Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

References

    1. Aljelehawy Q.H.A., Alshaibah L.H.H., Khafaji Z.K.A.A. Evaluation of virulence factors among Staphylococcus aureus strains isolated from patients with urinary tract infection in Al-Najaf Al-Ashraf teaching hospital. Cell. Mol. Biomed. Rep. 2021;1:78–87. doi: 10.55705/cmbr.2021.144995.1017. - DOI
    1. Ahmadi S., Ahmadi G., Ahmadi H. A review on antifungal and antibacterial activities of some medicinal plants. Micro Nano Bio Asp. 2022;1:10–17.
    1. Alavi M., Rai M. Antisense RNA, the modified CRISPR-Cas9, and metal/metal oxide nanoparticles to inactivate pathogenic bacteria. Cell. Mol. Biomed. Rep. 2021;1:52–59. doi: 10.55705/cmbr.2021.142436.1014. - DOI
    1. Amraei S., Ahmadi S. Recent studies on antimicrobial and anticancer activities of saponins: A mini-review. Nano Micro Bios. 2022;1:22–26.
    1. Muhammad I., Sale P.M., Salisu M.K., Muhammad T.M., Abubakar B., Maidala A.L., Nuwanyada E. Molecular analysis of Bio-makers of Chloroquine resistance in Plasmodium falciparum Isolate from Gombe Local Government Area, Gombe State, Nigeria. Cell. Mol. Biomed. Rep. 2022;2:42–55. doi: 10.55705/cmbr.2022.335753.1033. - DOI

LinkOut - more resources