Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex.

COVID-19 Coronavirus SARS-CoV-2 SARS-CoV-2 main protease molecular docking molecular dynamics simulations α-ketoamide

Journal

Computational biology and chemistry
ISSN: 1476-928X
Titre abrégé: Comput Biol Chem
Pays: England
ID NLM: 101157394

Informations de publication

Date de publication:
28 May 2020
Historique:
received: 17 04 2020
revised: 19 05 2020
accepted: 23 05 2020
pubmed: 3 6 2020
medline: 3 6 2020
entrez: 3 6 2020
Statut: aheadofprint

Résumé

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. In the absence of a vaccine, or an approved effective therapeutic, there is an intense interest in repositioning available drugs or designing small molecule antivirals. In this context, in silico modelling has proven to be an invaluable tool. An important target is the SARS-CoV-2 main protease (M

Identifiants

pubmed: 32485652
pii: S1476-9271(20)30420-5
doi: 10.1016/j.compbiolchem.2020.107292
pmc: PMC7253975
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

107292

Informations de copyright

Copyright © 2020 Elsevier Ltd. All rights reserved.

Références

Lancet. 2020 Feb 15;395(10223):514-523
pubmed: 31986261
FEBS J. 2014 Sep;281(18):4085-96
pubmed: 25039866
Lancet. 2020 Feb 15;395(10223):470-473
pubmed: 31986257
J Med Chem. 2006 Oct 19;49(21):6177-96
pubmed: 17034125
N Engl J Med. 2020 Mar 26;382(13):1199-1207
pubmed: 31995857
J Chem Inf Model. 2009 Feb;49(2):377-89
pubmed: 19434839
Lancet Infect Dis. 2020 Jul;20(7):776-777
pubmed: 32224313
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
J Comput Aided Mol Des. 2013 Mar;27(3):221-34
pubmed: 23579614
J Comput Chem. 2010 Mar;31(4):671-90
pubmed: 19575467
Am J Physiol Lung Cell Mol Physiol. 2011 Sep;301(3):L269-74
pubmed: 21665960
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Lancet Infect Dis. 2020 Jul;20(7):773
pubmed: 32171390
J Mol Biol. 2007 Sep 21;372(3):774-97
pubmed: 17681537
Lancet Respir Med. 2020 Apr;8(4):e20
pubmed: 32171067
Science. 2003 Jun 13;300(5626):1763-7
pubmed: 12746549
Lancet Infect Dis. 2020 May;20(5):533-534
pubmed: 32087114
Comput Sci Discov. 2012 Jul 26;5(1):
pubmed: 22905037
J Med Chem. 2020 May 14;63(9):4562-4578
pubmed: 32045235
Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41
pubmed: 11517324
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13190-5
pubmed: 14585926
J Chem Inf Model. 2008 May;48(5):1081-91
pubmed: 18465849
Science. 2020 Apr 24;368(6489):409-412
pubmed: 32198291
Chembiochem. 2020 Mar 2;21(5):730-738
pubmed: 32022370
EMBO J. 2002 Jul 1;21(13):3213-24
pubmed: 12093723
J Virol. 2005 Dec;79(24):15189-98
pubmed: 16306590
Nat Rev Microbiol. 2016 Aug;14(8):523-34
pubmed: 27344959
J Comput Chem. 2011 Aug;32(11):2359-68
pubmed: 21541964
N Engl J Med. 2020 Feb 20;382(8):692-694
pubmed: 31978293
J Chem Inf Model. 2014 Jul 28;54(7):1951-62
pubmed: 24850022
J Virol. 2008 Mar;82(5):2515-27
pubmed: 18094151
J Chem Inf Model. 2011 Jan 24;51(1):69-82
pubmed: 21117705
Virology. 2008 Mar 1;372(1):127-35
pubmed: 18022664
Nature. 2020 Jun;582(7811):289-293
pubmed: 32272481
Cell Biosci. 2020 Mar 16;10:40
pubmed: 32190290
J Comput Chem. 2005 Jul 15;26(9):915-31
pubmed: 15841474
J Chem Theory Comput. 2010 Feb 9;6(2):459-66
pubmed: 26617301
Cell. 2020 Apr 16;181(2):271-280.e8
pubmed: 32142651
Int J Oral Sci. 2020 Feb 24;12(1):8
pubmed: 32094336
MMWR Morb Mortal Wkly Rep. 2020 Mar 27;69(12):343-346
pubmed: 32214079
J Med Chem. 2009 May 28;52(10):3159-65
pubmed: 19385614

Auteurs

Julia Liang (J)

Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia.

Eleni Pitsillou (E)

Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia.

Chris Karagiannis (C)

School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia; School of Agriculture & Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia.

Kevion K Darmawan (KK)

School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia.

Ken Ng (K)

School of Agriculture & Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia.

Andrew Hung (A)

School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia.

Tom C Karagiannis (TC)

Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia. Electronic address: tom.karagiannis@monash.edu.

Classifications MeSH