Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy

Abstract

There are many RNA targets in the transcriptome to which small molecule chemical probes and lead therapeutics are desired. However, identifying compounds that bind and modulate RNA function in cellulo is difficult. Although rational design approaches have been developed, they are still in their infancies and leave many RNAs “undruggable”. In an effort to develop a small molecule library that is biased for binding RNA, we computationally identified “drug-like” compounds from screening collections that have favorable properties for binding RNA and for suitability as lead drugs. As proof-of-concept, this collection was screened for binding to and modulating the cellular dysfunction of the expanded repeating RNA (r(CUG)exp) that causes myotonic dystrophy type 1. Hit compounds bind the target in cellulo, as determined by the target identification approach Competitive Chemical Cross-Linking and Isolation by Pull-down (C-ChemCLIP), and selectively improve several disease-associated defects. The best compounds identified from our 320-member library are more potent in cellulo than compounds identified by high-throughput screening (HTS) campaigns against this RNA. Furthermore, the compound collection has a higher hit rate (9% compared to 0.01–3%), and the bioactive compounds identified are not charged; thus, RNA can be “drugged” with compounds that have favorable pharmacological properties. Finally, this RNA-focused small molecule library may serve as a useful starting point to identify lead “drug-like” chemical probes that affect the biological (dys)function of other RNA targets by direct target engagement.

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands

“…[7a, 8] In studies targeting r(CUG)-repeat sequences in 2015, Disney et al tested a drug-like, RNA-biased library of bis-benzimidazoles and similar core structures and found that bioactive molecules had statistically significant differences in topological polar surface area (tPSA) as well as hydrogen bond acceptors (HBA) and donors (HBD). [9] Inspired by this previous work and the recent surge in discoveries of biologically active RNA-targeting ligands, [10] we proposed to more broadly analyze the key guiding principles for specific RNA-targeting. In this work, we report the discovery of distinct physicochemical, structural, and spatial properties of RNA-targeted bioactive ligands, which are expected to facilitate the rapid discovery of RNA-targeted chemical probes and subsequent evaluation of the therapeutic potential of non-ribosomal RNAs.…”

Structure-Based Discovery of Small Molecules Binding to RNA

“…Some derivatives compete with aminoglycosides for binding to the bacterial rRNA A-site, others bind to the hepatitis C internal ribosomal entry site (IRES) and bis-benzimidazoles interact with CUG repeats that cause myotonic dystrophy type 1 [98]. Based on this knowledge a similarity search for small, druglike molecules containing the bis-benzimidazole or similar core structures was performed [99]. This resulted in a library of about 300 compounds with the potential to bind to RNA.…”

Biochemical and cell biological assays to identify and characterize DNA helicase inhibitors

“…Moreover, the WST-1 assay requires less time than alternative approaches such as measurement of DNA synthesis by BrdU incorporation. WST-1 assays are widely used to perform screens for compounds that have an effect on cell viability [18-20]. …”