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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Fragment-based inhibitor design for SARS-CoV2 main protease.

Priyanka Andola¹, Jishu Pagag¹, Durgam Laxman¹

¹School of Chemistry, University of Hyderabad, Hyderabad, 500046 India.

Structural Chemistry

|July 11, 2022

Summary

This study identifies potential inhibitors for the SARS-CoV-2 main protease using fragment-based drug discovery. Computational methods validated the stability and binding of these novel COVID-19 drug candidates.

Keywords:

Binding free energy Fragment-based drug discovery Mechanical stiffness Molecular docking Molecular dynamics simulations Normal mode analysis Principal component analysis SARS-CoV2 main protease Virtual screening

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Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

Area of Science:

Medicinal Chemistry
Computational Biology
Virology

Background:

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes COVID-19, a global pandemic with significant mortality.
Targeting the SARS-CoV-2 main protease is a key strategy for developing antiviral therapies.
The protease is essential for viral replication, cleaving polyproteins into functional units.

Purpose of the Study:

To identify novel hit molecule inhibitors for the SARS-CoV-2 main protease.
To utilize fragment-based drug discovery (FBDD) approach.
To leverage the crystal structure of a known chromene-based inhibitor (PDB_ID: 6M2N).

Main Methods:

Fragment-based drug discovery (FBDD) was employed.
Molecular docking and molecular dynamics simulations were used for validation.
Binding free energies, normal mode analysis, mechanical stiffness, and principal component analysis assessed complex stability.

Main Results:

Novel hit molecules targeting the SARS-CoV-2 main protease were identified.
Computational validation confirmed the stability and binding of designed inhibitors.
Detailed analyses provided insights into the molecular interactions and stability of the complexes.

Conclusions:

The study successfully identified potential inhibitors for SARS-CoV-2 main protease using FBDD.
Computational simulations validated the efficacy and stability of these drug candidates.
These findings contribute to the development of new therapeutic strategies against COVID-19.