Discovery of Small Molecules Targeting the Frameshifting Element RNA in SARS-CoV-2 Viral Genome

Targeting structured RNA elements in the SARS-CoV-2 viralgenomewith small molecules is an attractive strategy for pharmacologicalcontrol over viral replication. In this work, we report the discoveryof small molecules that target the frameshifting element (FSE) inthe SARS-CoV-2 RNA genome using high-throughput small-molecule microarray(SMM) screening. A new class of aminoquinazoline ligands for the SARS-CoV-2FSE are synthesized and characterized using multiple orthogonal biophysicalassays and structure-activity relationship (SAR) studies. Thiswork reveals compounds with mid-micromolar binding affinity (K (D) = 60 +/- 6 mu M) to the FSE RNA andsupports a binding mode distinct from previously reported FSE bindersMTDB and merafloxacin. In addition, compounds are active in in vitro dual-luciferase and in-cell dual-fluorescent-reporterframeshifting assays, highlighting the promise of targeting structuredelements of RNAs with druglike compounds to alter expression of viralproteins.

Automated summary

In this study, small molecules that target the frameshifting element (FSE) in the SARS-CoV-2 RNA genome were discovered and characterized using high-throughput small-molecule microarray (SMM) screening. These compounds showed mid-micromolar binding affinity to the FSE RNA and had a binding mode distinct from previously reported FSE binders. Furthermore, these compounds were active in in vitro and in-cell dual-fluorescent-reporter frameshifting assays, indicating the potential of targeting RNA structural elements with druglike compounds to alter viral protein expression.