1
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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2
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Bolding JE, Nielsen AL, Jensen I, Hansen TN, Ryberg LA, Jameson ST, Harris P, Peters GHJ, Denu JM, Rogers JM, Olsen CA. Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7. Angew Chem Int Ed Engl 2023; 62:e202314597. [PMID: 37873919 DOI: 10.1002/anie.202314597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
The sirtuins are NAD+ -dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.
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Affiliation(s)
- Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
- Current address: Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Iben Jensen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Line A Ryberg
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Immunology and Microbiology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Samuel T Jameson
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Chemistry, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Joseph M Rogers
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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3
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Tan S, Li X. Small-Molecule Fluorescent Probes for Detecting HDAC Activity. Chem Asian J 2022; 17:e202200835. [PMID: 36117388 DOI: 10.1002/asia.202200835] [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: 08/11/2022] [Revised: 09/15/2022] [Indexed: 11/05/2022]
Abstract
Histone deacetylases (HDACs) play critical roles in epigenetic modification. These enzymes can remove acetyl groups from the N-terminal lysine residues of histones, thereby regulating gene expression. Because of their great relevance to various diseases, numerous HDAC inhibitors have been developed. In this context, assays for HDAC activity are prerequisite. Due to the advantages of small-molecule fluorescent probes, researchers have developed many probes to detect HDAC activity for developing HDAC inhibitors. Based on the mechanism of action, two main types of small-molecule fluorescent probes are known. One type is based on binding affinity that are generally HDAC inhibitor-fluorophore conjugates. The other one is enzyme-activated probes, which act as HDAC substrates and show fluorogenic or ratiometric response after being deacetylated by HDACs.
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Affiliation(s)
- Shuyu Tan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
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4
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Roopa, Priya B, Bhalla V, Kumar M, Kumar N. Fluorescent molecular probe-based activity and inhibition monitoring of histone deacetylases. Chem Commun (Camb) 2021; 57:11153-11164. [PMID: 34613324 DOI: 10.1039/d1cc04034k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Extensive studies in recent decades have revealed that gene expression regulation is not limited to genetic mutations but also to processes that do not alter the genetic sequence. Post-translational histone modification is one of these processes in addition to DNA or RNA modifications. Histone modifications are essential in controlling histone functions and play a vital role in cellular gene expression. The reversible histone acetylation, regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is an example of such modifications. HDACs are involved in the deacetylation of histones and lead to the termination of gene expression. Although this cellular process is essential, upregulation of HDACs is found in numerous cancers. Therefore, research related to the activity and inhibition monitoring of HDACs is necessary to gain profound knowledge of these enzymes and evaluate the success of the therapeutic approach. In this perspective, methodology derived from fluorescent molecular probes is one of the preferable methods. Herein, we describe fluorescent probes developed to target HDACs by considering their activity and inhibition characteristics.
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Affiliation(s)
- Roopa
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Bhanu Priya
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Vandana Bhalla
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Manoj Kumar
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Naresh Kumar
- Department of Chemistry, SRM University, Delhi-NCR, Sonepat-131029, Haryana, India.
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García S, Mercado-Sánchez I, Bahena L, Alcaraz Y, García-Revilla MA, Robles J, Santos-Martínez N, Ordaz-Rosado D, García-Becerra R, Vazquez MA. Design of Fluorescent Coumarin-Hydroxamic Acid Derivatives as Inhibitors of HDACs: Synthesis, Anti-Proliferative Evaluation and Docking Studies. Molecules 2020; 25:molecules25215134. [PMID: 33158250 PMCID: PMC7662212 DOI: 10.3390/molecules25215134] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 01/02/2023] Open
Abstract
Coumarin-hydroxamic acid derivatives 7a-k were herein designed with a dual purpose: as antiproliferative agents and fluorescent probes. The compounds were synthesized in moderate yields (30-87%) through a simple methodology, biological evaluation was carried out on prostate (PC3) and breast cancer (BT-474 and MDA-MB-231) cell lines to determine the effects on cell proliferation and gene expression. For compounds 7c, 7e, 7f, 7i and 7j the inhibition of cancer cell proliferation was similar to that found with the reference compound at a comparable concentration (10 μM), in addition, their molecular docking studies performed on histone deacetylases 1, 6 and 8 showed strong binding to the respective active sites. In most cases, antiproliferative activity was accompanied by greater levels of cyclin-dependent kinase inhibitor p21, downregulation of the p53 tumor suppressor gene, and regulation of cyclin D1 gene expression. We conclude that compounds 7c, 7e, 7f, 7i and 7j may be considered as potential anticancer agents, considering their antiproliferative properties, their effect on the regulation of the genes, as well as their capacity to dock to the active sites. The fluorescent properties of compound 7j and 7k suggest that they can provide further insight into the mechanism of action.
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Affiliation(s)
- Santiago García
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Itzel Mercado-Sánchez
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Luis Bahena
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Yolanda Alcaraz
- Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (Y.A.); (J.R.)
| | - Marco A. García-Revilla
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Juvencio Robles
- Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (Y.A.); (J.R.)
| | - Nancy Santos-Martínez
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (N.S.-M.); (D.O.-R.)
| | - David Ordaz-Rosado
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (N.S.-M.); (D.O.-R.)
| | - Rocío García-Becerra
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Miguel A. Vazquez
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
- Correspondence: ; Tel.: +52-473-732-0006 (ext. 1419)
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Krieger V, Hamacher A, Cao F, Stenzel K, Gertzen CGW, Schäker-Hübner L, Kurz T, Gohlke H, Dekker FJ, Kassack MU, Hansen FK. Synthesis of Peptoid-Based Class I-Selective Histone Deacetylase Inhibitors with Chemosensitizing Properties. J Med Chem 2019; 62:11260-11279. [DOI: 10.1021/acs.jmedchem.9b01489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Viktoria Krieger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Fangyuan Cao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katharina Stenzel
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Christoph G. W. Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
- Center for Structural Studies (CSS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Linda Schäker-Hübner
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Medical Faculty, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Matthias U. Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Finn K. Hansen
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Medical Faculty, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
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Hori Y, Kikuchi K. Chemical Tools with Fluorescence Switches for Verifying Epigenetic Modifications. Acc Chem Res 2019; 52:2849-2857. [PMID: 31577127 DOI: 10.1021/acs.accounts.9b00349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Epigenetic DNA and histone modifications alter chromatin conformation and regulate gene expression. A major DNA modification is methylation, which is catalyzed by DNA methyltransferase (Dnmt) and results in gene suppression. Compared to DNA, histones undergo a greater variety of modification types, one of which is the acetylation of lysine. While histone acetyltransferase (HAT) catalyzes acetylation and activates gene expression, histone deacetylase (HDAC) removes the modification and causes gene suppression. As precise regulation of these epigenetic marks on DNA and histones is critical for cellular functions, their dysregulation causes various diseases including cancer, metabolic syndromes, immune diseases, and psychiatric diseases. Therefore, elucidation of the epigenetic phenomena is important not only in the field of biology but also in medical and pharmaceutical sciences. Furthermore, this field is also attracting industrial interest, because small-molecule inhibitors modulate enzymatic activity for epigenetic modification and are used for cancer treatment. Under these circumstances, various methods for detecting epigenetic modifications have been developed. However, most methods require cell lysis, which is not suitable for real-time detection of enzymatic activity. Since fluorescent probes are attractive chemical tools to solve this issue, chemists made considerable efforts to create fluorescent probes for epigenetics. To date, we have particularly focused on HDAC activity and DNA methylation and have developed fluorescent probes for their detection. The first part of this review describes our recent efforts to develop fluorescent probes for detecting HDAC activity. Since the discovery of HDAC activity in the late 1960s, no fluorescent probe has been developed that can detect enzymatic reactions in a simple, one-step procedure despite its biological and medical importance. We designed fluorescent probes to overcome this limitation by devising two different types of fluorescence switching mechanisms, which are based on aggregation-induced emission (AIE) and intramolecular transesterification. Using these probes, we detected HDAC activity simply by mixing the probes and HDAC for the first time. In the second part, a hybrid approach using a protein-labeling system was employed to detect DNA methylation in living cells. So far, live-cell detection of DNA methylation was conducted by imaging the localization of Fluorescent Proteins (FPs) fused to a methylated DNA-binding domain. However, FP lacks a fluorescence switch and emits fluorescence without binding to methylated DNA. We created a hybrid probe that comprises a fluorogen and a protein and enhances fluorescence intensity upon binding to methylated DNA. To create the hybrid probe, we applied our protein labeling system using the PYP-tag that we previously developed. This method successfully visualized methylated DNA in living cells and verified its dynamics during cell division. Both of the above-mentioned fluorescent probes have great potential for use not only in HDAC and DNA methylation but also in other epigenetics-associated modifications. For example, the mechanism of the HDAC probes can be used to detect histone demethylation. The hybrid probe can be converted to a sensor for imaging acetylated or methylated histones. In this review, we mainly describe how we designed the probes using chemical principles and solved the current obstacles with the probe design and discuss the future prospects of these probes.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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8
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Bandolik JJ, Hamacher A, Schrenk C, Weishaupt R, Kassack MU. Class I-Histone Deacetylase (HDAC) Inhibition is Superior to pan-HDAC Inhibition in Modulating Cisplatin Potency in High Grade Serous Ovarian Cancer Cell Lines. Int J Mol Sci 2019; 20:ijms20123052. [PMID: 31234549 PMCID: PMC6627993 DOI: 10.3390/ijms20123052] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/23/2023] Open
Abstract
High grade serous ovarian cancer (HGSOC) is the most common and aggressive ovarian cancer subtype with the worst clinical outcome due to intrinsic or acquired drug resistance. Standard treatment involves platinum compounds. Cancer development and chemoresistance is often associated with an increase in histone deacetylase (HDAC) activity. The purpose of this study was to examine the potential of HDAC inhibitors (HDACi) to increase platinum potency in HGSOC. Four HGSOC cell lines with different cisplatin sensitivity were treated with combinations of cisplatin and entinostat (class I HDACi), panobinostat (pan-HDACi), or nexturastat A (class IIb HDACi), respectively. Inhibition of class I HDACs by entinostat turned out superior in increasing cisplatin potency than pan-HDAC inhibition in cell viability assays (MTT), apoptosis induction (subG1), and caspase 3/7 activation. Entinostat was synergistic with cisplatin in all cell lines in MTT and caspase activation assays. MTT assays gave combination indices (CI values) < 0.9 indicating synergism. The effect of HDAC inhibitors could be attributed to the upregulation of pro-apoptotic genes (CDNK1A, APAF1, PUMA, BAK1) and downregulation of survivin. In conclusion, the combination of entinostat and cisplatin is synergistic in HGSOC and could be an effective strategy for the treatment of aggressive ovarian cancer.
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Affiliation(s)
- Jan J Bandolik
- Institute for Pharmaceutical and Medicinal Chemistry, University of Duesseldorf, 40225 Duesseldorf, Germany.
| | - Alexandra Hamacher
- Institute for Pharmaceutical and Medicinal Chemistry, University of Duesseldorf, 40225 Duesseldorf, Germany.
| | - Christian Schrenk
- Institute for Pharmaceutical and Medicinal Chemistry, University of Duesseldorf, 40225 Duesseldorf, Germany.
| | - Robin Weishaupt
- Institute for Computer Science, Computational Complexity and Cryptology, University of Duesseldorf, 40225 Duesseldorf, Germany.
| | - Matthias U Kassack
- Institute for Pharmaceutical and Medicinal Chemistry, University of Duesseldorf, 40225 Duesseldorf, Germany.
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9
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Li Y, Fang H, Hou Z, Sang L, Yang X. An in-line capillary electrophoresis assay for the high-throughput screening of histone deacetylase inhibitors. J Chromatogr A 2019; 1591:171-177. [DOI: 10.1016/j.chroma.2019.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 02/04/2023]
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10
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Shao D, Yao C, Kim MH, Fry J, Cohen RA, Costello CE, Matsui R, Seta F, McComb ME, Bachschmid MM. Improved mass spectrometry-based activity assay reveals oxidative and metabolic stress as sirtuin-1 regulators. Redox Biol 2019; 22:101150. [PMID: 30877853 PMCID: PMC6423473 DOI: 10.1016/j.redox.2019.101150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
Sirtuin-1 (SirT1) catalyzes NAD+-dependent protein lysine deacetylation and is a critical regulator of energy and lipid metabolism, mitochondrial biogenesis, apoptosis, and senescence. Activation of SirT1 mitigates metabolic perturbations associated with diabetes and obesity. Pharmacologic molecules, cellular redox, and nutritional states can regulate SirT1 activity. Technical barriers against measuring endogenous SirT1 activity have limited characterization of SirT1 in disease and its activation by small molecules. Herein, we developed a relative quantitative mass spectrometry-based technique for measuring endogenous SirT1 activity (RAMSSAY/RelAtive Mass Spectrometry Sirt1 Activity assaY) in cell and tissue homogenates using a biotin-labeled, acetylated p53-derived peptide as a substrate. We demonstrate that oxidative and metabolic stress diminish SirT1 activity in the hepatic cell line HepG2. Moreover, pharmacologic molecules including nicotinamide and EX-527 attenuate SirT1 activity; purported activators of SirT1, the polyphenol S17834, the polyphenol resveratrol, or the non-polyphenolic Sirtris compound SRT1720, failed to activate endogenous SirT1 significantly. Furthermore, we provide evidence that feeding a high fat high sucrose diet (HFHS) to mice inhibits endogenous SirT1 activity in mouse liver. In summary, we introduce a robust, specific and sensitive mass spectrometry-based assay for detecting and quantifying endogenous SirT1 activity using a biotin-labeled peptide in cell and tissue lysates. With this assay, we determine how pharmacologic molecules and metabolic and oxidative stress regulate endogenous SirT1 activity. The assay may also be adapted for other sirtuin isoforms. Fast, sensitive, and specific MALDI-TOF based sirtuin-1 activity assay applicable to cell and tissue lysates. Oxidative and metabolic stress inhibit Sirtuin-1 deacetylase activity. Purported activators of SirT1failed to significantly activate endogenous SirT1. The activity assay is adaptable to other sirtuin isoforms using specific synthetic peptides and assay conditions.
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Affiliation(s)
- Di Shao
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Chunxiang Yao
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA; Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA, USA
| | - Maya H Kim
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Jessica Fry
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Richard A Cohen
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA, USA
| | - Reiko Matsui
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Francesca Seta
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Mark E McComb
- Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA, USA
| | - Markus M Bachschmid
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA; Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA, USA.
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11
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Olesen SV, Rajabi N, Svensson B, Olsen CA, Madsen AS. An NAD +-Dependent Sirtuin Depropionylase and Deacetylase (Sir2La) from the Probiotic Bacterium Lactobacillus acidophilus NCFM. Biochemistry 2018; 57:3903-3915. [PMID: 29863862 DOI: 10.1021/acs.biochem.8b00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sirtuins, a group of NAD+-dependent deacylases, have emerged as the key connection between NAD+ metabolism and aging. This class of enzymes hydrolyzes a range of ε- N-acyllysine PTMs, and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacterium Lactobacillus acidophilus NCFM. Screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, demonstrated that one of the investigated proteins, Sir2La, is a bona fide NAD+-dependent sirtuin, catalyzing hydrolysis of acetyl-, propionyl-, and butyryllysine. Further substantiating the identity of Sir2La as a sirtuin, known sirtuin inhibitors, nicotinamide and suramin, as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. On the basis of steady-state kinetics, Sir2La showed a slight preference for propionyllysine (Kpro) over acetyllysine (Kac). For nonfluorogenic peptide substrates, the preference is driven by a remarkably low KM (280 nM vs 700 nM, for Kpro and Kac, respectively), whereas kcat was similar (21 × 10-3 s-1). Moreover, while NAD+ is a prerequisite for Sir2La-mediated deacylation, Sir2La has a very high KM for NAD+ compared to the expected levels of the dinucleotide in L. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl- and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.
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Affiliation(s)
- Sita V Olesen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
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12
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King K, Hauser AT, Melesina J, Sippl W, Jung M. Carbamates as Potential Prodrugs and a New Warhead for HDAC Inhibition. Molecules 2018; 23:E321. [PMID: 29393896 PMCID: PMC6017415 DOI: 10.3390/molecules23020321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 11/25/2022] Open
Abstract
We designed and synthesized carbamates of the clinically-approved HDAC (histone deacetylase) inhibitor vorinostat (suberoylanilide hydroxamic acid, SAHA) in order to validate our previously-proposed hypothesis that these carbamates might serve as prodrugs for hydroxamic acid containing HDAC inhibitors. Biochemical assays proved our new compounds to be potent inhibitors of histone deacetylases in vitro, and they also showed antiproliferative effects in leukemic cells. These results, as well as stability analysis led to the suggestion that the intact carbamates are inhibitors of histone deacetylases themselves, representing a new zinc-binding warhead in HDAC inhibitor design. This suggestion was further supported by the synthesis and evaluation of a carbamate derivative of the HDAC6-selective inhibitor bufexamac.
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Affiliation(s)
- Kristina King
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
| | - Alexander-Thomas Hauser
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
| | - Jelena Melesina
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany.
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany.
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
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13
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Fellows R, Denizot J, Stellato C, Cuomo A, Jain P, Stoyanova E, Balázsi S, Hajnády Z, Liebert A, Kazakevych J, Blackburn H, Corrêa RO, Fachi JL, Sato FT, Ribeiro WR, Ferreira CM, Perée H, Spagnuolo M, Mattiuz R, Matolcsi C, Guedes J, Clark J, Veldhoen M, Bonaldi T, Vinolo MAR, Varga-Weisz P. Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nat Commun 2018; 9:105. [PMID: 29317660 PMCID: PMC5760624 DOI: 10.1038/s41467-017-02651-5] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
The recently discovered histone post-translational modification crotonylation connects cellular metabolism to gene regulation. Its regulation and tissue-specific functions are poorly understood. We characterize histone crotonylation in intestinal epithelia and find that histone H3 crotonylation at lysine 18 is a surprisingly abundant modification in the small intestine crypt and colon, and is linked to gene regulation. We show that this modification is highly dynamic and regulated during the cell cycle. We identify class I histone deacetylases, HDAC1, HDAC2, and HDAC3, as major executors of histone decrotonylation. We show that known HDAC inhibitors, including the gut microbiota-derived butyrate, affect histone decrotonylation. Consistent with this, we find that depletion of the gut microbiota leads to a global change in histone crotonylation in the colon. Our results suggest that histone crotonylation connects chromatin to the gut microbiota, at least in part, via short-chain fatty acids and HDACs.
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Affiliation(s)
- Rachel Fellows
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jérémy Denizot
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK.,Université Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, F-63000, France
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, Istituto Europeo di Oncologia, 20139, Milano, Italy
| | - Payal Jain
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Elena Stoyanova
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Szabina Balázsi
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Zoltán Hajnády
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Anke Liebert
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Juri Kazakevych
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - José Luís Fachi
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - Fabio Takeo Sato
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - Willian R Ribeiro
- Department of Pharmaceutical Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil.,Chemical Biology Graduate Program, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil
| | - Caroline Marcantonio Ferreira
- Department of Pharmaceutical Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil
| | - Hélène Perée
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Raphaël Mattiuz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Csaba Matolcsi
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Joana Guedes
- Lymphocyte Signalling and Development, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jonathan Clark
- Biological Chemistry, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Marc Veldhoen
- Lymphocyte Signalling and Development, Babraham Institute, Cambridge, CB22 3AT, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, 1649-028, Portugal
| | - Tiziana Bonaldi
- Department of Experimental Oncology, Istituto Europeo di Oncologia, 20139, Milano, Italy.
| | | | - Patrick Varga-Weisz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK. .,School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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14
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Stenzel K, Hamacher A, Hansen FK, Gertzen CGW, Senger J, Marquardt V, Marek L, Marek M, Romier C, Remke M, Jung M, Gohlke H, Kassack MU, Kurz T. Alkoxyurea-Based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines. J Med Chem 2017; 60:5334-5348. [DOI: 10.1021/acs.jmedchem.6b01538] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Katharina Stenzel
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Finn K. Hansen
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Pharmaceutical/Medicinal
Chemistry, Institute of Pharmacy, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Christoph G. W. Gertzen
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Johanna Senger
- Institut
für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Viktoria Marquardt
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Department
of Neuropathology, Medical Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Division of Pediatric
Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer
Research Center (DKFZ), Moorenstraße
5, 40225 Düsseldorf, Germany
| | - Linda Marek
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin Marek
- Département
de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christophe Romier
- Département
de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Marc Remke
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Department
of Neuropathology, Medical Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Division of Pediatric
Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer
Research Center (DKFZ), Moorenstraße
5, 40225 Düsseldorf, Germany
| | - Manfred Jung
- Institut
für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Holger Gohlke
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Matthias U. Kassack
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Thomas Kurz
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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15
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Krieger V, Hamacher A, Gertzen CGW, Senger J, Zwinderman MRH, Marek M, Romier C, Dekker FJ, Kurz T, Jung M, Gohlke H, Kassack MU, Hansen FK. Design, Multicomponent Synthesis, and Anticancer Activity of a Focused Histone Deacetylase (HDAC) Inhibitor Library with Peptoid-Based Cap Groups. J Med Chem 2017; 60:5493-5506. [PMID: 28574690 DOI: 10.1021/acs.jmedchem.7b00197] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this work, we report the multicomponent synthesis of a focused histone deacetylase (HDAC) inhibitor library with peptoid-based cap groups and different zinc-binding groups. All synthesized compounds were tested in a cellular HDAC inhibition assay and an MTT assay for cytotoxicity. On the basis of their noteworthy activity in the cellular HDAC assays, four compounds were further screened for their inhibitory activity against recombinant HDAC1-3, HDAC6, and HDAC8. All four compounds showed potent inhibition of HDAC1-3 as well as significant inhibition of HDAC6 with IC50 values in the submicromolar concentration range. Compound 4j, the most potent HDAC inhibitor in the cellular HDAC assay, revealed remarkable chemosensitizing properties and enhanced the cisplatin sensitivity of the cisplatin-resistant head-neck cancer cell line Cal27CisR by almost 7-fold. Furthermore, 4j almost completely reversed the cisplatin resistance in Cal27CisR. This effect is related to a synergistic induction of apoptosis as seen in the combination of 4j with cisplatin.
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Affiliation(s)
- Viktoria Krieger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Johanna Senger
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Martijn R H Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9712 Groningen, The Netherlands
| | - Martin Marek
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM , 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM , 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , 9712 Groningen, The Netherlands
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Matthias U Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Finn K Hansen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf, Germany.,Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University , Brüderstraße 34, 04103 Leipzig, Germany
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16
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Godoy LD, Lucas JE, Bender AJ, Romanick SS, Ferguson BS. Targeting the epigenome: Screening bioactive compounds that regulate histone deacetylase activity. Mol Nutr Food Res 2017; 61. [PMID: 27981795 DOI: 10.1002/mnfr.201600744] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/07/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022]
Abstract
SCOPE Nutrigenomics is a rapidly expanding field that elucidates the link between diet-genome interactions. Recent evidence demonstrates that regulation of the epigenome, and in particular inhibition of histone deacetylases (HDACs), impact pathogenetic mechanisms involved in chronic disease. Few studies, to date, have screened libraries of bioactive compounds that act as epigenetic modifiers. This study screened a library of 131 natural compounds to determine bioactive compounds that inhibit Zn-dependent HDAC activity. METHODS AND RESULTS Using class-specific HDAC substrates, we screened 131 natural compounds for HDAC activity in bovine cardiac tissue. From this screen, we identified 18 bioactive compound HDAC inhibitors. Using our class-specific HDAC substrates, we next screened these 18 bioactive compounds against recombinant HDAC proteins. Consistent with inhibition of HDAC activity, these compounds were capable of inhibiting activity of individual HDAC isoforms. Lastly, we report that treatment of H9c2 cardiac myoblasts with bioactive HDAC inhibitors was sufficient to increase lysine acetylation as assessed via immunoblot. CONCLUSION This study provided the first step in identifying multiple bioactive compound HDAC inhibitors. Taken together, this report sets the stage for future exploration of these bioactive compounds as epigenetic regulators to potentially ameliorate chronic disease.
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Affiliation(s)
- Luis D Godoy
- Department Agriculture, Nutrition, & Veterinary Sciences, University of Nevada, Reno, NV, USA
| | - Julianna E Lucas
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Abigail J Bender
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | | | - Bradley S Ferguson
- Department Agriculture, Nutrition, & Veterinary Sciences, University of Nevada, Reno, NV, USA
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17
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Hau M, Zenk F, Ganesan A, Iovino N, Jung M. Cellular analysis of the action of epigenetic drugs and probes. Epigenetics 2017; 12:308-322. [PMID: 28071961 DOI: 10.1080/15592294.2016.1274472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small molecule drugs and probes are important tools in drug discovery, pharmacology, and cell biology. This is of course also true for epigenetic inhibitors. Important examples for the use of established epigenetic inhibitors are the study of the mechanistic role of a certain target in a cellular setting or the modulation of a certain phenotype in an approach that aims toward therapeutic application. Alternatively, cellular testing may aim at the validation of a new epigenetic inhibitor in drug discovery approaches. Cellular and eventually animal models provide powerful tools for these different approaches but certain caveats have to be recognized and taken into account. This involves both the selectivity of the pharmacological tool as well as the specificity and the robustness of the cellular system. In this article, we present an overview of different methods that are used to profile and screen for epigenetic agents and comment on their limitations. We describe not only diverse successful case studies of screening approaches using different assay formats, but also some problematic cases, critically discussing selected applications of these systems.
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Affiliation(s)
- Mirjam Hau
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany
| | - Fides Zenk
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - A Ganesan
- c School of Pharmacy, University of East Anglia , Norwich NR4 7TJ , United Kingdom.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
| | - Nicola Iovino
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Manfred Jung
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
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18
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016; 56:153-157. [DOI: 10.1002/anie.201608677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/07/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED; 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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19
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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20
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Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao SQ, Sun H. Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases. J Am Chem Soc 2016; 138:15596-15604. [DOI: 10.1021/jacs.6b07334] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yusheng Xie
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Jingyan Ge
- College
of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Haipeng Lei
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Bo Peng
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Huatang Zhang
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Danyang Wang
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Sijun Pan
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Ganchao Chen
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Lanfang Chen
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Yi Wang
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Hongyan Sun
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
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21
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HDAC Inhibitors as Epigenetic Regulators of the Immune System: Impacts on Cancer Therapy and Inflammatory Diseases. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8797206. [PMID: 27556043 PMCID: PMC4983322 DOI: 10.1155/2016/8797206] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/08/2016] [Accepted: 06/29/2016] [Indexed: 01/13/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are powerful epigenetic regulators that have enormous therapeutic potential and have pleiotropic effects at the cellular and systemic levels. To date, HDAC inhibitors are used clinically for a wide variety of disorders ranging from hematopoietic malignancies to psychiatric disorders, are known to have anti-inflammatory properties, and are in clinical trials for several other diseases. In addition to influencing gene expression, HDAC enzymes also function as part of large, multisubunit complexes which have many nonhistone targets, alter signaling at the cellular and systemic levels, and result in divergent and cell-type specific effects. Thus, the effects of HDAC inhibitor treatment are too intricate to completely understand with current knowledge but the ability of HDAC inhibitors to modulate the immune system presents intriguing therapeutic possibilities. This review will explore the complexity of HDAC inhibitor treatment at the cellular and systemic levels and suggest strategies for effective use of HDAC inhibitors in biomedical research, focusing on the ability of HDAC inhibitors to modulate the immune system. The possibility of combining the documented anticancer effects and newly emerging immunomodulatory effects of HDAC inhibitors represents a promising new combinatorial therapeutic approach for HDAC inhibitor treatments.
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22
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Gober IN, Waters ML. Supramolecular Affinity Labeling of Histone Peptides Containing Trimethyllysine and Its Application to Histone Deacetylase Assays. J Am Chem Soc 2016; 138:9452-9. [DOI: 10.1021/jacs.6b02836] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Isaiah N. Gober
- Department
of Chemistry,
CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department
of Chemistry,
CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
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23
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Zwick V, Simões-Pires C, Cuendet M. Cell-based multi-substrate assay coupled to UHPLC-ESI-MS/MS for a quick identification of class-specific HDAC inhibitors. J Enzyme Inhib Med Chem 2016; 31:209-214. [PMID: 27149362 DOI: 10.1080/14756366.2016.1180595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Histone deacetylases (HDAC) are involved in several diseases including cancer, cardiovascular and neurodegenerative disorders, and the search for inhibitors is a current topic in drug discovery. Four HDAC inhibitors have already been approved by the FDA for cancer therapy and others are under clinical studies. However, the clinical utility of some of them is limited because of unfavorable toxicities associated with their broad range of HDAC inhibitory effects. Toxicity could be decreased by using HDAC inhibitors with improved specificity. To date, the most popular screening assays are based on fluorescence-labeled substrates incubated with an enzymatic source (cells extracts or recombinant isoforms). Here, we describe a high-throughput cell-based UHPLC-ESI-MS/MS assay able to rapidly predict activity against HDAC1 and HDAC6 in a cell environment. This method is predicted to be a useful tool to accelerate the search for class-selective HDAC inhibitors in drug discovery.
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Affiliation(s)
- Vincent Zwick
- a School of Pharmaceutical Sciences, University of Geneva, University of Lausanne , Geneva , Switzerland
| | - Claudia Simões-Pires
- a School of Pharmaceutical Sciences, University of Geneva, University of Lausanne , Geneva , Switzerland
| | - Muriel Cuendet
- a School of Pharmaceutical Sciences, University of Geneva, University of Lausanne , Geneva , Switzerland
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24
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Jost JO, Hanswillemenke A, Schwarzer D. A miniaturized readout strategy for endogenous histone deacetylase activity. MOLECULAR BIOSYSTEMS 2016; 11:1820-3. [PMID: 26009008 DOI: 10.1039/c5mb00326a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone deacetylases are important drug targets, which are difficult to characterize due to their poor accessibility. We have developed a miniaturized assay for the multi-site readout of deacetylase activity and profiled the substrate selectivity of HDACs for acetylation sites on histone H4 and tumor suppressor protein p53.
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Affiliation(s)
- Jan Oliver Jost
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, 72076 Tuebingen, Germany.
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25
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Nilsson LM, Green LC, Muralidharan SV, Demir D, Welin M, Bhadury J, Logan DT, Walse B, Nilsson JA. Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins. Cancer Res 2016; 76:2376-83. [PMID: 26941288 DOI: 10.1158/0008-5472.can-15-2721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/18/2016] [Indexed: 11/16/2022]
Abstract
Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce differentiation in experimental systems, but their mechanisms of action and potential range of uses on that basis have not been developed. Here, we show that HMBA, a compound first tested in the oncology clinic over 25 years ago, acts as a selective bromodomain inhibitor. Biochemical and structural studies revealed an affinity of HMBA for the second bromodomain of BET proteins. Accordingly, both HMBA and the prototype BET inhibitor JQ1 induced differentiation of mouse erythroleukemia cells. As expected of a BET inhibitor, HMBA displaced BET proteins from chromatin, caused massive transcriptional changes, and triggered cell-cycle arrest and apoptosis in Myc-induced B-cell lymphoma cells. Furthermore, HMBA exerted anticancer effects in vivo in mouse models of Myc-driven B-cell lymphoma. This study illuminates the function of an early anticancer agent and suggests an intersection with ongoing clinical trials of BET inhibitor, with several implications for predicting patient selection and response rates to this therapy and starting points for generating BD2-selective BET inhibitors. Cancer Res; 76(8); 2376-83. ©2016 AACR.
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Affiliation(s)
- Lisa M Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Lydia C Green
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Somsundar Veppil Muralidharan
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Dağsu Demir
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | - Joydeep Bhadury
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | | | - Jonas A Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden.
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26
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Seidel J, Klockenbusch C, Schwarzer D. Investigating Deformylase and Deacylase Activity of Mammalian and Bacterial Sirtuins. Chembiochem 2016; 17:398-402. [DOI: 10.1002/cbic.201500611] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Cordula Klockenbusch
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB); University of Tübingen; Hoppe-Seyler-Strasse 4 72076 Tübingen Germany
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27
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Galleano I, Schiedel M, Jung M, Madsen AS, Olsen CA. A Continuous, Fluorogenic Sirtuin 2 Deacylase Assay: Substrate Screening and Inhibitor Evaluation. J Med Chem 2016; 59:1021-31. [PMID: 26788965 DOI: 10.1021/acs.jmedchem.5b01532] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sirtuins are important regulators of lysine acylation, which is implicated in cellular metabolism and transcriptional control. This makes the sirtuin class of enzymes interesting targets for development of small molecule probes with pharmaceutical potential. To achieve detailed profiling and kinetic insight regarding sirtuin inhibitors, it is important to have access to efficient assays. In this work, we report readily synthesized fluorogenic substrates enabling enzyme-economical evaluation of SIRT2 inhibitors in a continuous assay format as well as evaluation of the properties of SIRT2 as a long chain deacylase enzyme. Novel enzymatic activities of SIRT2 were thus established in vitro, which warrant further investigation, and two known inhibitors, suramin and SirReal2, were profiled against substrates containing ε-N-acyllysine modifications of varying length.
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Affiliation(s)
- Iacopo Galleano
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Matthias Schiedel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology, University of Copenhagen , Universitetsparken 2, DK-2100, Copenhagen, Denmark
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28
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Rodrigues DA, Ferreira-Silva GÀ, Ferreira ACS, Fernandes RA, Kwee JK, Sant'Anna CMR, Ionta M, Fraga CAM. Design, Synthesis, and Pharmacological Evaluation of Novel N-Acylhydrazone Derivatives as Potent Histone Deacetylase 6/8 Dual Inhibitors. J Med Chem 2016; 59:655-70. [PMID: 26705137 DOI: 10.1021/acs.jmedchem.5b01525] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This manuscript describes a novel class of N-acylhydrazone (NAH) derivatives that act as histone deacetylase (HDAC) 6/8 dual inhibitors and were designed from the structure of trichostatin A (1). Para-substituted phenyl-hydroxamic acids presented a more potent inhibition of HDAC6/8 than their meta analogs. In addition, the effect of compounds (E)-4-((2-(4-(dimethylamino)benzoyl)hydrazono)methyl)-N-hydroxybenzamide (3c) and (E)-4-((2-(4-(dimethylamino)benzoyl)-2-methylhydrazono)methyl)-N-hydroxybenzamide (3f) on the acetylation of α-tubulin revealed an increased level of acetylation. These two compounds also affected cell migration, indicating their inhibition of HDAC6. An analysis of the antiproliferative activity of these compounds, which presented the most potent activity, showed that compound 3c induced cell cycle arrest and 3g induced apoptosis through caspase 3/7 activation. These results suggest HDAC6/8 as a potential target of future molecular therapies for cancer.
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Affiliation(s)
| | - Guilherme À Ferreira-Silva
- Laboratório de Biologia Animal Integrativa, Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas , 37130-000 Alfenas, Minas Gerais, Brazil
| | - Ana C S Ferreira
- Coordenação de Pesquisa, Instituto Nacional de Câncer , 20231-050 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renan A Fernandes
- Coordenação de Pesquisa, Instituto Nacional de Câncer , 20231-050 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jolie K Kwee
- Coordenação de Pesquisa, Instituto Nacional de Câncer , 20231-050 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos M R Sant'Anna
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Rural do Rio de Janeiro , 23970-000 Seropédica, Rio de Janeiro, Brazil
| | - Marisa Ionta
- Laboratório de Biologia Animal Integrativa, Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas , 37130-000 Alfenas, Minas Gerais, Brazil
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29
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Howitz KT. Screening and profiling assays for HDACs and sirtuins. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 18:38-48. [PMID: 26723891 DOI: 10.1016/j.ddtec.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Epigenetic factors are enzymes or proteins that confer, remove or recognize covalent modifications to chromatin DNA or proteins. They can be divided into three broad groups, commonly referred to as the 'writers', 'erasers' and 'readers'. The HDACs and sirtuins, which remove acetyl groups from the ɛ-amino of protein lysine residues, fall into the 'eraser' category. Due to their important effects on gene expression and involvement in various disease states, these enzymes have been the subjects of many assay development efforts in recent years. Commonly used techniques include mass spectrometry, antibody-based methods and protease-coupled assays with fluorogenic peptide substrates. Recent advances include the development of synthetic substrates for the assay of various newly discovered non-acetyl deacylation activities among the sirtuins.
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Affiliation(s)
- Konrad T Howitz
- Reaction Biology Corporation, One Great Valley Parkway, Suite 2, Malvern, PA 19355, USA.
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30
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Rooker DR, Buccella D. Real-time detection of histone deacetylase activity with a small molecule fluorescent and spectrophotometric probe. Chem Sci 2015; 6:6456-6461. [PMID: 30090264 PMCID: PMC6054043 DOI: 10.1039/c5sc02704g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 07/30/2015] [Indexed: 02/01/2023] Open
Abstract
Histone deacetylases (HDACs) are central players in transcription regulation and important targets in cancer treatment. Activity assays are critical tools for the study of the function and regulation of these enzymes, as well as for the screening of potential inhibitors. We report a small-molecule probe for single-step, continuous detection of deacetylase activity based on an acetyl-lysine mimic functionalized with an amine-reactive fluorophore, designed to undergo rapid intramolecular imine formation upon deacetylation. The probe exhibits a bathochromic shift in the absorption spectrum and changes in fluorescence emission intensity that enable unprecedented real-time detection of HDAC activity of purified enzymes or in cell lysates, and offers a means to evaluate HDAC inhibitors via simple spectrophotometric or fluorescence readings without the need of additional reagents.
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Affiliation(s)
- Debra R Rooker
- Department of Chemistry , New York University , New York , New York 10003 , USA .
| | - Daniela Buccella
- Department of Chemistry , New York University , New York , New York 10003 , USA .
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31
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Wang Y, Chen Y, Wang H, Cheng Y, Zhao X. Specific Turn-On Fluorescent Probe with Aggregation-Induced Emission Characteristics for SIRT1 Modulator Screening and Living-Cell Imaging. Anal Chem 2015; 87:5046-9. [DOI: 10.1021/acs.analchem.5b01069] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yi Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Yaqi Chen
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Haibo Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Yiyu Cheng
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Xiaoping Zhao
- College
of Preclinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang China
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32
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Baba R, Hori Y, Kikuchi K. Intramolecular Long-Distance Nucleophilic Reactions as a Rapid Fluorogenic Switch Applicable to the Detection of Enzymatic Activity. Chemistry 2015; 21:4695-702. [DOI: 10.1002/chem.201406093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Indexed: 01/10/2023]
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33
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Tashima T, Murata H, Kodama H. Design and synthesis of novel and highly-active pan-histone deacetylase (pan-HDAC) inhibitors. Bioorg Med Chem 2014; 22:3720-31. [DOI: 10.1016/j.bmc.2014.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/02/2014] [Accepted: 05/03/2014] [Indexed: 12/25/2022]
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34
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Schutkowski M, Fischer F, Roessler C, Steegborn C. New assays and approaches for discovery and design of Sirtuin modulators. Expert Opin Drug Discov 2014; 9:183-99. [DOI: 10.1517/17460441.2014.875526] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Parbin S, Kar S, Shilpi A, Sengupta D, Deb M, Rath SK, Patra SK. Histone deacetylases: a saga of perturbed acetylation homeostasis in cancer. J Histochem Cytochem 2014; 62:11-33. [PMID: 24051359 PMCID: PMC3873803 DOI: 10.1369/0022155413506582] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In the current era of genomic medicine, diseases are identified as manifestations of anomalous patterns of gene expression. Cancer is the principal example among such maladies. Although remarkable progress has been achieved in the understanding of the molecular mechanisms involved in the genesis and progression of cancer, its epigenetic regulation, particularly histone deacetylation, demands further studies. Histone deacetylases (HDACs) are one of the key players in the gene expression regulation network in cancer because of their repressive role on tumor suppressor genes. Higher expression and function of deacetylases disrupt the finely tuned acetylation homeostasis in both histone and non-histone target proteins. This brings about alterations in the genes implicated in the regulation of cell proliferation, differentiation, apoptosis and other cellular processes. Moreover, the reversible nature of epigenetic modulation by HDACs makes them attractive targets for cancer remedy. This review summarizes the current knowledge of HDACs in tumorigenesis and tumor progression as well as their contribution to the hallmarks of cancer. The present report also describes briefly various assays to detect histone deacetylase activity and discusses the potential role of histone deacetylase inhibitors as emerging epigenetic drugs to cure cancer.
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Affiliation(s)
- Sabnam Parbin
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India (SP, SK, AS, DS, SKR, SKP)
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36
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Bürli RW, Luckhurst CA, Aziz O, Matthews KL, Yates D, Lyons KA, Beconi M, McAllister G, Breccia P, Stott AJ, Penrose SD, Wall M, Lamers M, Leonard P, Müller I, Richardson CM, Jarvis R, Stones L, Hughes S, Wishart G, Haughan AF, O'Connell C, Mead T, McNeil H, Vann J, Mangette J, Maillard M, Beaumont V, Munoz-Sanjuan I, Dominguez C. Design, synthesis, and biological evaluation of potent and selective class IIa histone deacetylase (HDAC) inhibitors as a potential therapy for Huntington's disease. J Med Chem 2013; 56:9934-54. [PMID: 24261862 DOI: 10.1021/jm4011884] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Inhibition of class IIa histone deacetylase (HDAC) enzymes have been suggested as a therapeutic strategy for a number of diseases, including Huntington's disease. Catalytic-site small molecule inhibitors of the class IIa HDAC4, -5, -7, and -9 were developed. These trisubstituted diarylcyclopropanehydroxamic acids were designed to exploit a lower pocket that is characteristic for the class IIa HDACs, not present in other HDAC classes. Selected inhibitors were cocrystallized with the catalytic domain of human HDAC4. We describe the first HDAC4 catalytic domain crystal structure in a "closed-loop" form, which in our view represents the biologically relevant conformation. We have demonstrated that these molecules can differentiate class IIa HDACs from class I and class IIb subtypes. They exhibited pharmacokinetic properties that should enable the assessment of their therapeutic benefit in both peripheral and CNS disorders. These selective inhibitors provide a means for evaluating potential efficacy in preclinical models in vivo.
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Affiliation(s)
- Roland W Bürli
- BioFocus , Chesterford Research Park, Saffron Walden, Essex, CB10 1XL, United Kingdom
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37
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Yu C, Wu Y, Zeng F, Li X, Shi J, Wu S. Hyperbranched Polyester-Based Fluorescent Probe for Histone Deacetylase via Aggregation-Induced Emission. Biomacromolecules 2013; 14:4507-14. [DOI: 10.1021/bm401548u] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Changmin Yu
- College of Materials Science & Engineering, State Key Laboratory of Luminescent Materials & Devices, South China University of Technology, Guangzhou 510640, China
| | - Yinglong Wu
- College of Materials Science & Engineering, State Key Laboratory of Luminescent Materials & Devices, South China University of Technology, Guangzhou 510640, China
| | - Fang Zeng
- College of Materials Science & Engineering, State Key Laboratory of Luminescent Materials & Devices, South China University of Technology, Guangzhou 510640, China
| | - Xizhen Li
- College of Materials Science & Engineering, State Key Laboratory of Luminescent Materials & Devices, South China University of Technology, Guangzhou 510640, China
| | - Jianbin Shi
- College of Materials Science & Engineering, College of Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shuizhu Wu
- College of Materials Science & Engineering, State Key Laboratory of Luminescent Materials & Devices, South China University of Technology, Guangzhou 510640, China
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38
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Lübke M, Jung M, Haufe G. New histone deacetylase inhibitors based on 4-fluoro-2-amino acid esters: Synthesis and activity. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Abstract
The effect of histone deacetylases (HDACs) on normal and aberrant gene expression has been studied widely, making these enzymes interesting targets for the treatment of cancer and other diseases. In this chapter, we present in vitro assays that are commonly used to detect HDAC activity that do not rely on radioactive substrates and are amenable for high-throughput testing in microtiter plates. The major focus is on in vitro screening, but we also provide protocols to monitor HDAC activity from cancer cells and peripheral white blood cells. We will discuss the advantages and drawbacks of the respective protocols and give general hints and suggestions that are valuable to obtain reliable and reproducible results.
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40
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Wu H, Liu S, Zhu W, Jiang J, Shen G, Yu R. A Sensitive Electrochemical Biosensor for Detection of Histone Deacetylase Activity Using an Acetylated Peptide. ELECTROANAL 2012. [DOI: 10.1002/elan.201200414] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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M. Jung. ChemMedChem 2012. [DOI: 10.1002/cmdc.201200280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Baba R, Hori Y, Mizukami S, Kikuchi K. Development of a Fluorogenic Probe with a Transesterification Switch for Detection of Histone Deacetylase Activity. J Am Chem Soc 2012; 134:14310-3. [DOI: 10.1021/ja306045j] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Reisuke Baba
- Graduate
School of Engineering and ‡Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871,
Japan
| | - Yuichiro Hori
- Graduate
School of Engineering and ‡Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871,
Japan
| | - Shin Mizukami
- Graduate
School of Engineering and ‡Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871,
Japan
| | - Kazuya Kikuchi
- Graduate
School of Engineering and ‡Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871,
Japan
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43
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Rye PT, Frick LE, Ozbal CC, Lamarr WA. Advances in label-free screening approaches for studying sirtuin-mediated deacetylation. ACTA ACUST UNITED AC 2011; 16:1217-26. [PMID: 21911826 DOI: 10.1177/1087057111420291] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The sirtuin enzymes, a class of NAD(+)-dependent histone deacetylases, are a focal point of epigenetic research because of their roles in regulating gene expression and cellular differentiation by deacetylating histones and a host of transcription factors, including p53. Here, the authors present two label-free screening methodologies to study sirtuin activity using high-throughput mass spectrometry. The first method involves the detection of native peptides and provides a platform for more detailed mechanistic studies by enabling the concurrent and direct measurement of multiple modification states. The second method obviates the need for substrate-specific assay development by measuring the O-acetyl-ADP-ribose co-product formed by sirtuin-dependent deacetylation. Both methodologies were applied to investigating the deacetylation of multiple-peptide substrates by multiple-sirtuin enzymes. Kinetic data, including binding constants, inhibition, and, in some cases, activation, are demonstrated to correlate well, both between the methodologies and with previous literature precedent. In addition, the ability to monitor sirtuin activity via O-acetyl-ADP-ribose production permits experimentation on whole-protein substrates. The deacetylation of whole-histone proteins by SIRT3, and inhibition thereof, is presented and demonstrates the feasibility of screening sirtuins using more biologically relevant molecules.
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Affiliation(s)
- Peter T Rye
- Agilent Technologies, Inc., Life Sciences Group, Wakefield, MA 01880, USA.
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Ilies M, Dowling DP, Lombardi PM, Christianson DW. Synthesis of a new trifluoromethylketone analogue of l-arginine and contrasting inhibitory activity against human arginase I and histone deacetylase 8. Bioorg Med Chem Lett 2011; 21:5854-8. [PMID: 21875805 DOI: 10.1016/j.bmcl.2011.07.100] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/25/2011] [Accepted: 07/26/2011] [Indexed: 01/12/2023]
Abstract
As part of our continuing search for new amino acid inhibitors of metalloenzymes, we now report the synthesis and biological evaluation of the trifluoromethylketone analogue of L-arginine, (S)-2-amino-8,8,8-trifluoro-7-oxo-octanoic acid (10). While this novel amino acid was initially designed as a potential inhibitor of human arginase I, it exhibits no measurable inhibitory activity against this enzyme. Surprisingly, however, 10 is a potent inhibitor of human histone deacetylase 8, with IC(50)=1.5 ± 0.2 μM. Additionally, 10 weakly inhibits the related bacterial enzyme, acetylpolyamine amidohydrolase, with IC(50)=110 ± 30 μM. The lack of inhibitory activity against human arginase I may result from unfavorable interactions of the bulky trifluoromethyl group of 10 in the constricted active site. Since the active site of histone deacetylase 8 is less constricted, we hypothesize that it accommodates 10 as the gem-diol, which mimics the tetrahedral intermediate and its flanking transition states in catalysis. Therefore, we suggest that 10 represents a new lead in the design of an amino acid or peptide-based inhibitor of histone deacetylases with simpler structure than previously studied trifluoromethylketones.
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Affiliation(s)
- Monica Ilies
- Department of Chemistry, Drexel University, Philadelphia, PA 19104-2875, USA
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45
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Discovery of polyoxometalate-based HDAC inhibitors with profound anticancer activity in vitro and in vivo. Eur J Med Chem 2011; 46:2477-84. [DOI: 10.1016/j.ejmech.2011.03.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/09/2011] [Accepted: 03/16/2011] [Indexed: 12/31/2022]
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46
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Lemon DD, Horn TR, Cavasin MA, Jeong MY, Haubold KW, Long CS, Irwin DC, McCune SA, Chung E, Leinwand LA, McKinsey TA. Cardiac HDAC6 catalytic activity is induced in response to chronic hypertension. J Mol Cell Cardiol 2011; 51:41-50. [PMID: 21539845 DOI: 10.1016/j.yjmcc.2011.04.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 04/12/2011] [Accepted: 04/14/2011] [Indexed: 02/07/2023]
Abstract
Small molecule histone deacetylase (HDAC) inhibitors block adverse cardiac remodeling in animal models of heart failure. The efficacious compounds target class I, class IIb and, to a lesser extent, class IIa HDACs. It is hypothesized that a selective inhibitor of a specific HDAC class (or an isoform within that class) will provide a favorable therapeutic window for the treatment of heart failure, although the optimal selectivity profile for such a compound remains unknown. Genetic studies have suggested that class I HDACs promote pathological cardiac remodeling, while class IIa HDACs are protective. In contrast, nothing is known about the function or regulation of class IIb HDACs in the heart. We developed assays to quantify catalytic activity of distinct HDAC classes in left and right ventricular cardiac tissue from animal models of hypertensive heart disease. Class I and IIa HDAC activity was elevated in some but not all diseased tissues. In contrast, catalytic activity of the class IIb HDAC, HDAC6, was consistently increased in stressed myocardium, but not in a model of physiologic hypertrophy. HDAC6 catalytic activity was also induced by diverse extracellular stimuli in cultured cardiac myocytes and fibroblasts. These findings suggest an unforeseen role for HDAC6 in the heart, and highlight the need for pre-clinical evaluation of HDAC6-selective inhibitors to determine whether this HDAC isoform is pathological or protective in the setting of cardiovascular disease.
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Affiliation(s)
- Douglas D Lemon
- Department of Medicine, Division of Cardiology, University of Colorado Denver, Aurora, CO, USA
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47
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Schlimme S, Hauser AT, Carafa V, Heinke R, Kannan S, Stolfa DA, Cellamare S, Carotti A, Altucci L, Jung M, Sippl W. Carbamate Prodrug Concept for Hydroxamate HDAC Inhibitors. ChemMedChem 2011; 6:1193-8. [DOI: 10.1002/cmdc.201100007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Indexed: 11/10/2022]
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48
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5-Aza-2'-deoxycytidine stress response and apoptosis in prostate cancer. Clin Epigenetics 2011; 2:339-48. [PMID: 22704346 PMCID: PMC3365594 DOI: 10.1007/s13148-010-0019-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 12/15/2010] [Indexed: 12/31/2022] Open
Abstract
While studying on epigenetic regulatory mechanisms (DNA methylation at C-5 of -CpG- cytosine and demethylation of methylated DNA) of certain genes (FAS, CLU, E-cadh, CD44, and Cav-1) associated with prostate cancer development and its better management, we noticed that the used in vivo dose of 5-aza-2'-deoxycytidine (5.0 to 10.0 nM, sufficient to inhibit DNA methyltransferase activity in vitro) helped in the transcription of various genes with known (steroid receptors, AR and ER; ER variants, CD44, CDH1, BRCA1, TGFβR1, MMP3, MMP9, and UPA) and unknown (DAZ and Y-chromosome specific) proteins and the respective cells remained healthy in culture. At a moderate dose (20 to 200 nM) of the inhibitor, cells remain growth arrested. Upon subsequent challenge with increased dose (0.5 to 5.0 μM) of the inhibitor, we observed that the cellular morphology was changing and led to death of the cells with progress of time. Analyses of DNA and anti-, pro-, and apoptotic factors of the affected cells revealed that the molecular events that went on are characteristics of programmed cell death (apoptosis).
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Wagner JM, Hackanson B, Lübbert M, Jung M. Histone deacetylase (HDAC) inhibitors in recent clinical trials for cancer therapy. Clin Epigenetics 2010; 1:117-136. [PMID: 21258646 PMCID: PMC3020651 DOI: 10.1007/s13148-010-0012-4] [Citation(s) in RCA: 320] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 10/19/2010] [Indexed: 12/15/2022] Open
Abstract
Heritable changes in gene expression that are not based upon alterations in the DNA sequence are defined as epigenetics. The most common mechanisms of epigenetic regulation are the methylation of CpG islands within the DNA and the modification of amino acids in the N-terminal histone tails. In the last years, it became evident that the onset of cancer and its progression may not occur only due to genetic mutations but also because of changes in the patterns of epigenetic modifications. In contrast to genetic mutations, which are almost impossible to reverse, epigenetic changes are potentially reversible. This implies that they are amenable to pharmacological interventions. Therefore, a lot of work in recent years has focussed on the development of small molecule enzyme inhibitors like DNA-methyltransferase inhibitors or inhibitors of histone-modifying enzymes. These may reverse misregulated epigenetic states and be implemented in the treatment of cancer or other diseases, e.g., neurological disorders. Today, several epigenetic drugs are already approved by the FDA and the EMEA for cancer treatment and around ten histone deacetylase (HDAC) inhibitors are in clinical development. This review will give an update on recent clinical trials of the HDAC inhibitors used systemically that were reported in 2009 and 2010 and will present an overview of different biomarkers to monitor the biological effects.
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Affiliation(s)
- Julia M. Wagner
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Björn Hackanson
- Department of Hematology/Oncology, University Medical Center Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology/Oncology, University Medical Center Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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50
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Nepravishta R, Bellomaria A, Polizio F, Paci M, Melino S. Reticulon RTN1-CCT Peptide: A Potential Nuclease and Inhibitor of Histone Deacetylase Enzymes. Biochemistry 2009; 49:252-8. [DOI: 10.1021/bi9012676] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | | | | | | | - Sonia Melino
- Department of Sciences and Chemical Technologies
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