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. 2022 Nov 29;10(12):3074.
doi: 10.3390/biomedicines10123074.

Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study

Mehran Alavi  1   2 , M R Mozafari  3 , Saba Ghaemi  4 , Morahem Ashengroph  1 , Fatemeh Hasanzadeh Davarani  5 , Mohammadreza Mohammadabadi  6
Affiliations

Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study

Mehran Alavi et al. Biomedicines. .

Abstract

Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.

Keywords: SARS-CoV-2; antiviral activity; natural compounds; severe pneumonia; transmembrane spike glycoprotein.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(a) Main parts of SARS-CoV-2, including spike (S1 and S2 subunits), nucleocapsid, membrane, envelope, and ssRNA. (b) Schematic image showing the replication cycle of SARS-CoV-2 in host cells. Distributed under the terms of the Creative Commons Attribution License (CC BY) [26].
Figure 2
Figure 2
(a) Spike glycoprotein (PDB ID: 6VSB), (b) Nsp15 (PDB ID: 6VWW), (c) epigallocatechin-3-gallate (EGCG), and (d) quercetin.
Figure 3
Figure 3
The best mode of the active site for the receptor of 6VSB (a) and its interaction with EGCG (b) based on the results of CB-Dock.
Figure 4
Figure 4
The best mode of the active site for the receptor of 6VWW (a) and its interaction with EGCG (b) based on the results of CB-Dock.
Figure 5
Figure 5
The best mode of the active site for the receptor of 6VSB (a) and its interaction with quercetin (b) according to the results of CB-Dock.
Figure 6
Figure 6
The best mode of the active site for the receptor of 6VWW (a) and its interaction with quercetin (b) according to the results of CB-Dock.
Figure 7
Figure 7
The best modes for the interaction between 6VSB and (a) EGCG and (b) quercetin as well as between 6VWW and (c) EGCG and (d) quercetin ligands based on the results of EDock.
Figure 8
Figure 8
The molecular structure (a,b), total electron density maps (c), 3D model of HOMO-LUMO molecular orbitals, and (d) contour plots (side view: left; front view: right) of EGCG.
Figure 9
Figure 9
The molecular structure (a,b), total electron density maps (c), 3D model of HOMO-LUMO molecular orbitals, and (d) contour plots (side view: left; front view: right) of quercetin.
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