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Banerjee S, Ghosh B, Jha T, Adhikari N. A patent review of histone deacetylase 8 (HDAC8) inhibitors (2013-present). Expert Opin Ther Pat 2024:1-27. [PMID: 39121339 DOI: 10.1080/13543776.2024.2391289] [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: 03/31/2024] [Revised: 06/14/2024] [Accepted: 08/08/2024] [Indexed: 08/11/2024]
Abstract
INTRODUCTION The processes and course of several fatal illnesses, such as cancer, inflammatory diseases, and neurological disorders are closely correlated with HDAC8. Therefore, novel HDAC8 inhibitors represent effective therapeutic possibilities that may help treat these conditions. To yet, there are not any such particular HDAC8 inhibitors available for sale. This review was conducted to examine recent HDAC8 inhibitors that have been patented over the last 10 years. AREAS COVERED This review focuses on HDAC8 inhibitor-related patents and their therapeutic applications that have been published within the last 10 years and are accessible through the Patentscope and Google Patents databases. EXPERT OPINION A handful of HDAC8 inhibitor-related patents have been submitted over the previous 10 years, more selective, and specific HDAC8 inhibitors that are intended to treat a variety of medical diseases. This could lead to the development of novel treatment approaches that target HDAC8. Employing theoretical frameworks and experimental procedures can reveal the creation of new HDAC8 inhibitors with enhanced pharmacokinetic characteristics. A thorough understanding of the role that HDAC8 inhibitors play in cancer, including the mechanisms behind HDAC8 in other disorders is necessary.
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Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Xiao Y, Awasthee N, Liu Y, Meng C, He MY, Hale S, Karki R, Lin Z, Mosterio M, Garcia BA, Kridel R, Liao D, Zheng G. Discovery of a Highly Potent and Selective HDAC8 Degrader: Advancing the Functional Understanding and Therapeutic Potential of HDAC8. J Med Chem 2024; 67:12784-12806. [PMID: 38949959 DOI: 10.1021/acs.jmedchem.4c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
HDAC8 plays crucial roles in biological processes, from gene regulation to cell motility, making it a highly desirable target for therapeutic intervention. HDAC8 also has deacetylase-independent activity which cannot be blocked by a conventional inhibitor. In this study, we report the discovery of YX862, a highly potent and selective hydrazide-based HDAC8-proteolysis targeting chimera (PROTAC) degrader. The selectivity is achieved through rational design of the warhead to spare HDAC3 activity from the previous HDAC3/8 dual degrader YX968. We demonstrate that the degradation of HDAC8 by YX862 increases acetylation levels of its nonhistone substrates such as SMC3 without significantly triggering histone PTM, supporting HDAC8's major role in nonhistone PTM regulation. YX862 exhibits promising on-target antiproliferative activity against DLBCL cells with higher potency than the HDAC8 selective inhibitor PCI-34051. As a selective HDAC8 degrader that avoids pan-HDAC inhibition, YX862 represents a valuable tool for exploring the biological and therapeutic potential of HDAC8.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Nikee Awasthee
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Chengcheng Meng
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Michael Y He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Seth Hale
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Rashmi Karki
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Megan Mosterio
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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Huang Y, Zhai G, Fu Y, Li Y, Zang Y, Lin Y, Zhang K. A proximity labeling-based orthogonal trap strategy identifies HDAC8 promotes cell motility by modulating cortactin acetylation. Cell Chem Biol 2024; 31:514-522.e4. [PMID: 38460516 DOI: 10.1016/j.chembiol.2024.02.003] [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: 04/19/2023] [Revised: 12/14/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
It is a challenge for the traditional affinity methods to capture transient interactions of enzyme-post-translational modification (PTM) substrates in vivo. Herein we presented a strategy termed proximity labeling-based orthogonal trap approach (ProLORT), relying upon APEX2-catalysed proximity labeling and an orthogonal trap pipeline as well as quantitative proteomics to directly investigate the transient interactome of enzyme-PTM substrates in living cells. As a proof of concept, ProLORT allows for robust evaluation of a known HDAC8 substrate, histone H3K9ac. By leveraging this approach, we identified numerous of putative acetylated proteins targeted by HDAC8, and further confirmed CTTN as a bona fide substrate in vivo. Next, we demonstrated that HDAC8 facilitates cell motility via deacetylation of CTTN at lysine 144 that attenuates its interaction with F-actin, expanding the underlying regulatory mechanisms of HDAC8. We developed a general strategy to profile the transient enzyme-substrate interactions mediated by PTMs, providing a powerful tool for identifying the spatiotemporal PTM-network regulated by enzymes in living cells.
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Affiliation(s)
- Yepei Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China; Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou 350014, Fujian Province, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
| | - Yun Fu
- Fujian Provincial Sperm bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Yanan Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yong Zang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, United States.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
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Fukuda M, Fujita Y, Hino Y, Nakao M, Shirahige K, Yamashita T. Inhibition of HDAC8 Reduces the Proliferation of Adult Neural Stem Cells in the Subventricular Zone. Int J Mol Sci 2024; 25:2540. [PMID: 38473789 DOI: 10.3390/ijms25052540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
In the adult mammalian brain, neurons are produced from neural stem cells (NSCs) residing in two niches-the subventricular zone (SVZ), which forms the lining of the lateral ventricles, and the subgranular zone in the hippocampus. Epigenetic mechanisms contribute to maintaining distinct cell fates by suppressing gene expression that is required for deciding alternate cell fates. Several histone deacetylase (HDAC) inhibitors can affect adult neurogenesis in vivo. However, data regarding the role of specific HDACs in cell fate decisions remain limited. Herein, we demonstrate that HDAC8 participates in the regulation of the proliferation and differentiation of NSCs/neural progenitor cells (NPCs) in the adult mouse SVZ. Specific knockout of Hdac8 in NSCs/NPCs inhibited proliferation and neural differentiation. Treatment with the selective HDAC8 inhibitor PCI-34051 reduced the neurosphere size in cultures from the SVZ of adult mice. Further transcriptional datasets revealed that HDAC8 inhibition in adult SVZ cells disturbs biological processes, transcription factor networks, and key regulatory pathways. HDAC8 inhibition in adult SVZ neurospheres upregulated the cytokine-mediated signaling and downregulated the cell cycle pathway. In conclusion, HDAC8 participates in the regulation of in vivo proliferation and differentiation of NSCs/NPCs in the adult SVZ, which provides insights into the underlying molecular mechanisms.
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Affiliation(s)
- Momoko Fukuda
- Department of Anatomy and Developmental Biology, School of Medicine, Shimane University, 89-1, Enya-cho, Izumo-shi 693-8501, Japan
| | - Yuki Fujita
- Department of Anatomy and Developmental Biology, School of Medicine, Shimane University, 89-1, Enya-cho, Izumo-shi 693-8501, Japan
| | - Yuko Hino
- Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Quarter A6, 171 77 Stockholm, Sweden
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3, Yamadaoka, Suita 565-0871, Japan
- Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita 565-0871, Japan
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Toro TB, Skripnikova EV, Bornes KE, Zhang K, Watt TJ. Endogenous expression of inactive lysine deacetylases reveals deacetylation-dependent cellular mechanisms. PLoS One 2023; 18:e0291779. [PMID: 37721967 PMCID: PMC10506724 DOI: 10.1371/journal.pone.0291779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
Acetylation of lysine residues is an important and common post-translational regulatory mechanism occurring on thousands of non-histone proteins. Lysine deacetylases (KDACs or HDACs) are a family of enzymes responsible for removing acetylation. To identify the biological mechanisms regulated by individual KDACs, we created HT1080 cell lines containing chromosomal point mutations, which endogenously express either KDAC6 or KDAC8 having single inactivated catalytic domain. Engineered HT1080 cells expressing inactive KDA6 or KDAC8 domains remained viable and exhibited enhanced acetylation on known substrate proteins. RNA-seq analysis revealed that many changes in gene expression were observed when KDACs were inactivated, and that these gene sets differed significantly from knockdown and knockout cell lines. Using GO ontology, we identified several critical biological processes associated specifically with catalytic activity and others attributable to non-catalytic interactions. Treatment of wild-type cells with KDAC-specific inhibitors Tubastatin A and PCI-34051 resulted in gene expression changes distinct from those of the engineered cell lines, validating this approach as a tool for evaluating in-cell inhibitor specificity and identifying off-target effects of KDAC inhibitors. Probing the functions of specific KDAC domains using these cell lines is not equivalent to doing so using previously existing methods and provides novel insight into the catalytic functions of individual KDACs by investigating the molecular and cellular changes upon genetic inactivation.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Elena V. Skripnikova
- Division of Basic and Pharmaceutical Sciences, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kiara E. Bornes
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kun Zhang
- Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, United States of America
- Bioinformatics Core, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
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Schweipert M, Amurthavasan A, Meyer-Almes FJ. Continuous enzyme activity assay for high-throughput classification of histone deacetylase 8 inhibitors. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:447-459. [PMID: 37455831 PMCID: PMC10344891 DOI: 10.37349/etat.2023.00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/24/2023] [Indexed: 07/18/2023] Open
Abstract
Aim Human histone deacetylase 8 (KDAC8) is a well-recognized pharmaceutical target in Cornelia de Lange syndrome and different types of cancer, particularly childhood neuroblastoma. Several classes of chemotypes have been identified, which interfere with the enzyme activity of KDAC8. These compounds have been identified under equilibrium or near equilibrium conditions for inhibitor binding to the target enzyme. This study aims for the classification of KDAC8 inhibitors according to the mode of action and identification of most promising lead compounds for drug development. Methods A continuous enzyme activity assay is used to monitor inhibition kinetics. Results A high-throughput continuous KDAC8 activity assay is developed that provides additional mechanistic information about enzyme inhibition enabling the classification of KDAC8 inhibitors according to their mode of action. Fast reversible inhibitors act as a molecular chaperone and are capable to rescue the enzyme activity of misfolded KDAC8, while covalent inactivators and slow dissociating inhibitors do not preserve KDAC8 activity. Conclusions The application of continuous KDAC8 activity assay reveals additional information about the mode of interaction with inhibitors, which can be used to classify KDAC8 inhibitors according to their mode of action. The approach is compatible with the high-throughput screening of compound libraries. Fast reversible inhibitors of KDAC8 act as molecular chaperones and recover enzyme activity from misfolded protein conformations. In contrast, slow-binding inhibitors and covalent inactivators of KDAC8 are not capable to recover enzyme activity.
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Affiliation(s)
- Markus Schweipert
- Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64295 Darmstadt, Germany
| | - Anuja Amurthavasan
- Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64295 Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64295 Darmstadt, Germany
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7
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Amin SA, Khatun S, Gayen S, Das S, Jha T. Are inhibitors of histone deacetylase 8 (HDAC8) effective in hematological cancers especially acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL)? Eur J Med Chem 2023; 258:115594. [PMID: 37429084 DOI: 10.1016/j.ejmech.2023.115594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Histone deacetylase 8 (HDAC8) aberrantly deacetylates histone and non-histone proteins. These include structural maintenance of chromosome 3 (SMC3) cohesin protein, retinoic acid induced 1 (RAI1), p53, etc and thus, regulating diverse processes such as leukemic stem cell (LSC) transformation and maintenance. HDAC8, one of the crucial HDACs, affects the gene silencing process in solid and hematological cancer progressions especially on acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). A specific HDAC8 inhibitor PCI-34051 showed promising results against both T-cell lymphoma and AML. Here, we summarize the role of HDAC8 in hematological malignancies, especially in AML and ALL. This article also introduces the structure/function of HDAC8 and a special attention has been paid to address the HDAC8 enzyme selectivity issue in hematological cancer especially against AML and ALL.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India; Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India.
| | - Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Sanjib Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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8
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Toro TB, Bornes KE, Watt TJ. Lysine Deacetylase Substrate Selectivity: Distinct Interaction Surfaces Drive Positive and Negative Selection for Residues Following Acetyllysine. Biochemistry 2023; 62:1464-1483. [PMID: 37043688 PMCID: PMC10157890 DOI: 10.1021/acs.biochem.3c00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Lysine acetylation is a post-translational modification that is reversed by lysine deacetylases (KDACs). The goal of this work was to identify determinants of substrate specificity for KDACs, focusing on short-range interactions occurring with residues immediately following the acetyllysine. Using a fluorescence-based in vitro assay, we determined the activity for each enzyme with a limited panel of derivative substrate peptides, revealing a distinct reactivity profile for each enzyme. We mapped the interaction surface for KDAC6, KDAC8, and KDAC1 with the +1 and +2 substrate residues (with respect to acetyllysine) based on enzyme-substrate interaction pairs observed in molecular dynamics simulations. Characteristic residues in each KDAC interact preferentially with particular substrate residues and correlate with either enhanced or inhibited activity. Although nonpolar aromatic residues generally enhanced activity with all KDACs, the manner in which each enzyme interacted with these residues is distinct. Furthermore, each KDAC has distinctive interactions that correlate with lower activity, primarily ionic in nature. KDAC8 exhibited the most diverse and widest range of effects, while KDAC6 was sensitive only to the +1 position and KDAC1 selectivity was primarily driven by negative selection. The substrate preferences were validated for KDAC6 and KDAC8 using a set of peptides derived from known acetylated proteins. Overall, we determined how KDAC6, KDAC8, and KDAC1 achieve substrate specificity with residues following the acetyllysine. These new insights into KDAC specificity will be critical for identifying novel substrates of particular KDACs, designing KDAC-specific inhibitors, and demonstrate a general framework for understanding substrate specificity for other enzyme classes.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Kiara E Bornes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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Herath KE, Kodikara IKM, Pflum MKH. Proteomics-based trapping with single or multiple inactive mutants reproducibly profiles histone deacetylase 1 substrates. J Proteomics 2023; 274:104807. [PMID: 36587730 DOI: 10.1016/j.jprot.2022.104807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
Histone deacetylase 1 (HDAC1) plays a key role in diverse cellular processes. With the aberrant expression of HDAC1 linked to many diseases, including cancers, HDAC inhibitors have been used successfully as therapeutics. HDAC1 has been predominantly associated with histone deacetylation and gene expression. Recently, non-histone substrates have revealed diverse roles of HDAC1 beyond epigenetics. To augment discovery of non-histone substrates, we introduced "substrate trapping" to enrich HDAC1 substrates using an inactive mutant. Herein, we performed a series of proteomics studies to test the robustness of HDAC1 substrate trapping. Based on our recent results documenting that different HDAC1 mutants preferentially bound different substrates, which suggested that multiple mutants could be used for efficient trapping, trapping with three single point mutants simultaneously identified several potential substrates uniquely compared to a single mutant alone. However, a greater number of biologically interesting hits were observed using only a single mutant, which suggests that the C151A HDAC1 mutant is the optimal trap. Importantly, comparing independent trials with a single mutant performed by different experimentalists and HEK293 cell populations, trapping was robust and reproducible. Based on the reproducible trapping data, carnosine N-methyltransferase 1 (CARNMT1) was validated as an HDAC1 substrate. The data document that mutant trapping is an effective method for discovery of unanticipated HDAC substrates. SIGNIFICANCE: Histone deacetylase (HDAC) proteins are well established epigenetic transcriptional regulators that deacetylate histone substrates to control gene expression. More recently, deacetylation of non-histone substrates has linked HDAC activity to functions outside of epigenetics. Given the use of HDAC inhibitor drugs as anti-cancer therapeutics, understanding the full functions of HDAC proteins in cell biology is essential to future drug design. To discover unanticipated non-histone substrates and further characterize HDAC functions, inactive mutants have been used to "trap" putative substrates, which were identified with mass spectrometry-based proteomics analysis. Here multiple trapping studies were performed to test the robustness of using inactive mutants and proteomics for HDAC substrate discovery. The data confirm the value of trapping mutants as effective tools to discover HDAC substrates and link HDAC activity to unexpected biological functions.
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Affiliation(s)
- Kavinda E Herath
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, United States of America
| | - Ishadi K M Kodikara
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, United States of America
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, United States of America.
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HAT- and HDAC-Targeted Protein Acetylation in the Occurrence and Treatment of Epilepsy. Biomedicines 2022; 11:biomedicines11010088. [PMID: 36672596 PMCID: PMC9856006 DOI: 10.3390/biomedicines11010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Epilepsy is a common and severe chronic neurological disorder. Recently, post-translational modification (PTM) mechanisms, especially protein acetylation modifications, have been widely studied in various epilepsy models or patients. Acetylation is regulated by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs catalyze the transfer of the acetyl group to a lysine residue, while HDACs catalyze acetyl group removal. The expression of many genes related to epilepsy is regulated by histone acetylation and deacetylation. Moreover, the acetylation modification of some non-histone substrates is also associated with epilepsy. Various molecules have been developed as HDAC inhibitors (HDACi), which have become potential antiepileptic drugs for epilepsy treatment. In this review, we summarize the changes in acetylation modification in epileptogenesis and the applications of HDACi in the treatment of epilepsy as well as the mechanisms involved. As most of the published research has focused on the differential expression of proteins that are known to be acetylated and the knowledge of whole acetylome changes in epilepsy is still minimal, a further understanding of acetylation regulation will help us explore the pathological mechanism of epilepsy and provide novel ideas for treating epilepsy.
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11
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Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
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Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
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12
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Identification of novel HDAC8 selective inhibitors through ligand and structure based studies: Exploiting the acetate release channel differences among class I isoforms. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 271] [Impact Index Per Article: 135.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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14
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Pagliazzo L, Caby S, Lancelot J, Salomé-Desnoulez S, Saliou JM, Heimburg T, Chassat T, Cailliau K, Sippl W, Vicogne J, Pierce RJ. Histone deacetylase 8 interacts with the GTPase SmRho1 in Schistosoma mansoni. PLoS Negl Trop Dis 2021; 15:e0009503. [PMID: 34843489 PMCID: PMC8670706 DOI: 10.1371/journal.pntd.0009503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/14/2021] [Accepted: 10/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Schistosoma mansoni histone deacetylase 8 (SmHDAC8) has elicited considerable interest as a target for drug discovery. Invalidation of its transcripts by RNAi leads to impaired survival of the worms in infected mice and its inhibition causes cell apoptosis and death. To determine why it is a promising therapeutic target the study of the currently unknown cellular signaling pathways involving this enzyme is essential. Protein partners of SmHDAC8 were previously identified by yeast two-hybrid (Y2H) cDNA library screening and by mass spectrometry (MS) analysis. Among these partners we characterized SmRho1, the schistosome orthologue of human RhoA GTPase, which is involved in the regulation of the cytoskeleton. In this work, we validated the interaction between SmHDAC8 and SmRho1 and explored the role of the lysine deacetylase in cytoskeletal regulation. Methodology/principal findings We characterized two isoforms of SmRho1, SmRho1.1 and SmRho1.2. Co- immunoprecipitation (Co-IP)/Mass Spectrometry (MS) analysis identified SmRho1 partner proteins and we used two heterologous expression systems (Y2H assay and Xenopus laevis oocytes) to study interactions between SmHDAC8 and SmRho1 isoforms. To confirm SmHDAC8 and SmRho1 interaction in adult worms and schistosomula, we performed Co-IP experiments and additionally demonstrated SmRho1 acetylation using a Nano LC-MS/MS approach. A major impact of SmHDAC8 in cytoskeleton organization was documented by treating adult worms and schistosomula with a selective SmHDAC8 inhibitor or using RNAi followed by confocal microscopy. Conclusions/significance Our results suggest that SmHDAC8 is involved in cytoskeleton organization via its interaction with the SmRho1.1 isoform. The SmRho1.2 isoform failed to interact with SmHDAC8, but did specifically interact with SmDia suggesting the existence of two distinct signaling pathways regulating S. mansoni cytoskeleton organization via the two SmRho1 isoforms. A specific interaction between SmHDAC8 and the C-terminal moiety of SmRho1.1 was demonstrated, and we showed that SmRho1 is acetylated on K136. SmHDAC8 inhibition or knockdown using RNAi caused extensive disruption of schistosomula actin cytoskeleton. Schistosoma mansoni is the major parasitic platyhelminth species causing intestinal schistosomiasis. Currently one drug, praziquantel, is the treatment of choice but its use in mass treatment programs means that the development of resistance is likely and renders imperative the development of new therapeutic agents. As new potential targets we have focused on lysine deacetylases, and in particular S. mansoni histone deacetylase 8 (SmHDAC8). Previous studies showed that reduction in the level of transcripts of SmHDAC8 by RNAi led to the impaired survival of the worms after the infection of mice. The analysis of the 3D structure of SmHDAC8 by X-ray crystallography showed that the catalytic domain structure diverges significantly from that of human HDAC8 and this was exploited to develop novel potential anti-schistosomal drugs. The biological roles of SmHDAC8 are unknown. For this reason, we previously characterized its protein binding partners and identified the schistosome orthologue of the human RhoA GTPase, suggesting the involvement of SmHDAC8 in the modulation of cytoskeleton organization. Here we investigated the interaction between SmHDAC8 and SmRho1 and identified two SmRho1 isoforms (SmRho1.1 and SmRho1.2). Our study showed that SmHDAC8 is involved in schistosome cytoskeleton organization.
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Affiliation(s)
- Lucile Pagliazzo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Stéphanie Caby
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Julien Lancelot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | | | - Jean-Michel Saliou
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Tino Heimburg
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Thierry Chassat
- Institut Pasteur de Lille - PLEHTA (Plateforme d’expérimentation et de Haute Technologie Animale), Lille, France
| | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (JV); (RJP)
| | - Raymond J. Pierce
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (JV); (RJP)
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15
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Toro TB, Swanier JS, Bezue JA, Broussard CG, Watt TJ. Lysine Deacetylase Substrate Selectivity: A Dynamic Ionic Interaction Specific to KDAC8. Biochemistry 2021; 60:2524-2536. [PMID: 34357750 DOI: 10.1021/acs.biochem.1c00384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lysine acetylation and deacetylation are critical for regulation of many cellular proteins. Despite the importance of this cycle, it is unclear how lysine deacetylase (KDAC) family members discriminate between acetylated proteins to react with a discrete set of substrates. Potential short-range interactions between KDAC8 and a known biologically relevant peptide substrate were identified using molecular dynamics (MD) simulations. Activity assays with a panel of peptides derived from this substrate supported a putative ionic interaction between arginine at the -1 substrate position and KDAC8 D101. Additional assays and MD simulations confirmed this novel interaction, which promotes deacetylation of substrates. Verification that a negatively charged residue at the 101 position is necessary for the ionic interaction and observed reactivity with the substrates was performed using KDAC8 derivatives. Notably, this interaction is specific to KDAC8, as KDAC1 and KDAC6 do not form this interaction and each KDAC has a different specificity profile with the peptide substrates, even though all KDACs could potentially form ionic interactions. When reacted with a panel of putative human KDAC substrates, KDAC8 preferentially deacetylated substrates containing an arginine at the -1 position. KDAC8 D101-R(-1) is a specific enzyme-substrate interaction that begins to explain how KDACs discriminate between potential substrates and how different KDAC family members can react with different subsets of acetylated proteins in cells. This multi-pronged approach will be extended to identify other critical interactions for KDAC8 substrate binding and determine critical interactions for other KDACs.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Jordan S Swanier
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Jada A Bezue
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Christian G Broussard
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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16
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Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM. A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat Commun 2020; 11:5783. [PMID: 33188197 PMCID: PMC7666118 DOI: 10.1038/s41467-020-19529-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor (https://bioconductor.org/packages/TPP2D). We hope that our method will facilitate prioritizing targets from thermal profiling experiments. 2D-thermal proteome profiling (2D-TPP) is a powerful assay for probing interactions of proteins with small molecules in their native context. Here the authors provide a statistical method for false discovery rate controlled analysis for 2D-TPP applications.
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Affiliation(s)
- Nils Kurzawa
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, 69120, Germany
| | - Isabelle Becher
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Sindhuja Sridharan
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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17
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Jänsch N, Sugiarto WO, Muth M, Kopranovic A, Desczyk C, Ballweg M, Kirschhöfer F, Brenner‐Weiss G, Meyer‐Almes F. Switching the Switch: Ligand Induced Disulfide Formation in HDAC8. Chemistry 2020; 26:13249-13255. [PMID: 32428298 PMCID: PMC7692948 DOI: 10.1002/chem.202001712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/11/2020] [Indexed: 01/10/2023]
Abstract
Human histone deacetylase 8 is a well-recognized target for T-cell lymphoma and particularly childhood neuroblastoma. PD-404,182 was shown to be a selective covalent inhibitor of HDAC8 that forms mixed disulfides with several cysteine residues and is also able to transform thiol groups to thiocyanates. Moreover, HDAC8 was shown to be regulated by a redox switch based on the reversible formation of a disulfide bond between cysteines Cys102 and Cys153 . This study on the distinct effects of PD-404,182 on HDAC8 reveals that this compound induces the dose-dependent formation of intramolecular disulfide bridges. Therefore, the inhibition mechanism of HDAC8 by PD-404,182 involves both, covalent modification of thiols as well as ligand mediated disulfide formation. Moreover, this study provides a deep molecular insight into the regulation mechanism of HDAC8 involving several cysteines with graduated capability to form reversible disulfide bridges.
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Affiliation(s)
- Niklas Jänsch
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
| | - Wisely Oki Sugiarto
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
| | - Marius Muth
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
- Institute of Functional Interfaces (IFG)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz Platz-176334Eggenstein-LeopoldshafenGermany
| | - Aleksandra Kopranovic
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
| | - Charlotte Desczyk
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
| | - Matthias Ballweg
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
| | - Frank Kirschhöfer
- Institute of Functional Interfaces (IFG)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz Platz-176334Eggenstein-LeopoldshafenGermany
| | - Gerald Brenner‐Weiss
- Institute of Functional Interfaces (IFG)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz Platz-176334Eggenstein-LeopoldshafenGermany
| | - Franz‐Josef Meyer‐Almes
- Department of Chemical Engineering and BiotechnologyUniversity of Applied Sciences DarmstadtStephanstraße 764295DarmstadtGermany
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18
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Spreafico M, Gruszka AM, Valli D, Mazzola M, Deflorian G, Quintè A, Totaro MG, Battaglia C, Alcalay M, Marozzi A, Pistocchi A. HDAC8: A Promising Therapeutic Target for Acute Myeloid Leukemia. Front Cell Dev Biol 2020; 8:844. [PMID: 33015043 PMCID: PMC7498549 DOI: 10.3389/fcell.2020.00844] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/06/2020] [Indexed: 12/23/2022] Open
Abstract
Histone deacetylase 8 (HDAC8), a class I HDAC that modifies non-histone proteins such as p53, is highly expressed in different hematological neoplasms including a subtype of acute myeloid leukemia (AML) bearing inversion of chromosome 16 [inv(16)]. To investigate HDAC8 contribution to hematopoietic stem cell maintenance and myeloid leukemic transformation, we generated a zebrafish model with Hdac8 overexpression and observed an increase in hematopoietic stem/progenitor cells, a phenotype that could be reverted using a specific HDAC8 inhibitor, PCI-34051 (PCI). In addition, we demonstrated that AML cell lines respond differently to PCI treatment: HDAC8 inhibition elicits cytotoxic effect with cell cycle arrest followed by apoptosis in THP-1 cells, and cytostatic effect in HL60 cells that lack p53. A combination of cytarabine, a standard anti-AML chemotherapeutic, with PCI resulted in a synergistic effect in all the cell lines tested. We, then, searched for a mechanism behind cell cycle arrest caused by HDAC8 inhibition in the absence of functional p53 and demonstrated an involvement of the canonical WNT signaling in zebrafish and in cell lines. Together, we provide the evidence for the role of HDAC8 in hematopoietic stem cell differentiation in zebrafish and AML cell lines, suggesting HDAC8 inhibition as a therapeutic target in hematological malignancies. Accordingly, we demonstrated the utility of a highly specific HDAC8 inhibition as a therapeutic strategy in combination with standard chemotherapy.
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Affiliation(s)
- Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Alicja M Gruszka
- Dipartimento di Oncologia Sperimentale, Istituto Europeo di Oncologia IRCCS, Milan, Italy
| | - Debora Valli
- Dipartimento di Oncologia Sperimentale, Istituto Europeo di Oncologia IRCCS, Milan, Italy
| | - Mara Mazzola
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | | | | | | | - Cristina Battaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Myriam Alcalay
- Dipartimento di Oncologia Sperimentale, Istituto Europeo di Oncologia IRCCS, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Anna Marozzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
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19
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Toro TB, Watt TJ. Critical review of non-histone human substrates of metal-dependent lysine deacetylases. FASEB J 2020; 34:13140-13155. [PMID: 32862458 DOI: 10.1096/fj.202001301rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal-dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large-scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC-substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non-catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell-based experimental strategies used to identify KDAC-substrate pairs and evaluate each for the purpose of directly identifying non-histone substrates of metal-dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non-histone substrate-KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well-established, while another thirteen pairs have both cell-based and in vitro evidence but lack independent replication and/or sufficient cell-based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
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20
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Du J, Li W, Liu B, Zhang Y, Yu J, Hou X, Fang H. An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators. Bioorg Med Chem 2020; 28:115607. [PMID: 32690262 DOI: 10.1016/j.bmc.2020.115607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022]
Abstract
Research interest in the development of histone deacetylase 8 (HDAC8) activators has substantially increased since loss-of-function HDAC8 mutations were found in patients with Cornelia de Lange syndrome (CdLS). A series of N-acetylthioureas (e.g., TM-2-51) have been identified as HDAC8-selective activators, among others; however, their activation mechanisms remain elusive. Herein, we performed molecular dynamics (MD) simulations and fragment-centric topographical mapping (FCTM) to investigate the mechanism of HDAC8 activation. Our results revealed that improper binding of the coumarin group of fluorescent substrates leads to the "flipping out" of catalytic residue Y306, which reduces the enzymatic activity of HDAC8 towards fluorescent substrates. A pocket between the coumarin group of the substrate and thed catalytic residue Y306 was filled with the activator TM-2-51, which not only enhanced binding between HDAC8 and the fluorescent substrate complex but also stabilized Y306 in a catalytically active conformation. Based on this newly proposed substrate-dependent activation mechanism, we performed structure-based virtual screening and successfully identified low-molecular-weight scaffolds as new HDAC8 activators.
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Affiliation(s)
- Jintong Du
- Shandong Cancer Hospital, Shandong University, Jinan, Shandong 250012, China; Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Wen Li
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Bo Liu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003, United States; NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, Shanghai 200122, China
| | - Jinming Yu
- Shandong Cancer Hospital, Shandong University, Jinan, Shandong 250012, China; Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China; Department of Chemistry, New York University, New York, NY 10003, United States.
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China.
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21
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Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability. Genes (Basel) 2020; 11:genes11050556. [PMID: 32429325 PMCID: PMC7288346 DOI: 10.3390/genes11050556] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) are evolutionary conserved enzymes which operate by removing acetyl groups from histones and other protein regulatory factors, with functional consequences on chromatin remodeling and gene expression profiles. We provide here a review on the recent knowledge accrued on the zinc-dependent HDAC protein family across different species, tissues, and human pathologies, specifically focusing on the role of HDAC inhibitors as anti-cancer agents. We will investigate the chemical specificity of different HDACs and discuss their role in the human interactome as members of chromatin-binding and regulatory complexes.
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22
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Saccoccia F, Brindisi M, Gimmelli R, Relitti N, Guidi A, Saraswati AP, Cavella C, Brogi S, Chemi G, Butini S, Papoff G, Senger J, Herp D, Jung M, Campiani G, Gemma S, Ruberti G. Screening and Phenotypical Characterization of Schistosoma mansoni Histone Deacetylase 8 ( SmHDAC8) Inhibitors as Multistage Antischistosomal Agents. ACS Infect Dis 2020; 6:100-113. [PMID: 31661956 DOI: 10.1021/acsinfecdis.9b00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Schistosomiasis (also known as bilharzia) is a neglected tropical disease caused by platyhelminths of the genus Schistosoma. The disease is endemic in tropical and subtropical areas of the world where water is infested by the intermediate parasite host, the snail. More than 800 million people live in endemic areas and more than 200 million are infected and require treatment. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment and transmission control being safe and very effective against adult worms of all the clinically relevant Schistosoma species. Unfortunately, it is ineffective on immature, juvenile worms; therefore, it does not prevent reinfection. Moreover, the risk of development and spread of drug resistance because of the widespread use of a single drug in such a large population represents a serious threat. Therefore, research aimed at identifying novel drugs to be used alone or in combination with PZQ are needed. Schistosoma mansoni histone deacetylase 8 (SmHDAC8) is a class I zinc-dependent HDAC, which is abundantly expressed in all stages of its life cycle, thus representing an interesting target for drug discovery. Through virtual screening and phenotypical characterization of selected hits, we discovered two main chemical classes of compounds characterized by the presence of a hydroxamate-based metal binding group coupled to a spiroindoline or a tricyclic thieno[3,2-b]indole core as capping groups. Some of the compounds of both classes were deeply investigated and showed to impair viability of larval, juvenile, and adult schistosomes, to impact egg production in vitro and/or to induce morphological alterations of the adult schistosome reproductive systems. Noteworthy, all of them inhibit the recombinant form of SmHDAC8 enzyme in vitro. Overall, we identified very interesting scaffolds, paving the way to the development of effective antischistosomal agents.
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Affiliation(s)
- Fulvio Saccoccia
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Margherita Brindisi
- Department of Excellence of Pharmacy, University of Napoli Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Roberto Gimmelli
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Nicola Relitti
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Alessandra Guidi
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - A Prasanth Saraswati
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Caterina Cavella
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Simone Brogi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulia Chemi
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Butini
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giuliana Papoff
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
| | - Johanna Senger
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Daniel Herp
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Sandra Gemma
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Campus A. Buzzati-Traverso, via E. Ramarini 32, 00015 Monterotondo (Rome), Italy
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23
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Wolff B, Jänsch N, Sugiarto WO, Frühschulz S, Lang M, Altintas R, Oehme I, Meyer-Almes FJ. Synthesis and structure activity relationship of 1, 3-benzo-thiazine-2-thiones as selective HDAC8 inhibitors. Eur J Med Chem 2019; 184:111756. [DOI: 10.1016/j.ejmech.2019.111756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 01/21/2023]
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24
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Leng KRW, Castañeda CA, Decroos C, Islam B, Haider SM, Christianson DW, Fierke CA. Phosphorylation of Histone Deacetylase 8: Structural and Mechanistic Analysis of the Phosphomimetic S39E Mutant. Biochemistry 2019; 58:4480-4493. [PMID: 31633931 PMCID: PMC6903415 DOI: 10.1021/acs.biochem.9b00653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylase (HDAC) enzymes that catalyze removal of acetyl-lysine post-translational modifications are frequently post-translationally modified. HDAC8 is phosphorylated within the deacetylase domain at conserved residue serine 39, which leads to decreased catalytic activity. HDAC8 phosphorylation at S39 is unique in its location and function and may represent a novel mode of deacetylation regulation. To better understand the impact of phosphorylation of HDAC8 on enzyme structure and function, we performed crystallographic, kinetic, and molecular dynamics studies of the S39E HDAC8 phosphomimetic mutant. This mutation decreases the level of deacetylation of peptides derived from acetylated nuclear and cytoplasmic proteins. However, the magnitude of the effect depends on the peptide sequence and the identity of the active site metal ion [Zn(II) vs Fe(II)], with the value of kcat/KM for the mutant decreasing 9- to >200-fold compared to that of wild-type HDAC8. Furthermore, the dissociation rate constant of the active site metal ion increases by ∼10-fold. S39E HDAC8 was crystallized in complex with the inhibitor Droxinostat, revealing that phosphorylation of S39, as mimicked by the glutamate side chain, perturbs local structure through distortion of the L1 loop. Molecular dynamics simulations of both S39E and phosphorylated S39 HDAC8 demonstrate that the perturbation of the L1 loop likely occurs because of the lost hydrogen bond between D29 and S39. Furthermore, the S39 perturbation causes structural changes that propagate through the protein scaffolding to influence function in the active site. These data demonstrate that phosphorylation plays an important regulatory role for HDAC8 by affecting ligand binding, catalytic efficiency, and substrate selectivity.
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Affiliation(s)
| | - Carol Ann Castañeda
- Interdepartmental Program in Chemical Biology, University of Michigan, 210 Washtenaw Avenue 4008 Life Sciences Institute, Ann Arbor, MI 48109
| | - Christophe Decroos
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104
| | - Barira Islam
- School of Pharmacy, University College London, 29-39 Brunswick Square London, WC1N 1AX, UK
| | - Shozeb M. Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square London, WC1N 1AX, UK
| | - David W. Christianson
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
- Interdepartmental Program in Chemical Biology, University of Michigan, 210 Washtenaw Avenue 4008 Life Sciences Institute, Ann Arbor, MI 48109
- Department of Chemistry, Texas A&M University, Jack K. Williams Administration Building, Suite 100 College Station, TX 77843
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25
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Preparation of a new construct of human histone deacetylase 8 for the crystallization of enzyme-inhibitor complexes. Methods Enzymol 2019. [PMID: 31606091 DOI: 10.1016/bs.mie.2019.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The metal-dependent histone deacetylases (HDACs) are critical regulatory enzymes that modulate myriad cellular processes. Implicated in cancer, neurodegenerative diseases, and other clinical disorders, various HDAC isozymes serve as validated drug targets. However, structural similarities among the HDAC isozymes challenge efforts in targeting a single isozyme for therapeutic intervention with an inhibitor. X-ray crystallography remains the premiere technique for studying the chemistry of isozyme-selective inhibition. While crystal structures of many HDAC-inhibitor complexes have been determined, especially with the class I isozyme HDAC8, the study of complexes with large inhibitors is complicated by flexible regions of the protein structure that can hinder crystallization. Here, we outline an approach for the identification of regions in HDAC8 that may hinder crystallization. We also describe protocols for the design and preparation of a truncated HDAC8 construct, HDAC8374, that enabled the successful crystallization and structure determination of the HDAC8-Trapoxin A complex at 1.24Å resolution.
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26
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Zhu YJ, Xu Q, Shao MY, Cao XY, Wu ZR, Chen YW, Bu H, Shi YJ. Decreased expression of HDAC8 indicates poor prognosis in patients with intrahepatic cholangiocarcinoma. Hepatobiliary Pancreat Dis Int 2019; 18:464-470. [PMID: 31402267 DOI: 10.1016/j.hbpd.2019.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 07/17/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is a highly malignant primary tumor in the liver, and the rates of incidence and mortality are rapidly increasing globally. Histone deacetylase 8 (HDAC8) is a transcriptional regulator and is associated with tumorigenesis of several tumor types. This study aimed to evaluate the correlation between HDAC8 expression and clinicopathological parameters in ICC patients. METHODS ICC tissues and corresponding nonmalignant bile duct tissues were obtained from 60 patients. HDAC8 and Ki-67 expression were evaluated by immunohistochemistry staining. HDAC8 expression and the clinicopathological features and prognosis of the patients were analyzed. The mRNA level of HDAC8 in ICC was further analyzed using data from The Cancer Genome Atlas (TCGA). RESULTS The expression of HDAC8 were lower in ICC tissues (39/60, 65%) than in the corresponding nonmalignant bile duct tissues (54/60, 90%) (P = 0.001). Low HDAC8 expression in ICC was significantly associated with lymph node metastases (47.6% vs. 17.9%, P = 0.015). In addition, the positive cells rate of HDAC8 was statistically and negatively correlated with the Ki-67 index in ICC lesions (r = -0.7660, P < 0.001). Importantly, the overall survival rate and recurrence-free survival rate in ICC patients with low HDAC8 expression were lower than those with high HDAC8 expression (P = 0.008 and P = 0.011, respectively). CONCLUSIONS Decreased HDAC8 expression in ICC is related to poor prognosis, and HDAC8 may be an independent prognostic indicator of ICC patients after curative resection.
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Affiliation(s)
- Yong-Jie Zhu
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qing Xu
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming-Yang Shao
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiao-Yue Cao
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen-Ru Wu
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China
| | - Yu-Wei Chen
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hong Bu
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yu-Jun Shi
- Laboratory of Pathology, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, China; Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu 610041, China.
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27
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Peng X, Liao G, Sun P, Yu Z, Chen J. An Overview of HDAC Inhibitors and their Synthetic Routes. Curr Top Med Chem 2019; 19:1005-1040. [DOI: 10.2174/1568026619666190227221507] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 01/19/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
Epigenetics play a key role in the origin, development and metastasis of cancer. Epigenetic processes include DNA methylation, histone acetylation, histone methylation, and histone phosphorylation, among which, histone acetylation is the most common one that plays important roles in the regulation of normal cellular processes, and is controlled by histone deacetylases (HDACs) and histone acetyltransferases (HATs). HDACs are involved in the regulation of many key cellular processes, such as DNA damage repair, cell cycle control, autophagy, metabolism, senescence and chaperone function, and can lead to oncogene activation. As a result, HDACs are considered to be an excellent target for anti-cancer therapeutics like histone deacetylase inhibitors (HDACi) which have attracted much attention in the last decade. A wide-ranging knowledge of the role of HDACs in tumorigenesis, and of the action of HDACi, has been achieved. The primary purpose of this paper is to summarize recent HDAC inhibitors and the synthetic routes as well as to discuss the direction for the future development of new HDAC inhibitors.
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Affiliation(s)
- Xiaopeng Peng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Guochao Liao
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
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28
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Meyer-Almes FJ. Determination of the binding mechanism of histone deacetylase inhibitors. Chem Biol Drug Des 2019; 93:1214-1250. [PMID: 30480375 DOI: 10.1111/cbdd.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
This article places its focus on methods and tools enabling the elucidation of the mechanism by which ligands, small-molecule inhibitors, or substrates interact with zinc-containing bacterial or human members of the histone deacetylase family (HDACs). These methods include biochemical and biophysical approaches and can be subdivided into equilibrium and kinetic methods. More information about the exact mode of action can be obtained by combining these methods with specific mutant variants of the enzymes and/or series of structural similar ligands. All available equilibrium and kinetic data including additional information from 3D structures of HDAC-ligand complexes can be beneficially combined in a data analysis procedure called Integrated Global-Fit analysis eventually providing the most likely binding mechanism.
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Affiliation(s)
- Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Darmstadt, Germany
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29
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Uba AI, Weako J, Keskin Ö, Gürsoy A, Yelekçi K. Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:1751-1760. [PMID: 31057077 DOI: 10.1080/07391102.2019.1615989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Histone deacetylase (HDAC) 8 has been implicated as a potential therapeutic target in a variety of cancers, neurodegenerative disorders, metabolic dysregulation and autoimmune and inflammatory diseases. Several nonselective HDAC inhibitors have been co-crystallized with HDAC8. Molecular dynamics (MD) studies may yield valuable information on the structural stabilities of the complexes over time as determined by various pharmacophore features of the co-crystallized inhibitors. Here, using 11 unmodified X-ray crystal structures of human HDAC8 (complexes) structure-based pharmacophore models were built and clustered based on distance - a function of the number of common pharmacophore features and the root-mean-squared displacement between the matching features. Based on this information, a total of seven complexes (1T64, 1W22, 3RQD, 3SFF, 3F0R, 5VI6 and 5FCW) were submitted to unrestrained 50 ns-MD simulations using nanoscale MD (NAMD) software. 1T64 (HDAC8 in complex with TSA) was found to show the highest stability over time, presumably because of the TSA's ability to span HDAC8 catalytic channel and form a strong ionic interaction with zinc metal ion. Other stable complexes were 1W22, 3SFF, 3F0R and 5FCW. However, 3RQD and 5VI6 showed relative instability over 50 ns time period. This may be attributed to bulkiness of the capping groups of both largazole thiol and trapoxin A, making them unable to fit well into the active site of HDAC8. They rather formed steric clashes with residues on loop regions near the entrance to the channel. Thus, 1T64 and similar crystal structures may be good candidates for HDAC8 structural dynamics studies and inhibitor design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
| | - Jackson Weako
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Özlem Keskin
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Attila Gürsoy
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
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30
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Porter NJ, Christianson DW. Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases. Curr Opin Struct Biol 2019; 59:9-18. [PMID: 30743180 DOI: 10.1016/j.sbi.2019.01.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Nicholas J Porter
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States.
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31
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Nalawansha DA, Zhang Y, Herath K, Pflum MKH. HDAC1 Substrate Profiling Using Proteomics-Based Substrate Trapping. ACS Chem Biol 2018; 13:3315-3324. [PMID: 30421914 PMCID: PMC6563814 DOI: 10.1021/acschembio.8b00737] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylase (HDAC) proteins are overexpressed in multiple diseases, including cancer, and have emerged as anticancer drug targets. HDAC proteins regulate cellular processes, such as the cell cycle, apoptosis, and cell proliferation, by deacetylating histone and non-histone substrates. Although a plethora of acetylated proteins have been identified using large-scale proteomic approaches, the HDAC proteins responsible for their dynamic deacetylation have been poorly studied. For example, few substrates of HDAC1 have been identified, which is mainly due to the scarcity of substrate identification tools. We recently developed a mutant trapping strategy to identify novel substrates of HDAC1. Herein, we introduce an improved version of the trapping method that uses mass spectrometry (MS)-based proteomics to identify multiple substrates simultaneously. Among the substrate hits, CDK1, AIFM1, MSH6, and RuvB-like 1 were identified as likely HDAC1 substrates. These newly discovered HDAC1 substrates are involved in various biological processes, suggesting novel functions of HDAC1 apart from epigenetics. Substrate trapping combined with MS-based proteomics provides an efficient approach to HDAC1 substrate identification and contributes to the full characterization of HDAC function in normal and disease states.
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Affiliation(s)
| | - Yuchen Zhang
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
| | - Kavinda Herath
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202
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32
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Murray LA, Sheng X, Cristea IM. Orchestration of protein acetylation as a toggle for cellular defense and virus replication. Nat Commun 2018; 9:4967. [PMID: 30470744 PMCID: PMC6251895 DOI: 10.1038/s41467-018-07179-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Emerging evidence highlights protein acetylation, a prevalent lysine posttranslational modification, as a regulatory mechanism and promising therapeutic target in human viral infections. However, how infections dynamically alter global cellular acetylation or whether viral proteins are acetylated remains virtually unexplored. Here, we establish acetylation as a highly-regulated molecular toggle of protein function integral to the herpesvirus human cytomegalovirus (HCMV) replication. We offer temporal resolution of cellular and viral acetylations. By interrogating dynamic protein acetylation with both protein abundance and subcellular localization, we discover finely tuned spatial acetylations across infection time. We determine that lamin acetylation at the nuclear periphery protects against virus production by inhibiting capsid nuclear egress. Further studies within infectious viral particles identify numerous acetylations, including on the viral transcriptional activator pUL26, which we show represses virus production. Altogether, this study provides specific insights into functions of cellular and viral protein acetylations and a valuable resource of dynamic acetylation events. The dynamics of protein acetylation during infection remains unexplored. Here, Murray et al. characterize spatio-temporal acetylations of both cellular and viral proteins during HCMV infection, providing new functional insights into the host-virus acetylome that might help identify new antiviral targets.
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Affiliation(s)
- L A Murray
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - X Sheng
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - I M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA.
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33
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Jänsch N, Meyners C, Muth M, Kopranovic A, Witt O, Oehme I, Meyer-Almes FJ. The enzyme activity of histone deacetylase 8 is modulated by a redox-switch. Redox Biol 2018; 20:60-67. [PMID: 30292946 PMCID: PMC6174833 DOI: 10.1016/j.redox.2018.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 01/05/2023] Open
Abstract
Enzymes from the histone deacetylase (HDAC) family are highly regulated by different mechanisms. However, only very limited knowledge exists about the regulation of HDAC8, an established target in multiple types of cancer. A previous dedicated study of HDAC class I enzymes identified no redox-sensitive cysteinyl thiol in HDAC8. This is in contrast to the observation that HDAC8 preparations show different enzyme activities depending on the addition of reducing agents. In the light of the importance of HDAC8 in tumorigenesis a possible regulation by redox signaling was investigated using biochemical and biophysical methods combined with site directed mutagenesis. The occurrence of a characteristic disulfide bond under oxidizing conditions is associated with a complete but reversible loss of enzyme activity. Cysteines 102 and 153 are the integral components of the redox-switch. A possible regulation of HDAC8 by redox signal transduction is suggested by the observed relationship between inhibition of reactive oxygen species generating NOX and concomitant increased HDAC8 activity in neuroblastoma tumor cells. The slow kinetics for direct oxidation of HDAC8 by hydrogen peroxide suggests that transmitters of oxidative equivalents are required to transfer the H2O2 signal to HDAC8.
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Affiliation(s)
- Niklas Jänsch
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Christian Meyners
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Marius Muth
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Aleksandra Kopranovic
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Olaf Witt
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, D-69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany; German Cancer Research Consortium (DKTK), Germany
| | - Ina Oehme
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, D-69120 Heidelberg, Germany; German Cancer Research Consortium (DKTK), Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany.
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34
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Ferrari L, Bragato C, Brioschi L, Spreafico M, Esposito S, Pezzotta A, Pizzetti F, Moreno‐Fortuny A, Bellipanni G, Giordano A, Riva P, Frabetti F, Viani P, Cossu G, Mora M, Marozzi A, Pistocchi A. HDAC8 regulates canonical Wnt pathway to promote differentiation in skeletal muscles. J Cell Physiol 2018; 234:6067-6076. [DOI: 10.1002/jcp.27341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Cinzia Bragato
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
- PhD Program in Neuroscience, University of Milano‐Bicocca Milano Italy
| | - Loredana Brioschi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Simona Esposito
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Alex Pezzotta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Fabrizio Pizzetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Artal Moreno‐Fortuny
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
- Developmental Genetics, Department of Biomedicine University of Basel Basel Switzerland
| | - Gianfranco Bellipanni
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
- Department of Medicine Surgery & Neuroscience, University of Siena Siena Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Flavia Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Paola Viani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
| | - Anna Marozzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
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35
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Ha SD, Solomon O, Akbari M, Sener A, Kim SO. Histone deacetylase 8 protects human proximal tubular epithelial cells from hypoxia-mimetic cobalt- and hypoxia/reoxygenation-induced mitochondrial fission and cytotoxicity. Sci Rep 2018; 8:11332. [PMID: 30054507 PMCID: PMC6063935 DOI: 10.1038/s41598-018-29463-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023] Open
Abstract
Cell death by hypoxia followed by reoxygenation (H/R) is responsible for tissue injury in multiple pathological conditions. Recent studies found that epigenetic reprogramming mediated by histone deacetylases (HDACs) is implicated in H/R-induced cell death. However, among 18 different isoforms comprising 4 classes (I-IV), the role of each HDAC in cell death is largely unknown. This study examined the role of HDAC8, which is the most distinct isoform of class I, in the hypoxia mimetic cobalt- and H/R-induced cytotoxicity of human proximal tubular HK-2 cells. Using the HDAC8-specific activator TM-2-51 (TM) and inhibitor PCI34051, we found that HDAC8 played a protective role in cytotoxicity. TM or overexpression of wild-type HDAC8, but not a deacetylase-defective HDAC8 mutant, prevented mitochondrial fission, loss of mitochondrial transmembrane potential and release of cytochrome C into the cytoplasm. TM suppressed expression of dynamin-related protein 1 (DRP1) which is a key factor required for mitochondrial fission. Suppression of DRP1 by HDAC8 was likely mediated by decreasing the level of acetylated histone H3 lysine 27 (a hallmark of active promoters) at the DRP1 promoter. Collectively, this study shows that HDAC8 inhibits cytotoxicity induced by cobalt and H/R, in part, through suppressing DRP1 expression and mitochondrial fission.
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Affiliation(s)
- Soon-Duck Ha
- Department of Microbiology & Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, 1400 Western Road, London, Ontario, N6G 2V4, Canada
| | - Ori Solomon
- Department of Microbiology & Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, 1400 Western Road, London, Ontario, N6G 2V4, Canada
| | - Masoud Akbari
- Department of Microbiology & Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, 1400 Western Road, London, Ontario, N6G 2V4, Canada
- Department of Surgery, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Alp Sener
- Department of Microbiology & Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, 1400 Western Road, London, Ontario, N6G 2V4, Canada
- Department of Surgery, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Sung Ouk Kim
- Department of Microbiology & Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, 1400 Western Road, London, Ontario, N6G 2V4, Canada.
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36
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Vanaja GR, Ramulu HG, Kalle AM. Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6. Cell Commun Signal 2018; 16:20. [PMID: 29716651 PMCID: PMC5930436 DOI: 10.1186/s12964-018-0231-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/13/2018] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) are involved in epigenetic gene regulation via deacetylation of acetylated lysine residues of both histone and non-histone proteins. Among the 18 HDACs identified in humans, HDAC8, a class I HDAC, is best understood structurally and enzymatically. However, its precise subcellular location, function in normal cellular physiology, its protein partners and substrates still remain elusive. METHODS The subcellular localization of HDAC8 was studied using immunofluorescence and confocal imaging. The binding parterns were identified employing immunoprecipitation (IP) followed by MALDI-TOF analysis and confirmed using in-silico protein-protein interaction studies, HPLC-based in vitro deacetylation assay, intrinsic fluorescence spectrophotometric analysis, Circular dichroism (CD) and Surface Plasmon Resonance (SPR). Functional characterization of the binding was carried out using immunoblot and knockdown by siRNA. Using one way ANOVA statistical significance (n = 3) was determined. RESULTS Here, we show that HDAC8 and its phosphorylated form (pHDAC8) localized predominantly in the cytoplasm in cancerous, HeLa, and non-cancerous (normal), HEK293T, cells, although nucleolar localization was observed in HeLa cells. The study identified Alpha tubulin as a novel interacting partner of HDAC8. Further, the results indicated binding and deacetylation of tubulin at ac-lys40 by HDAC8. Knockdown of HDAC8 by siRNA, inhibition of HDAC8 and/or HDAC6 by PCI-34051 and tubastatin respectively, cell-migration, cell morphology and cell cycle analysis clearly explained HDAC8 as tubulin deacetylase in HeLa cells and HDAC6 in HEK 293 T cells. CONCLUSIONS HDAC8 shows functional redundancy with HDAC6 when overexpressed in cervical cancer cells, HeLa, and deacetylaes ac-lys40 of alpha tubulin leading to cervical cancer proliferation and progression.
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Affiliation(s)
- G R Vanaja
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, TS, 500046, India
| | | | - Arunasree M Kalle
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, TS, 500046, India.
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37
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A kinome-wide RNAi screen identifies ALK as a target to sensitize neuroblastoma cells for HDAC8-inhibitor treatment. Cell Death Differ 2018. [PMID: 29515255 PMCID: PMC6261943 DOI: 10.1038/s41418-018-0080-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prognosis of advanced stage neuroblastoma patients remains poor and, despite intensive therapy, the 5-year survival rate remains less than 50%. We previously identified histone deacetylase (HDAC) 8 as an indicator of poor clinical outcome and a selective drug target for differentiation therapy in vitro and in vivo. Here, we performed kinome-wide RNAi screening to identify genes that are synthetically lethal with HDAC8 inhibitors. These experiments identified the neuroblastoma predisposition gene ALK as a candidate gene. Accordingly, the combination of the ALK/MET inhibitor crizotinib and selective HDAC8 inhibitors (3–6 µM PCI-34051 or 10 µM 20a) efficiently killed neuroblastoma cell lines carrying wildtype ALK (SK-N-BE(2)-C, IMR5/75), amplified ALK (NB-1), and those carrying the activating ALK F1174L mutation (Kelly), and, in cells carrying the activating R1275Q mutation (LAN-5), combination treatment decreased viable cell count. The effective dose of crizotinib in neuroblastoma cell lines ranged from 0.05 µM (ALK-amplified) to 0.8 µM (wildtype ALK). The combinatorial inhibition of ALK and HDAC8 also decreased tumor growth in an in vivo zebrafish xenograft model. Bioinformatic analyses revealed that the mRNA expression level of HDAC8 was significantly correlated with that of ALK in two independent patient cohorts, the Academic Medical Center cohort (n = 88) and the German Neuroblastoma Trial cohort (n = 649), and co-expression of both target genes identified patients with very poor outcome. Mechanistically, HDAC8 and ALK converge at the level of receptor tyrosine kinase (RTK) signaling and their downstream survival pathways, such as ERK signaling. Combination treatment of HDAC8 inhibitor with crizotinib efficiently blocked the activation of growth receptor survival signaling and shifted the cell cycle arrest and differentiation phenotype toward effective cell death of neuroblastoma cell lines, including sensitization of resistant models, but not of normal cells. These findings reveal combined targeting of ALK and HDAC8 as a novel strategy for the treatment of neuroblastoma.
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38
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Toro TB, Painter RG, Haynes RA, Glotser EY, Bratton MR, Bryant JR, Nichols KA, Matthew-Onabanjo AN, Matthew AN, Bratcher DR, Perry CD, Watt TJ. Purification of metal-dependent lysine deacetylases with consistently high activity. Protein Expr Purif 2018; 141:1-6. [PMID: 28843507 PMCID: PMC5624855 DOI: 10.1016/j.pep.2017.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/22/2017] [Indexed: 11/25/2022]
Abstract
Metal-dependent lysine deacetylases (KDACs) are involved in regulation of numerous biological and disease processes through control of post-translational acetylation. Characterization of KDAC activity and substrate identification is complicated by inconsistent activity of prepared enzyme and a range of multi-step purifications. We describe a simplified protocol based on two-step affinity chromatography. The purification method is appropriate for use regardless of expression host, and we demonstrate purification of several representative members of the KDAC family as well as a selection of mutated variants. The purified proteins are highly active and consistent across preparations.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Richard G Painter
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Rashad A Haynes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Elena Y Glotser
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Melyssa R Bratton
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Jenae R Bryant
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Kyara A Nichols
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Asia N Matthew-Onabanjo
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Ashley N Matthew
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Derek R Bratcher
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Chanel D Perry
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
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39
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Toro TB, Edenfield SA, Hylton BJ, Watt TJ. Chelatable trace zinc causes low, irreproducible KDAC8 activity. Anal Biochem 2018; 540-541:9-14. [PMID: 29100752 PMCID: PMC5712482 DOI: 10.1016/j.ab.2017.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/09/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022]
Abstract
Acetylation is an important regulatory mechanism in cells, and emphasis is being placed on identifying substrates and small molecule modulators of this post-translational modification. However, the reported in vitro activity of the lysine deacetylase KDAC8 is inconsistent across experimental setups, even with the same substrate, complicating progress in the field. We detected trace levels of zinc, a known inhibitor of KDAC8 when present in excess, even in high-quality buffer reagents, at concentrations that are sufficient to significantly inhibit the enzyme under common reaction conditions. We hypothesized that trace zinc in solution could account for the observed variability in KDAC8 activity. We demonstrate that addition of chelators, including BSA, EDTA, and citrate, and/or the use of a phosphate-based buffer instead of the more common tris-based buffer, eliminates the inhibition from low levels of zinc as well as the dependence of specific activity on enzyme concentration. This results in high KDAC8 activity that is consistent across buffer systems, even using low concentrations of enzyme. We report conditions that are suitable for several assays to increase both enzyme activity and reproducibility. Our results have significant implications for approaches used to identify substrates and small molecule modulators of KDAC8 and interpretation of existing data.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Samantha A Edenfield
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Brandon J Hylton
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
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40
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Castañeda CA, Wolfson NA, Leng KR, Kuo YM, Andrews AJ, Fierke CA. HDAC8 substrate selectivity is determined by long- and short-range interactions leading to enhanced reactivity for full-length histone substrates compared with peptides. J Biol Chem 2017; 292:21568-21577. [PMID: 29109148 PMCID: PMC5766737 DOI: 10.1074/jbc.m117.811026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/05/2017] [Indexed: 01/03/2023] Open
Abstract
Histone deacetylases (HDACs) catalyze deacetylation of acetyl-lysine residues within proteins. To date, HDAC substrate specificity and selectivity have been largely estimated using peptide substrates. However, it is unclear whether peptide substrates accurately reflect the substrate selectivity of HDAC8 toward full-length proteins. Here, we compare HDAC8 substrate selectivity in the context of peptides, full-length proteins, and protein-nucleic acid complexes. We demonstrate that HDAC8 catalyzes deacetylation of tetrameric histone (H3/H4) substrates with catalytic efficiencies that are 40-300-fold higher than those for corresponding peptide substrates. Thus, we conclude that additional contacts with protein substrates enhance catalytic efficiency. However, the catalytic efficiency decreases for larger multiprotein complexes. These differences in HDAC8 substrate selectivity for peptides and full-length proteins suggest that HDAC8 substrate preference is based on a combination of short- and long-range interactions. In summary, this work presents detailed kinetics for HDAC8-catalyzed deacetylation of singly-acetylated, full-length protein substrates, revealing that HDAC8 substrate selectivity is determined by multiple factors. These insights provide a foundation for understanding recognition of full-length proteins by HDACs.
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Affiliation(s)
| | | | - Katherine R Leng
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Yin-Ming Kuo
- the Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | | | - Carol A Fierke
- From the Program in Chemical Biology and
- the Departments of Biological Chemistry and
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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41
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Caby S, Pagliazzo L, Lancelot J, Saliou JM, Bertheaume N, Pierce RJ, Roger E. Analysis of the interactome of Schistosoma mansoni histone deacetylase 8. PLoS Negl Trop Dis 2017; 11:e0006089. [PMID: 29155817 PMCID: PMC5722368 DOI: 10.1371/journal.pntd.0006089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/08/2017] [Accepted: 10/31/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Histone deacetylase 8 from Schistosoma mansoni (SmHDAC8) is essential to parasite growth and development within the mammalian host and is under investigation as a target for the development of selective inhibitors as novel schistosomicidal drugs. Although some protein substrates and protein partners of human HDAC8 have been characterized, notably indicating a role in the function of the cohesin complex, nothing is known of the partners and biological function of SmHDAC8. METHODOLOGY/PRINCIPAL FINDINGS We therefore employed two strategies to characterize the SmHDAC8 interactome. We first used SmHDAC8 as a bait protein in yeast two-hybrid (Y2H) screening of an S. mansoni cDNA library. This allowed the identification of 49 different sequences encoding proteins. We next performed co-immunoprecipitation (Co-IP) experiments on parasite extracts with an anti-SmHDAC8 antibody. Mass spectrometry (MS) analysis allowed the identification of 160 different proteins. CONCLUSIONS/SIGNIFICANCE SmHDAC8 partners are involved in about 40 different processes, included expected functions such as the cohesin complex, cytoskeleton organization, transcriptional and translational regulation, metabolism, DNA repair, the cell cycle, protein dephosphorylation, proteolysis, protein transport, but also some proteasome and ribosome components were detected. Our results show that SmHDAC8 is a versatile deacetylase, potentially involved in both cytosolic and nuclear processes.
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Affiliation(s)
- Stéphanie Caby
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Lucile Pagliazzo
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Julien Lancelot
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Jean-Michel Saliou
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Nicolas Bertheaume
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Raymond J. Pierce
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
| | - Emmanuel Roger
- Univ. Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille (CIIL), F-59000 Lille, France
- * E-mail:
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42
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Lopez JE, Haynes SE, Majmudar JD, Martin BR, Fierke CA. HDAC8 Substrates Identified by Genetically Encoded Active Site Photocrosslinking. J Am Chem Soc 2017; 139:16222-16227. [PMID: 29035536 DOI: 10.1021/jacs.7b07603] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The histone deacetylase family comprises 18 enzymes that catalyze deacetylation of acetylated lysine residues; however, the specificity and substrate profile of each isozyme remains largely unknown. Due to transient enzyme-substrate interactions, conventional co-immunoprecipitation methods frequently fail to identify enzyme-specific substrates. Additionally, compensatory mechanisms often limit the ability of knockdown or chemical inhibition studies to achieve significant fold changes observed by acetylation proteomics methods. Furthermore, measured alterations do not guarantee a direct link between enzyme and substrate. Here we present a chemical crosslinking strategy that incorporates a photoreactive, non-natural amino acid, p-benzoyl-l-phenylalanine, into various positions of the structurally characterized isozyme histone deacetylase 8 (HDAC8). After covalent capture, co-immunoprecipitation, and mass spectrometric analysis, we identified a subset of HDAC8 substrates from human cell lysates, which were further validated for catalytic turnover. Overall, this chemical crosslinking approach identified novel HDAC8-specific substrates with high catalytic efficiency, thus presenting a general strategy for unbiased deacetylase substrate discovery.
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Affiliation(s)
- Jeffrey E Lopez
- Program in Chemical Biology, ‡Department of Chemistry, and §Department of Biological Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sarah E Haynes
- Program in Chemical Biology, ‡Department of Chemistry, and §Department of Biological Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Jaimeen D Majmudar
- Program in Chemical Biology, ‡Department of Chemistry, and §Department of Biological Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Brent R Martin
- Program in Chemical Biology, ‡Department of Chemistry, and §Department of Biological Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Carol A Fierke
- Program in Chemical Biology, ‡Department of Chemistry, and §Department of Biological Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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43
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Castaneda CA, Lopez JE, Joseph CG, Scholle MD, Mrksich M, Fierke CA. Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism. Biochemistry 2017; 56:5663-5670. [PMID: 28937750 DOI: 10.1021/acs.biochem.7b00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demonstrate that both HDAC8 activity and substrate selectivity for a diverse range of peptide substrates depend on the identity of the active site metal ion. Varied deacetylase activities of Fe(II)- and Zn(II)-HDAC8 toward an array of peptide substrates were identified using self-assembled monolayers for matrix-assisted laser desorption ionization (SAMDI) mass spectrometry. Subsequently, the metal dependence of deacetylation of peptides of biological interest was measured using an in vitro peptide assay. While Fe(II)-HDAC8 is generally more active than Zn(II)-HDAC8, the Fe(II)/Zn(II) HDAC8 activity ratio varies widely (from 2 to 150) among the peptides tested. These data provide support for the hypothesis that HDAC8 may undergo metal switching in vivo that, in turn, may regulate its activity. However, future studies are needed to explore the identity of the metal ion bound to HDAC8 in cells under varied conditions.
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Affiliation(s)
- Carol Ann Castaneda
- Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeffrey E Lopez
- Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Caleb G Joseph
- Department of Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Michael D Scholle
- Department of Chemistry and Department of Biomedical Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry and Department of Biomedical Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Carol A Fierke
- Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States.,Department of Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.,Department of Chemistry and Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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44
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Evolutionary relationships among protein lysine deacetylases of parasites causing neglected diseases. INFECTION GENETICS AND EVOLUTION 2017; 53:175-188. [DOI: 10.1016/j.meegid.2017.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022]
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45
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Toro TB, Bryant JR, Watt TJ. Lysine Deacetylases Exhibit Distinct Changes in Activity Profiles Due to Fluorophore Conjugation of Substrates. Biochemistry 2017; 56:4549-4558. [PMID: 28749131 PMCID: PMC5937523 DOI: 10.1021/acs.biochem.7b00270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity. Here, we have compared the activity of several KDACs, representing all major classes of KDACs, with substrates in the presence and absence of AMC as well as peptides for which tryptophan has been substituted for AMC. Our results unequivocally demonstrate that AMC has a significant effect on activity for all KDACs tested. Furthermore, in neither the nature of the effect nor the magnitude is consistent across KDACs, making it impossible to predict the effect of AMC on a particular enzyme-substrate pair. AMC did not affect acetyllysine preference in a multiply acetylated substrate. In contrast, AMC significantly enhanced KDAC6 substrate affinity, greatly reduced Sirt1 activity, eliminated the substrate sequence specificity of KDAC4, and had no consistent effect with KDAC8 substrates. These results indicate that profiling of KDAC activity with labeled peptides is unlikely to produce biologically relevant data.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Jenae R. Bryant
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
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Ha SD, Cho W, Kim SO. HDAC8 Prevents Anthrax Lethal Toxin-induced Cell Cycle Arrest through Silencing PTEN in Human Monocytic THP-1 Cells. Toxins (Basel) 2017; 9:E162. [PMID: 28509866 PMCID: PMC5450710 DOI: 10.3390/toxins9050162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 02/08/2023] Open
Abstract
Anthrax lethal toxin (LeTx) is a cytotoxic virulence factor that causes cell cycle arrest and cell death in various cell types. However, susceptibility to the cytotoxic effects varies depending on cell types. In proliferating monocytes, LeTx has only transient cytotoxic effects due to activation of the phosphoinositide 3-kinase (PI3K)-AKT-mediated adaptive responses. To date, the mechanism of LeTx in activating PI3K-AKT signaling axis is unknown. This study shows that the histone deacetylase 8 (HDAC8) is involved in activating PI3K-AKT signaling axis through down-regulating the phosphatase and tensin homolog 1 (PTEN) in human monocytic THP-1 cells. The HDAC8-specific activator TM-2-51 and inhibitor PCI-34051 enhanced and prevented, respectively, AKT activation and cell cycle progression in LeTx-treated cells. Furthermore, HDAC8 induced tri-methylation of histone H3 lysine 27 (H3K27me3), which is known to suppress PTEN expression, through at least in part down-regulating the H3K27me3 eraser Jumonji Domain Containing (JMJD) 3. Importantly, the JMJD3-specific inhibitor GSK-J4 induced AKT activation and protected cell cycle arrest in LeTx-treated cells, regardless the presence of HDAC8 activity. Collectively, this study for the first time demonstrated that HDAC8 activity determines susceptibility to cell cycle arrest induced by LeTx, through regulating the PI3K-PTEN-AKT signaling axis.
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Affiliation(s)
- Soon-Duck Ha
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6G 2V4, Canada.
| | - Woohyun Cho
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6G 2V4, Canada.
| | - Sung Ouk Kim
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6G 2V4, Canada.
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47
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Nalawansha DA, Pflum MKH. LSD1 Substrate Binding and Gene Expression Are Affected by HDAC1-Mediated Deacetylation. ACS Chem Biol 2017; 12:254-264. [PMID: 27977115 DOI: 10.1021/acschembio.6b00776] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine Specific Demethylase 1 (LSD1) catalyzes the demethylation of histone 3 to regulate gene expression. With a fundamental role in gene regulation, LSD1 is involved in multiple cellular processes, including embryonic development, cell proliferation, and metastasis. Significantly, LSD1 is overexpressed in multiple cancers and has emerged as a potential anticancer drug target. LSD1 is typically found in association with another epigenetic enzyme, histone deacetylase (HDAC). HDAC and LSD1 inhibitor compounds have been tested as combination anticancer agents. However, the functional link between LSD1 and HDAC has yet to be understood in detail. Here, we used a substrate trapping strategy to identify cellular substrates of HDAC1. Using inactive HDAC1 mutants, we identified LSD1 as an HDAC1 substrate. HDAC1 mediated deacetylation of LSD1 at K374 in the substrate binding lobe, which affected the histone 3 binding and gene expression activity of LSD1. The mechanistic link between HDAC1 and LSD1 established here suggests that HDAC inhibitors influence LSD1 activity, which will ultimately guide drug design targeting epigenetic enzymes.
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Affiliation(s)
- Dhanusha A. Nalawansha
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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48
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Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol 2017; 1561:139-169. [PMID: 28236237 DOI: 10.1007/978-1-4939-6798-8_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding. Rosetta FlexPepDock was built to generate precise models of protein-peptide complex structures, by effectively addressing the challenge of the considerable conformational flexibility of the peptide. Rosetta FlexPepBind is an extension of this protocol that allows characterizing peptide-binding affinities and specificities of various biological systems, based on the structural models generated by Rosetta FlexPepDock. We provide detailed descriptions and guidelines for the usage of these protocols, and on a specific example, we highlight the variety of different challenges that can be met and the questions that can be answered with Rosetta FlexPepDock.
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49
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Ingham O, Paranal RM, Smith WB, Escobar RA, Yueh H, Snyder T, Porco JA, Bradner JE, Beeler AB. Development of a Potent and Selective HDAC8 Inhibitor. ACS Med Chem Lett 2016; 7:929-932. [PMID: 27774131 PMCID: PMC5066159 DOI: 10.1021/acsmedchemlett.6b00239] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/19/2016] [Indexed: 12/19/2022] Open
Abstract
A novel, isoform-selective inhibitor of histone deacetylase 8 (HDAC8) has been discovered by the repurposing of a diverse compound collection. Medicinal chemistry optimization led to the identification of a highly potent (0.8 nM) and selective inhibitor of HDAC8.
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Affiliation(s)
- Oscar
J. Ingham
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ronald M. Paranal
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
| | - William B. Smith
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
| | - Randolph A. Escobar
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Han Yueh
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tracy Snyder
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John A. Porco
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - James E. Bradner
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aaron B. Beeler
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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50
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Targeting histone deacetylase 8 as a therapeutic approach to cancer and neurodegenerative diseases. Future Med Chem 2016; 8:1609-34. [PMID: 27572818 DOI: 10.4155/fmc-2016-0117] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Histone deacetylase 8 (HDAC8), a unique class I zinc-dependent HDAC, is an emerging target in cancer and other diseases. Its substrate repertoire extends beyond histones to many nonhistone proteins. Besides being a deacetylase, HDAC8 also mediates signaling via scaffolding functions. Aberrant expression or deregulated interactions with transcription factors are critical in HDAC8-dependent cancers. Many potent HDAC8-selective inhibitors with cellular activity and anticancer effects have been reported. We present HDAC8 as a druggable target and discuss inhibitors of different chemical scaffolds with cellular effects. Furthermore, we review HDAC8 activators that revert activity of mutant enzymes. Isotype-selective HDAC8 targeting in patients with HDAC8-relevant cancers is challenging, however, is promising to avoid adverse side effects as observed with pan-HDAC inhibitors.
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