We present the crystal structure of the catalytic SET domain of G9a-like protein (GLP) in complex with BIX-01294. The inhibitor is bound in the substrate peptide groove at the location where the histone H3 residues (Lys4 to Arg8) N-terminal to the target lysine would occupy. The inhibitor is positioned in place by residues specific for G9a and GLP using planar stacking contacts, polar hydrogen bonds and van der Waals interactions.

Worker and queen bees are genetically indistinguishable. However, queen bees are fertile, larger and have a longer lifespan than their female worker counterparts. Differential feeding of larvae with royal jelly controls this caste switching. There is emerging evidence that the queen-bee phenotype is driven by epigenetic mechanisms. In this study, we show that royal jelly-the secretion produced by the hypopharyngeal and mandibular glands of worker bees-has histone deacetylase inhibitor (HDACi) activity. A fatty acid, (E)-10-hydroxy-2-decenoic acid (10HDA), which accounts for up to 5% of royal jelly, harbours this HDACi activity. Furthermore, 10HDA can reactivate the expression of epigenetically silenced genes in mammalian cells. Thus, the epigenetic regulation of queen-bee development is probably driven, in part, by HDACi activity in royal jelly.

Lysine and arginine methyltransferases participate in the post-translational modification of histones and regulate key cellular functions. So far only one arginine methyltransferase inhibitor discovered by random screening was available. We present the first target-based approach to protein arginine methyltransferase (PRMT) inhibitors. Homology models of human and Aspergillus nidulans PRMT1 were generated from available X-ray structures of rat PRMTs. The NCI diversity set was filtered by a target-based virtual screening to identify PRMT inhibitors. Employing a fungal PRMT for screening and a human enzyme for validation, we have identified seven inhibitors of PRMTs in vitro. Hit validation was achieved for two new inhibitors by antibody mediated detection of histone hypomethylation as well as Western blotting in cancer cells. Functional activity was proven by an observed block of estrogen receptor activation. Thus, valuable chemical tools and potential drug candidates could be identified.

Dynamic histone lysine methylation involves the activities of modifying enzymes (writers), enzymes removing modifications (erasers) and readers of the histone code. One common feature of these activities is the recognition of lysines in methylated and unmethylated states, whether they are substrates, reaction products or binding partners. We applied the concept of adding a lysine mimic to an established inhibitor (BIX-01294) of histone H3 lysine 9 methyltransferases G9a and G9a-like protein (GLP) by including a 5-aminopentyloxy moiety, which is inserted into the target lysinebinding channel and becomes methylated by GLP, albeit slowly. The compound enhanced its potency in vitro and reduced cell toxicity in vivo. We suggest that adding a lysine or methyllysine mimic should be considered in the design of small molecule inhibitors for other methyl-lysine writers, erasers and readers. Author Contributions Y.C. performed SET-domain enzyme purifications, mass spectrometry-based inhibition assays, ITC measurements, crystallization, and participated in X-ray data collection; T.G. performed compound design, chemical synthesis, and wrote the method of chemical synthesis; A.K.U. performed Jumonji demethylation assays; J.R.H. collected X-ray data, determined structures and performed structural refinements; A.S. and M.T.B. performed Fas reactivation; J.L. performed Glide docking and contributed to compound design; A.S. assisted with compound design; X.Z developed and optimized mass spectrometry-based assay; Y.S. performed cell toxicity assay; J.P.S. coordinated synthesis and modeling activities, contributed to compound design, and wrote method of molecular modeling and legend of supplementary figure S6; X.C. organized and designed the scope of the study, participated in designing compounds with T.G., and wrote the manuscript; all were involved in analyzing data and helped in revising the manuscript. PDB accession numbersThe coordinates and structure factor for human GLP catalytic domain bound with E72, E67, and E11, respectively, and AdoHcy have been deposited with accession numbers3MO5, 3MO2, and 3MO0.

Epigenetics is defined as heritable changes to the transcriptome that are independent of changes in the genome. The biochemical modifications that govern epigenetics are DNA methylation and posttranslational histone modifications. Among the histone modifications, acetylation and deacetylation are well characterized, whereas the fields of histone methylation and especially demethylation are still in their infancy. This is particularly true with regard to drug discovery. There is strong evidence that these modifications play an important role in the maintenance of transcription as well as in the development of certain diseases. This article gives an overview of the mechanisms of action of histone methyltransferases and demethylases, their role in the formation of certain diseases, and available inhibitors. Special emphasis is placed on the strategies that led to the first inhibitors which are currently available and the screening approaches that were used in that process.