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Small molecule epigenetics

Laurie K Svoboda, Selina Shiqing K Teh, Sudha Sud, Samuel Kerk, Aaron Zebolsky, Sydney Treichel, Dafydd Thomas, Christopher J Halbrook, Ho-Joon Lee, Daniel Kremer, Li Zhang, Szymon Klossowski, Armand R Bankhead, Brian Magnuson, Mats Ljungman, Tomasz Cierpicki, Jolanta Grembecka, Costas A Lyssiotis, Elizabeth R Lawlor
Developmental transcription programs are epigenetically regulated by multi-protein complexes, including the menin- and MLL-containing trithorax (TrxG) complexes, which promote gene transcription by depositing the H3K4me3 activating mark at target gene promoters. We recently reported that in Ewing sarcoma, MLL1 (lysine methyltransferase 2A, KMT2A) and menin are overexpressed and function as oncogenes. Small molecule inhibition of the menin-MLL interaction leads to loss of menin and MLL1 protein expression and to inhibition of growth and tumorigenicity...
April 19, 2018: Journal of Pathology
Na Shen, Fei Yan, Jiuxia Pang, Zhe Gao, Aref Al-Kali, Christy L Haynes, Mark R Litzow, Shujun Liu
Gold nanoparticles (AuNPs) with adsorbed high-density lipoprotein (HDL) have been utilized to deliver oligonucleotides, yet HDL-AuNPs functionalized with small-molecule inhibitors have not been systematically explored. Here, we report an AuNP-based therapeutic system (HDL-AuNPs-BMS) for acute myeloid leukemia (AML) by delivering BMS309403 (BMS), a small molecule that selectively inhibits AML-promoting factor fatty acid-binding protein 4. To synthesize HDL-AuNPs-BMS, we use AuNP as a template to control conjugate size ensuring a spherical shape to engineer HDL-like nanoparticles containing BMS...
April 18, 2018: ACS Applied Materials & Interfaces
Michael J Bennett, Yiqin Wu, Amogh Boloor, Jennifer Matuszkiewicz, Shawn M O'Connell, Lihong Shi, Ryan K Stansfield, Joselyn R Del Rosario, James M Veal, David J Hosfield, Jiangchun Xu, Stephen W Kaldor, Jeffrey A Stafford, Juan M Betancort
The bromodomain and extra-terminal (BET) family of epigenetic proteins has attracted considerable attention in drug discovery given its involvement in regulating gene transcription. Screening a focused small molecule library based on the bromodomain pharmacophore resulted in the identification of 2-methylisoquinoline-1-one as a novel BET bromodomain-binding motif. Structure guided SAR exploration resulted in >10,000-fold potency improvement for the BRD4-BD1 bromodomain. Lead compounds exhibited excellent potencies in both biochemical and cellular assays in MYC-dependent cell lines...
April 10, 2018: Bioorganic & Medicinal Chemistry Letters
Mary A Morse, Karla K Balogh, Sarah A Brendle, Colin A Campbell, Mao X Chen, Rebecca C Furze, Isobel L Harada, Ian D Holyer, Umesh Kumar, Kevin Lee, Rab K Prinjha, Martin Rüdiger, Jon Seal, Simon Taylor, Jason Witherington, Neil D Christensen
The DNA papillomaviruses infect squamous epithelium and can cause persistent, benign and sometimes malignant hyperproliferative lesions. Effective antiviral drugs to treat human papillomavirus (HPV) infection are lacking and here we investigate the anti-papillomavirus activity of novel epigenetic targeting drugs, BET bromodomain inhibitors. Bromodomain and Extra-Terminal domain (BET) proteins are host proteins which regulate gene transcription, they bind acetylated lysine residues in histones and non-histone proteins via bromodomains, functioning as scaffold proteins in the formation of transcriptional complexes at gene regulatory regions...
April 10, 2018: Antiviral Research
Hongzhi Lin, Qihang Li, Qi Li, Jie Zhu, Kai Gu, Xueyang Jiang, Qianqian Hu, Feng Feng, Wei Qu, Yao Chen, Haopeng Sun
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...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
Showkat Ahmad Dar, Manoj Kumar
RNA activation (RNAa) is the process of enhancing selective gene expression at transcriptional level using double stranded RNAs, targeting gene promoter. These RNA molecules are usually twenty-one nucleotides long and termed as small activating RNAs (saRNAs). They are involved in gene regulation, epigenetics gain-of-function studies and as have potential therapeutic application for various diseases especially cancer. RNAa is opposite to RNA interference (RNAi) in functionality however; both processes share some protein machinery...
April 3, 2018: Journal of Molecular Biology
Tanushree Pal, Asmita Sharda, Bharat Khade, C S Ramaa, Sanjay Gupta
Cancer chemotherapy is associated with limitations like dose dependent host-tissue toxicity, multiple drug resistance and tumor heterogeneity. Hence, it is imperative to unearth novel targets to cure cancer. At present, 'pharmaco-epigenomics' constitutes the hope in cancer treatment owing to epigenetic deregulation- a reversible process, suspected of playing a role in malignancy. In this research work, we have used the fundamentals of drug repurposing for a set of our previously synthesized difluorinated propanediones and evaluated them for their histone methyltransferase inhibitory potential in leukemic cell lines...
April 4, 2018: Anti-cancer Agents in Medicinal Chemistry
Ma Hui, Zhang Jian, Zheng Peiyuan, Wu Zhenwei, Zhang Huibin
The bromodomain proteins, known as the key targets in epigenetics, are 'readers' of acetylated lysine of histones. As a member of bromodomain proteins, bromodomain-containing protein 9 (BRD9) is a subunit of mammalian SWI/SNF chromatin remodeling complexes. However, the biological functions and the potential application in therapeutics of BRD9 remain ambiguous due to a lack of selective small molecule inhibitors of BRD9. Recently, series of chemical ligands against BRD9 were developed by different research institutes...
April 5, 2018: Future Medicinal Chemistry
Joshua Denham, Adrian J Gray, John Scott-Hamilton, Amanda D Hagstrom, Aron J Murphy
Small non-coding RNAs (ncRNAs) are emerging as important molecules for normal biological processes and are deregulated in disease. Exercise training is a powerful therapeutic strategy that prevents cardiometabolic disease and improves cardiorespiratory fitness and performance. Despite the known systemic health benefits of exercise training, the underlying molecular mechanisms are incompletely understood. Recent evidence suggests a role for epigenetic mechanisms, such as microRNAs, but whether other small ncRNAs are modulated by chronic exercise training is unknown...
April 2018: Physiological Reports
Suresh Bugide, Michael R Green, Narendra Wajapeyee
Natural killer (NK) cell-mediated tumor cell eradication could inhibit tumor initiation and progression. However, the factors that regulate NK cell-mediated cancer cell eradication remain unclear. We determined that hepatocellular carcinoma (HCC) cells exhibit transcriptional down-regulation of NK group 2D (NKG2D) ligands and are largely resistant to NK cell-mediated eradication. Because the down-regulation of NKG2D ligands occurred at the transcriptional level, we tested 32 chemical inhibitors of epigenetic regulators for their ability to re-express NKG2D ligands and enhance HCC cell eradication by NK cells and found that Enhancer of zeste homolog 2 (EZH2) was a transcriptional repressor of NKG2D ligands...
March 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
Alexander-Thomas Hauser, Dina Robaa, Manfred Jung
DNA and histone methylation belong to the key regulatory components in the epigenetic machinery, and dysregulations of these processes have been associated with various human diseases. Small molecule modulators of these epigenetic targets are highly valuable both as chemical probes to study the biological roles of the target proteins, and as potential therapeutics. Indeed, recent years have seen the discovery of chemical modulators of several epigenetic targets, some of which are already marketed drugs or undergoing clinical trials...
March 23, 2018: Current Opinion in Chemical Biology
Paul Brennan, David Bowkett, Romain Talon, Cynthia Tallant, Chris Schofield, Gordon Bruton, Frank von Delft, Stefan Knapp
Epigenetics is of rapidly growing field in drug discovery. Of particular interest is the role of post-translational modifications to histone and the proteins that read, write, and erase such modifications. The development of inhibitors for reader domains has focused on single domains. One of the major difficulties of designing inhibitors for reader domains, is that with the notable exception of bromodomains, they tend not to possess a well enclosed binding site amenable to small molecule inhibition. As many of the proteins in epigenetic regulation have multiple domains there are opportunities for designing inhibitors that bind at a domain-domain interface which provide a more suitable interaction pocket...
March 26, 2018: ChemMedChem
Ewelina Kulikowski, Christopher Halliday, Jan Johansson, Mike Sweeney, Kenneth Lebioda, Norman Wong, Mathias Haarhaus, Vincent Brandenburg, Srinivasan Beddhu, Marcello Tonelli, Carmine Zoccali, Kamyar Kalantar-Zadeh
BACKGROUND/AIMS: The association between serum alkaline phosphatase (ALP) with adverse cardiovascular outcomes, in Chronic Kidney Disease (CKD) patients has previously been reported and may be a result of increased vascular calcification and inflammation. Here we report, for the first time, the effects of pharmacologic epigenetic modulation on levels of ALP and kidney function via a novel oral small molecule BET inhibitor, apabetalone, in CKD patients. METHODS: A post-hoc analysis evaluated patients with estimated glomerular filtration rate (eGFR) <60 mL/min/1...
March 16, 2018: Kidney & Blood Pressure Research
Xiang Li, Erchang Shang, Qiang Dong, Yingfeng Li, Jing Zhang, Shaohua Xu, Zuodong Zhao, Wei Shao, Cong Lv, Yong Zheng, Hailin Wang, Xiaoguang Lei, Bing Zhu, Zhuqiang Zhang
Regulation of gene expression by epigenetic modifications such as DNA methylation is crucial for developmental and disease processes, including cell differentiation and cancer development. Genes repressed by DNA methylation can be derepressed by various compounds that target DNA methyltransferases, histone deacetylases, and other regulatory factors. However, some additional, unknown mechanisms that promote DNA methylation-mediated gene silencing may exist. Chemical agents that can counteract the effects of epigenetic repression that is not regulated by DNA methyltransferases or histone deacetylases therefore may be of research interest...
March 20, 2018: Journal of Biological Chemistry
Jebi Sudan, Meenakshi Raina, Ravinder Singh
Plants have evolved various defense mechanisms including morphological adaptations, cellular pathways, specific signalling molecules and inherent immunity to endure various abiotic stresses during different growth stages. Most of the defense mechanisms are controlled by stress-responsive genes by transcribing and translating specific genes. However, certain modifications of DNA and chromatin along with small RNA-based mechanisms have also been reported to regulate the expression of stress-responsive genes and constitute another line of defense for plants in their struggle against stresses...
March 2018: 3 Biotech
Srikanth Appikonda, Kaushik N Thakkar, Parantu K Shah, Sharon Y R Dent, Jannik N Andersen, Michelle Craig Barton
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...
March 9, 2018: Journal of Biological Chemistry
Danny C Lenstra, Abbas H K Al Temimi, Jasmin Mecinović
Histone lysine methyltransferases G9a and GLP are validated targets for the development of new epigenetic drugs. Most, if not all, inhibitors of G9a and GLP target the histone substrate binding site or/and the S-adenosylmethionine cosubstrate binding site. Here, we report an alternative approach for inhibiting the methyltransferase activity of G9a and GLP. For proper folding and enzymatic activity, G9a and GLP contain structural zinc fingers, one of them being adjacent to the S-adenosylmethionine binding site...
February 24, 2018: Bioorganic & Medicinal Chemistry Letters
Jan Novak, Julie Bienertová Vašků, Miroslav Souček
The human genome contains about 22 000 protein-coding genes that are transcribed to an even larger amount of messenger RNAs (mRNA). Interestingly, the results of the project ENCODE from 2012 show, that despite up to 90 % of our genome being actively transcribed, protein-coding mRNAs make up only 2-3 % of the total amount of the transcribed RNA. The rest of RNA transcripts is not translated to proteins and that is why they are referred to as "non-coding RNAs". Earlier the non-coding RNA was considered "the dark matter of genome", or "the junk", whose genes has accumulated in our DNA during the course of evolution...
2018: Vnitr̆ní Lékar̆ství
Jing Zhang, Ming Jin, Xiaoyu Chen, Rui Zhang, Yanxia Huang, Hui Liu, Jinshui Zhu
OBJECTIVES: MicroRNAs (miRNAs) as small non-coding RNA molecules act by negatively regulating their target genes. Recent studies have shown that protein phosphatase Mg2+/Mn2+-dependent 1F (PPM1F) plays a critical role in cancer metastasis. But, the regulation mechanisms of PPM1F by miRNAs in gastric cancer (GC) remain undefined. METHODS: The correlation of PPM1F or miR-590-3p (miR-590) expression with clinicopathological features and prognosis of the patients with GC was analysed by TCGA RNA-sequencing data...
February 22, 2018: Cell Proliferation
Primoz Knap, Toma Tebaldi, Francesca Di Leva, Marta Biagioli, Mauro Dalla Serra, Gabriella Viero
Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i...
November 3, 2017: Toxins
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