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Begum MK, Konja D, Singh S, Chlopicki S, Wang Y. Endothelial SIRT1 as a Target for the Prevention of Arterial Aging: Promises and Challenges. J Cardiovasc Pharmacol 2021; 78:S63-S77. [PMID: 34840264 DOI: 10.1097/fjc.0000000000001154] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022]
Abstract
ABSTRACT SIRT1, a member of the sirtuin family of longevity regulators, possesses potent activities preventing vascular aging. The expression and function of SIRT1 in endothelial cells are downregulated with age, in turn causing early vascular aging and predisposing various vascular abnormalities. Overexpression of SIRT1 in the vascular endothelium prevents aging-associated endothelial dysfunction and senescence, thus the development of hypertension and atherosclerosis. Numerous efforts have been directed to increase SIRT1 signaling as a potential strategy for different aging-associated diseases. However, the complex mechanisms underlying the regulation of SIRT1 have posed a significant challenge toward the design of specific and effective therapeutics. This review aimed to provide a summary on the regulation and function of SIRT1 in the vascular endothelium and to discuss the different approaches targeting this molecule for the prevention and treatment of age-related cardiovascular and cerebrovascular diseases.
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Affiliation(s)
- Musammat Kulsuma Begum
- The State Key Laboratory of Pharmaceutical Biotechnology
- The Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
| | - Daniels Konja
- The State Key Laboratory of Pharmaceutical Biotechnology
- The Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
| | - Sandeep Singh
- The State Key Laboratory of Pharmaceutical Biotechnology
- The Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland; and
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Yu Wang
- The State Key Laboratory of Pharmaceutical Biotechnology
- The Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong SAR, China
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Gupta R, Kumar P. Computational Analysis Indicates That PARP1 Acts as a Histone Deacetylases Interactor Sharing Common Lysine Residues for Acetylation, Ubiquitination, and SUMOylation in Alzheimer's and Parkinson's Disease. ACS OMEGA 2021; 6:5739-5753. [PMID: 33681613 PMCID: PMC7931403 DOI: 10.1021/acsomega.0c06168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/12/2021] [Indexed: 05/28/2023]
Abstract
Aim/Hypothesis : Lysine residues are known for the post-translational modifications (PTMs) such as acetylation, ubiquitination, and SUMOylation. In acetylation, histone deacetylase (HDAC) and its interactors cause transcriptional deregulation and cause mitochondrial dysfunction, apoptosis, inflammatory response, and cell-cycle impairment that cause brain homeostasis and neuronal cell death. Other regulatory PTMs involved in the pathogenesis of neurodegenerative diseases (NDDs) are ubiquitination and SUMOylation for the degradation of the misfolded proteins. Thus, we aim to investigate the potential acetylation/ubiquitination/SUMOylation crosstalk sites in the HDAC interactors, which cause NDDs. Furthermore, we aim to identify the influence of PTMs on the structural features of proteins and the impact of putative lysine mutation on disease susceptibility. Last, we aim to examine the impact of the putative mutation on acetylated lysine for ubiquitination and SUMOylation. Results : Herein, we integrate 1455 genes, 3094 genes, and 1940 genes related to HDAC interactors, Alzheimer's disease (AD), and Parkinson's disease (PD), respectively. Furthermore, the protein-protein interaction and PTM integrations from different databases identified 32 proteins that are associated with HDAC, AD, and PD with 1489 potential lysine-modified sites. HDAC interactors poly(ADP-ribose) polymerase 1 (PARP1), nucleophosmin (NPM1), and cyclin-dependent kinase 1 (CDK1) involved in the progression of NDDs and 64 and 75% of PTM sites in PARP1, NPM1, and CDK1 fall into coiled and ordered regions, respectively. Moreover, 15 putative lysine sites have been found in the crosstalk and K148, K249, K528, K637, K700, and K796 of PARP1 are crosstalk hotspots. Conclusion : The loss of acetylated hotspot sites results in the loss of ubiquitination and SUMOylation function on nearby sites, which is relatively higher when compared to the gain of function.
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3
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Nielsen AL, Rajabi N, Kudo N, Lundø K, Moreno-Yruela C, Bæk M, Fontenas M, Lucidi A, Madsen AS, Yoshida M, Olsen CA. Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration. RSC Chem Biol 2021; 2:612-626. [PMID: 34458803 PMCID: PMC8341974 DOI: 10.1039/d0cb00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme. Here, we report a collection of chemical probes that are potent, selective, stable in serum, water-soluble, and inhibit SIRT2-mediated deacetylation and demyristoylation in cells. Compared to the current landscape of SIRT2 inhibitors, this is a unique ensemble of features built into a single compound. We expect the developed chemotypes to find broad application in the interrogation of SIRT2 functions in both healthy and diseased cells, and to provide a foundation for the development of future therapeutics. Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. Here, we developed small peptide-based inhibitors of its activity in living cells in culture.![]()
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Affiliation(s)
- Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Norio Kudo
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Kathrine Lundø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B DK-2200 Copenhagen Denmark
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Alessia Lucidi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
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Aggarwal S, Banerjee SK, Talukdar NC, Yadav AK. Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. Front Genet 2020; 11:356. [PMID: 32425973 PMCID: PMC7204943 DOI: 10.3389/fgene.2020.00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/24/2020] [Indexed: 01/07/2023] Open
Abstract
Sirtuins are protein deacetylases that play a protective role in cardiovascular diseases (CVDs), as well as many other diseases. Absence of sirtuins can lead to hyperacetylation of both nuclear and mitochondrial proteins leading to metabolic dysregulation. The protein post-translational modifications (PTMs) are known to crosstalk among each other to bring about complex phenotypic outcomes. Various PTM types such as acetylation, ubiquitination, and phosphorylation, and so on, drive transcriptional regulation and metabolism, but such crosstalks are poorly understood. We integrated protein–protein interactions (PPI) and PTMs from several databases to integrate information on 1,251 sirtuin-interacting proteins, of which 544 are associated with cardiac diseases. Based on the ∼100,000 PTM sites obtained for sirtuin interactors, we observed that the frequency of PTM sites (83 per protein), as well as PTM types (five per protein), is higher than the global average for human proteome. We found that ∼60–70% PTM sites fall into ordered regions. Approximately 83% of the sirtuin interactors contained at least one competitive crosstalk (in situ) site, with half of the sites occurring in CVD-associated proteins. A large proportion of identified crosstalk sites were observed for acetylation and ubiquitination competition. We identified 614 proteins containing PTM hotspots (≥5 PTM sites) and 133 proteins containing crosstalk hotspots (≥3 crosstalk sites). We observed that a large proportion of disease-associated sequence variants were found in PTM motifs of CVD proteins. We identified seven proteins (TP53, LMNA, MAPT, ATP2A2, NCL, APEX1, and HIST1H3A) containing disease-associated variants in PTM and crosstalk hotspots. This is the first comprehensive bioinformatics analysis on sirtuin interactors with respect to PTMs and their crosstalks. This study forms a platform for generating interesting hypotheses that can be tested for a deeper mechanistic understanding gained or derived from big-data analytics.
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Affiliation(s)
- Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.,Division of Life Sciences, Institute of Advanced Study in Science and Technology, Guwahati, India.,Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Sanjay K Banerjee
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Narayan Chandra Talukdar
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Guwahati, India.,Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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5
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Bæk M, Martín‐Gago P, Laursen JS, Madsen JLH, Chakladar S, Olsen CA. Photo Cross-Linking Probes Containing ϵ-N-Thioacyllysine and ϵ-N-Acyl-(δ-aza)lysine Residues. Chemistry 2020; 26:3862-3869. [PMID: 31922630 PMCID: PMC7154546 DOI: 10.1002/chem.201905338] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications (PTMs) are important in the regulation of protein function, trafficking, localization, and marking for degradation. This work describes the development of peptide activity/affinity-based probes for the discovery of proteins that recognize novel acyl-based PTMs on lysine residues in the proteome. The probes contain surrogates of ϵ-N-acyllysine by introduction of either hydrazide or thioamide functionalities to circumvent hydrolysis of the modification during the experiments. In addition to the modified PTMs, the developed chemotypes were analyzed with respect to the effect of peptide sequence. The photo cross-linking conditions and subsequent functionalization of the covalent adducts were systematically optimized by applying fluorophore labeling and gel electrophoresis (in-gel fluorescence measurements). Finally, selected probes, containing the ϵ-N-glutaryllysine and ϵ-N-myristoyllysine analogues, were successfully applied for the enrichment of native, endogenous proteins from cell lysate, recapitulating the expected interactions of SIRT5 and SIRT2, respectively. Interestingly, the latter mentioned was able to pull down two different splice variants of SIRT2, which has not been achieved with a covalent probe before. Based on this elaborate proof-of-concept study, we expect that the technology will have broad future applications for pairing of novel PTMs with the proteins that target them in the cell.
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Affiliation(s)
- Michael Bæk
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jonas S. Laursen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Julie L. H. Madsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Saswati Chakladar
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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Monaldi D, Rotili D, Lancelot J, Marek M, Wössner N, Lucidi A, Tomaselli D, Ramos-Morales E, Romier C, Pierce RJ, Mai A, Jung M. Structure–Reactivity Relationships on Substrates and Inhibitors of the Lysine Deacylase Sirtuin 2 from Schistosoma mansoni (SmSirt2). J Med Chem 2019; 62:8733-8759. [DOI: 10.1021/acs.jmedchem.9b00638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Daria Monaldi
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Dante Rotili
- Dipartimento di Chimica e Tecnologie del Farmaco, “Sapienza” Università di Roma, 00185 Rome, Italy
| | - Julien Lancelot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 8204—CIIL—Centre d’Infection et d’Immunité de Lille, 59000 Lille, France
| | - Martin Marek
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Nathalie Wössner
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Alessia Lucidi
- Dipartimento di Chimica e Tecnologie del Farmaco, “Sapienza” Università di Roma, 00185 Rome, Italy
| | - Daniela Tomaselli
- Dipartimento di Chimica e Tecnologie del Farmaco, “Sapienza” Università di Roma, 00185 Rome, Italy
| | - Elizabeth Ramos-Morales
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Raymond J. Pierce
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 8204—CIIL—Centre d’Infection et d’Immunité de Lille, 59000 Lille, France
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, “Sapienza” Università di Roma, 00185 Rome, Italy
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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7
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MicroRNAs and histone deacetylase inhibition-mediated protection against inflammatory β-cell damage. PLoS One 2018; 13:e0203713. [PMID: 30260972 PMCID: PMC6160007 DOI: 10.1371/journal.pone.0203713] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/24/2018] [Indexed: 01/22/2023] Open
Abstract
Inflammatory β-cell failure contributes to type 1 and type 2 diabetes pathogenesis. Pro-inflammatory cytokines cause β-cell dysfunction and apoptosis, and lysine deacetylase inhibitors (KDACi) prevent β-cell failure in vitro and in vivo, in part by reducing NF-κB transcriptional activity. We investigated the hypothesis that the protective effect of KDACi involves transcriptional regulation of microRNAs (miRs), potential new targets in diabetes treatment. Insulin-producing INS1 cells were cultured with or without the broad-spectrum KDACi Givinostat, prior to exposure to the pro-inflammatory cytokines IL-1β and IFN-γ for 6 h or 24 h, and miR expression was profiled with miR array. Thirteen miRs (miR-7a-2-3p, miR-29c-3p, miR-96-5p, miR-101a-3p, miR-140-5p, miR-146a-5p, miR-146b-5p, miR-340-5p, miR-384-5p, miR-455-5p, miR-466b-2-3p, miR-652-5p, and miR-3584-5p) were regulated by both cytokines and Givinostat, and nine were examined by qRT-PCR. miR-146a-5p was strongly regulated by cytokines and KDACi and was analyzed further. miR-146a-5p expression was induced by cytokines in rat and human islets. Cytokine-induced miR-146a-5p expression was specific for INS1 and β-TC3 cells, whereas α-TC1 cells exhibited a higher basal expression. Transfection of INS1 cells with miR-146a-5p reduced cytokine signaling, including the activity of NF-κB and iNOS promoters, as well as NO production and protein levels of iNOS and its own direct targets TNF receptor associated factor 6 (TRAF6) and interleukin-1 receptor-associated kinase 1 (IRAK1). miR-146a-5p was elevated in the pancreas of diabetes-prone BB-DP rats at diabetes onset, suggesting that miR-146a-5p could play a role in type 1 diabetes development. The miR array of cytokine-exposed INS1 cells rescued by KDACi revealed several other miRs potentially involved in cytokine-induced β-cell apoptosis, demonstrating the strength of this approach.
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8
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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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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10
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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Madsen AS, Andersen C, Daoud M, Anderson KA, Laursen JS, Chakladar S, Huynh FK, Colaço AR, Backos DS, Fristrup P, Hirschey MD, Olsen CA. Investigating the Sensitivity of NAD+-dependent Sirtuin Deacylation Activities to NADH. J Biol Chem 2016; 291:7128-41. [PMID: 26861872 DOI: 10.1074/jbc.m115.668699] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Indexed: 11/06/2022] Open
Abstract
Protein lysine posttranslational modification by an increasing number of different acyl groups is becoming appreciated as a regulatory mechanism in cellular biology. Sirtuins are class III histone deacylases that use NAD(+)as a co-substrate during amide bond hydrolysis. Several studies have described the sirtuins as sensors of the NAD(+)/NADH ratio, but it has not been formally tested for all the mammalian sirtuinsin vitro To address this problem, we first synthesized a wide variety of peptide-based probes, which were used to identify the range of hydrolytic activities of human sirtuins. These probes included aliphatic ϵ-N-acyllysine modifications with hydrocarbon lengths ranging from formyl (C1) to palmitoyl (C16) as well as negatively charged dicarboxyl-derived modifications. In addition to the well established activities of the sirtuins, "long chain" acyllysine modifications were also shown to be prone to hydrolytic cleavage by SIRT1-3 and SIRT6, supporting recent findings. We then tested the ability of NADH, ADP-ribose, and nicotinamide to inhibit these NAD(+)-dependent deacylase activities of the sirtuins. In the commonly used 7-amino-4-methylcoumarin-coupled fluorescence-based assay, the fluorophore has significant spectral overlap with NADH and therefore cannot be used to measure inhibition by NADH. Therefore, we turned to an HPLC-MS-based assay to directly monitor the conversion of acylated peptides to their deacylated forms. All tested sirtuin deacylase activities showed sensitivity to NADH in this assay. However, the inhibitory concentrations of NADH in these assays are far greater than the predicted concentrations of NADH in cells; therefore, our data indicate that NADH is unlikely to inhibit sirtuinsin vivo These data suggest a re-evaluation of the sirtuins as direct sensors of the NAD(+)/NADH ratio.
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Affiliation(s)
- Andreas S Madsen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark, the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark,
| | - Christian Andersen
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Mohammad Daoud
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kristin A Anderson
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Jonas S Laursen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Saswati Chakladar
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Frank K Huynh
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Ana R Colaço
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Donald S Backos
- the Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Peter Fristrup
- the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Matthew D Hirschey
- the Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, and
| | - Christian A Olsen
- From the Center for Biopharmaceuticals, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark, the Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark,
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12
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Toro TB, Pingali S, Nguyen TP, Garrett DS, Dodson KA, Nichols KA, Haynes RA, Payton-Stewart F, Watt TJ. KDAC8 with High Basal Velocity Is Not Activated by N-Acetylthioureas. PLoS One 2016; 11:e0146900. [PMID: 26745872 PMCID: PMC4706426 DOI: 10.1371/journal.pone.0146900] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/24/2015] [Indexed: 12/04/2022] Open
Abstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Recently, a series of N-acetylthioureas were synthesized and reported to enhance the activity of KDAC8 with a fluorogenic substrate. To determine if the activation was general, we synthesized three of the most potent N-acetylthioureas and measured their effect with peptide substrates and the fluorogenic substrate under multiple reaction conditions and utilizing two enzyme purification approaches. No activation was observed for any of the three N-acetylthioureas under any assayed conditions. Further characterization of KDAC8 kinetics with the fluorogenic substrate yielded a kcat/KM of 164 ± 17 in the absence of any N-acetylthioureas. This catalytic efficiency is comparable to or higher than that previously reported when KDAC8 was activated by the N-acetylthioureas, suggesting that the previously reported activation effect may be due to use of an enzyme preparation that contains a large fraction of inactive enzyme. Further characterization with a less active preparation and additional substrates leads us to conclude that N-acetylthioureas are not true activators of KDAC8 and only increase activity if the enzyme preparation is below the maximal basal activity.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Subramanya Pingali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Thao P. Nguyen
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Destane S. Garrett
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Kyra A. Dodson
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Kyara A. Nichols
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Rashad A. Haynes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Florastina Payton-Stewart
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
- * E-mail:
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13
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Madsen AS, Olsen CA. A potent trifluoromethyl ketone histone deacetylase inhibitor exhibits class-dependent mechanism of action. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00451a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic evaluation of HDAC inhibitors containing different zinc-binding chemotypes demonstrates that trifluoromethyl ketone-containing compounds can inhibit individual HDAC isozymes via differential mechanisms.
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Affiliation(s)
- Andreas S. Madsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology
- University of Copenhagen
- Copenhagen
- Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals and Department of Drug Design & Pharmacology
- University of Copenhagen
- Copenhagen
- Denmark
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14
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Toro TB, Watt TJ. KDAC8 substrate specificity quantified by a biologically relevant, label-free deacetylation assay. Protein Sci 2015; 24:2020-32. [PMID: 26402585 DOI: 10.1002/pro.2813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/21/2015] [Accepted: 09/20/2015] [Indexed: 01/25/2023]
Abstract
Analysis of the human proteome has identified thousands of unique protein sequences that contain acetylated lysine residues in vivo. These modifications regulate a variety of biological processes and are reversed by the lysine deacetylase (KDAC) family of enzymes. Despite the known prevalence and importance of acetylation, the details of KDAC substrate recognition are not well understood. While several methods have been developed to monitor protein deacetylation, none are particularly suited for identifying enzyme-substrate pairs of label-free substrates across the entire family of lysine deacetylases. Here, we present a fluorescamine-based assay which is more biologically relevant than existing methods and amenable to probing substrate specificity. Using this assay, we evaluated the activity of KDAC8 and other lysine deacetylases, including a sirtuin, for several peptides derived from known acetylated proteins. KDAC8 showed clear preferences for some peptides over others, indicating that the residues immediately surrounding the acetylated lysine play an important role in substrate specificity. Steady-state kinetics suggest that the sequence surrounding the acetylated lysine affects binding affinity and catalytic rate independently. Our results provide direct evidence that potential KDAC8 substrates previously identified through cell based experiments can be directly deacetylated by KDAC8. Conversely, the data from this assay did not correlate well with predictions from previous screens for KDAC8 substrates using less biologically relevant substrates and assay conditions. Combining results from our assay with mass spectrometry-based experiments and cell-based experiments will allow the identification of specific KDAC-substrate pairs and lead to a better understanding of the biological consequences of these interactions.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana, 70125
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana, 70125
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15
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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16
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Chen B, Zang W, Wang J, Huang Y, He Y, Yan L, Liu J, Zheng W. The chemical biology of sirtuins. Chem Soc Rev 2015; 44:5246-64. [DOI: 10.1039/c4cs00373j] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article reviews the tremendous accomplishments achieved during the past few years in the field of chemical biology for the physiologically and therapeutically important sirtuin family of Nε-acyl-lysine deacylase enzymes.
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Affiliation(s)
- Bing Chen
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Wenwen Zang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Juan Wang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yajun Huang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yanhua He
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Lingling Yan
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Jiajia Liu
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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17
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Villadsen JS, Kitir B, Wich K, Friis T, Madsen AS, Olsen CA. An azumamide C analogue without the zinc-binding functionality. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00252k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have attracted considerable attention due to their promise as therapeutic agents.
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Affiliation(s)
| | - Betül Kitir
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
| | | | - Tina Friis
- Department of Clinical Biochemistry
- Immunology and Genetics (KBIG)
- Statens Serum Institut
- Copenhagen
- Denmark
| | - Andreas S. Madsen
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
| | - Christian A. Olsen
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
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