Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in  Pichia pastoris

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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. Recombinant 3CL ^pro was expressed in Pichia pastoris GS115 as a 42 kDa protein that displayed a K _m of 15 ± 2 μM with Dabcyl-KTSAVLQSGFRKME-Edans as substrate. Purified 3CL ^pro was used for inhibition and kinetic assays with seven flavonoid compounds. The IC ₅₀ of six flavonoid compounds were 47–381 μM. Quercetin, epigallocatechin gallate and gallocatechin gallate (GCG) displayed good inhibition toward 3CL ^pro with IC ₅₀ values of 73, 73 and 47 μM, respectively. GCG showed a competitive inhibition pattern with K _i 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 3CL ^pro and the galloyl moiety at 3-OH position was required for 3CL ^pro inhibition activity.

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Characterization of a novel coronavirus associated with severe acute respiratory syndrome.

P Rota (2003)

In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.

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Reduced surface: an efficient way to compute molecular surfaces.

Jay Olson, Bernd M Sanner, J Spehner (1996)

Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analytical representation of only the solvent-accessible surface. There are a few programs that compute the analytical representation of the solvent-excluded surface, but they often have problems handling singular cases of self-intersecting surfaces and tend to fail on large molecules (more than 10,000 atoms). We describe here a program called MSMS, which is shown to be fast and reliable in computing molecular surfaces. It relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. The four algorithms composing MSMS are described and their complexity is analyzed. Special attention is given to the handling of self-intersecting parts of the solvent-excluded surface called singularities. The program has been compared with Connolly's program PQMS [M.L. Connolly (1993) Journal of Molecular Graphics, Vol. 11, pp. 139-141] on a set of 709 molecules taken from the Brookhaven Data Base. MSMS was able to compute topologically correct surfaces for each molecule in the set. Moreover, the actual time spent to compute surfaces is in agreement with the theoretical complexity of the program, which is shown to be O[n log(n)] for n atoms. On a Hewlett-Packard 9000/735 workstation, MSMS takes 0.73 s to produce a triangulated solvent-excluded surface for crambin (1 crn, 46 residues, 327 atoms, 4772 triangles), 4.6 s for thermolysin (3tln, 316 residues, 2437 atoms, 26462 triangles), and 104.53 s for glutamine synthetase (2gls, 5676 residues, 43632 atoms, 476665 triangles).

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Is Open Access

GenBank

Dennis A Benson, Ilene Karsch-Mizrachi, David Lipman … (2010)

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

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Contributors

Doman Kim: +82-62-5301844 , +82-62-5301949 , dmkim@jnu.ac.kr

Journal

Journal ID (nlm-ta): Biotechnol Lett

Journal ID (iso-abbrev): Biotechnol. Lett

Title: Biotechnology Letters

Publisher: Springer Netherlands (Dordrecht )

ISSN (Print): 0141-5492

ISSN (Electronic): 1573-6776

Publication date (Electronic): 15 February 2012

Publication date (Print): 2012

Volume: 34

Issue: 5

Pages: 831-838

Affiliations

[1 ]GRID grid.14005.30, ISNI 0000000103569399, 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

[2 ]GRID grid.266100.3, ISNI 0000000121074242, Department of Pediatrics, , University of California, ; San Diego, CA 92103 USA

[3 ]GRID grid.445114.1, Biotechnology Faculty, , Hanoi Open University, ; 46 Ta Quang Buu street, Hai Ba Trung District, Hanoi, Vietnam

[4 ]GRID grid.249967.7, ISNI 0000000406363099, Eco-Friendly Biomaterial Research Center, , Korea Research Institute of Bioscience and Biotechnology, ; Jeongeup, 580-185 Republic of Korea

[5 ]GRID grid.411733.3, ISNI 000000040532811X, Department of Physics, , Gangeung-wonju National University, ; Gangneung, 210-702 Republic of Korea

[6 ]GRID grid.249964.4, ISNI 0000000105235253, Global Science Experimental Data Hub Center, , Korea Institute of Science and Technology Information, ; Daejeon, 805-306 Republic of Korea

[7 ]GRID grid.258151.a, ISNI 0000000107081323, State Key Laboratory of Food Science and Technology, , Jiangnan University, ; 214122 Jiangsu, China

Article

Publisher ID: 845

DOI: 10.1007/s10529-011-0845-8

PMC ID: 7087583

PubMed ID: 22350287

SO-VID: 7e9cc69d-4346-44fe-a785-311375ff66a8

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This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

History

Date received : 24 October 2011

Date accepted : 22 December 2011

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ScienceOpen disciplines: Biotechnology

Keywords: flavonoid,molecular docking,pichia pastoris,protease,severe acute respiratory syndrome (sars)

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ScienceOpen disciplines: Biotechnology

Keywords: flavonoid, molecular docking, pichia pastoris, protease, severe acute respiratory syndrome (sars)

Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in Pichia pastoris

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Microbiology Society: Coronaviruses

Most cited references 10

Characterization of a novel coronavirus associated with severe acute respiratory syndrome.

Reduced surface: an efficient way to compute molecular surfaces.

GenBank

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