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Design and Discovery of new pyrimidine coupled nitrogen aromatic rings as chelating groups of JMJD3 Inhibitors
Abstract
The histone methylation on lysine residues is one of the most studied post-translational modifications, and its aberrant states have been associated with many human diseases. In 2012, Kruidenier et al. reported GSK-J1 as a selective Jumonji H3K27 demethylase (JMJD3 and UTX) inhibitor. However, there is limited information on the structure–activity relationship of this series of compounds. Moreover, there are few scaffolds reported as chelating groups for Fe(II) ion in Jumonji demethylase inhibitors development. To further elaborate the structure–activity relationship of selective JMJD3 inhibitors and to explore the novel chelating groups for Fe(II) ion, we initialized a medicinal chemistry modification based on the GSK-J1 structure. Finally, we found that several compounds bearing different chelating groups showed similar activities with respect to GSK-J1 and excellent metabolic stability in liver microsomes. The ethyl ester prodrugs of these inhibitors also showed a better activity than GSK-J4 for inhibition of TNF-α production in LPS-stimulated murine macrophage cell line Raw 264.7 cells. Taking together, the current study not only discovered alternative potent JMJD3 inhibitors, but also can benefit other researchers to design new series of Jumonji demethylase inhibitors based on the identified chelating groups.
... In addition, we demonstrated that GSK-J4 could prevent thyroid cell apoptosis induced by TNF-α. A similar study suggested that GSK-J4 could prevent the apoptosis of human and mouse pancreatic islet cells in vitro by reducing the level of inducible nitric oxide synthase in cells [29]. Another research found that JMJD3 has an antiapoptotic effect on osteoblasts. ...
Hashimoto’s thyroiditis (HT) is an autoimmune illness caused by a combination of genetic, epigenetic, and environmental factors. The pathogenesis of HT is not fully elucidated, especially in epigenetics. The epigenetic regulator Jumonji domain-containing protein D3 (JMJD3) has been extensively investigated in immunological disorders. This study has been performed to explore the roles and potential mechanisms of JMJD3 in HT. Thyroid samples from patients and healthy subjects were collected. We first analyzed the expression of JMJD3 and chemokines in the thyroid gland using real-time PCR and immunohistochemistry. In vitro , the apoptosis effect of the JMJD3-specific inhibitor GSK-J4 on the thyroid epithelial cell line Nthy-ori 3-1 was evaluated using FITC Annexin V Detection kit. Reverse transcription-polymerase chain reaction and Western blotting were applied to examine the inhibitory effect of GSK-J4 on the inflammation of thyrocytes. In the thyroid tissue of HT patients, JMJD3 messenger RNA and protein levels were substantially greater than in controls ( P < 0.05). Chemokines C–X–C motif chemokine ligand 10 (CXCL10) and C–C motif chemokine ligand 2 (CCL2) were elevated in HT patients, and thyroid cells with stimulation of tumor necrosis factor α (TNF-α). GSK-J4 could suppress TNF-α-induced synthesis of chemokines CXCL10 and CCL2 and prohibit thyrocyte apoptosis. Our results shed light on the potential role of JMJD3 in HT and indicate that JMJD3 may become a novel therapeutic target in HT treatment and prevention.
... Compound 2 showed higher potency and selectivity for KDM4C over other KDM subfamilies (Korczynska et al., 2016). Analogs of GSK-J1 (3) (Kruidenier et al., 2012) preserving the β-amino acid and changing the 2-(pyridine-2-yl)pyrimidine scaffold were developed and found to exhibit better activity at TNF-α production than parent 3 (Hu et al., 2016). Benzoxazole (4) was shown to inhibit KDM6 subfamily member JMJD3 and to induce the cell cycle arrest in the S-phase on A375 melanoma cells (Giordano et al., 2019). ...
Aberrant epigenetic modifications are involved in cancer development. Jumonji C domain-containing histone lysine demethylases (KDMs) are found mainly up-regulated in breast, prostate, and colon cancer. Currently, growing interest is focusing on the identification and development of new inhibitors able to block the activity of KDMs and thus reduce tumor progression. KDM4A is known to play a role in several cellular physiological processes, and was recently found overexpressed in a number of pathological states, including cancer. In this work, starting from the structure of purpurogallin 9aa, previously identified as a natural KDM4A inhibitor, we synthesized two main sets of compound derivatives in order to improve their inhibitory activity against KDM4A in vitro and in cells, as well as their antitumor action. Based on the hypothetical biogenesis of the 5-oxo-5H-benzo[7]annulene skeleton of the natural product purpurogallin (Salfeld, 1960; Horner et al., 1961; Dürckheimer and Paulus, 1985; Tanaka et al., 2002; Yanase et al., 2005) the pyrogallol and catechol units were first combined with structural modifications at different positions of the aryl ring using enzyme-mediated oxidative conditions, generating a series of benzotropolone analogs. Two of the synthetic analogs of purpurogallin, 9ac and 9bc, showed an efficient inhibition (50 and 80%) of KDM4A in enzymatic assays and in cells by increasing levels of its specific targets, H3K9me3/2 and H3K36me3. However, these two compounds/derivatives did not induce cell death. We then synthesized a further set of analogs of these two compounds with greater structural diversification. The most potent of these analogs, 9bf, displayed the highest KDM4A inhibitory enzymatic activity in vitro (IC50 of 10.1 and 24.37 μM) in colon cancer cells, and the strongest antitumor action in several solid and hematological human cancer cell lines with no toxic effect in normal cells. Our findings suggest that further development of this compound and its derivatives may lead to the identification of new therapeutic antitumor agents acting through inhibition of KDM4A.
... Indeed, concerning JMJD3, up to date, only one JMJD3/UTX binder has been reported, GSK-J1, 1 along with a series of its derivatives showing a similar or lower activity. 18 Recently, we identified the quinoline-5,8 dicarboxylic acid scaffold as new potential lead compound for the development of JMJD3 inhibitors, using a fragment-based approach. 19 This chemical core is endowed with an unprecedented selectivity toward the proposed biological target and a relevant inhibition potency in the micromolar range. ...
JMJD3 is a member of the KDM6 subfamily and catalyzes the demethylation of lysine 27 on histone H3 (H3K27). This protein was identified as a useful tool in understanding the role of epigenetics in inflammatory conditions and in cancer as well. Guided by a virtual fragment screening approach, we identified the benzoxazole scaffold as a new hit suitable for the development of tighter JMJD3 inhibitors. Compounds were synthesized by a microwave-assisted one-pot reaction under catalyst and solvent-free conditions. Among these, compound 8 presented the highest inhibitory activity (IC 50 = 1.22 ± 0.22 μM) in accordance with molecular modeling calculations. Moreover, 8 induced the cycle arrest in S-phase on A375 melanoma cells.
... 13 Structure−activity relationship (SAR) studies of GSK-J1 led to the identification of thiazolo-, pyrazolo-, and triazolopyrimidine derivatives, which showed similar or reduced potency. 14 As claimed in a recent article by Nowak et al., 15 although potent inhibitors have been identified for most KDM subfamilies, the identification of selective and cell-permeable inhibitors remains a challenge. McAllister et al. 16 have reviewed KDM inhibitors developed since 2014 and pointed out that the vast majority of the identified inhibitors are OGA competitors and are all derivatives of a reduced number of metal-chelating fragments. ...
In the search for new demethylase inhibitors we have developed a multi-step protocol for in silico screening. Millions of poses generated by high-throughput docking or 3D-pharmacophore search are first minimized by a classical force field and then filtered by semiempirical quantum mechanical calculations of the interaction energy with a selected set of functional groups in the binding site. The final ranking includes solvation effects, which are evaluated in the continuum dielectric approximation (finite-difference Poisson equation). Application of the multi-step protocol to the JMJD3 jumonji demethylase has resulted in a dozen low-micromolar inhibitors belonging to five different chemical classes. We have solved the crystal structure of the JMJD3 inhibitor 8 in the complex with UTX (a demethylase in the same sub-family as JMJD3), which validates the predicted binding mode. Compound 8 is a promising candidate for future optimization as it has a favorable ligand efficiency of 0.32 kcal/mol per non-hydrogen atom.
... Administration of 66b significantly reduced the expression of 16 in 34 LPS-driven cytokines by PCR array. Xiong et al. designed and synthesized a series of derivatives of 66a to study the detail of SAR of this scaffold of selective KDM6 inhibitors 130 . The representative compound 67a had an equivalent potency against 66a (IC 50 ¼ 0.15 lM versus 0.15 lM). ...
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
... [1] Recently,aseries of GSK-J1 derivatives was reported, showing activity similar to or lower than that of the reference compound. [10] Thus, the discovery of small molecules that are able to selectively modulate the biological functiono f JMJD3 is very attractive, in that they will shed light on itsr ole, both in normal biological processes and under diseasec onditions, expanding the cancert herapy toolkit. ...
The quinoline-5,8 dicarboxylic acid scaffold has been identified by a fragment-based approach as new potential lead compound for the development of JMJD3 inhibitors. Among them, 3-(2,4-dimethoxypyrimidin-5-yl)quinoline-5,8-dicarboxylic acid (compound 3) shows low micromolar inhibitory activity against Jumonji domain-containing protein 3 (JMJD3). The experimental evaluation of inhibitory activity against seven related isoforms of JMJD3 highlighted an unprecedented selectivity toward the biological target of interest.
... Likely candidates to establish demethylation of H3K4me1/2 to establish the unmethylated state are limited, and we previously showed that expression of LSD1 (KDM1), a H3K4me2/1 demethylase [45], did indeed alter TRIM24-regulated gene expression in MCF7 cells [7]. Recent studies linking ER and enzymes that modulate histone methylation, UTX, LSD1 and MLL2 in ER-positive breast cancer cells suggest that histone methylation and demethylation is an important regulatory node that may yield to recently developed inhibitors of these enzymes [46][47][48][49]. Multiple histone acetyltransferases, including CBP/p300 [50] and GCN5 [51], may acetylate H3K23, and ERa has been shown to promote chromatin acetylation by recruiting CBP/p300 [52,53]. ...
Proteins with domains that recognize and bind post-translational modifications (PTMs) of histones are collectively termed epigenetic readers. Numerous interactions between specific reader protein domains and histone PTMs and their regulatory outcomes have been reported, but little is known about how reader proteins may in turn be modulated by these interactions. Tripartite motif-containing protein 24 (TRIM24) is a histone reader aberrantly expressed in multiple cancers. Here, our investigation revealed functional crosstalk between histone acetylation and TRIM24 SUMOylation. Binding of TRIM24 to chromatin via its tandem PHD-bromodomain, which recognizes unmethylated lysine 4 and acetylated lysine 23 of histone H3 (H3K4me0/K23ac), led to TRIM24 SUMOylation at lysine residues 723 and 741. Inactivation of the bromodomain, either by mutation or with a small-molecule inhibitor, IACS-9571, abolished TRIM24 SUMOylation. Conversely, inhibition of histone deacetylation markedly increased TRIM24's interaction with chromatin and its SUMOylation. Of note, gene expression profiling of MCF7 cells expressing wild type versus SUMO-deficient TRIM24 identified cell adhesion as the major pathway regulated by the cross-talk between chromatin acetylation and TRIM24 SUMOylation. In conclusion, our findings establish a new link between histone H3 acetylation and SUMOylation of the reader protein TRIM24, a functional connection that may bear on TRIM24's oncogenic function and may inform future studies of PTM cross-talk between histones and epigenetic regulators.
... In vivo administration of GSK-J4 killed the TAL1-positive primary human leukemia cells in a patientderived xenotransplant (PDX) model [139]. Novel KDM6B inhibitors modified from the previously identified pan-KDM6 inhibitor GSK-J1 have been reported recently and the ethyl ester prodrugs of these inhibitors showed better activity than GSK-J4 in a cell-based functional assay [141]. However, it is noteworthy that GSK-J1/J4 may also inhibit KDM5B and KDM5C at higher concentrations [142]. ...
Histone proteins constitute the core component of the nucleosome, the basic unit of chromatin. Chemical modifications of histone proteins affect their interaction with genomic DNA, the accessibility of recognized proteins, and the recruitment of enzymatic complexes to activate or diminish specific transcriptional programs to modulate cellular response to extracellular stimuli or insults. Methylation of histone proteins was demonstrated 50 years ago; however, the biological significance of each methylated residue and the integration between these histone markers are still under intensive investigation. Methylation of histone H3 on lysine 27 (H3K27) is frequently found in the heterochromatin and conceives a repressive marker that is linked with gene silencing. The identification of enzymes that add or erase the methyl group of H3K27 provides novel insights as to how this histone marker is dynamically controlled under different circumstances. Here we summarize the methyltransferases and demethylases involved in the methylation of H3K27 and show the new evidence by which the H3K27 methylation can be established via an alternative mechanism. Finally, the progress of drug development targeting H3K27 methylation-modifying enzymes and their potential application in cancer therapy are discussed.
... 682 A study that explored the SAR by replacing the pyridine ring of GSK-J1 with other potential chelating heterocycles was also published. 703 Several compounds featuring a pyrazole or triazole ring instead of the pyridine ring with IC 50 values of 0.15−0.27 μM were identified. ...
Post-translational modifications of histones by protein methyltransferases (PMTs) and histone demethylases (KDMs) play an important role in the regulation of gene expression and transcription and are implicated in cancer and many other diseases. Many of these enzymes also target various nonhistone proteins impacting numerous crucial biological pathways. Given their key biological functions and implications in human diseases, there has been a growing interest in assessing these enzymes as potential therapeutic targets. Consequently, discovering and developing inhibitors of these enzymes has become a very active and fast-growing research area over the past decade. In this review, we cover the discovery, characterization, and biological application of inhibitors of PMTs and KDMs with emphasis on key advancements in the field. We also discuss challenges, opportunities, and future directions in this emerging, exciting research field.
... Recent studies linking ER and enzymes that modulate histone methylation, UTX, LSD1 and MLL2 in ER-positive breast cancer cells suggest that histone methylation and demethylation is an Drug Discovery Today: Technologies | Vol. 19,2016 important regulatory node that may yield to recently developed inhibitors of these enzymes [46][47][48][49]. Multiple histone acetyltransferases, including CBP/p300 [50] and GCN5 [51], may acetylate H3K23, and ERa has been shown to promote chromatin acetylation by recruiting CBP/p300 [52,53]. ...
Tripartite Motif-containing protein 24 (TRIM24) functions as an E3 ligase targeting p53 for ubiquitination, a histone ‘reader’ that interacts with a specific signature of histone post-translational modifications and a co-regulator of nuclear receptor-regulated transcription. Although mouse models of Trim24 depletion suggest that TRIM24 may be a liver-specific tumor suppressor, several studies show that human TRIM24 is an oncogene when aberrantly over expressed. This review focuses on the mechanisms of TRIM24 functions in oncogenesis and metabolic reprogramming, which underlie recent interest in therapeutic targeting of aberrant TRIM24 in human cancers.
... Due to the limited information on the structureactivity relationship of GSK-J1 and its isomers, Hu et al., initialized a medicinal chemistry modification based on GSK-J1 structure, and they finally identified several compounds which exhibited similar activities as with GSK-J1. The inhibition of these compounds on LPS-stimulated genes was also proven in macrophages [80]. Some other inhibitors of JmjC demethylases have been identified including the α-ketoglutaric acid mimics N-oxalylglycine [81], methylstat [82], and catechols [83]. ...
Aberrant epigenetic reprogramming occurs frequently in the development of tumors. Histone H3 lysine 27 trimethylation (H3K27me3) exerts a repressive epigenetic mark on a large number of genes. UTX and JMJD3 are the only two histone demethylases which activate gene expression via demethylating H3K27me3 to H3K27me2 or H3K27me1. Current studies show that dysregulation of these two proteins are heavily linked to oncogenesis in various tissue types. Accumulating evidence suggested that there is remarkable therapeutic potential of targeting JMJD3 or UTX in different types of cancer. Herein, we shall give a brief review on the functional roles of JMJD3 and UTX in cancers and evaluate the available compounds and agents targeting UTX and JMJD3. Finally, we also discuss the several modalities that target UTX and JMJD3 for cancer therapy. This review will help to develop novel strategies to abolish or restore effects of UTX and JMJD3 in the pathogenesis of cancer.
Epigenetic modifications play a fundamental role in the regulation of gene expression and cell fate. During the development of cancer, epigenetic modifications appear that favor cell proliferation and migration, but at the same time prevent differentiation and apoptosis, among other processes. KDM6B is a histone demethylase that specifically removes methyl groups from H3K27me3, thus allowing re-expression of its target genes. It is currently known that KDM6B can act as both a tumor suppressor and an oncogene depending on the cellular context. Therefore, in this work we summarize the current knowledge of the role that KDM6B plays in different oncological contexts, and we try to orient it towards its clinical application.
Fe(II)/α-ketoglutarate-dependent lysine demethylases (KDMs) are attractive drug targets for several diseases including cancer. In this study, we designed and screened ortho-substituted anilides that are expected to function as Fe(II) chelators, and identified ortho-hydroxy anilide as a novel scaffold for KDM5A inhibitors. Treatment of human lung cancer A549 cells with a prodrug form of 4-carboxy-2-hydroxy-formanilide (9c) increased trimethylated lysine 4 on histone H3 level, suggesting KDM5 inhibition in the cells.
We describe in this study a rhodium(III) complex 1 as a new JMJD3 inhibitor and proinflammatory mediator. Complex 1 selectively inhibited the demethylation of H3K27me3 over other similar substrates, indicating its selectivity for JMJD3 over other histone demethylases, including JMJD2D and KDM5A. In terms of mechanism, complex 1 inhibited the JMJD3-H3K27me3 interaction in mouse macrophage cells and down-regulated the expression of TNF-α. To our knowledge, complex 1 is the first metal-based inhibitor of JMJD3 activity and only the second class of JMJD3 inhibitor reported overall.
1,2,3,4-Tetrahydroisoquinolines bearing phenacyl group at the nitrogen atom in their reaction with benzyne in acetonitrile undergo ring expansion to give 1H-3-benzazepines.
New synthetic methods to prepare seven-membered heterocyclic compounds containing one or more of the heteroatoms N, O, or S are covered. Aromatic systems containing at least one N atom were the focus of many reports. Research was often driven by the search for new bioactive heterocycles for use in medicinal chemistry and for the synthesis of natural products. Notable synthetic methods included transition metal-catalyzed, cycloaddition, ring-expansion, cascade-type, and C–H functionalization processes. A number of reviews in the field were also published.
The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.
Epigenetics is one of the most rapidly expanding fields in biology. The recent characterization of a human DNA methylome at single nucleotide resolution, the discovery of the CpG island shores, the finding of new histone variants and modifications, and the unveiling of genome-wide nucleosome positioning maps highlight the accelerating speed of discovery over the past two years. Increasing interest in epigenetics has been accompanied by technological breakthroughs that now make it possible to undertake large-scale epigenomic studies. These allow the mapping of epigenetic marks, such as DNA methylation, histone modifications and nucleosome positioning, which are critical for regulating gene and noncoding RNA expression. In turn, we are learning how aberrant placement of these epigenetic marks and mutations in the epigenetic machinery is involved in disease. Thus, a comprehensive understanding of epigenetic mechanisms, their interactions and alterations in health and disease, has become a priority in biomedical research.
The lysine-specific histone demethylase 1 (LSD1) is a chromatin modifying enzyme that specifically removes methyl groups from lysine 4 of histone 3 (H3-K4) and induces transcriptional repression. However, limited knowledge exists, regarding the existence and significance of LSD1 in the brain. We identified the distribution of LSD1 and H3-K4 mono-, di-, and tri-methylation in the brain of rats, respectively. The temporal and spatial distribution of LSD1 during ischemic brain injury was also explored. LSD1 immunoreactive cells were nucleus positive and were concentrated in the neurons of the hippocampus, cerebral cortex, striatum and amagdala. The distributions of H3-K4 mono-, di-, and tri-methylation exhibited exactly the same pattern as LSD1. LSD1 expression was induced both region and cell specifically after ischemic/perfusion, and complied with the two-peak mode of expression. These studies revealed a tightly regulated distribution for LSD1 in the brain of rats under ischemic insult, suggesting a critical role in neuron function.
Epigenetic mechanisms, which involve DNA and histone modifications, result in the heritable silencing of genes without a change in their coding sequence. The study of human disease has focused on genetic mechanisms, but disruption of the balance of epigenetic networks can cause several major pathologies, including cancer, syndromes involving chromosomal instabilities, and mental retardation. The development of new diagnostic tools might reveal other diseases that are caused by epigenetic alterations. Great potential lies in the development of 'epigenetic therapies'--several inhibitors of enzymes controlling epigenetic modifications, specifically DNA methyltransferases and histone deacetylases, have shown promising anti-tumorigenic effects for some malignancies.
The covalent modification of histones is closely associated with regulation of gene transcription. Chromatin modifications have been suggested to represent an epigenetic code that is dynamically 'written' and 'erased' by specialized proteins, and 'read', or interpreted, by proteins that translate the code into gene expression changes. Initially thought to be an irreversible process, histone methylation is now known to be reversed by demethylases, FAD dependent amineoxidases and by iron(II)-alpha-ketoglutarate dependent deoxygenases of the Jumonji family. Altered histone demethylase activities have been associated with human disease, including cancer. The first wave of novel investigational drugs directed against KDM1A has recently entered the clinic, and the first specific inhibitor targeting a Jumonji KDM is advancing in preclinical regulatory studies.
Copyright © 2015 Elsevier Ltd. All rights reserved.
The Jumonji (Jmj) family of demethylases has a crucial role in regulating epigenetic processes through the removal of methyl groups from histone tails. The ability of Jmj demethylases to recognize their targets selectively has been elegantly addressed by structural studies. Reviewing recent structural literature, we provide an overview of selectivity mechanisms that demethylases use, including specific residues, methylation states and contextual requirements. We also report the presence of a common JmjN support domain across the family. The ability to use structural information for this enzyme class will be a crucial component of future drug discovery.
Copyright © 2014. Published by Elsevier Ltd.
Parkinson's disease (PD) is the second most common age-related neurodegenerative disease, but its pathogenesis is not fully understood. The selective neuronal cell death in PD has been considered to result from a complex interaction between genetic and environmental factors, but the nature of the relationship between the two chief modifiers remains to be elucidated. There is a growing body of evidence supporting the role of epigenetics in the development and progression of many neurodegenerative diseases including PD. Epigenetic modification refers to changes in gene expression or function without changes in DNA sequence, which mainly includes DNA methylation, post-modifications of histone, and non-coding RNAs. In this review, we will focus on the abnormal epigenetic modifications involved in the pathogenesis of PD and their implications for the development of future diagnostic and therapeutic strategies.
Copyright © 2014 Elsevier B.V. All rights reserved.
Lysine acetylation is a fundamental post-translational modification that plays an important role in control of gene transcription in chromatin in an ordered fashion. The bromodomain, the conserved structural module present in transcription-associated proteins, functions exclusively to recognize acetyl-lysine on histones and non-histone proteins. The structural analyses of bromodomains’ recognition of lysine-acetylated peptides derived from histones and cellular proteins provide detailed insights into the differences and unifying features of biological ligand binding selectivity by the bromodomains. Newly developed small molecule inhibitors targeting bromodomain proteins further highlight the functional importance of bromodomain/acetyl-lysine binding as a key mechanism in orchestrating molecular interactions and regulation in chromatin biology and gene transcription. These new studies argue that modulating bromodomain/acetyl-lysine interactions with small-molecule chemicals offer new opportunities to control gene expression in a wide array of human diseases including cancer and inflammation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
It has recently been demonstrated that the genes controlling the epigenetic programmes that are required for maintaining chromatin structure and cell identity include genes that drive human cancer. This observation has led to an increased awareness of chromatin-associated proteins as potentially interesting drug targets. The successful introduction of DNA methylation and histone deacetylase (HDAC) inhibitors for the treatment of specific subtypes of cancer has paved the way for the use of epigenetic therapy. Here, we highlight key biological findings demonstrating the roles of members of the histone lysine demethylase class of enzymes in the development of cancers, discuss the potential and challenges of therapeutically targeting them, and highlight emerging small-molecule inhibitors of these enzymes.
A plethora of groundbreaking studies have demonstrated the importance of chromatin-associated proteins and post-translational modifications of histones, proteins and DNA (so-called epigenetic modifications) for transcriptional control and normal development. Disruption of epigenetic control is a frequent event in disease, and the first epigenetic-based therapies for cancer treatment have been approved. A generation of new classes of potent and specific inhibitors for several chromatin-associated proteins have shown promise in preclinical trials. Although the biology of epigenetic regulation is complex, new inhibitors such as these will hopefully be of clinical use in the coming years.
This paper presents the design and development of a ground-based microwave radiometer system (MWR) for the offshore oil platform. It will be used to provide long time series of geophysical parameters such as the sea-surface temperature, the near-surface wind speed and the sea ice type. The ground-based MWR is a five-frequency, dual-polarized microwave radiometer which is a total power type microwave radiometer based on a heterodyne receiver. It operates at 6.8 GHz, 10.7 GHz, 18.7 GHz, 23.8 GHz and 37 GHz, respectively. The scanning mode adopts circular scan in a vertical plane. During each period, two-point calibration is performed to calibrate the receiver gain and noise. The antenna beam directs different angles and the blackbody used in calibration to obtain measurement data and calibration data. The ground-based MWR consists of three units: antenna and receiver unit, electronic unit and power supply unit. Antenna and receiver unit collects emission from the atmosphere. It is constructed with several RF components, which include voltage-controlled oscillator, high power amplifier, directional coupler, RF switch, band-pass filter, isolators, detectors and mixers. The received signal is down-converted by the double side band mixer to Intermediate Frequency, and then the IF signals are down-converted to Low Frequency by the detector and integrator. The electronic unit digitizes the LF signal, controls the scanning mechanism and measures physical temperature of the hot target for calibration, and takes charge of communication with a remote computer. The power supply unit performs DC/DC conversion, distributes the DC lines to various sub assemblies and switches. In paper, the basic principle and technical specifications of microwave radiometer will be briefly introduced, and the block diagram and detail design parameters of the proposed system will be described. The system followed radiometer electronics design and achieved exacting stability and high accuracy requirements.
Selective inhibitors of Jumonji domain-containing protein (JMJD) histone demethylases are candidate anticancer agents as well as potential tools for elucidating the biological functions of JMJDs. On the basis of the crystal structure of JMJD2A and a homology model of JMJD2C, we designed and prepared a series of hydroxamate analogues bearing a tertiary amine. Enzyme assays using JMJD2C, JMJD2A, and prolyl hydroxylases revealed that hydroxamate analogue 8 is a potent and selective JMJD2 inhibitor, showing 500-fold greater JMJD2C-inhibitory activity and more than 9100-fold greater JMJD2C-selectivity compared with the lead compound N-oxalylglycine 2. Compounds 17 and 18, prodrugs of compound 8, each showed synergistic growth inhibition of cancer cells in combination with an inhibitor of lysine-specific demethylase 1 (LSD1). These findings suggest that combination treatment with JMJD2 inhibitors and LSD1 inhibitors may represent a novel strategy for anticancer chemotherapy.
For a physiologically realistic joint range of motion and therefore range of muscle fiber lengths, only part of the whole muscle force-length curve can be used in vivo; that is, only a section of the force-length curve is expressed. Previous work has determined that the expressed section of the force-length curve for individual muscles can vary between subjects; however, the degree of intersubject variability is different for different muscles. This study determined the expressed section of both the rectus femoris and gastrocnemius--muscles with very different ratios of tendon slack length to muscle fiber optimum length--for 28 nonspecifically trained subjects to test the hypothesis that the value of this ratio affects the amount of variability in the expressed section. The force-length curves of the two muscles were reconstructed from moment-angle data using the method of Herzog & ter Keurs (1988). There was no relationship between the expressed sections of the force-length curve for the two muscles. Less variability was found in the expressed section of the gastrocnemius compared with the rectus femoris, supporting the hypothesis. The lack of relationship between the expressed sections of the two muscles has implications for motor control and for training muscle for rehabilitation.
Ferrous ion and 2-oxoglutarate (2OG) oxygenases catalyze the demethylation of N(epsilon)-methylated lysine residues in histones. Here we report studies on the inhibition of the JMJD2 subfamily of histone demethylases, employing binding analyses by nondenaturing mass spectrometry (MS), dynamic combinatorial chemistry coupled to MS, turnover assays, and crystallography. The results of initial binding and inhibition assays directed the production and analysis of a set of N-oxalyl-d-tyrosine derivatives to explore the extent of a subpocket at the JMJD2 active site. Some of the inhibitors were shown to be selective for JMJD2 over the hypoxia-inducible factor prolyl hydroxylase PHD2. A crystal structure of JMJD2A in complex with one of the potent inhibitors was obtained; modeling other inhibitors based on this structure predicts interactions that enable improved inhibition for some compounds.
Epigenetics is rising to prominence in biology as a mechanism by which environmental factors have intermediate-term effects on gene expression without changing the underlying genetic sequence. This can occur through the selective methylation of DNA bases and modification of histones. There are wide-ranging implications for the gene-environment debate and epigenetic mechanisms are causing a reevaluation of many traditional concepts such as heritability. The reversible nature of epigenetics also provides plausible treatment or prevention prospects for diseases previously thought hard-coded into the genome. Here, we consider how growing knowledge of epigenetics is altering our understanding of biology and medicine, and its implications for future research.
Recent studies indicate that histone lysine methylation is subject to enzyme-catalyzed reversion, and jumonji C (JmjC) domain-containing proteins have been identified as one of the members of histone demethylases. Although an increasing number of histone demethylases have been identified and biochemically characterized, their biological functions are poorly characterized. To elucidate the physiological functions, we generated the knockout mouse model of dimethylated or monomethylated histone 3 lysine 9 (H3K9me2/1)-specific JmjC domain-containing histone demethylase 2A (JHDM2A; also known as JMJD1A and KDM3A) and showed that JHDM2A is essential for spermatogenesis. Jhdm2a-deficient mice exhibited impaired postmeiotic chromatin condensation, which caused infertility, even though the hormonal levels were maintained. Further molecular and biochemical analysis revealed that JHDM2A directly bound to the core promoter regions of transition nuclear protein 1 (Tnp1) and protamine 1 (Prm1) genes, and it induced the transcriptional activation of these genes by removing H3K9 methylation, which is known as a silencing marker of gene transcription. This work uncovered a role for JHDM2A in spermatogenesis and identified 2 downstream genes that are critical for sperm nuclear condensation. In addition, we also showed that JHDM2A plays a role in regulating fat metabolic gene expression in muscle and brown fat tissue, and the knockout mice exhibited obesity and hyperlipidemia. Thus, JHDM2A possesses organ/tissue-specific target genes, and impairment of this molecule cannot be compensated by other JmjC-containing histone demethylases, suggesting the importance of this molecule in vivo.
Posttranslational modifications of histone N-terminal tails impact chromatin structure and gene transcription. While the extent of histone acetylation is determined by both acetyltransferases and deacetylases, it has been unclear whether histone methylation is also regulated by enzymes with opposing activities. Here, we provide evidence that LSD1 (KIAA0601), a nuclear homolog of amine oxidases, functions as a histone demethylase and transcriptional corepressor. LSD1 specifically demethylates histone H3 lysine 4, which is linked to active transcription. Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant derepression of target genes, suggesting that LSD1 represses transcription via histone demethylation. The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases.