/s41598-024-57795-4] [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: 12/01/2023] [Accepted: 03/21/2024] [Indexed: 05/08/2024] Open
Abstract
The present work elicits a novel approach to combating COVID-19 by synthesizing a series of azo-anchored 3,4-dihydroimidazo[4,5-b]indole derivatives. The envisaged methodology involves the L-proline-catalyzed condensation of para-amino-functionalized azo benzene, indoline-2,3-dione, and ammonium acetate precursors with pertinent aryl aldehyde derivatives under ultrasonic conditions. The structures of synthesized compounds were corroborated through FT-IR, 1H NMR, 13C NMR, and mass analysis data. Molecular docking studies assessed the inhibitory potential of these compounds against the main protease (Mpro) of SARS-CoV-2. Remarkably, in silico investigations revealed significant inhibitory action surpassing standard drugs such as Remdesivir, Paxlovid, Molnupiravir, Chloroquine, Hydroxychloroquine (HCQ), and (N3), an irreversible Michael acceptor inhibitor. Furthermore, the highly active compound was also screened for cytotoxicity activity against HEK-293 cells and exhibited minimal toxicity across a range of concentrations, affirming its favorable safety profile and potential suitability. The pharmacokinetic properties (ADME) of the synthesized compounds have also been deliberated. This study paves the way for in vitro and in vivo testing of these scaffolds in the ongoing battle against SARS-CoV-2.
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Affiliation(s)
- Deepika Geedkar
- School of Chemical Sciences, Devi Ahilya University, Indore, Madhya Pradesh, India
| | - Ashok Kumar
- School of Chemical Sciences, Devi Ahilya University, Indore, Madhya Pradesh, India
| | - Pratibha Sharma
- School of Chemical Sciences, Devi Ahilya University, Indore, Madhya Pradesh, India.
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Esam Z, Akhavan M, Lotfi M, Bekhradnia A. Synthesis and In Silico Investigation of Isatin-Based Schiff Bases as Potential Inhibitors for Promising Targets against SARS-CoV-2. ChemistrySelect 2022; 7:e202201983. [PMID: 36718466 PMCID: PMC9878032 DOI: 10.1002/slct.202201983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022]
Abstract
Despite the significant development in vaccines and therapeutics cocktails, there is no specific treatment available for coronavirus disease 2019 (COVID-19), caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Targeting the main protease (Mpro) of SARS-CoV-2, which possesses a key role in producing the essential viral structural and functional proteins, can be considered an efficient way to control this potentially lethal infection. Recently, some of Michael acceptor-pharmacophore containing inhibitors have been suggested as successful suppressors of the main protease. Here, we synthesized the Isatin-based Schiff bases possessing the structural pattern of a Michael acceptor-like portion employing synthesis procedures. In silico investigation of these compounds was not limited to the main protease. We have also evaluated their possible inhibitory activity against the other identified druggable targets using homology modeling, molecular docking, and molecular dynamics simulations. Our investigations revealed that the dimethyl biguanide carrying Schiff bases of Isatin-derivatives have the best binding mode and interaction energy. The dimethyl biguanide moiety-containing compounds have formed promising interactions with the key amino acid residues Cys145 and HIS41 of Mpro with a binding free energy of -7.6 kcal/mol which was lower than the positive control compound Carmofur (-6.3 kcal/mol). It also leads to the higher affinity and the much inhibitory potential against the SARS-CoV-2 RdRp and Spike glycoproteins, human TMPRSS2, and ACE2 receptors.
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Affiliation(s)
- Zohreh Esam
- Pharmaceutical Sciences Research CenterDepartment of Medicinal ChemistryFaculty of PharmacyMazandaran University of Medical SciencesSariIran
| | - Malihe Akhavan
- Pharmaceutical Sciences Research CenterDepartment of Medicinal ChemistryFaculty of PharmacyMazandaran University of Medical SciencesSariIran
| | - Maryam Lotfi
- The Multiscale Modeling Lab, ITQB NOVAAv. da Republica2780-157OeirasPortugal
| | - Ahmadreza Bekhradnia
- Pharmaceutical Sciences Research CenterDepartment of Medicinal ChemistryFaculty of PharmacyMazandaran University of Medical SciencesSariIran,Department of chemistry and biochemistry103CBBMontana State UniversityBozemanMT59717USA
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Bagde H, Dhopte A. Effects of Plant Metabolites on the Growth of COVID-19 (Coronavirus Disease-19) Including Omicron Strain. Cureus 2022; 14:e26549. [PMID: 35936126 PMCID: PMC9348519 DOI: 10.7759/cureus.26549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
According to recent reports out of India, a new strain of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) B1.1.529 Omicron virus has emerged. In comparison to the Wuhan (WHU) strain and the delta variant, this variant showed a far stronger effect on the angiotensin converting enzyme2 (ACE2) receptor. There are several medicinal compounds in plant metabolites, and their diverse chemical structures make them ideal for the treatment of serious illnesses. It's possible that some of these could be useful alternative pharmaceuticals, as well as a starting point for the repurposing of existing medications and new chemical discoveries. SARS-CoV-2 infection triggered a worldwide epidemic of the severe acute respiratory syndrome (SARS). There have been trials for different therapies for SARS-CoV-2 and so also there are recent announcements of extensive research into the development of viable medicines for this global health calamity. After a thorough examination of plant-derived treatments for COVID-19, investigators in the current study decided to focus on plant-derived secondary metabolites (PSMs). According to some researchers, new MDR (Multi-Drug Resistant) antibiotics may one day be developed due to the adaptability of secondary metabolites. Identifying plant metabolites that can treat a wide range of viral infections was one of the study's aims. Many natural medications that could be recommended for the treatment of COVID-19 were discovered as a result of this research, including remedies from plant families, viral candidates that are susceptible, antiviral assays, and mechanisms of therapeutic action. The findings of this study will inspire further research and speed up the development of new antiviral plant-based medications.
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Komissarov A, Karaseva M, Roschina M, Kostrov S, Demidyuk I. The SARS-CoV-2 main protease doesn't induce cell death in human cells in vitro. PLoS One 2022; 17:e0266015. [PMID: 35609027 PMCID: PMC9129031 DOI: 10.1371/journal.pone.0266015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19) which has extremely rapidly spread worldwide. In order to develop the effective antiviral therapies, it is required to understand the molecular mechanisms of the SARS-CoV-2 pathogenesis. The main protease, or 3C-like protease (3CLpro), plays the essential role in the coronavirus replication that makes the enzyme a promising therapeutic target. Viral enzymes are known to be multifunctional. Particularly, 3CLpro of SARS-CoV was shown to induce apoptosis in addition to its main function. In the present study we analyzed the cytotoxicity of active SARS-CoV-2 3CLpro and its inactivated form upon their individual expression in four human cell lines. For this purpose, we constructed a protein biosensor which allows to detect the proteolytic activity of SARS-CoV-2 3CLpro and confirmed the expression of the active protease in all cell lines used. We studied viability and morphology of the cells and found that both active and inactivated enzyme variants induce no cell death in contrast to the homologous 3CL protease of SARS-CoV. These results indicate that SARS-CoV-2 3CLpro is unlikely contribute to the cytopathic effect observed during viral infection directly.
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Affiliation(s)
- Alexey Komissarov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Maria Karaseva
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Marina Roschina
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Sergey Kostrov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Ilya Demidyuk
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
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Sesquiterpenes and polyphenols with glucose-uptake stimulatory and antioxidant activities from the medicinal mushroom Sanghuangporus sanghuang. Chin J Nat Med 2021; 19:693-699. [PMID: 34561081 DOI: 10.1016/s1875-5364(21)60101-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Indexed: 12/20/2022]
Abstract
A chemical investigation on the fermentation products of Sanghuangporus sanghuang led to the isolation and identification of fourteen secondary metabolites (1-14) including eight sesquiterpenoids (1-8) and six polyphenols (9-14). Compounds 1-3 were sesquiterpenes with new structures which were elucidated based on NMR spectroscopy, high resolution mass spectrometry (HRMS) and electronic circular dichroism (ECD) data. All the isolates were tested for their stimulation effects on glucose uptake in insulin-resistant HepG2 cells, and cellular antioxidant activity. Compounds 9-12 were subjected to molecular docking experiment to primarily evaluate their anti-coronavirus (SARS-CoV-2) activity. As a result, compounds 9-12 were found to increase the glucose uptake of insulin-resistant HepG2 cells by 18.1%, 62.7%, 33.7% and 21.4% at the dose of 50 μmol·L-1, respectively. Compounds 9-12 also showed good cellular antioxidant activities with CAA50 values of 12.23, 23.11, 5.31 and 16.04 μmol·L-1, respectively. Molecular docking between COVID-19 Mpro and compounds 9-12 indicated potential SARS-CoV-2 inhibitory activity of these four compounds. This work provides new insights for the potential role of the medicinal mushroom S. sanghuang as drugs and functional foods.
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Yan S, Wu G. Potential 3-chymotrypsin-like cysteine protease cleavage sites in the coronavirus polyproteins pp1a and pp1ab and their possible relevance to COVID-19 vaccine and drug development. FASEB J 2021; 35:e21573. [PMID: 33913206 PMCID: PMC8206714 DOI: 10.1096/fj.202100280rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus (CoV) 3-chymotrypsin (C)-like cysteine protease (3CLpro ) is a target for anti-CoV drug development and drug repurposing because along with papain-like protease, it cleaves CoV-encoded polyproteins (pp1a and pp1ab) into nonstructural proteins (nsps) for viral replication. However, the cleavage sites of 3CLpro and their relevant nsps remain unclear, which is the subject of this perspective. Here, we address the subject from three standpoints. First, we explore the inconsistency in the cleavage sites and relevant nsps across CoVs, and investigate the function of nsp11. Second, we consider the nsp16 mRNA overlapping of the spike protein mRNA, and analyze the effect of this overlapping on mRNA vaccines. Finally, we study nsp12, whose existence depends on ribosomal frameshifting, and investigate whether 3CLpro requires a large number of inhibitors to achieve full inhibition. This perspective helps us to clarify viral replication and is useful for developing anti-CoV drugs with 3CLpro as a target in the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
| | - Guang Wu
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
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Chhetri A, Chettri S, Rai P, Sinha B, Brahman D. Exploration of inhibitory action of Azo imidazole derivatives against COVID-19 main protease (M pro): A computational study. J Mol Struct 2021; 1224:129178. [PMID: 32904625 PMCID: PMC7456803 DOI: 10.1016/j.molstruc.2020.129178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/29/2020] [Accepted: 08/30/2020] [Indexed: 12/23/2022]
Abstract
Four novel ionic liquid tagged azo-azomethine derivatives (L1-L4) have been prepared by the condensation reaction of azo-coupled ortho-vaniline precursor with amino functionalised imidazole derivative and the synthesized derivatives (L1-L4) have been characterized by different analytical and spectroscopic techniques. Molecular docking studies were carried out to ascertain the inhibitory action of studied ligands (L1-L4) against the Main Protease (6LU7) of novel coronavisrus (COVID-19). The result of the docking of L1-L4 showed a significant inhibitory action against the Main protease (Mpro) of SARS-CoV-2 and the binding energy (ΔG) values of the ligands (L1-L4) against the protein 6LU7 have found to be -7.7 Kcal/mole (L1), -7.0 Kcal/mole (L2), -7.9 Kcal/mole (L3), and -7.9 Kcal/mole (L4).The efficiency of the ligands has been compared with the FDA approved and clinically trial drugs such as remdesivir, Chloroquin and Hydroxychloroquin and native ligand N3 of main protease 6LU7 to ascertain the inhibitory potential of the studied ligands (L1-L4) against the protein 6LU7. Pharmacokinetic properties (ADME) of the ligands (L1-L4) have also been studied.
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Affiliation(s)
- Abhijit Chhetri
- Department of Microbiology, St. Joseph's College, Darjeeling, 734104, India
| | - Sailesh Chettri
- Department of Chemistry, St. Joseph's College, Darjeeling, 734104, India
| | - Pranesh Rai
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Biswajit Sinha
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Dhiraj Brahman
- Department of Chemistry, St. Joseph's College, Darjeeling, 734104, India
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Yan S, Wu G. Spatial and temporal roles of SARS-CoV PL pro -A snapshot. FASEB J 2021; 35:e21197. [PMID: 33368679 PMCID: PMC7883198 DOI: 10.1096/fj.202002271] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
SARS‐CoV and SARS‐CoV‐2 encode four structural and accessory proteins (spike, envelope, membrane and nucleocapsid proteins) and two polyproteins (pp1a and pp1ab). The polyproteins are further cleaved by 3C‐like cysteine protease (3CLpro) and papain‐like protease (PLpro) into 16 nonstructural proteins (nsps). PLpro is released from nsp3 through autocleavage, and then it cleaves the sites between nsp1/2, between nsp2/3 and between nsp3/4 with recognition motif of LXGG, and the sites in the C‐terminus of ubiquitin and of protein interferon‐stimulated gene 15 (ISG15) with recognition motif of RLRGG. Alone or together with SARS unique domain (SUD), PLpro can stabilize an E3 ubiquitin ligase, the ring‐finger, and CHY zinc‐finger domain‐containing 1 (RCHY1), through domain interaction, and thus, promote RCHY1 to ubiquitinate its target proteins including p53. However, a dilemma appears in terms of PLpro roles. On the one hand, the ubiquitination of p53 is good for SARS‐CoV because the ubiquitinated p53 cannot inhibit SARS‐CoV replication. On the other hand, the ubiquitination of NF‐κB inhibitor (IκBα), TNF receptor‐associated factors (TRAFs), and stimulator of interferon gene (STING), and the ISGylation of targeted proteins are bad for SARS‐CoV because these ubiquitination and ISGylation initiate the innate immune response and antiviral state. This mini‐review analyzes the dilemma and provides a snapshot on how the viral PLpro smartly manages its roles to avoid its simultaneously contradictory actions, which could shed lights on possible strategies to deal with SARS‐CoV‐2 infections.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of Bio-Refinery, Guangxi Academy of Sciences, Nanning, China
| | - Guang Wu
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of Bio-Refinery, Guangxi Academy of Sciences, Nanning, China
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Ghale-Noie ZN, Salmaninejad A, Bergquist R, Mollazadeh S, Hoseini B, Sahebkar A. Genetic Aspects and Immune Responses in Covid-19: Important Organ Involvement. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1327:3-22. [PMID: 34279825 DOI: 10.1007/978-3-030-71697-4_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the last two decades, the world has experienced outbreaks of three major coronaviruses with high morbidity and mortality rates. The most recent of these started in the form of an unusual viral pneumonia in Wuhan, China, and now the world is facing a serious pandemic. This new disease has been called COVID-19 and is caused by the SARS-CoV-2 virus. Understanding the specific genetic and phenotypic structure of SARS-CoV-2 in COVID-19 pathogenesis is vital in finding appropriate drugs and vaccines. With this in mind, this review sheds light on the virology, genetics, immune-responses, and mechanism of action of this virus.
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Affiliation(s)
- Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Robert Bergquist
- Formerly UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Benyamin Hoseini
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Health Information Technology, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Solnier J, Fladerer JP. Flavonoids: A complementary approach to conventional therapy of COVID-19? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2021; 20:773-795. [PMID: 32982616 PMCID: PMC7500502 DOI: 10.1007/s11101-020-09720-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/29/2020] [Indexed: 05/02/2023]
Abstract
COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential.
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Affiliation(s)
- Julia Solnier
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
| | - Johannes-Paul Fladerer
- Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University of Graz, Universitätsplatz 4, 8010 Graz, Austria
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Matveeva T, Khafizova G, Sokornova S. In Search of Herbal Anti-SARS-Cov2 Compounds. FRONTIERS IN PLANT SCIENCE 2020; 11:589998. [PMID: 33304368 PMCID: PMC7701093 DOI: 10.3389/fpls.2020.589998] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 05/14/2023]
Abstract
On March 11, 2020, the World Health Organization (WHO) announced that the spread of the new coronavirus had reached the stage of a pandemic. To date (23.10.2020), there are more than 40 million confirmed cases of the disease in the world, at the same time there is still no effective treatment for the disease. For management and treatment of SARS-Cov2, the development of an antiviral drug is needed. Since the representatives of all human cultures have used medicinal plants to treat viral diseases throughout their history, plants can be considered as sources of new antiviral drug compounds against emerging viruses. The huge metabolic potential of plants allows us to expect discovery of plant compounds for the prevention and treatment of coronavirus infection. This idea is supported by number of papers on the anti-SARS-Cov2 activity of plant extracts and specific compounds in the experiments in silico, in vitro, and in vivo. Here, we summarize information on methods and approaches aimed to search for anti-SARS-Cov2 compounds including cheminformatics, bioinformatics, genetic engineering of viral targets, interacting with drugs, biochemical approaches etc. Our mini-review may be useful for better planning future experiments (including rapid methods for screening compounds for antiviral activity, the initial assessment of the antiviral potential of various plant species in relation to certain pathogens, etc.) and giving a hand to those who are making first steps in this field.
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Affiliation(s)
- Tatiana Matveeva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Galina Khafizova
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Sofia Sokornova
- Department of Toxicology and Biotechnology, All-Russian Institute of Plant Protection, St. Petersburg, Russia
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Smit M, Marinosci A, Nicoletti GJ, Perneger T, Ragozzino S, Andrey DO, Stoeckle M, Jacquerioz F, Lebowitz D, Agoritsas T, Meyer B, Spechbach H, Salamun J, Back M, Schaubhut C, Fuchs S, Decosterd L, Battegay M, Guessous I, Chappuis F, Kaiser L, Labhardt ND, Calmy A. Efficacy of pragmatic same-day ring prophylaxis for adult individuals exposed to SARS-CoV-2 in Switzerland (COPEP): protocol of an open-label cluster randomised trial. BMJ Open 2020; 10:e040110. [PMID: 33184083 PMCID: PMC7662450 DOI: 10.1136/bmjopen-2020-040110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Lopinavir/ritonavir (LPV/r) has been proposed as repurposed drugs for pre-exposure and postexposure prophylaxis as well as therapy of COVID-19. Coronavirus postexposure prophylaxis (COPEP) trial aims at assessing their efficacy as postexposure ring-prophylaxis among adults exposed to SARS-CoV-2. METHODS AND ANALYSIS COPEP is a two-arm open-label cluster-randomised trial conducted in three cantons of Switzerland. Asymptomatic contacts (≥16 years) of individuals diagnosed with COVID-19 will be randomised (2:1) to either LPV/r (400 mg/100 mg two times per day) for 5 days, or a standard of care arm (no treatment). Asymptomatic individuals may be either SARS-CoV-2 positive or negative. Contacts living in the single household will form a cluster and will be randomised into the same arm. All participants will be followed-up for 21 days and undergo daily monitoring for COVID-19 symptoms. The primary endpoint is 21-day incidence of laboratory-confirmed COVID-19 with ≥1 compatible symptom, analysed in an intention-to-treat (ITT) analysis. The secondary endpoints include the 21-day incidence of COVID-19 as well as SARS-CoV-2 infection in a modified ITT analysis, excluding participants who had a positive SARS-CoV-2 RT-PCR from oropharyngeal swab and/or a positive SARS-CoV-2 IgG serology at baseline. Assuming a 21-day incidence for COVID-19 of 20% among contacts without postexposure chemoprophylaxis, to detect a relative risk reduction of 60% (ie, translating in an absolute reduction from 20% to 8%), with a power of 80%, an alpha of 5%. Accounting for design effect of cluster design of circa 1.1, we plan to enrol 200 participants to the LPV/r arm and 100 to the standard of care arm, 300 participants in total. ETHICS AND DISSEMINATION Ethics approval has been granted by the Commission Cantonale d'Ethique de la Recherche, Ethikkommission Nordwest- und Zentralschweiz and Comitato Etico Cantonale (ref 2020-00864) and Swissmedic (2020DR3056). Results from this trial will be disseminated via journal articles and presentations at national and international conferences. TRIAL REGISTRATION NUMBER Clinicaltrials.gov Registry (NCT04364022); Swiss National Clinical Trial Portal Registry (SNCTP 000003732). REGISTERED REPORT IDENTIFIER CCER 2020-0864.
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Affiliation(s)
- Mikaela Smit
- HIV Unit, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | | | - Thomas Perneger
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Clinical Epidemiology, Geneva University Hospitals, Geneva, Switzerland
| | - Silvio Ragozzino
- Department of Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Diego O Andrey
- HIV Unit, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Marcel Stoeckle
- Department of Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | | | - Dan Lebowitz
- Infection Control Programme, Geneva University Hospitals, Geneva, Switzerland
- Direction Generale de la Sante, Republique et Canton de Geneve, Geneva, Switzerland
| | - Thomas Agoritsas
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Herve Spechbach
- Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - Julien Salamun
- Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - Moritz Back
- Gesundheitsdepartement, Canton of Basel City, Basel, Switzerland
| | - Carla Schaubhut
- Gesundheitsdepartement, Canton of Basel City, Basel, Switzerland
| | - Simon Fuchs
- Gesundheitsdepartement, Canton of Basel City, Basel, Switzerland
| | - Laurent Decosterd
- Laboratory of Clinical Pharmacology, University of Lausanne, Lausanne, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Idris Guessous
- Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - François Chappuis
- Department of Primary Care, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Niklaus D Labhardt
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Alexandra Calmy
- HIV Unit, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
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13
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Chhetri A, Chettri S, Rai P, Mishra DK, Sinha B, Brahman D. Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (M pro: 6LU7). J Mol Struct 2020; 1225:129230. [PMID: 32963413 PMCID: PMC7499073 DOI: 10.1016/j.molstruc.2020.129230] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022]
Abstract
Six azo imidazole derivatives have been synthesized and characterized by spectroscopic and analytical tools. Inhibitory potential against main protease (6LU7) have been investigated using computational techniques. Binding energy of the ligands has found in the range −6.7 Kcal/mole to −8.1 Kcal/mole. The order of the ligands towards the protein 6LU7 are L5> L4≈L6>L1>L2>L3.
A series of six novel imidazole anchored azo-imidazole derivatives (L1-L6) have been prepared by the simple condensation reaction of azo-coupled ortho-vaniline precursor with amino functionalised imidazole derivative and the synthesized derivatives (L1-L6) have been characterized by different analytical and spectroscopic techniques. Molecular docking studies were carried out to ascertain the inhibitory action of studied ligands (L1-L6) against the Main Protease (6LU7) of novel coronavirus (COVID-19). The result of the docking of L1-L6 showed a significant inhibitory action against the Main protease (Mpro) of SARS-CoV-2 and the binding energy (ΔG) values of the ligands (L1-L6) against the protein 6LU7 have found to be -7.7 Kcal/mole (L1), -7.4 Kcal/mole (L2), -6.7 Kcal/mole (L3), -7.9 Kcal/mole (L4), -8.1 Kcal/mole (L5) and -7.9 Kcal/mole (L6). Pharmacokinetic properties (ADME) of the ligands (L1-L6) have also been studied.
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Affiliation(s)
- Abhijit Chhetri
- Department of Microbiology, St. Joseph's College, Darjeeling-734104, India
| | - Sailesh Chettri
- Department of Chemistry, St. Joseph's College, Darjeeling-734104, India
| | - Pranesh Rai
- Department of Chemistry, University of North Bengal, Darjeeling-734013, India
| | - Dipu Kumar Mishra
- Department of Chemistry, University of North Bengal, Darjeeling-734013, India
| | - Biswajit Sinha
- Department of Chemistry, University of North Bengal, Darjeeling-734013, India
| | - Dhiraj Brahman
- Department of Chemistry, St. Joseph's College, Darjeeling-734104, India
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14
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Razzaghi-Asl N, Ebadi A, Shahabipour S, Gholamin D. Identification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis. J Biomol Struct Dyn 2020; 39:6633-6648. [PMID: 32705953 PMCID: PMC7441780 DOI: 10.1080/07391102.2020.1797536] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Considering lack of validated therapeutic drugs or vaccines against contagious SARS-CoV2, various efforts have been focused on repurposing of existing drugs or identifying new agents. In an attempt to identify new and potential SARS-CoV2 inhibitors targeting specific enzyme of the pathogen, a few induced fit models of SARS-CoV2 main protease (Mpro) including N-aryl amide and aryl sulfonamide based fragments were subjected to a multi-step in silico strategy. Sub-structure query of co-crystallographic fragments provided numerous ZINC15 driven commercially available compounds that entered molecular docking stage to find binding interactions/modes inside Mpro active site. Docking results were reevaluated through time dependent stability of top-ranked ligand-protease complexes by molecular dynamics (MD) simulations within 50 ns. Relative contribution of interacted residues in binding to the most probable binding pose was estimated through amino acid decomposition analysis in B3LYP level of theory with Def2-TZVPP split basis set. In confirmation of docking results, MD simulations revealed less perceptible torsional distortions (more stable binding mode) in binding of ZINC_252512772 (ΔGb −9.18 kcal/mol) into Mpro active site. H-bond interactions and hydrophobic contacts were determinant forces in binding interactions of in silico hit. Quantum chemical calculations confirmed MD results and proved the pivotal role of a conserved residue (Glu166) in making permanent hydrogen bond (98% of MD simulations time) with ZINC_252512772. Drug-like physicochemical properties as well as desirable target binding interactions nominated ZINC_252512772 as a desirable in silico hit for further development toward SARS-CoV2 inhibitors. Highlights A few N-aryl amide/aryl sulfonamide based fragments were subjected to a multi-step in silico strategy to afford potential SARS-CoV2 Mpro inhibitors. MD simulations revealed less perceptible torsional distortions (more stable binding mode) in binding of ZINC_252512772 (ΔGb -9.18 kcal/mol) into Mpro active site. H-bond interactions and hydrophobic contacts were determinant forces in binding interactions of in silico hit. Quantum chemical calculations confirmed MD results and proved pivotal role of a conserved residue (Glu166) in making permanent hydrogen bond (98% of MD simulations time) with ZINC_252512772.
Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ahmad Ebadi
- Department of Medicinal Chemistry, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sara Shahabipour
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Danial Gholamin
- Students Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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15
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Lopinavir; A Potent Drug against Coronavirus Infection: Insight from Molecular Docking Study. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2017. [DOI: 10.5812/archcid.13823] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Aggarwal M, Sharma R, Kumar P, Parida M, Tomar S. Kinetic characterization of trans-proteolytic activity of Chikungunya virus capsid protease and development of a FRET-based HTS assay. Sci Rep 2015; 5:14753. [PMID: 26439734 PMCID: PMC4593962 DOI: 10.1038/srep14753] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/01/2015] [Indexed: 11/25/2022] Open
Abstract
Chikungunya virus (CHIKV) capsid protein (CVCP) is a serine protease that possesses cis-proteolytic activity essential for the structural polyprotein processing and plays a key role in the virus life cycle. CHIKV being an emerging arthropod-borne pathogenic virus, is a public health concern worldwide. No vaccines or specific antiviral treatment is currently available for chikungunya disease. Thus, it is important to develop inhibitors against CHIKV enzymes to block key steps in viral reproduction. In view of this, CVCP was produced recombinantly and purified to homogeneity. A fluorescence resonance energy transfer (FRET)-based proteolytic assay was developed for high throughput screening (HTS). A FRET peptide substrate (DABCYL-GAEEWSLAIE-EDANS) derived from the cleavage site present in the structural polyprotein of CVCP was used. The assay with a Z’ factor of 0.64 and coefficient of variation (CV) is 8.68% can be adapted to high throughput format for automated screening of chemical libraries to identify CVCP specific protease inhibitors. Kinetic parameters Km and kcat/Km estimated using FRET assay were 1.26 ± 0.34 μM and 1.11 × 103 M−1 sec−1 respectively. The availability of active recombinant CVCP and cost effective fluorogenic peptide based in vitro FRET assay may serve as the basis for therapeutics development against CHIKV.
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Affiliation(s)
- Megha Aggarwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Rajesh Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Manmohan Parida
- Division of Virology, Defence Research and Development Establishment, Gwalior 474002, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee-247667, India
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17
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Park JY, Ko JA, Kim DW, Kim YM, Kwon HJ, Jeong HJ, Kim CY, Park KH, Lee WS, Ryu YB. Chalcones isolated from Angelica keiskei inhibit cysteine proteases of SARS-CoV. J Enzyme Inhib Med Chem 2015; 31:23-30. [PMID: 25683083 DOI: 10.3109/14756366.2014.1003215] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two viral proteases of severe acute respiratory syndrome coronavirus (SARS-CoV), a chymotrypsin-like protease (3CL(pro)) and a papain-like protease (PL(pro)) are attractive targets for the development of anti-SARS drugs. In this study, nine alkylated chalcones (1-9) and four coumarins (10-13) were isolated from Angelica keiskei, and the inhibitory activities of these constituents against SARS-CoV proteases (3CL(pro) and PL(pro)) were determined (cell-free/based). Of the isolated alkylated chalcones, chalcone 6, containing the perhydroxyl group, exhibited the most potent 3CL(pro) and PL(pro) inhibitory activity with IC50 values of 11.4 and 1.2 µM. Our detailed protein-inhibitor mechanistic analysis of these species indicated that the chalcones exhibited competitive inhibition characteristics to the SARS-CoV 3CL(pro), whereas noncompetitive inhibition was observed with the SARS-CoV PL(pro).
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Affiliation(s)
- Ji-Young Park
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Jin-A Ko
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Dae Wook Kim
- b Division of Applied Life Science (BK21 program, IALS) , Graduate School of Gyeongsang National University , Jinju , Republic of Korea , and
| | - Young Min Kim
- c Department of Food Science & Technology and Functional Food Research Center , Chonnam National University , Gwangju , Republic of Korea
| | - Hyung-Jun Kwon
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Hyung Jae Jeong
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Cha Young Kim
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Ki Hun Park
- b Division of Applied Life Science (BK21 program, IALS) , Graduate School of Gyeongsang National University , Jinju , Republic of Korea , and
| | - Woo Song Lee
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
| | - Young Bae Ryu
- a Eco-friendly Bio Material Research Center, Korea Research Institute of Bioscience and Biotechnology , Jeongeup , Republic of Korea
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18
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Li SW, Yang TC, Lai CC, Huang SH, Liao JM, Wan L, Lin YJ, Lin CW. Antiviral activity of aloe-emodin against influenza A virus via galectin-3 up-regulation. Eur J Pharmacol 2014; 738:125-32. [DOI: 10.1016/j.ejphar.2014.05.028] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 02/01/2023]
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19
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Chen S, Chen L, Chen K, Shen X, Jiang H. Techniques used for the discovery of therapeutic compounds: The case of SARS. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 3:277-83. [PMID: 24980529 PMCID: PMC7105914 DOI: 10.1016/j.ddtec.2006.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is the etiological agent of SARS disease, which has ever severely menaced humans from the end of 2002 to June 2003. To date, great efforts have been made for the discovery of therapeutic compounds by using various technologies. In this report, we present a survey of these techniques and their applications in the development of promising anti-SARS agents.:
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Affiliation(s)
- Shuai Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xu Shen
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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20
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Zhang R, Zhang CT. A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics 2014; 15:78-94. [PMID: 24822026 PMCID: PMC4009844 DOI: 10.2174/1389202915999140328162433] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.
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Affiliation(s)
- Ren Zhang
- Center for Molecular Medicine and Genetics, Wayne State University Medical School, Detroit, MI 48201, USA
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, China
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21
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Neuman BW, Chamberlain P, Bowden F, Joseph J. Atlas of coronavirus replicase structure. Virus Res 2013; 194:49-66. [PMID: 24355834 PMCID: PMC7114488 DOI: 10.1016/j.virusres.2013.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022]
Abstract
Complete and up to date coverage of replicase protein structures for SARS-CoV. Discusses SARS-CoV structure in the context of other coronavirus structures. Summarizes data from a variety of structural methods to illuminate protein function. Uses models and predictions to fill gaps in the SARS-CoV structure. Discusses the high percentage of novel protein folds among SARS-CoV proteins.
The international response to SARS-CoV has produced an outstanding number of protein structures in a very short time. This review summarizes the findings of functional and structural studies including those derived from cryoelectron microscopy, small angle X-ray scattering, NMR spectroscopy, and X-ray crystallography, and incorporates bioinformatics predictions where no structural data is available. Structures that shed light on the function and biological roles of the proteins in viral replication and pathogenesis are highlighted. The high percentage of novel protein folds identified among SARS-CoV proteins is discussed.
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Affiliation(s)
| | | | - Fern Bowden
- School of Biological Sciences, University of Reading, Reading, UK
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22
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Kilianski A, Baker SC. Cell-based antiviral screening against coronaviruses: developing virus-specific and broad-spectrum inhibitors. Antiviral Res 2013; 101:105-12. [PMID: 24269477 PMCID: PMC3931262 DOI: 10.1016/j.antiviral.2013.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 10/31/2013] [Accepted: 11/09/2013] [Indexed: 01/19/2023]
Abstract
To combat the public health threat from emerging coronaviruses (CoV), the development of antiviral therapies with either virus-specific or pan-coronaviral activities is necessary. An important step in antiviral drug development is the screening of potential inhibitors in cell-based systems. The recent emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) necessitates adapting methods that have been used to identify antivirals against severe acute respiratory syndrome coronavirus (SARS-CoV) and developing new approaches to more efficiently screen antiviral drugs. In this article we review cell-based assays using infectious virus (BSL-3) and surrogate assays (BSL-2) that can be implemented to accelerate antiviral development against MERS-CoV and future emergent coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses."
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Affiliation(s)
- Andy Kilianski
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, United States
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, United States.
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23
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Park JY, Kim JH, Kwon JM, Kwon HJ, Jeong HJ, Kim YM, Kim D, Lee WS, Ryu YB. Dieckol, a SARS-CoV 3CL(pro) inhibitor, isolated from the edible brown algae Ecklonia cava. Bioorg Med Chem 2013; 21:3730-7. [PMID: 23647823 PMCID: PMC7126891 DOI: 10.1016/j.bmc.2013.04.026] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 12/11/2022]
Abstract
SARS-CoV 3CL(pro) plays an important role in viral replication. In this study, we performed a biological evaluation on nine phlorotannins isolated from the edible brown algae Ecklonia cava. The nine isolated phlorotannins (1-9), except phloroglucinol (1), possessed SARS-CoV 3CL(pro) inhibitory activities in a dose-dependently and competitive manner. Of these phlorotannins (1-9), two eckol groups with a diphenyl ether linked dieckol (8) showed the most potent SARS-CoV 3CL(pro) trans/cis-cleavage inhibitory effects (IC(50)s = 2.7 and 68.1 μM, respectively). This is the first report of a (8) phlorotannin chemotype significantly blocking the cleavage of SARS-CoV 3CL(pro) in a cell-based assay with no toxicity. Furthermore, dieckol (8) exhibited a high association rate in the SPR sensorgram and formed extremely strong hydrogen bonds to the catalytic dyad (Cys145 and His41) of the SARS-CoV 3CL(pro).
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Affiliation(s)
- Ji-Young Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Republic of Korea
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24
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Ye S, Xia H, Dong C, Cheng Z, Xia X, Zhang J, Zhou X, Hu Y. Identification and characterization of Iflavirus 3C-like protease processing activities. Virology 2012; 428:136-45. [PMID: 22534091 PMCID: PMC7111971 DOI: 10.1016/j.virol.2012.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/03/2012] [Accepted: 04/05/2012] [Indexed: 12/13/2022]
Abstract
Viral replication and capsid assembly in the viruses in the order Picornavirales requires polyprotein proteolytic processing by 3C or 3C-like (3CL) proteases. We identified and characterized the 3CL protease of Ectropis obliqua virus (EoV) of the newly established family Iflaviridae (order Picornavirales). The bacterially expressed EoV 3CL protease domain autocatalytically released itself from larger precursors by proteolytic cleavage, and cleavage sites were determined via N-terminal sequencing of the cleavage products. This protease also mediated trans-proteolytic activity and cleaved the polyprotein at the same specific positions. Moreover, we determined the critical catalytic residues (H2261, D2299, C2383) for the protease activity, and characterized the biochemical properties of EoV 3CL and its responses to various protease inhibitors. Our work is the first study to identify an iflaviral 3CL protease and further characterize it in detail and should foster our understanding of EoV and other iflaviruses.
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Affiliation(s)
| | | | | | | | | | | | - Xi Zhou
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yuanyang Hu
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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25
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Chuck CP, Chow HF, Wan DCC, Wong KB. Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses. PLoS One 2011; 6:e27228. [PMID: 22073294 PMCID: PMC3206940 DOI: 10.1371/journal.pone.0027228] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/12/2011] [Indexed: 01/22/2023] Open
Abstract
Background Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CLpro), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection. Methodology/Principal Findings Here, we profiled the substrate specificities of 3CLpro from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 19×8 of variants with single substitutions at P5 to P3' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CLpro prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1' and P2' positions. Despite 3CLpro from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CLpro prefers P4-Pro and SARS-CoV 3CLpro prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences ‘VARLQ↓SGF’ that can be cleaved efficiently by all 3CLpro with relative activity of 1.7 to 3.2, and ‘VPRLQ↓SGF’ that can be cleaved specifically by IBV 3CLpro with relative activity of 4.3. Conclusions/Significance The comprehensive substrate specificities of 3CLpro from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases.
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Affiliation(s)
- Chi-Pang Chuck
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hak-Fun Chow
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
| | - David Chi-Cheong Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kam-Bo Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail:
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26
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Activation and maturation of SARS-CoV main protease. Protein Cell 2011; 2:282-90. [PMID: 21533772 PMCID: PMC4875205 DOI: 10.1007/s13238-011-1034-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 04/07/2011] [Indexed: 12/30/2022] Open
Abstract
The worldwide outbreak of the severe acute respiratory syndrome (SARS) in 2003 was due to the transmission of SARS coronavirus (SARS-CoV). The main protease (Mpro) of SARS-CoV is essential for the viral life cycle, and is considered to be an attractive target of anti-SARS drug development. As a key enzyme for proteolytic processing of viral polyproteins to produce functional non-structure proteins, Mpro is first auto-cleaved out of polyproteins. The monomeric form of Mpro is enzymatically inactive, and it is activated through homo-dimerization which is strongly affected by extra residues to both ends of the mature enzyme. This review provides a summary of the related literatures on the study of the quaternary structure, activation, and self-maturation of Mpro over the past years.
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Khan S, Verma G, Sharma S. A novel Ca2+-activated protease from germinating Vigna radiata seeds and its role in storage protein mobilization. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:855-861. [PMID: 20149479 DOI: 10.1016/j.jplph.2010.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 01/20/2010] [Accepted: 01/20/2010] [Indexed: 05/28/2023]
Abstract
Calcium (Ca(2+))-dependent/activated proteases make decisive cleavages in proteins, affecting their further degradation/activation. Few such Ca(2+)-dependent proteases have been reported from plants, and none during germination-related events. Seeds are woken up from their quiescent state upon imbibition of water. The subsequent process of germination is strongly influenced by hormones (mainly gibberellins) and light, with both resulting in change in intracellular Ca(2+). We have investigated the effect of Ca(2+) on protease activity in extracts prepared from dry Vigna radiata (L.) Wilczec seeds and cotyledons 4, 24, 48 and 72h post-imbibition. Ca(2+)-activated protease activity is present at a very low level in dry seeds, rises with imbibition and peaks 24h post-imbibition. Subsequently, the activity rapidly declines, even as total protease activity continues to rise. Calcium activation of proteolysis was reversed by ethylene diamine tetraacetic acid (EDTA), ethylene glycol-bis (2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA), 1,10, phenanthroline, chlorpromazine and by beta-mercaptoethanol in a concentration-dependent manner. Protease activity was also inhibited by para chloro mercuribenzoate (pCMB) and l-trans-epoxysuccinyl-leucylamido(4-guanidino) butane (E 64), while phenyl methyl sulfonyl fluoride (PMSF) and pepstatin did not effect Ca(2+) activation. The protease could be separated from the calmodulin fraction by size-exclusion chromatography, while retaining its ability for Ca(2+) activation, excluding the possibility of activation through calmodulin-based pathways. The presence of a Ca(2+)-activated protease in the cotyledons suggests its role in a predetermined program of germination involving elevation of cytosolic Ca(2+) levels during germination. This protease could be an important enzyme interfacing cytoplasmic signaling events and initiation of storage protein mobilization during seed germination.
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Affiliation(s)
- Sadaf Khan
- Department of Biochemistry, Lucknow University, Lucknow 226007, India
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Monto A, Schooley RT, Lai JC, Sulkowski MS, Chung RT, Pawlotsky JM, McHutchison JG, Jacobson IM. Lessons from HIV therapy applied to viral hepatitis therapy: summary of a workshop. Am J Gastroenterol 2010; 105:989-1004; quiz 988, 1005. [PMID: 20087331 DOI: 10.1038/ajg.2009.726] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Therapies for hepatitis B virus (HBV) have continued to evolve, and new therapies for hepatitis C virus (HCV) will soon be available in clinical practice. These medications for hepatitis C will mark the first time that direct antivirals that target HCV functions have been used. When such drugs are used as single agents, previously existing mutants with reduced susceptibility to them are rapidly selected. The relationship between these drug-resistant mutants and "wild-type" virus is unclear, but resistant strains likely have the potential to maintain the progression of liver disease despite successful treatment of "wild-type" virus. Resistant HBV and now HCV are already a clinical problem. The same issue was recognized very early in the development of therapy against HIV, with azidothymidine-resistant mutants detected within the first weeks of therapy. Clinical investigation and a progressive understanding of the pathogenesis of the disease overcame this challenge and led to the substantial and durable benefits of antiretroviral therapy that are evident today. To bring experts from the fields of HIV and viral hepatitis virology and therapy together for interactive discussions about how to apply the lessons from HIV to the further development of viral hepatitis therapy, the American Association for the Study of Liver Diseases held a single-topic conference entitled "Viral Hepatitis Therapy: Lessons to be Learned From HIV" on 24-26 July 2008. This article summarizes that conference.
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Affiliation(s)
- Alexander Monto
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California 94121, USA.
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Chen S, Jonas F, Shen C, Hilgenfeld R, Higenfeld R. Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode. Protein Cell 2010; 1:59-74. [PMID: 21203998 PMCID: PMC4875104 DOI: 10.1007/s13238-010-0011-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/17/2009] [Indexed: 11/29/2022] Open
Abstract
The main protease (Mpro) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for transcleavage activity. However, the auto-processing mechanism of Mpro, i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” Mpro. Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature Mpro, are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and transcleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of Mpro appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of Mpro from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV Mpro.
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Affiliation(s)
- Shuai Chen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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Hu D, Shao C, Guan W, Su Z, Sun J. Studies on the interactions of Ti-containing polyoxometalates (POMs) with SARS-CoV 3CLpro by molecular modeling. J Inorg Biochem 2007; 101:89-94. [PMID: 17049610 PMCID: PMC7112571 DOI: 10.1016/j.jinorgbio.2006.08.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 08/14/2006] [Accepted: 08/17/2006] [Indexed: 11/28/2022]
Abstract
Ti-containing alpha-Keggin polyoxometalates (POMs) have been proved with properties of both anti-tumor and anti-HIV (human immunodeficiency virus). The potential anti-SARS (severe acute respiratory syndrome) activity of the POMs [alpha-PTi(2)W(10)O(40)](7-) isomers was investigated in this paper by molecular modeling method. The SARS 3c like protease, namely the SARS 3CL(pro) is the key function protease for virus replication as well as transcription and thus can be taken as one of the key targets for anti-SARS drug design. Affinity/Insight II was used to explore possible binding locations for POMs/3CL(pro) interaction. Charges in the POMs were obtained from density-functional theory (DFT) method. The results show that POMs bind with 3CL(pro) in the active site region with high affinity; POMs are more prone to bind with 3CL(pro) than with some organic compounds; for the POMs/3CL(pro)complex, the OTi(2) in POMs is the vital element for electrostatic interaction, and the electrostatic binding energy is strong enough to keep the complex stable.
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Affiliation(s)
- Donghua Hu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
- Traditional Chinese Medicine Institute of Traditional Chinese Medicine Collage of Changchun, Changchun 130017, China
| | - Chen Shao
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Wei Guan
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Zhongmin Su
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Jiazhong Sun
- State Key Laboratory of Theoretical and Computational Chemistry of Jilin University, Changchun 130000, China
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Xue X, Yang H, Shen W, Zhao Q, Li J, Yang K, Chen C, Jin Y, Bartlam M, Rao Z. Production of authentic SARS-CoV M(pro) with enhanced activity: application as a novel tag-cleavage endopeptidase for protein overproduction. J Mol Biol 2006; 366:965-75. [PMID: 17189639 PMCID: PMC7094453 DOI: 10.1016/j.jmb.2006.11.073] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 11/24/2006] [Indexed: 02/05/2023]
Abstract
The viral proteases have proven to be the most selective and useful for removing the fusion tags in fusion protein expression systems. As a key enzyme in the viral life-cycle, the main protease (Mpro) is most attractive for drug design targeting the SARS coronavirus (SARS-CoV), the etiological agent responsible for the outbreak of severe acute respiratory syndrome (SARS) in 2003. In this study, SARS-CoV Mpro was used to specifically remove the GST tag in a new fusion protein expression system. We report a new method to produce wild-type (WT) SARS-CoV Mpro with authentic N and C termini, and compare the activity of WT protease with those of three different types of SARS-CoV Mpro with additional residues at the N or C terminus. Our results show that additional residues at the N terminus, but not at the C terminus, of Mpro are detrimental to enzyme activity. To explain this, the crystal structures of WT SARS-CoV Mpro and its complex with a Michael acceptor inhibitor were determined to 1.6 Å and 1.95 Å resolution respectively. These crystal structures reveal that the first residue of this protease is important for sustaining the substrate-binding pocket and inhibitor binding. This study suggests that SARS-CoV Mpro could serve as a new tag-cleavage endopeptidase for protein overproduction, and the WT SARS-CoV Mpro is more appropriate for mechanistic characterization and inhibitor design.
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Affiliation(s)
- Xiaoyu Xue
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Yang
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Shen
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Qi Zhao
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jun Li
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Kailin Yang
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Cheng Chen
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Yinghua Jin
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Mark Bartlam
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China
| | - Zihe Rao
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China
- Nankai University, Tianjin 300071, China
- Corresponding author.
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Lin CW, Lin KH, Hsieh TH, Shiu SY, Li JY. Severe acute respiratory syndrome coronavirus 3C-like protease-induced apoptosis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2006; 46:375-80. [PMID: 16553810 PMCID: PMC7110344 DOI: 10.1111/j.1574-695x.2006.00045.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 10/06/2005] [Indexed: 01/30/2023]
Abstract
The pathogenesis of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is an important issue for the treatment and prevention of severe acute respiratory syndrome. Recently, SARS-CoV has been demonstrated to induce cell apoptosis in Vero-E6 cells. The possible role of SARS-CoV 3C-like protease (3CLpro) in virus-induced apoptosis is characterized in this study. Growth arrest and apoptosis via caspase-3 and caspase-9 activities were demonstrated in SARS-CoV 3CLpro -expressing human promonocyte cells. The fluorescence intensity of dihydrorhodamine 123 staining indicated that cellular reactive oxygen species were markedly increased in SARS-CoV 3CLpro -expressing cells. Moreover, in vivo signalling pathway assay indicated that 3CLpro increased the activation of the nuclear factor-kappa B-dependent reporter, but inhibited activator protein-1-dependent transcription. This finding is likely to be responsible for virus-induced apoptotic signalling.
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Affiliation(s)
- Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
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Lin CW, Tsai FJ, Tsai CH, Lai CC, Wan L, Ho TY, Hsieh CC, Chao PDL. Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds. Antiviral Res 2006; 68:36-42. [PMID: 16115693 PMCID: PMC7114321 DOI: 10.1016/j.antiviral.2005.07.002] [Citation(s) in RCA: 340] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Revised: 07/05/2005] [Accepted: 07/05/2005] [Indexed: 12/20/2022]
Abstract
The 3C-like protease (3CLpro) of SARS-coronavirus mediates the proteolytic processing of replicase polypeptides 1a and 1ab into functional proteins, becoming an important target for the drug development. In this study, Isatis indigotica root extract, five major compounds of I. indigotica root, and seven plant-derived phenolic compounds were tested for anti-SARS-CoV 3CLpro effects using cell-free and cell-based cleavage assays. Cleavage assays with the 3CLpro demonstrated that IC50 values were in micromolar ranges for I. indigotica root extract, indigo, sinigrin, aloe emodin and hesperetin. Sinigrin (IC50: 217 microM) was more efficient in blocking the cleavage processing of the 3CLpro than indigo (IC50: 752 microM) and beta-sitosterol (IC50: 1210 microM) in the cell-based assay. Only two phenolic compounds aloe emodin and hesperetin dose-dependently inhibited cleavage activity of the 3CLpro, in which the IC50 was 366 microM for aloe emodin and 8.3 microM for hesperetin in the cell-based assay.
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Affiliation(s)
- Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung 404, Taiwan, ROC
- Clinical Virology Laboratory, Department of Laboratory Medicine, China Medical University Hospital, Taichung 404, Taiwan, ROC
- Corresponding author. Fax: +886 4 22057414.
| | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung 404, Taiwan, ROC
- Corresponding author. Fax: +886 4 22057414.
| | - Chang-Hai Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung 404, Taiwan, ROC
| | - Chien-Chen Lai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung 404, Taiwan, ROC
| | - Lei Wan
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung 404, Taiwan, ROC
| | - Tin-Yun Ho
- Institute of Chinese Medical Science, China Medical University, Taichung 404, Taiwan, ROC
| | - Chang-Chi Hsieh
- Institute of Integration Chinese and Western Medicine, China Medical University, Taichung 404, Taiwan, ROC
| | - Pei-Dawn Lee Chao
- Department of Pharmacy, China Medical University, Taichung 404, Taiwan, ROC
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Brierley I, Dos Ramos FJ. Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res 2005; 119:29-42. [PMID: 16310880 PMCID: PMC7114087 DOI: 10.1016/j.virusres.2005.10.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 07/31/2005] [Accepted: 10/19/2005] [Indexed: 01/11/2023]
Abstract
Ribosomal frameshifting is a mechanism of gene expression used by several RNA viruses to express replicase enzymes. This article focuses on frameshifting in two human pathogens, the retrovirus human immunodeficiency virus type 1 (HIV-1) and the coronavirus responsible for severe acute respiratory syndrome (SARS). The nature of the frameshift signals of HIV-1 and the SARS–CoV will be described and the impact of this knowledge on models of frameshifting will be considered. The role of frameshifting in the replication cycle of the two pathogens and potential antiviral therapies targeting frameshifting will also be discussed.
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Affiliation(s)
- Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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Lin CW, Tsai FJ, Wan L, Lai CC, Lin KH, Hsieh TH, Shiu SY, Li JY. Binding interaction of SARS coronavirus 3CL(pro) protease with vacuolar-H+ ATPase G1 subunit. FEBS Lett 2005; 579:6089-94. [PMID: 16226257 PMCID: PMC7094641 DOI: 10.1016/j.febslet.2005.09.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/18/2005] [Accepted: 09/19/2005] [Indexed: 11/19/2022]
Abstract
The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is an important issue for treatment and prevention of SARS. Recently, SARS-CoV 3CL(pro) protease has been implied to be possible relevance to SARS-CoV pathogenesis. In this study, we intended to identify potential 3CL(pro)-interacting cellular protein(s) using the phage-displayed human lung cDNA library. The vacuolar-H+ ATPase (V-ATPase) G1 subunit that contained a 3CL(pro) cleavage site-like motif was identified as a 3CL(pro)-interacting protein, as confirmed using the co-immunoprecipitation assay and the relative affinity assay. In addition, our result also demonstrated the cleavage of the V-ATPase G1 fusion protein and the immunoprecipitation of cellular V-ATPase G1 by the 3CL(pro). Moreover, loading cells with SNARF-1 pH-sensitive dye showed that the intracellular pH in 3CL(pro)-expressing cells was significantly lower as compared to mock cells.
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Affiliation(s)
- Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung 404, Taiwan.
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Lin CW, Tsai CH, Tsai FJ, Chen PJ, Lai CC, Wan L, Chiu HH, Lin KH. Characterization of trans- and cis-cleavage activity of the SARS coronavirus 3CLpro protease: basis for the in vitro screening of anti-SARS drugs. FEBS Lett 2004; 574:131-7. [PMID: 15358553 PMCID: PMC7127318 DOI: 10.1016/j.febslet.2004.08.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 07/26/2004] [Accepted: 08/12/2004] [Indexed: 12/29/2022]
Abstract
Severe acute respiratory syndrome (SARS) has been globally reported. A novel coronavirus (CoV), SARS-CoV, was identified as the etiological agent of the disease. SARS-CoV 3C-like protease (3CLpro) mediates the proteolytic processing of replicase polypeptides 1a and 1ab into functional proteins, playing an important role in viral replication. In this study, we demonstrated the expression of the SARS-CoV 3CLpro in Escherichia coli and Vero cells, and then characterized the in vitro trans-cleavage and the cell-based cis-cleavage by the 3CLpro. Mutational analysis of the 3CLpro demonstrated the importance of His41, Cys145, and Glu166 in the substrate-binding subsite S1 for keeping the proteolytic activity. In addition, alanine substitution of the cleavage substrates indicated that Gln-(P1) in the substrates mainly determined the cleavage efficiency. Therefore, this study not only established the quantifiable and reliable assay for the in vitro and cell-based measurement of the 3CLpro activity, but also characterized the molecular interaction of the SARS-CoV 3CLpro with the substrates. The results will be useful for the rational development of the anti-SARS drugs.
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Affiliation(s)
- Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung 404, Taiwan, ROC.
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