Abstract
Plants are endowed with a large pool of structurally diverse small molecules known as secondary metabolites. The present study aims to virtually screen these plant secondary metabolites (PSM) for their possible anti-SARS-CoV-2 properties targeting four proteins/ enzymes which govern viral pathogenesis. Results of molecular docking with 4,704 ligands against four target proteins, and data analysis revealed a unique pattern of structurally similar PSM interacting with the target proteins. Among the top-ranked PSM which recorded lower binding energy (BE), > 50% were triterpenoids which interacted strongly with viral spike protein—receptor binding domain, > 32% molecules which showed better interaction with the active site of human transmembrane serine protease were belongs to flavonoids and their glycosides, > 16% of flavonol glycosides and > 16% anthocyanidins recorded lower BE against active site of viral main protease and > 13% flavonol glycoside strongly interacted with active site of viral RNA-dependent RNA polymerase. The primary concern about these PSM is their bioavailability. However, several PSM recorded higher bioavailability score and found fulfilling most of the drug-likeness characters as per Lipinski's rule (Coagulin K, Kamalachalcone C, Ginkgetin, Isoginkgetin, 3,3′-Biplumbagin, Chrysophanein, Aromoline, etc.). Natural occurrence, bio-transformation, bioavailability of selected PSM and their interaction with the target site of selected proteins were discussed in detail. Present study provides a platform for researchers to explore the possible use of selected PSM to prevent/ cure the COVID-19 by subjecting them for thorough in vitro and in vivo evaluation for the capabilities to interfering with the process of viral host cell recognition, entry and replication.
Highlights
Coronaviruses (CoV) are spherical or pleomorphic, enveloped, non-segmented particles contain positive-sense single-stranded RNA1
The data obtained from this study indicated the possibilities of developing flavonoid glycoside or triterpenoid based drug molecules targeting human TMPRSS2 which process SARS-CoV-2 spike protein and facilitate the entry of the virus into the host cell
It could be concluded that virtual screening of large number of plant secondary metabolites (PSM) through molecular docking is a promising preliminary step towards developing an effective drug against a desired target protein/ enzyme by understanding their structure–activity relationship
Summary
Coronaviruses (CoV) are spherical or pleomorphic, enveloped, non-segmented particles contain positive-sense single-stranded RNA1. Several CoV virus related diseases have been frequently reported in human and animals such as human CoV OC43, 299E, Bovin CoV, Canine CoV, Feline CoV, Porcine CoV, etc., indicating their increasing competence to expand their host r ange[3] Their capabilities to cause fatality in human was realized with the SARS outbreak occurred during 2002 and 20034,5. Researchers across the world attempting to identify/ develop drug molecule targeting several viral pathogenicity factors such as, spike protein-human Angiotensin-converting enzyme 2 (hACE2) mediated viral entry, main protease (Mpro), papain-like protease 2 (PLP2), RNA-dependent RNA polymerase (RdRp), SARS-CoV helicase, etc[11]. Repurposing the already available FDA approved drugs, use of plant-based herbal medicines, or edible plant parts rich in anti-viral PSM are other strategies appears to be promising under current situations
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