Artemisia afra for COVID-19

Coronavirus disease (COVID-19) is still a severe concern, especially in Africa with suboptimal intention rates of vaccination. This flagged the requirement of plant-based remedies as an alternative treatment. In this study we integrated metabolomics and chemometrics approaches with In silico and In vitro approaches to accelerate and unravel compounds from commonly used South African plants that may inhibit SARS-CoV-2 main protease. The selected commonly used plants, Artemisia afra and Artemisia annua, were found to be non-toxic against Vero cells, as determined by the resazurin cell viability assay. Metabolites profiling revealed eighty-one compounds and the top three hit compounds, quercetin 3-O-(6“-acetyl-glucoside), 2”-O-acetylrutin, and quercetin 3-(6”-malonyl-glucoside), had binding affinities of -9.3 kcal/mol, -9.5 kcal/mol, and -9.3 kcal/mol, respectively. The 2”-O-acetyl group of the rutin moiety and quercetin moiety produces a hydrogen bond with the amide nitrogen of His41 and with the side chain carboxylate of Cys145, respectively. Molecular dynamics simulations revealed a stable binding of the docked complexes. In silico observations were validated by In vitro bioassay, which flagged the ability of these compounds to inhibit SARS-CoV-2 3CLpro. The collected analysed data of this study does not only draw special attention to the surfaced 2”-O-acetylrutin as the best suitable inhibitor of SARS-CoV-2 3CLpro, but also indirectly reveals the importance of integrating metabolomics and chemometrics approaches with In silico and In vitro approaches to accelerate and unravel compounds from South African commonly used plants.

The expected progress in SARS-CoV-2 vaccinations, as anticipated in 2020 and 2021, has fallen short, exacerbating global disparities due to a lack of universally recognized “safe and effective” vaccines. This study focuses on extracts of South African medicinal plants, Artemisia annua and Artemisia afra, to identify metabolomic bioactive compounds inhibiting the binding of the SARS-CoV-2 spike protein to ACE2 receptors. The extracts were monitored for cytotoxicity using a resazurin cell viability assay and xCELLigence real-time cell analyzer. Chemical profiling was performed using UPLC-MS/MS, orthogonal projection to latent structures (OPLS), and evaluated using principle component analysis (PCA) models. Identified bioactive compounds were subjected to in vitro SARS-CoV-2 enzyme inhibition assay using standard methods and docked into the spike (S) glycoprotein of SARS-CoV-2 using Schrodinger® suite followed by molecular dynamics simulation studies. Cell viability assays revealed non-toxic effects of extracts on HEK293T cells at lower concentrations. Chemical profiling identified 81 bioactive compounds, with compounds like 6″-O-acetylglycitin, 25-hydroxyvitamin D3-26,23-lactone, and sesaminol glucoside showing promising binding affinity. Molecular dynamics simulations suggested less stable binding, but in vitro studies demonstrated the ability of these compounds to interfere with SARS-CoV-2 spike protein’s binding to the human ACE2 receptor. Sesaminol glucoside emerged as the most effective inhibitor against this interaction. This study emphasizes the importance of multiplatform metabolite profiling and chemometrics to understand plant extract composition. This finding is of immense significance in terms of unravelling metabolomics bioactive compounds inhibiting the binding of the SARS-CoV-2 spike protein to ACE2 receptors and holds promise for phytotherapeutics against SARS-CoV-2.