1
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Senanayaka D, Zeng D, Alishiri S, Martin WJ, Moore KI, Patel R, Luka Z, Hirschi A, Reiter NJ. Autoregulatory mechanism of enzyme activity by the nuclear localization signal of lysine-specific demethylase 1. J Biol Chem 2024; 300:107607. [PMID: 39084460 PMCID: PMC11388019 DOI: 10.1016/j.jbc.2024.107607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
The N-terminal region of the human lysine-specific demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple posttranslational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays reveal that LSD1's own electropositive NLS amino acids 107 to 120 inhibit demethylation activity on a model histone 3 lysine 4 dimethyl (H3K4me2) peptide (Kiapp ∼ 3.3 μM) and histone 3 lysine 4 dimethyl nucleosome substrates (IC50 ∼ 30.4 μM), likely mimicking the histone H3 tail. Further, when the identical, inhibitory NLS region contains phosphomimetic modifications, inhibition is partially relieved. Based upon these results and biophysical data, a regulatory mechanism for the LSD1-catalyzed demethylation reaction is proposed whereby NLS-mediated autoinhibition can occur through electrostatic interactions, and be partially relieved through phosphorylation that occurs proximal to the NLS. Taken together, the results highlight a dynamic and synergistic role for PTMs, intrinsically disordered regions, and structured regions near LSD1 active site and introduces the notion that phosphorylated mediated NLS regions can function to fine-tune chromatin modifying enzyme activity.
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Affiliation(s)
- Dulmi Senanayaka
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Danyun Zeng
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Sahar Alishiri
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - William J Martin
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Khadijah I Moore
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Roshni Patel
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alexander Hirschi
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nicholas J Reiter
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA.
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2
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Takada Y, Adachi K, Fujinaga Y, Yamashita Y, Itoh Y, Suzuki T. A Structure-Activity Relationship Study of SNAIL1 Peptides as Inhibitors of Lysine-Specific Demethylase 1. Chem Pharm Bull (Tokyo) 2024; 72:155-160. [PMID: 38296557 DOI: 10.1248/cpb.c23-00671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Peptides have recently garnered attention as middle-molecular-weight drugs with the characteristics of small molecules and macromolecules. Lysine-specific demethylase 1 (LSD1) is a potential therapeutic target for lung cancer, neuroblastoma, and leukemia, and some peptide-based LSD1 inhibitors designed based on the N-terminus of SNAIL1, a member of the SNAIL/SCRATCH family of transcription factors, have been reported. The N-terminus of SNAIL1 peptide acts as a cap of the catalytic site of LSD1, inhibiting interactions with LSD1. However, the structure-activity relationship (SAR) of these inhibitors is not yet fully understood. Therefore, in the present study, we aimed to uncover the SAR and to identify novel SNAIL1 peptide-based LSD1 inhibitors. We synthesized peptide inhibitor candidates based on truncating the N-terminus of SNAIL1 or substituting its amino acid residues. In the truncation study, we found that SNAIL1 1-16 (2), which was composed of 16 residues, strongly inhibited LSD1. Furthermore, we investigated the SAR at residues-3 and -5 from the N-terminus and found that peptides 2j and 2k, in which leucine 5 of the parent peptide is substituted with unnatural amino acids, cyclohexylalanine and norleucine, respectively, strongly inhibited LSD1. This result suggests that the hydrophobic interaction between the inhibitor peptides and LSD1 affects the LSD1-inhibitory activity. We believe that this SAR information provides a basis for the development of more potent LSD1 inhibitors.
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3
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Luo Q, Ma Y, Liang H, Feng Y, Liu N, Lian C, Zhu L, Ye Y, Liu Z, Hou Z, Chen S, Wang Y, Dai C, Song C, Zhang M, He Z, Xing Y, Zhong W, Li S, Wu J, Lu F, Yin F, Li Z. Covalent Peptide LSD1 Inhibitor Specifically Recognizes Cys360 in the Enzyme-Active Region. J Med Chem 2023; 66:15409-15423. [PMID: 37922441 DOI: 10.1021/acs.jmedchem.3c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a promising therapeutic target, especially in cancer treatment. Despite several LSD1 inhibitors being discovered for the cofactor pocket, none are FDA-approved. We aimed to develop stabilized peptides for irreversible LSD1 binding, focusing on unique cysteine residue Cys360 in LSD1 and SNAIL1. We created LSD1 C360-targeting peptides, like cyclic peptide S9-CMC1, using our Cysteine-Methionine cyclization strategy. S9-CMC1 effectively inhibited LSD1 at the protein level, as confirmed by MS analysis showing covalent bonding to Cys360. In cells, S9-CMC1 inhibited LSD1 activity, increasing H3K4me1 and H3K4me2 levels, leading to G1 cell cycle arrest and apoptosis and inhibiting cell proliferation. Remarkably, S9-CMC1 showed therapeutic potential in A549 xenograft animal models, regulating LSD1 activity and significantly inhibiting tumor growth with minimal organ damage. These findings suggest LSD1 C360 as a promising site for covalent LSD1 inhibitors' development.
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Affiliation(s)
- Qinhong Luo
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Yue Ma
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Huiting Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Yuan Feng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Na Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Chenshan Lian
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Lizhi Zhu
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yuxin Ye
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Sijin Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yaqi Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Chuan Dai
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Chunli Song
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Min Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zhipeng He
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Yun Xing
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Wanjin Zhong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Shuiming Li
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianlong Wu
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
| | - Fei Lu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
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4
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Baby S, Shinde SD, Kulkarni N, Sahu B. Lysine-Specific Demethylase 1 (LSD1) Inhibitors: Peptides as an Emerging Class of Therapeutics. ACS Chem Biol 2023; 18:2144-2155. [PMID: 37812385 DOI: 10.1021/acschembio.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aberrant expression of the epigenetic regulator lysine-specific demethylase 1 (LSD1) has been associated with the incidence of many diseases, particularly cancer, and it has evolved as a promising epigenetic target over the years for treatment. The advent of LSD1 inhibitor-based clinical utility began with tranylcypromine, and it is now considered an inevitable scaffold in the search for other irreversible novel LSD1 inhibitors (IMG-7289 or bomedemstat, ORY1001 or iadademstat, ORY-2001 or vafidemstat, GSK2879552, and INCB059872). Moreover, numerous reversible inhibitors for LSD1 have been reported in the literature, including clinical candidates CC-90011 (pulrodemstat) and SP-2577 (seclidemstat). There is parallel mining for peptide-based LSD1 inhibitors, which exploits the opportunities in the LSD1 substrate binding pocket. This Review highlights the research progress on reversible and irreversible peptide/peptide-derived LSD1 inhibitors. For the first time, we comprehensively organized the peptide-based LSD1 inhibitors from the design strategy. Peptide inhibitors of LSD1 are classified as H3 peptide and SNAIL1 peptide derivatives, along with miscellaneous peptides that include naturally occurring LSD1 inhibitors.
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Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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5
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Zheng C, Rej RK, Wang M, Huang L, Fernandez-Salas E, Yang CY, Wang S. Discovery of Pyrrolo[2,3- c]pyridines as Potent and Reversible LSD1 Inhibitors. ACS Med Chem Lett 2023; 14:1389-1395. [PMID: 37849536 PMCID: PMC10577893 DOI: 10.1021/acsmedchemlett.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
Lysine specific demethylase 1 (LSD1) acts as an epigenetic eraser by specifically demethylating mono- and histone 3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) residues. LSD1 has been pursued as a promising therapeutic target for the treatment of human cancer, and a number of LSD1 inhibitors have been advanced into clinical development. In the present study, we describe our discovery of pyrrolo[2,3-c]pyridines as a new class of highly potent and reversible LSD1 inhibitors, designed on the basis of a previously reported LSD1 inhibitor GSK-354. Among them, 46 shows an IC50 value of 3.1 nM in inhibition of LSD1 enzymatic activity and inhibits cell growth with IC50 values of 0.6 nM in the MV4;11 acute leukemia cell line and 1.1 nM in the H1417 small-cell lung cancer cell line. Compound 46 (LSD1-UM-109) is a novel, highly potent, and reversible LSD1 inhibitor and serves as a promising lead compound for further optimization.
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Affiliation(s)
- Canhui Zheng
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Rohan Kalyan Rej
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Mi Wang
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Liyue Huang
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Ester Fernandez-Salas
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Chao-Yie Yang
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
| | - Shaomeng Wang
- Department
of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United
States
- Department of Pharmacology, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
- Medicinal
Chemistry, College of Pharmacy, University
of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United
States
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6
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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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7
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Hu R, Hameed UFS, Sun X, Moorthy BS, Zhang W, Jeffrey PD, Zhou L, Ma X, Chen F, Pei J, Giri PK, Mou Y, Swaminathan K, Yuan P. A NR2E1-interacting peptide of LSD1 inhibits the proliferation of brain tumour initiating cells. Cell Prolif 2023; 56:e13350. [PMID: 36321378 DOI: 10.1111/cpr.13350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Elimination of brain tumour initiating cells (BTICs) is important for the good prognosis of malignant brain tumour treatment. To develop a novel strategy targeting BTICs, we studied NR2E1(TLX) involved self-renewal mechanism of BTICs and explored the intervention means. MATERIALS AND METHODS NR2E1 and its interacting protein-LSD1 in BTICs were studied by gene interference combined with cell growth, tumour sphere formation, co-immunoprecipitation and chromatin immunoprecipitation assays. NR2E1 interacting peptide of LSD1 was identified by Amide Hydrogen/Deuterium Exchange and Mass Spectrometry (HDX-MS) and analysed by in vitro functional assays. The in vivo function of the peptide was examined with intracranial mouse model by transplanting patient-derived BTICs. RESULTS We found NR2E1 recruits LSD1, a lysine demethylase, to demethylate mono- and di-methylated histone 3 Lys4 (H3K4me/me2) at the Pten promoter and repress its expression, thereby promoting BTIC proliferation. Using Amide Hydrogen/Deuterium Exchange and Mass Spectrometry (HDX-MS) method, we identified four LSD1 peptides that may interact with NR2E1. One of the peptides, LSD1-197-211 that locates at the LSD1 SWIRM domain, strongly inhibited BTIC proliferation by promoting Pten expression through interfering NR2E1 and LSD1 function. Furthermore, overexpression of this peptide in human BTICs can inhibit intracranial tumour formation. CONCLUSION Peptide LSD1-197-211 can repress BTICs by interfering the synergistic function of NR2E1 and LSD1 and may be a promising lead peptide for brain tumour therapy in future.
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Affiliation(s)
- Rong Hu
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Xiang Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | | | - Wen Zhang
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Li Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xin Ma
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fangjin Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Pankaj K Giri
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Yonggao Mou
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | | | - Ping Yuan
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
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8
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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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9
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Li B, Zhang X, Li J. Carrier-free supramolecular nanoassemblies of pure LSD1 inhibitor for effective anti-tumor therapy. Front Chem 2022; 10:1012882. [PMID: 36247676 PMCID: PMC9561089 DOI: 10.3389/fchem.2022.1012882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
The LSD1 protein is an oxidase that regulates protein methylation, which regulates gene expression and triggers tumors. Previously, inhibiting LSD1 has been found to be an effective treatment strategy for opposing tumors caused by overexpression of LSD1. Our recent study found that compound 17i was a suitable LSD1 inhibitor with potential anti-tumor activity. However, its extremely insoluble nature limits further validation of its anti-tumor activity at the clinical level. In this study, a unique carrier-free supramolecular nanoassemblies of pure compound 17i is expected to enhance therapeutic efficacy. Aqueous-insoluble compound 17i was mixed with a small quantity of DSPE-PEG2000 into an organic solvent and was prepared as nanoassemblies in water via the one-step nanoprecipitation method. The 17i nanoassemblies have a similar effect on its cytotoxicity when compared with 17i solution in vitro. Importantly, the PEGylated 17i nanoassemblies exhibit significant superiorities over 17i solutions in therapeutic efficiency, anti-tumor immune response and systemic toxicity in BALB/c mice bearing CT-26 colorectal tumors. We envision that the fabrication of pure drug nanoassemblies offers an efficient platform for reforming the undesirable characteristics of drug-like compounds to potentiate the anti-tumor therapeutic effect.
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Affiliation(s)
- Boao Li
- Department of Colorectal Surgery, Liaoning Cancer Hospital, Shenyang, China
| | - Xiangyu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- *Correspondence: Xiangyu Zhang, ; Jibin Li,
| | - Jibin Li
- Department of Colorectal Surgery, Liaoning Cancer Hospital, Shenyang, China
- *Correspondence: Xiangyu Zhang, ; Jibin Li,
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10
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Zhang X, Sun Y, Huang H, Wang X, Wu T, Yin W, Li X, Wang L, Gu Y, Zhao D, Cheng M. Identification of novel indole derivatives as highly potent and efficacious LSD1 inhibitors. Eur J Med Chem 2022; 239:114523. [PMID: 35732082 DOI: 10.1016/j.ejmech.2022.114523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 11/04/2022]
Abstract
Lysine-specific demethylase 1 (LSD1) is a FAD-dependent histone demethylase to catalyze the demethylation of H3K4 and H3K9 and thus is an attractive target for therapeutic cancer. Starting with a high micromolar compound 17i, structure-based optimization of novel indole derivatives is described by a bioelectronic isosteric strategy. Grounded by molecular modeling, medicinal chemistry has efficiently yielded low nanomolar LSD1 inhibitors. One of the compounds, B35, exhibited excellent LSD1 inhibition (IC50 = 0.050 ± 0.005 μM) and anti-proliferation against A549 cells (IC50 = 0.74 ± 0.14 μM). The further PK studies indicated compound B35 possessed favorable metabolic stability, in which the plasma t1/2 of p.o. and i.v. were 6.27 ± 0.72 h and 8.78 ± 1.31 h, respectively. Additionally, inhibitor B35 shows a strong antitumor effect and good safety in vivo. Meanwhile, compound B35 regulated genes are closely associated with transcriptional dislocation in cancer and PI3K/AKT pathway involving IGFBP3. Taken together, B35 could be a potent LSD1 inhibitor for further drug development.
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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, PR China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Hailan Huang
- Department of Physiology, Life Science and Biopharmaceutical Institution, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinran Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China; 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, PR China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Xiaojia Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Lin Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
| | - Yanting Gu
- Department of Physiology, Life Science and Biopharmaceutical Institution, Shenyang Pharmaceutical University, Shenyang, China.
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, PR China
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11
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Alsehli M, Aljuhani A, Ihmaid SK, El-Messery SM, Othman DIA, El-Sayed AAAA, Ahmed HEA, Rezki N, Aouad MR. Design and Synthesis of Benzene Homologues Tethered with 1,2,4-Triazole and 1,3,4-Thiadiazole Motifs Revealing Dual MCF-7/HepG2 Cytotoxic Activity with Prominent Selectivity via Histone Demethylase LSD1 Inhibitory Effect. Int J Mol Sci 2022; 23:ijms23158796. [PMID: 35955929 PMCID: PMC9369007 DOI: 10.3390/ijms23158796] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, an efficient multistep synthesis of novel aromatic tricyclic hybrids incorporating different biological active moieties, such as 1,3,4-thiadiazole and 1,2,4-triazole, was reported. These target scaffolds are characterized by having terminal lipophilic or hydrophilic parts, and their structures are confirmed by different spectroscopic methods. Further, the cytotoxic activities of the newly synthesized compounds were evaluated using in vitro MTT cytotoxicity screening assay against three different cell lines, including HepG-2, MCF-7, and HCT-116, compared with the reference drug Taxol. The results showed variable performance against cancer cell lines, exhibiting MCF-7 and HepG-2 selectivities by active analogs. Among these derivatives, 1,2,4-triazoles 11 and 13 and 1,3,4-thiadiazole 18 were found to be the most potent compounds against MCF-7 and HepG-2 cancer cells. Moreover, structure–activity relationship (SAR) studies led to the identification of some potent LSD1 inhibitors. The tested compounds showed good LSD1 inhibitory activities, with an IC50 range of 0.04–1.5 μM. Compounds 27, 23, and 22 were found to be the most active analogs with IC50 values of 0.046, 0.065, and 0.074 μM, respectively. In addition, they exhibited prominent selectivity against a MAO target with apparent cancer cell apoptosis, resulting in DNA fragmentation. This research provides some new aromatic-centered 1,2,4-triazole-3-thione and 1,3,4-thiadiazole analogs as highly effective anticancer agents with good LSD1 target selectivity.
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Affiliation(s)
- Mosa Alsehli
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Ateyatallah Aljuhani
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Saleh K. Ihmaid
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah 42353, Saudi Arabia
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Jadara University, Irbid 21110, Jordan
| | - Shahenda M. El-Messery
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Dina I. A. Othman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abdel-Aziz A. A. El-Sayed
- Biology Department, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawarah 42351, Saudi Arabia
- Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Hany E. A. Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah 42353, Saudi Arabia
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 35511, Egypt
- Correspondence: (H.E.A.A.); (N.R.)
| | - Nadjet Rezki
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
- Correspondence: (H.E.A.A.); (N.R.)
| | - Mohamed R. Aouad
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
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12
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He X, Zhang H, Zhang Y, Ye Y, Wang S, Bai R, Xie T, Ye XY. Drug discovery of histone lysine demethylases (KDMs) inhibitors (progress from 2018 to present). Eur J Med Chem 2022; 231:114143. [DOI: 10.1016/j.ejmech.2022.114143] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/19/2022]
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13
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Sacilotto N, Dessanti P, Lufino MMP, Ortega A, Rodríguez-Gimeno A, Salas J, Maes T, Buesa C, Mascaró C, Soliva R. Comprehensive in Vitro Characterization of the LSD1 Small Molecule Inhibitor Class in Oncology. ACS Pharmacol Transl Sci 2021; 4:1818-1834. [PMID: 34927013 DOI: 10.1021/acsptsci.1c00223] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 01/10/2023]
Abstract
Lysine-specific demethylase 1 (LSD1 or KDM1A) is a chromatin modifying enzyme playing a key role in the cell cycle and cell differentiation and proliferation through the demethylation of histones and nonhistone substrates. In addition to its enzymatic activity, LSD1 plays a fundamental scaffolding role as part of transcription silencing complexes such as rest co-repressor (CoREST) and nucleosome remodeling and deacetylase (NuRD). A host of classical amine oxidase inhibitors such as tranylcypromine, pargyline, and phenelzine together with LSD1 tool compounds such as SP-2509 and GSK-LSD1 have been extensively utilized in LSD1 mechanistic cancer studies. Additionally, several optimized new chemical entities have reached clinical trials in oncology such as ORY-1001 (iadademstat), GSK2879552, SP-2577 (seclidemstat), IMG-7289 (bomedemstat), INCB059872, and CC-90011 (pulrodemstat). Despite this, no single study exists that characterizes them all under the same experimental conditions, preventing a clear interpretation of published results. Herein, we characterize the whole LSD1 small molecule compound class as inhibitors of LSD1 catalytic activity, disruptors of SNAIL/GFI1 (SNAG)-scaffolding protein-protein interactions, inducers of cell differentiation, and potential anticancer treatments for hematological and solid tumors to yield an updated, unified perspective of this field. Our results highlight significant differences in potency and selectivity among the clinical compounds with iadademstat being the most potent and reveal that most of the tool compounds have very low activity and selectivity, suggesting some conclusions derived from their use should be taken with caution.
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Affiliation(s)
- Natalia Sacilotto
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Paola Dessanti
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Michele M P Lufino
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Alberto Ortega
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | | | - Jordi Salas
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Tamara Maes
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Carlos Buesa
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Cristina Mascaró
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
| | - Robert Soliva
- Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, 08940 Barcelona, Spain
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14
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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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15
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Design, synthesis and biological evaluation of novel benzofuran derivatives as potent LSD1 inhibitors. Eur J Med Chem 2021; 220:113501. [PMID: 33945992 DOI: 10.1016/j.ejmech.2021.113501] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a FAD-dependent enzyme, which has been proposed as a promising target for therapeutic cancer. Herein, a series of benzofuran derivatives were designed, synthesized and biochemical evaluated as novel LSD1 inhibitors based on scaffold hopping and conformational restriction strategy. Most of the compounds potently suppressed the enzymatic activities of LSD1 and potently inhibited tumor cells proliferation. In particular, the representative compound 17i exhibited excellent LSD1 inhibition at the molecular levels with IC50 = 0.065 μM, as well as anti-proliferation against MCF-7, MGC-803, H460, A549 and THP-1 tumor cells with IC50 values of 2.90 ± 0.32, 5.85 ± 0.35, 2.06 ± 0.27, 5.74 ± 1.03 and 6.15 ± 0.49 μM, respectively. The binding modes of these compounds were rationalized by molecular docking. Meanwhile, a preliminary druggability evaluation showed that compound 17i displayed favorable liver microsomal stability and weak inhibitory activity against CYPs at 10 μM. Remarkably, H460 xenograft tumors studies revealed that 17i demonstrated robust in vivo antitumor efficacy without significant side effects. All the results demonstrated that compound 17i could represent a promising lead for further development.
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16
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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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17
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Dai XJ, Liu Y, Xue LP, Xiong XP, Zhou Y, Zheng YC, Liu HM. Reversible Lysine Specific Demethylase 1 (LSD1) Inhibitors: A Promising Wrench to Impair LSD1. J Med Chem 2021; 64:2466-2488. [PMID: 33619958 DOI: 10.1021/acs.jmedchem.0c02176] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a flavin adenine dinucleotide (FAD)-dependent monoamine oxidase, lysine specific demethylase 1 (LSD1/KDM1A) functions as a transcription coactivator or corepressor to regulate the methylation of histone 3 lysine 4 and 9 (H3K4/9), and it has emerged as a promising epigenetic target for anticancer treatment. To date, numerous inhibitors targeting LSD1 have been developed, some of which are undergoing clinical trials for cancer therapy. Although only two reversible LSD1 inhibitors CC-90011 and SP-2577 are in the clinical stage, the past decade has seen remarkable advances in the development of reversible LSD1 inhibitors. Herein, we provide a comprehensive review about structures, biological evaluation, and structure-activity relationship (SAR) of reversible LSD1 inhibitors.
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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
| | - 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
| | - 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
| | - Ying Zhou
- 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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18
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Sun Y, Li N, Su M, Wang X, Zhao D, Xiong B, Zhou Y, Liu T, Chen YL. Divalent tranylcypromine derivative as lysine-specific demethylase 1 inhibitor. Med Chem Res 2021. [DOI: 10.1007/s00044-020-02689-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Kanouni T, Severin C, Cho RW, Yuen NYY, Xu J, Shi L, Lai C, Del Rosario JR, Stansfield RK, Lawton LN, Hosfield D, O’Connell S, Kreilein MM, Tavares-Greco P, Nie Z, Kaldor SW, Veal JM, Stafford JA, Chen YK. Discovery of CC-90011: A Potent and Selective Reversible Inhibitor of Lysine Specific Demethylase 1 (LSD1). J Med Chem 2020; 63:14522-14529. [DOI: 10.1021/acs.jmedchem.0c00978] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Toufike Kanouni
- Fount Therapeutics, LLC, San Diego, California 92130, United States
| | - Christophe Severin
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Robert W. Cho
- Quanticel Pharmaceuticels, San Francisco, California 94158, United States
| | - Natalie Y.-Y. Yuen
- Oric Pharmaceuticals, South San Francisco, California 94080, United States
| | - Jiangchun Xu
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Lihong Shi
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Chon Lai
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Joselyn R. Del Rosario
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | | | - Lee N. Lawton
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - David Hosfield
- University of Chicago, Chicago, Illinois 60637, United States
| | | | | | | | - Zhe Nie
- Schrödinger, Inc., San Diego, California 92121, United States
| | | | - James M. Veal
- 858 Therapeutics, Inc., San Diego, California 92121, United States
| | | | - Young K. Chen
- Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
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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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Yang J, Talibov VO, Peintner S, Rhee C, Poongavanam V, Geitmann M, Sebastiano MR, Simon B, Hennig J, Dobritzsch D, Danielson UH, Kihlberg J. Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1. ACS OMEGA 2020; 5:3979-3995. [PMID: 32149225 PMCID: PMC7057333 DOI: 10.1021/acsomega.9b03493] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme which regulates the methylation of Lys4 of histone 3 (H3) and is overexpressed in certain cancers. We used structures of H3 substrate analogues bound to LSD1 to design macrocyclic peptide inhibitors of LSD1. A linear, Lys4 to Met-substituted, 11-mer (4) was identified as the shortest peptide distinctly interacting with LSD1. It was evolved into macrocycle 31, which was >40 fold more potent (K i = 2.3 μM) than 4. Linear and macrocyclic peptides exhibited unexpected differences in structure-activity relationships for interactions with LSD1, indicating that they bind LSD1 differently. This was confirmed by the crystal structure of 31 in complex with LSD1-CoREST1, which revealed a novel binding mode at the outer rim of the LSD1 active site and without a direct interaction with FAD. NMR spectroscopy of 31 suggests that macrocyclization restricts its solution ensemble to conformations that include the one in the crystalline complex. Our results provide a solid basis for the design of optimized reversible LSD1 inhibitors.
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Affiliation(s)
- Jie Yang
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Vladimir O. Talibov
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Stefan Peintner
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Claire Rhee
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | | | - Matthis Geitmann
- Beactica
AB, Uppsala Business Park, Virdings allé 2, SE-75450 Uppsala, Sweden
| | | | - Bernd Simon
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Janosch Hennig
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Doreen Dobritzsch
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - U. Helena Danielson
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- Science
for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
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22
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Vinyard ME, Su C, Siegenfeld AP, Waterbury AL, Freedy AM, Gosavi PM, Park Y, Kwan EE, Senzer BD, Doench JG, Bauer DE, Pinello L, Liau BB. CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML. Nat Chem Biol 2019; 15:529-539. [PMID: 30992567 DOI: 10.1038/s41589-019-0263-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/03/2019] [Indexed: 12/13/2022]
Abstract
Understanding the mechanism of small molecules is a critical challenge in chemical biology and drug discovery. Medicinal chemistry is essential for elucidating drug mechanism, enabling variation of small molecule structure to gain structure-activity relationships (SARs). However, the development of complementary approaches that systematically vary target protein structure could provide equally informative SARs for investigating drug mechanism and protein function. Here we explore the ability of CRISPR-Cas9 mutagenesis to profile the interactions between lysine-specific histone demethylase 1 (LSD1) and chemical inhibitors in the context of acute myeloid leukemia (AML). Through this approach, termed CRISPR-suppressor scanning, we elucidate drug mechanism of action by showing that LSD1 enzyme activity is not required for AML survival and that LSD1 inhibitors instead function by disrupting interactions between LSD1 and the transcription factor GFI1B on chromatin. Our studies clarify how LSD1 inhibitors mechanistically operate in AML and demonstrate how CRISPR-suppressor scanning can uncover novel aspects of target biology.
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Affiliation(s)
- Michael E Vinyard
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Allison P Siegenfeld
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pallavi M Gosavi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Yongho Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Eugene E Kwan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Benjamin D Senzer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Luca Pinello
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Molecular Pathology Unit and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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23
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Ganesan A. Epigenetic drug discovery: a success story for cofactor interference. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0069. [PMID: 29685973 DOI: 10.1098/rstb.2017.0069] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Within the past two decades, seven epigenetic drugs have received regulatory approval and numerous other candidates are currently in clinical trials. Among the epigenetic targets are the writer and eraser enzymes that are, respectively, responsible for the reversible introduction and removal of structural modifications in the nucleosome. This review discusses the progress achieved in the design and development of inhibitors against the key writer and eraser pairs: DNA methyltransferases and Tet demethylases; lysine/arginine methyltransferases and lysine demethylases; and histone acetyltransferases and histone deacetylases. A common theme for the successful inhibition of these enzymes in a potent and selective manner is the targeting of the cofactors present in the active site, namely zinc and iron cations, S-adenosylmethione, nicotinamide adenine dinucleotide, flavin adenine dinucleotide and acetyl Coenzyme A.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK .,Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg im Breisgau, Germany
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24
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Kores K, Lešnik S, Bren U, Janežič D, Konc J. Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. J Chem Inf Model 2019; 59:2467-2478. [PMID: 30883115 DOI: 10.1021/acs.jcim.8b00981] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Resveratrol is a polyphenol known for its antioxidant and anti-inflammatory properties, which support its use as a treatment for variety of diseases. There are already known connections of resveratrol to chemoprevention of cancer because of its ability to prevent tumor initiation and inhibit tumor promotion and progression. Resveratrol is also believed to be important in cardiovascular diseases and neurological disorders, such as Alzheimer's disease. Using an inverse molecular docking approach, we sought to find new potential targets of resveratrol. Docking of resveratrol into each ProBiS predicted binding site of >38 000 protein structures from the Protein Data Bank was examined, and a number of novel potential targets into which resveratrol was docked successfully were found. These explain known actions or predict new effects of resveratrol. The results included three human proteins that are already known to bind resveratrol. A majority of proteins discovered however have no already described connections with resveratrol. We report new potential target human proteins and proteins connected with different organisms into which resveratrol can dock. Our results reveal previously unknown potential target human proteins, whose connection with cardiovascular and neurological disorders could lead to new potential treatments for variety of diseases. We believe that our research could help in future experimental studies on revestratol bioactivity in humans.
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Affiliation(s)
- Katarina Kores
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Urban Bren
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia.,National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Dušanka Janežič
- University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
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25
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Lee A, Borrello MT, Ganesan A. LSD
(Lysine‐Specific Demethylase): A Decade‐Long Trip from Discovery to Clinical Trials. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527809257.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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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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27
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Ma JL, Zhang T, Suo FZ, Chang J, Wan XB, Feng XJ, Zheng YC, Liu HM. Lysine-specific demethylase 1 activation by vitamin B2 attenuates efficacy of apatinib for proliferation and migration of gastric cancer cell MGC-803. J Cell Biochem 2018; 119:4957-4966. [PMID: 29384217 DOI: 10.1002/jcb.26741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/25/2018] [Indexed: 12/29/2022]
Abstract
B vitamins play an essential role in the biosynthesis of nucleotides, replication of DNA, supply of methyl-groups, growth and repair of cells, aberrancies of which have all been implicated in carcinogenesis. Although the potential role of vitamin B in relation to the risk of cancer, including breast, and colorectal cancer, has been investigated in several observational studies, the mechanism of action is still unclear. In this study, vitamin B2 exhibited efficient activation of LSD1 by occupying the active sites where FAD stands. Interestingly, vitamin B2 significantly downregulated expression of CD86, a sensitive surrogate biomarker of LSD1 inhibition, and showed marked activation of gastric cancer cell migration and invasion. Meanwhile, vitamin B2 induced activation of LSD1 may attenuate the proliferation inhibition, and anti-migration effects of apatinib in gastric cancer cells. These findings suggested that vitamin B supplementation may interfere with the efficacy of apatinib in patients with gastric cancer.
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Affiliation(s)
- Jin-Lian Ma
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
| | - Ting Zhang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
| | - Feng-Zhi Suo
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiao Chang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang-Bin Wan
- Henan Cancer Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Xue-Jian Feng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China.,National Center for International Research of Micro-nano Molding Technology & Key Laboratory for Micro Molding Technology of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, Henan, China
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28
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Probing the interaction of the p53 C-terminal domain to the histone demethylase LSD1. Arch Biochem Biophys 2017; 632:202-208. [PMID: 28784588 DOI: 10.1016/j.abb.2017.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022]
Abstract
The p53 transcription factor plays a central role in the regulation of the expression of several genes, and itself is post-translationally regulated through its different domains. Of particular relevance for p53 function is its intrinsically disordered C-terminal domain (CTD), representing a hotspot for post-translational modifications and a docking site for transcriptional regulators. For example, the histone H3 lysine demethylase 1 (LSD1) interacts with p53 via the p53-CTD for mutual regulation. To biochemically and functionally characterize this complex, we evaluated the in vitro interactions of LSD1 with several p53-CTD peptides differing in length and modifications. Binding was demonstrated through thermal shift, enzymatic and fluorescence polarization assays, but no enzymatic activity could be detected on methylated p53-CTD peptides in vitro. These experiments were performed using the wild-type enzyme and LSD1 variants that are mutated on three active-site residues. We found that LSD1 demethylase activity is inhibited by p53-CTD. We also noted that the association between the two proteins is mediated by mostly non-specific electrostatic interactions involving conserved active-site residues of LSD1 and a highly charged segment of the p53-CTD. We conclude that p53-CTD inhibits LSD1 activity and that the direct association between the two proteins can contribute to their functional cross-talk.
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29
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Abstract
![]()
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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30
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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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31
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Niwa H, Umehara T. Structural insight into inhibitors of flavin adenine dinucleotide-dependent lysine demethylases. Epigenetics 2017; 12:340-352. [PMID: 28277979 PMCID: PMC5453194 DOI: 10.1080/15592294.2017.1290032] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Until 2004, many researchers believed that protein methylation in eukaryotic cells was an irreversible reaction. However, the discovery of lysine-specific demethylase 1 in 2004 drastically changed this view and the concept of chromatin regulation. Since then, the enzymes responsible for lysine demethylation and their cellular substrates, biological significance, and selective regulation have become major research topics in epigenetics and chromatin biology. Many cell-permeable inhibitors for lysine demethylases have been developed, including both target-specific and nonspecific inhibitors. Structural understanding of how these inhibitors bind to lysine demethylases is crucial both for validation of the inhibitors as chemical probes and for the rational design of more potent, target-specific inhibitors. This review focuses on published small-molecule inhibitors targeted at the two flavin adenine dinucleotide-dependent lysine demethylases, lysine-specific demethylases 1 and 2, and how the inhibitors interact with the tertiary structures of the enzymes.
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Affiliation(s)
- Hideaki Niwa
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan
| | - Takashi Umehara
- a Epigenetics Drug Discovery Unit , RIKEN Center for Life Science Technologies , Suehiro-cho, Tsurumi, Yokohama , Kanagawa , Japan.,b PRESTO, Japan Science and Technology Agency (JST) , Honcho, Kawaguchi , Saitama , Japan
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32
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Amano Y, Umezawa N, Sato S, Watanabe H, Umehara T, Higuchi T. Activation of lysine-specific demethylase 1 inhibitor peptide by redox-controlled cleavage of a traceless linker. Bioorg Med Chem 2017; 25:1227-1234. [DOI: 10.1016/j.bmc.2016.12.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022]
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33
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Jambhekar A, Anastas JN, Shi Y. Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026484. [PMID: 28049654 DOI: 10.1101/cshperspect.a026484] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dynamic regulation of covalent modifications to histones is essential for maintaining genomic integrity and cell identity and is often compromised in cancer. Aberrant expression of histone lysine demethylases has been documented in many types of blood and solid tumors, and thus demethylases represent promising therapeutic targets. Recent advances in high-throughput chemical screening, structure-based drug design, and structure-activity relationship studies have improved both the specificity and the in vivo efficacy of demethylase inhibitors. This review will briefly outline the connection between demethylases and cancer and will provide a comprehensive overview of the structure, specificity, and utility of currently available demethylase inhibitors. To date, a select group of demethylase inhibitors is being evaluated in clinical trials, and additional compounds may soon follow from the bench to the bedside.
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Affiliation(s)
- Ashwini Jambhekar
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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34
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Marabelli C, Marrocco B, Mattevi A. The growing structural and functional complexity of the LSD1/KDM1A histone demethylase. Curr Opin Struct Biol 2016; 41:135-144. [DOI: 10.1016/j.sbi.2016.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
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35
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Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A. Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features. SCIENCE ADVANCES 2016; 2:e1601017. [PMID: 27626075 PMCID: PMC5017823 DOI: 10.1126/sciadv.1601017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.
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Affiliation(s)
- Valentina Speranzini
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Biagina Marrocco
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Mariantonietta Forgione
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alessia Lucidi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Parinaz Mehdipour
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139 Milan, Italy
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire CB10 1SD, U.K
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
- Pasteur Institute–Cenci Bolognetti Foundation, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
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Kilburg D, Gallicchio E. Recent Advances in Computational Models for the Study of Protein-Peptide Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:27-57. [PMID: 27567483 DOI: 10.1016/bs.apcsb.2016.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We review computational models and software tools in current use for the study of protein-peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic agents to target protein-protein interactions. Protein-protein interactions are pervasive in biological systems and are responsible for the regulation of critical functions within the cell. Mutations or dysregulation of expression can alter the network of interactions among proteins and cause diseases such as cancer. Protein-protein binding interfaces, which are often large, shallow, and relatively feature-less, are difficult to target with small-molecule inhibitors. Peptide derivatives based on the binding motifs present in the target protein complex are increasingly drawing interest as superior alternatives to conventional small-molecule inhibitors. However, the design of peptide-based inhibitors also presents novel challenges. Peptides are more complex and more flexible than standard medicinal compounds. They also tend to form more extended and more complex interactions with their protein targets. Computational modeling is increasingly being employed to supplement synthetic and biochemical work to offer guidance and energetic and structural insights. In this review, we discuss recent in silico structure-based and physics-based approaches currently employed to model protein-peptide interactions with a few examples of their applications.
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Affiliation(s)
- D Kilburg
- Brooklyn College, Brooklyn, NY, United States; The Graduate Center of the City University of New York, New York, NY, United States
| | - E Gallicchio
- Brooklyn College, Brooklyn, NY, United States; The Graduate Center of the City University of New York, New York, NY, United States.
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McAllister TE, England KS, Hopkinson RJ, Brennan PE, Kawamura A, Schofield CJ. Recent Progress in Histone Demethylase Inhibitors. J Med Chem 2016; 59:1308-29. [PMID: 26710088 DOI: 10.1021/acs.jmedchem.5b01758] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is increasing interest in targeting histone N-methyl-lysine demethylases (KDMs) with small molecules both for the generation of probes for target exploration and for therapeutic purposes. Here we update on previous reviews on the inhibition of the lysine-specific demethylases (LSDs or KDM1s) and JmjC families of N-methyl-lysine demethylases (JmjC KDMs, KDM2-7), focusing on the academic and patent literature from 2014 to date. We also highlight recent biochemical, biological, and structural studies which are relevant to KDM inhibitor development.
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Affiliation(s)
- Tom E McAllister
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
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Itoh Y, Aihara K, Mellini P, Tojo T, Ota Y, Tsumoto H, Solomon VR, Zhan P, Suzuki M, Ogasawara D, Shigenaga A, Inokuma T, Nakagawa H, Miyata N, Mizukami T, Otaka A, Suzuki T. Identification of SNAIL1 Peptide-Based Irreversible Lysine-Specific Demethylase 1-Selective Inactivators. J Med Chem 2016; 59:1531-44. [DOI: 10.1021/acs.jmedchem.5b01323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yukihiro Itoh
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Keisuke Aihara
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Paolo Mellini
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Toshifumi Tojo
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Yosuke Ota
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-Cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Viswas Raja Solomon
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Peng Zhan
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Miki Suzuki
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Daisuke Ogasawara
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Akira Shigenaga
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Tsubasa Inokuma
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Hidehiko Nakagawa
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Naoki Miyata
- Graduate
School of Pharmaceutical Sciences, Nagoya City University, 3-1
Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tamio Mizukami
- Graduate
School of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Akira Otaka
- Institute
of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan
| | - Takayoshi Suzuki
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
- CREST, Japan Science
and Technology Agency (JST), 4-1-8
Honcho Kawaguchi, Saitama 332-0012, Japan
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Wu F, Zhou C, Yao Y, Wei L, Feng Z, Deng L, Song Y. 3-(Piperidin-4-ylmethoxy)pyridine Containing Compounds Are Potent Inhibitors of Lysine Specific Demethylase 1. J Med Chem 2015; 59:253-263. [PMID: 26652247 DOI: 10.1021/acs.jmedchem.5b01361] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Methylation of histone lysine residues plays important roles in gene expression regulation as well as cancer initiation. Lysine specific demethylase 1 (LSD1) is responsible for maintaining balanced methylation levels at histone H3 lysine 4 (H3K4). LSD1 is a drug target for certain cancers, due to important functions of methylated H3K4 or LSD1 overexpression. We report the design, synthesis, and structure-activity relationships of 3-(piperidin-4-ylmethoxy)pyridine containing compounds as potent LSD1 inhibitors with Ki values as low as 29 nM. These compounds exhibited high selectivity (>160×) against related monoamine oxidase A and B. Enzyme kinetics and docking studies suggested they are competitive inhibitors against a dimethylated H3K4 substrate and provided a possible binding mode. The potent LSD1 inhibitors can increase cellular H3K4 methylation and strongly inhibit proliferation of several leukemia and solid tumor cells with EC50 values as low as 280 nM, while they had negligible effects on normal cells.
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Affiliation(s)
- Fangrui Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Chao Zhou
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yuan Yao
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Liping Wei
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Zizhen Feng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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40
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Wang X, Huang B, Suzuki T, Liu X, Zhan P. Medicinal chemistry insights in the discovery of novel LSD1 inhibitors. Epigenomics 2015; 7:1379-96. [PMID: 26646727 DOI: 10.2217/epi.15.86] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
LSD1 is an epigenetic modulator associated with transcriptional regulation of genes involved in a broad spectrum of key cellular processes, and its activity is often altered under pathological conditions. LSD1 inhibitors are considered to be candidates for therapy of cancer, viral diseases and neurodegeneration. Many LSD1 inhibitors with various scaffolds have been disclosed, and a few potent molecules are in different stages of clinical development. In this review, we summarize recent biological findings on the roles of LSD1 and the current understanding of the clinical significance of LSD1, and focus on the medicinal chemistry strategies used in the design and development of LSD1 inhibitors as drug-like epigenetic modulators since 2012, including a brief consideration of structure–activity relationships.
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Affiliation(s)
- Xueshun Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, PR China
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41
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Zhang X, Li M, Wang Y, Zhao Y. Insight into the binding mode of a novel LSD1 inhibitor by molecular docking and molecular dynamics simulations. J Recept Signal Transduct Res 2015; 35:363-9. [PMID: 26364657 DOI: 10.3109/10799893.2015.1049360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lysine-specific demethylase (LSD1) is an important enzyme for histone lysine methylation. Downregulated LSD1 expression has been linked to cancer proliferation, migration and invasion, indicating that it is an important target for anti-cancer medication. In the present study, the binding modes of a recent reported new series of LSD1 inhibitor were analyzed by using molecular docking and molecular dynamics simulations. A binding mode of these inhibitors was proposed based on the results. According to this binding mode, Thr628 can form two important hydrogen bonds with these inhibitors. Moreover, if the inhibitors can form an additional hydrogen bond with hydroxyl group of Ser289, the potency of the inhibitor can be greatly improved, such as the best inhibitor (compound 12d) in this series. Hydrophobic interactions between the inhibitors and LSD1 are also key contributor here, such as the interaction between the hydrophobic groups (benzene rings) of the inhibitors and the hydrophobic residues of LSD1 (including Val288, Val317, Val811, Ala814, Leu659, Trp751 and Tyr761). Based on the results and analysis, it may provide some useful information for future novel LSD1 inhibitor design.
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Affiliation(s)
- Xu Zhang
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Mo Li
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Yu Wang
- a Department of Thoracic Surgery , The Second Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China and
| | - Yi Zhao
- b Department of Oncology , The First Affiliated Hospital of Dalian Medical University , Dalian , Liaoning , P.R. China
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42
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Zheng YC, Ma J, Wang Z, Li J, Jiang B, Zhou W, Shi X, Wang X, Zhao W, Liu HM. A Systematic Review of Histone Lysine-Specific Demethylase 1 and Its Inhibitors. Med Res Rev 2015; 35:1032-71. [PMID: 25990136 DOI: 10.1002/med.21350] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/02/2015] [Accepted: 04/19/2015] [Indexed: 12/11/2022]
Abstract
Histone lysine-specific demethylase 1 (LSD1) is the first discovered and reported histone demethylase by Dr. Shi Yang's group in 2004. It is classified as a member of amine oxidase superfamily, the common feature of which is using the flavin adenine dinucleotide (FAD) as its cofactor. Since it is located in cell nucleus and acts as a histone methylation eraser, LSD1 specifically removes mono- or dimethylated histone H3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) through formaldehyde-generating oxidation. It has been indicated that LSD1 and its downstream targets are involved in a wide range of biological courses, including embryonic development and tumor-cell growth and metastasis. LSD1 has been reported to be overexpressed in variety of tumors. Inactivating LSD1 or downregulating its expression inhibits cancer-cell development. LSD1 targeting inhibitors may represent a new insight in anticancer drug discovery. This review summarizes recent studies about LSD1 and mainly focuses on the basic physiological function of LSD1 and its involved mechanisms in pathophysiologic conditions, as well as the development of LSD1 inhibitors as potential anticancer therapeutic agents.
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Affiliation(s)
- Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinlian Ma
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Zhiru Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Jinfeng Li
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Bailing Jiang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wenjuan Zhou
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xiaojing Shi
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Xixin Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Wen Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New drug R & D and Preclinical Safety, Zhengzhou University School of Pharmaceutical Sciences, 100 Kexue Avenue, Zhengzhou, Henan, 450001, P. R. China
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Hologram quantitative structure–activity relationship and comparative molecular interaction field analysis of aminothiazole and thiazolesulfonamide as reversible LSD1 inhibitors. Future Med Chem 2015; 7:1381-94. [DOI: 10.4155/fmc.15.68] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background: LSD-1 is an enzyme that removes methyl groups from lysine residues of histone proteins. LSD-1 inhibition decreases cellular proliferation and therefore represents a therapeutic target for cancer treatment. MAO and LSD-1 are both flavin adenine dinucleotide-dependent MAOs, and the MAO inhibitor, tranylcypromine, is currently undergoing clinical trials for cancer treatment because it acts as an irreversible LSD-1 inhibitor. Materials & methods: The present study investigated new reversible LSD-1 inhibitors, in order to develop novel selective anticancer agents. We constructed 2 and 3D quantitative structure–activity relationship models by using a series of 54 aminothiazole and thiazolesulfonamide derivatives. Results: The models were validated internally and externally (q2 , 0.691 and 0.701; r2 , 0.894 and 0.937; r2 test , 0.785 and 0.644, for 2 and 3D models, respectively). Fragment contribution maps, as well as steric and electrostatic contour maps were generated in order to obtain chemical information related to LSD-1 inhibition. Conclusion: The thiazolesulfonamide group was fundamental to the inhibition of LSD-1 by these compounds and that bulky and aromatic substituents at the thiazole ring were important for their steric and electrostatic interactions with the active site of LSD-1.
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44
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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45
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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46
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Mould DP, McGonagle AE, Wiseman DH, Williams EL, Jordan AM. Reversible inhibitors of LSD1 as therapeutic agents in acute myeloid leukemia: clinical significance and progress to date. Med Res Rev 2015; 35:586-618. [PMID: 25418875 DOI: 10.1002/med.21334] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the 10 years since the discovery of lysine-specific demethylase 1 (LSD1), this epigenetic eraser has emerged as an important target of interest in oncology. More specifically, research has demonstrated that it plays an essential role in the self-renewal of leukemic stem cells in acute myeloid leukemia (AML). This review will cover clinical aspects of AML, the role of epigenetics in the disease, and discuss the research that led to the first irreversible inhibitors of LSD1 entering clinical trials for the treatment of AML in 2014. We also review recent achievements and progress in the development of potent and selective reversible inhibitors of LSD1. These compounds differ in their mode of action from tranylcypromine derivatives and could facilitate novel biochemical studies to probe the pathways mediated by LSD1. In this review, we will critically evaluate the strengths and weaknesses of published series of reversible LSD1 inhibitors. Overall, while the development of reversible inhibitors to date has been less fruitful than that of irreversible inhibitors, there is still the possibility for their use to facilitate further research into the roles and functions of LSD1 and to expand the therapeutic applications of LSD1 inhibitors in the clinic.
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Affiliation(s)
- Daniel P Mould
- Department of Drug Discovery, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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47
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Monaldi D, Ruoppolo G, Tilset M, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts. Eur J Med Chem 2015; 94:163-74. [DOI: 10.1016/j.ejmech.2015.02.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 12/12/2022]
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48
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Ma LY, Zheng YC, Wang SQ, Wang B, Wang ZR, Pang LP, Zhang M, Wang JW, Ding L, Li J, Wang C, Hu B, Liu Y, Zhang XD, Wang JJ, Wang ZJ, Zhao W, Liu HM. Design, Synthesis, and Structure–Activity Relationship of Novel LSD1 Inhibitors Based on Pyrimidine–Thiourea Hybrids As Potent, Orally Active Antitumor Agents. J Med Chem 2015; 58:1705-16. [PMID: 25610955 DOI: 10.1021/acs.jmedchem.5b00037] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Li-Ying Ma
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Sai-Qi Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bo Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Zhi-Ru Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Lu-Ping Pang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Miao Zhang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jun-Wei Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Lina Ding
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Juan Li
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Cong Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Biao Hu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiao-Dan Zhang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jia-Jia Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Zhi-Jian Wang
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Wen Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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49
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Rodriguez V, Valente S, Rovida S, Rotili D, Stazi G, Lucidi A, Ciossani G, Mattevi A, Botrugno OA, Dessanti P, Mercurio C, Vianello P, Minucci S, Varasi M, Mai A. Pyrrole- and indole-containing tranylcypromine derivatives as novel lysine-specific demethylase 1 inhibitors active on cancer cells. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00507d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new series of pyrrole/indole-containing tranylcypromine analogues is reported as potent and selective LSD1 inhibitors active in leukemia.
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50
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Zhou C, Kang D, Xu Y, Zhang L, Zha X. Identification of Novel Selective Lysine-Specific Demethylase 1 (LSD1) Inhibitors Using a Pharmacophore-Based Virtual Screening Combined with Docking. Chem Biol Drug Des 2014; 85:659-71. [DOI: 10.1111/cbdd.12461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Chen Zhou
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Di Kang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Luyong Zhang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
| | - Xiaoming Zha
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
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