Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies
Abstract
:1. Introduction
2. Results
2.1. The Overall Architecture of the SARS-CoV-2 Main Protease
2.2. Molecular Docking
2.3. Drug-Likeness Prediction Studies
2.4. Molecular Docking Analysis
2.5. Molecular Dynamics Simulations
2.5.1. Effect of Ligands on Conformational Stability
2.5.2. Conformational Dynamics of Protein–Ligand Binding
2.5.3. Ligand-Induced Changes on Protein Dynamics
3. Discussion
4. Materials and Methods
4.1. Ligand Preparation
4.2. Protein Preparation and Grid Generation
4.3. Molecular Docking Simulation
4.4. Prime MM-GBSA for Affinity Prediction
4.5. Molecular Dynamics Simulation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Das, R.; Habiba, S.U.; Dash, R.; Seo, Y.; Woo, J. Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies. Int. J. Mol. Sci. 2023, 24, 3100. https://doi.org/10.3390/ijms24043100
Das R, Habiba SU, Dash R, Seo Y, Woo J. Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies. International Journal of Molecular Sciences. 2023; 24(4):3100. https://doi.org/10.3390/ijms24043100
Chicago/Turabian StyleDas, Raju, Sarmin Ummey Habiba, Raju Dash, Yohan Seo, and Joohan Woo. 2023. "Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies" International Journal of Molecular Sciences 24, no. 4: 3100. https://doi.org/10.3390/ijms24043100