An activity‑based high‑throughput screening platform for identifying functional modulators of OFF‑type riboswitches
Year: 2026
Type: preprint
Abstract: Structured regulatory RNAs, such as riboswitches, represent attractive yet challenging targets for small‑molecule discovery. Many existing screening approaches prioritize ligand binding over their function, such as controlling gene expression. Here, we describe an activity‑based high‑throughput screening platform designed to identify effector compounds of off‑type riboswitches by directly reporting transcriptional readthrough. The assay combines a miniaturized in vitro transcription system with a dual molecular beacon readout to enable discrimination between ligand‑induced riboswitch control and non‑specific effects such as transcriptional inhibition or fluorescence interference. Using a previously uncharacterized Staphylococcus aureus thiD thiamine pyrophosphate (TPP) riboswitch as a model, we validate the platform against a radiolabelled in vitro transcription readthrough assay and demonstrate robust performance in a miniaturized 1536-well format. Screening of several diverse compound libraries did not yield validated non‑native modulators under the assay conditions and the chemical space explored, consistent with previous predictions of low druggability for the TPP riboswitch. Importantly, these results highlight the utility of the platform as a stringent functional filter that enables the identification of riboswitches that operate at the transcriptional level, the identification of effector ligands of bacterial RNA targets, and the assessment of the functional ligandability of RNA targets, thereby aiding in target prioritization.
Source: ChemRxiv
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204856617