Bromodomain Inhibitor Design For Epigenetic Cancer Therapies and Chemical Probes

Chemical Epigenetics

Bromodomain Inhibitor Design

Chemical Epigenetics
Dual PrOF NMR Screen

     How our genetic information is manipulated and ultimately expressed as a heritable phenotype is a central question in the field of epigenetics. N-terminal modifications on conserved histone proteins are key regulators of transcription. Proteins that interpret these complex modifications known as the “histone code” are known to be essential for maintaining cellular homeostasis, or when dysregulated, they become drivers of disease. Chemical probes for these proteins are in high demand for treating disease and understanding new biology.

     Bromodomains are epigenetic protein modules that bind to acetyl groups on proteins including those of acetylated histones in nucleosomes, helping to interpret or “read” the histone code. Since the first report of a nanomolar inhibitor of bromodomains BRD2, 3, 4 and T in 2010, over 20 clinical trials have been initiated to test the efficacy of bromodomain inhibition in cancer, inflammation, and heart disease.  More selective probes within this class have lagged behind due to the high similarity in binding sites. From the few available inhibitors, studies have shown these molecules to be more efficacious and they are thought to lead to less toxic side effects.  Guided by initial PrOF NMR efforts, our research group has made initial efforts in developing more selective inhibitors for these bromodomain-containing proteins.  Many other  bromodomains lack specific chemical probes to validate their role in both health and disease, which we are actively pursuing using a combination of genetic code expansion approaches, synthetic chemistry, biophysics, structural biology and cell biology.

     We have currently applied our PrOF NMR method to three bromodomains, BRDT, BPTF, and BRD4. As a new advance, we have started to study multiple bromodomains at once to develop selective inhibitors.  See The Resonance, and have developed an inhibitor for the N-terminal brodomains of BRDT and BRD4 over its C-terminal bromdomains.  These studies are enabled by a combination of biophysical experiments, structural biology (NMR and X-ray) and cell-based experiments.  We have also helped develop a high potency pan-inhibitor for the BET family of bromodomains, BRD2, 3, 4 and T. A strong medicinal chemistry effort in our lab has now been established for improving our leads for these bromodomains. 

     We also discovered and synthesized the first small molecule inhibitor, we named AU1, for the bromodomain of BPTF to understand its role in regulating transcription.  BPTF has been recognized as an oncoprotein in melanoma, colorectal, breast, bladder, and lung cancer.  By providing a new chemical probe, we plan to illuminate the functional role of the bromodomain in various cancers.  Active efforts in next generation BPTF inhibitor development are underway to improve upon AU1. 

     At the fundamental level, due to weak binding interactions of histones for BPTF we aim to further characterize the interactions of post-translation modifications of histone variant interactions with bromodomains through synthesis of isolated histone peptides and fully synthetic nucleosomes to help address the “Histone Code” hypothesis. Several other projects on bromodomains are in early stages of development. These projects are highly interdisciplinary and expose students to cell biology experiments to study the effects of the inhibitors we synthesize on gene regulation.

 For further reading see:

4.  “Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells.” W. D. Frey, A. Chaudhry, P. F. Slepicka, A. M. Ouellette, S. E. Kirberger, W. C. K. Pomerantz, G. J. Hannon, and C. O. dos Santos*, Stem Cell Reports 2017, 9, 1-9.

 3.  “BET bromodomain inhibitors with one-step synthesis discovered from virtual screen.” A. Ayoub, L. M. L. Hawk, R. J. Herzig, J. Jiang, A. J. Wisniewski, C. T. Gee, P. Zhao, J. Zhu, N. Berndt, N. K. Offei-Addo, T. G. Scott, J. Qi, J. E. Bradner, T. R. Ward, E. Schönbrunn, G. I. Georg*, W. C. K. Pomerantz*, J. Med. Chem. 2017, 60, 4805-17.

 2.  Dual screening of BPTF and Brd4 using protein-observed fluorine NMR uncovers new bromodomain probe molecules. Andrew K. Urick, Laura M. L. Hawk, Melissa K. Cassel, Neeraj K. Mishra, Shuai Liu, Neeta Adhikari, Wei Zhang, Camila O. dos Santos, Jennifer L. Hall, and William C. K. Pomerantz* ACS. Chem. Biol. 2015, 10, 2246-56

1. “Fluorinated aromatic amino acids are sensitive probes for bromodomain ligand interactions”, N. K. Mishra, A. K. Urick, S. W. Ember, E. Schonbrunn, W. C. Pomerantz* ACS. Chem. Biol. 2014 9, 2755-60.