Inhibitor Scaffolds for 2-Oxoglutarate-Dependent Histone Lysine Demethylases

Rose, Nathan R.; Ng, Stanley S.; Mecinović, Jasmin; Liénard, Benoît M. R.; Bello, Simon H.; Sun, Zhe; McDonough, Michael A.; Oppermann, U.; Schofield, Christopher J.

doi:10.1021/jm800936s

Cited by 227 publications

(346 citation statements)

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“…Recent reports showed that PrCa cell lines respond to MAOA inhibitors, possibly via inhibition of KDM's (Flamand et al, 2010). Furthermore, the JmjC-domain containing KDMs including PHF8 were found to be repressed by compounds targeting the Fe (II)/a-ketoglutarate dependent oxygenases (Cloos et al, 2006;Smith et al, 2007;Rose et al, 2008). Taken together, such compounds and epigenetic therapeutic concepts may offer intriguing starting points for the development of novel epigenetic therapies for PrCa.…”

Section: Discussionmentioning

confidence: 97%

Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion

et al. 2011

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Our understanding of key epigenetic regulators involved in specific biological processes and cancers is still incomplete, despite great progress in genome-wide studies of the epigenome. Here, we carried out a systematic, genomewide analysis of the functional significance of 615 epigenetic proteins in prostate cancer (PrCa) cells. We used the high-content cell-spot microarray technology and siRNA silencing of PrCa cell lines for functional screening of cell proliferation, survival, androgen receptor (AR) expression, histone methylation and acetylation. Our study highlights subsets of epigenetic enzymes influencing different cancer cell phenotypes. Plant homeo domain (PHD) finger proteins have a key role in cell survival and histone methylation, whereas histone deacetylases were primarily involved in regulating AR expression. In contrast, JumonjiC-domain (JmjC) containing histone lysine demethylases (KDMs) mainly had an impact on cell proliferation. Our results show that the KDMs JARID1B, PHF8, KDM3A, KDM3B and KDM4A were highly expressed in clinical PrCa samples. The PHD-finger protein 8 (PHF8), a transcriptional coactivator with both PHD-and JmjC-domains, was moderately to strongly expressed in 80% of clinical PrCa samples, whereas 76% of normal and benign samples were negative or only showed weak PHF8 expression. Strong PHF8 expression correlated significantly with high Gleason grade and was borderline significant for poor prognosis. The results of functional PHF8 knockdown implicate a role in cell migration and invasion, as shown by cell motility and 3-D invasion assays. Our study suggests that various cellular phenotypes are regulated by distinct subsets of epigenetic enzymes. Proteins interpreting and modifying histone methylation, such as JmjC-domain and particularly PHDfinger proteins like PHF8, are activated in subsets of PrCa's and promote cancer relevant phenotypes.

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Section: Discussionmentioning

confidence: 97%

Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion

et al. 2011

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“…To evaluate whether compounds were inhibiting by binding to the active site (as opposed to, or in addition to, chelation of iron in solution), nondenaturing electrospray ionisation protein mass spectrometry (ESI MS) (Figure 2) was used to detect binding of compounds to the intact protein complex. [11] Although there are caveats on the use of mass spectrometry for screening binding strength, [17] the results of both assay methods correlated well (Table 1), with more potent compounds showing a stronger binding interaction with the protein complex by ESI MS.Previous work on inhibitors of the JMJD2 demethylases demonstrated that the parent compound 2,4-pyridinedicarboxylate is a 2OG-competitive inhibitor. This compound was shown by crystallographic analyses (PDB ID 2VD7) to bind the active-site metal via the pyridine nitrogen and the 2-carboxylate, while the 4-carboxylate is positioned to interact with the 2OG-binding residues Lys206 and Tyr132, effectively 'anchoring' the compound in the active site (see Figure 4).…”

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confidence: 85%

“…Although the situation with iron may be different to that for nickel (used for crystallography), these observations suggest that compounds such as 13a, 2,4-PDCA and 5-carboxy-8-hydroxyquinoline may inhibit JMJD2 Overall we have shown that modifications to the 4,4′-dicarboxy-2,2′-bipyridine template can result in substantial increases in potency against JMDJ2E (IC 50 of 6.6 μM for the lead compound 8a, while the most potent compound identified, 15c, had an IC 50 of 110 nM, which represents a 66-fold improvement in potency). [11] These increases in potency are, at least in part, likely mediated by both hydrophobic/π-π interactions and, in the case of some compounds (e.g. 13a), by electrostatic interactions.…”

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confidence: 99%

Inhibition of Histone Demethylases by 4‐Carboxy‐2,2′‐Bipyridyl Compounds

et al. 2011

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# These authors contributed equally to this work. Keywordsepigenetics; histone demethylase; bipyridyl; enzyme inhibitors; 2-oxoglutarate In eukaryotes, nuclear DNA is packaged into chromatin by binding to histones and associated factors. Covalent modifications to histone tails are associated with specific transcriptional states of the associated DNA. Acetylation of lysine side-chains normally correlates with transcriptional activation, while deacetylation leads to transcriptional silencing. The regulatory roles of methylation of lysine and arginine residues appear to be more complex. Methylation of certain lysine residues is associated with active transcription, while methylation of others is associated with silencing and heterochromatin formation. Each methylation 'mark' is placed, removed and 'interpreted' in a site-specific manner by histone methyltransferases, demethylases and methyl-binding domains, respectively. The biological functions of the individual enzymes are largely undefined, and are the focus of current investigations (for review see [1,2] The JmjC histone demethylases are 2-oxoglutarate (2OG) dependent oxygenases that catalyse N ε -lysyl demethylation via hydroxylation of the methyl group in a 2-oxoglutarate and Fe(II)-dependent manner (Scheme 1). Human 2OG oxygenases catalyse a range of reactions, including hydroxylation of amino acids, DNA and small molecules, and demethylation of proteins and DNA. [3] 2OG oxygenases show promise as therapeutic targets. An inhibitor of γ-butyrobetaine hydroxylase (BBOX) is used for the treatment of cardiovascular disease [4,5] and inhibitors of the hypoxia inducible factor (HIF) prolyl hydroxylases are in clinical trials for the treatment of anaemia. [6] Inhibitors of the collagen prolyl hydroxylases have also been evaluated as potential therapeutics for the treatment of liver fibrosis. [7,8] The discovery of the JmjC domain histone demethylases, and the suggestions that some of them are potential therapeutic targets for cancer treatment, [9] Figure 1). [10][11][12][13] Compounds which catalyse the ejection of a structural Zn(II) ion from the JMJD2 demethylases have also been reported ( Figure 1). [14] In a study describing various template inhibitors of the JmjC demethylases, we found that 2,2′-bipyridyl compounds with at least one 4-carboxylate group inhibit the histone demethylase JMJD2E. [11] A related series of compounds, 5,5′-dicarboxylate-2,2′-bipyridyls, is reported to inhibit the collagen prolyl-4-hydroxylases. [15] 2,2′-Bipyridine and bipyridyl compounds have also been used as inhibitors of the HIF hydroxylases. [16] Although it is likely that in some cases the enzyme inhibition effects of bipyridyl compounds result from metal chelation in solution, they also have the potential to inhibit via active site binding, as is the case for some 2OG oxygenases; however, to date there is no structural information on their mechanism of action. Here we report structure-activity relationship studies and analyses on bipyridyl inhibitors of JMJD2E.The bipyridyl com...

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“…The amounts of NADH generated can be measured by absorbance at wavelength of 340 nm 235 or by fluorescence emission at 465 nm. [236][237][238] In addition to the measurement of formaldehyde, demethylated histone peptide products can be directly measured by MALDI-MS, 237,238 thus providing an optional approach for counterscreen or secondary assays of primary hits.…”

Section: B Biochemical Assays For Methyltransferase and Demethylase mentioning

confidence: 99%

“…80 A few inhibitors have been reported for JMJD demethylases that demethylate specific lysines in the H3 tail ( Figure 18). 237,[284][285][286] The analog of α-ketoglutarate, oxalyglycine, has been reported to be a weak inhibitor against JMJD2C 83 and the catalytic core of JMJD2A(c-JMJD2A). 284 Recently, Rose and coworkers demonstrated that HDAC inhibitors and pyridine carboxylic acids such as compound 6a and 7 ( Figure 18) act as micromolar inhibitors against JMJD2E (IC 50 : 1.4 μM for 6a and 6.6 μM for 7).…”

Section: E Inhibitors Of Histone Lysine Demethylasesmentioning

confidence: 99%

Chemical and biochemical approaches in the study of histone methylation and demethylation

Luo

Wang

et al. 2010

Med. Res. Rev.

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Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic.

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Inhibitor Scaffolds for 2-Oxoglutarate-Dependent Histone Lysine Demethylases

Cited by 227 publications

References 16 publications

Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion

Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion

Inhibition of Histone Demethylases by 4‐Carboxy‐2,2′‐Bipyridyl Compounds

Chemical and biochemical approaches in the study of histone methylation and demethylation

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