Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations.
Comput Biol Med
; 146: 105572, 2022 07.
Article
in English
| MEDLINE | ID: covidwho-1814281
ABSTRACT
BACKGROUND:
The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus.METHODS:
To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. RESULTS ANDCONCLUSION:
All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Molecular Dynamics Simulation
/
COVID-19 Drug Treatment
Limits:
Humans
Language:
English
Journal:
Comput Biol Med
Year:
2022
Document Type:
Article
Affiliation country:
J.compbiomed.2022.105572
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