A recent study posted to the Research Square* preprint server, and currently under consideration at the Journal of Molecular Modeling, assessed the molecular dynamics of potentially active natural phytochemicals to target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro).
Study: Molecular dynamics and docking studies on potentially active natural phytochemicals for targeting SARS-CoV-2 Main Protease. Image Credit: Kateryna Kon/Shutterstock
This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources
Background
The morbidity and mortality caused by the coronavirus disease 2019 (COVID-19) pandemic have been significantly curbed by SARS-CoV-2 vaccines. However, there is considerable skepticism regarding vaccine-related health complications post-administration.
About the study
The present study investigated the effectiveness of phytochemical constituents, present in four medicinal herbs, in neutralizing SARS-CoV-2 Mpro and their mechanism of action.
The team employed the SARS-CoV-2 Mpro receptor that consisted of domains I and II having β-barrels while domain III had α-helices. Docking and visualization were performed on this receptor. Aegle marmelos, Coleus amboinicus, Aerva lanta, and Biophytum sensitivum constituting 20, 24, 17, and 26 phytochemicals, respectively, were used to obtain the phytochemicals.
The study then assessed the drug-likeness of the screened drugs, ensuring that each compound had 500 g/mol or less molecular weight, five or fewer hydrogen donors, less than 10 hydrogen acceptors, less than 10 rotatable bonds, less than 140 polar surface area (PSA), and less than 12 total hydrogen bond donors and acceptors.
Furthermore, the five pharmacokinetic properties, namely absorption, distribution, metabolism, excretion, and toxicity (ADME/T) of the drugs were also evaluated. A quantitative structure-activity relationship (QSAR) was used to calculate the ADME/T properties like aqueous solubility, cytochrome P450 inhibition (CYP250), blood-brain barrier penetration (BBB), hepatotoxicity, plasma protein binding (PPB), and human intestinal absorption.
The team chose the binding site of the Mpro according to the location of peptide inhibitor N3. Also, a hotspot was formed at the interaction site of the polar and nonpolar receptors using high throughput virtual screening (HTVS). Moreover, the binding energies (BEs) of the phytochemicals were calculated and molecular dynamics (MD) simulations of protein-ligand complexes with high docking values were performed.
Results
The study assessed 87 phytochemicals obtained from the four herbs. The binding energy for Aegle Marmelos phytochemicals ranged from −8.55 kcal/mol to -7.14 kcal/mol while the LibDock score ranged between 142.00 and 63.00. Notably, tigogenin, aegelinoside, and dehydromarmeli had the highest binding energies of -8.55 kcal/mol, -8.54 kcal/mol, and -8.53 kcal/mol, respectively.
Also, imperatorin, O-prenylhalfordinol, skimmianine, xanthotoxin, N-[2-ethoxy-2-(4-methoxyphenyl)ethyl]cinnamide, aeglemarmaelosine, aegeline, and anhydromarmeline had binding energies ranging from -8.41 kcal/mol to -8.06 kcal/mol.
An alpha-glucosidase inhibitor found in Aegle Marmelos called aegelinoside B, interacted with glutamic acid-166 (GLU166), glutamine-192 (GLN192), threonine-190 (THR190), arginine-188 (ARG188), and GLN189.
Out of the 17 phytochemicals present in Aerva lanata, a biologically active canthin-6-one alkaloid, called ervoside, had a LibDock score of 129.69 kcal/mol. Amino acids residues like tyrosine-54 (TYR54), histidine-172 (HIS172), cysteine-145 (CYS145), serine-144 (SER144), methionine-165 (MET165), and MET49 interacted with ervoside.
Another phytochemical called feruloyltyramine had a LibDock score of 123.22 kcal/mol and had three hydrogen bonds with the viral protein. Quercetin, with a LibDock score between 110 to 130 kcal/mol, exhibited protective effects against COVID-19-related kidney injuries as a result of its five hydrogen bonds with glycine-143 (GLY143), SER144, and MET165 amino acid residues.
Epicatechin, present in Biophytum sensitivum, had binding energy of -7.69 kcal/mol. Residues including HIS164, HIS163, SER144, phenylalanine-140 (PHE140), and asparagine-142 (ASN142) interacted with this ligand. Also, all the phytochemicals present in Coleus amboinicus had LibDock scores of less than 100.
All compounds except 3-hydroxy-4-methoxybenzoic acid had sufficient oral bioavailability to function efficiently as potential oral drugs. Either low, medium, high, or very high levels of BBB penetration were observed for most of the drugs except gamma sitosterol, 4′,7-Dimethoxykaempferol, stigmast-4-en-3-one, dl-Phenylephrine, 3-hydroxy-4-methoxybenzoic acid, ervoside, and methoxykaempferol. Also, gamma sitosterol, anhydromarmeline, and stigmast-4-en-3-one showed significant levels of plasma protein binding.
Conclusion
The study findings showed the potency of biochemical phytochemicals obtained from herbs in targeting the SARS-CoV-2 Mpro receptor.
According to this study, six of the active phytochemicals can be further assessed as potential Mpro inhibitors based on their significant docking scores. These efficient phytochemicals are ervoside and feruloyltyramine obtained from Aerva lanata, epicatechin from Biophytum sensitivum, and epoxyaurapten, marmin, and aegelinoside B from Aegle Marmelos.
The researchers believed that these results can form the foundation for further studies of medicinal herbs and their usage as a therapeutic device against SARS-CoV-2.
This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources
Article Revisions
- Jun 6 2023 - The preprint preliminary research paper that this article was based upon was accepted for publication in a peer-reviewed Scientific Journal. This article was edited accordingly to include a link to the final peer-reviewed paper, now shown in the sources section.
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