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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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2
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Shi Y, Yang Y, Xu S. Iridium-Catalyzed Enantioselective C(sp 3 )-H Borylation of Aminocyclopropanes. Angew Chem Int Ed Engl 2022; 61:e202201463. [PMID: 35194926 DOI: 10.1002/anie.202201463] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 12/17/2022]
Abstract
Transition-metal-catalyzed regio- and stereo-controllable C-H functionalization remains a formidable challenge in asymmetric catalysis. Herein, we disclose the first example of iridium-catalyzed C(sp3 )-H borylation of aminocyclopropanes by using simple imides as weakly coordinating directing groups under mild reaction conditions. The reaction proceeded via a six-membered iridacycle, affording a vast range of chiral aminocyclopropyl boronates. The current method features a broad spectrum of functional groups (36 examples) and high enantioselectivities (up to 99 %). We also demonstrated the synthetic utility by a preparative scale C-H borylation, C-B bond transformations, and conversion of the directing group.
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Affiliation(s)
- Yongjia Shi
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yuhuan Yang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Senmiao Xu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China
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3
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Shi Y, Yang Y, Xu S. Iridium‐Catalyzed Enantioselective C(sp
3
)−H Borylation of Aminocyclopropanes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yongjia Shi
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Lanzhou Institute of Chemical Physics Chinese Academy of Sciences Lanzhou 730000 China
| | - Yuhuan Yang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Lanzhou Institute of Chemical Physics Chinese Academy of Sciences Lanzhou 730000 China
| | - Senmiao Xu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Lanzhou Institute of Chemical Physics Chinese Academy of Sciences Lanzhou 730000 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education Hangzhou Normal University Hangzhou 311121 China
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4
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Teresa Borrello M, Benelkebir H, Lee A, Hin Tam C, Shafat M, Rushworth SA, Bowles KM, Douglas L, Duriez PJ, Bailey S, Crabb SJ, Packham G, Ganesan A. Synthesis of Carboxamide-Containing Tranylcypromine Analogues as LSD1 (KDM1A) Inhibitors Targeting Acute Myeloid Leukemia. ChemMedChem 2021; 16:1316-1324. [PMID: 33533576 DOI: 10.1002/cmdc.202000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/18/2020] [Indexed: 01/14/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) oxidatively removes methyl groups from histone proteins, and its aberrant activity has been correlated with cancers including acute myeloid leukemia (AML). We report a novel series of tranylcypromine analogues with a carboxamide at the 4-position of the aryl ring. These compounds, such as 5 a and 5 b with benzyl and phenethylamide substituents, respectively, had potent sub-micromolar IC50 values for the inhibition of LSD1 as well as cell proliferation in a panel of AML cell lines. The dose-dependent increase in cellular expression levels of H3K4me2, CD86, CD11b and CD14 supported a mechanism involving LSD1 inhibition. The tert-butyl and ethyl carbamate derivatives of these tranylcypromines, although inactive in LSD1 inhibition, were of similar potency in cell-based assays with a more rapid onset of action. This suggests that carbamates can act as metabolically labile tranylcypromine prodrugs with superior pharmacokinetics.
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Affiliation(s)
| | - Hanae Benelkebir
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Adam Lee
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Chak Hin Tam
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Manar Shafat
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Kristian M Bowles
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Leon Douglas
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Patrick J Duriez
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Sarah Bailey
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Simon J Crabb
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Graham Packham
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
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5
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Liang X, Yu P, Fu C, Shen Y. Organotin-catalyzed synthesis of hydroxyalkylamides from lactones via a ring-opening process. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Zhang Y, Li Y, Zhou W, Zhang M, Zhang Q, Jia R, Zhao J. Assembly of polysubstituted chiral cyclopropylamines via highly enantioselective Cu-catalyzed three-component cyclopropene alkenylamination. Chem Commun (Camb) 2020; 56:12250-12253. [PMID: 32929423 DOI: 10.1039/d0cc01060j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enabled by a commercial bisphosphine ligand, the Cu-catalyzed three-component cyclopropene alkenylamination with alkenyl organoboron reagent and hyroxyamine esters proceeds with exceptionally high enantioselectivity to deliver poly-substituted cis-1,2-alkenylcyclopropylamines that contain up to all three stereogenic centers on the cyclopropane.
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Affiliation(s)
- Yu Zhang
- Jilin Province Key Laboratory of Functional Organic Molecule Design & Synthesis, Department of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China.
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7
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Abstract
KDM5 family members (A, B, C and D) that demethylate H3K4me3 have been shown to be involved in human cancers. Here we performed screening for KDM5A inhibitors from chemical libraries using the AlphaScreen method and identified a battery of screening hits that inhibited recombinant KDM5A. These compounds were further subjected to cell-based screening using a reporter gene that responded to KDM5A inhibition and 6 compounds were obtained as candidate inhibitors. When further confirmation of their inhibition activity on cellular KDM5A was made by immunostaining H3K4me3 in KDM5A-overexpressing cells, ryuvidine clearly repressed H3K4me3 demethylation. Ryuvidine prevented generation of gefitinib-tolerant human small-cell lung cancer PC9 cells and also inhibited the growth of the drug-tolerant cells at concentrations that did not affect the growth of parental PC9 cells. Ryuvidine inhibited not only KDM5A but also recombinant KDM5B and C; KDM5B was the most sensitive to the inhibitor. These results warrant that ryuvidine may serve as a lead compound for KDM5 targeted therapeutics.
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8
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Lee A, Borrello MT, Ganesan A. LSD
(Lysine‐Specific Demethylase): A Decade‐Long Trip from Discovery to Clinical Trials. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527809257.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Ota Y, Suzuki T. Drug Design Concepts for LSD1-Selective Inhibitors. CHEM REC 2018; 18:1782-1791. [PMID: 30277644 DOI: 10.1002/tcr.201810031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022]
Abstract
Lysine-specific demethylase 1 (LSD1) is one of the flavin-dependent oxidases and is involved in many cellular processes by controlling the methylation of histone H3. Recently, it has been reported that LSD1 is associated with several diseases such as cancer, metabolic disorders, and psychiatric diseases. Thus, LSD1 is an attractive molecular target for the treatment of these diseases, and its inhibitors are predicted as therapeutic agents. Although a variety of LSD1 inhibitors have been reported to date, many of them show insufficient activities and selectivity toward LSD1. Meanwhile, we identified several LSD1-selective inhibitors using target-guided synthesis strategies based on our original ideas. Our LSD1 inhibitors show not only potent LSD1-selective inhibitory activities, but also unique bioactivities both in vitro and in vivo. This account highlights our drug design concepts for and identification of LSD1-selective inhibitors.
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Affiliation(s)
- Yosuke Ota
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
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10
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Design, Synthesis, and In Vitro Evaluation of Novel Histone H3 Peptide-Based LSD1 Inactivators Incorporating α,α-Disubstituted Amino Acids with γ-Turn-Inducing Structures. Molecules 2018; 23:molecules23051099. [PMID: 29734782 PMCID: PMC6099693 DOI: 10.3390/molecules23051099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 01/16/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) mainly removes methyl groups of mono- or di-methylated lysine residues at the fourth position of histone H3 to epigenetically regulate the expression of genes associated with several diseases, such as cancer. Therefore, LSD1 inactivators are expected to be used as therapeutic agents. In this study, to identify novel peptide-based LSD1 inactivators, we focused on the X-ray structure of LSD1 complexed with a H3 peptide-based suicide substrate. It has been proposed that a methylated histone substrate forms three consecutive γ-turn structures in the active pocket of LSD1. Based on this, we designed and synthesized novel histone H3 peptide-based LSD1 inactivators 2a⁻c by incorporating various α,α-disubstituted amino acids with γ-turn-inducing structures. Among synthetic peptides 2a⁻c, peptide 2b incorporating two 1-aminocyclohexanecarboxylic acids at both sides of a lysine residue bearing a trans-2-phenylcyclopropylamine (PCPA) moiety, which is a pharmacophore for LSD1 inactivation, was the most potent and selective LSD1 inactivator. These findings are useful for the further development of histone H3 peptide-based LSD1 inactivators.
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11
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Tomilov YV, Menchikov LG, Novikov RA, Ivanova OA, Trushkov IV. Methods for the synthesis of donor-acceptor cyclopropanes. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4787] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Ghosh AK, Sarkar A, Brindisi M. The Curtius rearrangement: mechanistic insight and recent applications in natural product syntheses. Org Biomol Chem 2018; 16:2006-2027. [PMID: 29479624 PMCID: PMC5864567 DOI: 10.1039/c8ob00138c] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Curtius rearrangement is a versatile reaction in which a carboxylic acid can be converted to an isocyanate through an acyl azide intermediate under mild conditions. The resulting stable isocyanate can then be readily transformed into a variety of amines and amine derivatives including urethanes and ureas. There have been wide-ranging applications of the Curtius rearrangement in the synthesis of natural products and their derivatives. Also, this reaction has been extensively utilized in the synthesis and application of a variety of biomolecules. In this review, we present mechanistic studies, chemical methodologies and reagents for the synthesis of isocyanates from carboxylic acids, the conversion of isocyanates to amines and amine derivatives, and their applications in the synthesis of bioactive natural products and their congeners.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Anindya Sarkar
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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13
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Song L, Merceron R, Gracia B, Quintana AL, Risseeuw MDP, Hulpia F, Cos P, Aínsa JA, Munier-Lehmann H, Savvides SN, Van Calenbergh S. Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors. J Med Chem 2018; 61:2753-2775. [DOI: 10.1021/acs.jmedchem.7b01570] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Romain Merceron
- VIB Center for Inflammation Research, Zwijnaarde, Ghent 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Begoña Gracia
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ainhoa Lucía Quintana
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Martijn D. P. Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen, Belgium
| | - José A. Aínsa
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28 Rue du Dr. Roux, Cedex 15 75724 Paris, France
| | - Savvas N. Savvides
- VIB Center for Inflammation Research, Zwijnaarde, Ghent 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
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14
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Ota Y, Miyamura S, Araki M, Itoh Y, Yasuda S, Masuda M, Taniguchi T, Sowa Y, Sakai T, Itami K, Yamaguchi J, Suzuki T. Design, synthesis and evaluation of γ-turn mimetics as LSD1-selective inhibitors. Bioorg Med Chem 2018; 26:775-785. [DOI: 10.1016/j.bmc.2017.12.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/25/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
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15
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Kakizawa T, Ota Y, Itoh Y, Suzuki T. Histone H3 peptides incorporating modified lysine residues as lysine-specific demethylase 1 inhibitors. Bioorg Med Chem Lett 2018; 28:167-169. [DOI: 10.1016/j.bmcl.2017.11.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/08/2017] [Accepted: 11/23/2017] [Indexed: 10/18/2022]
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16
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Castelli G, Pelosi E, Testa U. Targeting histone methyltransferase and demethylase in acute myeloid leukemia therapy. Onco Targets Ther 2017; 11:131-155. [PMID: 29343972 PMCID: PMC5749389 DOI: 10.2147/ott.s145971] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome. In fact, genes involved in DNA demethylation (such as DNMT3A, TET2, IDH1, and IDH2) or histone methylation and demethylation (EZH2, MLL, DOT1L) are frequently mutated in primary and secondary AML. Furthermore, some histone demethylases, such as LSD1, are frequently overexpressed in AML. These observations have strongly supported a major role of dysregulated epigenetic regulatory processes in leukemia onset and development. This conclusion was further supported by the observation that mutations in genes encoding epigenetic modifiers, such as DMT3A, ASXL1, TET2, IDH1, and IDH2, are usually acquired early and are present in the founding leukemic clone. These observations have contributed to development of the idea that targeting epigenetic abnormalities could represent a potentially promising strategy for the development of innovative treatments of AML. In this review, we analyze those proteins and their inhibitors that have already reached the first stages of clinical trials in AML, namely the histone methyltransferase DOT1L, the demethylase LSD1, and the MLL-interacting protein menin.
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Affiliation(s)
- Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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17
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Zalloum WA, Zalloum HM. Exploring the Active Center of the LSD1/CoREST Complex by Molecular Dynamics Simulation Utilizing Its Co-crystallized Co-factor Tetrahydrofolate as a Probe. J Chem Inf Model 2017; 57:3022-3031. [PMID: 29161028 DOI: 10.1021/acs.jcim.7b00256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic targeting of cancer is a recent effort to manipulate the gene without destroying the genetic material. Lysine-specific demethylase 1 (LSD1) is one of the enzymes associated with the chromatin for post-translational modifications, where it demethylates lysine amino acid in the chromatin H3 tail. Many studies showed that inhibiting LSD1 could potentially be used to treat cancer epigenetically. LSD1 is associated with its corepressor protein CoREST, and it uses tetrahydrofolate as a co-factor to accept CH2 from the demethylation process. In this study, the co-crystallized co-factor tetrahydrofolate was utilized to determine possible binding regions in the active center of the LSD1/CoREST complex. Also, the flexibility of the complex has been investigated by molecular dynamics simulation and subsequent analysis by clustering and principal component analysis. This research supported other studies and showed that LSD1/CoREST complex exists in two main conformational structures: open and closed. Furthermore, this study showed that tetrahydrofolate stably binds to the LSD1/CoREST complex, in its open conformation, at its entrance. It then binds to the core of the complex, inducing the closed conformation. Furthermore, the interactions of tetrahydrofolate to these two binding regions and the corresponding binding mode of tetrahydrofolate were investigated to be used in structure-based drug design.
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Affiliation(s)
- Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba , P.O. Box 2882, Amman 11821, Jordan
| | - Hiba M Zalloum
- Hamdi Mango Research Center for Scientific Research, The University of Jordan , Amman 11942, Jordan
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18
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Fluorinated tranylcypromine analogues as inhibitors of lysine-specific demethylase 1 (LSD1, KDM1A). Bioorg Med Chem Lett 2017; 27:2099-2101. [DOI: 10.1016/j.bmcl.2017.03.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 02/07/2023]
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19
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Niwa H, Umehara T. Structural insight into inhibitors of flavin adenine dinucleotide-dependent lysine demethylases. Epigenetics 2017; 12:340-352. [PMID: 28277979 PMCID: PMC5453194 DOI: 10.1080/15592294.2017.1290032] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Until 2004, many researchers believed that protein methylation in eukaryotic cells was an irreversible reaction. However, the discovery of lysine-specific demethylase 1 in 2004 drastically changed this view and the concept of chromatin regulation. Since then, the enzymes responsible for lysine demethylation and their cellular substrates, biological significance, and selective regulation have become major research topics in epigenetics and chromatin biology. Many cell-permeable inhibitors for lysine demethylases have been developed, including both target-specific and nonspecific inhibitors. Structural understanding of how these inhibitors bind to lysine demethylases is crucial both for validation of the inhibitors as chemical probes and for the rational design of more potent, target-specific inhibitors. This review focuses on published small-molecule inhibitors targeted at the two flavin adenine dinucleotide-dependent lysine demethylases, lysine-specific demethylases 1 and 2, and how the inhibitors interact with the tertiary structures of the enzymes.
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Affiliation(s)
- Hideaki Niwa
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan
| | - Takashi Umehara
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan.,b PRESTO, Japan Science and Technology Agency (JST) , Honcho, Kawaguchi , Saitama , Japan
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20
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Jambhekar A, Anastas JN, Shi Y. Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026484. [PMID: 28049654 DOI: 10.1101/cshperspect.a026484] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dynamic regulation of covalent modifications to histones is essential for maintaining genomic integrity and cell identity and is often compromised in cancer. Aberrant expression of histone lysine demethylases has been documented in many types of blood and solid tumors, and thus demethylases represent promising therapeutic targets. Recent advances in high-throughput chemical screening, structure-based drug design, and structure-activity relationship studies have improved both the specificity and the in vivo efficacy of demethylase inhibitors. This review will briefly outline the connection between demethylases and cancer and will provide a comprehensive overview of the structure, specificity, and utility of currently available demethylase inhibitors. To date, a select group of demethylase inhibitors is being evaluated in clinical trials, and additional compounds may soon follow from the bench to the bedside.
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Affiliation(s)
- Ashwini Jambhekar
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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21
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Sareddy GR, Viswanadhapalli S, Surapaneni P, Suzuki T, Brenner A, Vadlamudi RK. Novel KDM1A inhibitors induce differentiation and apoptosis of glioma stem cells via unfolded protein response pathway. Oncogene 2016; 36:2423-2434. [PMID: 27893719 DOI: 10.1038/onc.2016.395] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 12/15/2022]
Abstract
Glioma stem cells (GSCs) have a central role in glioblastoma (GBM) development and chemo/radiation resistance, and their elimination is critical for the development of efficient therapeutic strategies. Recently, we showed that lysine demethylase KDM1A is overexpressed in GBM. In the present study, we determined whether KDM1A modulates GSCs stemness and differentiation and tested the utility of two novel KDM1A-specific inhibitors (NCL-1 and NCD-38) to promote differentiation and apoptosis of GSCs. The efficacy of KDM1A targeting drugs was tested on purified GSCs isolated from established and patient-derived GBMs using both in vitro assays and in vivo orthotopic preclinical models. Our results suggested that KDM1A is highly expressed in GSCs and knockdown of KDM1A using shRNA-reduced GSCs stemness and induced the differentiation. Pharmacological inhibition of KDM1A using NCL-1 and NCD-38 significantly reduced the cell viability, neurosphere formation and induced apoptosis of GSCs with little effect on differentiated cells. In preclinical studies using orthotopic models, NCL-1 and NCD-38 significantly reduced GSCs-driven tumor progression and improved mice survival. RNA-sequencing analysis showed that KDM1A inhibitors modulate several pathways related to stemness, differentiation and apoptosis. Mechanistic studies showed that KDM1A inhibitors induce activation of the unfolded protein response (UPR) pathway. These results strongly suggest that selective targeting of KDM1A using NCL-1 and NCD-38 is a promising therapeutic strategy for elimination of GSCs.
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Affiliation(s)
- G R Sareddy
- The Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - S Viswanadhapalli
- The Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - P Surapaneni
- The Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - T Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,CREST, Japan Science and Technology Agency (JST), Saitama, Japan
| | - A Brenner
- Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,The Department of Hematology and Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - R K Vadlamudi
- The Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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22
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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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23
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Paluch BE, Naqash AR, Brumberger Z, Nemeth MJ, Griffiths EA. Epigenetics: A primer for clinicians. Blood Rev 2016; 30:285-95. [PMID: 26969414 DOI: 10.1016/j.blre.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/04/2016] [Accepted: 02/12/2016] [Indexed: 01/08/2023]
Abstract
With recent advances in cellular biology, we now appreciate that modifications to DNA and histones can have a profound impact on transcription and function, even in the absence of changes to DNA sequence. These modifications, now commonly referred to as "epigenetic" alterations, have changed how we understand cell behavior, reprogramming and differentiation and have provided significant insight into the mechanisms underlying carcinogenesis. Epigenetic alterations, to this point, are largely identified by changes in DNA methylation and hydroxymethylation as well as methylation, acetylation, and phosphorylation of histone tails. These modifications enable significant flexibility in gene expression, rather than just turning genes "ON" or "OFF." Herein we describe the epigenetic landscape in the regulation of gene expression with a particular focus on interrogating DNA methylation in myeloid malignancy.
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Affiliation(s)
- Benjamin E Paluch
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA.
| | - Abdul R Naqash
- Catholic Health, State University of New York at Buffalo (SUNY), 2157 Main Street, 14214 Buffalo, NY, USA.
| | - Zachary Brumberger
- University at Buffalo State University of New York, School of Medicine and Biomedical Sciences, 3435 Main Street, 14260 Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA
| | - Elizabeth A Griffiths
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA; Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA; Leukemia Division, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA.
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24
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Kakizawa T, Mizukami T, Itoh Y, Hasegawa M, Sasaki R, Suzuki T. Evaluation of phenylcyclopropylamine compounds by enzymatic assay of lysine-specific demethylase 2 in the presence of NPAC peptide. Bioorg Med Chem Lett 2016; 26:1193-5. [PMID: 26794039 DOI: 10.1016/j.bmcl.2016.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/06/2016] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
Lysine-specific demethylase 2 (LSD2) demethylates mono- and dimethylated Lys-4 of histone H3 (H3K4me1 and H3K4me2). NPAC protein is known to interact with LSD2 and promote its H3K4 demethylase activity. In this study, we established a demethylation assay system that utilizes recombinant LSD2 in the presence of a synthetic NPAC peptide. Several phenylcyclopropylamine (PCPA)-based inhibitors were examined for their LSD2 inhibitory activity in the LSD2 enzymatic assay with the NPAC peptide. The assay results showed that the PCPA derivatives, including NCD41, selectively inhibited LSD1 in preference to LSD2.
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Affiliation(s)
- Taeko Kakizawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo 169-8555, Japan
| | - Tamio Mizukami
- Graduate School of Bio-Science, Nagahama Institute of Bio-Science Technology, 1226 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Makoto Hasegawa
- Graduate School of Bio-Science, Nagahama Institute of Bio-Science Technology, 1226 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Ryuzo Sasaki
- Graduate School of Bio-Science, Nagahama Institute of Bio-Science Technology, 1226 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.
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25
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Itoh Y, Aihara K, Mellini P, Tojo T, Ota Y, Tsumoto H, Solomon VR, Zhan P, Suzuki M, Ogasawara D, Shigenaga A, Inokuma T, Nakagawa H, Miyata N, Mizukami T, Otaka A, Suzuki T. Identification of SNAIL1 Peptide-Based Irreversible Lysine-Specific Demethylase 1-Selective Inactivators. J Med Chem 2016; 59:1531-44. [DOI: 10.1021/acs.jmedchem.5b01323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yukihiro Itoh
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Keisuke Aihara
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Paolo Mellini
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Toshifumi Tojo
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Yosuke Ota
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-Cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Viswas Raja Solomon
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Peng Zhan
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Miki Suzuki
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Daisuke Ogasawara
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Akira Shigenaga
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Tsubasa Inokuma
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Hidehiko Nakagawa
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Naoki Miyata
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tamio Mizukami
- Graduate
School of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Akira Otaka
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Takayoshi Suzuki
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
- CREST, Japan Science
and Technology Agency (JST), 4-1-8
Honcho Kawaguchi, Saitama 332-0012, Japan
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26
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Miyamura S, Araki M, Ota Y, Itoh Y, Yasuda S, Masuda M, Taniguchi T, Sowa Y, Sakai T, Suzuki T, Itami K, Yamaguchi J. C–H activation enables a rapid structure–activity relationship study of arylcyclopropyl amines for potent and selective LSD1 inhibitors. Org Biomol Chem 2016; 14:8576-85. [DOI: 10.1039/c6ob01483f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potent and selective LSD1 inhibitors were synthesized rapidly by a C–H borylation and cross-coupling sequence.
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27
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Nowotarski SL, Pachaiyappan B, Holshouser SL, Kutz CJ, Li Y, Huang Y, Sharma SK, Casero RA, Woster PM. Structure-activity study for (bis)ureidopropyl- and (bis)thioureidopropyldiamine LSD1 inhibitors with 3-5-3 and 3-6-3 carbon backbone architectures. Bioorg Med Chem 2015; 23:1601-12. [PMID: 25725609 PMCID: PMC4396983 DOI: 10.1016/j.bmc.2015.01.049] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/16/2022]
Abstract
Methylation at specific histone lysine residues is a critical post-translational modification that alters chromatin architecture, and dysregulated lysine methylation/demethylation is associated with the silencing of tumor suppressor genes. The enzyme lysine-specific demethylase 1 (LSD1) complexed to specific transcription factors catalyzes the oxidative demethylation of mono- and dimethyllysine 4 of histone H3 (H3K4me and H3K4me2, respectively). We have previously reported potent (bis)urea and (bis)thiourea LSD1 inhibitors that increase cellular levels of H3K4me and H3K4me2, promote the re-expression of silenced tumor suppressor genes and suppress tumor growth in vitro. Here we report the design additional (bis)urea and (bis)thiourea LSD1 inhibitors that feature 3-5-3 or 3-6-3 carbon backbone architectures. Three of these compounds displayed single-digit IC50 values in a recombinant LSD1 assay. In addition, compound 6d exhibited an IC50 of 4.2μM against the Calu-6 human lung adenocarcinoma line, and 4.8μM against the MCF7 breast tumor cell line, in an MTS cell viability assay. Following treatment with 6b-6d, Calu-6 cells exhibited a significant increase in the mRNA expression for the silenced tumor suppressor genes SFRP2, HCAD and p16, and modest increases in GATA4 message. The compounds described in this paper represent the most potent epigenetic modulators in this series, and have potential for use as antitumor agents.
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Affiliation(s)
- Shannon L Nowotarski
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Boobalan Pachaiyappan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Steven L Holshouser
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Craig J Kutz
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Youxuan Li
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States
| | - Yi Huang
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Shiv K Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy, Wayne State University, 259 Mack Avenue, Detroit, MI 48202, United States
| | - Robert A Casero
- Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD 21231, United States
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President St., Charleston, SC 29425, United States.
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28
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Ahmed Khan MN, Tsumoto H, Itoh Y, Ota Y, Suzuki M, Ogasawara D, Nakagawa H, Mizukami T, Miyata N, Suzuki T. Design, synthesis, and biological activity of N-alkylated analogue of NCL1, a selective inhibitor of lysine-specific demethylase 1. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00330f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hybridization of NCL1 and compound 5 led to the identification of a potent lysine-specific demethylase 1 inhibitor 5.
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Affiliation(s)
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging
- Tokyo Metropolitan Institute of Gerontology
- Itabashi-ku
- Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Sakyo-ku
- Japan
| | - Yosuke Ota
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Sakyo-ku
- Japan
| | - Miki Suzuki
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Sakyo-ku
- Japan
| | - Daisuke Ogasawara
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Sakyo-ku
- Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences
- Nagoya City University
- Nagoya
- Japan
| | - Tamio Mizukami
- Graduate School of Bio-Science
- Nagahama Institute of Bio-Science and Technology
- Nagahama
- Japan
| | - Naoki Miyata
- Graduate School of Pharmaceutical Sciences
- Nagoya City University
- Nagoya
- Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Sakyo-ku
- Japan
- PRESTO
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29
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Tough DF, Lewis HD, Rioja I, Lindon MJ, Prinjha RK. Epigenetic pathway targets for the treatment of disease: accelerating progress in the development of pharmacological tools: IUPHAR Review 11. Br J Pharmacol 2014; 171:4981-5010. [PMID: 25060293 PMCID: PMC4253452 DOI: 10.1111/bph.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
The properties of a cell are determined both genetically by the DNA sequence of its genes and epigenetically through processes that regulate the pattern, timing and magnitude of expression of its genes. While the genetic basis of disease has been a topic of intense study for decades, recent years have seen a dramatic increase in the understanding of epigenetic regulatory mechanisms and a growing appreciation that epigenetic misregulation makes a significant contribution to human disease. Several large protein families have been identified that act in different ways to control the expression of genes through epigenetic mechanisms. Many of these protein families are finally proving tractable for the development of small molecules that modulate their function and represent new target classes for drug discovery. Here, we provide an overview of some of the key epigenetic regulatory proteins and discuss progress towards the development of pharmacological tools for use in research and therapy.
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Affiliation(s)
- David F Tough
- Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Epinova DPU, Stevenage, UK
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30
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Miyamura S, Araki M, Suzuki T, Yamaguchi J, Itami K. Stereodivergent Synthesis of Arylcyclopropylamines by Sequential CH Borylation and Suzuki-Miyaura Coupling. Angew Chem Int Ed Engl 2014; 54:846-51. [DOI: 10.1002/anie.201409186] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 11/11/2022]
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31
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Miyamura S, Araki M, Suzuki T, Yamaguchi J, Itami K. Stereodivergent Synthesis of Arylcyclopropylamines by Sequential CH Borylation and Suzuki-Miyaura Coupling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409186] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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32
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Mino K, Nishimura S, Ninomiya S, Tujii H, Matsumori Y, Tsuchida M, Hosoi M, Koseki K, Wada S, Hasegawa M, Sasaki R, Murakami-Yamaguchi Y, Narita H, Suzuki T, Miyata N, Mizukami T. Regulation of tissue factor pathway inhibitor-2 (TFPI-2) expression by lysine-specific demethylase 1 and 2 (LSD1 and LSD2). Biosci Biotechnol Biochem 2014; 78:1010-7. [PMID: 25036127 DOI: 10.1080/09168451.2014.910104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tissue factor pathway inhibitor-2 (TFPI-2) is a major inhibitor of extracellular matrix degradation. Decreases in TFPI-2 contribute to malignant tumor cell production, and TFPI-2 is a presumed tumor suppressor. TFPI-2 gene transcription is regulated by two epigenetic mechanisms: DNA methylation of the promoter and K4 methylation of histone 3 (H3). Lysine-specific demethylase 1 (LSD1) and LSD2 demethylate H3K4me2/1. LSD1 has been implicated in TFPI-2 regulation through both epigenetic mechanisms, but the involvement of LSD2 remains unknown. We prepared a monoclonal anti-LSD2 antibody that clearly distinguishes LSD2 from LSD1. Knockdown of LSD1 or LSD2 by siRNAs increased TFPI-2 protein and mRNA. Simultaneous knockdown of both LSD1 and LSD2 showed additive effects. Bisulfite sequencing revealed that CpG sites in the TFPI-2 promoter region were unmethylated. These results indicate that LSD2 also contributes to TFPI-2 regulation through histone modification, and that further studies of the involvement of LSD2 in tumor malignancy are warranted.
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Affiliation(s)
- Koshiki Mino
- a Graduate School of Bio-Science , Nagahama Institute of Bio-Science and Technology , Nagahama , Japan
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33
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Itoh Y, Ogasawara D, Ota Y, Mizukami T, Suzuki T. Synthesis, LSD1 Inhibitory Activity, and LSD1 Binding Model of Optically Pure Lysine-PCPA Conjugates. Comput Struct Biotechnol J 2014; 9:e201402002. [PMID: 24757500 PMCID: PMC3995212 DOI: 10.5936/csbj.201402002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/13/2014] [Accepted: 02/04/2014] [Indexed: 01/22/2023] Open
Abstract
Compounds that inhibit the catalytic function of lysine-specific demethylase 1 (LSD1) are interesting as therapeutic agents. Recently, we identified three lysine-phenylcyclopropylamine conjugates, NCD18, NCD25, and NCD41, which are potent LSD1 inactivators. However, in our previous study, because we tested those compounds as mixtures of (1S,2R)- and (1R,2S)-disubstituted cyclopropane rings, the relationship between the stereochemistry of the cyclopropane ring and their biological activity remained unknown. In this work, we synthesized optically active compounds of NCD18, NCD25, and NCD41 and evaluated their LSD1 inhibitory activities. In enzyme assays, the LSD1 inhibitory activities of (1R,2S)-NCD18 and (1R,2S)-NCD25 were approximately eleven and four times more potent than those of the corresponding (1S,2R)-isomers, respectively. On the other hand, (1S,2R)-NCD41 was four times more potent than (1R,2S)-NCD41. Binding simulation with LSD1 indicated that the aromatic rings of the compounds and the amino group of the cyclopropylamine were important for the interaction with LSD1, and that the stereochemistry of the 1,2-disubstituted cyclopropane ring affected the position of the aromatic rings and the hydrogen bond formation of the amino group in the LSD1 catalytic site. These findings are expected to contribute to the further development of LSD1 inactivators.
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Affiliation(s)
- Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-cho, Kita-ku, Kyoto 603-8334, Japan
| | - Daisuke Ogasawara
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-cho, Kita-ku, Kyoto 603-8334, Japan
| | - Yosuke Ota
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-cho, Kita-ku, Kyoto 603-8334, Japan
| | - Tamio Mizukami
- Graduate School of Bio-Science, Nagahama Institute of Bio-Science Technology, 1226 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-cho, Kita-ku, Kyoto 603-8334, Japan ; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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34
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Itoh Y, Miyata N, Suzuki T. Target-guided Synthesis: Medicinal Chemistry Strategy to Allow Target Enzymes Themselves to Synthesize their Own Inhibitors. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Small molecule epigenetic inhibitors targeted to histone lysine methyltransferases and demethylases. Q Rev Biophys 2013; 46:349-73. [PMID: 23991894 DOI: 10.1017/s0033583513000085] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Altered chromatin structures and dynamics are responsible for a range of human malignancies, among which the status of histone lysine methylation remains of paramount importance. Histone lysine methylation is maintained by the relative activities of sequence-specific methyltransferase (KMT) writers and demethylase (KDM) erasers, with aberrant enzymatic activities or expression profiles closely correlated with multiple human diseases. Hence, targeting these epigenetic enzymes should provide a promising avenue for pharmacological intervention of aberrantly marked sites within the epigenome. Here we present an up-to-date critical evaluation on the development and optimization of potent small molecule inhibitors targeted to histone KMTs and KDMs, with the emphasis on contributions of structural biology to development of epigenetic drugs for therapeutic intervention. We anticipate that ongoing advances in the development of epigenetic inhibitors should lead to novel drugs that site-specifically target KMTs and KDMs, key enzymes responsible for maintenance of the lysine methylation landscape in the epigenome.
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Ogasawara D, Itoh Y, Tsumoto H, Kakizawa T, Mino K, Fukuhara K, Nakagawa H, Hasegawa M, Sasaki R, Mizukami T, Miyata N, Suzuki T. Lysine-specific demethylase 1-selective inactivators: protein-targeted drug delivery mechanism. Angew Chem Int Ed Engl 2013; 52:8620-4. [PMID: 23824985 DOI: 10.1002/anie.201303999] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Daisuke Ogasawara
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Nishitakatsukasa-cho, Taishogun Kita-ku, Kyoto 603-8334, Japan
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Ogasawara D, Itoh Y, Tsumoto H, Kakizawa T, Mino K, Fukuhara K, Nakagawa H, Hasegawa M, Sasaki R, Mizukami T, Miyata N, Suzuki T. Lysine-Specific Demethylase 1-Selective Inactivators: Protein-Targeted Drug Delivery Mechanism. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Pajtler KW, Weingarten C, Thor T, Künkele A, Heukamp LC, Büttner R, Suzuki T, Miyata N, Grotzer M, Rieb A, Sprüssel A, Eggert A, Schramm A, Schulte JH. The KDM1A histone demethylase is a promising new target for the epigenetic therapy of medulloblastoma. Acta Neuropathol Commun 2013; 1:19. [PMID: 24252778 PMCID: PMC3893444 DOI: 10.1186/2051-5960-1-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 11/17/2022] Open
Abstract
Background Medulloblastoma is a leading cause of childhood cancer-related deaths. Current aggressive treatments frequently lead to cognitive and neurological disabilities in survivors. Novel targeted therapies are required to improve outcome in high-risk medulloblastoma patients and quality of life of survivors. Targeting enzymes controlling epigenetic alterations is a promising approach recently bolstered by the identification of mutations in histone demethylating enzymes in medulloblastoma sequencing efforts. Hypomethylation of lysine 4 in histone 3 (H3K4) is also associated with a dismal prognosis for medulloblastoma patients. Functional characterization of important epigenetic key regulators is urgently needed. Results We examined the role of the H3K4 modifying enzyme, KDM1A, in medulloblastoma, an enzyme also associated with malignant progression in the closely related tumor, neuroblastoma. Re-analysis of gene expression data and immunohistochemistry of tissue microarrays of human medulloblastomas showed strong KDM1A overexpression in the majority of tumors throughout all molecular subgroups. Interestingly, KDM1A knockdown in medulloblastoma cell lines not only induced apoptosis and suppressed proliferation, but also impaired migratory capacity. Further analyses revealed bone morphogenetic protein 2 (BMP2) as a major KDM1A target gene. BMP2 is known to be involved in development and differentiation of granule neuron precursor cells (GNCPs), one potential cell of origin for medulloblastoma. Treating medulloblastoma cells with the specific KDM1A inhibitor, NCL-1, significantly inhibited growth in vitro. Conclusion We provide the first evidence that a histone demethylase is functionally involved in the regulation of the malignant phenotype of medulloblastoma cells, and lay a foundation for future evaluation of KDM1A-inihibiting therapies in combating medulloblastoma.
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Chanthamath S, Nguyen DT, Shibatomi K, Iwasa S. Highly Enantioselective Synthesis of Cyclopropylamine Derivatives via Ru(II)-Pheox-Catalyzed Direct Asymmetric Cyclopropanation of Vinylcarbamates. Org Lett 2013; 15:772-5. [DOI: 10.1021/ol303404c] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Soda Chanthamath
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Dao Thi Nguyen
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Kazutaka Shibatomi
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Seiji Iwasa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan
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Itoh Y, Suzuki T, Miyata N. Small-molecular modulators of cancer-associated epigenetic mechanisms. MOLECULAR BIOSYSTEMS 2013; 9:873-96. [DOI: 10.1039/c3mb25410k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Hazeldine S, Pachaiyappan B, Steinbergs N, Nowotarski S, Hanson AS, Casero RA, Woster PM. Low molecular weight amidoximes that act as potent inhibitors of lysine-specific demethylase 1. J Med Chem 2012; 55:7378-91. [PMID: 22876979 DOI: 10.1021/jm3002845] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered enzyme lysine-specific demethylase 1 (LSD1) plays an important role in the epigenetic control of gene expression, and aberrant gene silencing secondary to LSD1 dysregulation is thought to contribute to the development of cancer. We reported that (bis)guanidines, (bis)biguanides, and their urea- and thiourea isosteres are potent inhibitors of LSD1 and induce the re-expression of aberrantly silenced tumor suppressor genes in tumor cells in vitro. We now report a series of small molecule amidoximes that are moderate inhibitors of recombinant LSD1 but that produce dramatic changes in methylation at the histone 3 lysine 4 (H3K4) chromatin mark, a specific target of LSD1, in Calu-6 lung carcinoma cells. In addition, these analogues increase cellular levels of secreted frizzle-related protein (SFRP) 2, H-cadherin (HCAD), and the transcription factor GATA4. These compounds represent leads for an important new series of drug-like epigenetic modulators with the potential for use as antitumor agents.
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Affiliation(s)
- Stuart Hazeldine
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, Michigan 48202, USA
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Khan MNA, Suzuki T, Miyata N. An overview of phenylcyclopropylamine derivatives: biochemical and biological significance and recent developments. Med Res Rev 2012; 33:873-910. [PMID: 22893613 DOI: 10.1002/med.21269] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
trans-2-Phencylcyclopropylamine (2-PCPA), a potent, clinically used antidepressant, affects monoamine neurotransmitter levels by inhibiting the main metabolizing enzymes, monoamine oxidases (MAOs). However, the antidepressant action of this compound was not fully explained by its effects on MAOs due to its wide variety of biological effects. 2-PCPA also affects depression-associated pathophysiological pathways, and linked with increased levels of trace amines in brain, upregulation of GABAB receptors (where GABA is gamma amino butyric acid), modulation of phospholipid metabolism, and interference with various cytochrome P450 (CYP) enzymes. Consequently, despite its adverse effects and limited clinical applicability, 2-PCPA has attracted interest as a structural scaffold for the development of mechanism-based inhibitors of various enzymes, including lysine-specific demethylase 1 (LSD1), which is a possible target for cancer chemotherapy. In the recent years, many reports have appeared in the literature based on 2-PCPA scaffold and their potential medicinal implications. This review mainly focuses on the medicinal chemistry aspects including drug design, structure-activity relationships (SAR), biological and biochemical properties, and mechanism of actions of 2-PCPA and its derivatives. Furthermore, we also highlight recent advance in this area and discuss their future applications for beneficial therapeutic effects.
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Oncoepigenomics: making histone lysine methylation count. Eur J Med Chem 2012; 56:179-94. [PMID: 22975593 DOI: 10.1016/j.ejmech.2012.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/01/2012] [Accepted: 08/04/2012] [Indexed: 12/30/2022]
Abstract
Increasing studies show that methylation of histone lysine residues is implicated in the development and progression of varying disease states such as schizophrenia, diabetes, and multiple human cancers. Targeting the specific enzymes responsible for these processes has fueled global investigation into the understanding and correction of epigenetic pathology. This review aims to assemble a timely account of the current progress against chromatin-modifying histone lysine methyltransferases (KMTs) and demethylases (KDMs) to inform ongoing and future efforts into this promising field. In particular, we report on their role in tumor growth and progression and the development of small molecules that modulate these enzymes.
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Abstract
Epigenetic regulation of gene expression is a dynamic and reversible process that establishes normal cellular phenotypes but also contributes to human diseases. At the molecular level, epigenetic regulation involves hierarchical covalent modification of DNA and the proteins that package DNA, such as histones. Here, we review the key protein families that mediate epigenetic signalling through the acetylation and methylation of histones, including histone deacetylases, protein methyltransferases, lysine demethylases, bromodomain-containing proteins and proteins that bind to methylated histones. These protein families are emerging as druggable classes of enzymes and druggable classes of protein-protein interaction domains. In this article, we discuss the known links with disease, basic molecular mechanisms of action and recent progress in the pharmacological modulation of each class of proteins.
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Affiliation(s)
- Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-Cho, Kita-ku, Kyoto 403-8334, Japan.
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