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Fang H, Li M, Yang J, Ma S, Zhang L, Yang H, Tang Q, Cao J, Yang W. Repressing iron overload ameliorates central post-stroke pain via the Hdac2-Kv1.2 axis in a rat model of hemorrhagic stroke. Neural Regen Res 2024; 19:2708-2722. [PMID: 38595289 PMCID: PMC11168507 DOI: 10.4103/nrr.nrr-d-23-01498] [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: 09/06/2023] [Revised: 11/21/2023] [Accepted: 02/04/2024] [Indexed: 04/11/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202412000-00027/figure1/v/2024-04-08T165401Z/r/image-tiff Thalamic hemorrhage can lead to the development of central post-stroke pain. Changes in histone acetylation levels, which are regulated by histone deacetylases, affect the excitability of neurons surrounding the hemorrhagic area. However, the regulatory mechanism of histone deacetylases in central post-stroke pain remains unclear. Here, we show that iron overload leads to an increase in histone deacetylase 2 expression in damaged ventral posterolateral nucleus neurons. Inhibiting this increase restored histone H3 acetylation in the Kcna2 promoter region of the voltage-dependent potassium (Kv) channel subunit gene in a rat model of central post-stroke pain, thereby increasing Kcna2 expression and relieving central pain. However, in the absence of nerve injury, increasing histone deacetylase 2 expression decreased Kcna2 expression, decreased Kv current, increased the excitability of neurons in the ventral posterolateral nucleus area, and led to neuropathic pain symptoms. Moreover, treatment with the iron chelator deferiprone effectively reduced iron overload in the ventral posterolateral nucleus after intracerebral hemorrhage, reversed histone deacetylase 2 upregulation and Kv1.2 downregulation, and alleviated mechanical hypersensitivity in central post-stroke pain rats. These results suggest that histone deacetylase 2 upregulation and Kv1.2 downregulation, mediated by iron overload, are important factors in central post-stroke pain pathogenesis and could serve as new targets for central post-stroke pain treatment.
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Affiliation(s)
- He Fang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengjie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jingchen Yang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shunping Ma
- Department of Nutrition, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Li Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Hongqi Yang
- Department of Neurology, Henan Provincial People’s Hospital, Zhengzhou, Henan Province, China
| | - Qiongyan Tang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Cao
- Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
- Neuroscience Research Institute, Zhengzhou University Academy of Medical Sciences, Zhengzhou, Henan Province, China
| | - Weimin Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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2
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Elitt CM, Ross MM, Wang J, Fahrni CJ, Rosenberg PA. Developmental regulation of zinc homeostasis in differentiating oligodendrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550230. [PMID: 37546881 PMCID: PMC10402100 DOI: 10.1101/2023.07.26.550230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Oligodendrocytes develop through well characterized stages and understanding pathways regulating their differentiation remains an active area of investigation. Zinc is required for the function of many enzymes, proteins and transcription factors, including those important in myelination and mitosis. Our previous studies using the ratiometric zinc sensor chromis-1 demonstrated a reduction in intracellular free zinc concentrations in mature oligodendrocytes compared with earlier stages (Bourassa et al., 2018). We performed a more detailed developmental study to better understand the temporal course of zinc homeostasis across the oligodendrocyte lineage. Using chromis-1, we found a transient increase in free zinc after developing oligodendrocytes were switched into differentiation medium. To gather other evidence for dynamic regulation of free zinc during oligodendrocyte development, qPCR was used to evaluate mRNA expression of the major zinc storage proteins metallothioneins (MTs), and metal regulatory transcription factor 1 (MTF-1) which controls expression of MTs. MT-1, MT-2 and MTF1 mRNAs were all increased several fold in mature oligodendrocytes compared to developing oligodendrocytes. To assess the depth of the zinc buffer, we assayed zinc release from intracellular stores using the oxidizing thiol reagent 2,2'-dithiodipyridine (DTDP). Exposure to DTDP resulted in a ∼100% increase in free zinc in developing oligodendrocytes but, paradoxically more modest ∼60% increase in mature oligodendrocytes despite the increased expression of MTs. These results suggest that zinc homeostasis is regulated during oligodendrocyte development, that oligodendrocytes are a useful model for studying zinc homeostasis in the central nervous system, and that regulation of zinc homeostasis may be important in oligodendrocyte differentiation.
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3
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How Theoretical Evaluations Can Generate Guidelines for Designing/Engineering Metalloproteins with Desired Metal Affinity and Selectivity. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010249. [PMID: 36615442 PMCID: PMC9822464 DOI: 10.3390/molecules28010249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Almost half of all known proteins contain metal co-factors. Crucial for the flawless performance of a metalloprotein is the selection with high fidelity of the cognate metal cation from the surrounding biological fluids. Therefore, elucidating the factors controlling the metal binding and selectivity in metalloproteins is of particular significance. The knowledge thus acquired not only contributes to better understanding of the intimate mechanism of these events but, also, significantly enriches the researcher's toolbox that could be used in designing/engineering novel metalloprotein structures with pre-programmed properties. A powerful tool in aid of deciphering the physical principles behind the processes of metal recognition and selectivity is theoretical modeling of metal-containing biological structures. This review summarizes recent findings in the field with an emphasis on elucidating the major factors governing these processes. The results from theoretical evaluations are discussed. It is the hope that the physical principles evaluated can serve as guidelines in designing/engineering of novel metalloproteins of interest to both science and industry.
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4
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Metal cofactor stabilization by a partner protein is a widespread strategy employed for amidase activation. Proc Natl Acad Sci U S A 2022; 119:e2201141119. [PMID: 35733252 PMCID: PMC9245657 DOI: 10.1073/pnas.2201141119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Construction and remodeling of the bacterial peptidoglycan (PG) cell wall must be carefully coordinated with cell growth and division. Central to cell wall construction are hydrolases that cleave bonds in peptidoglycan. These enzymes also represent potential new antibiotic targets. One such hydrolase, the amidase LytH in Staphylococcus aureus, acts to remove stem peptides from PG, controlling where substrates are available for insertion of new PG strands and consequently regulating cell size. When it is absent, cells grow excessively large and have division defects. For activity, LytH requires a protein partner, ActH, that consists of an intracellular domain, a large rhomboid protease domain, and three extracellular tetratricopeptide repeats (TPRs). Here, we demonstrate that the amidase-activating function of ActH is entirely contained in its extracellular TPRs. We show that ActH binding stabilizes metals in the LytH active site and that LytH metal binding in turn is needed for stable complexation with ActH. We further present a structure of a complex of the extracellular domains of LytH and ActH. Our findings suggest that metal cofactor stabilization is a general strategy used by amidase activators and that ActH houses multiple functions within a single protein.
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5
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Osko JD, Christianson DW. Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6. Acta Crystallogr F Struct Biol Commun 2020; 76:428-437. [PMID: 32880591 PMCID: PMC7470039 DOI: 10.1107/s2053230x20010250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022] Open
Abstract
The zinc hydrolase histone deacetylase 6 (HDAC6) is unique among vertebrate deacetylases in that it contains two catalytic domains, designated CD1 and CD2. Both domains are fully functional as lysine deacetylases in vitro. However, the in vivo function of only the CD2 domain is well defined, whereas that of the CD1 domain is more enigmatic. Three X-ray crystal structures of HDAC6 CD1-inhibitor complexes are now reported to broaden the understanding of affinity determinants in the active site. Notably, cocrystallization with inhibitors was facilitated by using active-site mutants of zebrafish HDAC6 CD1. The first mutant studied, H82F/F202Y HDAC6 CD1, was designed to mimic the active site of human HDAC6 CD1. The structure of its complex with trichostatin A was generally identical to that with the wild-type zebrafish enzyme. The second mutant studied, K330L HDAC6 CD1, was prepared to mimic the active site of HDAC6 CD2. It has previously been demonstrated that this substitution does not perturb inhibitor binding conformations in HDAC6 CD1; here, this mutant facilitated cocrystallization with derivatives of the cancer chemotherapy drug suberoylanilide hydroxamic acid (SAHA). These crystal structures allow the mapping of inhibitor-binding regions in the outer active-site cleft, where one HDAC isozyme typically differs from another. It is expected that these structures will help to guide the structure-based design of inhibitors with selectivity against HDAC6 CD1, which in turn will enable new chemical biology approaches to probe its cellular function.
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Affiliation(s)
- Jeremy D. Osko
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philaldelphia, PA 19104-6323, USA
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philaldelphia, PA 19104-6323, USA
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6
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Zessin M, Kutil Z, Meleshin M, Nováková Z, Ghazy E, Kalbas D, Marek M, Romier C, Sippl W, Bařinka C, Schutkowski M. One-Atom Substitution Enables Direct and Continuous Monitoring of Histone Deacylase Activity. Biochemistry 2019; 58:4777-4789. [PMID: 31682411 DOI: 10.1021/acs.biochem.9b00786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We developed a one-step direct assay for the determination of histone deacylase (HDAC) activity by substituting the carbonyl oxygen of the acyl moiety with sulfur, resulting in thioacylated lysine side chains. This modification is recognized by class I HDACs with different efficiencies ranging from not accepted for HDAC1 to kinetic constants similar to that of the parent oxo substrate for HDAC8. Class II HDACs can hydrolyze thioacylated substrates with approximately 5-10-fold reduced kcat values, which resembles the effect of thioamide substitution in metallo-protease substrates. Class IV HDAC11 accepts thiomyristoyl modification less efficiently with an ∼5-fold reduced specificity constant. On the basis of the unique spectroscopic properties of thioamide bonds (strong absorption in spectral range of 260-280 nm and efficient fluorescence quenching), HDAC-mediated cleavage of thioamides could be followed by ultraviolet-visible and fluorescence spectroscopy in a continuous manner. The HDAC activity assay is compatible with microtiter plate-based screening formats up to 1536-well plates with Z' factors of >0.75 and signal-to-noise ratios of >50. Using thioacylated lysine residues in p53-derived peptides, we optimized substrates for HDAC8 with a catalytic efficiency of >250000 M-1 s-1, which are more than 100-fold more effective than most of the known substrates. We determined inhibition constants of several inhibitors for human HDACs using thioacylated peptidic substrates and found good correlation with the values from the literature. On the other hand, we could introduce N-methylated, N-acylated lysine residues as inhibitors for HDACs with an IC50 value of 1 μM for an N-methylated, N-myristoylated peptide derivative and human HDAC11.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Zora Nováková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Ehab Ghazy
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Diana Kalbas
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Martin Marek
- Departement de Biologie Structurale Integrative, Institut de Genetique et Biologie Moleculaire et Cellulaire (IGBMC) , Universite de Strasbourg (UDS), CNRS, INSERM , 1 rue Laurent Fries, B.P. 10142 , 67404 Illkirch Cedex IGBMC, France
| | - Christophe Romier
- Departement de Biologie Structurale Integrative, Institut de Genetique et Biologie Moleculaire et Cellulaire (IGBMC) , Universite de Strasbourg (UDS), CNRS, INSERM , 1 rue Laurent Fries, B.P. 10142 , 67404 Illkirch Cedex IGBMC, France
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
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7
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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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8
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Elitt CM, Fahrni CJ, Rosenberg PA. Zinc homeostasis and zinc signaling in white matter development and injury. Neurosci Lett 2019; 707:134247. [PMID: 31059767 DOI: 10.1016/j.neulet.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/08/2023]
Abstract
Zinc is an essential dietary micronutrient that is abundant in the brain with diverse roles in development, injury, and neurological diseases. With new imaging tools and chelators selectively targeting zinc, the field of zinc biology is rapidly expanding. The importance of zinc homeostasis is now well recognized in neurodegeneration, but there is emerging data that zinc may be equally important in white matter disorders. This review provides an overview of zinc biology, including a discussion of clinical disorders of zinc deficiency, different zinc pools, zinc biomarkers, and methods for measuring zinc. It emphasizes our limited understanding of how zinc is regulated in oligodendrocytes and white matter. Gaps in knowledge about zinc transporters and zinc signaling are discussed. Zinc-induced oligodendrocyte injury pathways relevant to white matter stroke, multiple sclerosis, and white matter injury of prematurity are reviewed and examples of zinc-dependent proteins relevant to myelination highlighted. Finally, a novel ratiometric zinc sensor is reviewed, revealing new information about mobile zinc during oligodendrocyte differentiation. With a better understanding of zinc biology in oligodendrocytes, new therapeutic targets for white matter disorders may be possible and the necessary tools to appropriately study zinc are finally available.
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Affiliation(s)
- Christopher M Elitt
- Boston Children's Hospital, Department of Neurology and the F.M. Kirby Neurobiology Center, 300 Longwood Avenue, Boston, MA, United States; Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.
| | - Christoph J Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Paul A Rosenberg
- Boston Children's Hospital, Department of Neurology and the F.M. Kirby Neurobiology Center, 300 Longwood Avenue, Boston, MA, United States; Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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9
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Cheshmedzhieva D, Toshev N, Gerova M, Petrov O, Dudev T. Hydroxamic acid derivatives as histone deacetylase inhibitors: a DFT study of their tautomerism and metal affinities/selectivities. J Mol Model 2018; 24:114. [PMID: 29691666 DOI: 10.1007/s00894-018-3651-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/09/2018] [Indexed: 01/28/2023]
Abstract
Hydroxamic acids are regarded as potent inhibitors of histone deacetylases (HDAC), and can therefore be used to reduce malignancy growth and size in affected organisms. Although there is a substantial body of information on the structures, syntheses, and biological activities of HDAC inhibitors, several important questions regarding their physicochemical properties and metal affinities/selectivities remain answered. First, how do the conformation and ionization of the hydroxamic group depend on its chemical composition and the dielectric properties of the medium? Second, how do these factors affect the affinities and selectivities of HDAC inhibitors for essential biogenic metal cations? Third, what is the preferred deprotonation site of the hydroxamic moiety and its mode of binding to the metal cation? The present work addressed these questions by performing density functional calculations combined with polarizable continuum model computations. The geometry, deprotonation pattern, metal-binding mode, and metal affinity/selectivity of SAHA, a typical HDAC inhibitor, were examined, and key factors affecting its ligation properties were elucidated. Sulfur- and selenium-containing analogs of SAHA were also modeled for the first time, and their potential as efficient metal-binding entities (to Mg2+, Fe2+, and Zn2+ cations) was assessed. The present calculations shed light on the thermodynamics of the binding of HDAC inhibitors to metal ions, and suggest techniques for enhancing their metal-ligating properties.
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Affiliation(s)
- D Cheshmedzhieva
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - N Toshev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - M Gerova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - O Petrov
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - T Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria.
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10
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Ho YH, Wang KJ, Hung PY, Cheng YS, Liu JR, Fung ST, Liang PH, Chern JW, Yu CW. A highly HDAC6-selective inhibitor acts as a fluorescent probe. Org Biomol Chem 2018; 16:7820-7832. [DOI: 10.1039/c8ob00966j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
HDAC6 receives great attention because of its therapeutic potential for the treatment of various diseases.
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Affiliation(s)
- Yi-Hsun Ho
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | - Kuang-Jui Wang
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | | | - Yi-Sheng Cheng
- Institute of Plant Biology
- College of Life Science
- National Taiwan University
- Taipei 106
- Taiwan
| | - Jia-Rong Liu
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | - Sheang-Tze Fung
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | - Pi-Hui Liang
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | - Ji-Wang Chern
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
| | - Chao-Wu Yu
- School of Pharmacy
- College of Medicine
- and Center for Innovative Therapeutics Discovery
- National Taiwan University
- Taipei 100
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11
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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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12
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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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13
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Dudev T, Nikolova V. Determinants of Fe2+ over M2+ (M = Mg, Mn, Zn) Selectivity in Non-Heme Iron Proteins. Inorg Chem 2016; 55:12644-12650. [DOI: 10.1021/acs.inorgchem.6b01822] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
| | - Valia Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
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14
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Hai Y, Christianson DW. Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat Chem Biol 2016; 12:741-7. [PMID: 27454933 PMCID: PMC4990478 DOI: 10.1038/nchembio.2134] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/11/2016] [Indexed: 12/11/2022]
Abstract
Histone deacetylase 6 (HDAC6) is a critical target for drug design due to its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens and CD1 and CD2 from Danio rerio HDAC6, and we correlate these structures with activity measurements using a panel of 13 different substrates. The catalytic activity of CD2 from both species exhibits broad substrate specificity, whereas that of CD1 is highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yield unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with 8 different inhibitors, including Belinostat and Panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-[(2-hydroxyethyl)(phenyl)amino]-2-oxoethyl)benzamide, reveal surprising new insight regarding changes in Zn2+ coordination and isozyme-specific inhibition.
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Affiliation(s)
- Yang Hai
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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15
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Daniel KB, Sullivan ED, Chen Y, Chan JC, Jennings PA, Fierke CA, Cohen SM. Dual-Mode HDAC Prodrug for Covalent Modification and Subsequent Inhibitor Release. J Med Chem 2015; 58:4812-21. [PMID: 25974739 PMCID: PMC4467547 DOI: 10.1021/acs.jmedchem.5b00539] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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Histone deacetylase inhibitors (HDACi)
target abnormal epigenetic
states associated with a variety of pathologies, including cancer.
Here, the development of a prodrug of the canonical broad-spectrum
HDACi suberoylanilide hydroxamic acid (SAHA) is described. Although
hydroxamic acids are utilized universally in the development of metalloenzyme
inhibitors, they are considered to be poor pharmacophores with reduced
activity in vivo. We developed a prodrug of SAHA by appending a promoiety,
sensitive to thiols, to the hydroxamic acid warhead (termed SAHA-TAP).
After incubation of SAHA-TAP with an HDAC, the thiol of a conserved
HDAC cysteine residue becomes covalently tagged with the promoiety,
initiating a cascade reaction that leads to the release of SAHA. Mass
spectrometry and enzyme kinetics experiments validate that the cysteine
residue is covalently appended with the TAP promoiety. SAHA-TAP demonstrates
cytotoxicity activity against various cancer cell lines. This strategy
represents an original prodrug design with a dual mode of action for
HDAC inhibition.
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Affiliation(s)
- Kevin B Daniel
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Yao Chen
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Joshua C Chan
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Patricia A Jennings
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Seth M Cohen
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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