High-throughput screening to identify inhibitors of lysine demethylases

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Authors: Molly Gale and Qin Yan
Date: Feb. 2015
From: Epigenomics(Vol. 7, Issue 1)
Publisher: Future Medicine Ltd.
Document Type: Report
Length: 5,728 words
Lexile Measure: 1730L

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Author(s): Molly Gale aff1 , Qin Yan [*] aff1


High-throughput screening; JmjC; KDM; lysine demethylase; LSD1; small-molecule inhibitor

Lysine demethylases (KDMs) and their counterparts lysine methyltransferases (KMTs) dynamically regulate lysine methylation in cells, of which the most studied form is histone lysine methylation. The methylation states of particular lysines in histone tails contribute significantly to transcriptional regulation. In general, methylation at histone H3 lysine 4 (H3K4) and H3K36 is associated with active transcription, while methylation at H3K9, H3K27 and H4K20 is thought to repress transcription [1 ]. Changes in methylation at these sites can have important biological consequences. In addition to histones, increasing numbers of proteins have been found to be mono-, di- and tri-methylated on lysine residues [ 2,3 ], and certain KDMs have been discovered to act on these residues, often with significant cellular outcomes. For instance, demethylation of p53 by LSD1 represses p53 function through blocking interaction between p53 and 53BP1 [ 4 ] and demethylation of RelA by KDM2A inhibits NF-κB activity [ 5,6 ].

About 20 mammalian KDMs have been discovered so far, each exhibiting specificity for particular histone and/or nonhistone substrates (reviewed here [7 ]). These KDMs fall into two classes: flavin adenine dinucleotide-dependent oxidases, discovered in 2004 [8 ] and Jumonji-C (JmjC) domain-containing enzymes, first identified in 2006 [ 9 ]. LSD1 and related enzymes function through flavin adenine dinucleotide oxidation of the methylated amine. In contrast, the JmjC domain-containing KDMs demethylate through a hydroxylation reaction with cofactors Fe 2+ and [alpha]-ketoglutarate [10 ].

Mutations or changes in expression of particular KDMs are associated with many types of cancer, inflammation and X-linked intellectual disability [ 11-14 ]. For this reason, small-molecule modulators of KDM function are now in high demand for use in research to better understand the functions of KDMs and for development of anticancer therapies. Several inhibitors of select KDMs have already been developed. In fact, two inhibitors of LSD1 are currently in clinical trials for small-cell lung carcinoma (GlaxoSmithKline, clinicaltrials.gov identifier: NCT02034123) and acute myeloid leukemia (ORYZON, Barcelona, Spain). Specific and potent inhibitors of certain JmjC domain-containing KDMs have also been discovered, despite similarities in their catalytic sites in which Fe2+ is coordinated by [alpha]-ketoglutarate and three conserved residues: two histidines and one aspartic or glutamic acid [15 ]. Though small-molecule inhibitors whose mechanism of action involves general disruption of the active site, for instance iron chelators, may inhibit multiple JmjC domain-containing KDMs, unique traits of these enzymes have allowed for development of a number of relatively specific inhibitors. For extensive reviews of existing KDM inhibitors, see [10 ] and [16 ].

Many research teams have used structure-based virtual modeling and screening, medicinal chemistry and focused campaigns to identify inhibitors of KDMs (e.g., see [17-21 ]). However, this is not amenable for all KDMs and there are likely numerous undiscovered chemotypes that can specifically inhibit activity of particular KDMs. Therefore, High-throughput screening (HTS) has been employed to search for small-molecule inhibitors of these enzymes. Several different HTS platforms have been utilized for KDMs, each with particular...

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Gale Document Number: GALE|A409374827