Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking (CROSBI ID 295696)
Prilog u časopisu | izvorni znanstveni rad | međunarodna recenzija
Podaci o odgovornosti
Novak, Jurica ; Rimac, Hrvoje ; Kandagalla, Shivananda ; Pathak, Prateek ; Naumovich, Vladislav ; Grishina, Maria ; Potemkin, Vladimir
engleski
Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking
The SARS-CoV-2 3CL protease (3CLpro) shows a high similarity with 3CL proteases of other beta- coronaviruses, such as SARS and MERS. It is the main enzyme involved in generating various non- structural proteins that are important for viral replication and is one of the most important proteins responsible for SARS-CoV-2 virulence. In this study, we have conducted an ensemble docking of molecules from the DrugBank database using both the crystallographic structure of the SARS-CoV-2 3CLpro, as well as five conformations obtained after performing a cluster analysis of a 300 ns molecular dynamics (MD) simulation. This procedure elucidated the inappropriateness of the active site for non-covalent inhibitors, but it has also shown that there exists an additional, more favorable, allosteric binding site, which could be a better target for non-covalent inhibitors, as it could prevent dimerization and activation of SARS- CoV-2 3CLpro. Two such examples are radotinib and nilotinib, tyrosine kinase inhibitors already in usefor treatment of leukemia and which binding to the newly found allosteric binding site was also confirmed using MD simulations.
3CL protease ; molecular dynamics ; SARS-CoV-2 ; radotinib ; nilotinib
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Podaci o izdanju
40 (19)
2022.
9347-9360
objavljeno
0739-1102
1538-0254
10.1080/07391102.2021.1927845
Povezanost rada
Farmacija, Interdisciplinarne prirodne znanosti, Kemija