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In silico Screening of Potential SARS-CoV-2 Main Protease Inhibitors from Thymus schimperi.


ABSTRACT:

Background

COVID-19 is still instigating significant social and economic chaos worldwide; however, there is no approved antiviral drug yet. Here, we used in silico analysis to screen potential SARS-CoV-2 main protease (Mpro) inhibitors extracted from the essential oil of Thymus schimperi which could contribute to the discovery of potent anti-SARS-CoV-2 phytochemicals.

Methods

The absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles of compounds were determined through SwissADME and ProToxII servers. AutoDock tools were used for molecular docking analysis studies, while Chimera, DS studio, and LigPlot were used for post-docking studies. Molecular dynamic simulations were performed for 200 ns under constant pressure.

Results

All compounds exhibited a bioavailability score of ≥0.55 entailing that at least 55% of the drugs can be absorbed unchanged. Only five (9%), nine (16%) and two (3.6%) of the compounds showed active hepatotoxicity, carcinogenicity, and immunotoxicity, respectively. Except for flourazophore P, which showed a little mutagenicity, all other compounds did not show mutagenic properties. On the other hand, only pinene beta was found to have a little cytotoxicity. Five compounds demonstrated effective binding to the catalytic dyad of the SARS-CoV-2 Mpro substrate binding pocket, while two of them (geranylisobutanoate and 3-octane) are found to be the best hits that formed hydrogen bonds with Glu166 and Ser144 of SARS-CoV-2 Mpro.

Conclusion

Based on our in silico analysis, top hits from Thymus schimperi may serve as potential anti-SARS-CoV-2 compounds. Further in vitro and in vivo studies are recommended to characterize these compounds for clinical applications.

SUBMITTER: Mengist HM 

PROVIDER: S-EPMC9868284 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

In silico Screening of Potential SARS-CoV-2 Main Protease Inhibitors from <i>Thymus schimperi</i>.

Mengist Hylemariam Mihiretie HM   Khalid Zunera Z   Adane Fentahun F  

Advances and applications in bioinformatics and chemistry : AABC 20230118


<h4>Background</h4>COVID-19 is still instigating significant social and economic chaos worldwide; however, there is no approved antiviral drug yet. Here, we used in silico analysis to screen potential SARS-CoV-2 main protease (M<sup>pro</sup>) inhibitors extracted from the essential oil of <i>Thymus schimperi</i> which could contribute to the discovery of potent anti-SARS-CoV-2 phytochemicals.<h4>Methods</h4>The absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles of co  ...[more]

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