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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 modications. The study of these modications, 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 modications on tRNAs from
model organisms (e.g. E. coli and yeast) [2, 3]. However, studies of the biological role
of modied nucleotides en masse awaited the genomic era and the discovery of genes
for associated RNA-modifying enzymes or “writers.” The biology of some RNA modications is also regulated by proteins known as “readers” and “erasers,” which bind
and remove modications, respectively. In recent years, the investigation of RNA
modication 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 modication sites across the transcriptome – but also
propelled by the demonstration that RNA modications can be dynamic [4–6] and
serve to regulate biological processes in response to endogenous and external cues
[7–10]. Further, while signicant gaps exist in our fundamental understanding of
RNA modication biology, numerous studies have identied connections between
RNA modications, RNA-modifying enzymes, and human disease [11–20], spurring
interest from the pharmaceutical and biotechnology industries.
Over 170 structurally distinct RNA modications have been identied in nature
[21] and occur in all classes of RNA and all kingdoms of life [22]. Modications range from simple changes such as methylation on the nucleobases or the
ribose 2
modications involving the addition of amino acids or other small-molecule
metabolites, which can require multiple biosynthetic enzymes. The function of
RNA modications is determined by their specic 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, modications can directly or indirectly impact functionally signicant
RNA–protein interactions [23–25]. These molecular mechanisms underlie the
eects of RNA modications on coding and non-coding RNA transcripts, which in
turn can aect RNA metabolism [26, 27], splicing [28], and tracking [24, 25, 29],
as well as protein translation [30–33] (Figure 12.1). RNA modication-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 specic RNA modications has been associated
with mitochondrial [39–42] and neurological disorders [43–47], while dysregulated RNA modication pathways (often resulting from perturbations in RNA
modication-associated proteins) can contribute to cancer pathogenesis.
In this chapter, we highlight some of the most well-studied RNA modications
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 modication
pathways. Our goal is not to provide a comprehensive treatment of RNA modications – 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 modication 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 deciency 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 deciency 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 deciency 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 deciency, 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
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