Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.
Antiviral Agents
/ pharmacology
Betacoronavirus
/ enzymology
COVID-19
Coronavirus 3C Proteases
Coronavirus Infections
/ drug therapy
Cysteine Endopeptidases
/ metabolism
Humans
Ligands
Molecular Docking Simulation
Pandemics
Pneumonia, Viral
/ drug therapy
Protease Inhibitors
/ pharmacology
Protein Binding
SARS-CoV-2
User-Computer Interface
Viral Nonstructural Proteins
/ antagonists & inhibitors
Journal
Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704
Informations de publication
Date de publication:
10 Nov 2020
10 Nov 2020
Historique:
pubmed:
23
10
2020
medline:
20
11
2020
entrez:
22
10
2020
Statut:
ppublish
Résumé
In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CL
Identifiants
pubmed: 33090785
doi: 10.1021/acs.jctc.0c00634
pmc: PMC8015232
doi:
Substances chimiques
Antiviral Agents
0
Ligands
0
Protease Inhibitors
0
Viral Nonstructural Proteins
0
Cysteine Endopeptidases
EC 3.4.22.-
Coronavirus 3C Proteases
EC 3.4.22.28
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7160-7172Références
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Mol Pharm. 2019 Oct 7;16(10):4282-4291
pubmed: 31437001
Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12564-9
pubmed: 14528008
J Chem Phys. 2019 Oct 14;151(14):144113
pubmed: 31615247
Bioinformatics. 2013 Apr 1;29(7):845-54
pubmed: 23407358
J Med Chem. 2013 Jan 24;56(2):534-46
pubmed: 23231439
Nat Chem. 2020 Jul;12(7):581
pubmed: 32555379
Bioorg Med Chem Lett. 2008 Oct 15;18(20):5684-8
pubmed: 18796354
Biophys J. 1997 Mar;72(3):1047-69
pubmed: 9138555
J Chem Theory Comput. 2014 Jul 8;10(7):2813-23
pubmed: 26586508
FEBS J. 2014 Sep;281(18):4085-96
pubmed: 25039866
Phys Chem Chem Phys. 2016 Jun 1;18(22):14991-5004
pubmed: 27193067
J Chem Phys. 2019 Sep 28;151(12):124116
pubmed: 31575187
J Chem Theory Comput. 2006 Sep;2(5):1255-73
pubmed: 26626834
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Phys Chem Chem Phys. 2019 Jul 7;21(25):13826-13834
pubmed: 31211310
J Comput Chem. 2009 Dec;30(16):2785-91
pubmed: 19399780
J Chem Phys. 2019 Oct 14;151(14):144115
pubmed: 31615230
Phys Rev Lett. 2003 Oct 3;91(14):140601
pubmed: 14611511
Chem Commun (Camb). 2020 Aug 4;56(62):8854-8856
pubmed: 32633733
J Chem Theory Comput. 2010 Sep 14;6(9):2804-8
pubmed: 26616081
J Comput Aided Mol Des. 2020 May;34(5):601-633
pubmed: 31984465
Mini Rev Med Chem. 2012 Nov;12(13):1330-44
pubmed: 22625413
J Chem Inf Model. 2017 Jun 26;57(6):1240-1245
pubmed: 28586207
J Chem Phys. 2006 Oct 28;125(16):164101
pubmed: 17092057
J Chem Phys. 2015 Apr 21;142(15):154117
pubmed: 25903876
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
J Comput Chem. 2010 Apr 15;31(5):1106-16
pubmed: 19824035
Science. 1989 Jun 2;244(4908):1069-72
pubmed: 2727695
Chem Phys Lett. 2020 Jul;750:137489
pubmed: 32313296
J Chem Inf Model. 2005 Jan-Feb;45(1):177-82
pubmed: 15667143
J Chem Inf Model. 2016 Jun 27;56(6):1117-21
pubmed: 27231982
J Phys Chem B. 2009 Feb 26;113(8):2234-46
pubmed: 19146384
J Biomol Struct Dyn. 2020 Apr 20;:1-14
pubmed: 32266873
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13190-5
pubmed: 14585926
Phys Chem Chem Phys. 2016 Jun 1;18(22):15005-18
pubmed: 27193181
Science. 2020 Apr 24;368(6489):409-412
pubmed: 32198291
J Chem Theory Comput. 2015 Feb 10;11(2):423-35
pubmed: 26580905
J Chem Theory Comput. 2018 Jul 10;14(7):3890-3902
pubmed: 29874073
J Chem Theory Comput. 2017 May 9;13(5):1924-1933
pubmed: 28388038
J Chem Inf Model. 2020 Dec 28;60(12):5771-5780
pubmed: 32530282
J Cheminform. 2011 Oct 07;3:33
pubmed: 21982300
J Phys Chem B. 2010 Aug 19;114(32):10235-53
pubmed: 20701361
Protein Eng. 1995 Feb;8(2):127-34
pubmed: 7630882
J Chem Theory Comput. 2018 Dec 11;14(12):6544-6559
pubmed: 30404450
Biochemistry. 2006 Dec 12;45(49):14632-41
pubmed: 17144656
Nature. 2020 Jun;582(7811):289-293
pubmed: 32272481
Prog Med Chem. 2019;58:1-62
pubmed: 30879472
Methods Mol Biol. 2015;1215:173-209
pubmed: 25330964
J Comput Aided Mol Des. 2020 Apr;34(4):371-384
pubmed: 31624982
J Med Chem. 2016 Jul 28;59(14):6595-628
pubmed: 26878082
J Am Chem Soc. 2015 Feb 25;137(7):2695-703
pubmed: 25625324
Nature. 2020 Jul;583(7816):459-468
pubmed: 32353859
J Comput Aided Mol Des. 2018 Oct;32(10):937-963
pubmed: 30415285
J Comput Aided Mol Des. 2018 Oct;32(10):965-982
pubmed: 30128927
J Mol Graph Model. 2017 Jan;71:233-241
pubmed: 27984798
Proteins. 2010 Jun;78(8):1950-8
pubmed: 20408171
J Comput Aided Mol Des. 2020 Jun;34(6):635-639
pubmed: 32277315