Discovery of a Highly Selective Cell‐Active Inhibitor of the Histone Lysine Demethylases KDM2/7

Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell‐permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure–activity relationships, leading to the development of a small molecule with around 75‐fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.     

Control of gene expression with small molecules: biotin-mediated acylation of targeted lysine residues in recombinant yeast

Chemical inducers of dimerization (CIDs) are powerful tools for controlling diverse cellular processes. These small molecules typically form strong noncovalent interactions with proteins. We report a related approach involving covalent acylation of a specific lysine residue of a target protein by the small molecule biotin. To control protein-protein interactions with biotin, the biotin protein ligase BirA from E. coli was coexpressed in yeast with a streptavidin-LexA fusion protein and Avitag or BCCP biotin acceptor peptides fused to the B42 activation domain. The addition of biotin (10 nM) resulted in BirA-mediated biotinylation of the biotin acceptor protein, recruitment to LexA DNA sites, and maximal activation of reporter gene expression in this yeast tribrid system. The high potency, low toxicity, and low molecular weight of biotin as a covalent CID are attractive properties for controlling cellular processes.     

Forward chemical genetics: library scaffold design

With the unraveling of the entire human genome, it has become imperative to understand the function of the gene products, proteins. Within the past several years, chemical genetics has gained recognition as a powerful approach to study protein function by using small molecules as gene knock-out or knock-in mimics. Forward chemical genetics is a three-step process; the design and synthesis of a small molecule library represents the first step followed secondly by the search for novel phenotypes and then by isolation and identification of target protein(s). This review will focus on the first step, the design of the scaffold for small molecule libraries. It will also examine the connection between the choice of a scaffold and the propensity of that library to demonstrate enhanced biological activity when tested in certain cellular systems.