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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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Kneller DW, Phillips G, O’Neill HM, Tan K, Joachimiak A, Coates L, Kovalevsky A. Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro: insights into enzyme mechanism and drug design. IUCRJ 2020; 7:S2052252520012634. [PMID: 33063790 PMCID: PMC7553146 DOI: 10.1107/s2052252520012634] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL Mpro, is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL Mpro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N-ethylmaleimide. It is suggested that the zwitterionic Cys145-His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid-base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL Mpro inhibitors.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Hugh M. O’Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kemin Tan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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53
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Theerawatanasirikul S, Kuo CJ, Phecharat N, Chootip J, Lekcharoensuk C, Lekcharoensuk P. Structural-based virtual screening and in vitro assays for small molecules inhibiting the feline coronavirus 3CL protease as a surrogate platform for coronaviruses. Antiviral Res 2020; 182:104927. [PMID: 32910955 PMCID: PMC7476565 DOI: 10.1016/j.antiviral.2020.104927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
Feline infectious peritonitis (FIP) which is caused by feline infectious peritonitis virus (FIPV), a variant of feline coronavirus (FCoV), is a member of family Coronaviridae, together with severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. So far, neither effective vaccines nor approved antiviral therapeutics are currently available for the treatment of FIPV infection. Both human and animal CoVs shares similar functional proteins, particularly the 3CL protease (3CLpro), which plays the pivotal role on viral replication. We investigated the potential drug-liked compounds and their inhibitory interaction on the 3CLpro active sites of CoVs by the structural-bases virtual screening. Fluorescence resonance energy transfer (FRET) assay revealed that three out of twenty-eight compounds could hamper FIPV 3CLpro activities with IC50 of 3.57 ± 0.36 μM to 25.90 ± 1.40 μM, and Ki values of 2.04 ± 0.08 to 15.21 ± 1.76 μM, respectively. Evaluation of antiviral activity using cell-based assay showed that NSC629301 and NSC71097 could strongly inhibit the cytopathic effect and also reduced replication of FIPV in CRFK cells in all examined conditions with the low range of EC50 (6.11 ± 1.90 to 7.75 ± 0.48 μM and 1.99 ± 0.30 to 4.03 ± 0.60 μM, respectively), less than those of ribavirin and lopinavir. Analysis of FIPV 3CLpro-ligand interaction demonstrated that the selected compounds reacted to the crucial residues (His41 and Cys144) of catalytic dyad. Our investigations provide a fundamental knowledge for the further development of antiviral agents and increase the number of anti-CoV agent pools for feline coronavirus and other related CoVs. Virtual screening and molecular docking revealed three lead compounds bound to FIPV 3CLpro active site. The 3D structures of 3CLpro of coronaviruses including SARS-CoV-2 are highly conserved. These compounds showed inhibitory effects on the proteases of FIPV, PEDV, SARS-CoV and SARS-CoV-2. Their antiviral activities are better than Ribavirin and Lopinavir while comparable to GC376.
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Affiliation(s)
- Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Chih Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Nanthawan Phecharat
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Jullada Chootip
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Chalermpol Lekcharoensuk
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand; Center of Advanced Studies in Agriculture and Food, KU Institute, Thailand.
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54
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Discovery of M Protease Inhibitors Encoded by SARS-CoV-2. Antimicrob Agents Chemother 2020; 64:AAC.00872-20. [PMID: 32669265 PMCID: PMC7449189 DOI: 10.1128/aac.00872-20] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
The coronavirus (CoV) disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is a health threat worldwide. Viral main protease (Mpro, also called 3C-like protease [3CLpro]) is a therapeutic target for drug discovery. Herein, we report that GC376, a broad-spectrum inhibitor targeting Mpro in the picornavirus-like supercluster, is a potent inhibitor for the Mpro encoded by SARS-CoV-2, with a half-maximum inhibitory concentration (IC50) of 26.4 ± 1.1 nM. In this study, we also show that GC376 inhibits SARS-CoV-2 replication with a half-maximum effective concentration (EC50) of 0.91 ± 0.03 μM. Only a small portion of SARS-CoV-2 Mpro was covalently modified in the excess of GC376 as evaluated by mass spectrometry analysis, indicating that improved inhibitors are needed. Subsequently, molecular docking analysis revealed that the recognition and binding groups of GC376 within the active site of SARS-CoV-2 Mpro provide important new information for the optimization of GC376. Given that sufficient safety and efficacy data are available for GC376 as an investigational veterinary drug, expedited development of GC376, or its optimized analogues, for treatment of SARS-CoV-2 infection in human is recommended.
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55
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Jo S, Kim S, Kim DY, Kim MS, Shin DH. Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro. J Enzyme Inhib Med Chem 2020; 35:1539-1544. [PMID: 32746637 PMCID: PMC7470085 DOI: 10.1080/14756366.2020.1801672] [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] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been a pandemic disease of which the termination is not yet predictable. Currently, researches to develop vaccines and treatments is going on globally to cope with this disastrous disease. Main protease (3CLpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the good targets to find antiviral agents before vaccines are available. Some flavonoids are known to inhibit 3CLpro from SARS-CoV which causes SARS. Since their sequence identity is 96%, a similar approach was performed with a flavonoid library. Baicalin, herbacetin, and pectolinarin have been discovered to block the proteolytic activity of SARS-CoV-2 3CLpro. An in silico docking study showed that the binding modes of herbacetin and pectolinarin are similar to those obtained from the catalytic domain of SARS-CoV 3CLpro. However, their binding affinities are different due to the usage of whole SARS-CoV-2 3CLpro in this study. Baicalin showed an effective inhibitory activity against SARS-CoV-2 3CLpro and its docking mode is different from those of herbacetin and pectolinarin. This study suggests important scaffolds to design 3CLpro inhibitors to develop antiviral agents or health-foods and dietary supplements to cope with SARS-CoV-2.
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Affiliation(s)
- Seri Jo
- College of Pharmacy, Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Suwon Kim
- College of Pharmacy, Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dae Yong Kim
- N-BIOTEK, Bucheon-Si, Gyeong-gi, Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy, Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy, Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
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56
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten JJ, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:12682316. [PMID: 33200116 PMCID: PMC7668741 DOI: 10.26434/chemrxiv.12682316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/24/2020] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | | | | | | | | | | | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Justin J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
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57
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Torequl Islam M, Nasiruddin M, Khan IN, Mishra SK, Kudrat-E-Zahan M, Alam Riaz T, Ali ES, Rahman MS, Mubarak MS, Martorell M, Cho WC, Calina D, Docea AO, Sharifi-Rad J. A Perspective on Emerging Therapeutic Interventions for COVID-19. Front Public Health 2020; 8:281. [PMID: 32733837 PMCID: PMC7362761 DOI: 10.3389/fpubh.2020.00281] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022] Open
Abstract
Coronaviruses are enveloped positive-sense RNA viruses with an unusual large RNA genome and a unique replication mechanism, which are characterized by club-like spikes that protrude from their surface. An outbreak of a novel coronavirus 2019 infection has posed significant threat to the health and economies in the whole world. This article reviewed the viral replication, pathogenicity, prevention and treatment strategies. With a lack of approved treatment options for this virus, alternative approaches to control the spread of disease is in urgent need. This article also covers some management strategies which may be applied to this virus outbreak. Ongoing clinical studies related to possible treatments for COVID-19, potential vaccines, and alternative medication such as natural compounds are also discussed.
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Affiliation(s)
- Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Nasiruddin
- Department of Chemistry, Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Ishaq N. Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Siddhartha Kumar Mishra
- Cancer Biology Laboratory, Department of Zoology, School of Biological Sciences, Dr. Harisingh Gour Central University, Sagar, India
| | | | - Thoufiqul Alam Riaz
- Department of Pharmacology, School of Medicine, Institute of New Drug Development, Jeonbuk National University, Jeonju, South Korea
| | - Eunus S. Ali
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - M. Safiur Rahman
- Environmental and Atmospheric Chemistry Laboratory, Bangladesh Atomic Energy Commission, Dhaka, Bangladesh
| | | | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile
- Centre for Healthy Living, University of Concepción, Concepción, Chile
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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58
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Kneller DW, Phillips G, O'Neill HM, Jedrzejczak R, Stols L, Langan P, Joachimiak A, Coates L, Kovalevsky A. Structural plasticity of SARS-CoV-2 3CL M pro active site cavity revealed by room temperature X-ray crystallography. Nat Commun 2020; 11:3202. [PMID: 32581217 PMCID: PMC7314768 DOI: 10.1038/s41467-020-16954-7] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 disease caused by the SARS-CoV-2 coronavirus has become a pandemic health crisis. An attractive target for antiviral inhibitors is the main protease 3CL Mpro due to its essential role in processing the polyproteins translated from viral RNA. Here we report the room temperature X-ray structure of unliganded SARS-CoV-2 3CL Mpro, revealing the ligand-free structure of the active site and the conformation of the catalytic site cavity at near-physiological temperature. Comparison with previously reported low-temperature ligand-free and inhibitor-bound structures suggest that the room temperature structure may provide more relevant information at physiological temperatures for aiding in molecular docking studies.
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Affiliation(s)
- Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - Paul Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
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59
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Ghosh AK, Brindisi M, Shahabi D, Chapman ME, Mesecar AD. Drug Development and Medicinal Chemistry Efforts toward SARS-Coronavirus and Covid-19 Therapeutics. ChemMedChem 2020; 15:907-932. [PMID: 32324951 PMCID: PMC7264561 DOI: 10.1002/cmdc.202000223] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 infection is spreading at an alarming rate and has created an unprecedented health emergency around the globe. There is no effective vaccine or approved drug treatment against COVID-19 and other pathogenic coronaviruses. The development of antiviral agents is an urgent priority. Biochemical events critical to the coronavirus replication cycle provided a number of attractive targets for drug development. These include, spike protein for binding to host cell-surface receptors, proteolytic enzymes that are essential for processing polyproteins into mature viruses, and RNA-dependent RNA polymerase for RNA replication. There has been a lot of ground work for drug discovery and development against these targets. Also, high-throughput screening efforts have led to the identification of diverse lead structures, including natural product-derived molecules. This review highlights past and present drug discovery and medicinal-chemistry approaches against SARS-CoV, MERS-CoV and COVID-19 targets. The review hopes to stimulate further research and will be a useful guide to the development of effective therapies against COVID-19 and other pathogenic coronaviruses.
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Affiliation(s)
- Arun K. Ghosh
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Medicinal Chemistry and Molecular PharmacolgyPurdue UniversityWest LafayetteIN 47907USA
| | - Margherita Brindisi
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Excellence of PharmacyUniversity of Naples Federico II80131NaplesItaly
| | - Dana Shahabi
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
| | | | - Andrew D. Mesecar
- Department of ChemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of BiochemistryPurdue UniversityWest LafayetteIN 47907USA
- Department of Biological SciencesPurdue UniversityWest LafayetteIN 47907USA
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60
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In silico and in vitro analysis of small molecules and natural compounds targeting the 3CL protease of feline infectious peritonitis virus. Antiviral Res 2019; 174:104697. [PMID: 31863793 PMCID: PMC7114316 DOI: 10.1016/j.antiviral.2019.104697] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
The computational search of chemical libraries has been used as a powerful tool for the rapid discovery of candidate compounds. To find small molecules with anti-feline infectious peritonitis virus (FIPV) properties, we utilized a virtual screening technique to identify the active site on the viral protease for the binding of the available natural compounds. The protease 3CL (3CLpro) plays an important role in the replication cycle of FIPV and other viruses within the family Coronaviridae. The 15 best-ranked candidate consensus compounds, based on three docking tools, were evaluated for further assays. The protease inhibitor assay on recombinant FIPV 3CLpro was performed to screen the inhibitory effect of the candidate compounds with IC50 ranging from 6.36 ± 2.15 to 78.40 ± 2.60 μM. As determined by the cell-based assay, the compounds NSC345647, NSC87511, and NSC343256 showed better EC50 values than the broad-spectrum antiviral drug ribavirin and the protease inhibitor lopinavir, under all the test conditions including pre-viral entry, post-viral entry, and prophylactic activity. The NSC87511 particularly yielded the best selective index (>4; range of SI = 13.80-22.90). These results indicated that the natural small-molecular compounds specifically targeted the 3CLpro of FIPV and inhibited its replication. Structural modification of these compounds may generate a higher anti-viral potency for the further development of a novel therapy against FIP.
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61
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Jo S, Kim H, Kim S, Shin DH, Kim M. Characteristics of flavonoids as potent MERS-CoV 3C-like protease inhibitors. Chem Biol Drug Des 2019; 94:2023-2030. [PMID: 31436895 PMCID: PMC7162010 DOI: 10.1111/cbdd.13604] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/18/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022]
Abstract
Middle East respiratory syndrome-coronavirus (MERS-CoV) is a zoonotic virus transmitted between animals and human beings. It causes MERS with high mortality rate. However, no vaccine or specific treatment is currently available. Since antiviral activity of some flavonoids is known, we applied a flavonoid library to probe inhibitory compounds against MERS-CoV 3C-like protease (3CLpro). Herbacetin, isobavachalcone, quercetin 3-β-d-glucoside and helichrysetin were found to block the enzymatic activity of MERS-CoV 3CLpro. The binding of the four flavonoids was also confirmed independently using a tryptophan-based fluorescence method. The systematic comparison of the binding affinity of flavonoids made it possible to infer their scaffolds and functional groups required to bind with MERS-CoV 3CLpro. An induced-fit docking analysis revealed that S1 and S2 sites play a role in interaction with flavonoids. The experimental and computational study showed that flavonol and chalcone are favourite scaffolds to bind with the catalytic site of MERS-CoV 3CLpro. It was also deduced that some flavonoid derivatives with hydrophobic or carbohydrate attached to their core structures have a good inhibitory effect. Therefore, we suggest that flavonoids with these characteristics can be used as templates to develop potent MERS-CoV 3CLpro inhibitors.
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Affiliation(s)
- Seri Jo
- College of Pharmacy and Graduates School of Pharmaceutical SciencesEwha Womans UniversitySeoulKorea
| | - Hyojin Kim
- College of Pharmacy and Graduates School of Pharmaceutical SciencesEwha Womans UniversitySeoulKorea
| | - Suwon Kim
- College of Pharmacy and Graduates School of Pharmaceutical SciencesEwha Womans UniversitySeoulKorea
| | - Dong Hae Shin
- College of Pharmacy and Graduates School of Pharmaceutical SciencesEwha Womans UniversitySeoulKorea
| | - Mi‐Sun Kim
- College of Pharmacy and Graduates School of Pharmaceutical SciencesEwha Womans UniversitySeoulKorea
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62
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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63
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Kumar V, Shin JS, Shie JJ, Ku KB, Kim C, Go YY, Huang KF, Kim M, Liang PH. Identification and evaluation of potent Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL Pro inhibitors. Antiviral Res 2017; 141:101-106. [PMID: 28216367 PMCID: PMC7113684 DOI: 10.1016/j.antiviral.2017.02.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 01/25/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe acute respiratory illness with fever, cough and shortness of breath. Up to date, it has resulted in 1826 human infections, including 649 deaths. Analogous to picornavirus 3C protease (3Cpro), 3C-like protease (3CLpro) is critical for initiation of the MERS-CoV replication cycle and is thus regarded as a validated drug target. As presented here, our peptidomimetic inhibitors of enterovirus 3Cpro (6b, 6c and 6d) inhibited 3CLpro of MERS-CoV and severe acute respiratory syndrome coronavirus (SARS-CoV) with IC50 values ranging from 1.7 to 4.7 μM and from 0.2 to 0.7 μM, respectively. In MERS-CoV-infected cells, the inhibitors showed antiviral activity with EC50 values ranging from 0.6 to 1.4 μM, by downregulating the viral protein production in cells as well as reducing secretion of infectious viral particles into culture supernatants. They also suppressed other α- and β-CoVs from human and feline origin. These compounds exhibited good selectivity index (over 70 against MERS-CoV) and could lead to the development of broad-spectrum antiviral drugs against emerging CoVs and picornaviruses.
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Affiliation(s)
- Vathan Kumar
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jin Soo Shin
- Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Keun Bon Ku
- Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Chonsaeng Kim
- Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yun Young Go
- Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Meehyein Kim
- Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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64
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Pillaiyar T, Manickam M, Namasivayam V, Hayashi Y, Jung SH. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J Med Chem 2016; 59:6595-628. [PMID: 26878082 PMCID: PMC7075650 DOI: 10.1021/acs.jmedchem.5b01461] [Citation(s) in RCA: 509] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CL(pro), has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CL(pro) chemotherapies discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small molecule inhibitors of SARS-CoV 3CL(pro). Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Manoj Manickam
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Vigneshwaran Namasivayam
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Yoshio Hayashi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Sang-Hun Jung
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
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65
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Kumar V, Tan KP, Wang YM, Lin SW, Liang PH. Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors. Bioorg Med Chem 2016; 24:3035-3042. [PMID: 27240464 PMCID: PMC7079562 DOI: 10.1016/j.bmc.2016.05.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome (SARS) led to a life-threatening form of atypical pneumonia in late 2002. Following that, Middle East Respiratory Syndrome (MERS-CoV) has recently emerged, killing about 36% of patients infected globally, mainly in Saudi Arabia and South Korea. Based on a scaffold we reported for inhibiting neuraminidase (NA), we synthesized the analogues and identified compounds with low micromolar inhibitory activity against 3CL(pro) of SARS-CoV and MERS-CoV. Docking studies show that a carboxylate present at either R(1) or R(4) destabilizes the oxyanion hole in the 3CL(pro). Interestingly, 3f, 3g and 3m could inhibit both NA and 3CL(pro) and serve as a starting point to develop broad-spectrum antiviral agents.
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Affiliation(s)
- Vathan Kumar
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Kian-Pin Tan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Ying-Ming Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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66
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Ye G, Deng F, Shen Z, Luo R, Zhao L, Xiao S, Fu ZF, Peng G. Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Virology 2016; 494:225-35. [PMID: 27128350 PMCID: PMC7111274 DOI: 10.1016/j.virol.2016.04.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/16/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CLpro), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CLpro and a molecular complex between an inactive PEDV 3CLpro variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CLpro. The dimerization of PEDV 3CLpro is similar to that of other Alphacoronavirus 3CLpros but has several differences from that of SARS-CoV 3CLpro from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CLpros, which may provide new insights into the recognition of substrates by 3CLpros in various coronavirus genera. The substrate binding mechanism of PEDV 3CLpro has been characterized. The large buried surface area is responsible for dimerization of PEDV 3CLpro. Non-conserved motifs cause different cleavage between PEDV and SARS-CoV 3CLpros.
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Affiliation(s)
- Gang Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China.
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67
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Kuo C, Liang P. Characterization and Inhibition of the Main Protease of Severe Acute Respiratory Syndrome Coronavirus. CHEMBIOENG REVIEWS 2015. [PMCID: PMC7159133 DOI: 10.1002/cben.201400031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chih‐Jung Kuo
- National Chung Hsing University, College of Veterinary Medicine, Department of Veterinary Medicine, Taichung 402, Taiwan
| | - Po‐Huang Liang
- National Chung Hsing University, College of Veterinary Medicine, Department of Veterinary Medicine, Taichung 402, Taiwan
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68
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Lim L, Shi J, Mu Y, Song J. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain. PLoS One 2014; 9:e101941. [PMID: 25036652 PMCID: PMC4103764 DOI: 10.1371/journal.pone.0101941] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/13/2014] [Indexed: 11/18/2022] Open
Abstract
Previously we revealed that the extra domain of SARS 3CLpro mediated the catalysis via different mechanisms. While the R298A mutation completely abolished the dimerization, thus resulting in the inactive catalytic machinery, N214A inactivated the enzyme by altering its dynamics without significantly perturbing its structure. Here we studied another mutant with S284-T285-I286 replaced by Ala (STI/A) with a 3.6-fold activity increase and slightly enhanced dimerization. We determined its crystal structure, which still adopts the dimeric structure almost identical to that of the wild-type (WT), except for slightly tighter packing between two extra-domains. We then conducted 100-ns molecular dynamics (MD) simulations for both STI/A and WT, the longest reported so far for 3CLpro. In the simulations, two STI/A extra domains become further tightly packed, leading to a significant volume reduction of the nano-channel formed by residues from both catalytic and extra domains. The enhanced packing appears to slightly increase the dynamic stability of the N-finger and the first helix residues, which subsequently triggers the redistribution of dynamics over residues directly contacting them. This ultimately enhances the dynamical stability of the residues constituting the catalytic dyad and substrate-binding pockets. Further correlation analysis reveals that a global network of the correlated motions exists in the protease, whose components include all residues identified so far to be critical for the dimerization and catalysis. Most strikingly, the N214A mutation globally decouples this network while the STI/A mutation alters the correlation pattern. Together with previous results, the present study establishes that besides the classic structural allostery, the dynamic allostery also operates in the SARS 3CLpro, which is surprisingly able to relay the perturbations on the extra domain onto the catalytic machinery to manifest opposite catalytic effects. Our results thus imply a promising avenue to design specific inhibitors for 3CL proteases by disrupting their dynamic correlation network.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Jiahai Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
- * E-mail:
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69
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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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70
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Traditional Chinese medicine herbal extracts of Cibotium barometz, Gentiana scabra, Dioscorea batatas, Cassia tora, and Taxillus chinensis inhibit SARS-CoV replication. J Tradit Complement Med 2014; 1:41-50. [PMID: 24716104 PMCID: PMC3942999 DOI: 10.1016/s2225-4110(16)30055-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Development of anti-severe acute respiratory syndrome associated coronavirus (SARS-CoV) agents is pivotal to prevent the reemergence of the life-threatening disease, SARS. In this study, more than 200 extracts from Chinese medicinal herbs were evaluated for anti-SARS-CoV activities using a cell-based assay that measured SARS-CoV-induced cytopathogenic effect (CPE) in vitro on Vero E6 cells. Six herbal extracts, one each from Gentianae Radix (龍膽 lóng dǎn; the dried rhizome of Gentiana scabra), Dioscoreae Rhizoma (山藥 shān yào; the tuber of Dioscorea batatas), Cassiae Semen (決明子 jué míng zǐ; the dried seed of Cassia tora) and Loranthi Ramus (桑寄生 sāng jì shēng; the dried stem, with leaf of Taxillus chinensis) (designated as GSH, DBM, CTH and TCH, respectively), and two from Rhizoma Cibotii (狗脊 gǒu jǐ; the dried rhizome of Cibotium barometz) (designated as CBE and CBM), were found to be potent inhibitors of SARS-CoV at concentrations between 25 and 200 μg/ml. The concentrations of the six extracts needed to inhibit 50% of Vero E6 cell proliferation (CC50) and 50% of viral replication (EC50) were determined. The resulting selective index values (SI = CC50/EC50) of the most effective extracts CBE, GSH, DBM, CTH and TCH were > 59.4, > 57.5, > 62.1, > 59.4, and > 92.9, respectively. Among these extracts, CBM and DBM also showed significant inhibition of SARS-CoV 3CL protease activity with IC50 values of 39 μg/ml and 44 μg/ml, respectively. Our findings suggest that these six herbal extracts may have potential as candidates for future development of anti-SARS therapeutics.
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71
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Lee H, Mittal A, Patel K, Gatuz JL, Truong L, Torres J, Mulhearn DC, Johnson ME. Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings. Bioorg Med Chem 2014; 22:167-77. [PMID: 24332657 PMCID: PMC3971864 DOI: 10.1016/j.bmc.2013.11.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/12/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022]
Abstract
We have used a combination of virtual screening (VS) and high-throughput screening (HTS) techniques to identify novel, non-peptidic small molecule inhibitors against human SARS-CoV 3CLpro. A structure-based VS approach integrating docking and pharmacophore based methods was employed to computationally screen 621,000 compounds from the ZINC library. The screening protocol was validated using known 3CLpro inhibitors and was optimized for speed, improved selectivity, and for accommodating receptor flexibility. Subsequently, a fluorescence-based enzymatic HTS assay was developed and optimized to experimentally screen approximately 41,000 compounds from four structurally diverse libraries chosen mainly based on the VS results. False positives from initial HTS hits were eliminated by a secondary orthogonal binding analysis using surface plasmon resonance (SPR). The campaign identified a reversible small molecule inhibitor exhibiting mixed-type inhibition with a K(i) value of 11.1 μM. Together, these results validate our protocols as suitable approaches to screen virtual and chemical libraries, and the newly identified compound reported in our study represents a promising structural scaffold to pursue for further SARS-CoV 3CLpro inhibitor development.
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Anuradha Mittal
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Joseph L Gatuz
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Lena Truong
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Jaime Torres
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Debbie C Mulhearn
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607, USA.
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72
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Kumar V, Jung YS, Liang PH. Anti-SARS coronavirus agents: a patent review (2008 - present). Expert Opin Ther Pat 2013; 23:1337-48. [PMID: 23905913 DOI: 10.1517/13543776.2013.823159] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION A novel coronavirus (CoV), unlike previous typical human coronaviruses (HCoVs), was identified as causative agent for severe acute respiratory syndrome (SARS). SARS first surfaced as a pandemic in late 2002 and originated in southern China. SARS-CoV rapidly spread to > 30 countries by 2003, infecting nearly 8,000 people and causing around 800 fatalities. After 10 years of silence, a 2012 report alarmed researchers about the emergence of a new strain of CoV causing SARS-like disease. AREAS COVERED To combat SARS, scientists applied for patents on various therapeutic agents, including small-molecule inhibitors targeting the essential proteases, helicase and other proteins of the virus, natural products, approved drugs, molecules binding to the virus, neutralizing antibodies, vaccines, anti-sense RNA, siRNA and ribozyme against SARS-CoV. In this article, the patents published from 2008 to the present for the new therapeutics that could potentially be used in the prophylaxis and treatment of SARS are reviewed. EXPERT OPINION The therapeutic interventions or prophylaxis discussed in this review seems to offer promising solutions to tackle SARS. Rather than being complacent about the results, we should envisage how to transform them into drug candidates that may be useful in combating SARS and related viral infections in the future.
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Affiliation(s)
- Vathan Kumar
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica , Taipei 115 , Taiwan R.O.C
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73
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Muramatsu T, Kim YT, Nishii W, Terada T, Shirouzu M, Yokoyama S. Autoprocessing mechanism of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CLpro) from its polyproteins. FEBS J 2013; 280:2002-13. [PMID: 23452147 PMCID: PMC7164132 DOI: 10.1111/febs.12222] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/25/2013] [Indexed: 11/17/2022]
Abstract
Like many other RNA viruses, severe acute respiratory syndrome coronavirus (SARS‐CoV) produces polyproteins containing several non‐structural proteins, which are then processed by the viral proteases. These proteases often exist within the polyproteins, and are excised by their own proteolytic activity (‘autoprocessing’). It is important to investigate the autoprocessing mechanism of these proteases from the point of view of anti‐SARS‐CoV drug design. In this paper, we describe a new method for investigating the autoprocessing mechanism of the main protease (Mpro), which is also called the 3C‐like protease (3CLpro). Using our method, we measured the activities, under the same conditions, of the mature form and pro‐forms with the N‐terminal pro‐sequence, the C‐terminal pro‐sequence or both pro‐sequences, toward the pro‐form with both N‐ and C‐terminal pro‐sequences. The data indicate that the pro‐forms of the enzyme have proteolytic activity, and are stimulated by the same proteolytic activity. The stimulation occurs in two steps, with approximately eightfold stimulation by N‐terminal cleavage, approximately fourfold stimulation by C‐terminal cleavage, and 23‐fold stimulation by the cleavage of both termini, compared to the pro‐form with both the N‐ and C‐terminal pro‐sequences. Such cleavage mainly occurs in a trans manner; i.e. the pro‐form dimer cleaves the monomeric form. The stimulation by N‐terminal pro‐sequence removal is due to the cis (intra‐dimer and inter‐protomer) effect of formation of the new N‐terminus, whereas that by C‐terminal cleavage is due to removal of its trans (inter‐dimer) inhibitory effect. A numerical simulation of the maturation pathway is presented.
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74
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Kim Y, Mandadapu SR, Groutas WC, Chang KO. Potent inhibition of feline coronaviruses with peptidyl compounds targeting coronavirus 3C-like protease. Antiviral Res 2013; 97:161-8. [PMID: 23219425 PMCID: PMC3563934 DOI: 10.1016/j.antiviral.2012.11.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/18/2012] [Accepted: 11/15/2012] [Indexed: 12/21/2022]
Abstract
Feline coronavirus infection is common among domestic and exotic felid species and usually associated with mild or asymptomatic enteritis; however, feline infectious peritonitis (FIP) is a fatal disease of cats that is caused by systemic infection with a feline infectious peritonitis virus (FIPV), a variant of feline enteric coronavirus (FECV). Currently, there is no specific treatment approved for FIP despite the importance of FIP as the leading infectious cause of death in young cats. During the replication process, coronavirus produces viral polyproteins that are processed into mature proteins by viral proteases, the main protease (3C-like [3CL] protease) and the papain-like protease. Since the cleavages of viral polyproteins are an essential step for virus replication, blockage of viral protease is an attractive target for therapeutic intervention. Previously, we reported the generation of broad-spectrum peptidyl inhibitors against viruses that possess a 3C or 3CL protease. In this study, we further evaluated the antiviral effects of the peptidyl inhibitors against feline coronaviruses, and investigated the interaction between our protease inhibitor and a cathepsin B inhibitor, an entry blocker, against a feline coronavirus in cell culture. Herein we report that our compounds behave as reversible, competitive inhibitors of 3CL protease, potently inhibited the replication of feline coronaviruses (EC(50) in a nanomolar range) and, furthermore, combination of cathepsin B and 3CL protease inhibitors led to a strong synergistic interaction against feline coronaviruses in a cell culture system.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, 66506, USA.
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75
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Kim Y, Lovell S, Tiew KC, Mandadapu SR, Alliston KR, Battaile KP, Groutas WC, Chang KO. Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses. J Virol 2012; 86:11754-62. [PMID: 22915796 PMCID: PMC3486288 DOI: 10.1128/jvi.01348-12] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/12/2012] [Indexed: 01/19/2023] Open
Abstract
Phylogenetic analysis has demonstrated that some positive-sense RNA viruses can be classified into the picornavirus-like supercluster, which includes picornaviruses, caliciviruses, and coronaviruses. These viruses possess 3C or 3C-like proteases (3Cpro or 3CLpro, respectively), which contain a typical chymotrypsin-like fold and a catalytic triad (or dyad) with a Cys residue as a nucleophile. The conserved key sites of 3Cpro or 3CLpro may serve as attractive targets for the design of broad-spectrum antivirals for multiple viruses in the supercluster. We previously reported the structure-based design and synthesis of potent protease inhibitors of Norwalk virus (NV), a member of the Caliciviridae family. We report herein the broad-spectrum antiviral activities of three compounds possessing a common dipeptidyl residue with different warheads, i.e., an aldehyde (GC373), a bisulfite adduct (GC376), and an α-ketoamide (GC375), against viruses that belong to the supercluster. All compounds were highly effective against the majority of tested viruses, with half-maximal inhibitory concentrations in the high nanomolar or low micromolar range in enzyme- and/or cell-based assays and with high therapeutic indices. We also report the high-resolution X-ray cocrystal structures of NV 3CLpro-, poliovirus 3Cpro-, and transmissible gastroenteritis virus 3CLpro- GC376 inhibitor complexes, which show the compound covalently bound to a nucleophilic Cys residue in the catalytic site of the corresponding protease. We conclude that these compounds have the potential to be developed as antiviral therapeutics aimed at a single virus or multiple viruses in the picornavirus-like supercluster by targeting 3Cpro or 3CLpro.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Kok-Chuan Tiew
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - Kevin P. Battaile
- IMCA-CAT Hauptman-Woodward Medical Research Institute, Argonne, Illinois, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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76
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Functional protease assay using liquid crystals as a signal reporter. Biosens Bioelectron 2012; 35:174-179. [DOI: 10.1016/j.bios.2012.02.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 11/22/2022]
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77
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Nguyen TTH, Woo HJ, Kang HK, Nguyen VD, Kim YM, Kim DW, Ahn SA, Xia Y, Kim D. Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in Pichia pastoris. Biotechnol Lett 2012; 34:831-8. [PMID: 22350287 PMCID: PMC7087583 DOI: 10.1007/s10529-011-0845-8] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/22/2011] [Indexed: 12/03/2022]
Abstract
The 3C-like protease (3CLpro) of severe acute respiratory syndrome associated coronavirus (SARS-CoV) is vital for SARS-CoV replication and is a promising drug target. Recombinant 3CLpro was expressed in Pichia pastoris GS115 as a 42 kDa protein that displayed a Km of 15 ± 2 μM with Dabcyl-KTSAVLQSGFRKME-Edans as substrate. Purified 3CLpro was used for inhibition and kinetic assays with seven flavonoid compounds. The IC50 of six flavonoid compounds were 47–381 μM. Quercetin, epigallocatechin gallate and gallocatechin gallate (GCG) displayed good inhibition toward 3CLpro with IC50 values of 73, 73 and 47 μM, respectively. GCG showed a competitive inhibition pattern with Ki value of 25 ± 1.7 μM. In molecular docking experiments, GCG displayed a binding energy of −14 kcal mol−1 to the active site of 3CLpro and the galloyl moiety at 3-OH position was required for 3CLpro inhibition activity.
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Affiliation(s)
- Thi Thanh Hanh Nguyen
- School of Biological Sciences and Technology and the Research Institute for Catalysis, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 500-757 Republic of Korea
- Department of Pediatrics, University of California, San Diego, CA 92103 USA
| | - Hye-Jin Woo
- School of Biological Sciences and Technology and the Research Institute for Catalysis, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 500-757 Republic of Korea
- Department of Pediatrics, University of California, San Diego, CA 92103 USA
| | - Hee-Kyoung Kang
- School of Biological Sciences and Technology and the Research Institute for Catalysis, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 500-757 Republic of Korea
- Department of Pediatrics, University of California, San Diego, CA 92103 USA
| | - Van Dao Nguyen
- Biotechnology Faculty, Hanoi Open University, 46 Ta Quang Buu street, Hai Ba Trung District, Hanoi, Vietnam
| | - Young-Min Kim
- Eco-Friendly Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 580-185 Republic of Korea
| | - Do-Won Kim
- Department of Physics, Gangeung-wonju National University, Gangneung, 210-702 Republic of Korea
| | - Sul-Ah Ahn
- Global Science Experimental Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 805-306 Republic of Korea
| | - Yongmei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Jiangsu, China
| | - Doman Kim
- School of Biological Sciences and Technology and the Research Institute for Catalysis, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 500-757 Republic of Korea
- Department of Pediatrics, University of California, San Diego, CA 92103 USA
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78
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Ramajayam R, Tan KP, Liang PH. Recent development of 3C and 3CL protease inhibitors for anti-coronavirus and anti-picornavirus drug discovery. Biochem Soc Trans 2011; 39:1371-5. [PMID: 21936817 DOI: 10.1042/bst0391371] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SARS-CoV (severe acute respiratory syndrome-associated coronavirus) caused infection of ~8000 people and death of ~800 patients around the world during the 2003 outbreak. In addition, picornaviruses such as enterovirus, coxsackievirus and rhinovirus also can cause life-threatening diseases. Replication of picornaviruses and coronaviruses requires 3Cpro (3C protease) and 3CLpro (3C-like protease) respectively, which are structurally analogous with chymotrypsin-fold, but the former is a monomer and the latter is dimeric due to an extra third domain for dimerization. Subtle structural differences in the S2 and S3 pockets of these proteases make inhibitors selective, but some dual inhibitors have been discovered. Our findings as summarized in the present review provide new potential anti-coronavirus and anti-picornavirus therapeutic agents and a clue to convert 3CLpro inhibitors into 3Cpro inhibitors and vice versa.
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Affiliation(s)
- R Ramajayam
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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79
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Kanoatov M, Krylov SN. DNA adsorption to the reservoir walls causing irreproducibility in studies of protein-DNA interactions by methods of kinetic capillary electrophoresis. Anal Chem 2011; 83:8041-5. [PMID: 21923122 DOI: 10.1021/ac202048y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate kinetic studies of protein-DNA interactions and highly efficient selection of DNA aptamers for protein targets. Here, we report a previously unnoticed source of error that affects the precision and accuracy of KCE-based measurements. The error manifests itself in cases that require the use of low concentrations of DNA. In such measurements, the reproducibility of the signal generated by the same fluorescently labeled DNA sample can have a relative standard deviation (RSD) as high as 40%. We have investigated the cause of the irreproducibility and found that it is attributed to DNA adsorption to the surface of the sample vials, in which protein-DNA mixtures are prepared prior to a KCE experiment. The use of commercially available "high DNA recovery" sample vials does not resolve the problem. We have found that the problem can be significantly alleviated by the passivation of the vial surface with blocking agents, such as masking DNA or bovine serum albumin (BSA). The described adsorption of DNA to the surface of sample vials may also be important in other procedures that deal with low DNA concentrations, such as aptamer selection and quantitative PCR.
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Affiliation(s)
- Mirzo Kanoatov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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80
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Abstract
The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the in vitro and in vivo settings in which they have been employed.
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Affiliation(s)
- Christopher R Drake
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA, 94107, USA
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81
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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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82
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Shi J, Han N, Lim L, Lua S, Sivaraman J, Wang L, Mu Y, Song J. Dynamically-driven inactivation of the catalytic machinery of the SARS 3C-like protease by the N214A mutation on the extra domain. PLoS Comput Biol 2011; 7:e1001084. [PMID: 21390281 PMCID: PMC3044768 DOI: 10.1371/journal.pcbi.1001084] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 01/18/2011] [Indexed: 11/18/2022] Open
Abstract
Despite utilizing the same chymotrypsin fold to host the catalytic machinery, coronavirus 3C-like proteases (3CLpro) noticeably differ from picornavirus 3C proteases in acquiring an extra helical domain in evolution. Previously, the extra domain was demonstrated to regulate the catalysis of the SARS-CoV 3CLpro by controlling its dimerization. Here, we studied N214A, another mutant with only a doubled dissociation constant but significantly abolished activity. Unexpectedly, N214A still adopts the dimeric structure almost identical to that of the wild-type (WT) enzyme. Thus, we conducted 30-ns molecular dynamics (MD) simulations for N214A, WT, and R298A which we previously characterized to be a monomer with the collapsed catalytic machinery. Remarkably, three proteases display distinctive dynamical behaviors. While in WT, the catalytic machinery stably retains in the activated state; in R298A it remains largely collapsed in the inactivated state, thus implying that two states are not only structurally very distinguishable but also dynamically well separated. Surprisingly, in N214A the catalytic dyad becomes dynamically unstable and many residues constituting the catalytic machinery jump to sample the conformations highly resembling those of R298A. Therefore, the N214A mutation appears to trigger the dramatic change of the enzyme dynamics in the context of the dimeric form which ultimately inactivates the catalytic machinery. The present MD simulations represent the longest reported so far for the SARS-CoV 3CLpro, unveiling that its catalysis is critically dependent on the dynamics, which can be amazingly modulated by the extra domain. Consequently, mediating the dynamics may offer a potential avenue to inhibit the SARS-CoV 3CLpro. Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century which has not only caused rapid infection and death, but also triggered a dramatic social crisis. Its 3C-like protease is crucial for reproducing virus and thus represents a top target for drug design. Interestingly, unlike 3C protease such as from picorovirus, the SARS protease evolutionarily acquired a C-terminal extra domain with previously-unknown function. Immediately after SARS outbreak, we revealed that the extra domain was able to regulate the catalysis by controlling the dimerization essential for activity. Here, we studied one mutant with only slightly-weakened dimerization but almost completely abolished activity. We determined its three-dimensional structure but very unexpectedly it is almost identical to that of the wild-type enzyme. Therefore, we initiated 30-ns molecular dynamic simulations for five forms of the enzyme and the results demonstrate that the dynamical changes in this mutant are responsible for its inactivation. Therefore, the extra domain can also control the catalysis by modulating the enzyme dynamics. This is not only of fundamental significance to understanding how enzymes evolve, but also implies a novel avenue for design of anti-SARS molecules.
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Affiliation(s)
- Jiahai Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Nanyu Han
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Shixiong Lua
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - J. Sivaraman
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore
- * E-mail: (JS); (YM)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine and National University of Singapore, Singapore
- * E-mail: (JS); (YM)
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83
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Kuo CJ, Shih YP, Kan D, Liang PH. Engineering a novel endopeptidase based on SARS 3CL(pro). Biotechniques 2011; 47:1029-32. [PMID: 20041855 PMCID: PMC7081961 DOI: 10.2144/000113303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A 3C-like protease (3CLpro) from the severe acute respiratory syndrome–coronavirus (SARS-CoV) is required for viral replication, cleaving the replicase polyproteins at 11 sites with the conserved Gln↓(Ser, Ala, Gly) sequences. In this study, we developed a mutant 3CLpro (T25G) with an expanded S1′ space that demonstrates 43.5-fold better kcat/Km compared with wild-type in cleaving substrates with a larger Met at P1′ and is suitable for tag removal from recombinant fusion proteins. Two vectors for expressing fusion proteins with the T25G recognition site (Ala-Val-Leu-Gln↓Met) in Escherichia coli and yeast were constructed. Identical cloning sites were used in these vectors for parallel cloning. PstI was chosen as a 5′ cloning site because it overlapped the nucleotide sequence encoding the protease site and avoided addition of extra amino acids at the N terminus of recombinant proteins. 3CLpro (T25G) was found to have a 3-fold improvement over TEVpro in tag cleavage at each respective preferred cleavage site.
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Affiliation(s)
- Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica and Core Facility of Recombinant Protein Production, Taipei, Taiwan
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84
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Ramajayam R, Tan KP, Liu HG, Liang PH. Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors. Bioorg Med Chem 2010; 18:7849-54. [PMID: 20947359 PMCID: PMC7127448 DOI: 10.1016/j.bmc.2010.09.050] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 09/20/2010] [Accepted: 09/21/2010] [Indexed: 11/23/2022]
Abstract
A series of pyrazolone compounds as possible SARS-CoV 3CL protease inhibitors were designed, synthesized, and evaluated by in vitro protease assay using fluorogenic substrate peptide in which several showed potent inhibition against the 3CL protease. Interestingly, one of the inhibitors was also active against 3C protease from coxsackievirus B3. These inhibitors could be potentially developed into anti-coronaviral and anti-picornaviral agents.
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Affiliation(s)
- R. Ramajayam
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
| | - Kian-Pin Tan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Hun-Ge Liu
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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85
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Ramajayam R, Tan KP, Liu HG, Liang PH. Synthesis, docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease. Bioorg Med Chem Lett 2010; 20:3569-72. [PMID: 20494577 PMCID: PMC7126861 DOI: 10.1016/j.bmcl.2010.04.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Revised: 04/20/2010] [Accepted: 04/27/2010] [Indexed: 11/20/2022]
Abstract
A series of 2-(benzylthio)-6-oxo-4-phenyl-1,6-dihydropyrimidine as SARS-CoV 3CL protease inhibitors were developed and their potency was evaluated by in vitro protease inhibitory assays. Two candidates had encouraging results for the development of new anti-SARS compounds.
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Affiliation(s)
- R Ramajayam
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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86
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Barrila J, Gabelli SB, Bacha U, Amzel LM, Freire E. Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro) . Biochemistry 2010; 49:4308-17. [PMID: 20420403 DOI: 10.1021/bi1002585] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Coronaviruses are responsible for a significant proportion of annual respiratory and enteric infections in humans and other mammals. The most prominent of these viruses is the severe acute respiratory syndrome coronavirus (SARS-CoV) which causes acute respiratory and gastrointestinal infection in humans. The coronavirus main protease, 3CL(pro), is a key target for broad-spectrum antiviral development because of its critical role in viral maturation and high degree of structural conservation among coronaviruses. Dimerization is an indispensable requirement for the function of SARS 3CL(pro) and is regulated through mechanisms involving both direct and long-range interactions in the enzyme. While many of the binding interactions at the dimerization interface have been extensively studied, those that are important for long-range control are not well-understood. Characterization of these dimerization mechanisms is important for the structure-based design of new treatments targeting coronavirus-based infections. Here we report that Asn28, a residue 11 A from the closest residue in the opposing monomer, is essential for the enzymatic activity and dimerization of SARS 3CL(pro). Mutation of this residue to alanine almost completely inactivates the enzyme and results in a 19.2-fold decrease in the dimerization K(d). The crystallographic structure of the N28A mutant determined at 2.35 A resolution reveals the critical role of Asn28 in maintaining the structural integrity of the active site and in orienting key residues involved in binding at the dimer interface and substrate catalysis. These findings provide deeper insight into complex mechanisms regulating the activity and dimerization of SARS 3CL(pro).
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Affiliation(s)
- Jennifer Barrila
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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87
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Zhang S, Zhong N, Xue F, Kang X, Ren X, Chen J, Jin C, Lou Z, Xia B. Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease. Protein Cell 2010; 1:371-383. [PMID: 21203949 PMCID: PMC4875095 DOI: 10.1007/s13238-010-0044-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 03/18/2010] [Indexed: 01/07/2023] Open
Abstract
Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses. The main protease (M(pro)) of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing. M(pro) is initially produced as part of viral polyproteins and it is matured by autocleavage. Here, we report that, with the addition of an N-terminal extension peptide, M(pro) can form a domain-swapped dimer. After complete removal of the extension peptide from the dimer, the mature M(pro) self-assembles into a novel super-active octamer (AO-M(pro)). The crystal structure of AO-M(pro) adopts a novel fold with four domain-swapped dimers packing into four active units with nearly identical conformation to that of the previously reported M(pro) active dimer, and 3D domain swapping serves as a mechanism to lock the active conformation due to entanglement of polypeptide chains. Compared with the previously well characterized form of M(pro), in equilibrium between inactive monomer and active dimer, the stable AO-M(pro) exhibits much higher proteolytic activity at low concentration. As all eight active sites are bound with inhibitors, the polyvalent nature of the interaction between AO-M(pro) and its polyprotein substrates with multiple cleavage sites, would make AO-M(pro) functionally much more superior than the M(pro) active dimer for polyprotein processing. Thus, during the initial period of SARS-CoV infection, this novel active form AOM(pro) should play a major role in cleaving polyproteins as the protein level is extremely low. The discovery of AOM(pro) provides new insights about the functional mechanism of M(pro) and its maturation process.
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Affiliation(s)
- Shengnan Zhang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Nan Zhong
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Fei Xue
- Structural Biology Laboratory, Tsinghua University, Beijing, 100084 China
| | - Xue Kang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Xiaobai Ren
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Jiaxuan Chen
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Life Sciences, Peking University, Beijing, 100871 China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China ,College of Life Sciences, Peking University, Beijing, 100871 China
| | - Zhiyong Lou
- Structural Biology Laboratory, Tsinghua University, Beijing, 100084 China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871 China ,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China ,College of Life Sciences, Peking University, Beijing, 100871 China
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88
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SARS-CoV 3CLpro inhibitory effects of quinone-methide triterpenes from Tripterygium regelii. Bioorg Med Chem Lett 2010; 20:1873-6. [PMID: 20167482 PMCID: PMC7127101 DOI: 10.1016/j.bmcl.2010.01.152] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 12/29/2009] [Accepted: 01/29/2010] [Indexed: 11/23/2022]
Abstract
Quinone-methide triterpenes, celastrol (1), pristimerin (2), tingenone (3), and iguesterin (4) were isolated from Triterygium regelii and dihydrocelastrol (5) was synthesized by hydrogenation under palladium catalyst. Isolated quinone-methide triterpenes (1–4) and 5 were evaluated for SARS-CoV 3CLpro inhibitory activities and showed potent inhibitory activities with IC50 values of 10.3, 5.5, 9.9, and 2.6 μM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC50 = 21.7 μM). As a result, quinone-methide moiety in A-ring and more hydrophobic E-ring assist to exhibit potent activity. Also, all quinone-methide triterpenes 1–4 have proven to be competitive by the kinetic analysis.
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89
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Ahn TY, Kuo CJ, Liu HG, Ha DC, Liang PH, Jung YS. Synthesis and Evaluation of Benzoquinolinone Derivatives as SARS-CoV 3CL Protease Inhibitors. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.01.087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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90
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Marguerre AK, Krämer R. Lanthanide-based fluorogenic peptide substrate for the highly sensitive detection of thermolysin. Bioorg Med Chem Lett 2009; 19:5757-9. [DOI: 10.1016/j.bmcl.2009.07.152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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91
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Hu T, Zhang Y, Li L, Wang K, Chen S, Chen J, Ding J, Jiang H, Shen X. Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure. Virology 2009; 388:324-34. [PMID: 19409595 PMCID: PMC7103376 DOI: 10.1016/j.virol.2009.03.034] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 03/06/2009] [Accepted: 03/30/2009] [Indexed: 01/01/2023]
Abstract
The 3C-like protease of SARS coronavirus (SARS-CoV 3CLpro) is vital for SARS-CoV replication and is a promising drug target. It has been extensively proved that only the dimeric enzyme is active. Here we discovered that two adjacent mutations (Ser139_Ala and Phe140_Ala) on the dimer interface resulted in completely different crystal structures of the enzyme, demonstrating the distinct roles of these two residues in maintaining the active conformation of SARS-CoV 3CLpro. S139A is a monomer that is structurally similar to the two reported monomers G11A and R298A. However, this mutant still retains a small fraction of dimer in solution, which might account for its remaining activity. F140A is a dimer with the most collapsed active pocket discovered so far, well-reflecting the stabilizing role of this residue. Moreover, a plausible dimerization mechanism was also deduced from structural analysis. Our work is expected to provide insight on the dimerization–function relationship of SARS-CoV 3CLpro.
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Affiliation(s)
- Tiancen Hu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Yu Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Lianwei Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Kuifeng Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Shuai Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Jing Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- Corresponding authors. Fax: +86 21 50806918.
| | - Xu Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- Corresponding authors. Fax: +86 21 50806918.
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92
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Saxena SK, Mishra N, Saxena R. Advances in antiviral drug discovery and development: Part II: Advancements in antiviral drug development. Future Virol 2009. [DOI: 10.2217/fvl.09.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Shailendra K Saxena
- Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500 007 (AP), India
| | - Niraj Mishra
- Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500 007 (AP), India
| | - Rakhi Saxena
- Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500 007 (AP), India
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93
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Sao K, Murata M, Fujisaki Y, Umezaki K, Mori T, Niidome T, Katayama Y, Hashizume M. A novel protease activity assay using a protease-responsive chaperone protein. Biochem Biophys Res Commun 2009; 383:293-7. [PMID: 19341711 DOI: 10.1016/j.bbrc.2009.03.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Protease activity assays are important for elucidating protease function and for developing new therapeutic agents. In this study, a novel turbidimetric method for determining the protease activity using a protease-responsive chaperone protein is described. For this purpose, a recombinant small heat-shock protein (sHSP) with an introduced Factor Xa protease recognition site was synthesized in bacteria. This recombinant mutant, FXa-HSP, exhibited chaperone-like activity at high temperatures in cell lysates. However, the chaperone-like activity of FXa-HSP decreased dramatically following treatment with Factor Xa. Protein precipitation was subsequently observed in the cell lysates. The reaction was Factor Xa concentration-dependent and was quantitatively suppressed by a specific inhibitor for Factor Xa. Protein aggregation was detected by a simple method based on turbidimetry. The results clearly demonstrate that this assay is an effective, easy-to-use method for determining protease activities without the requirement of labeling procedures and the use of radioisotopes.
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Affiliation(s)
- Kentaro Sao
- Kyushu University, Motooka Nishi-ku, Fukuoka, Japan
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94
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Regnier T, Sarma D, Hidaka K, Bacha U, Freire E, Hayashi Y, Kiso Y. New developments for the design, synthesis and biological evaluation of potent SARS-CoV 3CL(pro) inhibitors. Bioorg Med Chem Lett 2009; 19:2722-7. [PMID: 19362479 PMCID: PMC4436079 DOI: 10.1016/j.bmcl.2009.03.118] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/24/2009] [Accepted: 03/25/2009] [Indexed: 11/25/2022]
Abstract
A series of trifluoromethyl, benzothiazolyl or thiazolyl ketone-containing peptidic compounds as SARS-CoV 3CL protease inhibitors were developed and their potency was evaluated by in vitro protease inhibitory assays. Three candidates had encouraging results for the development of new anti-SARS compounds.
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Affiliation(s)
- Thomas Regnier
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Japan
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95
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Lee CC, Kuo CJ, Ko TP, Hsu MF, Tsui YC, Chang SC, Yang S, Chen SJ, Chen HC, Hsu MC, Shih SR, Liang PH, Wang AHJ. Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds. J Biol Chem 2009; 284:7646-55. [PMID: 19144641 PMCID: PMC2658058 DOI: 10.1074/jbc.m807947200] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human coxsackievirus (CV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. In picornavirus, a chymotrypsin-like protease (3C(pro)) is required for viral replication by processing the polyproteins, and thus it is regarded as an antiviral drug target. A 3C-like protease (3CL(pro)) also exists in human coronaviruses (CoV) such as 229E and the one causing severe acute respiratory syndrome (SARS). To combat SARS, we previously had developed peptidomimetic and zinc-coordinating inhibitors of 3CL(pro). As shown in the present study, some of these compounds were also found to be active against 3C(pro) of CV strain B3 (CVB3). Several crystal structures of 3C(pro) from CVB3 and 3CL(pro) from CoV-229E and SARS-CoV in complex with the inhibitors were solved. The zinc-coordinating inhibitor is tetrahedrally coordinated to the His(40)-Cys(147) catalytic dyad of CVB3 3C(pro). The presence of specific binding pockets for the residues of peptidomimetic inhibitors explains the binding specificity. Our results provide a structural basis for inhibitor optimization and development of potential drugs for antiviral therapies.
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Affiliation(s)
- Cheng-Chung Lee
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Chih-Jung Kuo
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Tzu-Ping Ko
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Min-Feng Hsu
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Yao-Chen Tsui
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Shih-Cheng Chang
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Syaulan Yang
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Shu-Jen Chen
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Hua-Chien Chen
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Ming-Chu Hsu
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Shin-Ru Shih
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Po-Huang Liang
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
| | - Andrew H.-J. Wang
- Structural Biology Program, Institute of
Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan,
Institute of Biological Chemistry, National
Core Facility of High-Throughput Protein Crystallography, and Taiwan
International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,
Institute of Biochemical Sciences, National Taiwan University, Taipei 10617,
Taiwan, Department of Medical Biotechnology and Laboratory
Science, Chang Gung University, and Clinical Virology
Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333,
Taiwan, and TaiGen Biotechnology, Taipei 114, Taiwan
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96
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Peng X, Chen H, Draney DR, Volcheck W, Schutz-Geschwender A, Olive DM. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Anal Biochem 2009; 388:220-8. [PMID: 19248753 DOI: 10.1016/j.ab.2009.02.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 02/09/2009] [Accepted: 02/17/2009] [Indexed: 10/21/2022]
Abstract
We report here a novel, water-soluble, nonfluorescent dye that efficiently quenches fluorescence from a broad range of visible and near-infrared (NIR) fluorophores in Förster resonance energy transfer (FRET) systems. A model FRET-based caspase-3 assay system was used to test the performance of the quencher dye. Fluorogenic caspase-3 substrates were prepared by conjugating the quencher, IRDye QC-1, to a GDEVDGAK peptide in combination with fluorescein (emission maximum approximately 540 nm), Cy3 (approximately 570 nm), Cy5 (approximately 670 nm), IRDye 680 (approximately 700 nm), IRDye 700DX (approximately 690 nm), or IRDye 800CW (approximately 790 nm). The Förster distance R(0) values are calculated as 41 to 65A for these dye/quencher pairs. The fluorescence quenching efficiencies of these peptides were determined by measuring the fluorescence change on complete cleavage by recombinant caspase-3 and ranged from 97.5% to 98.8%. The fold increase in fluorescence on caspase cleavage of the fluorogenic substrates ranged from 40 to 83 depending on the dye/quencher pair. Because IRDye QC-1 effectively quenches both the NIR fluorophores (e.g., IRDye 700DX, IRDye 680, IRDye 800CW) and the visible fluorophores (e.g., fluorescein, Cy3, Cy5), it should find broad applicability in FRET assays using a wide variety of fluorescent dyes.
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97
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Kuo CJ, Liu HG, Lo YK, Seong CM, Lee KI, Jung YS, Liang PH. Individual and common inhibitors of coronavirus and picornavirus main proteases. FEBS Lett 2009; 583:549-55. [PMID: 19166843 PMCID: PMC7094298 DOI: 10.1016/j.febslet.2008.12.059] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 12/17/2008] [Accepted: 12/23/2008] [Indexed: 11/08/2022]
Abstract
Picornaviruses (PV) and coronaviruses (CoV) are positive‐stranded RNA viruses which infect millions of people worldwide each year, resulting in a wide range of clinical outcomes. As reported in this study, using high throughput screening against ∼6800 small molecules, we have identified several novel inhibitors of SARS‐CoV 3CLpro with IC50 of low μM. Interestingly, one of them equally inhibited both 3Cpro and 3CLpro from PV and CoV, respectively. Using computer modeling, the structural features of these compounds as individual and common protease inhibitors were elucidated to enhance our knowledge for developing anti‐viral agents against PV and CoV.
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Affiliation(s)
- Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, ROC
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98
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Verschueren KHG, Pumpor K, Anemüller S, Chen S, Mesters JR, Hilgenfeld R. A structural view of the inactivation of the SARS coronavirus main proteinase by benzotriazole esters. ACTA ACUST UNITED AC 2008; 15:597-606. [PMID: 18559270 PMCID: PMC7110992 DOI: 10.1016/j.chembiol.2008.04.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 04/16/2008] [Accepted: 04/17/2008] [Indexed: 01/04/2023]
Abstract
The main proteinase (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus is a principal target for the design of anticoronaviral compounds. Benzotriazole esters have been reported as potent nonpeptidic inhibitors of the enzyme, but their exact mechanism of action remains unclear. Here we present crystal structures of SARS-CoV Mpro, the active-site cysteine of which has been acylated by benzotriazole esters that act as suicide inhibitors. In one of the structures, the thioester product has been hydrolyzed and benzoic acid is observed to bind to the hydrophobic S2 pocket. This structure also features the enzyme with a shortened N-terminal segment (“amputated N finger”). The results further the understanding of the important role of the N finger for catalysis as well as the design of benzotriazole inhibitors with improved specificity.
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Affiliation(s)
- Koen H G Verschueren
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
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99
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Kuo CJ, Shie JJ, Fang JM, Yen GR, Hsu JTA, Liu HG, Tseng SN, Chang SC, Lee CY, Shih SR, Liang PH. Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents. Bioorg Med Chem 2008; 16:7388-98. [PMID: 18583140 PMCID: PMC7125518 DOI: 10.1016/j.bmc.2008.06.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/07/2008] [Accepted: 06/10/2008] [Indexed: 10/31/2022]
Abstract
Human enterovirus (EV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. A peptidomimetic inhibitor AG7088 was developed to inhibit the 3C protease of rhinovirus (a member of the family), a chymotrypsin-like protease required for viral replication, by forming a covalent bond with the active site Cys residue. In this study, we have prepared the recombinant 3C protease from EV71 (TW/2231/98), a particular strain which causes severe outbreaks in Asia, and developed inhibitors against the protease and the viral replication. For inhibitor design, the P3 group of AG7088, which is not interacting with the rhinovirus protease, was replaced with a series of cinnamoyl derivatives directly linked to P2 group through an amide bond to simplify the synthesis. While the replacement caused decreased potency, the activity can be largely improved by substituting the alpha,beta-unsaturated ester with an aldehyde at the P1' position. The best inhibitor 10b showed EC(50) of 18 nM without apparent toxicity (CC(50)>25 microM). Our study provides potent inhibitors of the EV71 3C protease as anti-EV71 agents and facilitates the combinatorial synthesis of derivatives for further improving the inhibitory activity.
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Key Words
- ev, enterovirus
- rv, rhinovirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- ninta, nickel nitrilo-tri-acetic acid
- dabcyl, 4-(4-dimethylaminophenylazo)benzoic acid
- edans, 5-[(2-aminoethyl)amino]naphthalene-1-sulfonic acid
- boc, tert-butyloxycarbonyl
- cbz, benzyloxycarbonyl
- mes, 2-n-morpholono-ethanesulfonic acid
- dmem, dulbecco’s modified eagle’s medium
- fbs, fetal bovine serum
- protease
- picornaviridae
- inhibitor
- enterovirus
- computer modeling
- fluorogenic substrate
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Affiliation(s)
- Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jim-Min Fang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Guei-Rung Yen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Chu-Nan, Taiwan
| | - John T.-A. Hsu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Chu-Nan, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hun-Ge Liu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
| | - Sung-Nain Tseng
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
| | - Shih-Cheng Chang
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Ching-Yin Lee
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Shin-Ru Shih
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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100
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Bacha U, Barrila J, Gabelli SB, Kiso Y, Mario Amzel L, Freire E. Development of broad-spectrum halomethyl ketone inhibitors against coronavirus main protease 3CL(pro). Chem Biol Drug Des 2008; 72:34-49. [PMID: 18611220 PMCID: PMC2597651 DOI: 10.1111/j.1747-0285.2008.00679.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 05/27/2008] [Indexed: 11/28/2022]
Abstract
Coronaviruses comprise a large group of RNA viruses with diverse host specificity. The emergence of highly pathogenic strains like the SARS coronavirus (SARS-CoV), and the discovery of two new coronaviruses, NL-63 and HKU1, corroborates the high rate of mutation and recombination that have enabled them to cross species barriers and infect novel hosts. For that reason, the development of broad-spectrum antivirals that are effective against several members of this family is highly desirable. This goal can be accomplished by designing inhibitors against a target, such as the main protease 3CL(pro) (M(pro)), which is highly conserved among all coronaviruses. Here 3CL(pro) derived from the SARS-CoV was used as the primary target to identify a new class of inhibitors containing a halomethyl ketone warhead. The compounds are highly potent against SARS 3CL(pro) with K(i)'s as low as 300 nM. The crystal structure of the complex of one of the compounds with 3CL(pro) indicates that this inhibitor forms a thioether linkage between the halomethyl carbon of the warhead and the catalytic Cys 145. Furthermore, Structure Activity Relationship (SAR) studies of these compounds have led to the identification of a pharmacophore that accurately defines the essential molecular features required for the high affinity.
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Affiliation(s)
- Usman Bacha
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jennifer Barrila
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yoshiaki Kiso
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina‐ku, Kyoto 607‐8412, Japan
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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