Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity

Abstract

The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure–activity relationships across genomic RNA. Binding compounds can be identified and optimized into structure-specific ligands by using sequence-based design with various modes of action, for example, inhibiting translation or directing pre-mRNA splicing outcomes. In addition, strategies to direct protein activity against an RNA of interest via chemically induced proximity is a burgeoning area that has been validated both in cells and in preclinical animal models, and we describe that it may allow rapid access to new avenues to affect RNA biology. These approaches and the unique modes of action suggest that more RNAs are potentially amenable to targeting than proteins.

Introduction

Although ∼80% of the human genome is transcribed into RNA, only 1% is translated into protein [1], suggesting that there are more opportunities to affect biology at the transcriptional level (Fig. 1). Furthermore, RNA has diverse functions tied to its structure [2], including regulating pre-mRNA splicing outcomes [3], cellular localization [4], phase separation [5], and microRNA (miRNA) biogenesis [6,7]. Indeed, RNA-targeting oligonucleotide-based modalities have garnered Food and Drug Administration (FDA) approval, including those that target RNAs associated with central nervous system disorders such as spinal muscular atrophy (SMA) [8] and liver disease [9]. Although these medicines have transformed patients' lives, their transcriptome-wide implementation has been limited to tissues readily amenable to oligonucleotide targeting, that is, direct delivery to the central nervous system, liver, or kidney.

Highly structured regions in RNA are often functional [10], and the three-dimensional shapes they adopt could provide small-molecule binding pockets [11], occupied by compounds with complementarity of size, shape, stacking, and charge. Although there are challenges associated with small-molecule targeting of RNA, small molecules can be penetrant to a variety of tissues, and often, lead compounds can be medicinally optimized to enhance target engagement [12] and minimize suboptimal features [13]. Herein, we discuss lead drug and chemical probe discovery against RNA targets on a genome-wide scale to elicit effects on the proteome (Table 1): downregulation of ‘undruggable’ proteins by targeting RNA structures in untranslated regions, upregulation of proteins by targeting miRNAs that repress their expression, and altering the ratio of protein isoforms by influencing pre-mRNA splicing outcomes. Collectively, targeting RNA structures with small molecules can indeed be an effective way to study and control biology.