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Drugging the Epitranscriptome
Tanner W. Eggert and Ralph E. Kleiner
Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Washington Road, Princeton, NJ 08544, USA
12.1 Introduction
The properties of cellular RNA are modulated by a diverse array of post­transcriptional modications. The study of these modications, collectively known as the RNA epitranscriptome, dates back to the discovery of pseudouridine in 1951 [1], and work in subsequent decades has led to the characterization of the chemical structure of numerous abundant RNA modications on tRNAs from model organisms (e.g. E. coli and yeast) [2, 3]. However, studies of the biological role of modied nucleotides en masse awaited the genomic era and the discovery of genes for associated RNA-modifying enzymes or “writers.” The biology of some RNA mod­ications is also regulated by proteins known as “readers” and “erasers,” which bind and remove modications, respectively. In recent years, the investigation of RNA modication chemistry and biology has enjoyed a renaissance – in large part driven by technological advances in liquid chromatography-mass spectrometry (LC-MS) and high-throughput RNA sequencing that have alleviated some of the analytical challenges in characterizing modication sites across the transcriptome – but also propelled by the demonstration that RNA modications can be dynamic [4–6] and serve to regulate biological processes in response to endogenous and external cues [7–10]. Further, while signicant gaps exist in our fundamental understanding of RNA modication biology, numerous studies have identied connections between RNA modications, RNA-modifying enzymes, and human disease [11–20], spurring interest from the pharmaceutical and biotechnology industries.
Over 170 structurally distinct RNA modications have been identied in nature [21] and occur in all classes of RNA and all kingdoms of life [22]. Modica­tions range from simple changes such as methylation on the nucleobases or the ribose 2 modications involving the addition of amino acids or other small-molecule metabolites, which can require multiple biosynthetic enzymes. The function of RNA modications is determined by their specic chemical structure and molec­ular context, but generally, they can impact RNA structure through modulation of
′
-OH, isomerization, deamination, or hydrogenation, to more complex
321
RNA as a Drug Target: The Next Frontier for Medicinal Chemistry, First Edition. Edited by John Schneekloth and Martin Pettersson. © 2024 WILEY-VCH GmbH. Published 2024 by WILEY-VCH GmbH.
322 12 Drugging the Epitranscriptome
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Figure 12.1 Roles of mRNA modifications.
hydrogen bonding (i.e. base pairing), base stacking, and nucleotide conformation. In addition, modications can directly or indirectly impact functionally signicant RNA–protein interactions [23–25]. These molecular mechanisms underlie the eects of RNA modications on coding and non-coding RNA transcripts, which in turn can aect RNA metabolism [26, 27], splicing [28], and tracking [24, 25, 29], as well as protein translation [30–33] (Figure 12.1). RNA modication-dependent perturbations in gene expression programs have been shown to impact embryonic development [34–36], learning and memory [37], and immune system func­tion [16, 38]. The absence of specic RNA modications has been associated with mitochondrial [39–42] and neurological disorders [43–47], while dysregu­lated RNA modication pathways (often resulting from perturbations in RNA modication-associated proteins) can contribute to cancer pathogenesis.
In this chapter, we highlight some of the most well-studied RNA modications on mRNA, tRNA, and rRNA (Figure 12.2), discuss their roles in disease, and touch upon the therapeutic approaches in motion to target and exploit RNA modication pathways. Our goal is not to provide a comprehensive treatment of RNA modica­tions – many excellent reviews have emerged on this topic in recent years [11–18, 20, 43, 48–59]. We seek to provide a brief account of the state of inhibitor development and therapeutic use cases for modifying enzymes, identify areas for further study, and speculate on the future of pharmaceutical development in the eld of epitran­scriptomics. Several biotechnology companies have been established in the last 5+ years to develop drugs to target RNA modication writers. Others are developing strategies to repurpose endogenous RNA-modifying enzymes or tRNAs to facilitate transcript recoding (Table 12.1). If successful, these approaches will represent new modalities for disease treatment.
(b)
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(a)
(c)
Figure 12.2 Human RNA modifications on tRNA, rRNA, and mRNA. (a) Human tRNA modifications and the positions where they occur. (b) Select rRNA modification structures. (c) Select mRNA modification structures.
Table 12.1 Companies targeting or exploiting RNA modifications.
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Company Est. Disease Area(s) Target(s) Approach Status
Accent Tx 2017 Oncology (CRC, endometrial, gastric)
ADARx Pharmaceuticals 2019 alpha-1 antitrypsin deciency ADAR1 Oligo-based ADAR recruitment N/A A2I Tx/AtomWise 2020 Immuno-oncology (NSCLC, TNBC) ADAR1 Small molecule N/A Covant Tx/Boehringer
Ingelheim Edigene 2015 Usher syndrome type 2, Hurler syndrome ADAR1 Oligo-based ADAR recruitment Discovery EPICS Tx 2018 Oncology (AML, solid tumors) METTL3 Small molecule Pre-clinical Gotham Tx (858 Tx) 2017 Oncology METTL3 Small molecule N/A Gossamer Bio 2015 Immuno-oncology ADAR1 Small molecule Discovery Korro Bio/Genevant 2018 alpha-1 antitrypsin deciency ADAR1 Oligo-based ADAR recruitment Discovery ProQR/Eli lilly 2012 Cholestatic disorders, cardiovascular,
Shape Tx 2018 Parkinson’s, Alzheimer’s, alpha-1
STORM Tx/Exelixis 2015 Oncology (solid tumors)
Wave Life Sciences 2012 alpha-1 antitrypsin deciency ADAR1 Oligo-based ADAR recruitment Pre-clinical 858 Tx 2019 Oncology (solid tumors) ADAR1 Small molecule Pre-clinical
Oncology (AML) Oncology (HNSCC, NSCLC, PD-(L)1)
2017 Immuno-oncology ADAR1 Small molecule N/A
metabolic, neurodegenerative
antitrypsin deciency, Rett syndrome
Oncology (solid tumors)
DHX9 METTL3 ADAR1
ADAR1 Oligo-based ADAR recruitment Pre-clinical
ADAR1 mRNA Premature stop codons Gene replacement
METTL3
ADAR1
Small molecule Small molecule Small molecule
Oligo-based ADAR recruitment
Engineered suppressor tRNAs
Tailored gene expression
Small molecule
Small molecule
Pre-clinical Pre-clinical Pre-clinical
N/A
N/A
N/A Phase 1
N/A