Epigenetic regulation of gene expression is a dynamic and reversible process that establishes normal cellular phenotypes but also contributes to human diseases. At the molecular level, epigenetic regulation involves hierarchical covalent modification of DNA and the proteins that package DNA, such as histones. Here, we review the key protein families that mediate epigenetic signalling through the acetylation and methylation of histones, including histone deacetylases, protein methyltransferases, lysine demethylases, bromodomain-containing proteins and proteins that bind to methylated histones. These protein families are emerging as druggable classes of enzymes and druggable classes of protein-protein interaction domains. In this article, we discuss the known links with disease, basic molecular mechanisms of action and recent progress in the pharmacological modulation of each class of proteins.

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Bromo and extra terminal (BET) proteins (BRD2, BRD3, BRD4 and BRDT) are transcriptional regulators required for efficient expression of several growth promoting and anti-apoptotic genes as well as for cell cycle progression. BET proteins are recruited to transcriptionally active chromatin via their two N-terminal bromodomains (BRDs), a protein interaction module that specifically recognizes acetylated lysine residues in histones H3 and H4. Inhibition of the BET-histone interaction results in transcriptional down-regulation of a number of oncogenes providing a novel pharmacological strategy for the treatment of cancer. Here we present a potent and highly selective dihydroquinazoline-2-one inhibitor, PFI-1 that efficiently blocks the interaction of BET BRDs with acetylated histone tails. Co-crystal structures showed that PFI-1 acts as an acetyl-lysine (Kac) mimetic inhibitor efficiently occupying the Kac binding site in BRD4 and BRD2. PFI-1 has antiproliferative effects on leukaemic cell lines and efficiently abrogates their clonogenic growth. Exposure of sensitive cell lines with PFI-1 results in G1 cell cycle arrest, down-regulation of MYC expression as well as induction of apoptosis and induces differentiation of primary leukaemic blasts. Intriguingly, cells exposed to PFI-1 showed significant down-regulation of Aurora B kinase, thus attenuating phosphorylation of the Aurora substrate H3S10 providing an alternative strategy for the specific inhibition of this well established oncology target.

The posttranslational modification of chromatin through acetylation at selected histone lysine residues is governed by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The significance of this subset of the epigenetic code is interrogated and interpreted by an acetyllysine-specific protein–protein interaction with bromodomain reader modules. Selective inhibition of the bromo and extra C-terminal domain (BET) family of bromodomains with a small molecule is feasible, and this may represent an opportunity for disease intervention through the recently disclosed antiproliferative and anti-inflammatory properties of such inhibitors. Herein, we describe the discovery and structure–activity relationship (SAR) of a novel, small-molecule chemical probe for BET family inhibition that was identified through the application of structure-based fragment assessment and optimization techniques. This has yielded a potent, selective compound with cell-based activity (PFI-1) that may further add to the understanding of BET family function within the bromodomains.

This novel screening system supersedes current in vitro fibroplasia models, as a fast, quantitative and non-destructive technique. This method distinguishes a reduction in collagen I deposition, excluding collagen cross-linking, and allows full evaluation of inhibitors of C-proteinase/BMP-1 and other matrix metalloproteinases.

Significance Protein methyltransferases constitute an emerging but undercharacterized class of therapeutic targets with diverse roles in normal human biology and disease. Small-molecule “chemical probes” can be powerful tools for the functional characterization of such enzymes, and here we report the discovery of ( R )-PFI-2—a first-in-class, potent, highly selective, and cell-active inhibitor of the methyltransferase activity of SETD7 [SET domain containing (lysine methyltransferase) 7]—and two related compounds for control and chemoproteomics studies. We used these compounds to characterize the role of SETD7 in signaling, in the Hippo pathway, that controls cell growth and organ size. Our work establishes a chemical biology tool kit for the study of the diverse roles of SETD7 in cells and further validates protein methyltransferases as a druggable target class.

The APC tumour suppressor gene is the most commonly mutated gene in colorectal cancer (CRC). Loss of Apc in intestinal stem cells (ISCs) drives aberrant Wnt signalling and adenoma formation in mice 1 . We previously showed that a reduction in WNT-ligand secretion increases the ability of Apc-mutant ISCs to colonise a crypt (fixation) and accelerate tumourigenesis 2 . Here, we investigate key mechanistic processes whereby Apc-mutant cells gain a clonal advantage over wild-type counterparts to achieve fixation. We find that Apc-mutant cells are enriched for transcripts encoding several secreted Wnt antagonists, with Notum being the most highly expressed. Indeed, conditioned medium from Apc-mutant cells suppresses the growth of wild-type organoids in a Notum-dependent manner. Furthermore, Notum-secreting mutant clones actively inhibit the proliferation of surrounding wild-type crypt cells and drive their differentiation, thereby outcompeting them from the niche. Importantly, genetic or pharmacological inhibition of Notum is sufficient to abrogate the expansion of Apcmutant cells and their ability to form intestinal adenomas. Taken together, we demonstrate Notum as a key mediator during the early stages of mutation fixation, which can be targeted to restore wild-type cell competition and thus, offer novel preventative strategies for high-risk patients. MainThe colonic epithelium displays one of the highest mutation rates of all tissues 3,4 , with lossof-function mutations in the APC tumour suppressor considered a key early event in colorectal cancer (CRC) initiation 5 . For a mutation to be maintained within a crypt, it needs to become "fixed", by mutant cells outcompeting wild-type intestinal stem cells (ISC) from the crypt 6,7 .Previous studies revealed that Apc loss (or Kras activation) confer a clonal advantage to ISCs 7,8, increasing their probability of fixation/winning within the crypt and, in the case of Apc mutation, driving adenoma formation. Even though APC-deficient clones have an increased probability of "winning", they can still be stochastically eliminated from the ISC pool i.e. lose.This suggests uncovering the molecular mechanisms by which APC-deficient cells outcompete wild-type cells could lead to novel chemo-preventative approaches.APC is a negative regulator of Wnt signalling that functions as an integral part of the destruction complex, which directs the phosphorylation and degradation of β-catenin 9 . Since Apc-mutant tumours exhibit constitutive Wnt-pathway activation, we first sought to identify genes differentially upregulated in Apc-mutant cells relative to the normal intestinal epithelium.For this, we performed transcriptomic analysis of tumours that develop in VillinCre ER ;Apc fl/+ (hereafter VilCre ER ;Apc fl/+ ) mice following the sporadic loss of the remaining copy of Apc 10 , akin to human CRC 11 . As expected, Wnt-target genes were highly upregulated in these Apcmutant tumours (Extended Data Fig. 1a). The most highly upregulated gene was Notum (Fig. 1a), which encodes a secreted WNT...

The ability to cross the blood brain barrier (BBB), sometimes expressed as BBB+ and BBB-, is a very important property in drug design. Several computational methods have been employed for the prediction of BBB-penetrating (BBB+) and nonpenetrating (BBB-) compounds with overall accuracies from 75 to 97%. However, most of these models use a large number of descriptors (67-199), and it is not easy to implement the models in order to predict values of BBB+/-. In this work, 19 simple molecular descriptors calculated from Algorithm Builder and fragmentation schemes were used for the analysis of 1593 BBB+/- data. The results show that hydrogen-bonding properties of compounds play a very important role in modeling BBB penetration. Several BBB models based on hydrogen-bonding properties, such as Abraham descriptors, polar surface area (PSA), and number of hydrogen bonding donors and acceptors, have been built using binomial-PLS analysis. The results show that the overall classification accuracy for a training set is over 90%, and overall prediction accuracy for a test set is over 95%.