Development of novel cellular histone-binding and chromatin-displacement assays for bromodomain drug discovery

Epigenetics & Chromatin

Jannik N. Andersen²  Mary K. Geck Do¹  Wylie S. Palmer¹  Philip Jones¹  Michelle Barton³  Jessica Tyler³  Giulio Draetta¹  Carlo Toniatti¹  Joseph R. Marszalek¹  Timothy P. Heffernan¹  Shiming Jiang³  Trang N. Tieu¹  Shuping Zhao¹  Bhavatarini Vangamudi¹  Srikanth Appikonda³  Hannah E. Shepard¹  Jennifer P. Bardenhagen¹  Elisabetta Leo¹  Xi Shi¹  Maria Kost-Alimova¹  Yanai Zhan¹ 

[1] Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston 77230, TX, USA;XTuit Pharmaceuticals, 700 Main Street, Cambridge 02139, MA, USA;Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston 77230, TX, USA

关键词: IACS-6558;    IACS-9571;    Bromodomain inhibitor;    TRIM24;    In situ cell extraction;    AlphaScreen;    AlphaLISA;    Chromatin drug-target displacement;    Bromodomain–histone-binding assays;   

Others  :  1227238
DOI  :  10.1186/s13072-015-0026-4

 received in 2015-06-29, accepted in 2015-09-01,  发布年份 2015

【 摘 要 】

Background

Proteins that ‘read’ the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably, the first BET bromodomain-based therapies have entered clinical trials and there is a broad interest in dissecting the therapeutic relevance of other bromodomain-containing proteins in human disease. Typically, drug development is facilitated and expedited by high-throughput screening, where assays need to be sensitive, robust, cost-effective and scalable. However, for bromodomains, which lack catalytic activity that otherwise can be monitored (using classical enzymology), the development of cell-based, drug-target engagement assays has been challenging. Consequently, cell biochemical assays have lagged behind compared to other protein families (e.g., histone deacetylases and methyltransferases).

Results

Here, we present a suite of novel chromatin and histone-binding assays using AlphaLISA, in situ cell extraction and fluorescence-based, high-content imaging. First, using TRIM24 as an example, the homogenous, bead-based AlphaScreen technology was modified from a biochemical peptide-competition assay to measure binding of the TRIM24 bromodomain to endogenous histone H3 in cells (AlphaLISA). Second, a target agnostic, high-throughput imaging platform was developed to quantify the ability of chemical probes to dissociate endogenous proteins from chromatin/nuclear structures. While overall nuclear morphology is maintained, the procedure extracts soluble, non-chromatin-bound proteins from cells with drug-target displacement visualized by immunofluorescence (IF) or microscopy of fluorescent proteins. Pharmacological evaluation of these assays cross-validated their utility, sensitivity and robustness. Finally, using genetic and pharmacological approaches, we dissect domain contribution of TRIM24, BRD4, ATAD2 and SMARCA2 to chromatin binding illustrating the versatility/utility of the in situ cell extraction platform.

Conclusions

In summary, we have developed two novel complementary and cell-based drug-target engagement assays, expanding the repertoire of pharmacodynamic assays for bromodomain tool compound development. These assays have been validated through a successful TRIM24 bromodomain inhibitor program, where a micromolar lead molecule (IACS-6558) was optimized using cell-based assays to yield the first single-digit nanomolar TRIM24 inhibitor (IACS-9571). Altogether, the assay platforms described herein are poised to accelerate the discovery and development of novel chemical probes to deliver on the promise of epigenetic-based therapies.

【 授权许可】

   
2015 Zhan et al.

【 图 表 】

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