Integrative In Silico and In Vitro Screening of Low Molecular Weight Compounds Targeting SARS-CoV-2 RNA Elements

An approach combining virtual and nuclear magnetic resonance (NMR)-based screening is presented here to identify low molecular weight molecules (small molecules) targeting viral RNA elements from the SARS-CoV-2 genome. The so-called high-resolution RNA structural Fragment Assembly of RNA with Full-Atom Refinement 2 (FARFAR2) ensembles of the conserved 5^'-terminal stem-loop 1 (SL1) and the pseudoknot of the -1 programed frameshift element are used as targets for binding of small molecules of three different virtual libraries of compounds. The resulting hits predicted by virtual screening are probed for their binding to the two RNA elements by ligand- and target-based NMR experiments. The results demonstrate that the integration of virtual and experimental NMR screening efficiently identifies RNA-binding small molecules as start molecular entities to advance RNA-targeted antiviral therapies in an efficient manner. The strategy does not only apply to SARS-CoV-2, but also provides a rapid, highly specific route to discovering therapeutics for other RNA-based pathogens, highlighting the critical role of RNA structural data in enriching virtual drug discovery efforts.