1
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Han D, Lu J, Fan B, Lu W, Xue Y, Wang M, Liu T, Cui S, Gao Q, Duan Y, Xu Y. Lysine-Specific Demethylase 1 Inhibitors: A Comprehensive Review Utilizing Computer-Aided Drug Design Technologies. Molecules 2024; 29:550. [PMID: 38276629 PMCID: PMC10821146 DOI: 10.3390/molecules29020550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising therapeutic target for treating various cancers (such as breast cancer, liver cancer, etc.) and other diseases (blood diseases, cardiovascular diseases, etc.), owing to its observed overexpression, thereby presenting significant opportunities in drug development. Since its discovery in 2004, extensive research has been conducted on LSD1 inhibitors, with notable contributions from computational approaches. This review systematically summarizes LSD1 inhibitors investigated through computer-aided drug design (CADD) technologies since 2010, showcasing a diverse range of chemical scaffolds, including phenelzine derivatives, tranylcypromine (abbreviated as TCP or 2-PCPA) derivatives, nitrogen-containing heterocyclic (pyridine, pyrimidine, azole, thieno[3,2-b]pyrrole, indole, quinoline and benzoxazole) derivatives, natural products (including sanguinarine, phenolic compounds and resveratrol derivatives, flavonoids and other natural products) and others (including thiourea compounds, Fenoldopam and Raloxifene, (4-cyanophenyl)glycine derivatives, propargylamine and benzohydrazide derivatives and inhibitors discovered through AI techniques). Computational techniques, such as virtual screening, molecular docking and 3D-QSAR models, have played a pivotal role in elucidating the interactions between these inhibitors and LSD1. Moreover, the integration of cutting-edge technologies such as artificial intelligence holds promise in facilitating the discovery of novel LSD1 inhibitors. The comprehensive insights presented in this review aim to provide valuable information for advancing further research on LSD1 inhibitors.
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Affiliation(s)
- Di Han
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Baoyi Fan
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Wenfeng Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yiwei Xue
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Meiting Wang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Shaoli Cui
- School of Forensic, Xinxiang Medical University, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Yingchao Duan
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
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2
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Li D, Liang H, Wei Y, Xiao H, Peng X, Pan W. Exploring the potential of histone demethylase inhibition in multi-therapeutic approaches for cancer treatment. Eur J Med Chem 2024; 264:115999. [PMID: 38043489 DOI: 10.1016/j.ejmech.2023.115999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
Histone demethylases play a critical role in gene transcription regulation and have been implicated in cancer. Numerous reports have highlighted the overexpression of histone demethylases, such as LSD1 and JmjC, in various malignant tumor tissues, identifying them as effective therapeutic targets for cancer treatment. Despite many histone demethylase inhibitors entering clinical trials, their clinical efficacy has been limited. Therefore, combination therapies based on histone demethylase inhibitors, along with other modulators like dual-acting inhibitors, have gained significant attention and made notable progress in recent years. In this review, we provide an overview of recent advances in drug discovery targeting histone demethylases, focusing specifically on drug combination therapy and histone demethylases-targeting dual inhibitors. We discuss the rational design, pharmacodynamics, pharmacokinetics, and clinical status of these approaches. Additionally, we summarize the co-crystal structures of LSD1 inhibitors and their target proteins as well as describe the corresponding binding interactions. Finally, we also provided the challenges and future directions for utilizing histone demethylases in cancer therapy, such as PROTACs and molecular glue etc.
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Affiliation(s)
- Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Hailiu Liang
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China
| | - Yifei Wei
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China
| | - Hao Xiao
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
| | - Xiaopeng Peng
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
| | - Wanyi Pan
- School of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ganzhou, 341000, China.
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3
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Xu X, Tian X, Song L, Xie J, Liao JC, Meeks JJ, Wu XR, Gin GE, Wang B, Uchio E, Zi X. Kawain Inhibits Urinary Bladder Carcinogenesis through Epigenetic Inhibition of LSD1 and Upregulation of H3K4 Methylation. Biomolecules 2023; 13:521. [PMID: 36979456 PMCID: PMC10046577 DOI: 10.3390/biom13030521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Epidemiological evidence suggests that kava (Piper methysticum Forst) drinks may reduce the risk of cancer in South Pacific Island smokers. However, little is known about the anti-carcinogenic effects of kava on tobacco smoking-related bladder cancer and its underlying mechanisms. Here we show that dietary feeding of kawain (a major active component in kava root extracts) to mice either before or after hydroxy butyl(butyl) nitrosamine (OH-BBN) carcinogen exposure slows down urinary bladder carcinogenesis and prolongs the survival of the OH-BBN-exposed mice. OH-BBN-induced bladder tumors exhibit significantly increased expression of lysine-specific demethylase 1 (LSD1), accompanied by decreased levels of H3K4 mono-methylation compared to normal bladder epithelium, whereas dietary kawain reverses the effects of OH-BBN on H3K4 mono-methylation. Human bladder cancer tumor tissues at different pathological grades also show significantly increased expression of LSD1 and decreased levels of H3K4 mono-methylation compared to normal urothelium. In addition, kava root extracts and the kavalactones kawain and methysticin all increase the levels of H3K4 mono- and di-methylation, leading to inhibitory effects on cell migration. Taken together, our results suggest that modification of histone lysine methylation may represent a new approach to bladder cancer prevention and treatment and that kavalactones may be promising agents for bladder cancer interception in both current and former smokers.
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Affiliation(s)
- Xia Xu
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
| | - Xuejiao Tian
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
| | - Liankun Song
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Jun Xie
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
| | - Joseph C. Liao
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Joshua J. Meeks
- Jesse Brown VA Medical Center, 820 S Damen Ave, Chicago, IL 60612, USA
| | - Xue-Ru Wu
- Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA
| | - Greg E. Gin
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Beverly Wang
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92868, USA
| | - Edward Uchio
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
| | - Xiaolin Zi
- Department of Urology, University of California, Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
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4
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Das ND, Niwa H, Umehara T. Chemical Inhibitors Targeting the Histone Lysine Demethylase Families with Potential for Drug Discovery. EPIGENOMES 2023; 7:epigenomes7010007. [PMID: 36975603 PMCID: PMC10048553 DOI: 10.3390/epigenomes7010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/21/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The dynamic regulation of histone methylation and demethylation plays an important role in the regulation of gene expression. Aberrant expression of histone lysine demethylases has been implicated in various diseases including intractable cancers, and thus lysine demethylases serve as promising therapeutic targets. Recent studies in epigenomics and chemical biology have led to the development of a series of small-molecule demethylase inhibitors that are potent, specific, and have in vivo efficacy. In this review, we highlight emerging small-molecule inhibitors targeting the histone lysine demethylases and their progress toward drug discovery.
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5
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Noce B, Di Bello E, Fioravanti R, Mai A. LSD1 inhibitors for cancer treatment: Focus on multi-target agents and compounds in clinical trials. Front Pharmacol 2023; 14:1120911. [PMID: 36817147 PMCID: PMC9932783 DOI: 10.3389/fphar.2023.1120911] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Histone lysine-specific demethylase 1 (LSD1/KDM1A) was first identified in 2004 as an epigenetic enzyme able to demethylate specific lysine residues of histone H3, namely H3K4me1/2 and H3K9me1/2, using FAD as the cofactor. It is ubiquitously overexpressed in many types of cancers (breast, gastric, prostate, hepatocellular, and esophageal cancer, acute myeloid leukemia, and others) leading to block of differentiation and increase of proliferation, migration and invasiveness at cellular level. LSD1 inhibitors can be grouped in covalent and non-covalent agents. Each group includes some hybrid compounds, able to inhibit LSD1 in addition to other target(s) at the same time (dual or multitargeting compounds). To date, 9 LSD1 inhibitors have entered clinical trials, for hematological and/or solid cancers. Seven of them (tranylcypromine, iadademstat (ORY-1001), bomedemstat (IMG-7289), GSK-2879552, INCB059872, JBI-802, and Phenelzine) covalently bind the FAD cofactor, and two are non-covalent LSD1 inhibitors [pulrodemstat (CC-90011) and seclidemstat (SP-2577)]. Another TCP-based LSD1/MAO-B dual inhibitor, vafidemstat (ORY-2001), is in clinical trial for Alzheimer's diseases and personality disorders. The present review summarizes the structure and functions of LSD1, its pathological implications in cancer and non-cancer diseases, and the identification of LSD1 covalent and non-covalent inhibitors with different chemical scaffolds, including those involved in clinical trials, highlighting their potential as potent and selective anticancer agents.
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Affiliation(s)
- Beatrice Noce
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Di Bello
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Rossella Fioravanti
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,*Correspondence: Rossella Fioravanti,
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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6
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Song Y, Wang S, Yu B. Structural and Functional Landscape of FAD-Dependent Histone Lysine Demethylases for New Drug Discovery. J Med Chem 2023; 66:71-94. [PMID: 36537915 DOI: 10.1021/acs.jmedchem.2c01324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules targeting the flavin adenine dinucleotide (FAD)-dependent histone lysine demethylase LSD family have displayed therapeutic promise against various diseases. Nine clinical candidates targeting the classic demethylase-dependent functions of the LSD family are currently being investigated for treating cancers, neurodegenerative diseases, etc. Moreover, targeting noncatalytic functions of LSDs also represents an emerging strategy for treating human diseases. In this Perspective, we provide full structural and functional landscape of the LSD family and action modes of different types of LSD inhibitors including natural products, peptides, and synthetic compounds, aiming to reveal new druggable space for the design of new LSD inhibitors. Particularly, we first classify these inhibitors into three types based on their unique binding modes. Additionally, the strategies targeting the demethylase-independent functions of LSDs are also briefly discussed. This Perspective may benefit the discovery of new LSD inhibitors for probing LSD biology and/or treating human diseases.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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7
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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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8
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Zeng Z, Zhu J, Deng X, Chen H, Jin Y, Miclet E, Alezra V, Wan Y. Customized Reversible Stapling for Selective Delivery of Bioactive Peptides. J Am Chem Soc 2022; 144:23614-23621. [PMID: 36530144 DOI: 10.1021/jacs.2c10949] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have developed a new concept for reversible peptide stapling that involves macrocyclization between two amino groups and decyclization promoted via dual 1,4-elimination. Depending on the trigger moiety, this strategy could be employed to selectively deliver peptides to either intracellular or extracellular targets. As a proof of concept, a peptide inhibitor targeting a lysine-specific demethylase 1 (LSD1) was temporarily cyclized to enhance its stability and ability to cross the cell membrane. Once inside the cells, the biologically active linear peptide was released under reducing environment. Moreover, we have developed reversibly stapled peptides using antimicrobial peptides (RStAMPs) whose bioactive helical conformation can be temporarily destabilized by stapling the peptide backbone. The resulting helix-distorted RStAMPs are nontoxic and highly resistant to protease hydrolysis, while at the infection site, RStAMPs can be rapidly activated by the overproduced H2O2 through the dual 1,4-elimination. The latter restored the helical structure of the native peptide and its antimicrobial activity. This work illustrates a highly valuable macrocyclization strategy for the peptide community and should greatly benefit the field of peptide delivery.
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Affiliation(s)
- Zizhen Zeng
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
| | - Jibao Zhu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
| | - Xiaoyu Deng
- Minist Educ, Key Lab Modern Preparat TCM, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
| | - Huanwen Chen
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
| | - Yi Jin
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
| | - Emeric Miclet
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 4 Place Jussieu, Cedex 05, Paris 75252, France
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, Université Paris-Saclay, Paris 91400, Orsay, France
| | - Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, P. R. China
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9
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Gilmore SA, Tam D, Cheung TL, Snyder C, Farand J, Dick R, Matles M, Feng JY, Ramirez R, Li L, Yu H, Xu Y, Barnes D, Czerwieniec G, Brendza KM, Appleby TC, Birkus G, Willkom M, Kobayashi T, Paoli E, Labelle M, Boesen T, Tay CH, Delaney WE, Notte GT, Schmitz U, Feierbach B. Characterization of a KDM5 small molecule inhibitor with antiviral activity against hepatitis B virus. PLoS One 2022; 17:e0271145. [PMID: 36477212 PMCID: PMC9728921 DOI: 10.1371/journal.pone.0271145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B (CHB) is a global health care challenge and a major cause of liver disease. To find new therapeutic avenues with a potential to functionally cure chronic Hepatitis B virus (HBV) infection, we performed a focused screen of epigenetic modifiers to identify potential inhibitors of replication or gene expression. From this work we identified isonicotinic acid inhibitors of the histone lysine demethylase 5 (KDM5) with potent anti-HBV activity. To enhance the cellular permeability and liver accumulation of the most potent KDM5 inhibitor identified (GS-080) an ester prodrug was developed (GS-5801) that resulted in improved bioavailability and liver exposure as well as an increased H3K4me3:H3 ratio on chromatin. GS-5801 treatment of HBV-infected primary human hepatocytes reduced the levels of HBV RNA, DNA and antigen. Evaluation of GS-5801 antiviral activity in a humanized mouse model of HBV infection, however, did not result in antiviral efficacy, despite achieving pharmacodynamic levels of H3K4me3:H3 predicted to be efficacious from the in vitro model. Here we discuss potential reasons for the disconnect between in vitro and in vivo efficacy, which highlight the translational difficulties of epigenetic targets for viral diseases.
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Affiliation(s)
- Sarah A. Gilmore
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Danny Tam
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Tara L. Cheung
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Chelsea Snyder
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Julie Farand
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Ryan Dick
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Mike Matles
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Joy Y. Feng
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Ricardo Ramirez
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Li Li
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Helen Yu
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Yili Xu
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Dwight Barnes
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Gregg Czerwieniec
- Gilead Sciences, Inc., Foster City, California, United States America
| | | | - Todd C. Appleby
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Gabriel Birkus
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Madeleine Willkom
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Tetsuya Kobayashi
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Eric Paoli
- Gilead Sciences, Inc., Foster City, California, United States America
| | | | - Thomas Boesen
- EpiTherapeutics ApS, Copenhagen, Denmark
- Novo Nordisk A/S, Bagsvaerd, Denmark
| | - Chin H. Tay
- Gilead Sciences, Inc., Foster City, California, United States America
| | | | - Gregory T. Notte
- Gilead Sciences, Inc., Foster City, California, United States America
| | - Uli Schmitz
- Gilead Sciences, Inc., Foster City, California, United States America
- * E-mail:
| | - Becket Feierbach
- Gilead Sciences, Inc., Foster City, California, United States America
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10
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Niwa H, Watanabe C, Sato S, Harada T, Watanabe H, Tabusa R, Fukasawa S, Shiobara A, Hashimoto T, Ohno O, Nakamura K, Tsuganezawa K, Tanaka A, Shirouzu M, Honma T, Matsuno K, Umehara T. Structure–Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2. ACS Med Chem Lett 2022; 13:1485-1492. [PMID: 36105323 PMCID: PMC9465824 DOI: 10.1021/acsmedchemlett.2c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
![]()
trans-2-Phenylcycloproylamine (trans-PCPA) has been used as the scaffold to develop covalent-binding
inhibitors against lysine-specific demethylase 1 (LSD1/KDM1A), a therapeutic
target for several cancers. However, the effects of different structural
moieties on the inhibitory activity, selectivity, and reactivity of
these derivatives, including the cis isomers, against
LSD1 and its paralogue LSD2/KDM1B are not fully understood. Here we
synthesized 65 cis- and trans-PCPA
derivatives and evaluated their inhibitory activity against LSD1 and
LSD2. One of the derivatives, 7c (cis-4-Br-2,5-F2-PCPA; S1024), inhibited LSD1
and LSD2 with Ki values of 0.094 μM
and 8.4 μM, respectively, and increased the level of dimethylated
histone H3 at K4 in CCRF-CEM cells. A machine learning-based regression
model (Q2 = 0.61) to predict LSD1-inhibitory
activity was also constructed and showed a good prediction accuracy
(R2 = 0.81) for 12 test-set compounds,
including 7c. The present methodology would be useful
when designing covalent-binding inhibitors for other enzymes.
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Affiliation(s)
- Hideaki Niwa
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Toshiyuki Harada
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryo Tabusa
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Shunsuke Fukasawa
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Ayane Shiobara
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Tomoko Hashimoto
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Osamu Ohno
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Kana Nakamura
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Tsuganezawa
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kenji Matsuno
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women’s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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11
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Liu X, Zhang Z, She N, Zhai J, Zhao Y, Wang C. Combination of multiple methods and views for recognition, transportation, and structure-guided modification of lysine-specific demethylase phenylcyclopropylamine inhibitor. Phys Chem Chem Phys 2022; 24:13806-13823. [PMID: 35612608 DOI: 10.1039/d2cp01197b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine-Specific Demethylase 1 (LSD1) is a typical histone-specific demethylase, which plays an important role in protein methylation modification. It is a member of the amine oxidase family (MAO) that specifically removes methyl groups from monomethylated H3K4, dimethylated H3K4 and H3K9 sites associated with tumorigenesis. Phenylcyclopropylamine derivatives are a class of specific LSD1 inhibitors, drawing attention due to their high efficiency. Here, extensive molecular dynamics (MD) simulations are combined with a three-dimensional quantitative structure-activity relationship (3D-QSAR) in order to design a new phenylcyclopropylamine inhibitor from multiple perspectives. In a ligand-oriented point of view, a 3D-QSAR model with comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) can be built based on the 55 phenylcyclopropylamine compounds targeting LSD1 obtained experimentally. The aromatic and piperazine rings are identified as the potential key groups regulating the activity of the compounds. In an interaction-oriented view, the representative compound is defined with the highest inhibitory efficiency. The binding and delivery mechanism and conformational dependence of activity, including channel and dynamic properties, are studied using RAMD and umbrella sampling technologies. The direct hydrogen bond and conjugated interactions are identified as a major driving force in this procedure. The dominant region of the phenylcyclopropylamine influences the free energy and detects the key residues in recognition and delivery. On the basis of both the ligand and interaction, a series of new inhibitor structures were designed, and two of them showed better efficiency. In order to select the inhibitor with a longer residence time, a comparison is conducted between the designed inhibitors and the experimentally obtained inhibitor from the perspective of static binding and dynamic delivery properties. This work creates new guidance for the phenylcyclopropylamine inhibitor design of LDS1 by combining the ligand and receptor, considering both static and dynamic properties. This scheme could be applied in other inhibitor design systems.
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Affiliation(s)
- Xiaoyuan Liu
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Jihang Zhai
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China.
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12
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Koda Y, Sato S, Yamamoto H, Niwa H, Watanabe H, Watanabe C, Sato T, Nakamura K, Tanaka A, Shirouzu M, Honma T, Fukami T, Koyama H, Umehara T. Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles. ACS Med Chem Lett 2022; 13:848-854. [PMID: 35586426 PMCID: PMC9109268 DOI: 10.1021/acsmedchemlett.2c00120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) is a promising therapeutic target for the treatment of cancers. Several derivatives of tranylcypromine (trans-2-phenylcyclopropylamine) have been developed as LSD1 inhibitors. One such derivative is S2157; however, this compound has a high hERG channel inhibitory activity and a low microsomal stability, making it unsuitable as a drug candidate. Here, using an in silico hERG inhibition prediction model, we designed, synthesized, and evaluated a novel series of S2157 derivatives characterized by modifications of the benzyloxy and piperazine groups. Among the synthesized derivatives, a compound possessing 2-fluoropyridine and 2,8-diaza-spiro[4.5]decane groups (compound 10) showed the most desirable activities, and its eutomer, S1427, was isolated by the optical resolution of 10. In addition to potent LSD1 inhibitory activity, S1427 exhibited desirable hERG channel inhibition and microsomal stability profiles.
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Affiliation(s)
- Yasuko Koda
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Yamamoto
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Niwa
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Tomohiro Sato
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kana Nakamura
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takehiro Fukami
- RIKEN Program for Drug Discovery and Medical Technology Platforms, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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13
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Santos A, Colaço AR, Nielsen AB, Niu L, Strauss M, Geyer PE, Coscia F, Albrechtsen NJW, Mundt F, Jensen LJ, Mann M. A knowledge graph to interpret clinical proteomics data. Nat Biotechnol 2022; 40:692-702. [PMID: 35102292 PMCID: PMC9110295 DOI: 10.1038/s41587-021-01145-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/01/2021] [Indexed: 12/14/2022]
Abstract
Implementing precision medicine hinges on the integration of omics data, such as proteomics, into the clinical decision-making process, but the quantity and diversity of biomedical data, and the spread of clinically relevant knowledge across multiple biomedical databases and publications, pose a challenge to data integration. Here we present the Clinical Knowledge Graph (CKG), an open-source platform currently comprising close to 20 million nodes and 220 million relationships that represent relevant experimental data, public databases and literature. The graph structure provides a flexible data model that is easily extendable to new nodes and relationships as new databases become available. The CKG incorporates statistical and machine learning algorithms that accelerate the analysis and interpretation of typical proteomics workflows. Using a set of proof-of-concept biomarker studies, we show how the CKG might augment and enrich proteomics data and help inform clinical decision-making.
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Affiliation(s)
- Alberto Santos
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Li-Ka Shing Big Data Institute, University of Oxford, Oxford, UK.
- Center for Health Data Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Ana R Colaço
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Annelaura B Nielsen
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lili Niu
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maximilian Strauss
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- OmicEra Diagnostics GmbH, Planegg, Germany
| | - Philipp E Geyer
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- OmicEra Diagnostics GmbH, Planegg, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabian Coscia
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nicolai J Wewer Albrechtsen
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department for Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Filip Mundt
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Juhl Jensen
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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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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15
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Sun Y, Lv R, Wu T, Zhang X, Sun Y, Yan J, Zhang Z, Zhao D, Cheng M. Design, synthesis, and biological evaluation of coumarin analogs as novel LSD1 inhibitors. Arch Pharm (Weinheim) 2021; 355:e2100311. [PMID: 34862974 DOI: 10.1002/ardp.202100311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/23/2023]
Abstract
The abnormal expression of lysine-specific histone demethylase 1 (LSD1) is associated with different cancer types, and it is increasingly recognized as a potential therapeutic target in oncology. Here, utilizing core hopping and conformational restriction strategies, we designed and synthesized a series of coumarin analogs that were shown to be potent LSD1 inhibitors in the enzyme assay. Furthermore, several potent compounds were selected to evaluate their antiproliferative activity on A549 cells and MGC-803 cells with high expression of LSD1. Among them, YX10 showed an anticlonogenic effect on A549 cells and MGC-803 cells, with IC50 values of 1.52 ± 0.16 and 0.98 ± 0.18 μM, respectively. Modeling suggested that the inhibitors would bind to the active site of the protein located around the key residues of Asp555 and Lys661. Meanwhile, a preliminary druggability evaluation showed that compound YX10 showed favorable liver microsomal and moderate plasma stability and weak inhibitory activity against cytochrome P450 isoforms at 10 μM. All the results indicated that compound YX10 could represent a promising lead compound for further development.
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Affiliation(s)
- Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ruicheng Lv
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jiangkun Yan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ziheng Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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16
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Zhang X, Wang X, Wu T, Yin W, Yan J, Sun Y, Zhao D. Therapeutic potential of targeting LSD1/ KDM1A in cancers. Pharmacol Res 2021; 175:105958. [PMID: 34718134 DOI: 10.1016/j.phrs.2021.105958] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/21/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
Abstract
LSD1 was the first histone demethylase identified by Professor Shi Yang and his team members in 2004. LSD1 employs FAD as its cofactor, which catalyzes the demethylation of H3K4 and H3K9. It is aberrantly overexpressed in different types of cancers and is associated with the growth, invasion, and metastasis of cancer cells. The knockout or inhibition of LSD1 could effectively suppress tumor development, and thus, it has become an attractive molecular target for cancer therapy. Moreover, many LSD1 inhibitors have been developed in preclinical and clinical trials to treat solid tumors and hematological malignancy. This study made an extensive review of the research obtained from the literature retrieval of electronic databases, such as PubMed, Web of Science, RCSB PDB, ClinicalTrials.gov, and EU clinical trials register. This review summarizes recent studies on the advances of LSD1 inhibitors in the literature, covering January 2015 to June 2021. It focuses on the function of LSD1 in tumor cells, summarizes the crystal structures of homo sapiens LSD1, reviews the structural characteristics of LSD1 inhibitors, compares the screening methods of LSD1 inhibitors, and proposes guidelines for the future exploitation of LSD1 inhibitors.
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Affiliation(s)
- Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China
| | - Xinran Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Chaoyang District, Beijing 102488, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China
| | - Jiangkun Yan
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, P. R. China.
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. QSAR Modeling, Molecular Docking and Molecular Dynamics Simulations Studies of Lysine-Specific Demethylase 1 (LSD1) Inhibitors as Anticancer Agents. Anticancer Agents Med Chem 2021; 21:987-1018. [PMID: 32698753 DOI: 10.2174/1871520620666200721134010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/07/2020] [Accepted: 05/17/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone Lysine Demetylases1 (LSD1) is a promising medication to treat cancer, which plays a crucial role in epigenetic modulation of gene expression. Inhibition of LSD1with small molecules has emerged as a vital mechanism to treat cancer. OBJECTIVE In the present research, molecular modeling investigations, such as CoMFA, CoMFA-RF, CoMSIA and HQSAR, molecular docking and Molecular Dynamics (MD) simulations were carried out on some tranylcypromine derivatives as LSD1 inhibitors. METHODS The QSAR models were carried out on a series of Tranylcypromine derivatives as data set via the SYBYL-X2.1.1 program. Molecular docking and MD simulations were carried out by the MOE software and the SYBYL program, respectively. The internal and external predictability performances related to the generated models for these LSD1 inhibitors were justified by evaluating cross-validated correlation coefficient (q2), noncross- validated correlation coefficient (r2ncv) and predicted correlation coefficient (r2pred) of the training and test set molecules, respectively. RESULTS The CoMFA (q2, 0.670; r2ncv, 0.930; r2pred, 0.968), CoMFA-RF (q2, 0.694; r2ncr, 0.926; r2pred, 0.927), CoMSIA (q2, 0.834; r2ncv, 0.956; r2pred, 0.958) and HQSAR models (q2, 0.854; r2ncv, 0.900; r2pred, 0.728) for training as well as the test set of LSD1 inhibition resulted in significant findings. CONCLUSION These QSAR models were found to be perfect and strong with better predictability. Contour maps of all models were generated and it was proven by molecular docking studies and molecular dynamics simulation that the hydrophobic, electrostatic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determining the structure-activity relationship. These theoretical results are possibly beneficial to design new strong LSD1 inhibitors with enhanced activity to treat cancer.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Esfandiar Heidarian
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
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18
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Kitagawa H, Kikuchi M, Sato S, Watanabe H, Umezawa N, Kato M, Hisamatsu Y, Umehara T, Higuchi T. Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity. J Med Chem 2021; 64:3707-3719. [PMID: 33754721 DOI: 10.1021/acs.jmedchem.0c01371] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Peptides are attractive drug candidates, but their utility is greatly limited by their inherent susceptibility to proteolytic degradation and their inability to pass through the cell membrane. Here, we employ a strategy of temporary cyclization to develop a cell-active lysine-specific demethylase 1 (LSD1/KDM1A) inhibitor peptide. We first identified a highly potent LSD1-inhibitory linear peptide, with the assistance of X-ray crystal structure data of inhibitor peptide-bound LSD1·CoREST. The peptide was converted to a redox-activatable cyclic peptide incorporating cell-penetrating peptide (CPP), expecting selective activation under intracellular reducing conditions. The cyclic peptide moiety exhibited enhanced stability to protease and was converted to the linear, unmodified LSD1 inhibitor peptide under reducing conditions. The cyclic peptide with CPP inhibited the proliferation of human acute myeloid leukemia cells (HL-60) in the low micromolar concentration range.
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Affiliation(s)
- Hiroki Kitagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Maiko Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
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19
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The circadian machinery links metabolic disorders and depression: A review of pathways, proteins and potential pharmacological interventions. Life Sci 2020; 265:118809. [PMID: 33249097 DOI: 10.1016/j.lfs.2020.118809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Circadian rhythms are responsible for regulating a number of physiological processes. The central oscillator is located within the suprachiasmatic nucleus (SCN) of the hypothalamus and the SCN synchronises the circadian clocks that are found in our peripheral organs through neural and humoral signalling. At the molecular level, biological clocks consist of transcription-translation feedback loops (TTFLs) and these pathways are influenced by transcription factors, post-translational modifications, signalling pathways and epigenetic modifiers. When disruptions occur in the circadian machinery, the activities of the proteins implicated in this network and the expression of core clock or clock-controlled genes (CCGs) can be altered. Circadian misalignment can also arise when there is desychronisation between our internal clocks and environmental stimuli. There is evidence in the literature demonstrating that disturbances in the circadian rhythm contribute to the pathophysiology of several diseases and disorders. This includes the metabolic syndrome and recently, it has been suggested that the 'circadian syndrome' may be a more appropriate term to use to not only describe the cardio-metabolic risk factors but also the associated comorbidities. Here we overview the molecular architecture of circadian clocks in mammals and provide insight into the effects of shift work, exposure to artificial light, food intake and stress on the circadian rhythm. The relationship between circadian rhythms, metabolic disorders and depression is reviewed and this is a topic that requires further investigation. We also describe how particular proteins involved in the TTFLs can be potentially modulated by small molecules, including pharmacological interventions and dietary compounds.
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20
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Dai XJ, Liu Y, Xiong XP, Xue LP, Zheng YC, Liu HM. Tranylcypromine Based Lysine-Specific Demethylase 1 Inhibitor: Summary and Perspective. J Med Chem 2020; 63:14197-14215. [PMID: 32931269 DOI: 10.1021/acs.jmedchem.0c00919] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone lysine-specific demethylase 1 (LSD1/KDM1A) has become an important and promising anticancer target since it was first identified in 2004 and specially demethylates lysine residues of histone H3K4me1/2 and H3K9me1/2. LSD1 is ubiquitously overexpressed in diverse cancers, and abrogation of LSD1 results in inhibition of proliferation, invasion, and migration in cancer cells. Over the past decade, a number of biologically active small-molecule LSD1 inhibitors have been developed. To date, six trans-2-phenylcyclopropylamine (TCP)-based LSD1 inhibitors (including TCP, ORY-1001, GSK-2879552, INCB059872, IMG-7289, and ORY-2001) that covalently bind to the flavin adenine dinucleotide (FAD) within the LSD1 catalytic cavity have already entered into clinical trials. Here, we provide an overview about the structures, activities, and structure-activity relationship (SAR) of TCP-based LSD1 inhibitors that mainly covers the literature from 2008 to date. The opportunities, challenges, and future research directions in this emerging and promising field are also discussed.
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Affiliation(s)
- Xing-Jie Dai
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiao-Peng Xiong
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Lei-Peng Xue
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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21
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Gao S, Chen S, Han D, Wang Z, Li M, Han W, Besschetnova A, Liu M, Zhou F, Barrett D, Luong MP, Owiredu J, Liang Y, Ahmed M, Petricca J, Patalano S, Macoska JA, Corey E, Chen S, Balk SP, He HH, Cai C. Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer. Nat Genet 2020; 52:1011-1017. [PMID: 32868907 PMCID: PMC7541538 DOI: 10.1038/s41588-020-0681-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/24/2020] [Indexed: 11/09/2022]
Abstract
FOXA1 functions as a pioneer transcription factor by facilitating the access to chromatin for steroid hormone receptors, such as androgen receptor and estrogen receptor1-4, but mechanisms regulating its binding to chromatin remain elusive. LSD1 (KDM1A) acts as a transcriptional repressor by demethylating mono/dimethylated histone H3 lysine 4 (H3K4me1/2)5,6, but also acts as a steroid hormone receptor coactivator through mechanisms that are unclear. Here we show, in prostate cancer cells, that LSD1 associates with FOXA1 and active enhancer markers, and that LSD1 inhibition globally disrupts FOXA1 chromatin binding. Mechanistically, we demonstrate that LSD1 positively regulates FOXA1 binding by demethylating lysine 270, adjacent to the wing2 region of the FOXA1 DNA-binding domain. Acting through FOXA1, LSD1 inhibition broadly disrupted androgen-receptor binding and its transcriptional output, and dramatically decreased prostate cancer growth alone and in synergy with androgen-receptor antagonist treatment in vivo. These mechanistic insights suggest new therapeutic strategies in steroid-driven cancers.
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Affiliation(s)
- Shuai Gao
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, Canada
| | - Dong Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Zifeng Wang
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Muqing Li
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Wanting Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Anna Besschetnova
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Mingyu Liu
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Feng Zhou
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA.,Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - David Barrett
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - My Phu Luong
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Jude Owiredu
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA.,Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Yi Liang
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, Canada
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, Canada
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Jill A Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Sen Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, Canada.
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA.
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22
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Niwa H, Sato S, Handa N, Sengoku T, Umehara T, Yokoyama S. Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. ChemMedChem 2020; 15:787-793. [PMID: 32166890 DOI: 10.1002/cmdc.202000014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/21/2020] [Indexed: 01/19/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the demethylation of histone H3 and regulates gene expression. Because it is implicated in the regulation of diseases such as acute myeloid leukemia, potent LSD1-specific inhibitors have been pursued. Trans-2-phenylcyclopropylamine (2-PCPA)-based inhibitors featuring substitutions on the amino group have emerged, with sub-micromolar affinities toward LSD1 and high selectivities over monoamine oxidases (MAOs). We synthesized two N-alkylated 2-PCPA-based LSD1 inhibitors, S2116 and S2157, based on the previously developed S2101. S2116 and S2157 exhibited enhanced potency for LSD1 by 2.0- to 2.6-fold, as compared with S2101. In addition, they exhibited improved selectivity over MAOs. Structural analyses of LSD1 co-crystallized with S2101, S2116, S2157, or another N-alkylated inhibitor (FCPA-MPE) confirmed that the N-substituents enhance the potency of a 2-PCPA-based inhibitor of LSD1, without constituting the adduct formed with FAD.
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Affiliation(s)
- Hideaki Niwa
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, 230-0045, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Shin Sato
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, 230-0045, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Noriko Handa
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan
| | - Toru Sengoku
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama, 230-0045, Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, 230-0045, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama, 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama, 230-0045, Japan.,RIKEN Yokoyama Laboratory, Yokohama, 230-0045, Japan
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23
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Cuyàs E, Gumuzio J, Verdura S, Brunet J, Bosch-Barrera J, Martin-Castillo B, Alarcón T, Encinar JA, Martin ÁG, Menendez JA. The LSD1 inhibitor iadademstat (ORY-1001) targets SOX2-driven breast cancer stem cells: a potential epigenetic therapy in luminal-B and HER2-positive breast cancer subtypes. Aging (Albany NY) 2020; 12:4794-4814. [PMID: 32191225 PMCID: PMC7138538 DOI: 10.18632/aging.102887] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022]
Abstract
SOX2 is a core pluripotency-associated transcription factor causally related to cancer initiation, aggressiveness, and drug resistance by driving the self-renewal and seeding capacity of cancer stem cells (CSC). Here, we tested the ability of the clinically proven inhibitor of the lysine-specific demethylase 1 (LSD1/KDM1A) iadademstat (ORY-100) to target SOX2-driven CSC in breast cancer. Iadademstat blocked CSC-driven mammosphere formation in breast cancer cell lines that are dependent on SOX2 expression to maintain their CSC phenotype. Iadademstat prevented the activation of an LSD1-targeted stemness-specific SOX2 enhancer in CSC-enriched 3-dimensional spheroids. Using high-throughput transcriptional data available from the METABRIC dataset, high expression of SOX2 was significantly more common in luminal-B and HER2-enriched subtypes according to PAM50 classifier and in IntClust1 (high proliferating luminal-B) and IntClust 5 (luminal-B and HER2-amplified) according to integrative clustering. Iadademstat significantly reduced mammospheres formation by CSC-like cells from a multidrug-resistant luminal-B breast cancer patient-derived xenograft but not of those from a treatment-naïve luminal-A patient. Iadademstat reduced the expression of SOX2 in luminal-B but not in luminal-A mammospheres, likely indicating a selective targeting of SOX2-driven CSC. The therapeutic relevance of targeting SOX2-driven breast CSC suggests the potential clinical use of iadademstat as an epigenetic therapy in luminal-B and HER2-positive subtypes.
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Affiliation(s)
- Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Joan Brunet
- Medical Oncology, Catalan Institute of Oncology (ICO), Girona, Spain.,Department of Medical Sciences, Medical School University of Girona, Girona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Joaquim Bosch-Barrera
- Medical Oncology, Catalan Institute of Oncology (ICO), Girona, Spain.,Department of Medical Sciences, Medical School University of Girona, Girona, Spain
| | | | - Tomás Alarcón
- ICREA, Barcelona, Spain.,Centre de Recerca Matemàtica (CRM), Barcelona, Spain.,Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain.,Barcelona Graduate School of Mathematics (BGSMath), Barcelona, Spain
| | - José Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain
| | | | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
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24
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Pitsillou E, Liang J, Hung A, Karagiannis TC. Chromatin modification by olive phenolics: In silico molecular docking studies utilising the phenolic groups categorised in the OliveNet™ database against lysine specific demethylase enzymes. J Mol Graph Model 2020; 97:107575. [PMID: 32126499 DOI: 10.1016/j.jmgm.2020.107575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
Extra virgin olive oil is the principal source of dietary fat in the Mediterranean diet and is considered to have beneficial health effects. There is evidence to suggest that the phenolic compounds within Olea europaea have the ability to inhibit lysine-specific demethylase 1 (LSD1). This is an epigenetic enzyme that removes methyl groups from histone proteins and regulates gene transcription. Conversely, SET domain-containing protein 7 (SETD7) has opposing enzymatic activity and is a histone methyltransferase. Due to the involvement of these proteins in a number of pathological processes, including cancer and diabetes, further research needs to be conducted into the way in which they can be targeted. A large number of phenolic compounds (>200) have been identified in Olea europaea. To help expedite the discovery of promising lead compounds, in this study, in silico molecular docking methods were used to investigate the molecular binding properties of the phenolic compounds obtained from the OliveNet™ database to LSD1 and its variants, LSD2, and SETD7. Numerous Olea europaea phenolic compounds were predicted to bind to the epigenetic enzymes and several had stronger binding affinities than the LSD1 and SETD7 positive control inhibitors. The protein-ligand interactions of the phenolic compounds were also compared to known inhibitors and the molecular docking results suggest that the flavonoids, secoiridoids and glucosides may bind particularly strongly to the epigenetic regulators. Overall, several ligands were identified as lead compounds from this research and their potential inhibitory activity could be validated further in the laboratory.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia; School of Science, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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25
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Zeng W, Tan X, Yu Y, Chen GQ, Zhang X. Copper-Catalyzed Asymmetric Hydrosilylation of β-Nitroethyl Aryl Ketones. Org Lett 2020; 22:858-862. [DOI: 10.1021/acs.orglett.9b04339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weijun Zeng
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
| | - Xuefeng Tan
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
| | - Yang Yu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
| | - Gen-Qiang Chen
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
| | - Xumu Zhang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518000, People’s Republic of China
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26
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Wang Z, Gao S, Han D, Han W, Li M, Cai C. LSD1 Activates PI3K/AKT Signaling Through Regulating p85 Expression in Prostate Cancer Cells. Front Oncol 2019; 9:721. [PMID: 31428587 PMCID: PMC6688199 DOI: 10.3389/fonc.2019.00721] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/19/2019] [Indexed: 11/13/2022] Open
Abstract
Lysine specific demethylase 1 (LSD1) functions as a transcriptional repressor through demethylating active histone marks such as mono- or di-methylated histone 3 lysine 4 (H3K4) and interacting with histone deacetylases. However, LSD1 can also act as an activator through demethylating repressive histone marks and possibly non-histone proteins. In prostate cancer (PCa) cells, LSD1 mediates the transcriptional activity of androgen receptor (AR), a ligand dependent nuclear transcription factor that drives PCa initiation and progression to the castration-resistant prostate cancer (CRPC). However, it is unclear whether LSD1 also regulates other growth promoting pathways independent of AR signaling in PCa cells. In this study, we show that LSD1 can activate PI3K/AKT pathways in absence of androgen stimulation, and we further demonstrate that LSD1 transcriptionally regulates the expression of PI3K regulatory subunit, p85, possibly through epigenetic reprogramming of enhancer landscape in PCa cells. Our study suggests that LSD1 has dual functions in promoting PCa development, that it enhances AR signaling through its coactivator function, and that it activates PI3K/AKT signaling through increasing p85 gene expression.
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Affiliation(s)
| | | | | | | | | | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, United States
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27
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Anan K, Hino S, Shimizu N, Sakamoto A, Nagaoka K, Takase R, Kohrogi K, Araki H, Hino Y, Usuki S, Oki S, Tanaka H, Nakamura K, Endo F, Nakao M. LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation. Nucleic Acids Res 2019; 46:5441-5454. [PMID: 29618057 PMCID: PMC6009677 DOI: 10.1093/nar/gky234] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023] Open
Abstract
The metabolic properties of cells are formed under the influence of environmental factors such as nutrients and hormones. Although such a metabolic program is likely initiated through epigenetic mechanisms, the direct links between metabolic cues and activities of chromatin modifiers remain largely unknown. In this study, we show that lysine-specific demethylase-1 (LSD1) controls the metabolic program in myogenic differentiation, under the action of catabolic hormone, glucocorticoids. By using transcriptomic and epigenomic approaches, we revealed that LSD1 bound to oxidative metabolism and slow-twitch myosin genes, and repressed their expression. Consistent with this, loss of LSD1 activity during differentiation enhanced the oxidative capacity of myotubes. By testing the effects of various hormones, we found that LSD1 levels were decreased by treatment with the glucocorticoid dexamethasone (Dex) in cultured myoblasts and in skeletal muscle from mice. Mechanistically, glucocorticoid signaling induced expression of a ubiquitin E3 ligase, JADE-2, which was responsible for proteasomal degradation of LSD1. Consequently, in differentiating myoblasts, chemical inhibition of LSD1, in combination with Dex treatment, synergistically de-repressed oxidative metabolism genes, concomitant with increased histone H3 lysine 4 methylation at these loci. These findings demonstrated that LSD1 serves as an epigenetic regulator linking glucocorticoid action to metabolic programming during myogenic differentiation.
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Affiliation(s)
- Kotaro Anan
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Noriaki Shimizu
- Division of Rheumatology, Center for Antibody and Vaccine Therapy, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Akihisa Sakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Katsuya Nagaoka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ryuta Takase
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Kensaku Kohrogi
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hirotaka Araki
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate school of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hirotoshi Tanaka
- Division of Rheumatology, Center for Antibody and Vaccine Therapy, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Fumio Endo
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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28
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Li Y, Tao L, Zuo Z, Zhou Y, Qian X, Lin Y, Jie H, Liu C, Li Z, Zhang H, Zhang H, Cen X, Yang S, Zhao Y. ZY0511, a novel, potent and selective LSD1 inhibitor, exhibits anticancer activity against solid tumors via the DDIT4/mTOR pathway. Cancer Lett 2019; 454:179-190. [DOI: 10.1016/j.canlet.2019.03.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/09/2019] [Accepted: 03/29/2019] [Indexed: 11/24/2022]
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29
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Lipase-catalyzed hydrolytic resolution of trans-2-(3,4-difluorophenyl)cyclopropyl azolides, a key building block for Ticagrelor synthesis. J Taiwan Inst Chem Eng 2019. [DOI: 10.1016/j.jtice.2019.02.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Synthesis, structure-activity relationship studies and biological characterization of new [1,2,4]triazolo[1,5-a]pyrimidine-based LSD1/KDM1A inhibitors. Eur J Med Chem 2019; 167:388-401. [DOI: 10.1016/j.ejmech.2019.02.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/13/2019] [Accepted: 02/10/2019] [Indexed: 02/03/2023]
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31
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Li ZR, Wang S, Yang L, Yuan XH, Suo FZ, Yu B, Liu HM. Experience-based discovery (EBD) of aryl hydrazines as new scaffolds for the development of LSD1/KDM1A inhibitors. Eur J Med Chem 2019; 166:432-444. [DOI: 10.1016/j.ejmech.2019.01.075] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/01/2019] [Accepted: 01/29/2019] [Indexed: 01/22/2023]
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32
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Li L, Li R, Wang Y. Identification of selective and reversible LSD1 inhibitors with anti-metastasis activity by high-throughput docking. Bioorg Med Chem Lett 2019; 29:544-548. [PMID: 30611617 DOI: 10.1016/j.bmcl.2018.12.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 02/08/2023]
Abstract
The overexpression of lysine specific demethylase 1 (LSD1) has been reported in various human tumors. There is increasing interest in targeting LSD1 with small molecules for cancer treatment. A released structure of an LSD1 kinase domain in complex with FAD was used to set up a low-cost high-throughput docking protocol for quick identification of LSD1 inhibitors. The most promising hit L05 was confirmed to be a potent, selective and reversible LSD1 inhibitor and displayed marked inhibition of colorectal cells migration without significant cytotoxicity.
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Affiliation(s)
- Lijun Li
- Department of General Surgery, Taizhou People's Hospital, Taizhou 225300, PR China.
| | - Ruizhe Li
- Department of Sport and Health Science, Nanjing Sport Institute, Nanjing 210000, PR China
| | - Yumei Wang
- Department of Emergency Internal Medicine, Taizhou People's Hospital, Taizhou 225300, PR China
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Saito S, Kikuchi J, Koyama D, Sato S, Koyama H, Osada N, Kuroda Y, Akahane K, Inukai T, Umehara T, Furukawa Y. Eradication of Central Nervous System Leukemia of T-Cell Origin with a Brain-Permeable LSD1 Inhibitor. Clin Cancer Res 2018; 25:1601-1611. [PMID: 30518632 DOI: 10.1158/1078-0432.ccr-18-0919] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/28/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE Lysine-specific demethylase 1 (LSD1) regulates several biological processes via the bifunctional modulation of enhancer functions. Recently, we reported that LSD1 overexpression is a founder abnormality of T-cell leukemogenesis and is maintained in fully transformed T-cell acute lymphoblastic leukemia (T-ALL) cells. On the basis of this finding, we attempted to develop novel LSD1 inhibitors effective for T-ALL with central nervous system (CNS) involvement. EXPERIMENTAL DESIGN We chemically modified the prototype LSD inhibitor tranylcypromine (TCP) and screened for cytotoxicity against TCP-resistant T-ALL cell lines. In vivo efficacy of novel LSD1 inhibitors was examined in immunodeficient mice transplanted with luciferase-expressing T-ALL cell lines, which faithfully reproduce human T-ALL with CNS involvement. RESULTS We found robust cytotoxicity against T-ALL cells, but not normal bone marrow progenitors, for two N-alkylated TCP derivatives, S2116 and S2157. The two compounds induced apoptosis in TCP-resistant T-ALL cells in vitro and in vivo by repressing transcription of the NOTCH3 and TAL1 genes through increased H3K9 methylation and reciprocal H3K27 deacetylation at superenhancer regions. Both S2116 and S2157 significantly retarded the growth of T-ALL cells in xenotransplanted mice and prolonged the survival of recipients as monotherapy and in combination with dexamethasone. Notably, S2157 could almost completely eradicate CNS leukemia because of its ability to efficiently pass through the blood-brain barrier. CONCLUSIONS These findings provide a molecular basis and rationale for the inclusion of a brain-permeable LSD1 inhibitor, S2157, in treatment strategies for T-ALL with CNS involvement.
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Affiliation(s)
- Shiori Saito
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Jiro Kikuchi
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Daisuke Koyama
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Shin Sato
- Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Naoki Osada
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Yoshiaki Kuroda
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Takashi Umehara
- Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yusuke Furukawa
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.
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34
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Yang GJ, Lei PM, Wong SY, Ma DL, Leung CH. Pharmacological Inhibition of LSD1 for Cancer Treatment. Molecules 2018; 23:E3194. [PMID: 30518104 PMCID: PMC6320820 DOI: 10.3390/molecules23123194] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Lysine-specific demethylase 1A (LSD1, also named KDM1A) is a demethylase that can remove methyl groups from histones H3K4me1/2 and H3K9me1/2. It is aberrantly expressed in many cancers, where it impedes differentiation and contributes to cancer cell proliferation, cell metastasis and invasiveness, and is associated with inferior prognosis. Pharmacological inhibition of LSD1 has been reported to significantly attenuate tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. This review will present the structural aspects of LSD1, its role in carcinogenesis, a comparison of currently available approaches for screening LSD1 inhibitors, a classification of LSD1 inhibitors, and its potential as a drug target in cancer therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Pui-Man Lei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Suk-Yu Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
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35
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Umezawa N, Tsuji K, Sato S, Kikuchi M, Watanabe H, Horai Y, Yamaguchi M, Hisamatsu Y, Umehara T, Higuchi T. Inhibition of FAD-dependent lysine-specific demethylases by chiral polyamine analogues. RSC Adv 2018; 8:36895-36902. [PMID: 35558920 PMCID: PMC9088916 DOI: 10.1039/c8ra07879c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/19/2018] [Indexed: 01/23/2023] Open
Abstract
Lysine-specific demethylases 1 and 2 (LSD1 and LSD2) are flavoenzyme demethylases, and their inhibitors are considered as potential chemical tools and anticancer agents. Here we report polyamine-based inhibitors of LSD1 and LSD2. In the initial screening, partially constrained polyamine 2 which contains three trans-cyclopentane units with a total of six stereogenic centers, showed the most potent LSD1-inhibitory activity. We then prepared a set of optical isomers of 2 and evaluated their inhibitory activities toward LSD1, LSD2, monoamine oxidases A and B (MAO-A and MAO-B). Optical isomers of 2 showed LSD1-inhibitory activity with K i values of 2.2 to 6.4 μM, and LSD2-inhibitory activity with K i values of 4.4 to 39 μM; there was a general preference for LSD1 to LSD2. All of them showed weak to negligible inhibition of MAO-A and MAO-B. This selectivity seemed to reflect the differences in the size and shape of the catalytic cavity of target enzymes, and our strategy of employing a set of optical isomers appears to be an effective approach for exploring the structural features of this family of enzymes. Polyamine 9 showed most potent LSD1-inhibitory activity (K i = 2.2 μM in vitro), and it also inhibited the proliferation of HL-60 cells (IC50 = 49 μM). On the other hand, 12 was the most potent inhibitors of LSD2 with in vitro K i values of 4.4 μM.
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Affiliation(s)
- Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
| | - Kasumi Tsuji
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, Tsurumi-kuYokohamaKanagawa 230-0045Japan
| | - Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, Tsurumi-kuYokohamaKanagawa 230-0045Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, Tsurumi-kuYokohamaKanagawa 230-0045Japan
| | - Yuhei Horai
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
| | - Masashi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
| | - Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, Tsurumi-kuYokohamaKanagawa 230-0045Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University3-1 Tanabe-dori, Mizuho-kuNagoya 467-8603Japan
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Xu S, Zhou C, Liu R, Zhu Q, Xu Y, Lan F, Zha X. Optimization of 5-arylidene barbiturates as potent, selective, reversible LSD1 inhibitors for the treatment of acute promyelocytic leukemia. Bioorg Med Chem 2018; 26:4871-4880. [PMID: 30153955 DOI: 10.1016/j.bmc.2018.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 02/08/2023]
Abstract
Histone lysine specific demethylase 1 (LSD1) is overexpressed in diverse hematologic disorders and recognized as a promising target for blood medicines. In this study, molecular docking-based virtual screening united with bioevaluation was utilized to identify novel skeleton of 5-arylidene barbiturate as small-molecule inhibitors of LSD1. Among the synthesized derivatives, 12a exhibited reversible and potent inhibition (IC50 = 0.41 μM) and high selectivity over the MAO-A and MAO-B. Notably, 12a strongly induced differentiation effect on acute promyelocytic leukemia NB4 cell line and distinctly escalated the methylation level on histone 3 lysine 4 (H3K4). Our findings indicate that 5-arylidene barbiturate may represent a new skeleton of LSD1 inhibitors and 12a deserve as a promising agent for the further research.
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Affiliation(s)
- Siyuan Xu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Chen Zhou
- Department of Pharmaceutical Engineering, Department of Biomedical Engineering, Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China
| | - Rongfeng Liu
- Shanghai ChemPartner Co. Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Qihua Zhu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Department of Pharmaceutical Engineering, Department of Biomedical Engineering, Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China.
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Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-( p-tolyl)pyridin-3-yl]benzonitrile. Molecules 2018; 23:molecules23071538. [PMID: 29949906 PMCID: PMC6099836 DOI: 10.3390/molecules23071538] [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] [Received: 05/28/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 11/17/2022] Open
Abstract
Because lysine-specific demethylase 1 (LSD1) regulates the maintenance of cancer stem cell properties, small-molecule inhibitors of LSD1 are expected to be useful for the treatment of several cancers. Reversible inhibitors of LSD1 with submicromolar inhibitory potency have recently been reported, but their exact binding modes are poorly understood. In this study, we synthesized a recently reported reversible inhibitor, 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile, which bears a 4-piperidinylmethoxy group, a 4-methylphenyl group, and a 4-cyanophenyl group on a pyridine ring, and determined the crystal structure of LSD1 in complex with this inhibitor at 2.96 Å. We observed strong electron density for the compound, showing that its cyano group forms a hydrogen bond with Lys661, which is a critical residue in the lysine demethylation reaction located deep in the catalytic center of LSD1. The piperidine ring interacts with the side chains of Asp555 and Asn540 in two conformations, and the 4-methylphenyl group is bound in a hydrophobic pocket in the catalytic center. Our elucidation of the binding mode of this compound can be expected to facilitate the rational design of more-potent reversible LSD1 inhibitors.
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38
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Yeh Y, Tzeng Y, Tsai S. Quantitative Improvements and Insights into CALB‐Catalyzed Resolution of
trans
‐ and
cis
‐2‐Phenylcyclopropyl Azolides. ChemistrySelect 2018. [DOI: 10.1002/slct.201800578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan‐Ru Yeh
- Institute of Biochemical and Biomedical EngineeringChang Gung University, Kwei-Shan District Tao-Yuan City 33302 Taiwan, R.O.C
| | - Yi‐Jia Tzeng
- Department of Chemical and Materials EngineeringChang Gung University, Kwei-Shan District Tao-Yuan City 33302 Taiwan, R.O.C
| | - Shau‐Wei Tsai
- Institute of Biochemical and Biomedical EngineeringChang Gung University, Kwei-Shan District Tao-Yuan City 33302 Taiwan, R.O.C
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39
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Xi J, Xu S, Zhang L, Bi X, Ren Y, Liu YC, Gu Y, Xu Y, Lan F, Zha X. Design, synthesis and biological activity of 4-(4-benzyloxy)phenoxypiperidines as selective and reversible LSD1 inhibitors. Bioorg Chem 2018. [PMID: 29524666 DOI: 10.1016/j.bioorg.2018.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine specific demethylase 1 (LSD1) plays a vital role in epigenetic regulation of gene activation and repression in several human cancers and is recognized as a promising antitumor therapeutic target. In this paper, a series of 4-(4-benzyloxy)phenoxypiperidines were synthesized and evaluated. Among the tested compounds, compound 10d exhibited the potent and reversible inhibitory activity against LSD1 in vitro (IC50 = 4 μM). Molecular docking was conducted to predict its binding mode. Furthermore, 10d displayed it could inhibit migration of HCT-116 colon cancer cells and A549 lung cancer cells. Taken together, 10d deserves further investigation as a hit-to-lead for the treatment of LSD1 associated tumors.
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Affiliation(s)
- Jiayue Xi
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Siyuan Xu
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China
| | - Lulu Zhang
- Department of Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, PR China
| | - Xueyuan Bi
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yanshen Ren
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Yueqing Gu
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Fei Lan
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China.
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40
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Lysine-specific demethylase 1 inhibitors prevent teratoma development from human induced pluripotent stem cells. Oncotarget 2018; 9:6450-6462. [PMID: 29464084 PMCID: PMC5814224 DOI: 10.18632/oncotarget.24030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/02/2018] [Indexed: 02/02/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) are creating great expectations for regenerative medicine. However, safety strategies must be put in place to guard against teratoma formation after transplantation of hiPSC-derived cells into patients. Recent studies indicate that epigenetic regulators act at the initial step of tumorigenesis. Using gain-of-function and loss-of-function approaches, we show here that the expression and function of lysine-specific demethylase 1 (LSD1) are tightly regulated in hiPSCs, and their deregulation underlies the development of teratomas. Consistent with these results, we demonstrate that an LSD1 inhibitor, S2157, prevented teratoma formation from hiPSCs transplanted into immunodeficient mice. This novel action of LSD1 and the effects of its inhibition potentially allow for the development of new clinical applications and therapeutic strategies using hiPSCs.
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41
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Kalin JH, Wu M, Gomez AV, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe JWR, Mattevi A, Alani RM, Cole PA. Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors. Nat Commun 2018; 9:53. [PMID: 29302039 PMCID: PMC5754352 DOI: 10.1038/s41467-017-02242-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023] Open
Abstract
Here we report corin, a synthetic hybrid agent derived from the class I HDAC inhibitor (entinostat) and an LSD1 inhibitor (tranylcypromine analog). Enzymologic analysis reveals that corin potently targets the CoREST complex and shows more sustained inhibition of CoREST complex HDAC activity compared with entinostat. Cell-based experiments demonstrate that corin exhibits a superior anti-proliferative profile against several melanoma lines and cutaneous squamous cell carcinoma lines compared to its parent monofunctional inhibitors but is less toxic to melanocytes and keratinocytes. CoREST knockdown, gene expression, and ChIP studies suggest that corin's favorable pharmacologic effects may rely on an intact CoREST complex. Corin was also effective in slowing tumor growth in a melanoma mouse xenograft model. These studies highlight the promise of a new class of two-pronged hybrid agents that may show preferential targeting of particular epigenetic regulatory complexes and offer unique therapeutic opportunities.
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Affiliation(s)
- Jay H Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrea V Gomez
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Yun Song
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Jayanta Das
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dawn Hayward
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nkosi Adejola
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mingxuan Wu
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Izabela Panova
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hye Jin Chung
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Edward Kim
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Holly J Roberts
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Polina Prusevich
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Louise Fairall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Charles Milano
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Abdulkerim Eroglu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Charlotte M Proby
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Albena T Dinkova-Kostova
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Wayne W Hancock
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sergio Valente
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Antonello Mai
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Nicole M Anders
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michelle A Rudek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yong Hu
- Department of Oncology, BioDuro LLC, Shanghai, 200131, China
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - John W R Schwabe
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy.
| | - Rhoda M Alani
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Xiong Y, Wang E, Huang Y, Guo X, Yu Y, Du Q, Ding X, Sun Y. Inhibition of Lysine-Specific Demethylase-1 (LSD1/KDM1A) Promotes the Adipogenic Differentiation of hESCs Through H3K4 Methylation. Stem Cell Rev Rep 2017; 12:298-304. [PMID: 27059868 PMCID: PMC4879152 DOI: 10.1007/s12015-016-9650-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Given their totipotency, human embryonic stem cells (hESCs) can differentiate into all types of cells, including adipocytes, and provide an excellent research model for studying diseases associated with the metabolism of adipocytes, such as obesity and diabetes mellitus. Epigenetic regulation, including DNA methylation and histone modification, plays an essential role in the development and differentiation of hESCs. Lysine-specific demethylase 1 (LSD1), a well-characterized histone-modifying enzyme, demethylates dimethylated histone H3 lysine 4 (H3K4) through a flavin adenine dinucleotide (FAD)-dependent oxidative reaction. LSD1 affects the growth and differentiation of human and mouse ES cells, and the deletion of this gene in mice leads to embryonic lethality. Here, we investigated the functional role of LSD1 during the adipogenic differentiation of hESCs involving the demethylation of H3K4. We also found that treating hESCs with the LSD1 inhibitor CBB1007 promotes the adipogenic differentiation of hESCs.
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Affiliation(s)
- Yujing Xiong
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Enyin Wang
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yan Huang
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xiaoyi Guo
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yiping Yu
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Qingyun Du
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xiaoyan Ding
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai, 200031, People's Republic of China
| | - Yingpu Sun
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China.
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43
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He Y, Bao B, Li H. Using zebrafish as a model to study the role of epigenetics in hearing loss. Expert Opin Drug Discov 2017; 12:967-975. [PMID: 28682135 DOI: 10.1080/17460441.2017.1340270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The rapid progress of bioinformatics and high-throughput screening techniques in recent years has led to the identification of many candidate genes and small-molecule drugs that have the potential to make significant contributions to our understanding of the developmental and pathological processes of hearing, but it remains unclear how these genes and regulatory factors are coordinated. Increasing evidence suggests that epigenetic mechanisms are essential for establishing gene expression profiles and likely play an important role in the development of inner ear and in the pathology of hearing-associated diseases. Zebrafish are a valuable and tractable in vivo model organism for monitoring changes in the epigenome and for identifying new epigenetic processes and drug molecules that can influence vertebrate development. Areas covered: In this review, the authors focus on zebrafish as a model to summarize recent findings concerning the roles of epigenetics in the development, regeneration, and protection of hair cells. Expert opinion: Using the zebrafish model in combination with high-throughput screening and genome-editing technologies to investigate the function of epigenetics in hearing is crucial to help us better understand the molecular and genetic mechanisms of auditory development and function. It will also contribute to the development of new strategies to restore hearing loss.
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Affiliation(s)
- Yingzi He
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China
| | - Beier Bao
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China
| | - Huawei Li
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,b Institutes of Biomedical Sciences , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China.,d Shanghai Engineering Research Centre of Cochlear Implant , Shanghai , China.,e The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science , Fudan University , Shanghai , China
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Xi J, Xu S, Wu L, Ma T, Liu R, Liu YC, Deng D, Gu Y, Zhou J, Lan F, Zha X. Design, synthesis and biological activity of 3-oxoamino-benzenesulfonamides as selective and reversible LSD1 inhibitors. Bioorg Chem 2017; 72:182-189. [PMID: 28460360 DOI: 10.1016/j.bioorg.2017.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/30/2017] [Accepted: 04/13/2017] [Indexed: 12/09/2022]
Abstract
Lysine specific demethylase 1 (LSD1) is a flavin-dependent amine oxidase that selectively removes one or two methyl groups from H3 at Lys4 and is recognized as a promising therapeutic target for cancer and other diseases. Here, a series of 3-oxoamino-benzenesulfonamides were synthesized and evaluated for their inhibitory activity against LSD1. Compounds 7b and 7h showed the most potent inhibition with the IC50 values of 9.5 and 6.9μM, respectively. Furthermore, the LSD1 inhibition of 7b and 7h were reversible and selective. Docking study presented the possible binding mode between 7b, 7h and the LSD1 active site. Taken together, 3-oxoamino-benzenesulfonamides may represent a new class of reversible LSD1 inhibitors and 7b and 7h were two hit compounds deserved further structural optimization.
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Affiliation(s)
- Jiayue Xi
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Siyuan Xu
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China
| | - Liming Wu
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Tianfang Ma
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Rongfeng Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Dawei Deng
- Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yueqing Gu
- Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Fei Lan
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Department of Biochemical Engineering, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
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45
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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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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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47
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Amano Y, Kikuchi M, Sato S, Yokoyama S, Umehara T, Umezawa N, Higuchi T. Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1. Bioorg Med Chem 2017; 25:2617-2624. [PMID: 28336409 DOI: 10.1016/j.bmc.2017.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) is a flavoenzyme demethylase, which removes mono- and dimethyl groups from histone H3 Lys4 (H3K4) or Lys9 (H3K9) in complexes with several nuclear proteins. Since LSD1 is implicated in the tumorigenesis and progression of various cancers, LSD1-specific inhibitors are considered as potential anti-cancer agents. A modified H3 peptide with substitution of Lys4 to Met [H3K4M] is already known to be a potent competitive inhibitor of LSD1. In this study, we synthesized a series of H3K4M peptide derivatives and evaluated their LSD1-inhibitory activities in vitro. We found that substitutions of the N-terminal amino acid with amino acids having a larger side chain were generally not tolerated, but substitution of Ala1 to Ser unexpectedly resulted in more potent inhibitory activity toward LSD1. X-ray crystallographic analysis of H3K4M derivatives bound to the LSD1·CoREST complex revealed the presence of additional hydrogen bonding between the N-terminal Ser residue of the H3 peptide derivative and LSD1. The present structural and biochemical findings will be helpful for obtaining more potent peptidic inhibitors of LSD1.
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Affiliation(s)
- Yuichi Amano
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Masaki Kikuchi
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shin Sato
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Umehara
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan.
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
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Vianello P, Sartori L, Amigoni F, Cappa A, Fagá G, Fattori R, Legnaghi E, Ciossani G, Mattevi A, Meroni G, Moretti L, Cecatiello V, Pasqualato S, Romussi A, Thaler F, Trifiró P, Villa M, Botrugno OA, Dessanti P, Minucci S, Vultaggio S, Zagarrí E, Varasi M, Mercurio C. Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure–Activity Relationship. J Med Chem 2017; 60:1693-1715. [DOI: 10.1021/acs.jmedchem.6b01019] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Paola Vianello
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Luca Sartori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Federica Amigoni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Anna Cappa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giovanni Fagá
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Raimondo Fattori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elena Legnaghi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giuseppe Ciossani
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Giuseppe Meroni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Loris Moretti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Valentina Cecatiello
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- IFOM- The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milano, Italy
| | - Sebastiano Pasqualato
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Alessia Romussi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Florian Thaler
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paolo Trifiró
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Manuela Villa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Oronza A. Botrugno
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Dessanti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Department
of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefania Vultaggio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elisa Zagarrí
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Mario Varasi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Ciro Mercurio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Genextra Group, DAC s.r.l., Via
Adamello 16, 20139 Milano, Italy
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49
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Abstract
Cancer cell hallmarks are underpinned by transcriptional programmes operating in the context of a dynamic and complicit epigenomic environment. Somatic alterations of chromatin modifiers are among the most prevalent cancer perturbations. There is a pressing need for targeted chemical probes to dissect these complex, interconnected gene regulatory circuits. Validated chemical probes empower mechanistic research while providing the pharmacological proof of concept that is required to translate drug-like derivatives into therapy for cancer patients. In this Review, we describe chemical probe development for epigenomic effector proteins that are linked to cancer pathogenesis. By annotating these reagents, we aim to share our perspectives on an informative 'epigenomic toolbox' of broad utility to the research community.
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Affiliation(s)
- Jake Shortt
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
- School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, Australia
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
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50
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Theisen ER, Pishas KI, Saund RS, Lessnick SL. Therapeutic opportunities in Ewing sarcoma: EWS-FLI inhibition via LSD1 targeting. Oncotarget 2017; 7:17616-30. [PMID: 26848860 PMCID: PMC4951237 DOI: 10.18632/oncotarget.7124] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing sarcoma is an aggressive primary pediatric bone tumor, often diagnosed in adolescents and young adults. A pathognomonic reciprocal chromosomal translocation results in a fusion gene coding for a protein which derives its N-terminus from a FUS/EWS/TAF15 (FET) protein family member, commonly EWS, and C-terminus containing the DNA-binding domain of an ETS transcription factor, commonly FLI1. Nearly 85% of cases express the EWS-FLI protein which functions as a transcription factor and drives oncogenesis. As the primary genomic lesion and a protein which is not expressed in normal cells, disrupting EWS-FLI function is an attractive therapeutic strategy for Ewing sarcoma. However, transcription factors are notoriously difficult targets for the development of small molecules. Improved understanding of the oncogenic mechanisms employed by EWS-FLI to hijack normal cellular programming has uncovered potential novel approaches to pharmacologically block EWS-FLI function. In this review we examine targeting the chromatin regulatory enzymes recruited to conspire in oncogenesis with a focus on the histone lysine specific demethylase 1 (LSD1). LSD1 inhibitors are being aggressively investigated in acute myeloid leukemia and the results of early clinical trials will help inform the future use of LSD1 inhibitors in sarcoma. High LSD1 expression is observed in Ewing sarcoma patient samples and mechanistic and preclinical data suggest LSD1 inhibition globally disrupts the function of EWS-ETS proteins.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Cancer Therapeutics Laboratory, Centre for Personalized Cancer Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Ranajeet S Saund
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Pediatric Hematology/Oncology/Bone Marrow Transplant at The Ohio State University, Columbus, Ohio, USA
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