Histone demethylating agents as potential <i>S</i>-adenosyl-<scp>l</scp>-methionine-competitors

Navakauskienė, Rūta; Mori, Mattia; Christodoulou, Michael S.; Zentelytė, Aistė; Botta, Bruno; Via, Lisa Dalla; Ricci, Francesca; Damia, Giovanna; Passarella, Daniele; Zilio, C.; Martinet, Nadine

doi:10.1039/c6md00170j

Cited by 6 publications

(13 citation statements)

References 43 publications

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“…It was not possible to identify partially unmethylated RAR alleles due to the lack of sensitivity of the allele-calling software. The HPLC-MS/MS assay is not suitable as a screening tool but its results corresponded relatively well with the results obtained using the 5-mC DNA ELISA™ (ZYMO Research, USA) according to the manufacturer's instructions previously [6,8]. For unmethylated alleles (0.13 µM 5-azacytidine treated cells), a 35% decrease in global 5mC content was detected by ELISA compared with a 48% decrease detected by HPLC-MS/MS.…”

Section: Sirtuin Inhibitionmentioning

confidence: 56%

“…Western blot analysis was used to identify small molecules with the ability to decrease me3H3K9 and/or me3H3K27 levels in MCF7 cells treated as described previously [8]. Briefly, cells were cultured for 48 h as described in Section 2.1 and nuclear proteins were then investigated by Western blot analysis using antibodies for the specific detection of me3H3K9 and me3H3K27.…”

Section: Histone H3k9 and K27 Studiesmentioning

confidence: 99%

“…Changes in the levels of me3HK27 and me3H3K9 were expressed as a percentage of the levels in the positive controls (MCF7 cells treated with BIX-01294 and with 3-deazaneplanocin A (DZNep); untreated cells served as the negative control. The catalytic activity of the KDM G9 was measured for (S)-evodiamine only with the EpiQuik™ KDM/Inhibition Assay (Epigentek, USA) as previously reported [8].…”

Section: Histone H3k9 and K27 Studiesmentioning

confidence: 99%

“…DZNep acts as a SAM hydrolase inhibitor to induce the accumulation of SAH and also functions as a KDM EZH2 inhibitor. BIX-01294 is a G9a-like protein and G9a KDM inhibitor that does not compete with SAM [8]. Entinostat, valproic acid, anacardic acid and tenovin 6 have localized DNA demethylating activities that cannot be explained by SAM-or SAH-based mechanisms (Table 1).…”

Section: Dna Methylation Studiesmentioning

confidence: 99%

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New Insights into the Epigenetic Activities of Natural Compounds

Vidaković¹,

Marinello²,

Lahtela‐Kakkonen³

et al. 2018

obm genet

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Background: With their varied pharmacophores, natural products are interesting tools to open the drug discovery pipeline. Several plant secondary metabolites are components of the human diet and have reported epigenetic activities. In this study, we screened a small natural compound library for epigenetic activities. Methods: Seventy-one different natural products plus 17 controls collected from all collaborating laboratories were screened. Localized DNA methylation (DNAm) was studied on a stretch of the retinoic acid receptor gene RAR. All genomic 5-methylated cytosine (5mC) bases were then detected by high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). DNA methyl transferase 1 (DNMT1) enzymatic activity was measured for selected compounds. Level of histone H3 trimethylation at lysine 9 and 27 (me3H3K9 and me3H3K27) was measured by Western blot analysis. Global histone deacetylase inhibition (HDAC) was assayed first using a bioluminescent resonance energy transfer-based (BRET) assay and then with enzymatic fluorescence based-assays for most HDAC class 1. HDAC6 inhibition was measured by Western blot analysis. Sirtuin (Sirt2) inhibition was assessed first with a thermal shift assay and then using the enzymatic SIRTainty™ Class III HDAC assay for Sirt1 and Sirt2. Results: Diosmetin, (S)-equol, umbelliferone, papaverin and L-carnitine were identified as novel DNA demethylating agents. Emodin, rhein, aloin and D-glucuronic acid were identified as novel histone H3 demethylating compounds. Previously undescribed Sirt activation by apigenin, biochanin B, robinin, pinocembrin, aureusidine, brucine and boldine was also detected. Conclusions: High-throughput alpha screens are used for initial studies of diverse compound libraries; however, this approach has significant disadvantages for the study of DNAm. Indeed, finding unmethylated RARalleles in one cell line does not indicate the activity of the compound at the level of the entire genome over a given time-frame and a given dose. Measurement of DNMT1 activity is not useful since most natural compounds are not direct enzymatic inhibitors. When studying histone methylation, Western blot analysis is laborious

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Section: Sirtuin Inhibitionmentioning

confidence: 56%

Section: Histone H3k9 and K27 Studiesmentioning

confidence: 99%

Section: Histone H3k9 and K27 Studiesmentioning

confidence: 99%

Section: Dna Methylation Studiesmentioning

confidence: 99%

See 2 more Smart Citations

New Insights into the Epigenetic Activities of Natural Compounds

Vidaković¹,

Marinello²,

Lahtela‐Kakkonen³

et al. 2018

obm genet

View full text Add to dashboard Cite

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“…FLAP (Fingerprints for Ligands and Proteins) is a virtual screening algorithm developed and licensed by Molecular Discovery Ltd. (http://www.moldiscovery.com). Several VS campaigns have been successfully performed with FLAP and are reported in the literature, as well as binding mode prediction and rationalization . Initially, the approach uses the GRID force field to evaluate the type, strength and direction of the interactions that a cavity is capable of making.…”

Section: Methodsmentioning

confidence: 99%

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case

et al. 2016

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Repurposing and repositioning drugs has become a frequently pursued and successful strategy in the current era, as new chemical entities are increasingly difficult to find and get approved. Herein we report an integrated BioGPS/FLAPdock pipeline for rapid and effective off-target identification and drug repurposing. Our method is based on the structural and chemical properties of protein binding sites, that is, the ligand image, encoded in the GRID molecular interaction fields (MIFs). Protein similarity is disclosed through the BioGPS algorithm by measuring the pockets' overlap according to which pockets are clustered. Co-crystallized and known ligands can be cross-docked among similar targets, selected for subsequent in vitro binding experiments, and possibly improved for inhibitory potency. We used human thymidylate synthase (TS) as a test case and searched the entire RCSB Protein Data Bank (PDB) for similar target pockets. We chose casein kinase IIα as a control and tested a series of its inhibitors against the TS template. Ellagic acid and apigenin were identified as TS inhibitors, and various flavonoids were selected and synthesized in a second-round selection. The compounds were demonstrated to be active in the low-micromolar range.

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Imidazo[2,1-b]benzothiazol Derivatives as Potential Allosteric Inhibitors of the Glucocorticoid Receptor

Christodoulou

Dapiaggi

Ghiringhelli

et al. 2018

ACS Med. Chem. Lett.

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Glucocorticoid receptor (GCR) transactivation reporter gene assays were used as an initial high-throughput screening on a diversified library of 1200 compounds for their evaluation as GCR antagonists. A class of imidazo[2,1-]benzothiazole and imidazo[2,1-]benzoimidazole derivatives were identified for their ability to modulate GCR transactivation and anti-inflammatory transrepression effects utilizing GCR and NF-κB specific reporter gene assays. Modeling studies on the crystallographic structure of the GCR ligand binding domain provided three new analogues bearing the tetrahydroimidazo[2,1-]benzothiazole scaffold able to antagonize the GCR in the presence of dexamethasone (DEX) and also defined their putative binding into the GCR structure. Both mRNA level measures of GCR itself and its target gene GILZ, on cells treated with the new analogues, showed a GCR transactivation inhibition, thus suggesting a potential allosteric inhibition of the GCR.

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Histone demethylating agents as potential S-adenosyl-l-methionine-competitors

Cited by 6 publications

References 43 publications

New Insights into the Epigenetic Activities of Natural Compounds

New Insights into the Epigenetic Activities of Natural Compounds

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case

Imidazo[2,1-b]benzothiazol Derivatives as Potential Allosteric Inhibitors of the Glucocorticoid Receptor

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