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.