Small-molecule drugs as RNA-targeted degraders

Given the numerous crucial roles of RNA molecules in disease initiation and progression, RNAs have emerged as promising therapeutic targets for many diseases. Tong et al. report their discovery¹ of small-molecule bioactive degraders that selectively bind to disease-associated RNAs and recruit ribonuclease (RNase) enzymes to facilitate the degradation of RNAs. They have demonstrated the therapeutic potential of RNA degraders in the animal models of different cancers. The findings pave the way to target the development of novel RNA-targeted small-molecule drugs.

Despite considerable advances in drug discovery, there are only hundreds of proteins that have been targeted by approved drugs, compared to the estimated 20,000 human genes. To widen the scope of druggable targets, sustained research efforts have been devoted to modulating the challenging “undruggable” targets in novel ways. Targeting cellular RNA represents one such emerging strategy with the potential to expand the scope that can be drugged. There are multiple different classes of RNA molecules, contributing to various and essential biological functions. Messenger RNA (mRNA) and ribosomal RNA are involved in gene expression and protein synthesis. Noncoding RNAs are critical for the regulation of transcription and translation, such as long noncoding RNA, microRNA (miRNA), and antisense RNAs. Recent evidence has illustrated the important roles of RNA in various diseases, including neurodegenerative diseases, cancer, genetic disorders, and viral infections.²

A range of natural RNA-processing mechanisms have been leveraged to develop RNA-based therapeutics. They provide potential ways to specifically inhibit the expression of disease-related genes and prevent the translation of corresponding proteins. The most well-known RNA-based therapeutics include small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs).³ The siRNAs are double-stranded RNA molecules with 20–25 nucleotides. The ASOs are short synthetic single-stranded DNA or RNA. Both siRNAs and ASOs are gene silencers designed to target RNA molecules in a sequence-specific manner. However, one of the challenges that hindered their clinical application is their limited in vivo stability and cellular permeability due to their large molecular weight. Drug delivery systems are required to deliver the therapeutics intracellularly and systemically.⁴

Small molecules usually follow Lipinski's rule of five and face no such impediments. Compared to oligonucleotides, small-molecule drugs targeting RNAs have the advantage of nonimmunogenic and lower molecular weight. This makes them more effective in cell penetration and overcomes the delivery challenges of RNA-based therapeutics. Orally delivered small molecules also significantly increase patient comfort and compliance. Traditionally, small molecules have been primarily limited to targeting proteins. Selectively modulating RNA has been a considerable challenge.⁵ Evrysdi is a Food and Drug Administration-approved small-molecule drug that targets disease-causing RNA. Evrysdi represents a milestone for the treatment of neurodegenerative disease spinal muscular atrophy (SMA). SMA is caused by a deficiency in survival motor neuron (SMN) protein. Evrysdi works by modulating the pre-mRNA splicing of the compensatory gene SMN2 and increasing the protein expression of SMN2, which is usually expressed at a very low level.

Recently, Tong et al. reported a strategy to target oncogenic RNAs using bifunctional small molecules termed ribonuclease-targeting chimeras.¹ They employed a screening approach to identify RNA-binding small molecules. These natural-product-like small molecules are capable of binding to disease-associated RNAs with high affinity and selectivity. However, most of the binding sites on the RNAs were nonfunctional. Therefore, the RNA-binding small molecules would be unlikely to modulate the cellular levels or the activities of the RNA molecules. The challenge is how to convert these inactive RNA binders into bioactive small molecules. The researchers conjugated the RNA binder with a second RNase-recruiting molecule. The optimized molecule thus contains an RNA-binding module and an RNase recruitment module joined by a chemical linker (Figure 1A). The bifunctional small molecules are capable of recruiting the cellular enzyme RNase L, which induces the degradation of the target RNAs (Figure 1B). The designed RNA degraders are reminiscent of proteolysis targeting chimeras (PROTACs). The PROTACs are small molecules composed of a protein-binding module and a ubiquitin ligase recruitment module, which target proteins for proteasomal degradation (Figure 1C).

The researchers demonstrated the effectiveness of their strategy by targeting three important cancer-associated RNAs: miRNA-155, JUN, and MYC mRNAs.¹ The three genes are overexpressed and drive the growth of many different cancers. Directly targeting the proteins of JUN and MYC using small molecules is extremely challenging due to the intrinsically disordered protein structures. The bioactive RNA degraders effectively reduced the cellular levels of these targeted RNAs in a dose-dependent manner. In vitro studies validated that the RNA degraders reduced the proliferation and growth of multiple cancer cell lines. In vivo studies confirmed that they inhibited the colonization and invasion of cancer cells in mouse models. These results highlighted the potential therapeutic applications of bioactive RNA degraders in treating various cancers.

Moreover, some challenges need to be addressed in the future. One is the potential off-target effects of small molecules. Whether they bind other RNAs or protein targets should be carefully evaluated. Another is further optimizing the cellular uptake and bioavailability of the RNA-targeted degraders because of their high molecular weight compared to oral drugs. In addition, the precise mechanism that governs how small molecules bind to the folded RNA structures could be investigated. Understanding the intricate RNA folding and three-dimensional structures should guide the rational design of small molecules that modulate RNA function. Finally, the activity of RNA degraders is influenced by the endogenous expression level of RNase L, which varies among different cell lines. The RNA degraders might have no biological effect in cells with low RNase L expression.

In summary, Tong et al. successfully developed RNA-binding and RNase-recruiting bioactive degraders that can target oncogenic RNAs.¹ The ability to selectively degrade disease-associated RNAs using small molecules expands our strategies in the field of drug discovery. This research marks a significant step forward in developing novel therapeutics for traditionally undruggable targets.

Both authors have read and approved the final manuscript.

Jun Zou is an editorial staff of MedComm – Future Medicine. Jun Zou was not involved in the journal's review of, or decisions related to, this manuscript.

Not applicable.