Molecular docking analysis of selected phytochemicals against SARS-CoV-2 Mpro receptor

Abstract

Presently world is on a war with the novel coronavirus and with no immediate treatments available the scourge caused by the SARS-CoV-2 is increasing day by day. A lot of researches are going on for the potential drug candidate that could help the healthcare system in this fight. Plants are a natural data bank of bioactive compounds. Many phytochemicals are being studied for various ailments including cancer, bacterial and viral infections, etc. The present study aims to screen 38 bioactive compounds from 5 selected plants viz., Azadirachta indica , Curcuma longa , Zingiber officinale , Ocimum basilicum and Panax ginseng against SARS-CoV-2. Lipinski’s rule was taken as the foundation for initial screening. Shortlisted compounds were subjected to molecular docking study with M pro receptor present in SARS-CoV-2. The study identified that gedunin, epoxyazadiradione, nimbin and ginsenosides have potential to inhibit M pro activity and their binding energies are − 9.51 kcal/mol, − 8.47 kcal/mol, − 8.66 kcal/mol and − 9.63 kcal/mol respectively. Based on bioavailability radar studies gedunin and epoxyazadiradione are the two most potent compounds which are used for molecular dynamics simulation studies. Molecular dynamics studies showed that gedunin is more potent than epoxyazadiradione. To find the effectiveness and to propose the exact mechanism, in-vitro studies can be further performed on gedunin.

Use of vitamin/zinc supplements, medicinal plants, and immune boosting drinks during COVID-19 pandemic: A pilot study from Benha city, Egypt

“…The other examined medicinal plants ( Origanum majorana , Carum carvi , Glycyrrhiza glabra , Ocimum basilicum ) were used but less frequently. Such plants have also been shown to possess immune enhancement effects ( Garg et al, 2020 ; Mardani et al, 2016 ; Sun et al, 2019 ; Yousefi et al, 2021 ). Thus, the use of available and natural boosters of the immune system that help in the management of COVID19 should be encouraged.…”

Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach

“…This showed about 36 phytochemicals per plant species. Similarly, few studies reported the main protease binding potential of only A. Indica phytochemicals, but they considered less number of phytochemicals ( Garg et al., 2020 ; Adegbola et al., 2021 ; Umar et al., 2021 ). Lim et al.…”

“…This showed about 36 phytochemicals per plant species. Similarly, few studies reported the main protease binding potential of only A. Indica phytochemicals, but they considered less number of phytochemicals (Garg et al, 2020;Adegbola et al, 2021;Umar et al, 2021). Lim et al (2021) suggested A. indica as a potential herbal source of anti-SARS-CoV-2 agent with a multimodal efficacy of antiviral, anti-inflammatory, and immunomodulatory properties.…”

Phytochemical Analysis and Cellular Uptake Study of an Ayurvedic Formulation, Vyaghryadi Kashayam Used in the Clinical Management of COVID-19.

“…Screening of the phytochemicals, as obtained from LC-MS/MS QTOF analysis, revealed that seven phytochemicals that are present in VK have been reported previously for potential activity against SARS-CoV-2. These are 6-gingerol [22], 6-shogoal [22], Diacetoxy-4 -gingerdiol [23], gallic acid [24], magnoflorine [24], solasonine [25] and solamargine [25]. The binding site of these phytochemicals from the previous reports and the plant sources of these are summarised in Table 3.…”