Insights from computational studies on the potential of natural compounds as inhibitors against SARS-CoV-2 spike omicron variant

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a major global health emergency, with more than six million deaths worldwide. It is becoming increasingly challenging to treat COVID-19 due to the emergence of novel variants. The omicron variant is capable to evade defences and spread quickly. Among many validated COVID-19 targets, the spike (S) protein plays an important role in receptor recognition (via the S1 subunit) and membrane fusion (via the S2 subunit). The S protein is one of the vital targets for the development of drugs to combat this illness. In this research, we applied various computational methods such as molecular docking, molecular dynamics, MM-GBSA calculations, and ADMET prediction to identify potential natural products from Saudi medicinal plants against the spike omicron variant. As a result, three compounds (LTS0002490, LTS0117007, and LTS0217912) were identified with better binding affinity to the spike omicron variant compared to the reference compound (VE607). In addition, these compounds showed stable interactions with the target during molecular dynamics simulations for 140 ns. Last, these compounds have optimal ADMET properties. We suggest that these compounds may be considered promising hits to treat COVID-19 if experimentally validated.

KEYWORDS:

• COVID-19
• omicron variant
• natural compounds
• MDS
• ADMET

Acknowledgements

The author acknowledges Mme Katia Dekimeche from Schrodinger for the technical support and help.

Disclosure statement

No potential conflict of interest was reported by the author.

Data availability statement

The original contributions presented in the study are included in the article. Further inquiries can be directed to the corresponding author.

Supplementary material

Supplemental data for this article can be accessed at: https://doi.org/10.1080/1062936X.2022.2152486

Additional information

Funding

The author reported there is no funding associated with the work featured in this article.