Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro).

Journal of Biomolecular Structure & Dynamics
Shruti KoulgiRajendra Joshi

Abstract

The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site ...Continue Reading

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Citations

Nov 5, 2020·Briefings in Bioinformatics·Serena DotoloRoberto Tagliaferri
Mar 20, 2021·Biomedical Journal·Shasank Sekhar SwainWalter Luyten
Apr 6, 2021·Biochemistry and Biophysics Reports·Tamim Ahsan, Abu Ashfaqur Sajib
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Nov 4, 2021·Journal of Chemical Information and Modeling·P Bernát SzabóJuan J Nogueira

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Methods Mentioned

BETA
X-ray
PLIP

Software Mentioned

UCSF Chimera
LigPlus
SWEETLEAD
PyEmma
AMBER
AMBERTOOLS
LIG
HADDOCK
- LIG
Ensemble

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