LC-Q-TOF-MS phenolic profiling, data mining for antiviral compounds, and in silico analysis against SARS-CoV-2 in heritage-pigmented rice metabolome

Viral infections are constantly causing a threat to global health. Ayurvedic health practitioners have been using pigmented rice to cure infectious diseases. This study aimed to identify bioactive polyphenols in 24 Indian heritage pigmented rice varieties (IHPRV) using LC-Q-TOF-MS-based metabolomic profiling. The study identified 132 diverse polyphenols with flavonoids (61 %) constituting a major category. Karupa kavuni (BKk), a black rice variety, contained the highest number of identified phenolic metabolites (72), followed by Kesari (red rice, 71). Chemometric analysis highlighted 67 abundant phenolic metabolites across the samples. Data mining through literature screening and database search, revealed 23 out of the 67 compounds to show significant antiviral activity. Of these, 20 were reported to have anti-SARS-CoV-2 virus activity. Of the 20, 9 were also reported to have activity against other viruses. The remaining 3 showed activity against non-SARS-CoV-2 viruses. Scaffolds of 23 compounds with reported antiviral activity and the remaining 20 lacking studies, were taken ahead for ADME profiling. Molecular docking analysis carried out for 14 abundant bioavailable polyphenols showed five exhibiting a strong binding affinity (-7.02 to -7.53 kcal/mol) with SARS-CoV-2 Mpro. Both data mining and molecular docking results were considered for ranking IHPRV with antiviral potency. BKk ranked highest (10), followed by red varieties (Kesari, Poonghar, and Kuzhiadichan) (6–7), and two brown varieties (5). These findings lay a foundation for developing drugs, functional food products, and nutraceuticals, utilizing top-ranked samples with antiviral phenolic metabolites for viral defense and immune support. [Display omitted] •Metabolomic analysis revealed 132 polyphenols in 24 IHPRV with 67 being abundant.•Data mining identified twenty phenolic metabolites with anti-SARS-CoV-2 activity.•Five additional polyphenols in the IHPRV metabolome showed good binding affinity with SARS-CoV-2 Mpro.•The black rice variety, Karupa kavuni, was identified as the most potent antiviral variety.