Abstract

Recent studies have highlighted the role of distinct RNA mechanisms in several pathologies, opening new avenues for therapeutic intervention. Emerging data highlights the importance of epitranscriptomic mechanisms such as RNA methylation and RNA-editing along with the discovery of coding and non-coding RNA transcripts that modulate numerous cellular processes. Current drug discovery assays for many RNA-related targets rely on cumbersome labels such as antibodies, fluorescent reporters, or radioisotopes that drive up costs and generate high rates of false positive data. Here, we describe a label-free and ultra high-throughput assay that combines self-assembled monolayers (SAMs) with matrix assisted laser desorption ionization (MALDI) mass spectrometry—a technique termed SAMDI—that offers unique and quantitative solutions for RNA drug discovery. We first showcase the development of a robust SAMDI assay to measure METTL3/14 RNA methyltransferase activities. Next we describe an innovative assay that measures RNA editing activities. Finally, we highlight an affinity selection mass spectrometry approach to reveal non-covalent small molecules binders to distinct RNA transcripts. Each approach is amenable to an ultra high-throughput readout capable of screening millions of compounds per week. Taken together, SAMDI is an enabling technology to drive RNA drug discovery towards the clinic.