Molecular Docking and Dynamics Simulations Study of Selected Phytoconstituents of “Pangi” (Pangium edule Reinw) Leaf as Anti-SARS-CoV-2

Abstract

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.

Village-level Processing of Pangi (Pangium edule Reinw.) Seeds by the Obu Manuvu Improves the Edibility and Level of Some Nutritional Factors [RESEARCH NOTE]

“…The main product of this plant is the endosperm of its fruit seed which is usually consumed as a spice or an added ingredient to several local dishes. However, its consumption is compromised by its relatively high amount of cyanogen, making it poisonous and unsafe to eat (Deshpande et al 2000;Sailah et al 2021). Cyanogen is an antinutrient that limits the optimum utilization of plant food sources because of its adverse effects on human health.…”

“…This can provide the chemical basis as to how Pangi seeds become edible and safe for consumption after processing. Although review of literature does not reveal records on food poisoning cases from Pangi seeds in the Philippine setting, there are references stating that fresh Pangi fruit and seeds are high in hydrogen cyanide which is a deadly poison (Deshpande et al 2000;Etoh 2001;Sailah et al 2021). Furthermore, interviews with the Obu Manuvu community revealed that consuming unprocessed Pangi seeds results in poisoning for both humans and animals.…”