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Li J, Lin C, Zhou X, Zhong F, Zeng P, Yang Y, Zhang Y, Yu B, Fan X, McCormick PJ, Fu R, Fu Y, Jiang H, Zhang J. Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332. J Virol 2022; 96:e0201321. [PMID: 35389231 DOI: 10.1101/2021.11.05.467529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genera of coronaviruses is the substrate-binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332, developed by Pfizer, is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here, we report three crystal structures of the main protease of SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome (MERS)-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of the main protease harbors multiple inhibitor-binding sites, where PF-07321332 occupies subsites S1, S2, and S4 and appears more restricted than other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of the main proteases from different coronaviruses. Given the importance of the main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals. IMPORTANCE The current pandemic of multiple variants has created an urgent need for effective inhibitors of SARS-CoV-2 to complement vaccine strategies. PF-07321332, developed by Pfizer, is the first orally administered coronavirus-specific main protease inhibitor approved by the FDA. We solved the crystal structures of the main protease of SARS-CoV-2, SARS-CoV, and MERS-CoV that bound to the PF-07321332, suggesting PF-07321332 is a broad-spectrum inhibitor for coronaviruses. Structures of the main protease inhibitor complexes present an opportunity to discover safer and more effective inhibitors for COVID-19.
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Affiliation(s)
- Jian Li
- College of Pharmaceutical Sciences, Gannan Medical Universitygrid.440714.2, Ganzhou, China
| | - Cheng Lin
- School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China
| | - Xuelan Zhou
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China
| | - Fanglin Zhong
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, China
| | - Yang Yang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, China
| | - Yuting Zhang
- School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China
| | - Bo Yu
- School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China
| | - Xiaona Fan
- College of Pharmaceutical Sciences, Gannan Medical Universitygrid.440714.2, Ganzhou, China
| | - Peter J McCormick
- William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Rui Fu
- Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang Universitygrid.260463.5, Nanchang, China
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2
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Lata S, Akif M. Comparative protein structure network analysis on 3CL pro from SARS-CoV-1 and SARS-CoV-2. Proteins 2021; 89:1216-1225. [PMID: 33983654 PMCID: PMC8242809 DOI: 10.1002/prot.26143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/10/2021] [Accepted: 05/05/2021] [Indexed: 12/29/2022]
Abstract
The main protease Mpro, 3CLpro is an important target from coronaviruses. In spite of having 96% sequence identity among Mpros from SARS‐CoV‐1 and SARS‐CoV‐2; the inhibitors used to block the activity of SARS‐CoV‐1 Mpro so far, were found to have differential inhibitory effect on Mpro of SARS‐CoV‐2. The possible reason could be due to the difference of few amino acids among the peptidases. Since, overall 3‐D crystallographic structure of Mpro from SARS‐CoV‐1 and SARS‐CoV‐2 is quite similar and mapping a subtle structural variation is seemingly impossible. Hence, we have attempted to study a structural comparison of SARS‐CoV‐1 and SARS‐CoV‐2 Mpro in apo and inhibitor bound states using protein structure network (PSN) based approach at contacts level. The comparative PSNs analysis of apo Mpros from SARS‐CoV‐1 and SARS‐CoV‐2 uncovers small but significant local changes occurring near the active site region and distributed throughout the structure. Additionally, we have shown how inhibitor binding perturbs the PSG and the communication pathways in Mpros. Moreover, we have also investigated the network connectivity on the quaternary structure of Mpro and identified critical residue pairs for complex formation using three centrality measurement parameters along with the modularity analysis. Taken together, these results on the comparative PSN provide an insight into conformational changes that may be used as an additional guidance towards specific drug development.
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Affiliation(s)
- Surabhi Lata
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohd Akif
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Lockbaum GJ, Reyes AC, Lee JM, Tilvawala R, Nalivaika EA, Ali A, Kurt Yilmaz N, Thompson PR, Schiffer CA. Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. Viruses 2021; 13:174. [PMID: 33503819 PMCID: PMC7911568 DOI: 10.3390/v13020174] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 01/08/2023] Open
Abstract
Viral proteases are critical enzymes for the maturation of many human pathogenic viruses and thus are key targets for direct acting antivirals (DAAs). The current viral pandemic caused by SARS-CoV-2 is in dire need of DAAs. The Main protease (Mpro) is the focus of extensive structure-based drug design efforts which are mostly covalent inhibitors targeting the catalytic cysteine. ML188 is a non-covalent inhibitor designed to target SARS-CoV-1 Mpro, and provides an initial scaffold for the creation of effective pan-coronavirus inhibitors. In the current study, we found that ML188 inhibits SARS-CoV-2 Mpro at 2.5 µM, which is more potent than against SAR-CoV-1 Mpro. We determined the crystal structure of ML188 in complex with SARS-CoV-2 Mpro to 2.39 Å resolution. Sharing 96% sequence identity, structural comparison of the two complexes only shows subtle differences. Non-covalent protease inhibitors complement the design of covalent inhibitors against SARS-CoV-2 main protease and are critical initial steps in the design of DAAs to treat CoVID 19.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; (G.J.L.); (A.C.R.); (J.M.L.); (R.T.); (E.A.N.); (A.A.); (N.K.Y.); (P.R.T.)
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4
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Shi TH, Huang YL, Chen CC, Pi WC, Hsu YL, Lo LC, Chen WY, Fu SL, Lin CH. Andrographolide and its fluorescent derivative inhibit the main proteases of 2019-nCoV and SARS-CoV through covalent linkage. Biochem Biophys Res Commun 2020; 533:467-473. [PMID: 32977949 PMCID: PMC7447262 DOI: 10.1016/j.bbrc.2020.08.086] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 08/22/2020] [Indexed: 01/10/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by 2019 novel coronavirus (2019-nCoV) has been a crisis of global health, whereas the effective vaccines against 2019-nCoV are still under development. Alternatively, utilization of old drugs or available medicine that can suppress the viral activity or replication may provide an urgent solution to suppress the rapid spread of 2019-nCoV. Andrographolide is a highly abundant natural product of the medicinal plant, Andrographis paniculata, which has been clinically used for inflammatory diseases and anti-viral therapy. We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (Andro- NBD), suppressed the main protease (Mpro) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Moreover, Andro-NBD was shown to covalently link its fluorescence to these proteases. Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys145 of either 2019-nCoV Mpro or SARS-CoV Mpro. Consistently, molecular modeling analysis supported the docking of andrographolide within the catalytic pockets of both viral Mpros. Considering that andrographolide is used in clinical practice with acceptable safety and its diverse pharmacological activities that could be beneficial for attenuating COVID-19 symptoms, extensive investigation of andrographolide on the suppression of 2019-nCoV as well as its application in COVID-19 therapy is suggested.
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Affiliation(s)
- Tzu-Hau Shi
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan; Biomedical Industry Ph.D. Program, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yi-Long Huang
- Aging and Health Research Center, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chiao-Che Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yu-Ling Hsu
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Lee-Chiang Lo
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Shu-Ling Fu
- Institute of Traditional Medicine, National Yang-Ming University, Taipei, 112, Taiwan.
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan; Aging and Health Research Center, National Yang-Ming University, Taipei, 112, Taiwan; Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, 112, Taiwan.
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Abstract
There were severe panics caused by Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome-Coronavirus. Therefore, researches targeting these viruses have been required. Coronaviruses (CoVs) have been rising targets of some flavonoids. The antiviral activity of some flavonoids against CoVs is presumed directly caused by inhibiting 3C-like protease (3CLpro). Here, we applied a flavonoid library to systematically probe inhibitory compounds against SARS-CoV 3CLpro. Herbacetin, rhoifolin and pectolinarin were found to efficiently block the enzymatic activity of SARS-CoV 3CLpro. The interaction of the three flavonoids was confirmed using a tryptophan-based fluorescence method, too. An induced-fit docking analysis indicated that S1, S2 and S3' sites are involved in binding with flavonoids. The comparison with previous studies showed that Triton X-100 played a critical role in objecting false positive or overestimated inhibitory activity of flavonoids. With the systematic analysis, the three flavonoids are suggested to be templates to design functionally improved inhibitors.
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Affiliation(s)
- Seri Jo
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Suwon Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
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Shitrit A, Zaidman D, Kalid O, Bloch I, Doron D, Yarnizky T, Buch I, Segev I, Ben-Zeev E, Segev E, Kobiler O. Conserved interactions required for inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sci Rep 2020; 10:20808. [PMID: 33257760 PMCID: PMC7704658 DOI: 10.1038/s41598-020-77794-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands' interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50 µM concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.
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Affiliation(s)
- Alina Shitrit
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Daniel Zaidman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | | | - Itai Bloch
- Biotechnology Department, Migal - Galilee Research Institute, Kiryat-Shmona, Israel
| | - Dvir Doron
- Chemical & Computational Toxicology, Non-Clinical Development, Global R&D, Teva Pharmaceutical Industries Ltd., Netanya, Israel
| | - Tali Yarnizky
- Tali Yarnizky Scientific Consulting, Maccabim-Reut, Israel
| | - Idit Buch
- Emendo Biotherapeutics Ltd., Ness Ziona, Israel
| | | | - Efrat Ben-Zeev
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Segev
- Department of Applied Mathematics, Faculty of Science, Holon Institute of Technology, Holon, Israel
| | - Oren Kobiler
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel.
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7
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Koudelka T, Boger J, Henkel A, Schönherr R, Krantz S, Fuchs S, Rodríguez E, Redecke L, Tholey A. N-Terminomics for the Identification of In Vitro Substrates and Cleavage Site Specificity of the SARS-CoV-2 Main Protease. Proteomics 2020; 21:e2000246. [PMID: 33111431 PMCID: PMC7645863 DOI: 10.1002/pmic.202000246] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/21/2020] [Indexed: 01/11/2023]
Abstract
The genome of coronaviruses, including SARS‐CoV‐2, encodes for two proteases, a papain like (PLpro) protease and the so‐called main protease (Mpro), a chymotrypsin‐like cysteine protease, also named 3CLpro or non‐structural protein 5 (nsp5). Mpro is activated by autoproteolysis and is the main protease responsible for cutting the viral polyprotein into functional units. Aside from this, it is described that Mpro proteases are also capable of processing host proteins, including those involved in the host innate immune response. To identify substrates of the three main proteases from SARS‐CoV, SARS‐CoV‐2, and hCoV‐NL63 coronviruses, an LC‐MS based N‐terminomics in vitro analysis is performed using recombinantly expressed proteases and lung epithelial and endothelial cell lysates as substrate pools. For SARS‐CoV‐2 Mpro, 445 cleavage events from more than 300 proteins are identified, while 151 and 331 Mpro derived cleavage events are identified for SARS‐CoV and hCoV‐NL63, respectively. These data enable to better understand the cleavage site specificity of the viral proteases and will help to identify novel substrates in vivo. All data are available via ProteomeXchange with identifier PXD021406.
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Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research and BioanalyticsInstitute for Experimental Medicine, Christian‐Albrechts‐Universität zu KielKiel24105Germany
| | - Juliane Boger
- Institute of BiochemistryUniversity of LuebeckLuebeck23562Germany
| | | | - Robert Schönherr
- Institute of BiochemistryUniversity of LuebeckLuebeck23562Germany
- Photon ScienceDeutsches Elektronen Synchrotron (DESY)Hamburg22607Germany
| | - Stefanie Krantz
- Experimental Trauma Surgery, Department of Trauma Surgery and OrthopedicsUniversity Medical Center Schleswig‐HolsteinKiel24105Germany
| | - Sabine Fuchs
- Experimental Trauma Surgery, Department of Trauma Surgery and OrthopedicsUniversity Medical Center Schleswig‐HolsteinKiel24105Germany
| | - Estefanía Rodríguez
- Virology DepartmentBernhard Nocht Institute for Tropical MedicineGerman Center for Infection Research (DZIF), Partner site Hamburg‐Lübeck‐Borstel‐Riems, Hamburg, GermanyHamburg20359Germany
| | - Lars Redecke
- Institute of BiochemistryUniversity of LuebeckLuebeck23562Germany
- Photon ScienceDeutsches Elektronen Synchrotron (DESY)Hamburg22607Germany
| | - Andreas Tholey
- Systematic Proteome Research and BioanalyticsInstitute for Experimental Medicine, Christian‐Albrechts‐Universität zu KielKiel24105Germany
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Bzówka M, Mitusińska K, Raczyńska A, Samol A, Tuszyński JA, Góra A. Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design. Int J Mol Sci 2020; 21:E3099. [PMID: 32353978 PMCID: PMC7247150 DOI: 10.3390/ijms21093099] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 11/25/2022] Open
Abstract
The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mixed-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar severe acute respiratory syndrome (SARS) Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins showed major differences in both shape and size, indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding site's conformational changes during the simulation time indicated its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicated that the virus' mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Agata Raczyńska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Aleksandra Samol
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Jack A. Tuszyński
- Department of Physics, University of Alberta, Edmont, AB T6G 2E1, Canada
- DIMEAS, Politecnino di Torino, Corso Duca degli Abruzzi, 24, 10129 Turin, Italy
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland
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Yoshizawa SI, Hattori Y, Kobayashi K, Akaji K. Evaluation of an octahydroisochromene scaffold used as a novel SARS 3CL protease inhibitor. Bioorg Med Chem 2019; 28:115273. [PMID: 31926775 PMCID: PMC7127348 DOI: 10.1016/j.bmc.2019.115273] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/11/2019] [Accepted: 12/14/2019] [Indexed: 12/28/2022]
Abstract
An octahydroisochromene scaffold has been introduced into a known SARS 3CL protease inhibitor as a novel hydrophobic core to interact with the S2 pocket of the protease. An alkyl or aryl substituent was also introduced at the 1-position of the octahydroisochromene scaffold and expected to introduce additional interactions with the protease. Sharpless–Katsuki asymmetric epoxidation and Sharpless asymmetric dihydroxylation were employed to construct the octahydroisochromene scaffold. The introductions of the P1 site His-al and the substituent at 1-position was achieved using successive reductive amination reactions. Our initial evaluations of the diastereo-isomeric mixtures (16a–d) revealed that the octahydroisochromene moiety functions as a core hydrophobic scaffold for the S2 pocket of the protease and the substituent at the 1-position may form additional interactions with the protease. The inhibitory activities of the diastereoisomerically-pure inhibitors (3a–d) strongly suggest that a specific stereo-isomer of the octahydroisochromene scaffold, (1S, 3S) 3b, directs the P1 site imidazole, the warhead aldehyde, and substituent at the 1-position of the fused ring to their appropriate pockets in the protease.
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Affiliation(s)
- Shin-Ichiro Yoshizawa
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Yasunao Hattori
- Center for Instrumental Analysis, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kazuya Kobayashi
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
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10
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Niemeyer D, Mösbauer K, Klein EM, Sieberg A, Mettelman RC, Mielech AM, Dijkman R, Baker SC, Drosten C, Müller MA. The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species. PLoS Pathog 2018; 14:e1007296. [PMID: 30248143 PMCID: PMC6171950 DOI: 10.1371/journal.ppat.1007296] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/04/2018] [Accepted: 08/26/2018] [Indexed: 12/22/2022] Open
Abstract
SARS-coronavirus (CoV) is a zoonotic agent derived from rhinolophid bats, in which a plethora of SARS-related, conspecific viral lineages exist. Whereas the variability of virulence among reservoir-borne viruses is unknown, it is generally assumed that the emergence of epidemic viruses from animal reservoirs requires human adaptation. To understand the influence of a viral factor in relation to interspecies spillover, we studied the papain-like protease (PLP) of SARS-CoV. This key enzyme drives the early stages of infection as it cleaves the viral polyprotein, deubiquitinates viral and cellular proteins, and antagonizes the interferon (IFN) response. We identified a bat SARS-CoV PLP, which shared 86% amino acid identity with SARS-CoV PLP, and used reverse genetics to insert it into the SARS-CoV genome. The resulting virus replicated like SARS-CoV in Vero cells but was suppressed in IFN competent MA-104 (3.7-fold), Calu-3 (2.6-fold) and human airway epithelial cells (10.3-fold). Using ectopically-expressed PLP variants as well as full SARS-CoV infectious clones chimerized for PLP, we found that a protease-independent, anti-IFN function exists in SARS-CoV, but not in a SARS-related, bat-borne virus. This PLP-mediated anti-IFN difference was seen in primate, human as well as bat cells, thus independent of the host context. The results of this study revealed that coronavirus PLP confers a variable virulence trait among members of the species SARS-CoV, and that a SARS-CoV lineage with virulent PLPs may have pre-existed in the reservoir before onset of the epidemic.
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Affiliation(s)
- Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Kirstin Mösbauer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Eva M. Klein
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Andrea Sieberg
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Robert C. Mettelman
- Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
| | - Anna M. Mielech
- Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
| | - Ronald Dijkman
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Marcel A. Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research, associated partner Charité, Berlin, Germany
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11
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Daczkowski CM, Dzimianski JV, Clasman JR, Goodwin O, Mesecar AD, Pegan SD. Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species. J Mol Biol 2017; 429:1661-1683. [PMID: 28438633 PMCID: PMC5634334 DOI: 10.1016/j.jmb.2017.04.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/04/2017] [Accepted: 04/18/2017] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) encode multifunctional papain-like proteases (PLPs) that have the ability to process the viral polyprotein to facilitate RNA replication and antagonize the host innate immune response. The latter function involves reversing the post-translational modification of cellular proteins conjugated with either ubiquitin (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). Ub is known to be highly conserved among eukaryotes, but surprisingly, ISG15 is highly divergent among animals. The ramifications of this sequence divergence to the recognition of ISG15 by coronavirus PLPs at a structural and biochemical level are poorly understood. Therefore, the activity of PLPs from SARS-CoV, MERS-CoV, and mouse hepatitis virus was evaluated against seven ISG15s originating from an assortment of animal species susceptible, and not, to certain coronavirus infections. Excitingly, our kinetic, thermodynamic, and structural analysis revealed an array of different preferences among PLPs. Included in these studies is the first insight into a coronavirus PLP's interface with ISG15 via SARS-CoV PLpro in complex with the principle binding domain of human ISG15 (hISG15) and mouse ISG15s (mISG15s). The first X-ray structure of the full-length mISG15 protein is also reported and highlights a unique, twisted hinge region of ISG15 that is not conserved in hISG15, suggesting a potential role in differential recognition. Taken together, this new information provides a structural and biochemical understanding of the distinct specificities among coronavirus PLPs observed and addresses a critical gap of how PLPs can interact with ISG15s from a wide variety of species.
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Affiliation(s)
- Courtney M Daczkowski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA
| | - John V Dzimianski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA
| | - Jozlyn R Clasman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Octavia Goodwin
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA
| | - Andrew D Mesecar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Scott D Pegan
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA.
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12
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Teruya K, Hattori Y, Shimamoto Y, Kobayashi K, Sanjoh A, Nakagawa A, Yamashita E, Akaji K. Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold. Biopolymers 2016; 106:391-403. [PMID: 26572934 PMCID: PMC7159131 DOI: 10.1002/bip.22773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 02/03/2023]
Abstract
Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2) = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016.
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Affiliation(s)
- Kenta Teruya
- Department of NeurochemistryTohoku University Graduate School of MedicineAoba‐Ku Sendai980‐8575Japan
| | - Yasunao Hattori
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Yasuhiro Shimamoto
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Kazuya Kobayashi
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | | | - Atsushi Nakagawa
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Kenichi Akaji
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
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13
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Chen L, Chen S, Gui C, Shen J, Shen X, Jiang H. Discovering Severe Acute Respiratory Syndrome Coronavirus 3CL Protease Inhibitors: Virtual Screening, Surface Plasmon Resonance, and Fluorescence Resonance Energy Transfer Assays. ACTA ACUST UNITED AC 2016; 11:915-21. [PMID: 17092912 PMCID: PMC9050464 DOI: 10.1177/1087057106293295] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An integrated system has been developed for discovering potent inhibitors of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CLpro) by virtual screening correlating with surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) technologies-based assays. The authors screened 81,287 small molecular compounds against SPECS database by virtual screening; 256 compounds were subsequently selected for biological evaluation. Through SPR technology-based assay, 52 from these 256 compounds were discovered to show binding to SARS-CoV 3CLpro. The enzymatic inhibition activities of these 52 SARS-CoV 3CLpro binders were further applied to FRET-based assay, and IC50 values were determined. Based on this integrated assay platform, 8 new SARS-CoV 3CLpro inhibitors were discovered. The fact that the obtained IC50 values for the inhibitors are in good accordance with the discovered dissociation equilibrium constants (KDs) assayed by SPR implied the reliability of this platform. Our current work is hoped to supply a powerful approach in the discovery of potent SARS-CoV 3CLpro inhibitors, and the determined inhibitors could be used as possible lead compounds for further research.
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Affiliation(s)
- Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chunshan Gui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xu Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Address reprint requests to: Xu Shen Drug Discovery and Design Center State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 E-mail: or
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Konno H, Wakabayashi M, Takanuma D, Saito Y, Akaji K. Design and synthesis of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease. Bioorg Med Chem 2016; 24:1241-54. [PMID: 26879854 PMCID: PMC7111485 DOI: 10.1016/j.bmc.2016.01.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 01/19/2023]
Abstract
Synthesis of serine derivatives having the essential functional groups for the inhibitor of SARS 3CL protease and evaluation of their inhibitory activities using SARS 3CL R188I mutant protease are described. The lead compounds, functionalized serine derivatives, were designed based on the tetrapeptide aldehyde and Bai's cinnamoly inhibitor, and additionally performed with simulation on GOLD softwear. Structure activity relationship studies of the candidate compounds were given reasonable inhibitors ent-3 and ent-7k against SARS 3CL R188I mutant protease. These inhibitors showed protease selectivity and no cytotoxicity.
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Affiliation(s)
- Hiroyuki Konno
- Department of Biological Engineering, Graduate School of Science and Technology, Yamagata University, Yonezawa, Yamagata 992-8510, Japan.
| | - Masaki Wakabayashi
- Department of Biological Engineering, Graduate School of Science and Technology, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Daiki Takanuma
- Department of Biological Engineering, Graduate School of Science and Technology, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Yota Saito
- Department of Biological Engineering, Graduate School of Science and Technology, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8414, Japan.
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16
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Shimamoto Y, Hattori Y, Kobayashi K, Teruya K, Sanjoh A, Nakagawa A, Yamashita E, Akaji K. Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors. Bioorg Med Chem 2015; 23:876-90. [PMID: 25614110 PMCID: PMC7111320 DOI: 10.1016/j.bmc.2014.12.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 01/07/2023]
Abstract
The design and evaluation of a novel decahydroisoquinolin scaffold as an inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)) are described. Focusing on hydrophobic interactions at the S2 site, the decahydroisoquinolin scaffold was designed by connecting the P2 site cyclohexyl group of the substrate-based inhibitor to the main-chain at the α-nitrogen atom of the P2 position via a methylene linker. Starting from a cyclohexene enantiomer obtained by salt resolution, trans-decahydroisoquinolin derivatives were synthesized. All decahydroisoquinolin inhibitors synthesized showed moderate but clear inhibitory activities for SARS 3CL(pro), which confirmed the fused ring structure of the decahydroisoquinolin functions as a novel scaffold for SARS 3CL(pro) inhibitor. X-ray crystallographic analyses of the SARS 3CL(pro) in a complex with the decahydroisoquinolin inhibitor revealed the expected interactions at the S1 and S2 sites, as well as additional interactions at the N-substituent of the inhibitor.
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Affiliation(s)
- Yasuhiro Shimamoto
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Yasunao Hattori
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kazuya Kobayashi
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kenta Teruya
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Sakyo-ku, Kyoto 606-0823, Japan
| | - Akira Sanjoh
- R&D Center, Protein Wave Co., Nara 631-0006, Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
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17
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Wong KB, Wan DCC, Chow HF. Substrate specificity and rational design of peptidomimetic inhibitors for SARS coronavirus main protease. Hong Kong Med J 2014; 20 Suppl 4:18-21. [PMID: 25224113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- K B Wong
- School of Life Sciences, The Chinese University of Hong Kong
| | - D C C Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - H F Chow
- Department of Chemistry, The Chinese University of Hong Kong
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18
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Chuck CP, Ke ZH, Chen C, Wan DCC, Chow HF, Wong KB. Profiling of substrate-specificity and rational design of broad-spectrum peptidomimetic inhibitors for main proteases of coronaviruses. Hong Kong Med J 2014; 20 Suppl 4:22-25. [PMID: 25224114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- C P Chuck
- School of Life Sciences, The Chinese University of Hong Kong
| | - Z H Ke
- Department of Chemistry, The Chinese University of Hong Kong
| | - C Chen
- Department of Chemistry, The Chinese University of Hong Kong
| | - D C C Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - H F Chow
- Department of Chemistry, The Chinese University of Hong Kong
| | - K B Wong
- School of Life Sciences, The Chinese University of Hong Kong
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Ratia K, Kilianski A, Baez-Santos YM, Baker SC, Mesecar A. Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease. PLoS Pathog 2014; 10:e1004113. [PMID: 24854014 PMCID: PMC4031219 DOI: 10.1371/journal.ppat.1004113] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/28/2014] [Indexed: 01/16/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes a papain-like protease (PLpro) with both deubiquitinating (DUB) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response. Here we examine the structural basis for PLpro's ubiquitin chain and interferon stimulated gene 15 (ISG15) specificity. We present the X-ray crystal structure of PLpro in complex with ubiquitin-aldehyde and model the interaction of PLpro with other ubiquitin-chain and ISG15 substrates. We show that PLpro greatly prefers K48- to K63-linked ubiquitin chains, and ISG15-based substrates to those that are mono-ubiquitinated. We propose that PLpro's higher affinity for K48-linked ubiquitin chains and ISG15 stems from a bivalent mechanism of binding, where two ubiquitin-like domains prefer to bind in the palm domain of PLpro with the most distal ubiquitin domain interacting with a “ridge” region of the thumb domain. Mutagenesis of residues within this ridge region revealed that these mutants retain viral protease activity and the ability to catalyze hydrolysis of mono-ubiquitin. However, a select number of these mutants have a significantly reduced ability to hydrolyze the substrate ISG15-AMC, or be inhibited by K48-linked diubuiquitin. For these latter residues, we found that PLpro antagonism of the nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway is abrogated. This identification of key and unique sites in PLpro required for recognition and processing of diubiquitin and ISG15 versus mono-ubiquitin and protease activity provides new insight into ubiquitin-chain and ISG15 recognition and highlights a role for PLpro DUB and deISGylase activity in antagonism of the innate immune response. All coronaviruses such as the SARS virus and the recently identified Middle East Respiratory Syndrome (MERS) virus encode in their genomes at least one papain-like protease (PLpro) enzyme that has two distinct functions in viral pathogenesis. The first function is to process the viral polyprotein into individual proteins that are essential for viral replication. The second function is to remove ubiquitin and ISG15 proteins from host cell proteins, which likely helps coronaviruses short circuit the host's innate immune response. The 3-dimensional structure of SARS virus PLpro in complex with a human ubiquitin analog was determined and reveals how coronavirus PLpro enzymes strip ubiquitin and ISG15 from host cell proteins at the molecular level. A series of amino acid residues involved in interactions between PLpro and ubiquitin were mutated to identify which interactions are important only for the recognition of ubiquitin and ISG15 modified proteins by PLpro and not for recognition and cleaving of the viral polyprotein. The 3D structure of SARS PLpro with ubiquitin-aldehyde sheds significant new light into how PLpro interacts with ubiquitin-like molecules and provides a molecular road map for performing similar studies on other deadly coronaviruses such as MERS.
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Affiliation(s)
- Kiira Ratia
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, Illinois, United States of America
| | - Andrew Kilianski
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Yahira M. Baez-Santos
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Andrew Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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21
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Báez-Santos Y, Barraza SJ, Wilson MW, Agius MP, Mielech AM, Davis NM, Baker SC, Larsen SD, Mesecar AD. X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases. J Med Chem 2014; 57:2393-412. [PMID: 24568342 PMCID: PMC3983375 DOI: 10.1021/jm401712t] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 12/01/2022]
Abstract
Structure-guided design was used to generate a series of noncovalent inhibitors with nanomolar potency against the papain-like protease (PLpro) from the SARS coronavirus (CoV). A number of inhibitors exhibit antiviral activity against SARS-CoV infected Vero E6 cells and broadened specificity toward the homologous PLP2 enzyme from the human coronavirus NL63. Selectivity and cytotoxicity studies established a more than 100-fold preference for the coronaviral enzyme over homologous human deubiquitinating enzymes (DUBs), and no significant cytotoxicity in Vero E6 and HEK293 cell lines is observed. X-ray structural analyses of inhibitor-bound crystal structures revealed subtle differences between binding modes of the initial benzodioxolane lead (15g) and the most potent analogues 3k and 3j, featuring a monofluoro substitution at para and meta positions of the benzyl ring, respectively. Finally, the less lipophilic bis(amide) 3e and methoxypyridine 5c exhibit significantly improved metabolic stability and are viable candidates for advancing to in vivo studies.
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Affiliation(s)
- Yahira
M. Báez-Santos
- Department
of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907, United States
| | - Scott J. Barraza
- Vahlteich
Medicinal Chemistry Core and Department of Medicinal Chemistry, College
of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael W. Wilson
- Vahlteich
Medicinal Chemistry Core and Department of Medicinal Chemistry, College
of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael P. Agius
- Vahlteich
Medicinal Chemistry Core and Department of Medicinal Chemistry, College
of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna M. Mielech
- Department
of Microbiology and Immunology, Loyola University
Chicago Stritch School of Medicine, Maywood, Illinois 60153, United States
| | - Nicole M. Davis
- Department
of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907, United States
| | - Susan C. Baker
- Department
of Microbiology and Immunology, Loyola University
Chicago Stritch School of Medicine, Maywood, Illinois 60153, United States
| | - Scott D. Larsen
- Vahlteich
Medicinal Chemistry Core and Department of Medicinal Chemistry, College
of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew D. Mesecar
- Department
of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907, United States
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22
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Sun Y, Wang Z, Tao J, Wang Y, Wu A, Yang Z, Wang K, Shi L, Chen Y, Guo D. Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase. Antiviral Res 2014; 104:156-64. [PMID: 24530452 PMCID: PMC7119097 DOI: 10.1016/j.antiviral.2014.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 12/17/2022]
Abstract
A yeast-based system for screening of coronavirus N7-MTases inhibitors was developed. Sinefungin is not an ideal antiviral inhibitor. Three natural extracts were observed to specifically inhibit the N7-MTases of coronavirus.
The 5′-cap structure is a distinct feature of eukaryotic mRNAs and is important for RNA stability and protein translation by providing a molecular signature for the distinction of self or non-self mRNA. Eukaryotic viruses generally modify the 5′-end of their RNAs to mimic the cellular mRNA structure, thereby facilitating viral replication in host cells. However, the molecular organization and biochemical mechanisms of the viral capping apparatus typically differ from its cellular counterpart, which makes viral capping enzymes attractive targets for drug discovery. Our previous work showed that SARS coronavirus (SARS-CoV) non-structural protein 14 represents a structurally novel and unique guanine-N7-methyltransferase (N7-MTase) that is able to functionally complement yeast cellular N7-MTase. In the present study, we developed a yeast-based system for identifying and screening inhibitors against coronavirus N7-MTase using both 96-well and 384-well microtiter plates. The MTase inhibitors previously identified by in vitro biochemical assays were tested, and some, such as sinefungin, effectively suppressed N7-MTase in the yeast system. However, other compounds, such as ATA and AdoHcy, did not exert an inhibitory effect within a cellular context. These results validated the yeast assay system for inhibitor screening yet also demonstrated the difference between cell-based and in vitro biochemical assays. The yeast system was applied to the screening of 3000 natural product extracts, and three were observed to more potently inhibit the activity of coronavirus than human N7-MTase.
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Affiliation(s)
- Ying Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zidao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jiali Tao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Andong Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Ziwen Yang
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Kaimei Wang
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Liqiao Shi
- Biological Pesticide Engineering Research Center, Hubei Academy of Agricultural Science, Hubei 430072, PR China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China.
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Subissi L, Imbert I, Ferron F, Collet A, Coutard B, Decroly E, Canard B. SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets. Antiviral Res 2014; 101:122-30. [PMID: 24269475 PMCID: PMC7113864 DOI: 10.1016/j.antiviral.2013.11.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/22/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
The SARS (severe acute respiratory syndrome) pandemic caused ten years ago by the SARS-coronavirus (SARS-CoV) has stimulated a number of studies on the molecular biology of coronaviruses. This research has provided significant new insight into many mechanisms used by the coronavirus replication-transcription complex (RTC). The RTC directs and coordinates processes in order to replicate and transcribe the coronavirus genome, a single-stranded, positive-sense RNA of outstanding length (∼27-32kilobases). Here, we review the up-to-date knowledge on SARS-CoV replicative enzymes encoded in the ORF1b, i.e., the main RNA-dependent RNA polymerase (nsp12), the helicase/triphosphatase (nsp13), two unusual ribonucleases (nsp14, nsp15) and RNA-cap methyltransferases (nsp14, nsp16). We also review how these enzymes co-operate with other viral co-factors (nsp7, nsp8, and nsp10) to regulate their activity. These last ten years of research on SARS-CoV have considerably contributed to unravel structural and functional details of one of the most fascinating replication/transcription machineries of the RNA virus world. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses".
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Affiliation(s)
- Lorenzo Subissi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Isabelle Imbert
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - François Ferron
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Axelle Collet
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Etienne Decroly
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Canard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France.
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Thanigaimalai P, Konno S, Yamamoto T, Koiwai Y, Taguchi A, Takayama K, Yakushiji F, Akaji K, Chen SE, Naser-Tavakolian A, Schön A, Freire E, Hayashi Y. Development of potent dipeptide-type SARS-CoV 3CL protease inhibitors with novel P3 scaffolds: design, synthesis, biological evaluation, and docking studies. Eur J Med Chem 2013; 68:372-84. [PMID: 23994330 PMCID: PMC7115411 DOI: 10.1016/j.ejmech.2013.07.037] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/17/2013] [Accepted: 07/20/2013] [Indexed: 01/17/2023]
Abstract
We report the design and synthesis of a series of dipeptide-type inhibitors with novel P3 scaffolds that display potent inhibitory activity against SARS-CoV 3CLpro. A docking study involving binding between the dipeptidic lead compound 4 and 3CLpro suggested the modification of a structurally flexible P3 N-(3-methoxyphenyl)glycine with various rigid P3 moieties in 4. The modifications led to the identification of several potent derivatives, including 5c-k and 5n with the inhibitory activities (Ki or IC50) in the submicromolar to nanomolar range. Compound 5h, in particular, displayed the most potent inhibitory activity, with a Ki value of 0.006 μM. This potency was 65-fold higher than the potency of the lead compound 4 (Ki=0.39 μM). In addition, the Ki value of 5h was in very good agreement with the binding affinity (16 nM) observed in isothermal titration calorimetry (ITC). A SAR study around the P3 group in the lead 4 led to the identification of a rigid indole-2-carbonyl unit as one of the best P3 moieties (5c). Further optimization showed that a methoxy substitution at the 4-position on the indole unit was highly favorable for enhancing the inhibitory potency.
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Affiliation(s)
- Pillaiyar Thanigaimalai
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
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Ren Z, Yan L, Zhang N, Guo Y, Yang C, Lou Z, Rao Z. The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current effective inhibitor targeting a 3C-like protease. Protein Cell 2013; 4:248-50. [PMID: 23549610 PMCID: PMC4875521 DOI: 10.1007/s13238-013-2841-3] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Zhilin Ren
- College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
- Structural Biology Laboratory and MOE Laboratory of Protein Science, School of Medicine and Life Science, Tsinghua University, Beijing, 100084 China
| | - Liming Yan
- College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
| | - Ning Zhang
- Emerging Infection Disease Program, High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457 China
| | - Yu Guo
- Structural Biology Laboratory and MOE Laboratory of Protein Science, School of Medicine and Life Science, Tsinghua University, Beijing, 100084 China
| | - Cheng Yang
- Structural Biology Laboratory and MOE Laboratory of Protein Science, School of Medicine and Life Science, Tsinghua University, Beijing, 100084 China
- Emerging Infection Disease Program, High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457 China
| | - Zhiyong Lou
- College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
| | - Zihe Rao
- College of Pharmacy and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 China
- Structural Biology Laboratory and MOE Laboratory of Protein Science, School of Medicine and Life Science, Tsinghua University, Beijing, 100084 China
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101 China
- Emerging Infection Disease Program, High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457 China
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Park JY, Kim JH, Kwon JM, Kwon HJ, Jeong HJ, Kim YM, Kim D, Lee WS, Ryu YB. Dieckol, a SARS-CoV 3CL(pro) inhibitor, isolated from the edible brown algae Ecklonia cava. Bioorg Med Chem 2013; 21:3730-7. [PMID: 23647823 PMCID: PMC7126891 DOI: 10.1016/j.bmc.2013.04.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 12/11/2022]
Abstract
SARS-CoV 3CL(pro) plays an important role in viral replication. In this study, we performed a biological evaluation on nine phlorotannins isolated from the edible brown algae Ecklonia cava. The nine isolated phlorotannins (1-9), except phloroglucinol (1), possessed SARS-CoV 3CL(pro) inhibitory activities in a dose-dependently and competitive manner. Of these phlorotannins (1-9), two eckol groups with a diphenyl ether linked dieckol (8) showed the most potent SARS-CoV 3CL(pro) trans/cis-cleavage inhibitory effects (IC(50)s = 2.7 and 68.1 μM, respectively). This is the first report of a (8) phlorotannin chemotype significantly blocking the cleavage of SARS-CoV 3CL(pro) in a cell-based assay with no toxicity. Furthermore, dieckol (8) exhibited a high association rate in the SPR sensorgram and formed extremely strong hydrogen bonds to the catalytic dyad (Cys145 and His41) of the SARS-CoV 3CL(pro).
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Affiliation(s)
- Ji-Young Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Republic of Korea
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Cho JK, Curtis-Long MJ, Lee KH, Kim DW, Ryu HW, Yuk HJ, Park KH. Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa. Bioorg Med Chem 2013; 21:3051-7. [PMID: 23623680 PMCID: PMC7126831 DOI: 10.1016/j.bmc.2013.03.027] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 11/22/2022]
Abstract
SARS-CoV papain-like protease (PLpro) is an important antiviral target due to its key roles in SARS virus replication. The MeOH extracts of the fruits of the Paulownia tree yielded many small molecules capable of targeting PLpro. Five of these compounds were new geranylated flavonoids, tomentin A, tomentin B, tomentin C, tomentin D, tomentin E (1-5). Structure analysis of new compounds (1-5) by NMR showed that they all contain a 3,4-dihydro-2H-pyran moiety. This chemotype is very rare and is derived from cyclization of a geranyl group with a phenol functionality. Most compounds (1-12) inhibited PLpro in a dose dependent manner with IC50's raging between 5.0 and 14.4 μM. All new compounds having the dihydro-2H-pyran group showed better inhibition than their parent compounds (1 vs 11, 2 vs 9, 4 vs 12, 5 vs 6). In kinetic studies, 1-12 emerged to be reversible, mixed inhibitors.
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Affiliation(s)
- Jung Keun Cho
- Division of Applied Life Science (BK21 program), IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
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Adedeji AO, Singh K, Sarafianos SG. Structural and biochemical basis for the difference in the helicase activity of two different constructs of SARS-CoV helicase. Cell Mol Biol (Noisy-le-grand) 2012; 58:114-121. [PMID: 23273200 PMCID: PMC3612351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 10/05/2012] [Indexed: 06/01/2023]
Abstract
The non—structural protein 13 (nsp13) of Severe Acute Respiratory Syndrome Coronavirus (SARS—CoV) is a helicase that separates double—stranded RNA or DNA with a 5'—3' polarity, using the energy of nucleotide hydrolysis. We have previously determined the minimal mechanism of helicase function by nsp13 where we demonstrated that the enzyme unwinds nucleic acid in discrete steps of 9.3 base—pairs each with a catalytic rate of 30 steps per second. In that study we used different constructs of nsp13 (GST and H6 constructs). GST—nsp13 showed much more efficient nucleic acid unwinding than the H6—tagged counterpart. At 0.1 second, more than 50% of the ATP is hydrolyzed by GST—nsp13 compared to less than 5% ATP hydrolysis by H6—nsp13. Interestingly, the two constructs have the same binding affinity for nucleic acids. We, therefore propose that the difference in the catalytic efficiency of these two constructs is due to the interference of ATP binding by the histidine tag at the amino—terminus of nsp13.
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Affiliation(s)
- Adeyemi O. Adedeji
- Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Stefan G. Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri School of Medicine, Columbia, MO 65211, USA
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Park JY, Kim JH, Kim YM, Jeong HJ, Kim DW, Park KH, Kwon HJ, Park SJ, Lee WS, Ryu YB. Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg Med Chem 2012; 20:5928-35. [PMID: 22884354 PMCID: PMC7127169 DOI: 10.1016/j.bmc.2012.07.038] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/23/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022]
Abstract
In the search for anti-SARS-CoV, tanshinones derived from Salvia miltiorrhiza were found to be specific and selective inhibitors for the SARS-CoV 3CL(pro) and PL(pro), viral cysteine proteases. A literature search for studies involving the seven isolated tanshinone hits showed that at present, none have been identified as coronaviral protease inhibitors. We have identified that all of the isolated tanshinones are good inhibitors of both cysteine proteases. However, their activity was slightly affected by subtle changes in structure and targeting enzymes. All isolated compounds (1-7) act as time dependent inhibitors of PL(pro), but no improved inhibition was observed following preincubation with the 3CL(pro). In a detail kinetic mechanism study, all of the tanshinones except rosmariquinone (7) were identified as noncompetitive enzyme isomerization inhibitors. However, rosmariquinone (7) showed a different kinetic mechanism through mixed-type simple reversible slow-binding inhibition. Furthermore, tanshinone I (5) exhibited the most potent nanomolar level inhibitory activity toward deubiquitinating (IC(50)=0.7 μM). Additionally, the inhibition is selective because these compounds do not exert significant inhibitory effects against other proteases including chymotrysin, papain, and HIV protease. These findings provide potential inhibitors for SARS-CoV viral infection and replication.
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Key Words
- ic50, the inhibitor concentration leading to 50% activity loss
- ki, inhibition constant
- kiapp, apparent ki
- k, rate constant
- vmax, maximum velocity
- km, michaelis-menten constant
- kobs, apparent first-order rate constant for the transition from vi to vs
- vi, initial velocity
- vs, steady-state rate
- sars, severe acute respiratory syndrome
- cov, coronavirus
- tanshinone
- sars-cov
- 3clpro
- plpro
- slow-binding inhibitor
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Affiliation(s)
- Ji-Young Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
- School of Biological Science and Biotechnology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Jang Hoon Kim
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Young Min Kim
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Hyung Jae Jeong
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Dae Wook Kim
- Division of Applied Life Science (BK 21 Program, IALS), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK 21 Program, IALS), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hyung-Jun Kwon
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Su-Jin Park
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Woo Song Lee
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
| | - Young Bae Ryu
- Infection Control Research Center, Korea Research Institute of Bioscience and Biotechnology, KRIBB, Jeongeup 580-185, Republic of Korea
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Ahn DG, Choi JK, Taylor DR, Oh JW. Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates. Arch Virol 2012; 157:2095-104. [PMID: 22791111 PMCID: PMC7086750 DOI: 10.1007/s00705-012-1404-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/24/2012] [Indexed: 11/26/2022]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) RNA genome is replicated by a virus-encoded RNA replicase, the key component of which is the nonstructural protein 12 (nsp12). In this report, we describe the biochemical properties of a full-length recombinant SARS-CoV nsp12 RNA-dependent RNA polymerase (RdRp) capable of copying viral RNA templates. The purified SARS-CoV nsp12 showed both primer-dependent and primer-independent RNA synthesis activities using homopolymeric RNA templates. The RdRp activity was strictly dependent on Mn2+. The nsp12 preferentially copied homopolymeric pyrimidine RNA templates in the absence of an added oligonucleotide primer. It was also able to initiate de novo RNA synthesis from the 3’-ends of both the plus- and minus-strand genome of SARS-CoV, using the 3’-terminal 36- and 37-nt RNA, respectively. The in vitro RdRp assay system established with a full-length nsp12 will be useful for understanding the mechanisms of coronavirus replication and for the development of anti-SARS-CoV agents.
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Affiliation(s)
- Dae-Gyun Ahn
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
| | - Jin-Kyu Choi
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
| | - Deborah R. Taylor
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892 USA
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
- Translational Research Center for Protein Function Control, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
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Yu MS, Lee J, Lee JM, Kim Y, Chin YW, Jee JG, Keum YS, Jeong YJ. Identification of myricetin and scutellarein as novel chemical inhibitors of the SARS coronavirus helicase, nsP13. Bioorg Med Chem Lett 2012; 22:4049-4054. [PMID: 22578462 DOI: 10.1016/j.bmcl.2012.04.08110.1016/j.bmcl.2012.04.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 04/09/2012] [Accepted: 04/17/2012] [Indexed: 05/22/2023]
Abstract
Severe acute respiratory syndrome (SARS) is an infectious disease with a strong potential for transmission upon close personal contact and is caused by the SARS-coronavirus (CoV). However, there are no natural or synthetic compounds currently available that can inhibit SARS-CoV. We examined the inhibitory effects of 64 purified natural compounds against the activity of SARS helicase, nsP13, and the hepatitis C virus (HCV) helicase, NS3h, by conducting fluorescence resonance energy transfer (FRET)-based double-strand (ds) DNA unwinding assay or by using a colorimetry-based ATP hydrolysis assay. While none of the compounds, examined in our study inhibited the DNA unwinding activity or ATPase activity of human HCV helicase protein, we found that myricetin and scutellarein potently inhibit the SARS-CoV helicase protein in vitro by affecting the ATPase activity, but not the unwinding activity, nsP13. In addition, we observed that myricetin and scutellarein did not exhibit cytotoxicity against normal breast epithelial MCF10A cells. Our study demonstrates for the first time that selected naturally-occurring flavonoids, including myricetin and scultellarein might serve as SARS-CoV chemical inhibitors.
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Affiliation(s)
- Mi-Sun Yu
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
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Adedeji AO, Marchand B, te Velthuis AJW, Snijder EJ, Weiss S, Eoff RL, Singh K, Sarafianos SG. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PLoS One 2012; 7:e36521. [PMID: 22615777 PMCID: PMC3352918 DOI: 10.1371/journal.pone.0036521] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/03/2012] [Indexed: 02/04/2023] Open
Abstract
The non-structural protein 13 (nsp13) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) is a helicase that separates double-stranded RNA (dsRNA) or DNA (dsDNA) with a 5′→3′ polarity, using the energy of nucleotide hydrolysis. We determined the minimal mechanism of helicase function by nsp13. We showed a clear unwinding lag with increasing length of the double-stranded region of the nucleic acid, suggesting the presence of intermediates in the unwinding process. To elucidate the nature of the intermediates we carried out transient kinetic analysis of the nsp13 helicase activity. We demonstrated that the enzyme unwinds nucleic acid in discrete steps of 9.3 base-pairs (bp) each, with a catalytic rate of 30 steps per second. Therefore the net unwinding rate is ∼280 base-pairs per second. We also showed that nsp12, the SARS-CoV RNA-dependent RNA polymerase (RdRp), enhances (2-fold) the catalytic efficiency of nsp13 by increasing the step size of nucleic acid (RNA/RNA or DNA/DNA) unwinding. This effect is specific for SARS-CoV nsp12, as no change in nsp13 activity was observed when foot-and-mouth-disease virus RdRp was used in place of nsp12. Our data provide experimental evidence that nsp13 and nsp12 can function in a concerted manner to improve the efficiency of viral replication and enhance our understanding of nsp13 function during SARS-CoV RNA synthesis.
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Affiliation(s)
- Adeyemi O. Adedeji
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Bruno Marchand
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Aartjan J. W. te Velthuis
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan Weiss
- Department of Microbiology, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Kamalendra Singh
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Stefan G. Sarafianos
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
- * E-mail:
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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: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Mukherjee P, Shah F, Desai P, Avery M. Inhibitors of SARS-3CLpro: virtual screening, biological evaluation, and molecular dynamics simulation studies. J Chem Inf Model 2011; 51:1376-92. [PMID: 21604711 PMCID: PMC3929308 DOI: 10.1021/ci1004916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SARS-CoV from the coronaviridae family has been identified as the etiological agent of Severe Acute Respiratory Syndrome (SARS), a highly contagious upper respiratory disease that reached epidemic status in 2002. SARS-3CL(pro), a cysteine protease indispensible to the viral life cycle, has been identified as one of the key therapeutic targets against SARS. A combined ligand and structure-based virtual screening was carried out against the Asinex Platinum collection. Multiple low micromolar inhibitors of the enzyme were identified through this search, one of which also showed activity against SARS-CoV in a whole cell CPE assay. Furthermore, multinanosecond explicit solvent simulations were carried out using the docking poses of the identified hits to study the overall stability of the binding site interactions as well as identify important changes in the interaction profile that were not apparent from the docking study. Cumulative analysis of the evaluated compounds and the simulation studies led to the identification of certain protein-ligand interaction patterns which would be useful in further structure based design efforts.
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Affiliation(s)
| | - Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS 38677
| | | | - Mitchell Avery
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS 38677
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Hanh Nguyen TT, Ryu HJ, Lee SH, Hwang S, Breton V, Rhee JH, Kim D. Virtual screening identification of novel severe acute respiratory syndrome 3C-like protease inhibitors and in vitro confirmation. Bioorg Med Chem Lett 2011; 21:3088-91. [PMID: 21470860 PMCID: PMC7126700 DOI: 10.1016/j.bmcl.2011.03.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/23/2011] [Accepted: 03/09/2011] [Indexed: 12/14/2022]
Abstract
The 3C-like protease (3CL(pro)) of severe acute respiratory syndrome associated coronavirus (SARS-CoV) is vital for SARS-CoV replication and is a promising drug target. Structure based virtual screening of 308307 chemical compounds was performed using the computation tool Autodock 3.0.5 on a WISDOM Production Environment. The top 1468 ranked compounds with free binding energy ranging from -14.0 to -17.09 kcal mol(-1) were selected to check the hydrogen bond interaction with amino acid residues in the active site of 3CL(pro). Fifty-three compounds from 35 main groups were tested in an in vitro assay for inhibition of 3CL(pro) expressed by Escherichia coli. Seven of the 53 compounds were selected; their IC(50) ranged from 38.57±2.41 to 101.38±3.27 μM. Two strong 3CL(pro) inhibitors were further identified as competitive inhibitors of 3CL(pro) with K(i) values of 9.11±1.6 and 9.93±0.44 μM. Hydrophobic and hydrogen bond interactions of compound with amino acid residues in the active site of 3CL(pro) were also identified.
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Affiliation(s)
- Thi Thanh Hanh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Hwa-Ja Ryu
- School of Biological Sciences and Technology and The Research Institute for Catalysis, Chonnam National University, Gwangju, Republic of Korea
| | - Se-Hoon Lee
- Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Soonwook Hwang
- Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Vincent Breton
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Joon Haeng Rhee
- Chonnam National University Medical School and Clinical Vaccine R&D Institute, Hwa-Sun, Republic of Korea
| | - Doman Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
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te Velthuis AJW, van den Worm SHE, Sims AC, Baric RS, Snijder EJ, van Hemert MJ. Zn(2+) inhibits coronavirus and arterivirus RNA polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture. PLoS Pathog 2010; 6:e1001176. [PMID: 21079686 PMCID: PMC2973827 DOI: 10.1371/journal.ppat.1001176] [Citation(s) in RCA: 543] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/01/2010] [Indexed: 02/06/2023] Open
Abstract
Increasing the intracellular Zn2+ concentration with zinc-ionophores like pyrithione (PT) can efficiently impair the replication of a variety of RNA viruses, including poliovirus and influenza virus. For some viruses this effect has been attributed to interference with viral polyprotein processing. In this study we demonstrate that the combination of Zn2+ and PT at low concentrations (2 µM Zn2+ and 2 µM PT) inhibits the replication of SARS-coronavirus (SARS-CoV) and equine arteritis virus (EAV) in cell culture. The RNA synthesis of these two distantly related nidoviruses is catalyzed by an RNA-dependent RNA polymerase (RdRp), which is the core enzyme of their multiprotein replication and transcription complex (RTC). Using an activity assay for RTCs isolated from cells infected with SARS-CoV or EAV—thus eliminating the need for PT to transport Zn2+ across the plasma membrane—we show that Zn2+ efficiently inhibits the RNA-synthesizing activity of the RTCs of both viruses. Enzymatic studies using recombinant RdRps (SARS-CoV nsp12 and EAV nsp9) purified from E. coli subsequently revealed that Zn2+ directly inhibited the in vitro activity of both nidovirus polymerases. More specifically, Zn2+ was found to block the initiation step of EAV RNA synthesis, whereas in the case of the SARS-CoV RdRp elongation was inhibited and template binding reduced. By chelating Zn2+ with MgEDTA, the inhibitory effect of the divalent cation could be reversed, which provides a novel experimental tool for in vitro studies of the molecular details of nidovirus replication and transcription. Positive-stranded RNA (+RNA) viruses include many important pathogens. They have evolved a variety of replication strategies, but are unified in the fact that an RNA-dependent RNA polymerase (RdRp) functions as the core enzyme of their RNA-synthesizing machinery. The RdRp is commonly embedded in a membrane-associated replication complex that is assembled from viral RNA, and viral and host proteins. Given their crucial function in the viral replicative cycle, RdRps are key targets for antiviral research. Increased intracellular Zn2+ concentrations are known to efficiently impair replication of a number of RNA viruses, e.g. by interfering with correct proteolytic processing of viral polyproteins. Here, we not only show that corona- and arterivirus replication can be inhibited by increased Zn2+ levels, but also use both isolated replication complexes and purified recombinant RdRps to demonstrate that this effect may be based on direct inhibition of nidovirus RdRps. The combination of protocols described here will be valuable for future studies into the function of nidoviral enzyme complexes.
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Affiliation(s)
- Aartjan J. W. te Velthuis
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H. E. van den Worm
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Amy C. Sims
- Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail: (ES); (MJvH)
| | - Martijn J. van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail: (ES); (MJvH)
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Abstract
BACKGROUND The 3C-like protease (3CL(pro)) of severe acute respiratory syndrome-coronavirus is required for autoprocessing of the polyprotein, and is a potential target for treating coronaviral infection. METHODOLOGY/PRINCIPAL FINDINGS To obtain a thorough understanding of substrate specificity of the protease, a substrate library of 198 variants was created by performing saturation mutagenesis on the autocleavage sequence at P5 to P3' positions. The substrate sequences were inserted between cyan and yellow fluorescent proteins so that the cleavage rates were monitored by in vitro fluorescence resonance energy transfer. The relative cleavage rate for different substrate sequences was correlated with various structural properties. P5 and P3 positions prefer residues with high β-sheet propensity; P4 prefers small hydrophobic residues; P2 prefers hydrophobic residues without β-branch. Gln is the best residue at P1 position, but observable cleavage can be detected with His and Met substitutions. P1' position prefers small residues, while P2' and P3' positions have no strong preference on residue substitutions. Noteworthy, solvent exposed sites such as P5, P3 and P3' positions favour positively charged residues over negatively charged one, suggesting that electrostatic interactions may play a role in catalysis. A super-active substrate, which combined the preferred residues at P5 to P1 positions, was found to have 2.8 fold higher activity than the wild-type sequence. CONCLUSIONS/SIGNIFICANCE Our results demonstrated a strong structure-activity relationship between the 3CL(pro) and its substrate. The substrate specificity profiled in this study may provide insights into a rational design of peptidomimetic inhibitors.
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Affiliation(s)
- Chi-Pang Chuck
- School of Biochemical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Lin-Tat Chong
- Department of Biochemistry and Molecular Biotechnology Programme, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Chao Chen
- Department of Chemistry, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Hak-Fun Chow
- Department of Chemistry, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - David Chi-Cheong Wan
- School of Biochemical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Kam-Bo Wong
- Department of Biochemistry and Molecular Biotechnology Programme, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR. Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog 2010; 6:e1000896. [PMID: 20463816 PMCID: PMC2865531 DOI: 10.1371/journal.ppat.1000896] [Citation(s) in RCA: 324] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 04/05/2010] [Indexed: 01/30/2023] Open
Abstract
Most RNA viruses lack the mechanisms to recognize and correct mutations that arise during genome replication, resulting in quasispecies diversity that is required for pathogenesis and adaptation. However, it is not known how viruses encoding large viral RNA genomes such as the Coronaviridae (26 to 32 kb) balance the requirements for genome stability and quasispecies diversity. Further, the limits of replication infidelity during replication of large RNA genomes and how decreased fidelity impacts virus fitness over time are not known. Our previous work demonstrated that genetic inactivation of the coronavirus exoribonuclease (ExoN) in nonstructural protein 14 (nsp14) of murine hepatitis virus results in a 15-fold decrease in replication fidelity. However, it is not known whether nsp14-ExoN is required for replication fidelity of all coronaviruses, nor the impact of decreased fidelity on genome diversity and fitness during replication and passage. We report here the engineering and recovery of nsp14-ExoN mutant viruses of severe acute respiratory syndrome coronavirus (SARS-CoV) that have stable growth defects and demonstrate a 21-fold increase in mutation frequency during replication in culture. Analysis of complete genome sequences from SARS-ExoN mutant viral clones revealed unique mutation sets in every genome examined from the same round of replication and a total of 100 unique mutations across the genome. Using novel bioinformatic tools and deep sequencing across the full-length genome following 10 population passages in vitro, we demonstrate retention of ExoN mutations and continued increased diversity and mutational load compared to wild-type SARS-CoV. The results define a novel genetic and bioinformatics model for introduction and identification of multi-allelic mutations in replication competent viruses that will be powerful tools for testing the effects of decreased fidelity and increased quasispecies diversity on viral replication, pathogenesis, and evolution. Quasispecies diversity is critical to virus fitness, adaptation, and pathogenesis. However, the relationship of fidelity to population diversity is less studied because viral systems with engineered differences in fidelity and bioinformatic methods that robustly measure and compare fidelity and diversity during replication and passage have not been available. Coronaviruses contain the largest and most complex RNA genomes, and encode multiple novel replicase nonstructural proteins (nsps). We previously demonstrated that murine hepatitis virus nsp14-exonuclease (ExoN) activity is required for replication fidelity. In the present report we have generated nsp14-ExoN inactivation mutants of SARS-coronavirus (S-ExoN) that have stable growth defects and dramatically decreased replication fidelity during replication in culture. We used the S-ExoN mutant viruses to define the diversity and stability of the genome during replication and passage, and to test the capacity of deep sequencing to track virus population diversity over time. The experiments demonstrate that viable S-ExoN mutants accumulate large numbers of predominantly unique mutations across the genome, and that increased diversity is continuous over passage. The results establish methods for direct comparison of consensus genome sequences with total population diversity and the impact on viral growth and adaptation.
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Affiliation(s)
- Lance D. Eckerle
- Departments of Pediatrics and Microbiology and Immunology and Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michelle M. Becker
- Departments of Pediatrics and Microbiology and Immunology and Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rebecca A. Halpin
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Kelvin Li
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eli Venter
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Xiaotao Lu
- Departments of Pediatrics and Microbiology and Immunology and Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Sana Scherbakova
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rachel L. Graham
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - David J. Spiro
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Mark R. Denison
- Departments of Pediatrics and Microbiology and Immunology and Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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Huang JD, Sun HZ, Tanner JA, Watt RM. Determination of the functions of the putative metal-binding domain of the SCV helicase. Hong Kong Med J 2009; 15 Suppl 6:15-16. [PMID: 19801711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Affiliation(s)
- J D Huang
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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Lee C, Lee JM, Lee NR, Kim DE, Jeong YJ, Chong Y. Investigation of the pharmacophore space of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) NTPase/helicase by dihydroxychromone derivatives. Bioorg Med Chem Lett 2009; 19:4538-41. [PMID: 19625187 PMCID: PMC7127646 DOI: 10.1016/j.bmcl.2009.07.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/01/2009] [Accepted: 07/03/2009] [Indexed: 11/24/2022]
Abstract
Aryl diketoacids have been identified as the first SARS-CoV NTPase/helicase inhibitors with a distinct pharmacophore featuring an arylmethyl group attached to a diketoacid. In order to search for the pharmacophore space around the diketoacid core, three classes of dihydroxychromone derivatives were prepared. Based on SAR study, an extended feature of the pharmacophore model of SARS-CoV NTPase/helicase was proposed which is constituted of a diketoacid core, a hydrophobic arylmethyl substituent, and a free catechol unit.
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Affiliation(s)
- Chaewoon Lee
- Department of Bioscience & Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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43
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Luo W, Su X, Gong S, Qin Y, Liu W, Li J, Yu H, Xu Q. Anti-SARS coronavirus 3C-like protease effects of Rheum palmatum L. extracts. Biosci Trends 2009; 3:124-126. [PMID: 20103835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The present study aims to clarify the inhibitive effect of the compounds from Rheum palmatum L. on the SARS-3CL protease. The SARS-CoV 3CL gene was amplified from RNA of the SARS virus by PCR. The SARS-CoV 3CL protease was purified from a colon bacillus recombinant. Drugs and 3CL protease were incubated together. The inhibition rate and IC(50) were calculated based on absorbance. Components from the Rheum palmatum L. had a high level of anti-SARS-CoV 3CL protease activity. The IC(50) was 13.76 +/- 0.03 microg/mL and the inhibition rate was up to 96%. In conclusion, extracts from Rheum palmatum L. have a high level of inhibitory activity against 3CL protease, suggesting that extracts from Rheum palmatum L. may represent a potential therapeutic for SARS.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chen P, Hu T, Jiang M, Guo D. [Synthesis in Escherichia coli cells and characterization of the active exoribonuclease of severe acute respiratory syndrome coronavirus]. Mol Biol (Mosk) 2009; 43:446-454. [PMID: 19548531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The nsp14 protein, an exoribonuclease of the DEDD superfamily encoded by severe acute respiratory syndrome coronavirus (SARS-CoV), was expressed in fusion with different affinity tags. The recombinant nspl4 proteins with either GST fusion or 6-histidine tag were shown to possess ribonuclease activity but nspl4 with a short MGHHHHHHGS tag sequence at the N-terminus increased the solubility of nspl4 protein and facilitated the protein purification. Mutations of the conserved residues of nspl4 resulted in significant attenuation but not abolishment of the ribonuclease activity. Combination of fluorescence and circular dichroism spectroscopy analyses showed that the conformational stability of nsp14 protein varied with many external factors such as pH, temperature and presence of denaturing chemicals. These results provide new information on the structural features and would be helpful for further characterization of this functionally important protein.
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Lee C, Lee JM, Lee NR, Jin BS, Jang KJ, Kim DE, Jeong YJ, Chong Y. Aryl diketoacids (ADK) selectively inhibit duplex DNA-unwinding activity of SARS coronavirus NTPase/helicase. Bioorg Med Chem Lett 2009; 19:1636-8. [PMID: 19233643 PMCID: PMC7127030 DOI: 10.1016/j.bmcl.2009.02.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/02/2009] [Accepted: 02/02/2009] [Indexed: 11/18/2022]
Abstract
As anti-HCV aryl diketoacids (ADK) are good metal chelators, we anticipated that ADKs might serve as potential inhibitors of SARS CoV (SCV) NTPase/helicase (Hel) by mimicking the binding modes of the bismuth complexes which effectively competes for the Zn(2+) ion binding sites in SCV Hel thereby disrupting and inhibiting both the NTPase and helicase activities. Phosphate release assay and FRET-based assay of the ADK analogues showed that the ADKs selectively inhibit the duplex DNA-unwinding activity without significant impact on the helicase ATPase activity. Also, antiviral activities of the ADKs were shown dependent upon the substituent. Taken together, these results suggest that there might be ADK-specific binding site in the SCV Hel, which warrants further investigations with diverse ADKs to provide valuable insights into rational design of specific SCV Hel inhibitors.
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Affiliation(s)
- Chaewoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Jin Moo Lee
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Na-Ra Lee
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Bong-Suk Jin
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Kyoung Jin Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yong-Joo Jeong
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Youhoon Chong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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Abstract
This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HIV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HIV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is limited to viruses that cause chronic disease, viruses that have the potential to cause large-scale epidemics, or viruses that are sufficiently ubiquitous that treating an acute infection would be beneficial even if the infection was ultimately self-limiting. Protease inhibitor development is most advanced for hepatitis C virus (HCV), and we also provide a review of HCV NS3/4A serine protease inhibitor development, including combination therapy and resistance. Finally, we discuss other viral proteases as potential drug targets, including those from Dengue virus, cytomegalovirus, rhinovirus, and coronavirus.
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Affiliation(s)
- Hans-Georg Kräusslich
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
| | - Ralf Bartenschlager
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
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Saikatendu KS, Joseph JS, Subramanian V, Clayton T, Griffith M, Moy K, Velasquez J, Neuman BW, Buchmeier MJ, Stevens RC, Kuhn P. Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3. Structure 2008; 13:1665-75. [PMID: 16271890 PMCID: PMC7126892 DOI: 10.1016/j.str.2005.07.022] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 07/26/2005] [Accepted: 07/31/2005] [Indexed: 11/19/2022]
Abstract
The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. The structure of this “X” domain, seen in many single-stranded RNA viruses, reveals a three-layered α/β/α core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1″-phosphate (Appr-1″-p). The SARS nsP3 domain readily removes the 1″ phosphate group from Appr-1″-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p.
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Affiliation(s)
- Kumar Singh Saikatendu
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Shi J, Sivaraman J, Song J. Mechanism for controlling the dimer-monomer switch and coupling dimerization to catalysis of the severe acute respiratory syndrome coronavirus 3C-like protease. J Virol 2008; 82:4620-9. [PMID: 18305031 PMCID: PMC2293028 DOI: 10.1128/jvi.02680-07] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 02/20/2008] [Indexed: 01/07/2023] Open
Abstract
Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 A. Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 3(10)-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.
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Affiliation(s)
- Jiahai Shi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.
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Mukherjee P, Desai P, Ross L, White EL, Avery MA. Structure-based virtual screening against SARS-3CL(pro) to identify novel non-peptidic hits. Bioorg Med Chem 2008; 16:4138-49. [PMID: 18343121 PMCID: PMC7127700 DOI: 10.1016/j.bmc.2008.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 01/04/2008] [Accepted: 01/07/2008] [Indexed: 01/01/2023]
Abstract
Severe acute respiratory syndrome is a highly infectious upper respiratory tract disease caused by SARS-CoV, a previously unidentified human coronavirus. SARS-3CL(pro) is a viral cysteine protease critical to the pathogen's life cycle and hence a therapeutic target of importance. The recently elucidated crystal structures of this enzyme provide an opportunity for the discovery of inhibitors through rational drug design. In the current study, Gold docking program was utilized to conduct extensive docking studies against the target crystal structure to develop a robust and predictive docking protocol. The validated docking protocol was used to conduct a structure-based virtual screening of the Asinex Platinum collection. Biological evaluation of a screened selection of compounds was carried out to identify novel inhibitors of the viral protease.
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Affiliation(s)
- Prasenjit Mukherjee
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, Faser 417, University, MS 38677, USA
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