Natural compounds from ethno-medicinal plants exhibit multiple binding activities on SARS-CoV-2 spike protein receptor-binding domains

Trizah Koyi Milugo^1,2*Bethwel Owuor³Patrick Wafula Okanya¹Kennedy Chepukosi¹Dr. George F. Obiero^1*

• ¹Technical University of Kenya, Nairobi, Kenya
• ²Disease Control and Elimination Theme, Medical Research Council The Gambia Unit (MRC), Banjul, Gambia
• ³Kisii University, Kisii, Kenya

Background: COVID-19, caused by SARS-CoV-2, is a communicable respiratory viral disease with no effective curative medicine. The structure of SARS-CoV-2 spike protein has conserved modules that facilitate both infection and fusion into human host cells. These modules serve as crucial targets for synthesized and natural antivirals and therapeutics. In this study, our objective was to explore the potential of ethno-medicinal practice and molecular modelling of phytochemicals in informing drug targets against COVID-19 infections.The study was conducted at four sites in western Kenya's Lake Victoria basin. We used purposive sampling and snowballing to identify traditional health practitioners (THPs) and documented their experience and response to COVID-19. Extracts from various medicinal plants identified by the THP were subjected to phytochemical analysis on Gas Chromatography-Massspectrometry (GC-MS). The resulting active phytochemicals were screened against SARS-CoV-2 S-protein in-silico using molecular modelling tools.Results: Seventeen (17) THPs with experience in response to COVID-19 were identified, of whom 92% had more than 10 years of experience in the practice of traditional medicine. Whereas 43 medical plants were identified and documented, only seven plants, prescribed consistently by all THPs were investigated further. Phytochemical analysis on GC-MS identified compounds belonging to different chemical classes: terpenes, alkanes, alkene, alcohols, acridone, pyrazine, and carboxylic acid esters. Molecular modelling revealed the S-protein to possess multiple active sites. The phytochemicals studied showed potential multiple conformers interacting with each of the S-protein active sites.Overall, we identified and modelled phytochemicals with the SARS-CoV-2 S-protein and explained their bioactivities as reported by traditional herbalists. The study underscores the beneficial contribution of traditional medicine in settings where access to comprehensive healthcare services for COVID-19 is limited. The identified plants and/or their phytochemicals could be targeted for conservation and future investigations including in-vivo studies targeting different aspects of the virus replication process, followed by the development of drugs with novel mode of action. The phytochemicals can also be screened for activities against other viruses in the Coronaviridae family.