Molecular docking and dynamics of phytochemicals from Chinese herbs with SARS-CoV-2 RdRp
Natural Product Communications
; 17(6), 2022.
Article
in English
| CAB Abstracts | ID: covidwho-1909973
ABSTRACT
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is causing coronavirus disease 2019 (COVID-19) pandemic. Ancient Chinese herbal formulas are effective for diseases caused by viral infection, and their effects on COVID-19 are currently being examined. To directly evaluate the role of Chinese herbs in inhibiting replication of SARS-CoV-2, we investigated how the phytochemicals from Chinese herbs interact with the viral RNA-dependent RNA polymerase (RdRP). Total 1025 compounds were screened, and then 181compounds were selected for molecular docking analysis. Four phytochemicals licorice glycoside E, diisooctyl phthalate, (-)-medicocarpin, and glycyroside showed good binding affinity with RdRp. The best complex licorice glycoside E/RdRp forms 3 hydrogen bonds, 4 hydrophobic interactions, 1 pair of Pi-cation/stacking, and 4 salt bridges. Furthermore, docking complexes licorice glycoside E/RdRp and diisooctyl phthalate/RdRp were optimized by molecular dynamics simulation to obtain the stable conformation. These studies indicate that they are promising as antivirals against SARS-CoV-2.
Prion, Viral, Bacterial and Fungal Pathogens of Humans [VV210]; Non-food/Non-feed Plant Products [SS200]; Pesticides and Drugs; Control [HH405]; Animal and in vitro Models for Pharmaceuticals [VV450]; enzymes; traditional Chinese medicines; garlic; medicinal plants; plant extracts; antiviral properties; pathogens; viral replication; DNA-directed RNA polymerase; glycosides; hydrogen bonding; Severe acute respiratory syndrome coronavirus 2; Allium sativum; Houttuynia cordata; Forsythia suspensa; Scutellaria baicalensis; Lonicera japonica; Fallopia japonica; Glycyrrhiza uralensis; Gentiana; plants; Severe acute respiratory syndrome-related coronavirus; Betacoronavirus; Coronavirinae; Coronaviridae; Nidovirales; positive-sense ssRNA Viruses; ssRNA Viruses; RNA Viruses; viruses; Allium; Amaryllidaceae; Asparagales; monocotyledons; angiosperms; Spermatophyta; eukaryotes; Houttuynia (Spermatophyta); Saururaceae; Piperales; magnoliids; Forsythia; Oleaceae; Lamiales; eudicots; Scutellaria; Lamiaceae; Lonicera; Caprifoliaceae; Dipsacales; Fallopia; Polygonaceae; Caryophyllales; Glycyrrhiza; Papilionoideae; Fabaceae; Fabales; Gentianaceae; Gentianales; Polygonum cuspidatum; Gentiana scabra; SARS-CoV-2; drug plants; medicinal herbs; officinal plants; honeysuckles; Japanese honeysuckle; Japanese knotweed; Reynoutria japonica; anti-viral properties; RNA polymerase; heterosides
Full text:
Available
Collection:
Databases of international organizations
Database:
CAB Abstracts
Topics:
Traditional medicine
Language:
English
Journal:
Natural Product Communications
Year:
2022
Document Type:
Article
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