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Nature evolves molecular interaction networks through persistent perturbation and selection, in stark contrast to drug discovery, which evaluates candidates one at a time by screening. Here, nature's highly parallel ligand-target search paradigm is recapitulated in a screen of a DNA-encoded library (DEL; 73,728 ligands) against a library of RNA structures (4,096 targets). In total, the screen evaluated ∼300 million interactions and identified numerous bona fide ligand-RNA three-dimensional fold target pairs. One of the discovered ligands bound a 5'GAG/3'CCC internal loop that is present in primary microRNA-27a (pri-miR-27a), the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand was cell active, potently and selectively inhibiting pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells. By exploiting evolutionary principles at the earliest stages of drug discovery, it is possible to identify high-affinity and selective target-ligand interactions and predict engagements in cells that short circuit disease pathways in preclinical disease models.

RNA plays important roles in regulating both health and disease biology in all kingdoms of life. Notably, RNA can form intricate three‐dimensional structures, and their biological functions are dependent on these structures. Targeting the structured regions of RNA with small molecules has gained increasing attention over the past decade, because it provides both chemical probes to study fundamental biology processes and lead medicines for diseases with unmet medical needs. Recent advances in RNA structure prediction and determination and RNA biology have accelerated the rational design and development of RNA‐targeted small molecules to modulate disease pathology. However, challenges remain in advancing RNA‐targeted small molecules towards clinical applications. This review summarizes strategies to study RNA structures, to identify small molecules recognizing these structures, and to augment the functionality of RNA‐binding small molecules. We focus on recent advances in developing RNA‐targeted small molecules as potential therapeutics in a variety of diseases, encompassing different modes of actions and targeting strategies. Furthermore, we present the current gaps between early‐stage discovery of RNA‐binding small molecules and their clinical applications, as well as a roadmap to overcome these challenges in the near future. [ABSTRACT FROM AUTHOR]

α-Synuclein is an important drug target for the treatment of Parkinson’s disease (PD), but it is an intrinsically disordered protein lacking typical small-molecule binding pockets. In contrast, the encoding SNCA mRNA has regions of ordered structure in its 5′ untranslated region (UTR). Here, we present an integrated approach to identify small molecules that bind this structured region and inhibit α-synuclein translation. A drug-like, RNA-focused compound collection was studied for binding to the 5′ UTR of SNCA mRNA, affording Synucleozid-2.0, a drug-like small molecule that decreases α-synuclein levels by inhibiting ribosomes from assembling onto SNCA mRNA. This RNA-binding small molecule was converted into a ribonuclease-targeting chimera (RiboTAC) to degrade cellular SNCA mRNA. RNA-seq and proteomics studies demonstrated that the RiboTAC (Syn-RiboTAC) selectively degraded SNCA mRNA to reduce its protein levels, affording a fivefold enhancement of cytoprotective effects as compared to Synucleozid-2.0. As observed in many diseases, transcriptome-wide changes in RNA expression are observed in PD. Syn-RiboTAC also rescued the expression of ~50% of genes that were abnormally expressed in dopaminergic neurons differentiated from PD patient–derived iPSCs. These studies demonstrate that the druggability of the proteome can be expanded greatly by targeting the encoding mRNAs with both small molecule binders and RiboTAC degraders. [ABSTRACT FROM AUTHOR]

The functional roles of structured RNAs in the regulation of biological processes, and hence RNA's potential as an effective therapeutic target, have only recently been appreciated. Robust and high‐throughput methods that identify potent RNA ligands are critical to the development of chemical probes and therapeutics. DNA‐encoded libraries (DEL) technology has emerged as a powerful tool for protein ligand discovery, and its ability to generate large, custom‐tailored, and novel chemical space offers unprecedented opportunities to discover the rules of RNA ligand design. In this review, we discuss the basic principles of DEL selection, current progress on the application of DEL to RNA targets, and the outlook of targeting RNA by DEL. [ABSTRACT FROM AUTHOR]

In 1990, a woman was wrongly convicted of poisoning her infant son and was sentenced to life in prison. Her conviction was based on laboratory work that wrongly identified ethylene glycol as present in her son's blood and in the formula he drank prior to his death. The actual cause of the infant's death, a metabolic disease, was eventually disclosed as a result of analytical work done by scientists who believed the mother was wrongly convicted. On the basis of the scientists' work, the conviction was overturned. This real-life case serves as the launching point for a biochemistry laboratory experiment, which uses polymerase chain reaction. Students design their own primers, amplify two biological samples, and analyze the results by gel electrophoresis to determine if their patient has a genetic mutation. This genetic mutation causes the metabolic disease, which if present can be used to "solve" the case. (Contains 1 table and 1 figure.)

Removing disease-causing expansion: Expansion in G4C2 RNA repeat in chromosome 9 open reading frame 72 (C9orf72) is one of the most common genetic causes of amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). To develop better therapeutics, Bush et al. developed and characterized a small molecule with dual function, able to bind the G4C2 expansion and to recruit an endonuclease to remove the expansion from the native RNA. The small molecule rescued typical cellular hallmarks of ALS/FTD in vitro in several patient-derived models and ameliorated ALS/FTD pathology in a mouse model. Removing pathological GC expansion using this dual-function small molecule could be an effective approach for treating C9orf72-mediated ALS/FTD. The most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD) is an expanded G4C2 RNA repeat [r(G4C2)exp] in chromosome 9 open reading frame 72 (C9orf72), which elicits pathology through several mechanisms. Here, we developed and characterized a small molecule for targeted degradation of r(G4C2)exp. The compound was able to selectively bind r(G4C2)exp's structure and to assemble an endogenous nuclease onto the target, provoking removal of the transcript by native RNA quality control mechanisms. In c9ALS patient–derived spinal neurons, the compound selectively degraded the mutant C9orf72 allele with limited off-targets and reduced quantities of toxic dipeptide repeat proteins (DPRs) translated from r(G4C2)exp. In vivo work in a rodent model showed that abundance of both the mutant allele harboring the repeat expansion and DPRs were selectively reduced by this compound. These results demonstrate that targeted small-molecule degradation of r(G4C2)exp is a strategy for mitigating c9ALS/FTD-associated pathologies and studying disease-associated pathways in preclinical models. [ABSTRACT FROM AUTHOR]