During the first days of fall, the Boston weather initially cooperated but quickly grew colder over the course of a packed 3 days at the Westin Waterfront hotel for the Targeting Epigenetic Readers track of the Discovery On Target 2013 conferences. This year a record number of attendees from basic science, clinical research, and industry presented their latest work in the rapidly expanding field of epigenetics. This year the field of epigenetic readers, driven by the exciting discovery of chemical inhibitors of BET bromodomain proteins, showed that it is treading the same ground once walked by HDACs.
Targeting Bromodomains in NUT Midline Carcinoma
Christopher French, Brigham and Women’s Hospital/Harvard Medical School
While inhibitors of BET bromodomains have achieved significant pre-clinical results in a variety of cancer types, Dr French demonstrated that NUT Midline Carcinoma represents perhaps the best target for these inhibitors. NMC is a rare cancer characterized by alterations in the NUT gene – the most common being fusions with Brd4 and Brd3, BET bromodomain proteins.
Dr French’s research showed that these fusions drive NMC by blocking differentiation of squamous cells, and suggested two possible mechanisms of action. The first by aberrant NUT recruitment of p300 to Brd4 chromatin sites, leading to decreased global histone acetylation due to this sequestration of p300. Notably, Dr French was able to reverse this in vitro with HDAC inhibitors, and even saw indications of a clinical response using HDAC inhibitors. The second proposed mechanism involves hyper-activation of Myc signaling driven by Brd4 recruitment to so-called “super-enhancers” of the MYC oncogene, which was shown by genetic knockdown of Myc and Brd4-NUT to be both necessary and sufficient for NMC cells to escape from differentiation.
These models suggest both that BET bromodomain inhibitors represent an excellent target for therapy in NMC, but that furthermore combination with HDAC inhibitors may potentiate therapeutic effects. Accordingly, clinical trials of BET bromodomain inhibitors in patients with NMC have already begun, and the results are eagerly anticipated.
Promoting Illiteracy: Inhibition of Methyl-Lysine Readers by Small Molecule Chemical Probes
Lindsey Ingerman James, UNC
One of the biggest steps forward for the field of epigenetic readers as a whole, was the development of the first potent, specific, inhibitor of a methyl-histone reader. Since the landmark publication of JQ-1, BET bromodomain inhibitors have proliferated and understandably focused the limelight on readers of acetyl-histone marks. However there are over 200 different proteins that recognize specific histone methylation marks, representing a vast untapped potential.
Dr James described her strategy for identifying and developing the first potent, specific inhibitor of a reader of mono and di-methylated histone H4K20. Rather than focusing on developing inhibitors for a specific reader, Dr James explained a strategy of screening compounds against a panel of all nine members of the MBT family of methyl-histone readers. This enabled for a faster iterative process, as derivatized compounds now had nine possible targets instead of just one.
Using this technique, the lab rapidly identified both a compound and a target, UNC1215 which bound potently to L3MBTL3 with over 50-fold specificity compared to other members of the MBT family. Dr James was able to show this compound specifically displaces this protein from chromatin and forms a 2:2 dimer, with two L3MBTL3 proteins binding two molecules of UNC1215. Future work focuses on improving the specificity of the compound and on using the compound as a probe to identify other potential readers of methyl-H4K20 in cells.
Inhibition of BET Proteins by Tandem Bromodomains with Coferons
Lee Arnold, Coferon Inc
A key feature of the conference was the high visibility of members of industry presenting their latest innovations, and one of the most fascinating presentations was by Dr Arnold of Coferon. There are several common problems that developers of small-molecule inhibitors have to deal with. First, a compound has to be developed that potently inhibits its target. Second, this compound needs to be specific for its target. Finally, this compound has certain physical limitations – size and electrostatic charge need to be minimized in order for the compound to easily be applied to a living organism and taken into cells.If fully realized, the technology being developed at Coferon promises to address all of these issues at once, and could potentially revolutionize how small molecule inhibitors are developed.
Effectively the Coferon technology works by doubling the practical size of small molecule inhibitors, using reversible covalent linkers. These linkers are engineered to dissociate at physiological conditions, creating two small molecules which individually bind weakly to their target. However once one molecule is bound, the affinity of the second molecule for the target is synergistically increased due to the added affinity of the linker between the two molecules. Through this clever engineering technology, Coferon has been able to circumvent size limitations for small molecule inhibitors, and consequently gain the increased potency and specificity of a larger inhibitor. Coferon has now set their sights on using this technology to develop next-generation BET bromodomain inhibitors.
Current inhibitors have little specificity between the Brd2/3/4 isoforms. Moreover, each protein contains two acetyl-lysine binding domains, each of which are targeted by current inhibitors. Coferon aims to leverage their unique technology to develop inhibitors that are not only isoform-specific, but also specific for individual binding domains, in order to dissect the mechanisms by which these proteins function.
**EpiGenie would like to thank Ryan Kuzmickas, who is a student in the Cichowski lab at Brigham and Women’s Hospital, for this conference coverage***