Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization

Abstract

Epigenetic therapies are being investigated for the treatment of cancer, cognitive disorders, metabolic alterations and autoinmune diseases. Among the different epigenetic target families, protein lysine methyltransferases (PKMTs), are especially interesting because it is believed that their inhibition may be highly specific at the functional level. Despite its relevance, there are currently known inhibitors against only 10 out of the 50 SET-domain containing members of the PKMT family. Accordingly, the identification of chemical probes for the validation of the therapeutic impact of epigenetic modulation is key. Moreover, little is known about the mechanisms that dictate their substrate specificity and ligand selectivity. Consequently, it is desirable to explore novel methods to characterize the pharmacological similarity of PKMTs, going beyond classical phylogenetic relationships. Such characterization would enable the prediction of ligand off-target effects caused by lack of ligand selectivity and the repurposing of known compounds against alternative targets. This is particularly relevant in the case of orphan targets with unreported inhibitors. Here, we first perform a systematic study of binding modes of cofactor and substrate bound ligands with all available SET domain-containing PKMTs. Protein ligand interaction fingerprints were applied to identify conserved hot spots and contact-specific residues across subfamilies at each binding site; a relevant analysis for guiding the design of novel, selective compounds. Then, a recently described methodology (GPCR-CoINPocket) that incorporates ligand contact information into classical alignment-based comparisons was applied to the entire family of 50 SET-containing proteins to devise pharmacological similarities between them. The main advantage of this approach is that it is not restricted to proteins for which crystallographic data with bound ligands is available. The resulting family organization from the separate analysis of both sites (cofactor and substrate) was retrospectively and prospectively validated. Of note, three hits (inhibition > 50% at 10 µM) were identified for the orphan NSD1.Electronic supplementary materialThe online version of this article (10.1186/s13321-018-0288-5) contains supplementary material, which is available to authorized users.

Development of Machine Learning Models for Accurately Predicting and Ranking the Activity of Lead Molecules to Inhibit PRC2 Dependent Cancer

“…Compound NCI694864 forms two hydrogen bonds with Trp624 and Cys663 residues. The backbone of Trp624 is derived from the conserved GXG motif of the SET domain and is crucial for ligand binding through hydrogen bonds [ 50 ]. Another important residue, Tyr111, was found to interact with these hits through hydrophobic interaction.…”

NSD1: A Lysine Methyltransferase between Developmental Disorders and Cancer

“…Using a luminescence screening platform that quantifies S-adenosyl homocysteine (which is produced during methyl transfer from S-adenosylmethionine used by NSD1 and other HMTs), researchers identified suramin and other scaffolds as potential inhibitors of the enzymatic NSD1 HMT activity [ 75 ]. A computational strategy incorporating ligand contact information into classical alignment-based comparisons applied to SET containing proteins revealed additional scaffolds that inhibited NSD1 activity [ 76 ].…”

Structure-Based Design and Characterization of the Highly Potent and Selective Covalent Inhibitors Targeting the Lysine Methyltransferases G9a/GLP

“…Protein lysine methyltransferases (PKMTs) are categorized as epigenetic writers that catalyze the transfer of one to three methyl groups from the cofactor S -adenosylmethionine (SAM) to the ε-amino group of specific lysine residues, including K3, K9, K20, K27, K36, and K79 on histones H3 and H4. , PKMTs have gained great attention because of their crucial functions in many biological processes, such as gene expression, transcriptional regulation, DNA replication, cellular signal transduction, and cell differentiation. − To date, more than 50 PKMTs have been identified . Among a myriad of PKMTs, G9a (also known as euchromatic histone methyltransferase 2, EHMT2) and G9a-like protein (GLP, also known as EHMT1) are two closely related proteins and were initially identified as H3K9 methyltransferases. , GLP shares 80% sequence identity with G9a in their respective SET domains and forms a heterodimer with G9a .…”