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.
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).