Chemical probes and drugs often bind to functional domains on disease-relevant proteins, but it can be difficult to understand their true 'on'- and 'off'-target effects when the target shares homologous domains with other proteins [1]. This is especially true of epigenetic protein families that mediate transcriptional signaling through the catalytic or scaffolding function of their structural domains, many of which are difficult to target selectively with small molecules because of their conserved binding sites [2]. My lab has developed chemical genetics approaches (Figure) to achieve single-target selectivity of chemical probes for the bromodomains of BET proteins Brd2, Brd3 and Brd4, a class of epigenetic readers of lysine acetylation and attractive cancer targets. First I will describe our ‘bump-and-hole’ approach to develop ET, an allele-specific derivative of the otherwise pan-selective BET bromodomain inhibitors JQ1 / I-BET762 [3]. ET achieves up to 540-fold selectivity for a BET bromodomain Leu/Ala mutation over wild-type. Application of the selective ET:L/A pair revealed that blockade of the first bromodomain of Brd4 is sufficient to displace the protein from chromatin [3]. I will next describe how we could achieve for the first time selective intracellular targeting of Brd4 over the homologous family members Brd2 and Brd3 via targeted protein degradation, by conjugating JQ1 to a potent and specific ligand that we had previously developed for the VHL E3 ubiquitin ligase [4]. Our proteolysis-targeting chimeric (PROTAC) molecule MZ1 achieves rapid and long-lasting preferential removal of Brd4 over Brd2 and Brd3, and induces a more profound anti-proliferative effect than BET inhibition in AML cancer cells [5]. References 1) Bunnage, M.E. et al. Nat. Chem. Biol. 11, 368–372 (2015) 2) Runcie, A.C. et al. Curr. Opin. Chem. Biol. 33, 186–194 (2016); Ciulli, A. Nat. Chem. Biol. 12(9), 659–660 (2016) 3) Baud, M.G.J. et al. Science 346, 638–641 (2014); Baud, M.G.J. et al. J. Med. Chem., 59, 1492–1500 (2016) 4) Galdeano, C. et al. J. Med. Chem. 57, 8657–8663 (2014); Frost, J. et al. Nat. Commun. 7, 13312 (2016) 5) Zengerle, M., Chan, K.-H. & Ciulli, A. ACS Chem. Biol. 10, 1770–1777 (2015)

Advanced chemical genetics for epigenetics: Bump-and-hole and PROTACs

253rd National Meeting (2017)

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