In silico Investigation of the Interactions of Thymol and Carvacrol on the Spike Protein of Omicron Variant and MPro Enzyme of Coronavirus
Öz
Many drug studies have been conducted against the coronavirus disease, which has affected the whole world since December 2019, and some studies have been carried out on natural treatment methods. Many ideas for curing coronavirus disease of T. vulgaris known as thyme plant have been presented, although there are gaps in the literature on the subject. In this work, the anti-severe acute respiratory syndrome coronavirus 2 potential of the major compounds of the T. vulgaris plant’s essential oil was investigated in silico. The major components of the T. vulgaris plant's essential oil are thymol and carvacrol. Using molecular docking experiments, we evaluated the effects of thymol and carvacrol in thyme essential oil on Omicron variant spike protein and main protease enzyme (Mpro) of severe acute respiratory syndrome coronavirus 2. We also used online databases to investigate the adsorption, distribution, metabolism, absorption, and toxic (ADMET) aspects of these two compounds. It was determined that thymol and carvacrol have strong binding affinity to the spike protein of the Omicron variant and the main protease enzyme. The compounds interact with target proteins through electrostatic, hydrogen bonds, and hydrophobic interactions. More promising findings are obtained when the contacts of carvacrol with target proteins are assessed in terms of the structure-activity relationship.
Anahtar Kelimeler
T. vulgaris, Thymol, Carvacrol, Severe acute respiratory syndrome coronavirus 2, Molecular Docking, ADMET
Kaynakça
- Alp, M & Alp, A.S. (2019). Medisinal Kimyaya Kısa Bir Giriş (1st ed.). Akademisyen Kitabevi.
- Amirghofran, Z., Ahmadi, H., Karimi, M. H. (2012). Immunomodulatory Activity of the Water Extract of Thymus vulgaris, Thymus daenensis, and Zataria multiflora on Dendritic Cells and T Cells Responses. Journal of Immunoassay and Immunochemistry, 33(4), 388–402. https://doi.org/10.1080/15321819.2012.655822.
- Banerjee, P., Eckert, A. O., Schrey, A. K., Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46, W257–W263. https://doi.org/10.1093/nar/gky318.
- Bank, R. P. D. RCSB PDB - 7T9J: Cryo-EM structure of the SARS-CoV-2 Omicron spike protein. Retrieved July 25, 2022, from https://www.rcsb.org/structure/7T9J.
- BIOVIA, Dassault Systèmes, (2021). BIOVA Discovery Studio Visualizer 2021, v21.1.0.20298, San Diego: Dassault Systèmes,
- Catella, C., Camero, M., Lucente, M.S., Fracchiolla, G., Sblano, S., Tempesta, M., Martella, V., Buonavoglia, C., Lanave, G. (2021). Virucidal and antiviral effects of Thymus vulgaris essential oil on feline coronavirus, Research in Veterinary Science, 137, 44-47. https://doi.org/10.1016/j.rvsc.2021.04.024.
- Narkhede R. R., Cheke R. S., Ambhore J. P., Shinde S. D., (2020). The Molecular Docking Study of Potential Drug Candidates Showing Anti-COVID-19 Activity by Exploring of Therapeutic Targets of SARS-CoV-2. Eurasian Journal of Medicine and Oncology. 4(3), 185-195.| DOI: 10.14744/ejmo.2020.31503.
- Daina, A., Michielin, O., Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717.
- Daoud, S., Alabed, S. J., Dahabiyeh, L. A. (2021). Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies. Acta Pharmaceutica, 71(2), 163–174. https://doi.org/10.2478/acph-2021-0016.
- Fakhar, Z., Khan, S., AlOmar, S. Y., Alkhuriji, A., Ahmad, A. (2021). ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19. Scientific Reports, 11(1), 234. https://doi.org/10.1038/s41598-020-79918-3.
kapsamında lisanslanmıştır.