Introduction to the themed collection on ‘Targeting RNA with small molecules’

For a long time, RNA was considered a mere intermediate in the transmission and expression of genetic information, during which DNA is transcribed into RNA, which is then translated into proteins. It is only in recent years that the essential role of RNA has become apparent, not only in transcription and translation, but also in the regulation of gene expression, underlying the potential of this nucleic acid as a therapeutic tool and target. The role of RNA as a tool is largely demonstrated by current events. For example, new SARS-CoV-2 vaccines are in fact messenger RNAs (mRNAs) which, once administered, enable the production of a viral protein by cells in order to induce an immune response. Further, the 2020 Nobel Prize in Chemistry awarded to Emmanuelle Charpentier and Jennifer Doudna also highlights RNA as a tool, since in the CIRSPR-Cas9 system, RNA plays an essential role in the recognition of target DNA by the Cas9 protein. Furthermore, the role of RNA as a therapeutic target is underlined by the FDA approval in 2020 of a risdiplam, which modifies the alternative splicing of the mRNA encoding the SMN2 protein, thereby correcting a genetic error in the synthesis of this protein responsible for spinal muscular atrophy, a serious genetic disease. It should be noted that most drugs currently on the market target proteins, and these represent an extremely small proportion (0.05%) of the total products encoded by the human genome. Non-coding RNAs – i.e. RNAs that do not induce but regulate protein synthesis, represent 70% of the genome. If these were to become more widely exploited targets, this would considerably increase the field of application of medicinal chemistry, and enable the discovery of new treatments for pathologies that are currently incurable. The pandemic caused by SARS-CoV-2, an RNA virus itself, underlines the importance of the studies involving this nucleic acid. In parallel, non-coding RNAs from this coronavirus are being studied as potential targets for new antivirals.

RNA is one of the most promising biological targets for innovative drug discovery in a wide range of pathologies. A variety of RNAs of therapeutic interest have already been identified. Among the most important ones are prokaryotic ribosomal RNA, which is the target for antibiotics commonly used in the clinic, viral RNAs such as the TAR, RRE and DIS RNAs of HIV-110, or oncogenic microRNAs which are closely involved in the development and progression of various cancers. Most of these RNAs are non-coding sequences organized in stem-loop structures where single-stranded regions forming loops and bulges are associated with double-stranded stem regions. This secondary structure leads to particular three-dimensional conformations in which the RNA double helix is distorted, inducing the formation of binding pockets suitable for specific interactions with peptides (the natural intracellular partners of RNAs) as well as with small molecules. Based on these considerations, three approaches are currently proposed and utilized to target RNAs of therapeutic interest: (i) the use of antisense oligonucleotides, (ii) the development of peptides and their analogues, and (iii) the use of natural and synthetic small molecules capable of binding specifically to a particular RNA sequence/structure. The use of antisense oligonucleotides is a well-established approach that leads to highly efficient and specific biochemical tools. However, their therapeutic application remains limited due to major pharmacodynamic/pharmacokinetic and bioavailability liabilities. Peptides and their analogues have also been proposed as promising RNA ligands, but as for oligonucleotides, bioavailability issues still need to be resolved for their use. Finally, small molecules represent an extremely interesting approach in terms of therapeutic application, as they could overcome the limitations associated with the use of oligonucleotides and peptides. All these approaches are complementary, and the feasibility of the small molecule approach has already been amply demonstrated. Indeed, several classes of antibiotics are commonly used clinically due to their ability to bind selectively to prokaryotic ribosomal RNA and inhibit protein synthesis in bacteria. These antibiotics include aminoglycosides, tetracyclines, macrolides and oxazilidinones. A number of analogues of these antibiotics have subsequently been developed not only as antimicrobials, but also as potential inhibitors of viral infections by binding to RNAs essential for viral replication, or as potential anticancer agents by binding to oncogenic RNAs such as microRNA precursors.

More generally, the work published to date on RNA targeting by small molecules demonstrates that it is possible to identify highly specific ligands for an RNA target. The main problem with the small-molecule approach is that rational design of RNA ligands specific for an RNA target is still difficult and limited. The majority of RNA-targeting ligands reported in the literature have been identified after screening large collections of molecules. Despite doubts about the actual selectivity of small molecules targeting RNAs and the change of paradigm that is required to discover RNA binders with therapeutic potential, new modalities continue to be developed using chemical tools to induce RNA cleavage and/or degradation. Furthermore, the targeting of RNA–protein interactions is an important part of the field where more specific compounds containing diverse scaffolds are to be expected.

The articles in this themed collection give an overview of the different approaches that can be used to develop small molecule RNA binders as well as inhibitors of RNA–protein interactions. First, review articles highlight the recent progress in the modulation of RNA splicing, the development of new bioactive compounds inspired by RNA-binding antibiotics and how it is possible to target proteins that affect RNA functioning. Furthermore, new methodologies to discover RNA binders, such as live cell screening, structure-based virtual screening and NMR-based screening are presented as cutting-edge methodologies to identify original and active RNA ligands. Finally, the design of new inhibitors of RNA-based biological processes is presented as a complementary approach to screening. These works contribute to the general knowledge about how to modulate RNA functions by small molecules and highlight the variety of methodologies and RNA targets that it is possible to be explored for new medicinal chemistry applications and how this field, still in its infancy, holds the promise for future developments.

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