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.

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Background: The novel coronavirus (2019-nCoV) causes a severe respiratory illness unknown to a human before. Its alarmingly quick transmission to many countries across the world has resulted in a global health emergency. Therefore, an imminent need for drugs to combat this disease has been increased. Worldwide collaborative efforts from scientists are underway to determine a therapy to treat COVID-19 infections and reduce mortality rates. Since herbal medicines and purified natural products have been reported to have antiviral activity against Coronaviruses (CoVs), this in silico evaluation was performed for identifying potential natural compounds with promising inhibitory activities against COVID-19. Methods: In this study, a High Throughput Virtual Screening (HTVS) protocol was used as a fast method for discovering novel drug candidates as potential COVID-19 main protease (Mpro) inhibitors. Over 180,000 natural product-based compounds were obtained from the ZINC database and virtually screened against the COVID-19 Mpro. In this study, the Glide docking program was applied for high throughput virtual screening. Also, Extra precision (XP) has been used following the induced-fit docking (IFD) approach. The ADME properties of all compounds were analyzed and a final selection was made based on the Lipinski rule of five. Also, molecular dynamics (MD) simulations were conducted for a virtual complex of the best scoring compound with COVID-19 protease. Results: Nineteen compounds were introduced as new potential inhibitors. Compound ZINC08765174 (1-[3-(1H-indol-3-yl) propanoyl]-N-(4-phenylbutan-2-yl)piperidine-3-carboxamide showed a strong binding affinity (-11.5 kcal/mol) to the COVID-19 Mpro comparing to peramivir (-9.8 kcal/mol) as a positive control. Conclusions: Based on these findings, nineteen compounds were proposed as possible new COVID-19 inhibitors, of which ZINC08765174 had a high affinity to Mpro. Furthermore, the promising ADME properties of the selected compounds emphasize their potential as attractive candidates for the treatments of COVID-19.

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Background: The novel coronavirus (2019-nCoV) causes a severe respiratory illness that was unknown in the human before. Its alarmingly quick transmission to many countries across the world resulted in a worldwide health emergency. It has caused a notable percentage of morbidity and mortality. Therefore, an imminent need for drugs to combat this disease has been increased. Global collaborative efforts from scientists are underway to find a therapy to treat infections and reduce death cases. Herbal medicines and purified natural products have been reported to have antiviral activity against Coronaviruses (CoVs).Methods: In this study, a High Throughput Virtual Screening (HTVS) protocol was used as a fast method on the discovery of novel drug candidates as the COVID-19 main protease inhibitors. Over 180,000 natural product-based compounds were obtained from the ZINC database and virtually screened against the COVID-19 main protease. In this study, the Glide docking program was applied for high throughput virtual screening. Extra precision (XP) and in a combination of Prime module, induced-fit docking (IFD) approach was also used. Additionally, the ADME properties of all compounds were analyzed, and the final selection was carried out based on the Lipinski rule of five. Results: The nineteen compounds were selected and introduced as new potential inhibitors. The compound ZINC08765174 (1-[3-(1H-indol-3-yl) propanoyl]-N-(4-phenylbutan-2-yl)piperidine-3-carboxamide) showed a strong binding affinity (-11.5 kcal/mol) to the crucial residues of COVID-19 main protease comparing to peramivir (-9.8 kcal/mol) as a positive control.Conclusions: The excellent ADME properties proposed the opportunity of this compound to be a promising candidate for the treatment of COVID-19.