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Published on: March 18, 2017
Fragment-Based Discovery of Potent RNA-Competitive Inhibitors of the DEAH-Box RNA Helicase DHX8
Benjamin J Read1, Caroline Ewens1, Federica Gigante1
1Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, LondonSM2 5GP, U.K.
Abstract:
Human DHX8 is a spliceosomal DEAH-box RNA helicase involved in releasing mRNA from the spliceosome and crucial in ensuring splicing fidelity. DHX8 was identified as a promising therapeutic oncology target due to its role in regulating stress-adaptive gene expression, including HSF1-dependent transcription, while having broader transcriptional effects in cells under oncogenic stress. We report the discovery of novel RNA-competitive DHX8 inhibitors based on a 2-(phenethylthio)nicotinic acid scaffold, which were optimized using a structure-guided design approach, following a biophysical fragment screen. This yielded compound 53 with nanomolar biochemical potency, good in vitro PK, and activity in a cellular target engagement assay. Optimizing inhibitor binding between Arg647 and the nonconserved His693, coupled with extending into a pocket in the DHX8 Winged-Helix domain, was crucial for potency improvement. By binding in the Winged-Helix domain, these inhibitors restrict the helicase domain's conformational plasticity, stabilizing a closed, inactive conformation while sterically blocking ssRNA translocation.
Insights
Researchers discovered new DHX8 inhibitors targeting cancer. These novel compounds show nanomolar potency and cellular activity, offering a promising therapeutic strategy for oncology by blocking RNA helicase function.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- Human DHX8 is a spliceosomal RNA helicase critical for mRNA release and splicing fidelity.
- DHX8 is a potential oncology target due to its role in stress-adaptive gene expression and oncogenic stress responses.
Purpose of the Study:
- To discover and optimize novel RNA-competitive inhibitors of DHX8.
- To elucidate the structure-activity relationships for DHX8 inhibition.
Main Methods:
- Structure-guided design based on biophysical fragment screening.
- Biochemical assays to determine inhibitor potency (nanomolar range).
- Cellular target engagement assays and in vitro pharmacokinetic studies.
Main Results:
- Identification of a novel 2-(phenethylthio)nicotinic acid scaffold for DHX8 inhibition.
- Compound 53 demonstrated nanomolar biochemical potency and cellular activity.
- Optimization involved targeting specific binding interactions within DHX8, including the Winged-Helix domain.
Conclusions:
- Novel DHX8 inhibitors were developed with potential as cancer therapeutics.
- Inhibitor binding to the Winged-Helix domain stabilizes an inactive conformation, blocking RNA translocation.
- These findings provide a foundation for further development of DHX8-targeted cancer therapies.
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