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In silico analysis of selected components of grapefruit seed extract against SARS-CoV-2 main protease Cover

In silico analysis of selected components of grapefruit seed extract against SARS-CoV-2 main protease

Open Access
|Jun 2021

Figures & Tables

Figure 1

A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand narirutin and their best mode binding interactions (B) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand narirutin and their best mode binding interactions (B) via PyMOL 2.4.

Figure 2

A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand naringin and their best mode binding interactions (B) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand naringin and their best mode binding interactions (B) via PyMOL 2.4.

Figure 3

A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID:6Y84) with ligand limonin and their best mode binding interactions (B) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID:6Y84) with ligand limonin and their best mode binding interactions (B) via PyMOL 2.4.

Figure 4

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand naringenin and their best mode binding interactions (b) via PyMOL 2.4
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand naringenin and their best mode binding interactions (b) via PyMOL 2.4

Figure 5

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand ascorbic acid and their best mode binding interactions (b) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand ascorbic acid and their best mode binding interactions (b) via PyMOL 2.4.

Figure 6

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand citric acid and their best mode binding interactions (b) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand citric acid and their best mode binding interactions (b) via PyMOL 2.4.

Figure 7

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand acetoside and their best mode binding interactions (b) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand acetoside and their best mode binding interactions (b) via PyMOL 2.4.

Figure 8

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand remdesivir and their best mode binding interactions (b) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand remdesivir and their best mode binding interactions (b) via PyMOL 2.4.

Figure 9

A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand gallic acid and their best mode binding interactions (b) via PyMOL 2.4.
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand gallic acid and their best mode binding interactions (b) via PyMOL 2.4.

Best docking scores (lowest binding energy) of selected compounds of grapefruit seed extract (GSE) as well as of the positive controls and their distance from best mode

Distance from best mode
LigandsAffinity (kcal/mol§)rmsd l.b.rmsd u.b
Narirutin-10.50.0000.000
Naringin-10.10.0000.000
Naringenin-8.20.0000.000
Limonin-9.90.0000.000
Ascorbic acid-6.70.0000.000
Citric acid-6.40.0000.000
Acetoside-10.00.0000.000
Remdesivir-9.60.0000.000
Gallic acid-6.40.0000.000
Language: English
Page range: 5 - 12
Published on: Jun 17, 2021
Published by: European Biotechnology Thematic Network Association
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2021 Belmina Saric, Nikolina Tomic, Abdurahim Kalajdzic, Naris Pojskic, Lejla Pojskic, published by European Biotechnology Thematic Network Association
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.