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Du S, Hu X, Menéndez-Arias L, Zhan P, Liu X. Target-based drug design strategies to overcome resistance to antiviral agents: opportunities and challenges. Drug Resist Updat 2024; 73:101053. [PMID: 38301487 DOI: 10.1016/j.drup.2024.101053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Viral infections have a major impact in human health. Ongoing viral transmission and escalating selective pressure have the potential to favor the emergence of vaccine- and antiviral drug-resistant viruses. Target-based approaches for the design of antiviral drugs can play a pivotal role in combating drug-resistant challenges. Drug design computational tools facilitate the discovery of novel drugs. This review provides a comprehensive overview of current drug design strategies employed in the field of antiviral drug resistance, illustrated through the description of a series of successful applications. These strategies include technologies that enhance compound-target affinity while minimizing interactions with mutated binding pockets. Furthermore, emerging approaches such as virtual screening, targeted protein/RNA degradation, and resistance analysis during drug design have been harnessed to curtail the emergence of drug resistance. Additionally, host targeting antiviral drugs offer a promising avenue for circumventing viral mutation. The widespread adoption of these refined drug design strategies will effectively address the prevailing challenge posed by antiviral drug resistance.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, PR China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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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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3
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Deng Z, Richardson DR. The Myc Family and the Metastasis Suppressor NDRG1: Targeting Key Molecular Interactions with Innovative Therapeutics. Pharmacol Rev 2023; 75:1007-1035. [PMID: 37280098 DOI: 10.1124/pharmrev.122.000795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
Cancer is a leading cause of death worldwide, resulting in ∼10 million deaths in 2020. Major oncogenic effectors are the Myc proto-oncogene family, which consists of three members including c-Myc, N-Myc, and L-Myc. As a pertinent example of the role of the Myc family in tumorigenesis, amplification of MYCN in childhood neuroblastoma strongly correlates with poor patient prognosis. Complexes between Myc oncoproteins and their partners such as hypoxia-inducible factor-1α and Myc-associated protein X (MAX) result in proliferation arrest and pro-proliferative effects, respectively. Interactions with other proteins are also important for N-Myc activity. For instance, the enhancer of zest homolog 2 (EZH2) binds directly to N-Myc to stabilize it by acting as a competitor against the ubiquitin ligase, SCFFBXW7, which prevents proteasomal degradation. Heat shock protein 90 may also be involved in N-Myc stabilization since it binds to EZH2 and prevents its degradation. N-Myc downstream-regulated gene 1 (NDRG1) is downregulated by N-Myc and participates in the regulation of cellular proliferation via associating with other proteins, such as glycogen synthase kinase-3β and low-density lipoprotein receptor-related protein 6. These molecular interactions provide a better understanding of the biologic roles of N-Myc and NDRG1, which can be potentially used as therapeutic targets. In addition to directly targeting these proteins, disrupting their key interactions may also be a promising strategy for anti-cancer drug development. This review examines the interactions between the Myc proteins and other molecules, with a special focus on the relationship between N-Myc and NDRG1 and possible therapeutic interventions. SIGNIFICANCE STATEMENT: Neuroblastoma is one of the most common childhood solid tumors, with a dismal five-year survival rate. This problem makes it imperative to discover new and more effective therapeutics. The molecular interactions between major oncogenic drivers of the Myc family and other key proteins; for example, the metastasis suppressor, NDRG1, may potentially be used as targets for anti-neuroblastoma drug development. In addition to directly targeting these proteins, disrupting their key molecular interactions may also be promising for drug discovery.
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Affiliation(s)
- Zhao Deng
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia (Z.D., D.R.R.), and Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan (D.R.R.)
| | - Des R Richardson
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia (Z.D., D.R.R.), and Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan (D.R.R.)
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Padalino G, Celatka CA, Rienhoff Jr. HY, Kalin JH, Cole PA, Lassalle D, Forde-Thomas J, Chalmers IW, Brancale A, Grunau C, Hoffmann KF. Chemical modulation of Schistosoma mansoni lysine specific demethylase 1 (SmLSD1) induces wide-scale biological and epigenomic changes. Wellcome Open Res 2023; 8:146. [PMID: 37520936 PMCID: PMC10375057 DOI: 10.12688/wellcomeopenres.18826.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 08/01/2023] Open
Abstract
Background: Schistosoma mansoni, a parasitic worm species responsible for the neglected tropical disease schistosomiasis, undergoes strict developmental regulation of gene expression that is carefully controlled by both genetic and epigenetic processes. As inhibition of S. mansoni epigenetic machinery components impairs key transitions throughout the parasite's digenetic lifecycle, a greater understanding of how epi-drugs affect molecular processes in schistosomes could lead to the development of new anthelmintics. Methods: In vitro whole organism assays were used to assess the anti-schistosomal activity of 39 Homo sapiens Lysine Specific Demethylase 1 (HsLSD1) inhibitors on different parasite life cycle stages. Moreover, tissue-specific stains and genomic analysis shed light on the effect of these small molecules on the parasite biology. Results: Amongst this collection of small molecules, compound 33 was the most potent in reducing ex vivo viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound 33 also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound 33 significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2 + stem cell progeny, S1 cells and late female germinal cells) associated with these ex vivo phenotypes. KEGG analyses further highlighted that chromatin structure of genes associated with sugar metabolism as well as TGF-beta and Wnt signalling were also significantly perturbed by compound 33 treatment. Conclusions: This work confirms the importance of histone methylation in S. mansoni lifecycle transitions, suggesting that evaluation of LSD1 - targeting epi-drugs may facilitate the search for next-generation anti-schistosomal drugs. The ability of compound 33 to modulate chromatin structure as well as inhibit parasite survival, oviposition and stem cell proliferation warrants further investigations of this compound and its epigenetic target SmLSD1.
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Affiliation(s)
- Gilda Padalino
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | | | | | - Jay H. Kalin
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Josephine Forde-Thomas
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Iain W. Chalmers
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | | | - Karl F. Hoffmann
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
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Zhang C, Wang Z, Shi Y, Yu B, Song Y. Recent advances of LSD1/KDM1A inhibitors for disease therapy. Bioorg Chem 2023; 134:106443. [PMID: 36857932 DOI: 10.1016/j.bioorg.2023.106443] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) dysregulation is closely associated with the pathological processes of various diseases, especially hematologic malignancies. Significant progresses have been made in the field of LSD1-targeted drug discovery. Nine LSD1 inhibitors including tranylcypromine, ORY-1001, ORY-2001, GSK-2879552, IMG-7289, INCB059872, TAK-418, CC-90011 and SP-2577 have entered clinical stage for disease treatment as either mono- or combinational therapy. This review updates LSD1 inhibitors reported during 2022. Design strategies, structure-activity relationship studies, binding model analysis and modes of action are highlighted. In particular, the unique multiple-copies binding mode of quinazoline derivatives paves new ways for the development of reversible LSD1 inhibitors by blocking the substrate entrance. The design strategy of clinical candidate TAK-418 also provides directions for further optimization of novel irreversible LSD1 inhibitors with low hematological side effects. The influence of the stereochemistry on the potency against LSD1 and its homolog LSD2 is briefly discussed. Finally, the challenges and prospects of LSD1-targeted drug discovery are also given.
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Affiliation(s)
- Chaofeng Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhiyuan Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuting Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Yihui Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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6
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Song Y, Wang S, Yu B. Structural and Functional Landscape of FAD-Dependent Histone Lysine Demethylases for New Drug Discovery. J Med Chem 2023; 66:71-94. [PMID: 36537915 DOI: 10.1021/acs.jmedchem.2c01324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules targeting the flavin adenine dinucleotide (FAD)-dependent histone lysine demethylase LSD family have displayed therapeutic promise against various diseases. Nine clinical candidates targeting the classic demethylase-dependent functions of the LSD family are currently being investigated for treating cancers, neurodegenerative diseases, etc. Moreover, targeting noncatalytic functions of LSDs also represents an emerging strategy for treating human diseases. In this Perspective, we provide full structural and functional landscape of the LSD family and action modes of different types of LSD inhibitors including natural products, peptides, and synthetic compounds, aiming to reveal new druggable space for the design of new LSD inhibitors. Particularly, we first classify these inhibitors into three types based on their unique binding modes. Additionally, the strategies targeting the demethylase-independent functions of LSDs are also briefly discussed. This Perspective may benefit the discovery of new LSD inhibitors for probing LSD biology and/or treating human diseases.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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7
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Yu X, Niu T, Liu C. Mechanism of LSD1 in oxygen-glucose deprivation/reoxygenation-induced pyroptosis of retinal ganglion cells via the miR-21-5p/NLRP12 axis. BMC Neurosci 2022; 23:63. [PMID: 36357913 PMCID: PMC9650888 DOI: 10.1186/s12868-022-00747-3] [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: 07/08/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
Background Retinal ganglion cells (RGCs) are important retinal neurons that connect visual receptors to the brain, and lysine-specific demethylase 1 (LSD1) is implicated in the development of RGCs. This study expounded the mechanism of LSD1 in oxygen-glucose deprivation/reoxygenation (OGD/R)-induced pyroptosis of RGCs. Methods Mouse RGCs underwent OGD/R exposure, and then RGC viability was examined using the cell counting kit-8 method. The mRNA levels of Caspase 1, the protein levels of NOD-like receptor family pyrin domain-containing 3 (NLRP3), N-terminal fragment of gasdermin D (GSDMD-N), and cleaved-Caspase1, and the concentrations of interleukin (IL)-1β and IL-18 were respectively examined. Subsequently, LSD1 expression was intervened to explore the underlying effect of LSD1 on OGD/R-induced pyroptosis of RGCs. Afterwards, the enrichments of LSD1 and histone H3 lysine 4 methylation (H3K4me) 1/2 on the microRNA (miR)-21-5p promoter were determined using chromatin-immunoprecipitation assay. And the binding interaction between miR-21-5p and NLRP12 was detected using dual-luciferase and RNA pull-down assays. Finally, the effects of miR-21-5p/NLRP12 on LSD1-mediated pyroptosis of RGCs were verified through functional rescue experiments. Results OGD/R treatment increased pyroptosis of RGCs and LSD1 expression. Silencing LSD1 declined levels of Caspase 1 mRNA, NLRP3, GSDMD-N, cleaved-Caspase1, IL-1β, and IL-18 and limited pyroptosis of OGD/R-treated RGCs. Mechanically, LSD1 suppressed miR-21-5p expression via demethylation of H3K4me2 on the miR-21-5p promoter to hamper the binding of miR-21-5p to NLRP12, and thereby increased NLRP12 expression. Silencing miR-21-5p or overexpressing NLRP12 facilitated OGD/R-induced pyroptosis of RGCs. Conclusion LSD1-mediated demethylation of H3K4me2 decreased miR-21-5p expression to increase NLRP12 expression, promoting pyroptosis of OGD/R-treated RGCs.
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Song Y, Zhang H, Yang X, Shi Y, Yu B. Annual review of lysine-specific demethylase 1 (LSD1/KDM1A) inhibitors in 2021. Eur J Med Chem 2022; 228:114042. [PMID: 34915312 DOI: 10.1016/j.ejmech.2021.114042] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising epigenetic target for disease treatment. Several LSD1 inhibitors have advanced into clinical trials. Following our last annual review on LSD1 inhibitors in 2020 (Eur. J. Med. Chem. 2021, 214, 113254), in this review we aim to update LSD1 inhibitors including natural products, synthetic compounds and cyclic peptides reported during 2021. Design strategies, structure-activity relationships, binding model analysis and modes of action are highlighted. In particular, two FDA-approved antihypertensive drugs raloxifene and fenoldopam were repurposed as reversible LSD1 inhibitors. The clinical candidate TAK-418 for treating neurodevelopmental disorders and PET imaging agent [18F]30 for LSD1 were identified. Moreover, dual inhibitors targeting both LSD1 and HDAC6 or tubulin displayed enhanced anti-cancer effects than single agents. These compounds further enrich the structural types of LSD1 inhibitors.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100000, China
| | - Huiqing Zhang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoke Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Yuting Shi
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100000, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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Zhou J, Wu S, Lee BG, Chen T, He Z, Lei Y, Tang B, Hirst JD. Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. Molecules 2021; 26:7492. [PMID: 34946572 PMCID: PMC8707381 DOI: 10.3390/molecules26247492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/01/2022] Open
Abstract
A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular fingerprints. The dataset, consisting of 931 molecules with LSD1 inhibition activity, was obtained from the ChEMBL database. An evaluation of several candidate algorithms on the main dataset revealed that the support vector regressor gave the best model, with a coefficient of determination (R2) of 0.703. Virtual screening, using this model, identified five predicted potent inhibitors from the ZINC database comprising more than 300,000 molecules. The virtual screening recovered a known inhibitor, RN1, as well as four compounds where activity against LSD1 had not previously been suggested. Thus, we performed a machine-learning-enabled virtual screening of LSD1 inhibitors using only the structural information of the molecules.
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Affiliation(s)
- Jiajun Zhou
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Shiying Wu
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Boon Giin Lee
- School of Computer Science, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China;
| | - Tianwei Chen
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Ziqi He
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Yukun Lei
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Bencan Tang
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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10
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Song Y, Yang X, Yu B. Repurposing antidepressants for anticancer drug discovery. Drug Discov Today 2021; 27:1924-1935. [PMID: 34728374 DOI: 10.1016/j.drudis.2021.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/23/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Drug repurposing is an attractive strategy for identifying new indications for existing drugs. Three approved antidepressants have advanced into clinical trials for cancer therapy. In particular, further medicinal chemistry efforts with tranylcypromine (TCP) have led to the discovery of several TCP-based histone lysine specific demethylase 1 (LSD1) inhibitors that display therapeutic promise for treating cancer in the clinic. Thus repurposing antidepressants could be a promising strategy for cancer treatment. In this review, we illustrate the anticancer mechanisms of action of antidepressants and also discuss the challenges and future directions of repurposing antidepressants for anticancer drug discovery, to provide an overview of approved antidepressant cancer therapies.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100000, China
| | - Xiaoke Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100000, China.
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11
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Matsuda S, Hattori Y, Matsumiya K, McQuade P, Yamashita T, Aida J, Sandiego CM, Gouasmat A, Carroll VM, Barret O, Tamagnan G, Koike T, Kimura H. Design, Synthesis, and Evaluation of [ 18F]T-914 as a Novel Positron-Emission Tomography Tracer for Lysine-Specific Demethylase 1. J Med Chem 2021; 64:12680-12690. [PMID: 34423983 DOI: 10.1021/acs.jmedchem.1c00653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Histone methylation is associated with the pathophysiology of neurodevelopmental disorders. Lysine-specific demethylase 1 (LSD1) catalyzes histone demethylation in a flavin adenine dinucleotide (FAD)-dependent manner. Thus, inhibiting LSD1 enzyme activity could offer a novel way to treat neurodevelopmental disorders. Assessing LSD1 target engagement using positron-emission tomography (PET) imaging could aid in developing therapeutic LSD1 inhibitors. In this study, PET probes based on 4-(2-aminocyclopropyl)benzamide derivatives that bind irreversibly to FAD found in LSD1 were examined. By optimizing the profiles of brain penetrance and brain-penetrant metabolites, T-914 (1g) was identified as a suitable PET tracer candidate. PET studies in nonhuman primates demonstrated that [18F]1g had heterogeneous brain uptake, which corresponded to known LSD1 expression levels. Moreover, brain uptake of [18F]1g was reduced by coadministration of unlabeled 1g, demonstrating blockable binding. These data suggest that [18F]1g warrants further investigation as a potential PET tracer candidate for assessing target engagement of LSD1.
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Affiliation(s)
- Satoru Matsuda
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasushi Hattori
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kouta Matsumiya
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Paul McQuade
- Quantitative Translational Science - Imaging, Takeda Pharmaceutical Company Limited, 40 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Tohru Yamashita
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jumpei Aida
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Christine M Sandiego
- Invicro, A Konica Minolta Company, 60 Temple Street, Suite 8A, New Haven, Connecticut 06510, United States
| | - Alexandra Gouasmat
- Invicro, A Konica Minolta Company, 60 Temple Street, Suite 8A, New Haven, Connecticut 06510, United States
| | - Vincent M Carroll
- Invicro, A Konica Minolta Company, 60 Temple Street, Suite 8A, New Haven, Connecticut 06510, United States
| | - Olivier Barret
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, 92265 Fontenay-aux-Roses, France
| | - Gilles Tamagnan
- XingImaging LLC, 760 Temple Street, New Haven, Connecticut 06510, United States
| | - Tatsuki Koike
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Haruhide Kimura
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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12
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Huang MJ, Guo JW, Fu YD, You YZ, Xu WY, Song TY, Li R, Chen ZT, Huang LH, Liu HM. Discovery of new tranylcypromine derivatives as highly potent LSD1 inhibitors. Bioorg Med Chem Lett 2021; 41:127993. [PMID: 33775841 DOI: 10.1016/j.bmcl.2021.127993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Tranylcypromine (TCP)-based structural modifications lead to the discovery of new LSD1 inhibitors, of which compounds 26b and 29b effectively inhibit LSD1 with the IC50 values of 17 and 11 nM, respectively and also show good selectivity over MAO-B. Mechanistic studies showed that compound 29b concentration-dependently induced H3K4me1/2 accumulation in LSD1 overexpressed MGC-803 cells and also inhibited metastasis of MGC-803 cells. Collectively, both compounds could be promising lead compounds for further investigation.
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Affiliation(s)
- Ming-Jie Huang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Jia-Wen Guo
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Yun-Dong Fu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Ya-Zhen You
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Wen-Yu Xu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Ting-Yu Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Ran Li
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Zi-Tong Chen
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Li-Hua Huang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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13
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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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14
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Ren Y, Ma Y, Cherukupalli S, Tavis JE, Menéndez-Arias L, Liu X, Zhan P. Discovery and optimization of benzenesulfonamides-based hepatitis B virus capsid modulators via contemporary medicinal chemistry strategies. Eur J Med Chem 2020; 206:112714. [PMID: 32949990 DOI: 10.1016/j.ejmech.2020.112714] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022]
Abstract
Hepatitis B is a vaccine-preventable, but potentially life-threatening liver infection caused by the Hepatitis B virus (HBV). It represents an important health burden, with 257 million active cases globally. Current HBV treatments using nucleos(t)ide analogs and pegylated interferons cannot alleviate the situation completely since they are unable to cure the infection or reduce the amount of viral covalently closed circular DNA (cccDNA). The HBV core protein is a small protein of 183 amino acids that participates in multiple essential functions in the HBV replicative cycle. Capsid assembly modulators that target the core protein are being developed. Sulfonamides are synthetic functional groups, found in several drugs. Herein, we provide a concise report focusing on the sulfamoylbenzamides as HBV capsid modulators, and medicinal chemistry strategies used in their design and development.
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Affiliation(s)
- Yujie Ren
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Yue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
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15
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Fang Y, Yang C, Yu Z, Li X, Mu Q, Liao G, Yu B. Natural products as LSD1 inhibitors for cancer therapy. Acta Pharm Sin B 2020; 11:S2211-3835(20)30616-X. [PMID: 32837872 PMCID: PMC7305746 DOI: 10.1016/j.apsb.2020.06.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Natural products generally fall into the biologically relevant chemical space and always possess novel biological activities, thus making them a rich source of lead compounds for new drug discovery. With the recent technological advances, natural product-based drug discovery is now reaching a new era. Natural products have also shown promise in epigenetic drug discovery, some of them have advanced into clinical trials or are presently being used in clinic. The histone lysine specific demethylase 1 (LSD1), an important class of histone demethylases, has fundamental roles in the development of various pathological conditions. Targeting LSD1 has been recognized as a promising therapeutic option for cancer treatment. Notably, some natural products with different chemotypes including protoberberine alkaloids, flavones, polyphenols, and cyclic peptides have shown effectiveness against LSD1. These natural products provide novel scaffolds for developing new LSD1 inhibitors. In this review, we mainly discuss the identification of natural LSD1 inhibitors, analysis of the co-crystal structures of LSD1/natural product complex, antitumor activity and their modes of action. We also briefly discuss the challenges faced in this field. We believe this review will provide a landscape of natural LSD1 inhibitors.
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Key Words
- AML, acute myeloid leukemia
- CCC, cut countercurrent chromatography
- CD11b, integrin alpha M
- CD14, cluster of differentiation 14
- CD86, cluster of differentiation 86
- COVID-19, coronavirus disease
- Cancer therapy
- CoREST, RE1-silencing transcription factor co-repressor
- Drug discovery
- EMT, epithelial–mesenchymal transition
- EVOO, extra virgin olive oil
- EdU, 5-ethynyl-20-deoxyuridine
- Epigenetic regulation
- FAD, flavin adenine dinucleotide
- FDA, U.S. Food and Drug Administration
- GGA, geranylgeranoic acid
- H3K4, histone H3 lysine 4
- H3K9, histone H3 lysine 9
- HDAC, histone deacetylase
- HRP, horseradish peroxidase
- Histone demethylase
- Kt, competitive inhibition constant
- LSD1 inhibitors
- LSD1, lysine-specific histone demethylase 1A
- MAO-A, monoamine oxidase A
- MHC, myosin heavy chain
- MMA, methylmalonic acid
- NAD, nicotinamide adenine dinucleotide
- NTRK2, neurotrophic receptor tyrosine kinase 2
- Natural products
- PDX, patient-derived xenograft
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SARs, structure–activity relationship studies
- SIRT1, sirtuin 1
- SOX2, sex determining region Y-box 2
- SPR, surface plasmon resonance
- TCP, tranylcypromine
- THF, tetrahydrofolate
- Tm, melting temperature
- iPS, induced pluripotent stem
- mRNA, messenger RNA
- siRNA, small interfering RNA
- ΔΨm, mitochondrial transmembrane potential
- α-MG, α-mangostin
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Affiliation(s)
- Yuan Fang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chao Yang
- Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaochuan Li
- The People's Hospital of Gaozhou, Gaozhou 525200, China
| | - Qingchun Mu
- The People's Hospital of Gaozhou, Gaozhou 525200, China
| | - Guochao Liao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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16
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Fang Y, Liao G, Yu B. LSD1/KDM1A inhibitors in clinical trials: advances and prospects. J Hematol Oncol 2019; 12:129. [PMID: 31801559 PMCID: PMC6894138 DOI: 10.1186/s13045-019-0811-9] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Histone demethylase LSD1 plays key roles during carcinogenesis, targeting LSD1 is becoming an emerging option for the treatment of cancers. Numerous LSD1 inhibitors have been reported to date, some of them such as TCP, ORY-1001, GSK-2879552, IMG-7289, INCB059872, CC-90011, and ORY-2001 currently undergo clinical assessment for cancer therapy, particularly for small lung cancer cells (SCLC) and acute myeloid leukemia (AML). This review is to provide a comprehensive overview of LSD1 inhibitors in clinical trials including molecular mechanistic studies, clinical efficacy, adverse drug reactions, and PD/PK studies and offer prospects in this field.
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Affiliation(s)
- Yuan Fang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China
| | - Guochao Liao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China.
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17
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Matsuda S, Baba R, Oki H, Morimoto S, Toyofuku M, Igaki S, Kamada Y, Iwasaki S, Matsumiya K, Hibino R, Kamada H, Hirakawa T, Iwatani M, Tsuchida K, Hara R, Ito M, Kimura H. T-448, a specific inhibitor of LSD1 enzyme activity, improves learning function without causing thrombocytopenia in mice. Neuropsychopharmacology 2019; 44:1505-1512. [PMID: 30580376 PMCID: PMC6785089 DOI: 10.1038/s41386-018-0300-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/29/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022]
Abstract
Dysregulation of histone H3 lysine 4 (H3K4) methylation has been implicated in the pathogenesis of several neurodevelopmental disorders. Targeting lysine-specific demethylase 1 (LSD1), an H3K4 demethylase, is therefore a promising approach to treat these disorders. However, LSD1 forms complexes with cofactors including growth factor independent 1B (GFI1B), a critical regulator of hematopoietic differentiation. Known tranylcypromine-based irreversible LSD1 inhibitors bind to coenzyme flavin adenine dinucleotide (FAD) and disrupt the LSD1-GFI1B complex, which is associated with hematotoxicity such as thrombocytopenia, representing a major hurdle in the development of LSD1 inhibitors as therapeutic agents. To discover LSD1 inhibitors with potent epigenetic modulation and lower risk of hematotoxicity, we screened small molecules that enhance H3K4 methylation by the inhibition of LSD1 enzyme activity in primary cultured rat neurons but have little impact on LSD1-GFI1B complex in human TF-1a erythroblasts. Here we report the discovery of a specific inhibitor of LSD1 enzyme activity, T-448 (3-((1S,2R)-2-(cyclobutylamino)cyclopropyl)-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide fumarate). T-448 has minimal impact on the LSD1-GFI1B complex and a superior hematological safety profile in mice via the generation of a compact formyl-FAD adduct. T-448 increased brain H3K4 methylation and partially restored learning function in mice with NMDA receptor hypofunction. T-448-type LSD1 inhibitors with improved safety profiles may provide unique therapeutic approaches for central nervous system disorders associated with epigenetic dysregulation.
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Affiliation(s)
- Satoru Matsuda
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Rina Baba
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Hideyuki Oki
- 0000 0001 0673 6017grid.419841.1Biomolecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Shinji Morimoto
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Masashi Toyofuku
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Shigeru Igaki
- 0000 0001 0673 6017grid.419841.1Biomolecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Yusuke Kamada
- 0000 0001 0673 6017grid.419841.1Biomolecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Shinji Iwasaki
- 0000 0001 0673 6017grid.419841.1Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Kota Matsumiya
- 0000 0001 0673 6017grid.419841.1Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Ryosuke Hibino
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Hiroko Kamada
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Takeshi Hirakawa
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Misa Iwatani
- 0000 0001 0673 6017grid.419841.1Biomolecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Ken Tsuchida
- 0000 0001 0673 6017grid.419841.1Extra Value Generation Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Ryujiro Hara
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Mitsuhiro Ito
- 0000 0001 0673 6017grid.419841.1Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Haruhide Kimura
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
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18
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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19
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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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20
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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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21
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Zhang S, Zhang J, Gao P, Sun L, Song Y, Kang D, Liu X, Zhan P. Efficient drug discovery by rational lead hybridization based on crystallographic overlay. Drug Discov Today 2018; 24:805-813. [PMID: 30529326 DOI: 10.1016/j.drudis.2018.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/29/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
In this review, we provide an overview of recent applications of crystallographic overlay-based molecular structure hybridization of lead compounds as a rational strategy for efficient drug discovery, with selected examples, and briefly discuss its advantages compared with other ligand-based methodologies.
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Affiliation(s)
- Shuo Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, 250012, Ji'nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China.
| | - 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, Ji'nan, 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, Ji'nan, Shandong, PR China.
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22
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Ota Y, Nakamura A, Elboray EE, Itoh Y, Suzuki T. Design, Synthesis, and Biological Evaluation of a Conjugate of 5-Fluorouracil and an LSD1 Inhibitor. Chem Pharm Bull (Tokyo) 2018; 67:192-195. [PMID: 30369513 DOI: 10.1248/cpb.c18-00577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Prodrug approaches are useful for enhancing the efficacies and reducing the side effects of anticancer drugs. Previously, we proposed a prodrug strategy for targeting cancers overexpressing lysine-specific demethylase 1 (LSD1), namely, conjugates of trans-2-phenylcyclopropylamine (PCPA, an LSD1 inhibitor) and anticancer drugs. In this study, we applied this prodrug strategy to the anticancer agent 5-fluorouracil (5-FU). In vitro assays showed that the PCPA-5-FU conjugate (1) released 5-FU upon the inhibition of LSD1. Furthermore, the conjugate (1) exerted an antiproliferative effect on colon cancer HCT116 cells. Thus, the PCPA-5-FU conjugate (1) was able to function as a prodrug of 5-FU, activated by LSD1 inhibition, and provided a useful new lead structure for further development.
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Affiliation(s)
- Yosuke Ota
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Arisa Nakamura
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Elghareeb E Elboray
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine.,Chemistry Department, Faculty of Science, South Valley University
| | - Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine.,CREST, Japan Science and Technology Agency (JST)
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Ota Y, Suzuki T. Drug Design Concepts for LSD1-Selective Inhibitors. CHEM REC 2018; 18:1782-1791. [PMID: 30277644 DOI: 10.1002/tcr.201810031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022]
Abstract
Lysine-specific demethylase 1 (LSD1) is one of the flavin-dependent oxidases and is involved in many cellular processes by controlling the methylation of histone H3. Recently, it has been reported that LSD1 is associated with several diseases such as cancer, metabolic disorders, and psychiatric diseases. Thus, LSD1 is an attractive molecular target for the treatment of these diseases, and its inhibitors are predicted as therapeutic agents. Although a variety of LSD1 inhibitors have been reported to date, many of them show insufficient activities and selectivity toward LSD1. Meanwhile, we identified several LSD1-selective inhibitors using target-guided synthesis strategies based on our original ideas. Our LSD1 inhibitors show not only potent LSD1-selective inhibitory activities, but also unique bioactivities both in vitro and in vivo. This account highlights our drug design concepts for and identification of LSD1-selective inhibitors.
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Affiliation(s)
- Yosuke Ota
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto, 606-0823, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
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24
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Alagarswamy K, Shinohara KI, Takayanagi S, Fukuyo M, Okabe A, Rahmutulla B, Yoda N, Qin R, Shiga N, Sugiura M, Sato H, Kita K, Suzuki T, Nemoto T, Kaneda A. Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide. Oncotarget 2018; 9:29316-29335. [PMID: 30034620 PMCID: PMC6047668 DOI: 10.18632/oncotarget.25451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/07/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β2P4) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β2PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10-10), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10-15) or WWCGWW sequences (P = 2 × 10-13). When treated with NCD38-β2P4, 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10-11), including significantly fewer GC-rich sequences (P < 1 × 10-15) and significantly more AT-rich sequences (P < 1 × 10-15) compared with NCD38 treatment. When treated with NCD38-β2PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10-11) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose.
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Affiliation(s)
| | - Ken-Ichi Shinohara
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Shihori Takayanagi
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Natsumi Yoda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Rui Qin
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoki Shiga
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masahiro Sugiura
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Sato
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Kazuko Kita
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuhiro Nemoto
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
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25
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Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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26
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Design, Synthesis, and In Vitro Evaluation of Novel Histone H3 Peptide-Based LSD1 Inactivators Incorporating α,α-Disubstituted Amino Acids with γ-Turn-Inducing Structures. Molecules 2018; 23:molecules23051099. [PMID: 29734782 PMCID: PMC6099693 DOI: 10.3390/molecules23051099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 01/16/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) mainly removes methyl groups of mono- or di-methylated lysine residues at the fourth position of histone H3 to epigenetically regulate the expression of genes associated with several diseases, such as cancer. Therefore, LSD1 inactivators are expected to be used as therapeutic agents. In this study, to identify novel peptide-based LSD1 inactivators, we focused on the X-ray structure of LSD1 complexed with a H3 peptide-based suicide substrate. It has been proposed that a methylated histone substrate forms three consecutive γ-turn structures in the active pocket of LSD1. Based on this, we designed and synthesized novel histone H3 peptide-based LSD1 inactivators 2a⁻c by incorporating various α,α-disubstituted amino acids with γ-turn-inducing structures. Among synthetic peptides 2a⁻c, peptide 2b incorporating two 1-aminocyclohexanecarboxylic acids at both sides of a lysine residue bearing a trans-2-phenylcyclopropylamine (PCPA) moiety, which is a pharmacophore for LSD1 inactivation, was the most potent and selective LSD1 inactivator. These findings are useful for the further development of histone H3 peptide-based LSD1 inactivators.
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27
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Xi J, Xu S, Zhang L, Bi X, Ren Y, Liu YC, Gu Y, Xu Y, Lan F, Zha X. Design, synthesis and biological activity of 4-(4-benzyloxy)phenoxypiperidines as selective and reversible LSD1 inhibitors. Bioorg Chem 2018. [PMID: 29524666 DOI: 10.1016/j.bioorg.2018.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine specific demethylase 1 (LSD1) plays a vital role in epigenetic regulation of gene activation and repression in several human cancers and is recognized as a promising antitumor therapeutic target. In this paper, a series of 4-(4-benzyloxy)phenoxypiperidines were synthesized and evaluated. Among the tested compounds, compound 10d exhibited the potent and reversible inhibitory activity against LSD1 in vitro (IC50 = 4 μM). Molecular docking was conducted to predict its binding mode. Furthermore, 10d displayed it could inhibit migration of HCT-116 colon cancer cells and A549 lung cancer cells. Taken together, 10d deserves further investigation as a hit-to-lead for the treatment of LSD1 associated tumors.
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Affiliation(s)
- Jiayue Xi
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China; Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Siyuan Xu
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China
| | - Lulu Zhang
- Department of Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, PR China
| | - Xueyuan Bi
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yanshen Ren
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
| | - Yueqing Gu
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Fei Lan
- Laboratory of Epigenetics, Institute of Biochemical Sciences, Fudan University, 131 Dong'An Road, Shanghai 200032, PR China.
| | - Xiaoming Zha
- Department of Pharmaceutical Engineering & Department of Biochemical Engineering, 639 Longmian Avenue, Nanjing 211198, PR China.
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28
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Ota Y, Miyamura S, Araki M, Itoh Y, Yasuda S, Masuda M, Taniguchi T, Sowa Y, Sakai T, Itami K, Yamaguchi J, Suzuki T. Design, synthesis and evaluation of γ-turn mimetics as LSD1-selective inhibitors. Bioorg Med Chem 2018; 26:775-785. [DOI: 10.1016/j.bmc.2017.12.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/25/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
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29
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Kakizawa T, Ota Y, Itoh Y, Suzuki T. Histone H3 peptides incorporating modified lysine residues as lysine-specific demethylase 1 inhibitors. Bioorg Med Chem Lett 2018; 28:167-169. [DOI: 10.1016/j.bmcl.2017.11.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/08/2017] [Accepted: 11/23/2017] [Indexed: 10/18/2022]
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30
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Duan YC, Ma YC, Qin WP, Ding LN, Zheng YC, Zhu YL, Zhai XY, Yang J, Ma CY, Guan YY. Design and synthesis of tranylcypromine derivatives as novel LSD1/HDACs dual inhibitors for cancer treatment. Eur J Med Chem 2017; 140:392-402. [PMID: 28987602 DOI: 10.1016/j.ejmech.2017.09.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022]
Abstract
Lysine specific demethylase 1 (LSD1) and Histone deacetylases (HDACs) are promising drug targets for cancers. Recent studies reveal an important functional interplay between LSD1 and HDACs, and there is evidence for the synergistic effect of combined LSD1 and HDAC inhibitors on cancers. Therefore, development of inhibitors targeting both LSD1 and HDACs might be a promising strategy for epigenetic therapy of cancers. We report herein the synthesis of a series of tranylcypromine derivatives as LSD1/HDACs dual inhibitors. Most compounds showed potent LSD1 and HDACs inhibitory activity, especially compound 7 displayed the most potent inhibitory activity against HDAC1 and HDAC2 with IC50 of 15 nM and 23 nM, as well as potent inhibition against LSD1 with IC50 of 1.20 μM. Compound 7 demonstrated stronger anti-proliferative activities than SAHA with IC50 values ranging from 0.81 to 4.28 μM against MGC-803, MCF-7, SW-620 and A-549 human cancer cell lines. Further mechanistic studies showed that compound 7 treatment in MGC-803 cells dose-dependently increased cellular H3K4 and H3K9 methylation, as well as H3 acetylation, decreased the mitochondrial membrane potential and induced remarkable apoptosis. Docking studies showed that compound 7 can be well docked into the active binding sites of LSD1 and HDAC2. This finding highlights the potential for the development of LSD1/HDACs dual inhibitors as novel anticancer drugs.
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Affiliation(s)
- Ying-Chao Duan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China.
| | - Yong-Cheng Ma
- Department of Pharmacy, Zhengzhou University People's Hospital, No. 7, Wei Wu Road, Zhengzhou, Henan, China
| | - Wen-Ping Qin
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Li-Na Ding
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying-Li Zhu
- Department of Pharmacy, Zhengzhou University People's Hospital, No. 7, Wei Wu Road, Zhengzhou, Henan, China
| | - Xiao-Yu Zhai
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Jing Yang
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Chao-Ya Ma
- Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yuan-Yuan Guan
- School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, China.
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31
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Abstract
LSD1 has become an important biologically validated epigenetic target for cancer therapy since its identification in 2004. LSD1 mediates many cellular signaling pathways and is involved in the initiation and development of cancers. Aberrant overexpression of LSD1 has been observed in different types of cancers, and inactivation by small molecules suppresses cancer cell differentiation, proliferation, invasion and migration. To date, a large number of LSD1 inhibitors have been reported, RG6016, GSK-2879552, INCB059872, IMG-7289 and CC-90011 are currently undergoing clinical assessment for the treatment of acute myeloid leukemia, small-cell lung cancer, etc. In this review, we briefly highlight recent advances of LSD1 inhibitors mainly covering the literatures from 2015 to 2017 and tentatively propose our perspectives on the design of new LSD1 inhibitors for cancer therapy.
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32
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Fluorinated tranylcypromine analogues as inhibitors of lysine-specific demethylase 1 (LSD1, KDM1A). Bioorg Med Chem Lett 2017; 27:2099-2101. [DOI: 10.1016/j.bmcl.2017.03.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 02/07/2023]
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33
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Zhang H, Tian Y, Kang D, Huo Z, Zhou Z, Liu H, De Clercq E, Pannecouque C, Zhan P, Liu X. Discovery of uracil-bearing DAPYs derivatives as novel HIV-1 NNRTIs via crystallographic overlay-based molecular hybridization. Eur J Med Chem 2017; 130:209-222. [DOI: 10.1016/j.ejmech.2017.02.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
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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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Abstract
The lysine-specific demethylase (LSD1) is a flavin-dependent amine oxidase that selectively removes one or two methyl groups from histone H3 at the Lys4 position. Along with histone deacetylases 1 and 2, LSD1 is involved in epigenetically silencing gene expression. LSD1 has been implicated as a potential therapeutic target in cancer and other diseases. In this chapter, we discuss several approaches to measure LSD1 demethylase activity and their relative strengths and limitations for inhibitor discovery and mechanistic characterization. In addition, we review the principal established chemical functional groups derived from monoamine oxidase inhibitors that have been investigated in the context of LSD1 as demethylase inhibitors. Finally, we highlight a few examples of recently developed LSD1 mechanism-based inactivators and their biomedical applications.
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Affiliation(s)
- D Hayward
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - P A Cole
- Johns Hopkins School of Medicine, Baltimore, MD, United States.
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36
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Miyamura S, Araki M, Ota Y, Itoh Y, Yasuda S, Masuda M, Taniguchi T, Sowa Y, Sakai T, Suzuki T, Itami K, Yamaguchi J. C–H activation enables a rapid structure–activity relationship study of arylcyclopropyl amines for potent and selective LSD1 inhibitors. Org Biomol Chem 2016; 14:8576-85. [DOI: 10.1039/c6ob01483f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potent and selective LSD1 inhibitors were synthesized rapidly by a C–H borylation and cross-coupling sequence.
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