Covid-19 is a global pandemic where an effective drug has yet to be found. A new coronavirus species, SARS-CoV-2 causes this disease. Several studies have been conducted on medicinal plant-based lead compounds to find antidotes for this virus. One of the fruits that with a high betacyanin content is super red dragon fruit produced by plant Hylocereus costaricensis. Betacyanin, besides having anti-inflammatory and immunomodulatory activities, also has antiviral activity. Therefore, this study aimed to evaluate betacyanin’s interaction with several SARS-CoV-2 receptors by observing its binding affinity and compared it with the nelfinavir and hydroxychloroquine sulfate that have been recommended for treating COVID-19. This research was an in silico study using computer software to assess binding affinity simulations based on molecular docking. The results of this study indicated that betacyanin had a good affinity with several receptors so that it has the potential to be developed as a lead compound to overcome COVID-19. Based on its binding affinity value, betacyanin’s ability was comparable to nelfinavir and hydroxychloroquine sulfate recommended by WHO as a therapeutic agent for COVID-19.
Herbal plants are often used as alternative medicine because they contain active compounds for the treatment of diseases and disorders with minimal side effects, and are easily obtained from the surrounding environment. Some of them have antiviral activity. This study aimed to analyze the potential of phytochemical compounds in the leaf of “pangi” (Pangium edule Reinw) as antiSARS-CoV-2 using molecular docking study. The drug- and lead-likeness properties of the selected compounds were obtained from the Swiss ADME and admetSAR online server tools. Molecular dynamics (MD) simulation of the selected ligand was carried out to validate the stability of the interaction. The results suggested that pangi leaves contain three compounds with remarkable binding affinities with Mpro (main protease) and RBD (receptor binding domain) were (5.beta.) pregnane-3,20.beta.-diol, 14.alpha.,18.alpha.-[4-methyl-3-oxo-(1-oxa-4-azabutane-1,4-diyl)]-, diacetate (PD), ethyl cholate (EC), and bis(3,5,5-trimethylhexyl) phthalate. Because EC will be metabolized in the body into cholic acid (Cho), this compound was then docked and validated using MD simulation. The compound has the best free binding energy (ΔG) with SARS-CoV-2 (–7.1 kcal/ mol with Mpro and –6.0 kcal/mol with RBD). Moreover, the compound is bound strongly to the active cavity of Mpro on Thr24, Thr26, His41, and Cys145 residues. The MM-GBSA calculation showed that the interaction of Cho with Mpro was higher than with RBD. According to the RMSD (root mean square deviation), RMSF (root mean square fluctuation), the radius of gyration (Rg), and intermolecular hydrogen bond (H-bond) analysis obtained from 50 ns MD simulations, Cho formed stable interactions with Mpro and RBD. The finding of this study indicated that Cho showed good anti-SARS-CoV-2 activity. The potential of the compound to inhibit the virus can serve as a starting point in the process of developing COVID-19 therapeutic natural medicine.
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