An activity‑based high‑throughput screening platform for identifying functional modulators of OFF‑type riboswitches
6 affiliations
- 1Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen, Norway, 5020
- 2Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic, 142 20
- 3RNA Group
- 4Université de Sherbrooke
- 5Department of Chemistry and Centre for Pharmacy, University of Bergen, Allégaten 41, Bergen, Norway, 5007
- 6Institute for Technical Microbiology
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.
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BibTeX
@misc{panchal2026activitybased,
title = {{An activity‑based high‑throughput screening platform for identifying functional modulators of OFF‑type riboswitches}},
author = {Vipul Panchal and Michaela Lisová and Daniel A. Lafontaine and Bengt Erik Haug and David Sedlak and Petr Bartunek and Matthias Mack and Ruth Brenk},
howpublished = {ChemRxiv},
year = {2026},
month = aug,
doi = {10.26434/chemrxiv.15008065/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008065/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - An activity‑based high‑throughput screening platform for identifying functional modulators of OFF‑type riboswitches
AU - Vipul Panchal
AU - Michaela Lisová
AU - Daniel A. Lafontaine
AU - Bengt Erik Haug
AU - David Sedlak
AU - Petr Bartunek
AU - Matthias Mack
AU - Ruth Brenk
PY - 2026
DA - 2026/08/31
PB - ChemRxiv
DO - 10.26434/chemrxiv.15008065/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008065/v1
AB - 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.
ER -