Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.
ANM
COVID-19
GNM
Volume Molar
Volume fluctuation
Voronoi
Journal
Computational biology and chemistry
ISSN: 1476-928X
Titre abrégé: Comput Biol Chem
Pays: England
ID NLM: 101157394
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
received:
04
01
2022
revised:
28
04
2022
accepted:
02
05
2022
pubmed:
1
6
2022
medline:
10
8
2022
entrez:
31
5
2022
Statut:
ppublish
Résumé
The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease M
Identifiants
pubmed: 35640480
pii: S1476-9271(22)00072-X
doi: 10.1016/j.compbiolchem.2022.107692
pmc: PMC9107165
pii:
doi:
Substances chimiques
Antiviral Agents
0
Drug Combinations
0
Lactams
0
Nitriles
0
Protease Inhibitors
0
nirmatrelvir and ritonavir drug combination
0
Ivermectin
70288-86-7
nirmatrelvir
7R9A5P7H32
Proline
9DLQ4CIU6V
Peptide Hydrolases
EC 3.4.-
Leucine
GMW67QNF9C
Ritonavir
O3J8G9O825
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
107692Informations de copyright
Copyright © 2022 Elsevier Ltd. All rights reserved.
Références
Int J Mol Sci. 2021 Aug 24;22(17):
pubmed: 34502033
Phys Chem Chem Phys. 2015 Apr 7;17(13):8499-508
pubmed: 25685984
J Phys Chem B. 2014 Nov 26;118(47):13554-63
pubmed: 25365737
J Infect Public Health. 2021 May;14(5):601-610
pubmed: 33848890
JAMA Intern Med. 2022 Apr 1;182(4):426-435
pubmed: 35179551
J Colloid Interface Sci. 2008 Jul 15;323(2):255-9
pubmed: 18502437
J Phys Chem Lett. 2020 May 21;11(10):3993-4000
pubmed: 32352786
J Biomol Struct Dyn. 2021 Sep;39(15):5735-5755
pubmed: 32679006
Biophys Chem. 2012 Feb;161:46-9
pubmed: 22133917
Protein Cell. 2022 Sep;13(9):689-693
pubmed: 34687004
Nat Commun. 2021 Feb 2;12(1):743
pubmed: 33531496
Nucleic Acids Res. 2015 Jul 1;43(W1):W225-30
pubmed: 25855813
Biochim Biophys Acta Mol Basis Dis. 2022 Feb 1;1868(2):166294
pubmed: 34687900
Gen Physiol Biophys. 2013 Mar;32(1):67-78
pubmed: 23531836
BMC Bioinformatics. 2013;14 Suppl 19:S5
pubmed: 24564434
Proteins. 2021 Nov;89(11):1425-1441
pubmed: 34169568
J Mol Struct. 2021 Jan 15;1224:129178
pubmed: 32904625
Biophys J. 2018 Feb 27;114(4):856-869
pubmed: 29490246
Chemphyschem. 2015 Dec 1;16(17):3555-71
pubmed: 26395255
Prog Biophys Mol Biol. 1984;44(3):181-214
pubmed: 6390520
Biopolymers. 1993 Jan;33(1):11-26
pubmed: 8427927
Comput Biol Chem. 2020 Dec;89:107372
pubmed: 32911432
Int J Antimicrob Agents. 2022 Mar;59(3):106542
pubmed: 35093538
J Pharm Sci. 2008 Sep;97(9):3494-517
pubmed: 18186490
Comput Struct Biotechnol J. 2022;20:1306-1344
pubmed: 35308802
J Chem Phys. 2006 Aug 7;125(5):054903
pubmed: 16942254
J Comput Chem. 2009 Dec;30(16):2785-91
pubmed: 19399780
PLoS Pathog. 2022 Jan 13;18(1):e1010171
pubmed: 35025963
Chempluschem. 2020 Dec;85(12):2657-2665
pubmed: 33305536
Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13327-13335
pubmed: 28592654
Viruses. 2021 Jan 25;13(2):
pubmed: 33503819
Biochim Biophys Acta. 2008 Nov;1784(11):1546-51
pubmed: 18773977
Comput Biol Med. 2022 Feb;141:105171
pubmed: 34968860
J Phys Chem B. 2015 Feb 5;119(5):1881-90
pubmed: 25590869
Phys Chem Chem Phys. 2010 Apr 28;12(16):4233-8
pubmed: 20379517
J Chem Phys. 2018 Jun 7;148(21):215102
pubmed: 29884062
J Biomol Struct Dyn. 2022 Sep;40(14):6243-6254
pubmed: 33525993
J Phys Chem B. 2018 Apr 5;122(13):3635-3646
pubmed: 29394062
Biophys Physicobiol. 2020 Oct 15;17:140-146
pubmed: 33240741
J Biomol Struct Dyn. 2015;33(11):2421-41
pubmed: 25967133
Front Chem. 2020 Nov 16;8:594009
pubmed: 33304884
J Biomol Struct Dyn. 2022 Apr;40(6):2851-2864
pubmed: 33131430
Inform Med Unlocked. 2021;23:100539
pubmed: 33623816
J Mol Struct. 2021 Dec 15;1246:131124
pubmed: 34305175
Sci Rep. 2014 Feb 06;4:4011
pubmed: 24500195
Inform Med Unlocked. 2021;23:100541
pubmed: 33649734
J Chem Inf Model. 2019 Aug 26;59(8):3545-3555
pubmed: 31365253
Future Med Chem. 2020 Oct;12(20):1815-1828
pubmed: 32787684
Biochemistry. 2004 Feb 10;43(5):1315-22
pubmed: 14756568
Int J Mol Sci. 2021 Dec 18;22(24):
pubmed: 34948390
J Mol Biol. 1996 Jul 26;260(4):588-603
pubmed: 8759322
Biophys Chem. 2016 Feb;209:1-8
pubmed: 26569082
Acc Chem Res. 2016 May 17;49(5):809-15
pubmed: 27110726
PLoS Comput Biol. 2020 Feb 13;16(2):e1007670
pubmed: 32053592
Biophys Chem. 2019 Mar;246:8-15
pubmed: 30597448
Proteins. 2021 Sep;89(9):1180-1192
pubmed: 33969540
Biopolymers. 1996 Nov;39(5):619-26
pubmed: 8875817
Biochemistry. 2016 Nov 29;55(47):6475-6483
pubmed: 27933780
PLoS One. 2012;7(1):e30038
pubmed: 22272272
J Phys Chem B. 2012 Apr 5;116(13):4098-105
pubmed: 22380610
Biochemistry. 1986 Oct 21;25(21):6563-71
pubmed: 3790543
Phys Chem Chem Phys. 2021 Mar 21;23(11):6746-6757
pubmed: 33711090
Eur J Med Chem Rep. 2022 Apr;4:100018
pubmed: 36593981
J Phys Chem B. 2018 Apr 19;122(15):4231-4238
pubmed: 29582658
Comput Biol Med. 2022 Mar;142:105245
pubmed: 35077937
J Phys Chem B. 2016 Sep 22;120(37):9903-12
pubmed: 27571383
Biophys J. 2014 Jul 15;107(2):435-447
pubmed: 25028885
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4282-7
pubmed: 15767576
Curr Opin Virol. 2021 Aug;49:36-40
pubmed: 34029993
Chem Sci. 2022 Feb 10;13(13):3674-3687
pubmed: 35432906
J Cheminform. 2011 Oct 07;3:33
pubmed: 21982300
Molecules. 2021 Feb 25;26(5):
pubmed: 33668914
Biophys Chem. 2003 Jun 1;104(2):489-99
pubmed: 12878316
Biophys Chem. 2021 Nov;278:106677
pubmed: 34428682
Antimicrob Agents Chemother. 2022 Jan 18;66(1):e0154321
pubmed: 34633839
Biochim Biophys Acta. 2004 Jul 1;1700(1):27-34
pubmed: 15210122
Nat Commun. 2022 Apr 27;13(1):2268
pubmed: 35477935
Chem Rev. 2017 Aug 23;117(16):10694-10725
pubmed: 28248491
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):426
pubmed: 30717654
Pharmaceuticals (Basel). 2022 Apr 02;15(4):
pubmed: 35455442
Proteins. 2008 Mar;70(4):1219-27
pubmed: 17847101
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W555-62
pubmed: 20478824
Biochemistry. 2012 Jul 24;51(29):5784-90
pubmed: 22732010
Bioinformatics. 2003 Nov 1;19(16):2112-21
pubmed: 14594717
ACS Comb Sci. 2020 Jun 8;22(6):297-305
pubmed: 32402186
Proc Natl Acad Sci U S A. 1983 Jan;80(2):622-6
pubmed: 6572909
Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9721-6
pubmed: 12097640
J Biomol Struct Dyn. 1998 Oct;16(2):397-411
pubmed: 9833677
Nature. 2021 Aug;596(7871):173-174
pubmed: 34341573
J Chem Phys. 2021 Feb 7;154(5):055102
pubmed: 33557542
J Am Chem Soc. 2017 Mar 15;139(10):3599-3602
pubmed: 28094513
J Chem Phys. 2006 Apr 7;124(13):134507
pubmed: 16613461
J Chem Phys. 2006 Feb 21;124(7):74704
pubmed: 16497067
J Mol Graph Model. 2022 Jan;110:108042
pubmed: 34653812
J Cheminform. 2021 Sep 20;13(1):70
pubmed: 34544500
J Enzyme Inhib Med Chem. 2021 Dec;36(1):1646-1650
pubmed: 34289752
Biochemistry. 2013 Jan 29;52(4):672-80
pubmed: 23293944
J Mol Liq. 2021 Oct 15;340:117284
pubmed: 34421159
J Chem Theory Comput. 2018 Feb 13;14(2):998-1008
pubmed: 29262685
J Med Chem. 2022 May 12;65(9):6499-6512
pubmed: 35352927
Sci Rep. 2021 Mar 10;11(1):5543
pubmed: 33692377
Structure. 2007 Nov;15(11):1357-63
pubmed: 17997961