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Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
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Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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2
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Park J, Lee K, Kim K, Yi SJ. The role of histone modifications: from neurodevelopment to neurodiseases. Signal Transduct Target Ther 2022; 7:217. [PMID: 35794091 PMCID: PMC9259618 DOI: 10.1038/s41392-022-01078-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and microRNA expression, play critical roles in cell differentiation and organ development through spatial and temporal gene regulation. Neurogenesis is a sophisticated and complex process by which neural stem cells differentiate into specialized brain cell types at specific times and regions of the brain. A growing body of evidence suggests that epigenetic mechanisms, such as histone modifications, allow the fine-tuning and coordination of spatiotemporal gene expressions during neurogenesis. Aberrant histone modifications contribute to the development of neurodegenerative and neuropsychiatric diseases. Herein, recent progress in understanding histone modifications in regulating embryonic and adult neurogenesis is comprehensively reviewed. The histone modifications implicated in neurodegenerative and neuropsychiatric diseases are also covered, and future directions in this area are provided.
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Affiliation(s)
- Jisu Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyubin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| | - Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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3
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Abstract
Introduction: Fatty liver disease, defined by the presence of liver fat infiltration, is part of a cluster of disorders that occur in the context of metabolic syndrome. Epigenetic factors - defined as stable and heritable changes in gene expression without changes in the DNA sequence - may not only play an important role in the disease development in adulthood, but they may start exerting their influence in the prenatal stage.Areas covered: By using systems biology approaches, we review the main epigenetic modifications and highlight their likely roles in the pathogenesis of nonalcoholic fatty liver disease.Expert opinion: Knowledge of the mechanisms by which epigenetic modifications participate in complex disorders would not only help scientists find novel therapeutic strategies but could also aid in implementing preventive care measures at gestation.
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Affiliation(s)
- Carlos Jose Pirola
- School of Medicine, Institute of Medical Research A Lanari, University of Buenos Aires, Buenos Aires, Argentina.,Department of Molecular Genetics and Biology of Complex Diseases, National Scientific and Technical Research Council (Conicet)-university of Buenos Aires. Institute of Medical Research (IDIM)
| | - Silvia Sookoian
- School of Medicine, Institute of Medical Research A Lanari, University of Buenos Aires, Buenos Aires, Argentina.,Department of Clinical and Molecular Hepatology, National Scientific and Technical Research Council (CONICET)-University of Buenos Aires. Institute of Medical Research (IDIM), Buenos Aires, Argentina
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Kamerzell TJ, Mikell B, Chen L, Elias H, Dawn B, MacRae C, Middaugh CR. The structural basis of histone modifying enzyme specificity and promiscuity: Implications for metabolic regulation and drug design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:189-243. [PMID: 35534108 DOI: 10.1016/bs.apcsb.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Histone modifying enzymes regulate chromatin architecture through covalent modifications and ultimately control multiple aspects of cellular function. Disruption of histone modification leads to changes in gene expression profiles and may lead to disease. Both small molecule inhibitors and intermediary metabolites have been shown to modulate histone modifying enzyme activity although our ability to identify successful drug candidates or novel metabolic regulators of these enzymes has been limited. Using a combination of large scale in silico screens and in vivo phenotypic analysis, we identified several small molecules and intermediary metabolites with distinctive HME activity. Our approach using unsupervised learning identifies the chemical fingerprints of both small molecules and metabolites that facilitate recognition by the enzymes active sites which can be used as a blueprint to design novel inhibitors. Furthermore, this work supports the idea that histone modifying enzymes sense intermediary metabolites integrating genes, environment and cellular physiology.
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Affiliation(s)
- Tim J Kamerzell
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States; Division of Internal Medicine, HCA MidWest Health, Overland Park, KS, United States; Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States; Applied AI Technologies, LLC, Overland Park, KS, United States.
| | - Brittney Mikell
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Lei Chen
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Harold Elias
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Calum MacRae
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
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5
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Souto JA, Sarno F, Nebbioso A, Papulino C, Álvarez R, Lombino J, Perricone U, Padova A, Altucci L, de Lera ÁR. A New Family of Jumonji C Domain-Containing KDM Inhibitors Inspired by Natural Product Purpurogallin. Front Chem 2020; 8:312. [PMID: 32523934 PMCID: PMC7261929 DOI: 10.3389/fchem.2020.00312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- José A Souto
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Federica Sarno
- Dipartimento di Medicina di Precisione, Università Degli Studi Della Campania "L. Vanvitelli", Naples, Italy
| | - Angela Nebbioso
- Dipartimento di Medicina di Precisione, Università Degli Studi Della Campania "L. Vanvitelli", Naples, Italy
| | | | - Rosana Álvarez
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | | | | | | | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università Degli Studi Della Campania "L. Vanvitelli", Naples, Italy
| | - Ángel R de Lera
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
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Zhao B, Liang Q, Ren H, Zhang X, Wu Y, Zhang K, Ma LY, Zheng YC, Liu HM. Discovery of pyrazole derivatives as cellular active inhibitors of histone lysine specific demethylase 5B (KDM5B/JARID1B). Eur J Med Chem 2020; 192:112161. [PMID: 32155529 DOI: 10.1016/j.ejmech.2020.112161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
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7
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Tsurumi A, Xue S, Zhang L, Li J, Li WX. Genome-wide Kdm4 histone demethylase transcriptional regulation in Drosophila. Mol Genet Genomics 2019; 294:1107-1121. [PMID: 31020413 PMCID: PMC6813854 DOI: 10.1007/s00438-019-01561-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/03/2019] [Indexed: 12/23/2022]
Abstract
The histone lysine demethylase 4 (Kdm4/Jmjd2/Jhdm3) family is highly conserved across species and reverses di- and tri-methylation of histone H3 lysine 9 (H3K9) and lysine 36 (H3K36) at the N-terminal tail of the core histone H3 in various metazoan species including Drosophila, C.elegans, zebrafish, mice and humans. Previous studies have shown that the Kdm4 family plays a wide variety of important biological roles in different species, including development, oncogenesis and longevity by regulating transcription, DNA damage response and apoptosis. Only two functional Kdm4 family members have been identified in Drosophila, compared to five in mammals, thus providing a simple model system. Drosophila Kdm4 loss-of-function mutants do not survive past the early 2nd instar larvae stage and display a molting defect phenotype associated with deregulated ecdysone hormone receptor signaling. To further characterize and identify additional targets of Kdm4, we employed a genome-wide approach to investigate transcriptome alterations in Kdm4 mutants versus wild-type during early development. We found evidence of increased deregulated transcripts, presumably associated with a progressive accumulation of H3K9 and H3K36 methylation through development. Gene ontology analyses found significant enrichment of terms related to the ecdysteroid hormone signaling pathway important in development, as expected, and additionally previously unidentified potential targets that warrant further investigation. Since Kdm4 is highly conserved across species, our results may be applicable more widely to other organisms and our genome-wide dataset may serve as a useful resource for further studies.
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Affiliation(s)
- Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, 50 Blossom St., Their 340, Boston, MA, 02114, USA.
- Department of Microbiology and Immunology, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Shriners Hospitals for Children-Boston®, 51 Blossom St., Boston, MA, 02114, USA.
| | - Shuang Xue
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Lin Zhang
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jinghong Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Willis X Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
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8
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Roatsch M, Hoffmann I, Abboud MI, Hancock RL, Tarhonskaya H, Hsu KF, Wilkins SE, Yeh TL, Lippl K, Serrer K, Moneke I, Ahrens TD, Robaa D, Wenzler S, Barthes NPF, Franz H, Sippl W, Lassmann S, Diederichs S, Schleicher E, Schofield CJ, Kawamura A, Schüle R, Jung M. The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases. ACS Chem Biol 2019; 14:1737-1750. [PMID: 31287655 DOI: 10.1021/acschembio.9b00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.
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Affiliation(s)
- Martin Roatsch
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Inga Hoffmann
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Martine I Abboud
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Rebecca L Hancock
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Sarah E Wilkins
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Serrer
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Isabelle Moneke
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
| | - Theresa D Ahrens
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Dina Robaa
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Sandra Wenzler
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Henriette Franz
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Wolfgang Sippl
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
- Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280 , 69120 Heidelberg , Germany
| | - Erik Schleicher
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Christopher J Schofield
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Roland Schüle
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
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9
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Monaghan L, Massett ME, Bunschoten RP, Hoose A, Pirvan PA, Liskamp RMJ, Jørgensen HG, Huang X. The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:705. [PMID: 31428579 PMCID: PMC6687838 DOI: 10.3389/fonc.2019.00705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/23/2022] Open
Abstract
Growing evidence has demonstrated that epigenetic dysregulation is a common pathological feature in human cancer cells. Global alterations in the epigenetic landscape are prevalent in malignant cells across different solid tumors including, prostate cancer, non-small-cell lung cancer, renal cell carcinoma, and in haemopoietic malignancy. In particular, DNA hypomethylation and histone hypoacetylation have been observed in acute myeloid leukemia (AML) patient blasts, with histone methylation being an emerging area of study. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification known to be involved in the regulation of a broad range of biological processes, including the formation of transcriptionally silent heterochromatin. Following the observation of its aberrant methylation status in hematological malignancy and several other cancer phenotypes, recent studies have associated H3K9me3 levels with patient outcome and highlighted key molecular mechanisms linking H3K9me3 profile with AML etiology in a number of large-scale meta-analysis. Consequently, the development and application of small molecule inhibitors which target the histone methyltransferases or demethylase enzymes known to participate in the oncogenic regulation of H3K9me3 in AML represents an advancing area of ongoing study. Here, we provide a comprehensive review on how this particular epigenetic mark is regulated within cells and its emerging role as a potential therapeutic target in AML, along with an update on the current research into advancing the generation of more potent and selective inhibitors against known H3K9 methyltransferases and demethylases.
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Affiliation(s)
- Laura Monaghan
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew E. Massett
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Alex Hoose
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Heather G. Jørgensen
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Xu Huang
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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10
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Xu X, Wang L, Hu L, Dirks WG, Zhao Y, Wei Z, Chen D, Li Z, Wang Z, Han Y, Wei L, Drexler HG, Hu Z. Small molecular modulators of JMJD1C preferentially inhibit growth of leukemia cells. Int J Cancer 2019; 146:400-412. [PMID: 31271662 DOI: 10.1002/ijc.32552] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 01/08/2023]
Abstract
Histone demethylases are promising therapeutic targets as they play fundamental roles for survival of Mixed lineage leukemia rearranged acute leukemia (MLLr AL). Here we focused on the catalytic Jumonji domain of histone H3 lysine 9 (H3K9) demethylase JMJD1C to screen for potential small molecular modulators from 149,519 natural products and 33,765 Chinese medicine components via virtual screening. JMJD1C Jumonji domain inhibitor 4 (JDI-4) and JDI-12 that share a common structural backbone were detected within the top 15 compounds. Surface plasmon resonance analysis showed that JDI-4 and JDI-12 bind to JMJD1C and its family homolog KDM3B with modest affinity. In vitro demethylation assays showed that JDI-4 can reverse the H3K9 demethylation conferred by KDM3B. In vivo demethylation assays indicated that JDI-4 and JDI-12 could induce the global increase of H3K9 methylation. Cell proliferation and colony formation assays documented that JDI-4 and JDI-12 kill MLLr AL and other malignant hematopoietic cells, but not leukemia cells resistant to JMJD1C depletion or cord blood cells. Furthermore, JDI-16, among multiple compounds structurally akin to JDI-4/JDI-12, exhibits superior killing activities against malignant hematopoietic cells compared to JDI-4/JDI-12. Mechanistically, JDI-16 not only induces apoptosis but also differentiation of MLLr AL cells. RNA sequencing and quantitative PCR showed that JDI-16 induced gene expression associated with cell metabolism; targeted metabolomics revealed that JDI-16 downregulates lactic acids, NADP+ and other metabolites. Moreover, JDI-16 collaborates with all-trans retinoic acid to repress MLLr AML cells. In summary, we identified bona fide JMJD1C inhibitors that induce preferential death of MLLr AL cells.
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Affiliation(s)
- Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,College of Bioscience and Technology, Weifang, Shandong, China
| | - Lin Wang
- The School of Physics and Optoelectronic Engineering, Weifang University, Weifang, Shandong, China
| | - Linda Hu
- Upstate Medical University, Syracuse, NY
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhishuai Wei
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Dexiang Chen
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Zhaoliang Li
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhanju Wang
- The Department of Hematology, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yangyang Han
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Liuya Wei
- College of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Hans G Drexler
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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11
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Li Z, Ding L, Li Z, Wang Z, Suo F, Shen D, Zhao T, Sun X, Wang J, Liu Y, Ma L, Zhao B, Geng P, Yu B, Zheng Y, Liu H. Development of the triazole-fused pyrimidine derivatives as highly potent and reversible inhibitors of histone lysine specific demethylase 1 (LSD1/KDM1A). Acta Pharm Sin B 2019; 9:794-808. [PMID: 31384539 PMCID: PMC6663923 DOI: 10.1016/j.apsb.2019.01.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Histone lysine specific demethylase 1 (LSD1) has been recognized as an important modulator in post-translational process in epigenetics. Dysregulation of LSD1 has been implicated in the development of various cancers. Herein, we report the discovery of the hit compound 8a (IC50 = 3.93 μmol/L) and further medicinal chemistry efforts, leading to the generation of compound 15u (IC50 = 49 nmol/L, and Ki = 16 nmol/L), which inhibited LSD1 reversibly and competitively with H3K4me2, and was selective to LSD1 over MAO-A/B. Docking studies were performed to rationalize the potency of compound 15u. Compound 15u also showed strong antiproliferative activity against four leukemia cell lines (OCL-AML3, K562, THP-1 and U937) as well as the lymphoma cell line Raji with the IC50 values of 1.79, 1.30, 0.45, 1.22 and 1.40 μmol/L, respectively. In THP-1 cell line, 15u significantly inhibited colony formation and caused remarkable morphological changes. Compound 15u induced expression of CD86 and CD11b in THP-1 cells, confirming its cellular activity and ability of inducing differentiation. The findings further indicate that targeting LSD1 is a promising strategy for AML treatment, the triazole-fused pyrimidine derivatives are new scaffolds for the development of LSD1/KDM1A inhibitors.
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Key Words
- AML treatment
- AML, acute myeloid leukemia
- ATRA, all-trans retinoic acid
- Antiproliferative ability
- BTK, Bruton׳s tyrosine kinase
- CDK, cyclin-dependent kinase
- CuAAC, copper-catalyzed azide-alkyne cycloadditions
- DABCO, triethylenediamine
- DCM, dichloromethane
- DIPEA, N,N-diisopropylethylamine
- DNMTs, DNA methyltransferases
- EA, ethyl acetate
- Epigenetic regulation
- EtOH, ethanol
- FAD, flavin adenine dinucleotide
- GSCs, glioma stem cells
- Histone demethylase
- LSD1
- LSD1, histone lysine specific demethylase 1
- MAO, monoamine oxidase
- MeOH, methanol
- Mercapto heterocycles
- PAINS, pan-assay interference compound
- Pyrimidine-triazole
- Rt, room temperature
- SAR, structure—activity relationship
- Structure–activity relationships (SARs)
- TCP, tranylcypromine
- TEA, triethylamine
- THF, terahydrofuran
- TLC, thin layer chromatography.
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Affiliation(s)
- Zhonghua Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Lina Ding
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Zhongrui Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Zhizheng Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Fengzhi Suo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Dandan Shen
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Taoqian Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Xudong Sun
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Junwei Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Ying Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Liying Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Bing Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Pengfei Geng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
- Corresponding authors.
| | - Yichao Zheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
- Corresponding authors.
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Co-Innovation Center of Henan Province for New Drug R&D and Preclinical Safety, Zhengzhou 450001, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China
- Corresponding authors.
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12
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Pippa S, Mannironi C, Licursi V, Bombardi L, Colotti G, Cundari E, Mollica A, Coluccia A, Naccarato V, La Regina G, Silvestri R, Negri R. Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. Molecules 2019; 24:molecules24091739. [PMID: 31060229 PMCID: PMC6540222 DOI: 10.3390/molecules24091739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background: KDM5 enzymes are H3K4 specific histone demethylases involved in transcriptional regulation and DNA repair. These proteins are overexpressed in different kinds of cancer, including breast, prostate and bladder carcinomas, with positive effects on cancer proliferation and chemoresistance. For these reasons, these enzymes are potential therapeutic targets. Methods: In the present study, we analyzed the effects of three different inhibitors of KDM5 enzymes in MCF-7 breast cancer cells over-expressing one of them, namely KDM5B/JARID1B. In particular we tested H3K4 demethylation (western blot); radio-sensitivity (cytoxicity and clonogenic assays) and damage accumulation (COMET assay and kinetics of H2AX phosphorylation). Results: we show that all three compounds with completely different chemical structures can selectively inhibit KDM5 enzymes and are capable of increasing sensitivity of breast cancer cells to ionizing radiation and radiation-induced damage. Conclusions: These findings confirm the involvement of H3K4 specific demethylases in the response to DNA damage, show a requirement of the catalytic function and suggest new strategies for the therapeutic use of their inhibitors.
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Affiliation(s)
- Simone Pippa
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", Italian National Research Council, 00185 Rome, Italy.
| | - Luca Bombardi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Enrico Cundari
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University "G. d' Annunzio" of Chieti, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valentina Naccarato
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
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13
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Guillade L, Sarno F, Tarhonskaya H, Nebbioso A, Alvarez S, Kawamura A, Schofield CJ, Altucci L, de Lera ÁR. Synthesis and Biological Evaluation of Tripartin, a Putative KDM4 Natural Product Inhibitor, and 1-Dichloromethylinden-1-ol Analogues. ChemMedChem 2018; 13:1949-1956. [PMID: 30047603 DOI: 10.1002/cmdc.201800377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Indexed: 12/17/2022]
Abstract
The natural product tripartin has been reported to inhibit the N-methyl-lysine histone demethylase KDM4A. A synthesis of tripartin starting from 3,5-dimethoxyphenylacrylic acid was developed, and the enantiomers were separated by chiral HPLC. We observed that both tripartin enantiomers manifested an apparent increase in H3K9me3 levels when dosed in cells, as measured by western blot analysis. Thus, there is no enantiomeric discrimination toward this natural product in terms of its effects on cellular histone methylation status. Interestingly, tripartin did not inhibit isolated KDM4A-E under our assay conditions (IC50 >100 μm). Tripartin analogues with a dichloromethylcarbinol group derived from the indanone scaffold were synthesized and found to be inactive against isolated recombinant KDM4 enzymes and in cell-based assays. Although the precise cellular mode of action of tripartin is unclear, our evidence suggests that it may affect histone methylation status via a mechanism other than direct inhibition of the KDM4 histone demethylases.
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Affiliation(s)
- Lucía Guillade
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Federica Sarno
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Angela Nebbioso
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Susana Alvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lucia Altucci
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Ángel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
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14
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Jones SE, Olsen L, Dorosz J, Seger ST, Andersson JL, Kristensen LH, Gajhede M. Peptides Derived from Histone 3 and Modified at Position 18 Inhibit Histone Demethylase KDM6 Enzymes. Chembiochem 2018; 19:1817-1822. [PMID: 29878441 DOI: 10.1002/cbic.201800185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/12/2022]
Abstract
The KDM6 subfamily of histone lysine demethylases has recently been implicated as a putative target in the treatment of a number of diseases; this makes the availability of potent and selective inhibitors important. Due to high sequence similarity of the catalytic domain of Jumonji C histone demethylases, the development of small-molecule, family-specific inhibitors has, however, proven challenging. One approach to achieve the selective inhibition of these enzymes is the use of peptides derived from the substrate, the histone 3 C terminus. Here we used computational methods to optimize such inhibitors of the KDM6 family. Through natural amino acid substitution, it is shown that a K18I variant of a histone H3 derived peptide significantly increases affinity towards the KDM6 enzymes. The crystal structure of KDM6B in complex with a histone 3 derived K18I peptide reveals a tighter fit of the isoleucine side chain, compared with that of the arginine. As a consequence, the peptide R17 residue also has increased hydrophilic interactions. These interactions of the optimized peptide are likely to be responsible for the increased affinity to the KDM6 enzymes.
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Affiliation(s)
- Sarah E Jones
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Lars Olsen
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Signe T Seger
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
| | - Jan L Andersson
- Nuevolution AB (publ.), Rønnegade 8, 2100, Copenhagen, Denmark
| | | | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
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15
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
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.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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16
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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17
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Kong L, Zhang P, Li W, Yang Y, Tian Y, Wang X, Chen S, Yang Y, Huang T, Zhao T, Tang L, Su B, Li F, Liu XS, Zhang F. KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells. Oncotarget 2018; 7:27959-74. [PMID: 27058897 PMCID: PMC5053702 DOI: 10.18632/oncotarget.8563] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/26/2016] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation plays an important role in tumor metastasis. KDM1A is a histone demethylase specific for H3K4me2/me1 demethylation, and has been found to be overexpressed in many cancers, including non-small cell lung cancer (NSCLC). However, the role of KDM1A in lung cancer remains unclear. Here, we show that KDM1A promotes cancer metastasis in NSCLC cells by repressing TIMP3 (tissue inhibitor of metalloproteinase 3) expression. Consistently with this, overexpression of TIMP3 inhibited MMP2 expression and JNK phosphorylation, both of which are known to be important for cell invasion and migration. Importantly, knockdown of TIMP3 in KDM1A-deficient cells rescued the metastatic capability of NSCLC cells. These findings were also confirmed by pharmacological inhibition assays. We further demonstrate that KDM1A removes H3K4me2 at the promoter of TIMP3, thus repressing the transcription of TIMP3. Finally, high expression of KDM1A and low expression of TIMP3 significantly correlate with a poor prognosis in NSCLC patients. This study establishes a mechanism by which KDM1A promotes cancer metastasis in NSCLC cells, and we suggest that KDM1A may be a potential therapeutic target for NSCLC treatment.
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Affiliation(s)
- Lingzhi Kong
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Wang Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yan Yang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Ye Tian
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xujun Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Sujun Chen
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yuxin Yang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianhao Huang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tian Zhao
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Liang Tang
- The Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Bo Su
- The Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Fei Li
- Department of Biology, New York University, New York, NY 10003, USA
| | - X Shirley Liu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
| | - Fan Zhang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.,School of Life Science and Technology, Tongji University, Shanghai 200092, China
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18
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Sun K, Peng JD, Suo FZ, Zhang T, Fu YD, Zheng YC, Liu HM. Discovery of tranylcypromine analogs with an acylhydrazone substituent as LSD1 inactivators: Design, synthesis and their biological evaluation. Bioorg Med Chem Lett 2017; 27:5036-5039. [PMID: 29037950 DOI: 10.1016/j.bmcl.2017.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/29/2017] [Accepted: 10/01/2017] [Indexed: 02/07/2023]
Abstract
Lysine specific demethylase 1 (LSD1), the first identified histone demethylase, plays an important role in epigenetic regulation of gene activation and repression, has been reported to be up-regulated and involved in numbers of solid malignant tumors. In this study, we identified a series of phenylalanyl hydrazones based LSD1 inhibitors, and the most potent one, compound 4q, can inactivate LSD1 with IC50 = 91.83 nM. In cellular level, compound 4q can induce the accumulation of CD86 as well as H3K4me2, and inhibit gastric cancer cell proliferation by inactivating LSD1. Our findings indicated that compound 4q may serve as a potential leading compound to target LSD1 overexpressed gastric cancer.
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Affiliation(s)
- Kai Sun
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jia-Di Peng
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Feng-Zhi Suo
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Ting Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yun-Dong Fu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Yi-Chao Zheng
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; National Center for International Research of Micro-nano Molding Technology & Key Laboratory for Micro Molding Technology of Henan Province, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.
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19
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Hayes A, Mok NY, Liu M, Thai C, Henley AT, Atrash B, Lanigan RM, Sejberg J, Le Bihan YV, Bavetsias V, Blagg J, Raynaud FI. Pyrido[3,4-d]pyrimidin-4(3H)-one metabolism mediated by aldehyde oxidase is blocked by C2-substitution. Xenobiotica 2017; 47:771-777. [PMID: 27618572 PMCID: PMC5526139 DOI: 10.1080/00498254.2016.1230245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022]
Abstract
1. We have previously described C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one derivatives as cell permeable inhibitors of the KDM4 and KDM5 subfamilies of JmjC histone lysine demethylases. 2. Although exemplar compound 1 exhibited moderate clearance in mouse liver microsomes, it was highly cleared in vivo due to metabolism by aldehyde oxidase (AO). Similar human and mouse AO-mediated metabolism was observed with the pyrido[3,4-d]pyrimidin-4(3H)-one scaffold and other C8-substituted derivatives. 3. We identified the C2-position as the oxidation site by LC-MS and 1H-NMR and showed that C2-substituted derivatives are no longer AO substrates. 4. In addition to the experimental data, these observations are supported by molecular modelling studies in the human AO protein crystal structure.
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Affiliation(s)
- Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - N. Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Ching Thai
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Alan T. Henley
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M. Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Jimmy Sejberg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I. Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
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20
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Chen YK, Bonaldi T, Cuomo A, Del Rosario JR, Hosfield DJ, Kanouni T, Kao SC, Lai C, Lobo NA, Matuszkiewicz J, McGeehan A, O’Connell SM, Shi L, Stafford JA, Stansfield RK, Veal JM, Weiss MS, Yuen NY, Wallace MB. Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS Med Chem Lett 2017; 8:869-874. [PMID: 28835804 DOI: 10.1021/acsmedchemlett.7b00220] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in the regulation of chromatin-related processes. Herein, we describe our discovery of a series of potent KDM4 inhibitors that are both cell permeable and antiproliferative in cancer models. The modulation of histone H3K9me3 and H3K36me3 upon compound treatment was verified by homogeneous time-resolved fluorescence assay and by mass spectroscopy detection. Optimization of the series using structure-based drug design led to compound 6 (QC6352), a potent KDM4 family inhibitor that is efficacious in breast and colon cancer PDX models.
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Affiliation(s)
- Young K. Chen
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Tiziana Bonaldi
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Alessandro Cuomo
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Joselyn R. Del Rosario
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - David J. Hosfield
- Ben
May Department for Cancer Research, University of Chicago, 929 East
57th Street, Chicago, Illinois 60637, United States
| | - Toufike Kanouni
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Shih-chu Kao
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Chon Lai
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Neethan A. Lobo
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Jennifer Matuszkiewicz
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Andrew McGeehan
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Shawn M. O’Connell
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Lihong Shi
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Jeffrey A. Stafford
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Ryan K. Stansfield
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - James M. Veal
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Michael S. Weiss
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Natalie Y. Yuen
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Michael B. Wallace
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
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21
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Liang J, Labadie S, Zhang B, Ortwine DF, Patel S, Vinogradova M, Kiefer JR, Mauer T, Gehling VS, Harmange JC, Cummings R, Lai T, Liao J, Zheng X, Liu Y, Gustafson A, Van der Porten E, Mao W, Liederer BM, Deshmukh G, An L, Ran Y, Classon M, Trojer P, Dragovich PS, Murray L. From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors. Bioorg Med Chem Lett 2017; 27:2974-2981. [PMID: 28512031 DOI: 10.1016/j.bmcl.2017.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/01/2017] [Accepted: 05/03/2017] [Indexed: 12/17/2022]
Abstract
A high-throughput screening (HTS) of the Genentech/Roche library identified a novel, uncharged scaffold as a KDM5A inhibitor. Lacking insight into the binding mode, initial attempts to improve inhibitor potency failed to improve potency, and synthesis of analogs was further hampered by the presence of a C-C bond between the pyrrolidine and pyridine. Replacing this with a C-N bond significantly simplified synthesis, yielding pyrazole analog 35, of which we obtained a co-crystal structure with KDM5A. Using structure-based design approach, we identified 50 with improved biochemical, cell potency and reduced MW and lower lipophilicity (LogD) compared with the original hit. Furthermore, 50 showed lower clearance than 9 in mice. In combination with its remarkably low plasma protein binding (PPB) in mice (40%), oral dosing of 50 at 5mg/kg resulted in unbound Cmax ∼2-fold of its cell potency (PC9 H3K4Me3 0.96μM), meeting our criteria for an in vivo tool compound from a new scaffold.
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Affiliation(s)
- Jun Liang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Sharada Labadie
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Birong Zhang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Snahel Patel
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - James R Kiefer
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Till Mauer
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Victor S Gehling
- Constellation Pharmaceuticals Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | | | - Richard Cummings
- Constellation Pharmaceuticals Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Tommy Lai
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jiangpeng Liao
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaoping Zheng
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yichin Liu
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Amy Gustafson
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Weifeng Mao
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Gauri Deshmukh
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Le An
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yingqing Ran
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Marie Classon
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | | | - Lesley Murray
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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22
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Basu Mallik S, Pai A, Shenoy RR, Jayashree BS. Novel flavonol analogues as potential inhibitors of JMJD3 histone demethylase-A study based on molecular modelling. J Mol Graph Model 2016; 72:81-87. [PMID: 28064082 DOI: 10.1016/j.jmgm.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/21/2016] [Accepted: 12/01/2016] [Indexed: 12/12/2022]
Abstract
Epigenetic modulation of gene expression has drawn enormous attention among researchers globally in the present scenario. Since their discovery, Jmj-C histone demethylases were identified as useful markers in understanding the role of epigenetics in inflammatory conditions and in cancer as well. This has created arousal of interest in search of suitable candidates. Potential inhibitors from various other scaffolds such as hydroxyquinolines, hydroxamic acids and triazolopyridines have already been identified and reported. In this direction, our present study attempts to target one of the important members of the family- namely JMJD3 (also known as KDM6B), that plays a pivotal role in inflammatory and immune reactions. Using molecular modeling approaches, myricetin analogues were identified as promising inhibitors of JMJD3. Extensive literature review showed myricetin as the most promising flavonol inhibitor for this enzyme. It served as a prototype for our study and modification of it's scaffold led to generation of analogues. The ZINC database was used as a repository for natural compounds and their analogues. Using similarity search options, 65 analogues of myricetin were identified and screened against JMJD3 (PDB ID: 4ASK), using the high throughput virtual screening and ligand docking tools in Maestro Molecular Modeling platform (version 10.5) from Schrödinger, LLC. 8 analogues out of 65 were identified as the most appropriate candidates which gave the best pose in ligand docking. Their binding mode and energy calculations were analysed using induced fit docking (IFD) and prime-MMGBSA tool, respectively. Thus, our findings highlight the most promising analogues of myricetin with comparable binding affinity as well as binding energy than their counterparts that could be taken for further optimisation as inhibitors of JMJD3 in both in vitro and in vivo screening studies.
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Affiliation(s)
- Sanchari Basu Mallik
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - Aravinda Pai
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - Rekha R Shenoy
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India
| | - B S Jayashree
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal, 576104, India.
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23
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Prickaerts P, Adriaens ME, Beucken TVD, Koch E, Dubois L, Dahlmans VEH, Gits C, Evelo CTA, Chan-Seng-Yue M, Wouters BG, Voncken JW. Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3. Epigenetics Chromatin 2016; 9:46. [PMID: 27800026 PMCID: PMC5080723 DOI: 10.1186/s13072-016-0086-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 08/30/2016] [Indexed: 12/15/2022] Open
Abstract
Background Trimethylation at histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) controls gene activity during development and differentiation. Whether H3K4me3 and H3K27me3 changes dynamically in response to altered microenvironmental conditions, including low-oxygen conditions commonly present in solid tumors, is relatively unknown. Demethylation of H3K4me3 and H3K27me3 is mediated by oxygen and 2-oxoglutarate dioxygenases enzymes, suggesting that oxygen deprivation (hypoxia) may influence histone trimethylation. Using the MCF7 breast epithelial adenocarcinoma cell model, we have determined the relationship between epigenomic and transcriptomic reprogramming as a function of fluctuating oxygen tension. Results We find that in MCF7, H3K4me3 and H3K27me3 marks rapidly increase at specific locations throughout the genome and are largely reversed upon reoxygenation. Whereas dynamic changes are relatively highest for H3K27me3 marking under hypoxic conditions, H3K4me3 occupation is identified as the defining epigenetic marker of transcriptional control. In agreement with the global increase of H3K27 trimethylation, we provide direct evidence that the histone H3K27me3 demethylase KDM6B/JMJD3 is inactivated by limited oxygen. In situ immunohistochemical analysis confirms a marked rise of histone trimethylation in hypoxic tumor areas. Acquisition of H3K27me3 at H3K4me3-marked loci results in a striking increase in “bivalent” epigenetic marking. Hypoxia-induced bivalency substantially overlaps with embryonal stem cell-associated genic bivalency and is retained at numerous loci upon reoxygenation. Transcriptional activity is selectively and progressively dampened at bivalently marked loci upon repeated exposure to hypoxia, indicating that this subset of genes uniquely maintains the potential for epigenetic regulation by KDM activity. Conclusions These data suggest that dynamic regulation of the epigenetic state within the tumor environment may have important consequences for tumor plasticity and biology. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0086-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peggy Prickaerts
- Department of Molecular Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Michiel E Adriaens
- Department of Bioinformatics (BiGCaT), Maastricht University Medical Centre, Maastricht, The Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Twan van den Beucken
- Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands.,Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada
| | - Elizabeth Koch
- Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Ludwig Dubois
- Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vivian E H Dahlmans
- Department of Molecular Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Caroline Gits
- Department of Molecular Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Chris T A Evelo
- Department of Bioinformatics (BiGCaT), Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Michelle Chan-Seng-Yue
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Bradly G Wouters
- Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands.,Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON Canada
| | - Jan Willem Voncken
- Department of Molecular Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
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24
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Substituted 2-(2-aminopyrimidin-4-yl)pyridine-4-carboxylates as potent inhibitors of JumonjiC domain-containing histone demethylases. Future Med Chem 2016; 8:1553-71. [DOI: 10.4155/fmc.15.188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background: Aberrant expression of iron(II)- and 2-oxoglutarate-dependent JumonjiC histone demethylases has been linked to cancer. Potent demethylase inhibitors are drug candidates and biochemical tools to elucidate the functional impact of demethylase inhibition. Methods & results: Virtual screening identified a novel lead scaffold against JMJD2A with low-micromolar potency in vitro. Analogs were acquired from commercial sources respectively synthesized in feedback with biological testing. Optimized compounds were transformed into cell-permeable prodrugs. A cocrystal x-ray structure revealed the mode of binding of these compounds as competitive to 2-oxoglutarate and confirmed kinetic experiments. Selectivity studies revealed a preference for JMJD2A and JARID1A over JMJD3. Conclusion: Virtual screening and rational structural optimization led to a novel scaffold for highly potent and selective JMJD2A inhibitors.
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25
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Morera L, Roatsch M, Fürst MCD, Hoffmann I, Senger J, Hau M, Franz H, Schüle R, Heinrich MR, Jung M. 4-Biphenylalanine- and 3-Phenyltyrosine-Derived Hydroxamic Acids as Inhibitors of the JumonjiC-Domain-Containing Histone Demethylase KDM4A. ChemMedChem 2016; 11:2063-83. [PMID: 27505861 DOI: 10.1002/cmdc.201600218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Indexed: 12/19/2022]
Abstract
Overexpression of the histone lysine demethylase KDM4A, which regulates H3K9 and H3K36 methylation states, has been related to the pathology of several human cancers. We found that a previously reported hydroxamate-based histone deacetylase (HDAC) inhibitor (SW55) was also able to weakly inhibit this demethylase with an IC50 value of 25.4 μm. Herein we report the synthesis and biochemical evaluations, with two orthogonal in vitro assays, of a series of derivatives of this lead structure. With extensive chemical modifications on the lead structure, also by exploiting the versatility of the radical arylation with aryldiazonium salts, we were able to increase the potency of the derivatives against KDM4A to the low-micromolar range and, more importantly, to obtain demethylase selectivity with respect to HDACs. Cell-permeable derivatives clearly showed a demethylase-inhibition-dependent antiproliferative effect against HL-60 human promyelocytic leukemia cells.
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Affiliation(s)
- Ludovica Morera
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Martin Roatsch
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Michael C D Fürst
- Department of Chemistry and Pharmacy, Friedrich Alexander University ErlangenNuremberg, Schuhstraße 19, 91052, Erlangen, Germany
| | - Inga Hoffmann
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Johanna Senger
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Mirjam Hau
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Henriette Franz
- Central Clinical Research, University Medical Center Freiburg, Breisacher Straße 66, 79106, Freiburg im Breisgau, Germany.,Institute of Anatomy and Cell Biology, Albert Ludwigs University Freiburg, Albertstraße 17, 79104, Freiburg im Breisgau, Germany
| | - Roland Schüle
- Central Clinical Research, University Medical Center Freiburg, Breisacher Straße 66, 79106, Freiburg im Breisgau, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Friedrich Alexander University ErlangenNuremberg, Schuhstraße 19, 91052, Erlangen, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert Ludwigs University Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany.
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26
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Lead optimization of a pyrazolo[1,5-a]pyrimidin-7(4H)-one scaffold to identify potent, selective and orally bioavailable KDM5 inhibitors suitable for in vivo biological studies. Bioorg Med Chem Lett 2016; 26:4036-41. [DOI: 10.1016/j.bmcl.2016.06.078] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/24/2022]
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27
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Turning on the Radio: Epigenetic Inhibitors as Potential Radiopriming Agents. Biomolecules 2016; 6:biom6030032. [PMID: 27384589 PMCID: PMC5039418 DOI: 10.3390/biom6030032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/09/2016] [Accepted: 06/27/2016] [Indexed: 01/02/2023] Open
Abstract
First introduced during the late 1800s, radiation therapy is fundamental to the treatment of cancer. In developed countries, approximately 60% of all patients receive radiation therapy (also known as the sixty percenters), which makes radioresistance in cancer an important and, to date, unsolved, clinical problem. Unfortunately, the therapeutic refractoriness of solid tumors is the rule not the exception, and the ubiquity of resistance also extends to standard chemotherapy, molecularly targeted therapy and immunotherapy. Based on extrapolation from recent clinical inroads with epigenetic agents to prime refractory tumors for maximum sensitivity to concurrent or subsequent therapies, the radioresistant phenotype is potentially reversible, since aberrant epigenetic mechanisms are critical contributors to the evolution of resistant subpopulations of malignant cells. Within the framework of a syllogism, this review explores the emerging link between epigenetics and the development of radioresistance and makes the case that a strategy of pre- or co-treatment with epigenetic agents has the potential to, not only derepress inappropriately silenced genes, but also increase reactive oxygen species production, resulting in the restoration of radiosensitivity.
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28
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Li Y, Tian X, Sui CG, Jiang YH, Liu YP, Meng FD. Interference of lysine-specific demethylase 1 inhibits cellular invasion and proliferation in vivo in gastric cancer MKN-28 cells. Biomed Pharmacother 2016; 82:498-508. [PMID: 27470390 DOI: 10.1016/j.biopha.2016.04.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/26/2016] [Accepted: 04/26/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Lysine-specific demethylase 1(LSD1), the first identified histone demethylase, plays an important role in the epigenetic regulation of gene activation and repression. Up-regulated LSD1expression has been reported in several malignant tumors.Our aim, therefore, was to better understand the mechanisms underlying the upregulation of LSD1 in gastric cancer. METHODS We used lentiviral shRNA to knockdown LSD1 in the gastric cancer MKN-28 cell line. Cell proliferation was measured by MTT assay while cell apoptosis was assessed by Annexin V-FITC/PI double staining flow cytometry. The invasive potential of gastric cancer cells was determined by matrigel invasion assay. Protein expression was detected by Western blot. In vivo, the effect of knocking down LSD1 on tumor growth and protein expression in gastric cancer cells in nude mice was investigated. RESULTS LSD1 knockdown in MKN-28 cell lines resulted in increasing the activity of cisplatin in vitro and the inhibition of cancer cell proliferation and invasion, and induced cell apoptosis. The expression of TGF-β1, VEGF, Bcl-2, β-catenin, p-ERK and p-Smad 2/3 proteins was inhibited in LSD1 knockdown cells. Moreover, in an in vivo model of gastric cancer, LSD1 knockdown suppressed tumor growth and protein expression. CONCLUSION LSD1 knockdown affected the fuction of gastric cancer MKN-28 cell line. LSD1 may be a latent target in the diagnosis and therapy of gastric cancer.
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Affiliation(s)
- Yan Li
- Department of Biotherapy, Cancer Research Institute, The First Affiliated Hospital of China Medical University, China
| | - Xin Tian
- Department of Biotherapy, Cancer Research Institute, The First Affiliated Hospital of China Medical University, China
| | - Cheng-Guang Sui
- Department of Biotherapy, Cancer Research Institute, The First Affiliated Hospital of China Medical University, China
| | - You-Hong Jiang
- Department of Biotherapy, Cancer Research Institute, The First Affiliated Hospital of China Medical University, China
| | - Yun-Peng Liu
- Department of Oncology, The First Affiliated Hospital of China Medical University, China
| | - Fan-Dong Meng
- Department of Biotherapy, Cancer Research Institute, The First Affiliated Hospital of China Medical University, China.
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29
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Zheng YC, Yu B, Chen ZS, Liu Y, Liu HM. TCPs: privileged scaffolds for identifying potent LSD1 inhibitors for cancer therapy. Epigenomics 2016; 8:651-66. [DOI: 10.2217/epi-2015-0002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Since the first lysine-specific demethylase (KDM), lysine-specific demethylase 1 (LSD1), was characterized in 2004, several families of KDMs have been identified. LSD1 can specifically demethylate H3K4me1/2, H3K9me1/2 as well as some nonhistone substrates. It has been demonstrated to be an oncogene as well as a drug target. Hence, tens of small-molecule LSD1 inhibitors have been designed, synthesized and applied for cancer treatment. However, the two LSD1 inhibitors that have been advanced into early phase clinical trials are trans-2-phenylcyclopropylamine (TCP) derivatives, which indicate that TCP is a druggable scaffold for LSD1 inhibitor. Here, we review the design, synthesis and properties of reported TCP-based LSD1 inhibitors as well as their biological roles.
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Affiliation(s)
- Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; Co-innovation Center of Henan Province for New drug R&D & Preclinical Safety; Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bin Yu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; Co-innovation Center of Henan Province for New drug R&D & Preclinical Safety; Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Zhe-Sheng Chen
- College of Pharmacy & Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York, NY 11439, USA
| | - Ying Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; Co-innovation Center of Henan Province for New drug R&D & Preclinical Safety; Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; Co-innovation Center of Henan Province for New drug R&D & Preclinical Safety; Institute of Drug Discovery & Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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30
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Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall K, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England K, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett J, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown N, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield C, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J. 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem 2016; 59:1388-409. [PMID: 26741168 PMCID: PMC4770324 DOI: 10.1021/acs.jmedchem.5b01635] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 11/29/2022]
Abstract
We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.
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Affiliation(s)
- Vassilios Bavetsias
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Rachel M. Lanigan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Gian Filippo Ruda
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Butrus Atrash
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Mark G. McLaughlin
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Anthony Tumber
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - N. Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Sally Dempster
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Katherine
J. Boxall
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Fiona Jeganathan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Stephanie B. Hatch
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Pavel Savitsky
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Srikannathasan Velupillai
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Tobias Krojer
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Katherine
S. England
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jimmy Sejberg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Ching Thai
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Adam Donovan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Akos Pal
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Giuseppe Scozzafava
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James
M. Bennett
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Catrine Johansson
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Aleksandra Szykowska
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carina Gileadi
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Nicola
A. Burgess-Brown
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Frank von Delft
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Udo Oppermann
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Zoe Walters
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Susan M. Westaway
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Rab K. Prinjha
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Oleg Fedorov
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | | | - Isaac M. Westwood
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Chas Bountra
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Susanne Müller
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rob L.
M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Paul E. Brennan
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Julian Blagg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
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31
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McAllister TE, England KS, Hopkinson RJ, Brennan PE, Kawamura A, Schofield CJ. Recent Progress in Histone Demethylase Inhibitors. J Med Chem 2016; 59:1308-29. [PMID: 26710088 DOI: 10.1021/acs.jmedchem.5b01758] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is increasing interest in targeting histone N-methyl-lysine demethylases (KDMs) with small molecules both for the generation of probes for target exploration and for therapeutic purposes. Here we update on previous reviews on the inhibition of the lysine-specific demethylases (LSDs or KDM1s) and JmjC families of N-methyl-lysine demethylases (JmjC KDMs, KDM2-7), focusing on the academic and patent literature from 2014 to date. We also highlight recent biochemical, biological, and structural studies which are relevant to KDM inhibitor development.
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Affiliation(s)
- Tom E McAllister
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
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32
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Westaway SM, Preston AGS, Barker MD, Brown F, Brown JA, Campbell M, Chung CW, Diallo H, Douault C, Drewes G, Eagle R, Gordon L, Haslam C, Hayhow TG, Humphreys PG, Joberty G, Katso R, Kruidenier L, Leveridge M, Liddle J, Mosley J, Muelbaier M, Randle R, Rioja I, Rueger A, Seal GA, Sheppard RJ, Singh O, Taylor J, Thomas P, Thomson D, Wilson DM, Lee K, Prinjha RK. Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-pyridine Carboxylate Derivatives. J Med Chem 2016; 59:1357-69. [PMID: 26771107 DOI: 10.1021/acs.jmedchem.5b01537] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Optimization of KDM6B (JMJD3) HTS hit 12 led to the identification of 3-((furan-2-ylmethyl)amino)pyridine-4-carboxylic acid 34 and 3-(((3-methylthiophen-2-yl)methyl)amino)pyridine-4-carboxylic acid 39 that are inhibitors of the KDM4 (JMJD2) family of histone lysine demethylases. Compounds 34 and 39 possess activity, IC50 ≤ 100 nM, in KDM4 family biochemical (RFMS) assays with ≥ 50-fold selectivity against KDM6B and activity in a mechanistic KDM4C cell imaging assay (IC50 = 6-8 μM). Compounds 34 and 39 are also potent inhibitors of KDM5C (JARID1C) (RFMS IC50 = 100-125 nM).
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Affiliation(s)
- Susan M Westaway
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Alex G S Preston
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Michael D Barker
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Fiona Brown
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Jack A Brown
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Matthew Campbell
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Chun-Wa Chung
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Hawa Diallo
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Clement Douault
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Gerard Drewes
- Cellzome GmbH, a GSK Company , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert Eagle
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Laurie Gordon
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Carl Haslam
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Thomas G Hayhow
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Philip G Humphreys
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Gerard Joberty
- Cellzome GmbH, a GSK Company , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roy Katso
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Laurens Kruidenier
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Melanie Leveridge
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - John Liddle
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Julie Mosley
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Marcel Muelbaier
- Cellzome GmbH, a GSK Company , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rebecca Randle
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Inma Rioja
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Anne Rueger
- Cellzome GmbH, a GSK Company , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gail A Seal
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Robert J Sheppard
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Onkar Singh
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Joanna Taylor
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Pamela Thomas
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Douglas Thomson
- Cellzome GmbH, a GSK Company , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David M Wilson
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Kevin Lee
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
| | - Rab K Prinjha
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K
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Ning B, Li W, Zhao W, Wang R. Targeting epigenetic regulations in cancer. Acta Biochim Biophys Sin (Shanghai) 2016; 48:97-109. [PMID: 26508480 PMCID: PMC4689160 DOI: 10.1093/abbs/gmv116] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022] Open
Abstract
Epigenetic regulation of gene expression is a dynamic and reversible process with DNA methylation, histone modifications, and chromatin remodeling. Recently, groundbreaking studies have demonstrated the importance of DNA and chromatin regulatory proteins from different aspects, including stem cell, development, and tumor genesis. Abnormal epigenetic regulation is frequently associated with diseases and drugs targeting DNA methylation and histone acetylation have been approved for cancer therapy. Although the network of epigenetic regulation is more complex than people expect, new potential druggable chromatin-associated proteins are being discovered and tested for clinical application. Here we review the key proteins that mediate epigenetic regulations through DNA methylation, the acetylation and methylation of histones, and the reader proteins that bind to modified histones. We also discuss cancer associations and recent progress of pharmacological development of these proteins.
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Affiliation(s)
- Bo Ning
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Wenyuan Li
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Wei Zhao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Rongfu Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
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34
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Abaoui M, Boutin M, Lavoie P, Auray-Blais C. Tandem mass spectrometry multiplex analysis of methylated and non-methylated urinary Gb3 isoforms in Fabry disease patients. Clin Chim Acta 2015; 452:191-8. [PMID: 26593248 DOI: 10.1016/j.cca.2015.11.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 11/15/2015] [Accepted: 11/18/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Fabry disease is a lysosomal storage disorder leading to the accumulation of glycosphingolipids in biological fluids and tissues. Globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3) are currently used for Fabry screening and diagnosis. However, these biomarkers are not always increased in Fabry patients with residual enzyme activity. We recently identified 7 urinary methylated Gb3-related isoforms. The aims of this study were (1) to develop and validate a novel LC-MS/MS method for the relative quantification of methylated and non-methylated Gb3 isoforms normalized to creatinine, (2) to evaluate these biomarkers in Fabry patients and healthy controls, and (3) to assess correlations between biomarker urinary excretion with age, gender, treatment and genotype of patients. METHODS Urine samples from 150 Fabry patients and 95 healthy controls were analyzed. Samples were purified and injected in the tandem mass spectrometer working in positive electrospray ionization. Relative quantification was performed for 15 methylated and non-methylated Gb3 isoforms. RESULTS Significant correlations (p<0.001) were established between Gb3 isoform concentrations, gender and treatment. Five patients with the late-onset cardiac mutation p.N215S showed abnormal concentrations of methylated Gb3 isoforms compared to their non-methylated homologues. CONCLUSIONS Methylated Gb3 isoforms might be helpful urinary biomarkers for Fabry patients with late-onset cardiac variant mutations.
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Affiliation(s)
- Mona Abaoui
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Michel Boutin
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pamela Lavoie
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada
| | - Christiane Auray-Blais
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Quebec J1H 5N4, Canada.
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35
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Ramachandran S, Ient J, Göttgens EL, Krieg AJ, Hammond EM. Epigenetic Therapy for Solid Tumors: Highlighting the Impact of Tumor Hypoxia. Genes (Basel) 2015; 6:935-56. [PMID: 26426056 PMCID: PMC4690023 DOI: 10.3390/genes6040935] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/18/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022] Open
Abstract
In the last few decades, epigenetics has emerged as an exciting new field in development and disease, with a more recent focus towards cancer. Epigenetics has classically referred to heritable patterns of gene expression, primarily mediated through DNA methylation patterns. More recently, it has come to include the reversible chemical modification of histones and DNA that dictate gene expression patterns. Both the epigenetic up-regulation of oncogenes and downregulation of tumor suppressors have been shown to drive tumor development. Current clinical trials for cancer therapy include pharmacological inhibition of DNA methylation and histone deacetylation, with the aim of reversing these cancer-promoting epigenetic changes. However, the DNA methyltransferase and histone deacetylase inhibitors have met with less than promising results in the treatment of solid tumors. Regions of hypoxia are a common occurrence in solid tumors. Tumor hypoxia is associated with increased aggressiveness and therapy resistance, and importantly, hypoxic tumor cells have a distinct epigenetic profile. In this review, we provide a summary of the recent clinical trials using epigenetic drugs in solid tumors, discuss the hypoxia-induced epigenetic changes and highlight the importance of testing the epigenetic drugs for efficacy against the most aggressive hypoxic fraction of the tumor in future preclinical testing.
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Affiliation(s)
- Shaliny Ramachandran
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford OX3 7DQ, UK.
| | - Jonathan Ient
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford OX3 7DQ, UK.
| | - Eva-Leonne Göttgens
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford OX3 7DQ, UK.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford OX3 7DQ, UK.
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Zheng YC, Ma J, Wang Z, Li J, Jiang B, Zhou W, Shi X, Wang X, Zhao W, Liu HM. A Systematic Review of Histone Lysine-Specific Demethylase 1 and Its Inhibitors. Med Res Rev 2015; 35:1032-71. [PMID: 25990136 DOI: 10.1002/med.21350] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/02/2015] [Accepted: 04/19/2015] [Indexed: 12/11/2022]
Abstract
Histone lysine-specific demethylase 1 (LSD1) is the first discovered and reported histone demethylase by Dr. Shi Yang's group in 2004. It is classified as a member of amine oxidase superfamily, the common feature of which is using the flavin adenine dinucleotide (FAD) as its cofactor. Since it is located in cell nucleus and acts as a histone methylation eraser, LSD1 specifically removes mono- or dimethylated histone H3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) through formaldehyde-generating oxidation. It has been indicated that LSD1 and its downstream targets are involved in a wide range of biological courses, including embryonic development and tumor-cell growth and metastasis. LSD1 has been reported to be overexpressed in variety of tumors. Inactivating LSD1 or downregulating its expression inhibits cancer-cell development. LSD1 targeting inhibitors may represent a new insight in anticancer drug discovery. This review summarizes recent studies about LSD1 and mainly focuses on the basic physiological function of LSD1 and its involved mechanisms in pathophysiologic conditions, as well as the development of LSD1 inhibitors as potential anticancer therapeutic agents.
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Affiliation(s)
- Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinlian Ma
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Zhiru Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinfeng Li
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Bailing Jiang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wenjuan Zhou
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xiaojing Shi
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xixin Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wen Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
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Hancock RL, Dunne K, Walport LJ, Flashman E, Kawamura A. Epigenetic regulation by histone demethylases in hypoxia. Epigenomics 2015; 7:791-811. [PMID: 25832587 DOI: 10.2217/epi.15.24] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The response to hypoxia is primarily mediated by the hypoxia-inducible transcription factor (HIF). Levels of HIF are regulated by the oxygen-sensing HIF hydroxylases, members of the 2-oxoglutarate (2OG) dependent oxygenase family. JmjC-domain containing histone lysine demethylases (JmjC-KDMs), also members of the 2OG oxygenase family, are key epigenetic regulators that modulate the methylation levels of histone tails. Kinetic studies of the JmjC-KDMs indicate they could also act in an oxygen-sensitive manner. This may have important implications for epigenetic regulation in hypoxia. In this review we examine evidence that the levels and activity of JmjC-KDMs are sensitive to oxygen availability, and consider how this may influence their roles in early development and hypoxic disease states including cancer and cardiovascular disease.
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Affiliation(s)
- Rebecca L Hancock
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Kate Dunne
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Louise J Walport
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Emily Flashman
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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Wang W, Marholz LJ, Wang X. Novel Scaffolds of Cell-Active Histone Demethylase Inhibitors Identified from High-Throughput Screening. ACTA ACUST UNITED AC 2015; 20:821-7. [PMID: 25883088 PMCID: PMC4475453 DOI: 10.1177/1087057115579637] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/10/2015] [Indexed: 12/27/2022]
Abstract
Jumonji C domain-containing histone demethylases (JHDMs) are epigenetic proteins capable of demethylating methylated lysine residues on histones proteins and for which high-quality chemical probes and eventual therapeutic leads are highly desirable. To expand the extent of known scaffolds targeting JHDMs, we initiated an unbiased high-throughput screening approach using a fluorescence polarization (FP)–based competitive binding assay we recently reported for JHDM1A (aka KDM2A). In total, 14,400 compounds in the HitFinder collection v.11 were screened, which represent all the distinct skeletons of the Maybridge Library. An eventual three compounds with two new scaffolds were discovered and further validated, which not only show in vitro binding for two different JHDMs, JHDM1A and JMJD2A (aka KDM4A), but also induce hypermethylation of their substrate in cells. These represent novel scaffolds as JHDM inhibitors and provide a basis for future optimization of affinity and selectivity.
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Affiliation(s)
- Wei Wang
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Laura J Marholz
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Xiang Wang
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
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Kristie TM. Dynamic modulation of HSV chromatin drives initiation of infection and provides targets for epigenetic therapies. Virology 2015; 479-480:555-61. [PMID: 25702087 DOI: 10.1016/j.virol.2015.01.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/25/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Upon infection, the genomes of herpesviruses undergo a striking transition from a non-nucleosomal structure to a chromatin structure. The rapid assembly and modulation of nucleosomes during the initial stage of infection results in an overlay of complex regulation that requires interactions of a plethora of chromatin modulation components. For herpes simplex virus, the initial chromatin dynamic is dependent on viral and host cell transcription factors and coactivators that mediate the balance between heterochromatic suppression of the viral genome and the euchromatin transition that allows and promotes the expression of viral immediate early genes. Strikingly similar to lytic infection, in sensory neurons this dynamic transition between heterochromatin and euchromatin governs the establishment, maintenance, and reactivation from the latent state. Chromatin dynamics in both the lytic infection and latency-reactivation cycles provides opportunities to shift the balance using small molecule epigenetic modulators to suppress viral infection, shedding, and reactivation from latency.
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Affiliation(s)
- Thomas M Kristie
- Molecular Genetics Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health Bld 33, Rm 3W20B.7 33 North Drive,, Bethesda, MA 20892, USA.
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Marholz LJ, Chang L, Old WM, Wang X. Development of substrate-selective probes for affinity pulldown of histone demethylases. ACS Chem Biol 2015; 10:129-37. [PMID: 25335116 PMCID: PMC4301071 DOI: 10.1021/cb5006867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
JmjC-domain
containing histone demethylases (JHDMs) play critical
roles in many key cellular processes and have been implicated in multiple
disease conditions. Each enzyme within this family is known to have
a strict substrate scope, specifically the position of the lysine
within the histone and its degree of methylation. While much progress
has been made in determining the substrates of each enzyme, new methods
with which to systematically profile each histone mark are greatly
needed. Novel chemical tools have the potential to fill this role
and, furthermore, can be used as probes to answer fundamental questions
about these enzymes and serve as potential therapeutic leads. In this
work, we first investigated three small-molecule probes differing
in the degree of “methylation state” and their differential
bindings to JHDM1A (an H3K36me1/2 demethylase) using a fluorescence
polarization-based competition assay. We then applied this specificity
toward the “methylation state” and combined it with
specificity toward lysine position in the design and synthesis of
a peptidic probe targeting H3K36me2 JHDMs. The probe is further functionalized
with a benzophenone cross-linking moiety and a biotin for affinity
purification. Results showed binding of the peptidic probe to JHDM1A
and specific enrichment of this protein in the presence of its native
histone substrates. Affinity purification pulldown experiments from
nuclear lysate coupled with mass spectrometry revealed the capability
of the probe to pull out and enrich JHDMs along with other epigenetic
proteins and transcriptional regulators.
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Affiliation(s)
- Laura J. Marholz
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Le Chang
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - William M. Old
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Xiang Wang
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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43
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Chin YW, Han SY. KDM4 histone demethylase inhibitors for anti-cancer agents: a patent review. Expert Opin Ther Pat 2014; 25:135-44. [PMID: 25468267 DOI: 10.1517/13543776.2014.991310] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION As epigenetic modulators, histone demethylases can be a therapeutic target in the area of oncology. KDM4 subfamily proteins are histone demethylases with a Jumonji domain. The subfamily consists of five functional members: KDM4A, KDM4B, KDM4C, KDM4D, and KDM4E. The role of the KDM4 subfamily proteins is reported in oncogenesis, and their overexpression in various tumor types is observed. Small molecule inhibitors for KDM4 proteins have great potential in anti-cancer therapy. AREAS COVERED A comprehensive review of the patents for KDM4 inhibitors is provided in this paper. Small molecule structural information and pharmacological effects are presented in the content. EXPERT OPINION The status of KDM4 inhibitor development is still in the early stages with small numbers of patents and journal articles. Future KDM4 inhibitor development should focus on obtaining selectivity between KDM4 subtypes, development of small molecules with in vivo activity, and extension of the therapeutic area of KDM4 inhibitors other than use in cancer therapy.
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Affiliation(s)
- Young-Won Chin
- Dongguk University-Seoul, College of Pharmacy and BK21PLUS R-FIND Team , Goyang, Gyeonggi-do 410-820 , Republic of Korea
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Leurs U, Lohse B, Rand KD, Ming S, Riise ES, Cole PA, Kristensen JL, Clausen RP. Substrate- and cofactor-independent inhibition of histone demethylase KDM4C. ACS Chem Biol 2014; 9:2131-8. [PMID: 25014588 PMCID: PMC4168794 DOI: 10.1021/cb500374f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Inhibition of histone demethylases
has within recent years advanced
into a new strategy for treating cancer and other diseases. Targeting
specific histone demethylases can be challenging, as the active sites
of KDM1A-B and KDM4A-D histone demethylases are highly conserved.
Most inhibitors developed up-to-date target either the cofactor- or
substrate-binding sites of these enzymes, resulting in a lack of selectivity
and off-target effects. This study describes the discovery of the
first peptide-based inhibitors of KDM4 histone demethylases that do
not share the histone peptide sequence or inhibit through substrate
competition. Through screening of DNA-encoded peptide libraries against
KDM1 and -4 histone demethylases by phage display, two cyclic peptides
targeting the histone demethylase KDM4C were identified and developed
as inhibitors by amino acid replacement, truncation, and chemical
modifications. Hydrogen/deuterium exchange mass spectrometry revealed
that the peptide-based inhibitors target KDM4C through substrate-independent
interactions located on the surface remote from the active site within
less conserved regions of KDM4C. The sites discovered in this study
provide a new approach of targeting KDM4C through substrate- and cofactor-independent
interactions and may be further explored to develop potent selective
inhibitors and biological probes for the KDM4 family.
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Affiliation(s)
| | | | | | - Shonoi Ming
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 316 Hunterian Building, Baltimore, Maryland 21205, United States
| | | | - Philip A. Cole
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 316 Hunterian Building, Baltimore, Maryland 21205, United States
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Simó-Riudalbas L, Esteller M. Targeting the histone orthography of cancer: drugs for writers, erasers and readers. Br J Pharmacol 2014; 172:2716-32. [PMID: 25039449 DOI: 10.1111/bph.12844] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/28/2014] [Accepted: 07/08/2014] [Indexed: 12/15/2022] Open
Abstract
Gene expression is dynamically controlled by epigenetics through post-translational modifications of histones, chromatin-associated proteins and DNA itself. All these elements are required for the maintenance of chromatin structure and cell identity in the context of a normal cellular phenotype. Disruption of epigenetic regulation is a common event in human cancer. Here, we review the key protein families that control epigenetic signalling through writing, erasing or reading specific post-translational modifications. By exploiting the leading role of epigenetics in tumour development and the reversibility of epigenetic modifications, promising novel epigenetic-based therapies are being developed. In this article, we highlight the emerging low MW inhibitors targeting each class of chromatin-associated protein, their current use in preclinical and clinical trials and the likelihood of their being approved in the near future.
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Affiliation(s)
- Laia Simó-Riudalbas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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Vianello P, Botrugno OA, Cappa A, Ciossani G, Dessanti P, Mai A, Mattevi A, Meroni G, Minucci S, Thaler F, Tortorici M, Trifiró P, Valente S, Villa M, Varasi M, Mercurio C. Synthesis, biological activity and mechanistic insights of 1-substituted cyclopropylamine derivatives: a novel class of irreversible inhibitors of histone demethylase KDM1A. Eur J Med Chem 2014; 86:352-63. [PMID: 25173853 DOI: 10.1016/j.ejmech.2014.08.068] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
Histone demethylase KDM1A (also known as LSD1) has become an attractive therapeutic target for the treatment of cancer as well as other disorders such as viral infections. We report on the synthesis of compounds derived from the expansion of tranylcypromine as a chemical scaffold for the design of novel demethylase inhibitors. These compounds, which are substituted on the cyclopropyl core moiety, were evaluated for their ability to inhibit KDM1A in vitro as well as to function in cells by modulating the expression of Gfi-1b, a well recognized KDM1A target gene. The molecules were all found to covalently inhibit KDM1A and to become increasingly selective against human monoamine oxidases MAO A and MAO B through the introduction of bulkier substituents on the cyclopropylamine ring. Structural and biochemical analysis of selected trans isomers showed that the two stereoisomers are endowed with similar inhibitory activities against KDM1A, but form different covalent adducts with the FAD co-enzyme.
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Affiliation(s)
- Paola Vianello
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Oronza A Botrugno
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Anna Cappa
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Paola Dessanti
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Antonello Mai
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, University "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Giuseppe Meroni
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Florian Thaler
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Marcello Tortorici
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Paolo Trifiró
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sergio Valente
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, University "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Manuela Villa
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Mario Varasi
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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A developmental genetic analysis of the lysine demethylase KDM2 mutations in Drosophila melanogaster. Mech Dev 2014; 133:36-53. [PMID: 25016215 DOI: 10.1016/j.mod.2014.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 06/11/2014] [Accepted: 06/17/2014] [Indexed: 12/19/2022]
Abstract
Post-translational modification of histones plays essential roles in the transcriptional regulation of genes in eukaryotes. Methylation on basic residues of histones is regulated by histone methyltransferases and histone demethylases, and misregulation of these enzymes has been linked to a range of diseases such as cancer. Histone lysine demethylase 2 (KDM2) family proteins have been shown to either promote or suppress tumorigenesis in different human malignancies. However, the roles and regulation of KDM2 in development are poorly understood, and the exact roles of KDM2 in regulating demethylation remain controversial. Since KDM2 proteins are highly conserved in multicellular animals, we analyzed the KDM2 ortholog in Drosophila. We have observed that dKDM2 is a nuclear protein and its level fluctuates during fly development. We generated three deficiency lines that disrupt the dKdm2 locus, and together with 10 transposon insertion lines within the dKdm2 locus, we characterized the developmental defects of these alleles. The alleles of dKdm2 define three phenotypic classes, and the intragenic complementation observed among these alleles and our subsequent analyses suggest that dKDM2 is not required for viability. In addition, loss of dKDM2 appears to have rather weak effects on histone H3 lysine 36 and 4 methylation (H3K36me and H3K4me) in the third instar wandering larvae, and we observed no effect on methylation of H3K9me2, H3K27me2 and H3K27me3 in dKdm2 mutants. Taken together, these genetic, molecular and biochemical analyses suggest that dKDM2 is not required for viability of flies, indicating that dKdm2 is likely redundant with other histone lysine demethylases in regulating normal development in Drosophila.
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48
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Tian X, Zhang S, Liu HM, Zhang YB, Blair CA, Mercola D, Sassone-Corsi P, Zi X. Histone lysine-specific methyltransferases and demethylases in carcinogenesis: new targets for cancer therapy and prevention. Curr Cancer Drug Targets 2014; 13:558-79. [PMID: 23713993 DOI: 10.2174/1568009611313050007] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 09/27/2012] [Accepted: 02/12/2013] [Indexed: 12/14/2022]
Abstract
Aberrant histone lysine methylation that is controlled by histone lysine methyltransferases (KMTs) and demethylases (KDMs) plays significant roles in carcinogenesis. Infections by tumor viruses or parasites and exposures to chemical carcinogens can modify the process of histone lysine methylation. Many KMTs and KDMs contribute to malignant transformation by regulating the expression of human telomerase reverse transcriptase (hTERT), forming a fused gene, interacting with proto-oncogenes or being up-regulated in cancer cells. In addition, histone lysine methylation participates in tumor suppressor gene inactivation during the early stages of carcinogenesis by regulating DNA methylation and/or by other DNA methylation independent mechanisms. Furthermore, recent genetic discoveries of many mutations in KMTs and KDMs in various types of cancers highlight their numerous roles in carcinogenesis and provide rare opportunities for selective and tumor-specific targeting of these enzymes. The study on global histone lysine methylation levels may also offer specific biomarkers for cancer detection, diagnosis and prognosis, as well as for genotoxic and non-genotoxic carcinogenic exposures and risk assessment. This review summarizes the role of histone lysine methylation in the process of cellular transformation and carcinogenesis, genetic alterations of KMTs and KDMs in different cancers and recent progress in discovery of small molecule inhibitors of these enzymes.
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Affiliation(s)
- Xuejiao Tian
- Department of Urology, University of California, Irvine, Orange CA 92868, USA
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Mannironi C, Proietto M, Bufalieri F, Cundari E, Alagia A, Danovska S, Rinaldi T, Famiglini V, Coluccia A, La Regina G, Silvestri R, Negri R. An high-throughput in vivo screening system to select H3K4-specific histone demethylase inhibitors. PLoS One 2014; 9:e86002. [PMID: 24489688 PMCID: PMC3906020 DOI: 10.1371/journal.pone.0086002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/03/2013] [Indexed: 12/15/2022] Open
Abstract
Background Histone demethylases (HDMs) have a prominent role in epigenetic regulation and are emerging as potential therapeutic cancer targets. The search for small molecules able to inhibit HDMs in vivo is very active but at the present few compounds were found to be specific for defined classes of these enzymes. Methodology/Principal Findings In order to discover inhibitors specific for H3K4 histone demethylation we set up a screening system which tests the effects of candidate small molecule inhibitors on a S.cerevisiae strain which requires Jhd2 demethylase activity to efficiently grow in the presence of rapamycin. In order to validate the system we screened a library of 45 structurally different compounds designed as competitive inhibitors of α -ketoglutarate (α-KG) cofactor of the enzyme, and found that one of them inhibited Jhd2 activity in vitro and in vivo. The same compound effectively inhibits human Jumonji AT-Rich Interactive Domain (JARID) 1B and 1D in vitro and increases H3K4 tri-methylation in HeLa cell nuclear extracts (NEs). When added in vivo to HeLa cells, the compound leads to an increase of tri-methyl-H3K4 (H3K4me3) but does not affect H3K9 tri-methylation. We describe the cytostatic and toxic effects of the compound on HeLa cells at concentrations compatible with its inhibitory activity. Conclusions/Significance Our screening system is proved to be very useful in testing putative H3K4-specific HDM inhibitors for the capacity of acting in vivo without significantly altering the activity of other important 2-oxoglutarate oxygenases.
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Affiliation(s)
- Cecilia Mannironi
- Istituto di Biologia e Patologia Molecolari Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Marco Proietto
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Francesca Bufalieri
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Enrico Cundari
- Istituto di Biologia e Patologia Molecolari Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Angela Alagia
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Svetlana Danovska
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Teresa Rinaldi
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Valeria Famiglini
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Antonio Coluccia
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Giuseppe La Regina
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Romano Silvestri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Rodolfo Negri
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- * E-mail:
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50
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Ye XW, Zheng YC, Duan YC, Wang MM, Yu B, Ren JL, Ma JL, Zhang E, Liu HM. Synthesis and biological evaluation of coumarin–1,2,3-triazole–dithiocarbamate hybrids as potent LSD1 inhibitors. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00031e] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Design of novel coumarin–1,2,3-triazole–dithiocarbamate hybrids as potent LSD1 inhibitors by introducing a coumarin scaffold.
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Affiliation(s)
- Xian-Wei Ye
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Yi-Chao Zheng
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Ying-Chao Duan
- School of Pharmacy
- Xinxiang Medical University
- Xinxiang 453003, P.R. China
| | - Meng-Meng Wang
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Bin Yu
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Jing-Li Ren
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Jin-Lian Ma
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - En Zhang
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
| | - Hong-Min Liu
- New Drug Research & Development Center
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou 450001, P.R. China
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