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Balao F, Medrano M, Bazaga P, Paun O, Alonso C. Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:1199-1212. [PMID: 39250311 DOI: 10.1111/plb.13713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024]
Abstract
The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress. We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5-Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness. In the long term, 5-Azacytidine treatment alone caused both hypo- and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context-specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level.
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Affiliation(s)
- F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - M Medrano
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - P Bazaga
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - C Alonso
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
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2
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Serhouni A, Calzaferri F, Bessina Y, van der Lee A, Arimondo PB, Louet M, Winum JY, Lopez M. 3-Halo-3-nitro-aza/thioflavanones: DNMT inhibitors with a two-site binding mode in the hDNMT3A catalytic pocket. Bioorg Med Chem 2024; 118:117988. [PMID: 39689413 DOI: 10.1016/j.bmc.2024.117988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 10/28/2024] [Accepted: 11/03/2024] [Indexed: 12/19/2024]
Abstract
Flavonoid derivatives are natural product analogues that have shown great interest for therapeutic applications as modulators of DNA methylation. In this article we report new synthesis pathways to access ten novel flavonoid derivatives (i.e. 3-halo-3-nitro-aza/thioflavanones) to be used as potential DNA methyltransferase inhibitors. These compounds have a micromolar inhibition against human DNA methyltransferase 3A in our in vitro fluorescence-based assay. Importantly, a docking study of representative compounds of this series in the enzyme pocket highlights a mode of interaction in the catalytic pocket of hDNMT3A that has never been described.
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Affiliation(s)
- Alexandra Serhouni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France
| | - Francesco Calzaferri
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France
| | - Yannick Bessina
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France
| | - Arie van der Lee
- Institut Européen des Membranes (IEM), UMR 5635 CNRS-Université de Montpellier, 300 avenue du Prof. E. Jeanbrau, 34296 Montpellier cedex 5, France
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, 75015 Paris, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-Université de Montpellier-ENSCM, 1919 route de Mende, 34296 Montpellier cedex 5, France.
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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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Barbachowska M, Arimondo PB. To target or not to target? The role of DNA and histone methylation in bacterial infections. Epigenetics 2023; 18:2242689. [PMID: 37731322 PMCID: PMC10515666 DOI: 10.1080/15592294.2023.2242689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/25/2023] [Indexed: 09/22/2023] Open
Abstract
Epigenetics describes chemical modifications of the genome that do not alter DNA sequence but participate in the regulation of gene expression and cellular processes such as proliferation, division, and differentiation of eukaryotic cell. Disruption of the epigenome pattern in a human cell is associated with different diseases, including infectious diseases. During infection pathogens induce epigenetic modifications in the host cell. This can occur by controlling expression of genes involved in immune response. That enables bacterial survival and replication within the host and evasion of the immune response. Methylation is an example of epigenetic modification that occurs on DNA and histones. Reasoning that DNA and histone methylation of human host cells plays a crucial role during pathogenesis, these modifications are promising targets for the development of alternative treatment strategies in infectious diseases. Here, we discuss the role of DNA and histone methyltransferases in human host cell upon bacterial infections. We further hypothesize that compounds targeting methyltransferases are tools to study epigenetics in the context of host-pathogen interactions and can open new avenues for the treatment of bacterial infections.
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Affiliation(s)
- Magdalena Barbachowska
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
- Universite Paris Cité, Ecole Doctorale MTCI, Paris, France
- Institut Pasteur, Pasteur- Paris University (PPU)- Oxford International Doctoral Program, Paris, France
| | - Paola B. Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
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Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Zheng Q, Wang H, Yan A, Yin F, Qiao X. DNA Methylation in Alcohol Use Disorder. Int J Mol Sci 2023; 24:10130. [PMID: 37373281 DOI: 10.3390/ijms241210130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Excessive drinking damages the central nervous system of individuals and can even cause alcohol use disorder (AUD). AUD is regulated by both genetic and environmental factors. Genes determine susceptibility to alcohol, and the dysregulation of epigenome drives the abnormal transcription program and promotes the occurrence and development of AUD. DNA methylation is one of the earliest and most widely studied epigenetic mechanisms that can be inherited stably. In ontogeny, DNA methylation pattern is a dynamic process, showing differences and characteristics at different stages. DNA dysmethylation is prevalent in human cancer and alcohol-related psychiatric disorders, resulting in local hypermethylation and transcriptional silencing of related genes. Here, we summarize recent findings on the roles and regulatory mechanisms of DNA methylation, the development of methyltransferase inhibitors, methylation alteration during alcohol exposure at different stages of life, and possible therapeutic options for targeting methylation in human and animal studies.
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Affiliation(s)
- Qingmeng Zheng
- Department of Pathology and Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Heng Wang
- Department of Pathology and Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - An Yan
- Department of Pathology and Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fangyuan Yin
- School of Medicine, College of Forensic Science, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaomeng Qiao
- Department of Pathology and Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
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7
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Liu M, Liu R, Wang R, Ba Y, Yu F, Deng Q, Huang H. Lead-induced neurodevelopmental lesion and epigenetic landscape: Implication in neurological disorders. J Appl Toxicol 2022. [PMID: 36433892 DOI: 10.1002/jat.4419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Lead (Pb) was implicated in multiple genotoxic, neuroepigenotoxic, and chromosomal-toxic mechanisms and interacted with varying synaptic plasticity pathways, likely underpinning previous reports of links between Pb and cognitive impairment. Epigenetic changes have emerged as a promising biomarker for neurological disorders, including cognitive disorders, Alzheimer's disease (AD), and Parkinson's disease (PD). In the present review, special attention is paid to neural epigenetic features and mechanisms that can alter gene expression patterns upon environmental Pb exposure in rodents, primates, and zebrafish. Epigenetic modifications have also been discussed in population studies and cell experiment. Further, we explore growing evidence of potential linkage between Pb-induced disruption of regulatory pathway and neurodevelopmental and neurological disorders both in vivo and in vitro. These findings uncover how epigenome in neurons facilitates the development and function of the brain in response to Pb insult.
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Affiliation(s)
- Mengchen Liu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Rundong Liu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Ruike Wang
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Yue Ba
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Fangfang Yu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Qihong Deng
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Hui Huang
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
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Discovery of novel non-nucleoside inhibitors with high potency and selectivity for DNA methyltransferase 3A. Eur J Med Chem 2022; 242:114646. [PMID: 36029561 DOI: 10.1016/j.ejmech.2022.114646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022]
Abstract
DNA methyltransferases (DNMTs) are important epigenetic regulatory enzymes involved in gene expression corresponding to many diseases including cancer. As one of the major enzymatically active mammalian DNMTs, DNMT3A has been regarded as an attractive target for the treatment of cancer particularly in hematological malignancy. Discovery of promising inhibitors toward this target with low toxicity, adequate activity and target selectivity is therefore pivotal in the development of novel cancer therapy and the inhibitory mechanism investigation. In this study, a multistep structure-based virtual screening and in vitro bioassays were conducted to search for potent novel DNMT3A inhibitors. Compound DY-46 was then identified as a promising new scaffold candidate (IC50 = 1.3 ± 0.22 μM) that can occupy both the SAM-cofactor pocket and the cytosine pocket of DNMT3A. Further similarity searching led to the discovery of compound DY-46-2 with IC50 of 0.39 ± 0.23 μM, which showed excellent selectivity against DNMT1 (33.3-fold), DNMT3B (269-fold) and G9a (over 1000-fold). These potent compounds significantly inhibited cancer cell proliferation and showed low cytotoxicity in peripheral blood mononuclear cells. This study provides a promising scaffold for the further development of DNMT3A inhibitors, and the possibility to design proper analogs with broad or specific selectivity.
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Gutiérrez JR, Salgadoa ARM, Arias MDÁ, Vergara HSJ, Rada WR, Gómez CMM. Epigenetic Modulators as Treatment Alternative to Diverse Types of Cancer. Curr Med Chem 2021; 29:1503-1542. [PMID: 34963430 DOI: 10.2174/0929867329666211228111036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/17/2021] [Accepted: 10/21/2021] [Indexed: 01/10/2023]
Abstract
DNA is packaged in rolls in an octamer of histones forming a complex of DNA and proteins called chromatin. Chromatin as a structural matrix of a chromosome and its modifications are nowadays considered relevant aspects for regulating gene expression, which has become of high interest in understanding genetic mechanisms regulating various diseases, including cancer. In various types of cancer, the main modifications are found to be DNA methylation in the CpG dinucleotide as a silencing mechanism in transcription, post-translational histone modifications such as acetylation, methylation and others that affect the chromatin structure, the ATP-dependent chromatin remodeling and miRNA-mediated gene silencing. In this review we analyze the main alterations in gene expression, the epigenetic modification patterns that cancer cells present, as well as the main modulators and inhibitors of each epigenetic mechanism and the molecular evolution of the most representative inhibitors, which have opened a promising future in the study of HAT, HDAC, non-glycoside DNMT inhibitors and domain inhibitors.
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Affiliation(s)
- Jorseth Rodelo Gutiérrez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Arturo René Mendoza Salgadoa
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Marcio De Ávila Arias
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Homero San- Juan- Vergara
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Wendy Rosales Rada
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
| | - Carlos Mario Meléndez Gómez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
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Yu X, Li M, Guo C, Wu Y, Zhao L, Shi Q, Song J, Song B. Therapeutic Targeting of Cancer: Epigenetic Homeostasis. Front Oncol 2021; 11:747022. [PMID: 34765551 PMCID: PMC8576334 DOI: 10.3389/fonc.2021.747022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
A large number of studies have revealed that epigenetics plays an important role in cancer development. However, the currently-developed epigenetic drugs cannot achieve a stable curative effect. Thus, it may be necessary to redefine the role of epigenetics in cancer development. It has been shown that embryonic development and tumor development share significant similarities in terms of biological behavior and molecular expression patterns, and epigenetics may be the link between them. Cell differentiation is likely a manifestation of epigenetic homeostasis at the cellular level. In this article, we introduced the importance of epigenetic homeostasis in cancer development and analyzed the shortcomings of current epigenetic treatment regimens. Understanding the dynamic process of epigenetic homeostasis in organ development can help us characterize cancer according to its differentiation stages, explore new targets for cancer treatment, and improve the clinical prognosis of patients with cancer.
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Affiliation(s)
- Xiaoyuan Yu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Menglu Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Guo
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuesheng Wu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Zhao
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Shi
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianbo Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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11
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Luviano N, Lopez M, Gawehns F, Chaparro C, Arimondo PB, Ivanovic S, David P, Verhoeven K, Cosseau C, Grunau C. The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor. Epigenetics Chromatin 2021; 14:48. [PMID: 34702322 PMCID: PMC8549274 DOI: 10.1186/s13072-021-00422-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. RESULTS Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. CONCLUSIONS Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.
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Affiliation(s)
- Nelia Luviano
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Univ Montpellier, ENSCM, Montpellier, France
- Epigenetic Targeting of Cancer (ETaC), CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
| | - Fleur Gawehns
- Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Paola B Arimondo
- Epigenetic Targeting of Cancer (ETaC), CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
- Epigenetic Chemical Biology (EpiChBio), Department Structural Biology and Chemistry, UMR 3523, CNRS, Institute Pasteur, 75015, Paris, France
| | - Slavica Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Patrice David
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Univ. Montpellier, CNRS - Université Paul Valéry Montpellier - EPHE, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Koen Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Céline Cosseau
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France.
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Carbajo-García MC, Corachán A, Segura-Benitez M, Monleón J, Escrig J, Faus A, Pellicer A, Cervelló I, Ferrero H. 5-aza-2'-deoxycitidine inhibits cell proliferation, extracellular matrix formation and Wnt/β-catenin pathway in human uterine leiomyomas. Reprod Biol Endocrinol 2021; 19:106. [PMID: 34233687 PMCID: PMC8265104 DOI: 10.1186/s12958-021-00790-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/18/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Uterine leiomyoma is a benign tumor with unclear pathogenesis and inaccurate treatment. This tumor exhibits altered DNA methylation related to disease progression. DNMT inhibitors as 5-aza-2'-deoxycytidine (5-aza-CdR), have been suggested to treat tumors in which DNA methylation is altered. We aimed to evaluate whether DNA methylation reversion with 5-aza-CdR reduces cell proliferation and extracellular matrix (ECM) formation in uterine leiomyoma cells to provide a potential treatment option. METHODS Prospective study using uterine leiomyoma and adjacent myometrium tissues and human uterine leiomyoma primary (HULP) cells (n = 16). In tissues, gene expression was analyzed by qRT-PCR and DNMT activity by ELISA. Effects of 5-aza-CdR treatment on HULP cells were assessed by CellTiter, western blot, and qRT-PCR. RESULTS DNMT1 gene expression was higher in uterine leiomyoma vs myometrium. Similarly, DNMT activity was greater in uterine leiomyoma and HULP cells (6.5 vs 3.8 OD/h/mg; 211.3 vs 63.7 OD/h/mg, respectively). After 5-aza-CdR treatment on HULP cells, cell viability was reduced, significantly so at 10 μM (85.3%). Treatment with 10 μM 5-aza-CdR on HULP cells significantly decreased expression of proliferation marker PCNA (FC = 0.695) and of ECM proteins (COLLAGEN I FC = 0.654; PAI-1, FC = 0.654; FIBRONECTIN FC = 0.733). 5-aza-CdR treatment also decreased expression of Wnt/β-catenin pathway final targets, including WISP1 protein expression (10 μM, FC = 0.699), c-MYC gene expression (2 μM, FC = 0.745 and 10 μM, FC = 0.728), and MMP7 gene expression (5 μM, FC = 0.520 and 10 μM, FC = 0.577). CONCLUSIONS 5-aza-CdR treatment inhibits cell proliferation, ECM formation, and Wnt/β-catenin signaling pathway targets in HULP cells, suggesting that DNA methylation inhibition is a viable therapeutic target in uterine leiomyoma.
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Affiliation(s)
- María Cristina Carbajo-García
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
- Departamento de Pediatría, Obstetricia y Ginecología, Universidad de Valencia, Valencia, Spain
| | - Ana Corachán
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
- Departamento de Pediatría, Obstetricia y Ginecología, Universidad de Valencia, Valencia, Spain
| | - Marina Segura-Benitez
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
- Departamento de Pediatría, Obstetricia y Ginecología, Universidad de Valencia, Valencia, Spain
| | - Javier Monleón
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Julia Escrig
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Amparo Faus
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
| | - Antonio Pellicer
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
- IVIRMA Rome, Rome, Italy
| | - Irene Cervelló
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
| | - Hortensia Ferrero
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain.
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13
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Nardella F, Halby L, Dobrescu I, Viluma J, Bon C, Claes A, Cadet-Daniel V, Tafit A, Roesch C, Hammam E, Erdmann D, Mairet-Khedim M, Peronet R, Mecheri S, Witkowski B, Scherf A, Arimondo PB. Procainamide-SAHA Fused Inhibitors of hHDAC6 Tackle Multidrug-Resistant Malaria Parasites. J Med Chem 2021; 64:10403-10417. [PMID: 34185525 DOI: 10.1021/acs.jmedchem.1c00821] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic post-translational modifications are essential for human malaria parasite survival and progression through its life cycle. Here, we present new functionalized suberoylanilide hydroxamic acid (SAHA) derivatives that chemically combine the pan-histone deacetylase inhibitor SAHA with the DNA methyltransferase inhibitor procainamide. A three- or four-step chemical synthesis was designed starting from cheap raw materials. Compared to the single drugs, the combined molecules showed a superior activity in Plasmodium and a potent inhibition against human HDAC6, exerting no cytotoxicity in human cell lines. These new compounds are fully active in multidrug-resistant Plasmodium falciparum Cambodian isolates. They target transmission of the parasite by inducing irreversible morphological changes in gametocytes and inhibiting exflagellation. The compounds are slow-acting and have an additive antimalarial effect in combination with fast-acting epidrugs and dihydroartemisinin. The lead compound decreases parasitemia in mice in a severe malaria model. Taken together, this novel fused molecule offers an affordable alternative to current failing antimalarial therapy.
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Affiliation(s)
- Flore Nardella
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France
| | - Irina Dobrescu
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Johanna Viluma
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France
| | - Corentin Bon
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France.,Ecole Doctorale MTCI ED563, Université de Paris, Sorbonne Paris Cité, Paris 75270, France
| | - Aurélie Claes
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Véronique Cadet-Daniel
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France
| | - Ambre Tafit
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France
| | - Camille Roesch
- Malaria Molecular Epidemiology Unit, Pasteur Institute in Cambodia, Phnom Penh 12201, Cambodia
| | - Elie Hammam
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Diane Erdmann
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France.,Ecole Doctorale MTCI ED563, Université de Paris, Sorbonne Paris Cité, Paris 75270, France
| | - Melissa Mairet-Khedim
- Malaria Molecular Epidemiology Unit, Pasteur Institute in Cambodia, Phnom Penh 12201, Cambodia
| | - Roger Peronet
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Salah Mecheri
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Pasteur Institute in Cambodia, Phnom Penh 12201, Cambodia
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, CNRS ERL 9195, INSERM Unit U1201, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, 28 Rue du Dr Roux, Paris 75015, France
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14
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Marques-Magalhães Â, Graça I, Miranda-Gonçalves V, Henrique R, Lopez M, Arimondo PB, Jerónimo C. Anti-neoplastic and demethylating activity of a newly synthetized flavanone-derived compound in Renal Cell Carcinoma cell lines. Biomed Pharmacother 2021; 141:111681. [PMID: 34139552 DOI: 10.1016/j.biopha.2021.111681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Renal Cell Carcinoma (RCC) is on the top 10 of the most incident cancers worldwide, being a third of patients diagnosed with advanced disease, for which no curative therapies are currently available. Thus, new effective therapeutic strategies are urgently needed. Herein, we tested the antineoplastic effect of newly synthesized 3-nitroflavanones (MLo1302) on RCC cell lines. 786-O, Caki2, and ACHN cell lines were cultured and treated with newly synthesized 3-nitroflavanones. IC50 values were calculated based on the effect on cell viability assessed by MTT assay, after 72 h of exposure. MLo1302 displayed antineoplastic properties in RCC cell lines through marked reduction of cell viability, increased apoptosis and DNA damage, and morphometric alterations indicating a less aggressive phenotype. MLo1302 induced a significant reduction of global DNA methylation and DNMT mRNA levels, increasing global DNA hydroxymethylation and TET expression. Moreover, MLo1302 decreased DNMT3A activity in RCC cell lines, demethylated and re-expressed hypermethylated genes in CAM-generated tumors. A marked in vivo decrease in tumor growth and angiogenesis was also disclosed. MLo1302 disclosed antineoplastic and demethylating activity in RCC cell lines, constituting a potential therapeutic agent for RCC patients.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Université de Montpellier, ENSCM UMR 5247, Montpellier 34296, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, Paris 75724, France
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal.
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15
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Role of protein-protein interactions in allosteric drug design for DNA methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:49-84. [PMID: 32312426 DOI: 10.1016/bs.apcsb.2019.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methyltransferases (DNMTs) not only play key roles in epigenetic gene regulation, but also serve as emerging targets for several diseases, especially for cancers. Due to the multi-domains of DNMT structures, targeting allosteric sites of protein-protein interactions (PPIs) is becoming an attractive strategy in epigenetic drug discovery. This chapter aims to review the major contemporary approaches utilized for the drug discovery based on PPIs in different dimensions, from the enumeration of allosteric mechanism to the identification of allosteric pockets. These include the construction of protein structure networks (PSNs) based on molecular dynamics (MD) simulations, performing elastic network models (ENMs) and perturbation response scanning (PRS) calculation, the sequence-based conservation and coupling analysis, and the allosteric pockets identification. Furthermore, we complement this methodology by highlighting the role of computational approaches in promising practical applications for the computer-aided drug design, with special focus on two DNMTs, namely, DNMT1 and DNMT3A.
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16
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Synthesis of novel 3-halo-3-nitroflavanones and their activities as DNA methyltransferase inhibitors in cancer cells. Eur J Med Chem 2020; 186:111829. [DOI: 10.1016/j.ejmech.2019.111829] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/23/2019] [Accepted: 10/26/2019] [Indexed: 12/27/2022]
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17
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[Chemical targeting of DNA and histone methylation in cancer: Novelties, hopes and promises]. Bull Cancer 2019; 106:823-833. [PMID: 31522746 DOI: 10.1016/j.bulcan.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 01/10/2023]
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18
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Ye F, Huang J, Wang H, Luo C, Zhao K. Targeting epigenetic machinery: Emerging novel allosteric inhibitors. Pharmacol Ther 2019; 204:107406. [PMID: 31521697 DOI: 10.1016/j.pharmthera.2019.107406] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Epigenetics has emerged as an extremely exciting fast-growing area of biomedical research in post genome era. Epigenetic dysfunction is tightly related with various diseases such as cancer and aging related degeneration, potentiating epigenetics modulators as important therapeutics targets. Indeed, inhibitors of histone deacetylase and DNA methyltransferase have been approved for treating blood tumor malignancies, whereas inhibitors of histone methyltransferase and histone acetyl-lysine recognizer bromodomain are in clinical stage. However, it remains a great challenge to discover potent and selective inhibitors by targeting catalytic site, as the same subfamily of epigenetic enzymes often share high sequence identity and very conserved catalytic core pocket. It is well known that epigenetic modifications are usually carried out by multi-protein complexes, and activation of catalytic subunit is often tightly regulated by other interactive protein component, especially in disease conditions. Therefore, it is not unusual that epigenetic complex machinery may exhibit allosteric regulation site induced by protein-protein interactions. Targeting allosteric site emerges as a compelling alternative strategy to develop epigenetic drugs with enhanced druggability and pharmacological profiles. In this review, we highlight recent progress in the development of allosteric inhibitors for epigenetic complexes through targeting protein-protein interactions. We also summarized the status of clinical applications of those inhibitors. Finally, we provide perspectives of future novel allosteric epigenetic machinery modulators emerging from otherwise undruggable single protein target.
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Affiliation(s)
- Fei Ye
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jing Huang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Cheng Luo
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, South Dong Qing Road, Guizhou 550025, China.
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
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19
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Yu J, Xie T, Wang Z, Wang X, Zeng S, Kang Y, Hou T. DNA methyltransferases: emerging targets for the discovery of inhibitors as potent anticancer drugs. Drug Discov Today 2019; 24:2323-2331. [PMID: 31494187 DOI: 10.1016/j.drudis.2019.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/18/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022]
Abstract
DNA methyltransferases (DNMTs) are a conserved family of cytosine methylases with crucial roles in epigenetic regulation. They have been considered as promising therapeutic targets for the epigenetic treatment of cancer. Therefore, DNMT inhibitors (DNMTis) have attracted considerable interest in recent years for the modulation of the aberrant DNA methylation pattern in a reversible way. In this review, we provide a structure-based overview of the therapeutic importance of DNMTs against different cancer types, and then summarize recently investigated DNMTis as well as their inhibitory mechanisms, focusing on recent advances in the development of DNMTis with specificity and/or selectivity using computational approaches.
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Affiliation(s)
- Jie Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tianli Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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20
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Nguyen HP, Stewart S, Kukwikila MN, Jones SF, Offenbartl‐Stiegert D, Mao S, Balasubramanian S, Beck S, Howorka S. A Photo-responsive Small-Molecule Approach for the Opto-epigenetic Modulation of DNA Methylation. Angew Chem Int Ed Engl 2019; 58:6620-6624. [PMID: 30773767 PMCID: PMC7027477 DOI: 10.1002/anie.201901139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Indexed: 12/12/2022]
Abstract
Controlling the functional dynamics of DNA within living cells is essential in biomedical research. Epigenetic modifications such as DNA methylation play a key role in this endeavour. DNA methylation can be controlled by genetic means. Yet there are few chemical tools available for the spatial and temporal modulation of this modification. Herein, we present a small-molecule approach to modulate DNA methylation with light. The strategy uses a photo-tuneable version of a clinically used drug (5-aza-2'-deoxycytidine) to alter the catalytic activity of DNA methyltransferases, the enzymes that methylate DNA. After uptake by cells, the photo-regulated molecule can be light-controlled to reduce genome-wide DNA methylation levels in proliferating cells. The chemical tool complements genetic, biochemical, and pharmacological approaches to study the role of DNA methylation in biology and medicine.
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Affiliation(s)
- Ha Phuong Nguyen
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | | | - Mikiembo N. Kukwikila
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Sioned Fôn Jones
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Shiqing Mao
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeUK
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeUK
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeUK
| | | | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
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21
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Nguyen HP, Stewart S, Kukwikila MN, Jones SF, Offenbartl‐Stiegert D, Mao S, Balasubramanian S, Beck S, Howorka S. A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ha Phuong Nguyen
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | | | - Mikiembo N. Kukwikila
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Sioned Fôn Jones
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Shiqing Mao
- Department of ChemistryUniversity of Cambridge Lensfield Road Cambridge UK
- Cancer Research (UK) Cambridge InstituteUniversity of Cambridge Robinson Way Cambridge UK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of Cambridge Lensfield Road Cambridge UK
- Cancer Research (UK) Cambridge InstituteUniversity of Cambridge Robinson Way Cambridge UK
| | | | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
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22
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Halby L, Marechal N, Pechalrieu D, Cura V, Franchini DM, Faux C, Alby F, Troffer-Charlier N, Kudithipudi S, Jeltsch A, Aouadi W, Decroly E, Guillemot JC, Page P, Ferroud C, Bonnefond L, Guianvarc'h D, Cavarelli J, Arimondo PB. Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0072. [PMID: 29685976 DOI: 10.1098/rstb.2017.0072] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathway starting from a protected bromomethylcytosine derivative to synthesize transition state analogues of the DNA methyltransferases. This approach led to seven 5-methylcytosine-adenosine compounds that were, surprisingly, inactive against hDNMT1, hDNMT3Acat, TRDMT1 and other RNA human and viral methyltransferases. Interestingly, compound 4 and its derivative 2 showed an inhibitory activity against PRMT4 in the micromolar range. Crystal structures showed that compound 4 binds to the PRMT4 active site, displacing strongly the S-adenosyl-l-methionine cofactor, occupying its binding site, and interacting with the arginine substrate site through the cytosine moiety that probes the space filled by a substrate peptide methylation intermediate. Furthermore, the binding of the compounds induces important structural switches. These findings open new routes for the conception of new potent PRMT4 inhibitors based on the 5-methylcytosine-adenosine scaffold.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Ludovic Halby
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France.,Maison Française d'Oxford, CNRS, MEAE, 2-10 Norham Road, Oxford, UK
| | - Nils Marechal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Céline Faux
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France
| | - Fréderic Alby
- Laboratoire Pierre Fabre, 3 avenue H. Curien, 31100 Toulouse, France
| | - Nathalie Troffer-Charlier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Wahiba Aouadi
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Etienne Decroly
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Jean-Claude Guillemot
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Patrick Page
- Epiremed SAS, 1 Rue des Pénitents Blancs, 31000 Toulouse, France
| | - Clotilde Ferroud
- Laboratoire de chimie moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers, 2 rue Conté, 75003 Paris, France
| | - Luc Bonnefond
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Dominique Guianvarc'h
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Paola B Arimondo
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France .,Churchill College, CB3 0DS Cambridge, UK
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23
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Lascano S, Lopez M, Arimondo PB. Natural Products and Chemical Biology Tools: Alternatives to Target Epigenetic Mechanisms in Cancers. CHEM REC 2018; 18:1854-1876. [PMID: 30537358 DOI: 10.1002/tcr.201800133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
DNA methylation and histone acetylation are widely studied epigenetic modifications. They are involved in numerous pathologies such as cancer, neurological disease, inflammation, obesity, etc. Since the discovery of the epigenome, numerous compounds have been developed to reverse DNA methylation and histone acetylation aberrant profile in diseases. Among them several were inspired by Nature and have a great interest as therapeutic molecules. In the quest of finding new ways to target epigenetic mechanisms, the use of chemical tools is a powerful strategy to better understand epigenetic mechanisms in biological systems. In this review we will present natural products reported as DNMT or HDAC inhibitors for anticancer treatments. We will then discuss the use of chemical tools that have been used in order to explore the epigenome.
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Affiliation(s)
- Santiago Lascano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, 28 rue du Docteur Roux, 75724, Paris cedex 15, France
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24
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Manara MC, Valente S, Cristalli C, Nicoletti G, Landuzzi L, Zwergel C, Mazzone R, Stazi G, Arimondo PB, Pasello M, Guerzoni C, Picci P, Nanni P, Lollini PL, Mai A, Scotlandi K. A Quinoline-Based DNA Methyltransferase Inhibitor as a Possible Adjuvant in Osteosarcoma Therapy. Mol Cancer Ther 2018; 17:1881-1892. [DOI: 10.1158/1535-7163.mct-17-0818] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/04/2017] [Accepted: 06/21/2018] [Indexed: 11/16/2022]
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25
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Hassanzadeh M, Kasymov R, Mahernia S, Adib M, Emperle M, Dukatz M, Bashtrykov P, Jeltsch A, Amanlou M. Discovery of Novel and Selective DNA Methyltransferase 1 Inhibitors by Pharmacophore and Docking-Based Virtual Screening. ChemistrySelect 2017. [DOI: 10.1002/slct.201701734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Malihe Hassanzadeh
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Rustem Kasymov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Shabnam Mahernia
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Mehdi Adib
- School of Chemistry; College of Science; University of Tehran; Tehran Iran
| | - Max Emperle
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Michael Dukatz
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Pavel Bashtrykov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Albert Jeltsch
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Massoud Amanlou
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
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26
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Halby L, Menon Y, Rilova E, Pechalrieu D, Masson V, Faux C, Bouhlel MA, David-Cordonnier MH, Novosad N, Aussagues Y, Samson A, Lacroix L, Ausseil F, Fleury L, Guianvarc'h D, Ferroud C, Arimondo PB. Rational Design of Bisubstrate-Type Analogues as Inhibitors of DNA Methyltransferases in Cancer Cells. J Med Chem 2017; 60:4665-4679. [PMID: 28463515 DOI: 10.1021/acs.jmedchem.7b00176] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant DNA hypermethylation of promoter of tumor suppressor genes is commonly observed in cancer, and its inhibition by small molecules is promising for their reactivation. Here we designed bisubstrate analogues-based inhibitors, by mimicking each substrate, the S-adenosyl-l-methionine and the deoxycytidine, and linking them together. This approach resulted in quinazoline-quinoline derivatives as potent inhibitors of DNMT3A and DNMT1, some showing certain isoform selectivity. We highlighted the importance of (i) the nature and rigidity of the linker between the two moieties for inhibition, as (ii) the presence of the nitrogen on the quinoline group, and (iii) of a hydrophobic group on the quinazoline. The most potent inhibitors induced demethylation of CDKN2A promoter in colon carcinoma HCT116 cells and its reactivation after 7 days of treatment. Furthermore, in a leukemia cell model system, we found a correlation between demethylation of the promoter induced by the treatment, chromatin opening at the promoter, and the reactivation of a reporter gene.
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Affiliation(s)
- Ludovic Halby
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Yoann Menon
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Elodie Rilova
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Dany Pechalrieu
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Véronique Masson
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Celine Faux
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Mohamed Amine Bouhlel
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, IRCL , 59045 Lille, France
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, IRCL , 59045 Lille, France
| | - Natacha Novosad
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Yannick Aussagues
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Arnaud Samson
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | | | - Fréderic Ausseil
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Laurence Fleury
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Dominique Guianvarc'h
- Laboratoire des BioMolécules, UMR 7203, Université Pierre et Marie Curie-Paris 6-ENS-CNRS , 4, place Jussieu, 75252 Paris Cedex 05, France
| | - Clotilde Ferroud
- Laboratoire de Chimie Moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers , 2 rue Conté, 75003 Paris, France
| | - Paola B Arimondo
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France.,Churchill College , CB3 0DS Cambridge, U.K
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