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Research Article
Sk. Md Nayeem
KRK Government Degree College
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4803-2955
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This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- This study involved the use of non-human vertebrates.
- The author has confirmed that all appropriate ethical guidelines for the handling and use of animals in research have been followed and details of the oversight board have been included in the text.
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
Molecular Dynamics simulation using Gromacs with OPLS-AA force field is performed for 100ns between SARS-CoV-2 main protease and Dexamethasone / Umifenovir drugs at 300 K/1 atm pressure. The trajectory of Root Mean Square Deviation (RMSD) and Radius of Gyration(Rg) emphasized the achievement of equilibrium and compactness. The drug-binding affinities on SARS-CoV-2 main protease are estimated via MM/PBSA method. The sign with magnitude of computed Gibbs free energy indicated the presence of strong interactions between SARS-CoV-2 and drugs of Dexamethasone / Umifenovir. The study revealed that the drug Dexamethasone is more effective over Umifenovir in binding SARS-CoV-2 main protease.
Keywords
SARS-CoV-2 protein, Dexamethasone, Umifenovir, molecular dynamics, Gromacs, Gibb's free energy, Interactions.
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This is a preprint. It has not completed peer review.
Research Article
Sk. Md Nayeem
KRK Government Degree College
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4803-2955
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 10 Jul, 2020
Community comments: 1
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Biomedical Engineering
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- This study involved the use of non-human vertebrates.
- The author has confirmed that all appropriate ethical guidelines for the handling and use of animals in research have been followed and details of the oversight board have been included in the text.
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
Molecular Dynamics simulation using Gromacs with OPLS-AA force field is performed for 100ns between SARS-CoV-2 main protease and Dexamethasone / Umifenovir drugs at 300 K/1 atm pressure. The trajectory of Root Mean Square Deviation (RMSD) and Radius of Gyration(Rg) emphasized the achievement of equilibrium and compactness. The drug-binding affinities on SARS-CoV-2 main protease are estimated via MM/PBSA method. The sign with magnitude of computed Gibbs free energy indicated the presence of strong interactions between SARS-CoV-2 and drugs of Dexamethasone / Umifenovir. The study revealed that the drug Dexamethasone is more effective over Umifenovir in binding SARS-CoV-2 main protease.
Figure 1
Figure 2
This preprint is available for download as a PDF.
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