Synthetic oligonucleotides as DHX8 inhibitors: An oligomimetic approach
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Embargo End Date
2026-12-19
ICR Authors
Authors
Cosgrove, E
Document Type
Thesis or Dissertation
Date
2025-12-19
Date Accepted
Abstract
This thesis presents the development of selective inhibitors and tool compounds targeting DEAH-Box Helicase 8 (DHX8), guided by an X-ray crystal structure of poly(A)6 RNA bound within the protein’s RNA-binding tunnel.1 To achieve this, chemically modified oligonucleotides (ONs) were designed and screened according to an oligomimetic approach—a novel approach intended to transform RNA-derived scaffolds into drug-like compounds with enhanced therapeutic potential. Compared to conventional small-molecule approaches, the oligomimetic framework has the potential to expand binding site coverage, overcome potency plateaus, potentially minimise toxicity, and improve selectivity. The development of oligomimetic DHX8 inhibitors in this thesis serves as a proof of concept for extending this approach to other disease relevant RNA-binding proteins (RBPs), which are notoriously difficult to drug due to their shallow, polar, and diffuse binding interfaces.
This strategy is a marriage between recent advances in ON therapeutics and a traditional medicinal chemistry approach to early-stage drug discovery. It involved systematic testing of poly(A)6 analogues incorporating single-point changes to the nucleobases, phosphates and ribose rings, followed by the evaluation of combined modifications to determine synergistic effects. Substitutions were based on ON modifications known to enhance cell permeability, bioavailability and nuclease stability.
This led to the identification of a poly(A)4-based minimum pharmacophore and several modified poly(A)4 derivatives, or oligomimetics, exhibiting improvements in potency of up to more than 1,000-fold in a biochemical competitive binding assay. Of these, oligomimetics 47, 56 and 57 were selected for further testing and demonstrated inhibitor-like functional activity in an ATPase assay, selectivity against DHX15, and cellular activity in an MCL1S/L alternative splicing assay. X-ray crystal structures of 47 and 56 were obtained, revealing a new intermediate conformational state of DHX8.
Overall, an oligomimetic approach was successfully employed in the discovery of selective DHX8 inhibitors from an RNA starting point. Compounds were initially screened in competitive binding assays based on Fluorescence Polarisation (FP) and/or Homogenous Time-Resolved Fluorescence (HTRF) and subsequently validated by Surface Plasmon Resonance (SPR) and, in some cases, Ligand-Observed NMR (LO-NMR). Results and hypotheses were supported by X-ray crystallography and in silico studies.
Citation
2025
DOI
Source Title
Publisher
Institute of Cancer Research (University Of London)
ISSN
eISSN
Collections
Research Team
Medicinal Chemistry 4