Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion

Abstract

A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r(CUG)exp, the causative agent of the most common form of adult-onset muscular dystrophy, myotonic dystrophy type 1 (DM1). A variety of uncharged and novel RNA binders were identified to selectively bind r(CUG)exp by using a two-color flow cytometry screen. The cellular activity of one binder was augmented by attaching it with a module that directly cleaves r(CUG)exp. In DM1 patient-derived muscle cells, the compound specifically bound r(CUG)exp and allele-specifically eliminated r(CUG)exp, improving disease-associated defects. The approaches herein can be used to identify and optimize ligands and bind RNA that can be further augmented for functionality including degradation.

Enolate–Azide [3 + 2]-Cycloaddition Reaction Suitable for DNA-Encoded Library Synthesis

“…Generally, DEL is synthesized by using the strategy of “split and pool.” The selected building blocks (BBs) and the corresponding encoding DNA tags are assembled via 3–4 rounds of interactive DNA-compatible chemical reactions and enzymatic ligation, and finally all of the DNA-conjugated chemicals are pooled together to efficiently generate the corresponding DEL. Currently, a series of hits targeting various types of drug targets such as kinase, enzymes, − chemokines, challenging protein and protein interactions (PPIs), − and RNA − have been selected from DELs. In addition, beyond the conventional hit selection campaign in drug discovery, DEL has emergingly served as a versatile fundamental technique that efficiently bridges biology and chemistry. − …”

Evaluation of the Topology Space of DNA-Encoded Libraries

“…Generally, the structures of DELs are defined on three levels: the library topology that describes the connectivity of the diversity elements (DEs), the reactions used to assemble them as well as the resulting linking fragments, and the choice of the building blocks (BBs) used at each DE (Figure ). Reports have shown the critical importance building block selection has on hit discovery especially in the case of focused libraries. − The exploration of on-DNA reactions for DEL synthesis is similarly important and is an active research area . Interestingly, however, the role of DEL topology remains unexplored.…”

Contemporary Progress and Opportunities in RNA-Targeted Drug Discovery

“…These discoveries have been made, in large part, due to technological advances in screening and chemical biology, aided by major advances in next-generation sequencing capabilities. Indeed, enabling technologies previously employed solely in the world of proteins, including mass spectrometry-based screening, small molecule microarrays, photoaffinity probes, ,,, and DNA-encoded libraries, ,, have now been unleashed for studying RNA–small molecule interactions. Representative examples of identified ligands and their discovery method are shown in Figure .…”