In silico study of potential SARS-CoV-2 antagonist from Clitoria Ternatea


Objectives: In this study, we implemented a structure-based virtual screening (VS) protocol in search of natural bioactive compounds in Clitoria ternatea that could inhibit the viral Mpro.

Methods: A library of twelve main bioactive compounds in Clitoria ternatea was created from PubChem database by minimizing ligand structure in PyRx software to increase the ligand flexibility. Molecular docking studies were performed by targeting Mpro (PDB ID: 6lu7) via Discovery Studio Visualiser and PyRx platforms. Top hits compounds were then selected to study their ADMET and druglikeness properties via pkCSM pharmacokinetics tool to understand the stability, interaction, conformational changes, and pharmaceutical relevant parameters.

Results: This investigation found that, in the molecular docking simulation, four bioactive compounds (procyanidin A2 (-9.3 kcal/mol), quercetin-3-rutinoside (-8.9 kcal/mol), delphinidin-3-O-glucoside (-8.3 kcal/mol) and ellagic acid (-7.4 kcal/mol)) showed producing the strongest binding affinity to the Mpro of SARS-CoV-2, as compared to positive control (N3 inhibitor) (-7.5 kcal/mol). These binding energies were found to be favorable for an efficient docking and resultant. Additionally, the stability of quercetin-3-rutinoside and ellagic acid is higher without any unfavourable bond. The ADMET and druglikeness of these two compounds were found that they are considered an effective and safe COVID-19 inhibitors through Lipinski’s Rule, absorption, distribution, metabolism and toxicity properties.

Conclusion: From these results, it was concluded that Clitoria ternatea possess potential therapeutic properties against COVID-19.


computational screening coronavirus disease 2019 molecular docking phytochemical severe acute respiratory syndrome coronavirus 2
Chun, C. Y., Khor, S. X. Y., Chia, A. Y. Y., & Tang, Y. Q. (2023). In silico study of potential SARS-CoV-2 antagonist from Clitoria Ternatea. International Journal of Health Sciences, 17(3), 3–10. Retrieved from
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