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Inhibition of COVID-19 RNA-Dependent RNA Polymerase by Natural Bioactive Compounds: Molecular Docking Analysis.

Article

Last updated: 22 Jan 2023

Subjects

-

Tags

Biochemistry

Abstract

Currently, no approved treatment for COVID-19 exists. However, phenolic compounds exhibit antiviral activity. This study aimed to evaluate the activities of polyphenolic compounds (gallic acid, quercetin, caffeine, resveratrol, naringenin, benzoic acid, oleuropein, and ellagic acid) as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (PDB ID 6M71) inhibitors. Molecular docking simulations of these polyphenols were performed using Autodock 4.0 and Chimera 1.8.1. Druglikeness and pharmacokinetic properties were calculated using the SWISSADME prediction website. Remdesivir and ribavirin were used for comparison. The docking analysis results, ranked by the binding energy value (ΔG) of the tested ligands toward SARS-CoV-2 polymerase, were remdesivir > gallic acid > quercetin > caffeine > ribavirin > resveratrol > naringenin > benzoic acid > oleuropein > ellagic acid, with binding energies of −8.51, −7.55, −7.17, −6.10, −6.01, −5.79, −5.69, −5.54, −4.94, and −4.59 kcal/mol, respectively. All tested polyphenols were predicted to form hydrogen bonds with one or two of the nucleotide triphosphate (NTP) entry channels at ARG 553, ARG 555, or LYS 545, except caffeine and oleuropein, which may influence the entry of substrate and divalent cations into the central active site cavity, thereby inhibiting enzyme activity. It appears promising that gallic acid and quercetin exhibited higher binding affinity than ribavirin toward the SARS-CoV-2 polymerase and expressed good druglikeness and pharmacokinetic properties. Additionally, resveratrol, naringenin, and benzoic and ellagic acids exhibited some efficacy as potential polymerase inhibitors. Further research is required to investigate the potential uses of these polyphenols in the treatment of COVID-19.

DOI

10.21608/ejchem.2021.45739.2947

Keywords

COVID-19, RNA-Dependent RNA Polymerase, bioactive compounds, Docking analysis

Authors

First Name

Nourhan

Last Name

Abdo

MiddleName

-

Affiliation

Food Technology Department, City of Scientific Research and Technological Applications

Email

nourhanm.abdo@gmail.com

City

-

Orcid

-

First Name

Olfat

Last Name

Moheyeldin

MiddleName

-

Affiliation

Department of Biochemistry, Faculty of Science, Alexandria University

Email

olfatmoheyeldin1@gmail.com

City

Alexandria

Orcid

-

First Name

Mohamed

Last Name

Shehata

MiddleName

G

Affiliation

City of Scientific Research andTechnological Applications

Email

gamalsng@gmail.com

City

-

Orcid

0000-0003-0760-5945

First Name

Sobhy

Last Name

El Sohaimy

MiddleName

-

Affiliation

1. Food Technology, City of Scientific Research and Technological Applications, Borg El Arab, Alex., Egypt. 2. Department of Technology and Orginization of Public Catering, South Ural State University, 454080 Chelyabinsh, Russia

Email

elsohaimys@gmail.com

City

Alexandria

Orcid

0000-0002-1657-5162

Volume

64

Article Issue

4

Related Issue

22914

Issue Date

2021-04-01

Receive Date

2020-10-13

Publish Date

2021-04-01

Page Start

1,989

Page End

2,001

Print ISSN

0449-2285

Online ISSN

2357-0245

Link

https://ejchem.journals.ekb.eg/article_142912.html

Detail API

https://ejchem.journals.ekb.eg/service?article_code=142912

Order

30

Type

Review Articles

Type Code

444

Publication Type

Journal

Publication Title

Egyptian Journal of Chemistry

Publication Link

https://ejchem.journals.ekb.eg/

MainTitle

-

Details

Type

Article

Created At

22 Jan 2023