PMC:7441777 / 5337-8775 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"Epidemiological studies repetitively suggested that consumption of bioactive compounds (e.g. vitamins, phytochemicals, polyphenols, flavonoids, flavonols, and carotenoids etc.) has beneficial activity on human health and could minimize the risk of various diseases starting from cancers to different viral infections (Khan et al., 2020; Szajdek \u0026 Borowska, 2008). Traditional natural compounds have been consumed since ancient times as they exhibit less toxicity, low-cost availability, minimum side-effects and are rich in therapeutic resources. Some of the previous findings also suggest that naturally occurring compounds possess a wide range of antiviral properties against RNA viruses, including polio-virus type 1, parainfluenza virus type 3, and respiratory syncytial virus by inhibiting their replication (Lin et al., 2014). In that context, Ahmed-Belkacem et al. have screened more than forty potent natural flavonoids for their polymerase inhibition activity using HCV-NS5 strain and among the different flavonoids, quercetagetin showed strong HCV replication inhibitory activity in vitro (Ahmed-Belkacem et al., 2014). Previously, song et al. reported that green tea catechins, by disrupting the membrane of the influenza virus, inhibited neuraminidase in the crude system (Song et al., 2005). On a separate report, Takashi et al. reported that EGCG, a green tea polyphenol can inhibit the endonuclease activity of influenza A virus RNA polymerase. EGCG is also reported to interfere with viral replication via modulating the cellular redox environment (Ho et al., 2009; Kuzuhara et al., 2009). Therefore, the existing scientific evidence strongly suggests that natural flavonoids/polyphenol can act against SARS-CoV-2 (Aanouz et al., 2020; Elfiky 2020b; Elmezayen et al., 2020; Enmozhi et al., 2020). Because of the time-consuming process of new synthetic/semi-synthetic drug development, drug repurposing of phytomolecules is an ideal alternative in this urgent situation as the latter process is economical and scalable in a very short period of time (Adeoye et al., 2020; Islam et al., 2020; Muralidharan et al., 2020; Sinha et al., 2020). Hence, a comprehensive understanding of their binding to SARS-CoV-2 RdRp can yield interesting findings that can further be capitalized to develop COVID-19 drugs. Nevertheless, the apparent lack of cytotoxicity of polyphenols at even significantly high concentrations makes them potential antiviral drug candidates. In the present study, we selected a hundred natural polyphenols to assess their potential to act as SARS-CoV-2 RdRp inhibitors. The selected library was then explored to evaluate the binding affinity of individual polyphenols towards RdRp of the SARS-CoV-2 by molecular docking using AutoDock vina. Among the selected polyphenols, theaflavin (TF1), theaflavin-3′-O-gallate (TF2a), theaflavin-3′-gallate (TF2b), theaflavin 3,3′-digallate (TF3), hesperidin, EGCG, myricetin, and quercetagetin were found to be docked in the active site of RdRp of the SARS-CoV-2 with a highly favourable affinity for the binding pocket. Further to get a better understanding of the dynamics of the complexes, we performed a 150-nanoseconds molecular dynamic simulation with those eight polyphenols. The binding free energy components were calculated by the MM-PBSA. Remdesivir (Hendaus, 2020) and GTP (a physiological nucleotide) were taken as positive controls to validate our 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