Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication
Tek Narsingh Malla, Suraj Pandey, Luis Aldama, Dennisse Feliz, Moraima Noda, Ishwor Poudyal, George N Phillips Jr, Emina A Stojković, Marius Schmidt
doi:10.1101/2021.05.02.442358
There is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known as main protease Mpro or 3CLpro. The shortest and the safest path to clinical use is the repurposing of drugs with binding affinity to PLpro or 3CLpro that have an established safety profile in humans. Several studies have reported crystal structures of SARS-CoV-2 main protease in complex with FDA approved drugs such as those used in treatment of hepatitis C. Here, we report the crystal structure of 3CLpro in complex Vitamin C (L-ascorbate) bound to the protein's active site at 2.5 Ångstrom resolution. The crystal structure of the Vitamin C 3CLpro complex may aid future studies on the effect of Vitamin C not only on the coronavirus main protease but on related proteases of other infectious viruses.
Supplementary Material Expression. The CoV-2 3CLpro sequence was synthetized (GenScript) for optimized expression in E. coli according to sequence information published previously (Zhang, Lin, Sun, et al., 2020) . In short, the N-terminus of 3CLpro is fused to glutathione-S-transferase (GST). It further has a 6-His tag at the c-terminus. The N-terminal GST will be autocatalytically cleaved off after expression due to an engineered 3CLpro cleavage sequence. Although the His tag can be cleaved off by a PreScission protease, the tag did not interfere with crystallization and consequently was left on. Overexpression and protein purification protocols were modified from previous reports. E. coli were grown to 0.8 OD 600 at 37 o in terrific broth. Expression was induced by 1 mmol/L IPTG at 25 o C. After 3 h of expression, the culture was induced a second time (1 mmol/L IPTG), and shaken overnight at 20 o C. The yield is about 80 mg for a 6 L culture. Cells were resuspended in lysis buffer (20mM Tris Base, 150 mmol/L NaCl, pH 7.8.). After lysis of the bacterial cells, debris was centrifuged at 50,000 g for 1 hour. The lysate was let stand at room temperature for 3 h (overnight is also possible). After this, the lysate was pumped through a column containing 15 mL of Talon Cobalt resin (TAKARA). The resin was washed without using imidazole using a wash cycle consisting of low salt (20 mmol/L Tris Base, 50 mmol/L NaCl, pH 7.8), high salt (20 mmol/L Tris Base, 1 mol/L NaCl, pH 7.8) and..
References
Adams, Afonine, Bunkoczi, Chen, Davis et al., PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr D Biol Crystallogr,
doi:10.1107/S0907444909052925
Banic, Colunga Biancatelli, Berrill, Marik, Prevention of Rabies by Vitamin C. Nature, Expert Rev Anti Infect Ther,
doi:10.1080/14787210.2020
Douangamath, Fearon, Gehrtz, Krojer, Lukacik et al., Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease, Nature Communications,
doi:10.1038/s41467-020-18709-w
Fowler Iii, Kim, Lepler, Malhotra, Debesa et al., Intravenous vitamin C as adjunctive therapy for enterovirus/rhinovirus induced acute respiratory distress syndrome, World J Crit Care Med,
doi:10.5492/wjccm.v6.i1.85
Furuya, Uozaki, Yamasaki, Arakawa, Arita et al., Antiviral effects of ascorbic and dehydroascorbic acids in vitro, Int J Mol Med
Gunther, Reinke, Fernandez-Garcia, Lieske, Lane et al., X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease, Science,
doi:10.1126/science.abf7945
Harakeh, Jariwalla, Pauling, Suppression of Human-Immunodeficiency-Virus Replication by Ascorbate in Chronically and Acutely Infected-Cells, Proc Natl Acad Sci U S A,
doi:10.1073/pnas.87
Hilgenfeld, From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design, Febs Journal,
doi:10.1111/febs.12936
Hoog, Smith, Qiu, Janson, Hellmig et al., Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex, Biochemistry,
doi:10.1021/bi9712697
Kneller, Galanie, Phillips, O'neill, Coates et al., Malleability of the SARS-CoV-2 3CL M(pro) Active-Site Cavity Facilitates Binding of Clinical Antivirals, Structure,
doi:10.1016/j.str.2020.10.007
Liebschner, Afonine, Moriarty, Poon, Sobolev et al., Polder maps: improving OMIT maps by excluding bulk solvent, Acta Crystallogr D Struct Biol,
doi:10.1107/S2059798316018210
Mescic Macan, Gazivoda Kraljevic, Raic-Malic, Therapeutic Perspective of Vitamin C and Its Derivatives, Antioxidants,
doi:10.3390/antiox8080247
Minor, Cymborowski, Otwinowski, Chruszcz, HKL-3000: the integration of data reduction and structure solution -from diffraction images to an initial model in minutes, Acta Crystallographica Section D-Structural Biology
Murshudov, Skubak, Lebedev, Pannu, Steiner et al., REFMAC5 for the refinement of macromolecular crystal structures, Acta Crystallogr D Biol Crystallogr,
doi:10.1107/S0907444911001314
Oeffner, Bunkoczi, Mccoy, Read, Improved estimates of coordinate error for molecular replacement, Acta Crystallographica Section D-Biological Crystallography,
doi:10.1107/S0907444913023512
Pauling, Vitamin C and the Common Cold
Ramajayam, Tan, Liang, Recent development of 3C and 3CL protease inhibitors for anti-coronavirus and anti-picornavirus drug discovery, Biochem Soc Trans,
doi:10.1042/BST0391371
Thomas, Patel, Bittel, Wolski, Wang et al., Effect of High-Dose Zinc and Ascorbic Acid Supplementation vs Usual Care on Symptom Length and Reduction Among Ambulatory Patients With SARS-CoV-2 Infection: The COVID A to Z Randomized Clinical Trial, JAMA Netw Open,
doi:10.1001/jamanetworkopen.2021.0369
Zhang, Lin, Kusov, Nian, Ma et al., alpha-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment, Journal of Medicinal Chemistry
Zhang, Lin, Sun, Curth, Drosten et al., Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors, Science
Zhao, Ling, Li, Peng, Huang et al., Beneficial aspects of high dose intravenous vitamin C on patients with COVID-19 pneumonia in severe condition: a retrospective case series study, Annals of Palliative Medicine,
doi:10.21037/apm-20-1387
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'DOI': '10.1038/s41467-020-18709-w',
'article-title': 'Crystallographic and electrophilic fragment screening of the SARS-CoV-2 '
'main protease',
'volume': '11',
'year': '2020',
'journal-title': 'Nature Communications'},
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'Lane, T. J. , Ginn, H. M. , Koua, H. M. , Ehrt, C. , Ewert, W. , '
'Oberthuer, D. , Yefanov, O. , Meier, S. , Lorenzen, K. , Krichel, B. , '
'Kopicki, J. D. , Gelisio, L. , Brehm, W. , Dunkel, I. , Seychell, B. , '
'Gieseler, H. , Norton-Baker, B. , Escudero-Perez, B. , Domaracky, M. , '
'Saouane, S. , Tolstikova, A. , White, T. A. , Hanle, A. , Groessler, M. '
', Fleckenstein, H. , Trost, F. , Galchenkova, M. , Gevorkov, Y. , Li, C. '
', Awel, S. , Peck, A. , Barthelmess, M. , Schluenzen, F. , Lourdu '
'Xavier, P. , Werner, N. , Andaleeb, H. , Ullah, N. , Falke, S. , '
'Srinivasan, V. , Franca, B. A. , Schwinzer, M. , Brognaro, H. , Rogers, '
'C. , Melo, D. , Zaitseva-Doyle, J. J. , Knoska, J. , Pena-Murillo, G. E. '
', Mashhour, A. R. , Hennicke, V. , Fischer, P. , Hakanpaa, J. , Meyer, '
'J. , Gribbon, P. , Ellinger, B. , Kuzikov, M. , Wolf, M. , Beccari, A. '
'R. , Bourenkov, G. , von Stetten, D. , Pompidor, G. , Bento, I. , '
'Panneerselvam, S. , Karpics, I. , Schneider, T. R. , Garcia-Alai, M. M. '
', Niebling, S. , Gunther, C. , Schmidt, C. , Schubert, R. , Han, H. , '
'Boger, J. , Monteiro, D. C. F. , Zhang, L. , Sun, X. , Pletzer-Zelgert, '
'J. , Wollenhaupt, J. , Feiler, C. G. , Weiss, M. S. , Schulz, E. C. , '
'Mehrabi, P. , Karnicar, K. , Usenik, A. , Loboda, J. , Tidow, H. , '
'Chari, A. , Hilgenfeld, R. , Uetrecht, C. , Cox, R. , Zaliani, A. , '
'Beck, T. , Rarey, M. , Gunther, S. , Turk, D. , Hinrichs, W. , Chapman, '
'H. N. , Pearson, A. R. , Betzel, C. , & Meents, A. (2021). X-ray '
'screening identifies active site and allosteric inhibitors of SARS-CoV-2 '
'main protease. Science. https://doi.org/10.1126/science.abf7945',
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'article-title': 'Malleability of the SARS-CoV-2 3CL M(pro) Active-Site Cavity '
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'year': '2020',
'journal-title': 'Structure'},
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'unstructured': 'Mescic Macan, A. , Gazivoda Kraljevic, T. , & Raic-Malic, S. (2019). '
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'(Basel), 8(8). https://doi.org/10.3390/antiox8080247',
'DOI': '10.3390/antiox8080247'},
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'volume': '62',
'year': '2006',
'journal-title': 'Acta Crystallographica Section D-Structural Biology'},
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'doi-asserted-by': 'crossref',
'first-page': '2209',
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'article-title': 'Improved estimates of coordinate error for molecular replacement',
'volume': '69',
'year': '2013',
'journal-title': 'Acta Crystallographica Section D-Biological Crystallography'},
{ 'key': '2021052211000682000_2021.05.02.442358v2.19',
'unstructured': 'Pauling, L. (1970). Vitamin C and the Common Cold. W. H. Freeman and '
'Company.'},
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'doi-asserted-by': 'crossref',
'unstructured': 'Sharma, A. , & Gupta, S. P. (2017). Fundamentals of Viruses and Their '
'Proteases. Viral Proteases and Their Inhibitors, 1–24. '
'https://doi.org/10.1016/B978-0-12-809712-0.00001-0',
'DOI': '10.1016/B978-0-12-809712-0.00001-0'},
{ 'issue': '2',
'key': '2021052211000682000_2021.05.02.442358v2.22',
'doi-asserted-by': 'crossref',
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'DOI': '10.1001/jamanetworkopen.2021.0369',
'article-title': 'Effect of High-Dose Zinc and Ascorbic Acid Supplementation vs Usual '
'Care on Symptom Length and Reduction Among Ambulatory Patients With '
'SARS-CoV-2 Infection: The COVID A to Z Randomized Clinical Trial',
'volume': '4',
'year': '2021',
'journal-title': 'JAMA Netw Open'},
{ 'key': '2021052211000682000_2021.05.02.442358v2.23',
'first-page': '4',
'article-title': 'A new coronavirus associated with human respiratory disease in China',
'volume': '579',
'year': '2020',
'journal-title': 'Nature'},
{ 'issue': '9',
'key': '2021052211000682000_2021.05.02.442358v2.24',
'doi-asserted-by': 'crossref',
'first-page': '4562',
'DOI': '10.1021/acs.jmedchem.9b01828',
'article-title': 'alpha-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and '
'Enterovirus Replication: Structure-Based Design, Synthesis, and '
'Activity Assessment',
'volume': '63',
'year': '2020',
'journal-title': 'Journal of Medicinal Chemistry'},
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'doi-asserted-by': 'crossref',
'first-page': '1599',
'DOI': '10.21037/apm-20-1387',
'article-title': 'Beneficial aspects of high dose intravenous vitamin C on patients with '
'COVID-19 pneumonia in severe condition: a retrospective case series '
'study',
'volume': '10',
'year': '2021',
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