Molecular Docking Investigation of Antiviral Herbal Compounds as Potential Inhibitors of SARS-CoV-2 Spike Receptor

Abstract

At the beginning of 2020, a new type of Coronavirus (Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)) dismayed the world and led to public health emergencies. This virus has caused a remarkable percentage of morbidity and mortality. Also, the lack of an effective treatment to fight this virus is another concern that should be given attention. Herbal medicines and purified natural products have been reported for their antiviral activity against SARS-CoV-2. In this study, molecular docking of effective compounds in the extracts and essential oils of Zingiber officinale, Glycyrrhiza glabra Sambucus nigra, Panax ginseng Ocimum basilicum, and Origanum vulgare was carried out to investigate their binding to the X-ray structure of the ACE2 binding domain of SARS-CoV-2. The Glide docking program was utilized for molecular docking with standard precision (SP) and extra precision (XP). Finally, 7 compounds- mainly belong to Panax ginseng-showed a higher docking score than some known antiviral compounds. Floralginsenoside B, which is extracted from Panax ginseng, indicated a strong binding affinity (-8.618 kcal/mol) to the crucial residues of the receptor binding domain of SARS-CoV-2 comparing to Doravirine (-7.2 kcal/mol), Hetacillin (-7.1 kcal/mol), Ketoprofen (-7.0 kcal/mol), and Mefloquine (-7.0 kcal/mol) reported in previous articles. Based on the excellent binding affinities of these herbal compounds, we concluded that these phytochemicals could be promising candidates for fighting against the COVID-19 pandemic.

Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods

“…Molecular docking studies are usually performed to study the preferred orientation of the bound drug(s) and the protein. − The model protein of the current report, myoglobin, is a single-polypeptide globular protein consisting of eight α-helices (subunits labeled as A–H). These subunits are connected through turns with an oxygen-binding heme group at the centre and a hydrophobic core. , Figures and (Figures S4–S9) show the possible docking results with drug–protein complex structures corresponding to SMZ–Mb and SDZ–Mb systems.…”

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

“…In a study of screening FDA-approved drugs, iron oxide nanoparticles were suggested for COVID-19 treatment . Existing drugs, such as amentoflavone, ledipasvir, tenofovir, levodopa, lopinavir, and ubrogepant, against S protein were investigated. − For natural products inhibiting S protein, studies focusing on indigenous food additives, herbal constituents, antioxidants, traditional medicinal plants, tea, and others − suggested potent inhibitors such as phycocyanobilin, phycoerythrobilin, phycourobilin, folic acid, hinokiflavone, and phytochemicals. Lastly, some other compounds are repurposed to inhibit the S protein.…”

A Review on Antiviral Plants Effective Against Different Virus Types

“…In a study conducted in Iran, the effects of essential oils of plant species belonging to different genera on SARS-CoV-2 were evaluated. It has been reported that the compounds obtained from Zingiber officinale, Glycyrrhiza glabra Sambucus nigra, Panax ginseng, Ocimum basilicum and Origanum vulgare used in the study exhibit significant binding strength on ACE2 [131]. In a study conducted in Italy, the effect of the extract obtained from Vitis vinifera on SARS-CoV-2 was examined.…”

“…Plants effective against coronavirus[42,61,68,[116][117][118][119][120][121][122][123][124][125][126][127][128][129][130][131][132][133][134][135].Aegle marmelos, Aesculus hippocastanum, Allium sativum, Aloe vera, Anastatica hierochuntica, Asteriscus hierochunticus, Azadirachta indica, Bombax ceiba, Camellia sinesis, Cannabis sativa, Cenostigma pluviosum subsp. peltophoroides, Cinnamomum verum, Citrus reticulata, Citrus sinensis, Cupressus sempervirens, Curcuma longa, Cyperus rotundus, Echinaceae purpurea, Eucalyptus globulus, Filipendula ulmaria, Gingko biloba, Glycyrrhiza glabra, Guaiacum officinale, Hibiscus sabdariffa, Houttuynia cordata, Juniperus oxycedrus, Justicia adhatoda, Kickxia aegyptiaca, Laurus nobilis, Mentha piperita, Moringa oleifera, Morus alba subsp.…”