Molecular docking study of fatty acids from Pliek U Oil in the inhibition of SARS-CoV-2 protein and enzymes

Abstract

This study aimed to analyze the fatty acid inPliek U oil andevaluate its inhibitor potential based on the interaction to several proteins and enzymes in SARS-CoV-2 using the in silico approach. Pliek U oil containing capric acid, caprylic acid, lauric acid, linoleic acid, myristic acid, oleic acid, and palmitic acids, with oleic acid as a dominant substance. Molecular docking analysis showed that linoleic acid has the best interaction to the receptors with the lowest binding affinity to 3CLpro (6LU7), Spike protein (6VXX), PLpro (6WX4), RdRp (6M71), E protein (5X29), and Spike Ectodomain Structure (6VYB) of -4.9, -5.8, -4.7, -4.3, -5.3 and -5.5 kcal/mol, respectively. The finding suggests that the binding of linoleic acid to the SARS-CoV-2 protein and enzyme may cause impairment of viral attachments to host cells, thus reducing infectivity in COVID-19 patients.

Green Synthesis and Antimicrobial Activities of Silver Nanoparticles Using Calotropis gigantea from Ie Seu-Um Geothermal Area, Aceh Province, Indonesia

“…Researchers have long studied plant extracts for their broad spectrum of medicinal properties such as anti-inflammatory [1], antibacterial [2,3], antifertility [4], termiticide, and nematicide activities [5]. Studies on plant extracts have recently gained more interest during the COVID-19 pandemic in the effort to find efficacious antiviral agents [6][7][8][9]. Notably, the bioactive compounds contained in plant extracts are strongly influenced by environmental factors [10].…”

Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2

“…Hydrophobic interaction is a reaction that causes protein structures to compact to prevent any contact with water or aqueous conditions [ 34 ]. Nonpolar amino acid residues that cluster together forming groups in the protein interior to avoid the residues from interacting with water is another definition of hydrophobic interaction.…”

“…The higher or more negative energy released from the ligand and receptor interactions, the more powerful the ligands adhere to the receptor. This is because ligand–receptor complex forms stable and strong non-covalent interactions which creates an opening to the cell leading to cell destruction as it interrupts cell metabolism and the replication of DNA [ 34 ]. In a very simple way, the Δ G value energy or the negativity of binding affinity is directly proportional to the stability of ligand–receptor complex formation.…”

Nasal application of sesame oil-based Anu taila as ‘biological mask’ for respiratory health during COVID-19

“…A similar study on seed proteins including sesame oil reported key molecules of sesame (Sesamin, sesaminol, sesamolin) having significantly good interaction with 3 important viral proteins (spike protein, M-pro, and ACE receptor site) [ 25 ]. Likewise, in a study conducted on all the fatty acids of coconut oil against viral proteins [ 26 ], fatty acids like capric acid, caprylic acid, lauric acid, linoleic acid, myristic acid, oleic acid, palmitic acid, and oleic acid exhibited good inhibition against 6 proteins of SARS-CoV-2 in binding to the host receptors. Surprisingly, despite the abundance of lauric acid (44%) in coconut oil, a stronger affinity was seen with linoleic acid(1%) against 5 of the 6 SARS-CoV-2 protein targets [ 26 ].…”

“…Likewise, in a study conducted on all the fatty acids of coconut oil against viral proteins [ 26 ], fatty acids like capric acid, caprylic acid, lauric acid, linoleic acid, myristic acid, oleic acid, palmitic acid, and oleic acid exhibited good inhibition against 6 proteins of SARS-CoV-2 in binding to the host receptors. Surprisingly, despite the abundance of lauric acid (44%) in coconut oil, a stronger affinity was seen with linoleic acid(1%) against 5 of the 6 SARS-CoV-2 protein targets [ 26 ]. Interestingly, sesame oil consists of about 41–48% linoleic acid and is the most abundant fatty acid seen in sesame oil in addition to other fatty acids like oleic acid (35–42%), palmitic acid (7–9%), and stearic acid (4–5%) [ 27 ].…”