Advanced Chemical Genetics for Epigenetics: Bump-and-hole and PROTACs

Alessio Ciulli

Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, DD1 5EH, Dundee, UK

Chemical genetics is the use of small molecules (chemical probes) to investigate the functions of gene products, through the modulation of protein activity. The difficulty in generating single-target selectivity has long been a thorn in the side of chemical genetics, and potentially limits its scope to study epigenetics. However recent developments in advanced forms of chemical genetics promise to bypass this, and other, limitations [1].
In my talk, I will first describe our development of a ‘bump-and-hole’ strategy with which we have engineered an allele-specific derivative (ET) of BET bromodomain inhibitor JQ1 that achieves up to 540-fold selectivity for a BET bromodomain Leu/Ala mutation [2]. Using this approach, we have showed that blockade of the first bromodomain of the BET protein Brd4 is sufficient to displace the protein from chromatin [2]. I will then describe how we could achieve for the first time selective intracellular targeting of Brd4 over the homologous BET family members Brd2 and Brd3 by conjugating the pan-selective ligand JQ1 to a potent and specific ligand that we had previously developed against the VHL E3 ubiquitin ligase [3]. 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 cancer cells [4].
The bump-and-hole approach now demonstrated successfully with BET bromodomains, may be applicable to other epigenetic domains and has potential to enhance target validation of epigenetic cancer targets in future. Meanwhile targeted protein degradation by PROTACs has been shown to be significantly more efficacious than standard domain inhibition, and has the potential to enhance on-target selectivity, with attractive untapped therapeutic potential.