1
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Santos JC, Dametto M, Masson AP, Faça VM, Bonacin R, Donadi EA, Passos GA. The AIRE G228W mutation disturbs the interaction of AIRE with its partner molecule SIRT1. Front Immunol 2022; 13:948419. [PMID: 36148232 PMCID: PMC9485725 DOI: 10.3389/fimmu.2022.948419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/11/2022] [Indexed: 12/02/2022] Open
Abstract
The autoimmune regulator (AIRE) protein functions as a tetramer, interacting with partner proteins to form the “AIRE complex,” which relieves RNA Pol II stalling in the chromatin of medullary thymic epithelial cells (mTECs). AIRE is the primary mTEC transcriptional controller, promoting the expression of a large set of peripheral tissue antigen genes implicated in the negative selection of self-reactive thymocytes. Under normal conditions, the SIRT1 protein temporarily interacts with AIRE and deacetylates K residues of the AIRE SAND domain. Once the AIRE SAND domain is deacetylated, the binding with SIRT1 is undone, allowing the AIRE complex to proceed downstream with the RNA Pol II to the elongation phase of transcription. Considering that the in silico and in vitro binding of the AIRE SAND domain with SIRT1 provides a powerful model system for studying the dominant SAND G228W mutation mechanism, which causes the autoimmune polyglandular syndrome-1, we integrated computational molecular modeling, docking, dynamics between the whole SAND domain with SIRT1, and surface plasmon resonance using a peptide harboring the 211 to 230 residues of the SAND domain, to compare the structure and energetics of binding/release between AIRE G228 (wild-type) and W228 (mutant) SAND domain to SIRT1. We observed that the G228W mutation in the SAND domain negatively influences the AIRE-SIRT1 interaction. The disturbed interaction might cause a disruption in the binding of the AIRE SAND domain with the SIRT1 catalytic site, impairing the AIRE complex to proceed downstream with RNA Pol II.
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Affiliation(s)
- Jadson C. Santos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Mariangela Dametto
- Renato Archer Information Technology Center (CTI Brazil), Ministry of Science, Technology and Innovation (MCTI), Campinas, SP, Brazil
| | - Ana Paula Masson
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Vitor M. Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Rodrigo Bonacin
- Renato Archer Information Technology Center (CTI Brazil), Ministry of Science, Technology and Innovation (MCTI), Campinas, SP, Brazil
| | - Eduardo A. Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Geraldo Aleixo Passos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
- Center for Cell-Based Therapy in Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
- *Correspondence: Geraldo Aleixo Passos,
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2
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Shao X, Kong W, Li Y, Zhang S. Quantitative structure-activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1's deacetylation substrates in diabetes mellitus. J Bioinform Comput Biol 2022; 20:2250008. [PMID: 35451939 DOI: 10.1142/s0219720022500081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD[Formula: see text]-dependent deacetylase involved in multiple glucose metabolism pathways and plays an important role in the pathogenesis of diabetes mellitus (DM). The enzyme specifically recognizes its deacetylation substrates' peptide segments containing a central acetyl-lysine residue as well as a number of amino acids flanking the central residue. In this study, we attempted to ascertain the minimal sequence requirement (MSR) around the central acetyl-lysine residue of SIRT1 substrate-recognition sites as well as the amino acid preference (AAP) at different residues of the MSR window through quantitative structure-activity relationship (QSAR) strategy, which would benefit our understanding of SIRT1 substrate specificity at the molecular level and is also helpful to rationally design substrate-mimicking peptidic agents against DM by competitively targeting SIRT1 active site. In this procedure, a large-scale dataset containing 6801 13-mer acetyl-lysine peptides (and their SIRT1-catalyized deacetylation activities) were compiled to train 10 QSAR regression models developed by systematic combination of machine learning methods (PLS and SVM) and five amino acids descriptors (DPPS, T-scale, MolSurf, [Formula: see text]-score, and FASGAI). The two best QSAR models (PLS+FASGAI and SVM+DPPS) were then employed to statistically examine the contribution of residue positions to the deacetylation activity of acetyl-lysine peptide substrates, revealing that the MSR can be represented by 5-mer acetyl-lysine peptides that meet a consensus motif X[Formula: see text]X[Formula: see text]X[Formula: see text](AcK)0X[Formula: see text]. Structural analysis found that the X[Formula: see text] and (AcK)0 residues are tightly packed against the enzyme active site and confer both stability and specificity for the enzyme-substrate complex, whereas the X[Formula: see text], X[Formula: see text] and X[Formula: see text] residues are partially exposed to solvent but can also effectively stabilize the complex system. Subsequently, a systematic deacetylation activity change profile (SDACP) was created based on QSAR modeling, from which the AAP for each residue position of MSR was depicted. With the profile, we were able to rationally design an SDACP combinatorial library with promising deacetylation activity, from which nine MSR acetyl-lysine peptides as well as two known SIRT1 acetyl-lysine peptide substrates were tested by using SIRT1 deacetylation assay. It is revealed that the designed peptides exhibit a comparable or even higher activity than the controls, although the former is considerably shorter than the latter.
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Affiliation(s)
- X Shao
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - W Kong
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - Y Li
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - S Zhang
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
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3
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Hendler A, Akiva E, Sandhu M, Goldberg D, Arbely E, Jackson CJ, Aharoni A. Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. Mol Biol Evol 2021; 38:545-556. [PMID: 32956445 PMCID: PMC7826192 DOI: 10.1093/molbev/msaa244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many enzymes that catalyze protein post-translational modifications can specifically modify multiple target proteins. However, little is known regarding the molecular basis and evolution of multispecificity in these enzymes. Here, we used a combined bioinformatics and experimental approaches to investigate the evolution of multispecificity in the sirtuin-1 (SIRT1) deacetylase. Guided by bioinformatics analysis of SIRT1 orthologs and substrates, we identified and examined important amino acid substitutions that have occurred during the evolution of sirtuins in Metazoa and Fungi. We found that mutation of human SIRT1 at these positions, based on sirtuin orthologs from Fungi, could alter its substrate specificity. These substitutions lead to reduced activity toward K382 acetylated p53 protein, which is only present in Metazoa, without affecting the high activity toward the conserved histone substrates. Results from ancestral sequence reconstruction are consistent with a model in which ancestral sirtuin proteins exhibited multispecificity, suggesting that the multispecificity of some metazoan sirtuins, such as hSIRT1, could be a relatively ancient trait.
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Affiliation(s)
- Adi Hendler
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
| | - Mahakaran Sandhu
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Dana Goldberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Arbely
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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4
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Rymarchyk S, Kang W, Cen Y. Substrate-Dependent Sensitivity of SIRT1 to Nicotinamide Inhibition. Biomolecules 2021; 11:312. [PMID: 33670751 PMCID: PMC7922766 DOI: 10.3390/biom11020312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
SIRT1 is the most extensively studied human sirtuin with a broad spectrum of endogenous targets. It has been implicated in the regulation of a myriad of cellular events, such as gene transcription, mitochondria biogenesis, insulin secretion as well as glucose and lipid metabolism. From a mechanistic perspective, nicotinamide (NAM), a byproduct of a sirtuin-catalyzed reaction, reverses a reaction intermediate to regenerate NAD+ through "base exchange", leading to the inhibition of the forward deacetylation. NAM has been suggested as a universal sirtuin negative regulator. Sirtuins have evolved different strategies in response to NAM regulation. Here, we report the detailed kinetic analysis of SIRT1-catalyzed reactions using endogenous substrate-based synthetic peptides. A novel substrate-dependent sensitivity of SIRT1 to NAM inhibition was observed. Additionally, SIRT1 demonstrated pH-dependent deacetylation with normal solvent isotope effects (SIEs), consistent with proton transfer in the rate-limiting step. Base exchange, in contrast, was insensitive to pH changes with no apparent SIEs, indicative of lack of proton transfer in the rate-limiting step. Consequently, NAM inhibition was attenuated at a high pH in proteated buffers. Our study provides new evidence for "activation by de-repression" as an effective sirtuin activation strategy.
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Affiliation(s)
- Stacia Rymarchyk
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
| | - Wenjia Kang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA;
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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5
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Hori Y, Nishiura M, Tao T, Baba R, Bull SD, Kikuchi K. Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues. Chem Sci 2021; 12:2498-2503. [PMID: 34164016 PMCID: PMC8179349 DOI: 10.1039/d0sc06551j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays. We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.![]()
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan .,IFReC, Osaka University Suita Osaka 565-0871 Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Tomomi Tao
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Reisuke Baba
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Steven D Bull
- Department of Chemistry, University of Bath Bath BA27AY UK
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan .,IFReC, Osaka University Suita Osaka 565-0871 Japan.,Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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6
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Moreno-Yruela C, Bæk M, Vrsanova AE, Schulte C, Maric HM, Olsen CA. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat Commun 2021; 12:62. [PMID: 33397936 PMCID: PMC7782793 DOI: 10.1038/s41467-020-20250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Adela-Eugenie Vrsanova
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Institute of Applied Biosciences & Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, D-76131, Karlsruhe, Germany.,Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Im Neuenhemier Feld 581, D-69120, Heidelberg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.
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7
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Ghirotto B, Terra FF, Câmara NOS, Basso PJ. Sirtuins in B lymphocytes metabolism and function. World J Exp Med 2019; 9:1-13. [PMID: 30705866 PMCID: PMC6354076 DOI: 10.5493/wjem.v9.i1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 01/05/2019] [Indexed: 02/06/2023] Open
Abstract
Sirtuins (SIRTs) are NAD+-dependent histone deacetylases and play a role in virtually all cell biological processes. As SIRTs functions vary according to their subtypes, they can either activate or inhibit signaling pathways upon different conditions or tissues. Recent studies have focused on metabolic effects performed by SIRTs in several cell types since specific metabolic pathways (e.g., aerobic glycolysis, oxidative phosphorylation, β-oxidation, glutaminolysis) are used to determine the cell fate. However, few efforts have been made to understand the role of SIRTs on B lymphocytes metabolism and function. These cells are associated with humoral immune responses by secreting larger amounts of antibodies after differentiating into antibody-secreting cells. Besides, both the SIRTs and B lymphocytes are potential targets to treat several immune-mediated disorders, including cancer. Here, we provide an outlook of recent studies regarding the role of SIRTs in general cellular metabolism and B lymphocytes functions, pointing out the future perspectives of this field.
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Affiliation(s)
- Bruno Ghirotto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fernanda Fernandes Terra
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Niels Olsen Saraiva Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Division of Nephrology, School of Medicine, Federal University of São Paulo, São Paulo 04023-062, Brazil
- Laboratory of Renal Physiology (LIM 16), School of Medicine, University of São Paulo, São Paulo 01246-903, Brazil
| | - Paulo José Basso
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
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8
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Olesen SV, Rajabi N, Svensson B, Olsen CA, Madsen AS. An NAD +-Dependent Sirtuin Depropionylase and Deacetylase (Sir2La) from the Probiotic Bacterium Lactobacillus acidophilus NCFM. Biochemistry 2018; 57:3903-3915. [PMID: 29863862 DOI: 10.1021/acs.biochem.8b00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sirtuins, a group of NAD+-dependent deacylases, have emerged as the key connection between NAD+ metabolism and aging. This class of enzymes hydrolyzes a range of ε- N-acyllysine PTMs, and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacterium Lactobacillus acidophilus NCFM. Screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, demonstrated that one of the investigated proteins, Sir2La, is a bona fide NAD+-dependent sirtuin, catalyzing hydrolysis of acetyl-, propionyl-, and butyryllysine. Further substantiating the identity of Sir2La as a sirtuin, known sirtuin inhibitors, nicotinamide and suramin, as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. On the basis of steady-state kinetics, Sir2La showed a slight preference for propionyllysine (Kpro) over acetyllysine (Kac). For nonfluorogenic peptide substrates, the preference is driven by a remarkably low KM (280 nM vs 700 nM, for Kpro and Kac, respectively), whereas kcat was similar (21 × 10-3 s-1). Moreover, while NAD+ is a prerequisite for Sir2La-mediated deacylation, Sir2La has a very high KM for NAD+ compared to the expected levels of the dinucleotide in L. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl- and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.
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Affiliation(s)
- Sita V Olesen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
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9
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Rajabi N, Galleano I, Madsen AS, Olsen CA. Targeting Sirtuins: Substrate Specificity and Inhibitor Design. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 154:25-69. [PMID: 29413177 DOI: 10.1016/bs.pmbts.2017.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine residues across the proteome are modified by posttranslational modifications (PTMs) that significantly enhance the structural and functional diversity of proteins. For lysine, the most abundant PTM is ɛ-N-acetyllysine (Kac), which plays numerous roles in regulation of important cellular functions, such as gene expression (epigenetic effects) and metabolism. A family of enzymes, namely histone deacetylases (HDACs), removes these PTMs. A subset of these enzymes, the sirtuins (SIRTs), represent class III HDAC and, unlike the rest of the family, these hydrolases are NAD+-dependent. Although initially described as deacetylases, alternative deacylase functions for sirtuins have been reported, which expands the potential cellular roles of this class of enzymes. Currently, sirtuins are investigated as therapeutic targets for the treatment of diseases that span from cancers to neurodegenerative disorders. In the present book chapter, we review and discuss the current literature on novel ɛ-N-acyllysine PTMs, targeted by sirtuins, as well as mechanism-based sirtuin inhibitors inspired by their substrates.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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10
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Bortell N, Basova L, Najera JA, Morsey B, Fox HS, Marcondes MCG. Sirtuin 1-Chromatin-Binding Dynamics Points to a Common Mechanism Regulating Inflammatory Targets in SIV Infection and in the Aging Brain. J Neuroimmune Pharmacol 2017; 13:163-178. [PMID: 29280055 DOI: 10.1007/s11481-017-9772-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 12/20/2022]
Abstract
Microglia and macrophages are the main non-neuronal subsets of myeloid origin in the brain, and are critical regulators in neurodegenerative disorders, where inflammation is a key factor. Since HIV infection results in neurological perturbations that are similar to those in aging, we examined microglial and infiltrating myeloid subsets in the search for changes that might resemble the ones in aging. For that, we used the SIV infection in rhesus macaques to model neuroAIDS. We found that Sirt-1, a molecule that impacts survival and health in many models, was decreased in cell preparations containing a majority of microglia and myeloid cells from the brain of infected macaques. The role of Sirt-1 in neuroAIDS is unknown. We hypothesized that Sirt-1 silencing functions are affected by SIV. Mapping of Sirt-1 binding patterns to chromatin revealed that the number of Sirt-1-bound genes was 29.6% increased in myeloid cells from infected animals with mild or no detectable neuropathology, but 51% was decreased in severe neuropathology, compared to controls. Importantly, Sirt-1-bound genes in controls largely participate in neuroinflammation. Promoters of type I IFN pathway genes IRF7, IRF1, IFIT1, and AIF1, showed Sirt-1 binding in controls, which was consistently lost after infection, together with higher transcription. Loss of Sirt-1 binding was also found in brains from old uninfected animals, suggesting a common regulation. The role of Sirt-1 in regulating these inflammatory markers was confirmed in two different in vitro models, where Sirt-1 blockage modulated IRF7, IRF1 and AIF1 levels both in human macrophage cell lines and in human blood-derived monocytes from various normal donors, stimulated with a TLR9 agonist. Our data suggests that Sirt-1-inflammatory gene silencing is disturbed by SIV infection, resembling aging in brains. These findings may impact our knowledge on the contribution of myeloid subsets to the neurological consequences of HIV infection, aggravated and overlapping with the aging process.
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Affiliation(s)
- Nikki Bortell
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Liana Basova
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA.,San Diego Biomedical Research Institute, 10865 Road to Cure, Suite 100, San Diego, CA, 92121, USA
| | - Julia A Najera
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Brenda Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5800, USA
| | - Maria Cecilia Garibaldi Marcondes
- Molecular and Cellular Neurosciences Department, The Scripps Research Institute, La Jolla, CA, USA. .,San Diego Biomedical Research Institute, 10865 Road to Cure, Suite 100, San Diego, CA, 92121, USA.
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11
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Gallego-Jara J, Écija Conesa A, de Diego Puente T, Lozano Terol G, Cánovas Díaz M. Characterization of CobB kinetics and inhibition by nicotinamide. PLoS One 2017; 12:e0189689. [PMID: 29253849 PMCID: PMC5734772 DOI: 10.1371/journal.pone.0189689] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022] Open
Abstract
Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
- * E-mail:
| | - Ana Écija Conesa
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
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12
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Zhai Z, Tang M, Yang Y, Lu M, Zhu WG, Li T. Identifying Human SIRT1 Substrates by Integrating Heterogeneous Information from Various Sources. Sci Rep 2017; 7:4614. [PMID: 28676654 PMCID: PMC5496887 DOI: 10.1038/s41598-017-04847-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
Most proteins undergo different kinds of modification after translation. Protein acetylation is one of the most crucial post-translational modifications, which causes direct or indirect impact on various biological activities in vivo. As a member of Class III HDACs, SIRT1 was the closest one to the yeast sir2 and drew most attention, while a small number of known SIRT1 substrates caused difficulties to clarify its function. In this work, we designed a novel computational method to screen SIRT1 substrates based on manually collected data and Support Vector Machines (SVMs). Unlike other approaches, we took both primary sequence and protein functional features into consideration. Through integrating functional features, the Matthews correlation coefficient (MCC) for the prediction increased from 0.10 to 0.65. The prediction results were verified by independent dataset and biological experiments. The validation results demostrated that our classifier could effectively identify SIRT1 substrates and filter appropriate candidates for further research. Furthermore, we provide online tool to support SIRT1 substrates prediction, which is freely available at http://bioinfo.bjmu.edu.cn/huac/.
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Affiliation(s)
- Zichao Zhai
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); State Key Laboratory of Natural and Biomimetic Drugs; Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yue Yang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ming Lu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); State Key Laboratory of Natural and Biomimetic Drugs; Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. .,Peking-Tsinghua University Center for Life Science; Peking University, Beijing, 100191, China. .,School of Medicine; Shenzhen University, Shenzhen, 518060, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. .,Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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13
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A Selective Cyclic Peptidic Human SIRT5 Inhibitor. Molecules 2016; 21:molecules21091217. [PMID: 27626398 PMCID: PMC6272981 DOI: 10.3390/molecules21091217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022] Open
Abstract
In the current study, we discovered that a side chain-to-side chain cyclic pentapeptide harboring a central Nε-carboxyethyl-thiocarbamoyl-lysine residue behaved as a strong and selective (versus human SIRT1/2/3/6) inhibitor against human SIRT5-catalyzed deacylation reaction. This compound was also found to be proteolytically much more stable than its linear counterpart. This compound could be a valuable lead for developing stronger, selective, metabolically stable, and cell permeable human SIRT5 inhibitors.
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14
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Abstract
Sirtuins are NAD(+)-dependent enzymes universally present in all organisms, where they play central roles in regulating numerous biological processes. Although early studies showed that sirtuins deacetylated lysines in a reaction that consumes NAD(+), more recent studies have revealed that these enzymes can remove a variety of acyl-lysine modifications. The specificities for varied acyl modifications may thus underlie the distinct roles of the different sirtuins within a given organism. This review summarizes the structure, chemistry, and substrate specificity of sirtuins with a focus on how different sirtuins recognize distinct substrates and thus carry out specific functions.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185;
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14850;
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15
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Chen B, Wang J, Huang Y, Zheng W. Human SIRT3 tripeptidic inhibitors containing N(ε)-thioacetyl-lysine. Bioorg Med Chem Lett 2015. [PMID: 26220157 DOI: 10.1016/j.bmcl.2015.07.008] [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] [Indexed: 11/17/2022]
Abstract
Built upon our lead pan-SIRT1/2/3 tripeptidic inhibitors that contain the catalytic mechanism-based sirtuin inhibitory warhead N(ε)-thioacetyl-lysine, three of their analogs (i.e., 7, 9, and 19) were discovered in the current study to exhibit a significantly enhanced SIRT3 inhibitory selectivity while maintaining the SIRT3 inhibitory potency. These compounds represent novel lead compounds for developing more potent and selective SIRT3 inhibitors of the catalytic mechanism-based type.
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Affiliation(s)
- Bing Chen
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Juan Wang
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Yajun Huang
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China.
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16
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The identification of high-affinity G protein-coupled receptor ligands from large combinatorial libraries using multicolor quantum dot-labeled cell-based screening. Future Med Chem 2015; 6:809-23. [PMID: 24941874 DOI: 10.4155/fmc.14.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs), which are involved in virtually every biological process, constitute the largest family of transmembrane receptors. Many top-selling and newly approved drugs target GPCRs. In this review, we aim to recapitulate efforts and progress in combinatorial library-assisted GPCR ligand discovery, particularly focusing on one-bead-one-compound library synthesis and quantum dot-labeled cell-based assays, which both effectively enhance the rapid identification of GPCR ligands with higher affinity and specificity.
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17
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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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18
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Rauh D, Fischer F, Gertz M, Lakshminarasimhan M, Bergbrede T, Aladini F, Kambach C, Becker CFW, Zerweck J, Schutkowski M, Steegborn C. An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms. Nat Commun 2014; 4:2327. [PMID: 23995836 DOI: 10.1038/ncomms3327] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 07/19/2013] [Indexed: 12/22/2022] Open
Abstract
Sirtuin enzymes regulate metabolism and aging processes through deacetylation of acetyl-lysines in target proteins. More than 6,800 mammalian acetylation sites are known, but few targets have been assigned to most sirtuin isoforms, hampering our understanding of sirtuin function. Here we describe a peptide microarray system displaying 6,802 human acetylation sites for the parallel characterisation of their modification by deacetylases. Deacetylation data for all seven human sirtuins obtained with this system reveal isoform-specific substrate preferences and deacetylation substrate candidates for all sirtuin isoforms, including Sirt4. We confirm malate dehydrogenase protein as a Sirt3 substrate and show that peroxiredoxin 1 and high-mobility group B1 protein are deacetylated by Sirt5 and Sirt1, respectively, at the identified sites, rendering them likely new in vivo substrates. Our microarray platform enables parallel studies on physiological acetylation sites and the deacetylation data presented provide an exciting resource for the identification of novel substrates for all human sirtuins.
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Affiliation(s)
- David Rauh
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University, Kurt-Mothes-Staße 3, 06120 Halle (Saale), Germany
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19
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Pumroy RA, Cingolani G. Jamming up the "β-staple": regulation of SIRT1 activity by its C-terminal regulatory segment (CTR). J Mol Biol 2014; 426:507-9. [PMID: 24269770 PMCID: PMC4405232 DOI: 10.1016/j.jmb.2013.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Ruth Anne Pumroy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.
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20
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Schutkowski M, Fischer F, Roessler C, Steegborn C. New assays and approaches for discovery and design of Sirtuin modulators. Expert Opin Drug Discov 2014; 9:183-99. [DOI: 10.1517/17460441.2014.875526] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Kuo HY, DeLuca TA, Miller WM, Mrksich M. Profiling deacetylase activities in cell lysates with peptide arrays and SAMDI mass spectrometry. Anal Chem 2013; 85:10635-10642. [PMID: 24088168 DOI: 10.1021/ac402614x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of arrays that can profile molecular activities in cells is important to understanding signaling pathways in normal and pathological settings. While oligonucleotide arrays are now routinely used to profile global gene expression, there is still a lack of tools for profiling enzyme activities in cell lysates. This paper describes the combination of peptide arrays formed on self-assembled monolayers and mass spectrometry to provide a label-free approach for identifying patterns of enzyme activities in cell lysates. The approach is demonstrated by profiling lysine deacetylase (KDAC) activities in cell lysates of the CHRF megakaryocytic (Mk) cell line. Class-specific deacetylase inhibitors were used to show that terminal Mk differentiation of CHRF cells is marked by a pronounced decrease in sirtuin activity and by little change in activity of KDACs 1-11. This work establishes a platform that can be used to identify changes in global activity profiles of cell lysates for a wide variety of enzymatic activities.
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Affiliation(s)
- Hsin-Yu Kuo
- Departments of Biomedical Engineering, Chemistry, Cell & Molecular Biology, Northwestern University, Evanston, Illinois 60208
| | - Teresa A DeLuca
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - William M Miller
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611
| | - Milan Mrksich
- Departments of Biomedical Engineering, Chemistry, Cell & Molecular Biology, Northwestern University, Evanston, Illinois 60208.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611
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22
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Cho CF, Behnam Azad B, Luyt LG, Lewis JD. High-throughput screening of one-bead-one-compound peptide libraries using intact cells. ACS COMBINATORIAL SCIENCE 2013; 15:393-400. [PMID: 23819541 DOI: 10.1021/co4000584] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Screening approaches based on one-bead-one-compound (OBOC) combinatorial libraries have facilitated the discovery of novel peptide ligands for cellular targeting in cancer and other diseases. Recognition of cell surface proteins is optimally achieved using live cells, yet screening intact cell populations is time-consuming and inefficient. Here, we evaluate the Complex Object Parametric Analyzer and Sorter (COPAS) large particle biosorter for high-throughput sorting of bead-bound human cell populations. When a library of RGD-containing peptides was screened against human cancer cells that express αvβ3 integrin, it was found that bead-associated cells are rapidly dissociated when sorted through the COPAS instrument. When the bound cells were reversibly cross-linked onto the beads, however, we demonstrated that cell/bead mixtures can be sorted quickly and accurately. This reversible cross-linking approach is compatible with matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based peptide sequence deconvolution. This approach should allow one to rapidly screen an OBOC library and identify novel peptide ligands against cell surface targets in their native conformation.
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Affiliation(s)
- Choi-Fong Cho
- Translational Prostate Cancer
Research Group, University of Alberta,
5-142C Katz Group Building, 114th Street and 87th Avenue, Edmonton,
AB, T6G 2E1 Canada
| | - Babak Behnam Azad
- Departments
of Chemistry, Oncology,
and Medical Imaging, Western University, London, ON, N6A 5C1 Canada
| | - Leonard G. Luyt
- Departments
of Chemistry, Oncology,
and Medical Imaging, Western University, London, ON, N6A 5C1 Canada
| | - John D. Lewis
- Translational Prostate Cancer
Research Group, University of Alberta,
5-142C Katz Group Building, 114th Street and 87th Avenue, Edmonton,
AB, T6G 2E1 Canada
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23
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Hintersteiner M, Auer M. A two-channel detection method for autofluorescence correction and efficient on-bead screening of one-bead one-compound combinatorial libraries using the COPAS fluorescence activated bead sorting system. Methods Appl Fluoresc 2013; 1:017001. [PMID: 29148437 DOI: 10.1088/2050-6120/1/1/017001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One-bead one-compound combinatorial library beads exhibit varying levels of autofluorescence after solid phase combinatorial synthesis. Very often this causes significant problems for automated on-bead screening using TentaGel beads and fluorescently labeled target proteins. Herein, we present a method to overcome this limitation when fluorescence activated bead sorting is used as the screening method. We have equipped the COPAS bead sorting instrument with a high-speed profiling unit and developed a spectral autofluorescence correction method. The correction method is based on a simple algebraic operation using the fluorescence data from two detection channels and is applied on-the-fly in order to reliably identify hit beads by COPAS bead sorting. Our method provides a practical tool for the fast and efficient isolation of hit beads from one-bead one-compound library screens using either fluorescently labeled target proteins or biotinylated target proteins. This method makes hit bead identification easier and more reliable. It reduces false positives and eliminates the need for time-consuming pre-sorting of library beads in order to remove autofluorescent beads.
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24
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Meledin R, Brik A, Aharoni A. Dissecting the roles of the N- and C-flanking residues of acetyllysine substrates for SIRT1 activity. Chembiochem 2013; 14:577-81. [PMID: 23426869 DOI: 10.1002/cbic.201200727] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Indexed: 11/09/2022]
Abstract
SIRT1 specificity: The multispecific SIRT1 enzyme catalyzes the deacetylation of acetyllysine residues within protein targets. However, little is known regarding the molecular basis for SIRT1 substrate recognition. Kinetic analysis of SIRT1 with a panel of peptide substrates shows the high importance of the region N-flanking the target acetyllysine and its high conservation through evolution.
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Affiliation(s)
- Roman Meledin
- Department of Life Sciences and the National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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25
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A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Mol Cell Biol 2013; 33:1487-502. [PMID: 23382074 DOI: 10.1128/mcb.00971-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex.
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26
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Abstract
Sir2 proteins, or sirtuins, are a family of enzymes that catalyze NAD(+)-dependent deacetylation reactions and can also process ribosyltransferase, demalonylase, and desuccinylase activities. More than 40 crystal structures of sirtuins have been determined, alone or in various liganded forms. These high-resolution architectural details lay the foundation for understanding the molecular mechanisms of catalysis, regulation, substrate specificity, and inhibition of sirtuins. In this minireview, we summarize these structural features and discuss their implications for understanding sirtuin function.
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Affiliation(s)
- Hua Yuan
- Program in Gene Expression and Regulation, The Wistar Institute, University of Pennsylvania,Philadelphia, Pennsylvania 19104, USA
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27
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Feldman JL, Dittenhafer-Reed KE, Denu JM. Sirtuin catalysis and regulation. J Biol Chem 2012; 287:42419-27. [PMID: 23086947 DOI: 10.1074/jbc.r112.378877] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sirtuins are a family of NAD(+)-dependent protein deacetylases/deacylases that dynamically regulate transcription, metabolism, and cellular stress response. Their general positive link with improved health span in mammals, potential regulation of pathways mediated by caloric restriction, and growing links to human disease have spurred interest in therapeutics that target their functions. Here, we review the current understanding of the chemistry of catalysis, biological targets, and endogenous regulation of sirtuin activity. We discuss recent efforts to generate small-molecule regulators of sirtuin activity.
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Affiliation(s)
- Jessica L Feldman
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.
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28
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Cha J, Lim J, Zheng Y, Tan S, Ang YL, Oon J, Ang MW, Ling J, Bode M, Lee SS. Process Automation toward Ultra-High-Throughput Screening of Combinatorial One-Bead-One-Compound (OBOC) Peptide Libraries. ACTA ACUST UNITED AC 2012; 17:186-200. [DOI: 10.1177/2211068211433503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Raghavan A, Shah ZA. Sirtuins in neurodegenerative diseases: a biological-chemical perspective. NEURODEGENER DIS 2011; 9:1-10. [PMID: 22041967 DOI: 10.1159/000329724] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/30/2011] [Indexed: 01/06/2023] Open
Abstract
Sirtuins, commonly known as NAD(+)-dependent class III histone deacetylase enzymes, have been extensively studied to evaluate their potential role in different disease states. Based on the published literature, sirtuins have been implicated in providing a myriad of intrinsic and extrinsic biological effects, which in turn may play an important role in the treatment of various disorders such as type II diabetes, obesity, cancer, aging and different neurodegenerative diseases. In particular, a number of studies have unequivocally supported the idea of sirtuins having therapeutic potential in neurodegenerative diseases such as stroke, ischemic brain injury, Alzheimer's disease, Parkinson's disease, Huntington's disease and amyotrophic lateral sclerosis. To exploit the therapeutic potential of sirtuins, their manipulation in terms of development of small-molecule modulators, inhibitors and analogs has increased dramatically since their inception, in both scientific and industrial worlds. Studies on the structure and catalytic core of sirtuins along with chemical mechanisms and substrate specificity have provided important input into the design and synthesis of sirtuin modulators. To study the role of sirtuins in the biological system, it has become extremely important to understand the molecular and chemical structure of sirtuins. In this review, we have discussed the biological role of sirtuins in various neurodegenerative diseases, and also provided an insight into their chemical structure.
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Affiliation(s)
- Aparna Raghavan
- Department of Medicinal and Biological Chemistry, University of Toledo College of Pharmacy and Pharmaceutical Sciences, Toledo, Ohio 43614, USA
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30
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Schlicker C, Boanca G, Lakshminarasimhan M, Steegborn C. Structure-based development of novel sirtuin inhibitors. Aging (Albany NY) 2011; 3:852-872. [PMID: 21937767 PMCID: PMC3227451 DOI: 10.18632/aging.100388] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 09/19/2011] [Indexed: 05/31/2023]
Abstract
Sirtuins are NAD+-dependent protein deacetylases regulating metabolism, stress responses, and aging processes. Mammalia possess seven Sirtuin isoforms, Sirt1-7, which differ in their subcellular localization and in the substrate proteins they deacetylate. The physiological roles of Sirtuins and their potential use as therapeutic targets for metabolic and aging-related diseases have spurred interest in the development of small-molecule Sirtuin modulators. Here, we describe an approach exploiting the structures available for four human Sirtuins for the development of isoform-specific inhibitors. Virtual docking of a compound library into the peptide binding pockets of crystal structures of Sirt2, 3, 5 and 6 yielded compounds potentially discriminating between these isoforms. Further characterization in activity assays revealed several inhibitory compounds with little isoform specificity, but also two compounds with micromolar potency and high specificity for Sirt2. Structure comparison and the predicted, shared binding mode of the Sirt2-specific compounds indicate a pocket extending from the peptide-binding groove as target side enabling isoform specificity. Our family-wide structure-based approach thus identified potent, Sirt2-specific inhibitors as well as lead structures and a target site for the development of compounds specific for other Sirtuin isoform, constituting an important step toward the identification of a complete panel of isoform-specific Sirtuin inhibitors.
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Affiliation(s)
- Christine Schlicker
- Department of Physiological Chemistry, Ruhr-University Bochum, Germany
- Present address: Department of Biophysics, Ruhr-University Bochum, Germany
| | - Gina Boanca
- Department of Biochemistry, University of Bayreuth, Germany
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31
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Fan Y, Hense M, Ludewig R, Weisgerber C, Scriba GK. Capillary electrophoresis-based sirtuin assay using non-peptide substrates. J Pharm Biomed Anal 2011; 54:772-8. [DOI: 10.1016/j.jpba.2010.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 10/18/2022]
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32
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Hirsch BM, Du Z, Li X, Sylvester JA, Wesdemiotis C, Wang Z, Zheng W. Potent sirtuin inhibition bestowed by l-2-amino-7-carboxamidoheptanoic acid (l-ACAH), a Nε-acetyl-lysine analog. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00212g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Blum CA, Ellis JL, Loh C, Ng PY, Perni RB, Stein RL. SIRT1 Modulation as a Novel Approach to the Treatment of Diseases of Aging. J Med Chem 2010; 54:417-32. [DOI: 10.1021/jm100861p] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Charles A. Blum
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - James L. Ellis
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Christine Loh
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Pui Yee Ng
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Robert B. Perni
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Ross L. Stein
- Sirtris, A GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, United States
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Iera JA, Jenkins LMM, Kajiyama H, Kopp JB, Appella DH. Solid-phase synthesis and screening of N-acylated polyamine (NAPA) combinatorial libraries for protein binding. Bioorg Med Chem Lett 2010; 20:6500-3. [PMID: 20932761 DOI: 10.1016/j.bmcl.2010.09.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/08/2010] [Accepted: 09/10/2010] [Indexed: 10/19/2022]
Abstract
Inhibitors for protein-protein interactions are challenging to design, in part due to the unique and complex architectures of each protein's interaction domain. Most approaches to develop inhibitors for these interactions rely on rational design, which requires prior structural knowledge of the target and its ligands. In the absence of structural information, a combinatorial approach may be the best alternative to finding inhibitors of a protein-protein interaction. Current chemical libraries, however, consist mostly of molecules designed to inhibit enzymes. In this manuscript, we report the synthesis and screening of a library based on an N-acylated polyamine (NAPA) scaffold that we designed to have specific molecular features necessary to inhibit protein-protein interactions. Screens of the library identified a member with favorable binding properties to the HIV viral protein R (Vpr), a regulatory protein from HIV, that is involved in numerous interactions with other proteins critical for viral replication.
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Affiliation(s)
- Jaclyn A Iera
- Laboratory of Bioorganic Chemistry and Kidney Disease Section, NIDDK, NIH, DHHS, Bethesda, MD 20892, United States
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35
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Modulation of histone H3 lysine 56 acetylation as an antifungal therapeutic strategy. Nat Med 2010; 16:774-80. [PMID: 20601951 DOI: 10.1038/nm.2175] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 06/03/2010] [Indexed: 12/12/2022]
Abstract
Candida albicans is a major fungal pathogen that causes serious systemic and mucosal infections in immunocompromised individuals. In yeast, histone H3 Lys56 acetylation (H3K56ac) is an abundant modification regulated by enzymes that have fungal-specific properties, making them appealing targets for antifungal therapy. Here we demonstrate that H3K56ac in C. albicans is regulated by the RTT109 and HST3 genes, which respectively encode the H3K56 acetyltransferase (Rtt109p) and deacetylase (Hst3p). We show that reduced levels of H3K56ac sensitize C. albicans to genotoxic and antifungal agents. Inhibition of Hst3p activity by conditional gene repression or nicotinamide treatment results in a loss of cell viability associated with abnormal filamentous growth, histone degradation and gross aberrations in DNA staining. We show that genetic or pharmacological alterations in H3K56ac levels reduce virulence in a mouse model of C. albicans infection. Our results demonstrate that modulation of H3K56ac is a unique strategy for treatment of C. albicans and, possibly, other fungal infections.
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36
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Lee SS, Lim J, Tan S, Cha J, Yeo SY, Agnew HD, Heath JR. Accurate MALDI-TOF/TOF sequencing of one-bead-one-compound peptide libraries with application to the identification of multiligand protein affinity agents using in situ click chemistry screening. Anal Chem 2010; 82:672-9. [PMID: 20000699 PMCID: PMC2829877 DOI: 10.1021/ac902195y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Combinatorial one-bead-one-compound (OBOC) peptide libraries are widely used for affinity screening, and the sequencing of peptides from hit beads is a key step in the process. For rapid sequencing, CNBr cleavage of the peptides from the beads, followed by de novo sequencing by MALDI-TOF/TOF, is explored. We report on a semiautomated sequencing algorithm and validate it through comparison against Edman degradation sequencing. The initial 44% sequencing success rate of the standard de novo sequencing software was improved to nearly 100%. The sequencing algorithm incorporates existing knowledge of amino acid chemistry and a new strategy for differentiating isobaric amino acids. We tested the algorithm by using MALDI-TOF/TOF to identify a peptide biligand affinity agent against the protein bovine carbonic anhydrase II, starting from comprehensive one-bead-one-compound peptide libraries comprised of non-natural and artificial amino acid components and using the strategy of in situ click/OBOC library screening.
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Affiliation(s)
- Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Sylvia Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Junhoe Cha
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Shi Yun Yeo
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Heather D. Agnew
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
| | - James R. Heath
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
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37
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Hirsch BM, Gallo CA, Du Z, Wang Z, Zheng W. Discovery of potent, proteolytically stable, and cell permeable human sirtuin peptidomimetic inhibitors containing Nε-thioacetyl-lysine. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00089b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Gurard-Levin ZA, Kim J, Mrksich M. Combining mass spectrometry and peptide arrays to profile the specificities of histone deacetylases. Chembiochem 2009; 10:2159-61. [PMID: 19688789 DOI: 10.1002/cbic.200900417] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zachary A Gurard-Levin
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60521, USA
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39
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Baur JA. Biochemical effects of SIRT1 activators. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1626-34. [PMID: 19897059 DOI: 10.1016/j.bbapap.2009.10.025] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 10/06/2009] [Accepted: 10/28/2009] [Indexed: 01/09/2023]
Abstract
SIRT1 is the closest mammalian homologue of enzymes that extend life in lower organisms. Its role in mammals is incompletely understood, but includes modulation of at least 34 distinct targets through its nicotinamide adenine dinucleotide (NAD(+))-dependent deacetylase activity. Recent experiments using small molecule activators and genetically engineered mice have provided new insight into the role of this enzyme in mammalian biology and helped to highlight some of the potentially relevant targets. The most widely employed activator is resveratrol, a small polyphenol that improves insulin sensitivity and vascular function, boosts endurance, inhibits tumor formation, and ameliorates the early mortality associated with obesity in mice. Many of these effects are consistent with modulation of SIRT1 targets, such as PGC1alpha and NFkappaB, however, resveratrol can also activate AMPK, inhibit cyclooxygenases, and influence a variety of other enzymes. A novel activator, SRT1720, as well as various methods to manipulate NAD(+) metabolism, are emerging as alternative methods to increase SIRT1 activity, and in many cases recapitulate effects of resveratrol. At present, further studies are needed to more directly test the role of SIRT1 in mediating beneficial effects of resveratrol, to evaluate other strategies for SIRT1 activation, and to confirm the specific targets of SIRT1 that are relevant in vivo. These efforts are especially important in light of the fact that SIRT1 activators are entering clinical trials in humans, and "nutraceutical" formulations containing resveratrol are already widely available.
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Affiliation(s)
- Joseph A Baur
- Institute for Diabetes, Obesity, and Metabolism, and Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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40
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Jamonnak N, Hirsch BM, Pang Y, Zheng W. Substrate specificity of SIRT1-catalyzed lysine Nepsilon-deacetylation reaction probed with the side chain modified Nepsilon-acetyl-lysine analogs. Bioorg Chem 2009; 38:17-25. [PMID: 19914676 DOI: 10.1016/j.bioorg.2009.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 10/13/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
Peptides containing L-N(epsilon)-acetyl-lysine (L-AcK) or its side chain modified analogs were prepared and assayed using SIRT1, the prototypical human silent information regulator 2 (Sir2) enzyme. While previous studies showed that the side chain acetyl group of L-AcK can be extended to bulkier acyl groups for Sir2 (including SIRT1)-catalyzed lysine N(epsilon)-deacylation reaction, our current study suggested that SIRT1-catalyzed deacetylation reaction had a very stringent requirement for the distance between the alpha-carbon and the side chain acetamido group, with that found in L-AcK being optimal. Moreover, our current study showed that SIRT1 catalyzed the stereospecific deacetylation of L-AcK versus its D-isomer. The results from our current study shall constitute another piece of important information to be considered when designing inhibitors for SIRT1 and Sir2 enzymes in general.
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Affiliation(s)
- Nuttara Jamonnak
- Department of Chemistry, University of Akron, 190 E. Buchtel Commons, Akron, OH 44325, USA
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41
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Chen W, Xu D, Liu L, Peng C, Zhu Y, Ma W, Bian A, Li Z, Jin Z, Zhu S, Xu C, Wang L. Ultrasensitive Detection of Trace Protein by Western Blot Based on POLY-Quantum Dot Probes. Anal Chem 2009; 81:9194-8. [DOI: 10.1021/ac901429a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Wei Chen
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Dinghua Xu
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Liqiang Liu
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Chifang Peng
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Yingyue Zhu
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Wei Ma
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Ai Bian
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Zhe Li
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Zhengyu Jin
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Shuifang Zhu
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Chuanlai Xu
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Libing Wang
- School of Food Science and Technology, State Key Lab of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
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42
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Medintz IL, Farrell D, Susumu K, Trammell SA, Deschamps JR, Brunel FM, Dawson PE, Mattoussi H. Multiplex Charge-Transfer Interactions between Quantum Dots and Peptide-Bridged Ruthenium Complexes. Anal Chem 2009; 81:4831-9. [DOI: 10.1021/ac900412j] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Dorothy Farrell
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Kimihiro Susumu
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Scott A. Trammell
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Jeffrey R. Deschamps
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Florence M. Brunel
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Philip E. Dawson
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Hedi Mattoussi
- Center for Bio/Molecular Science and Engineering, Code 6900, Division of Optical Sciences, Code 5611, Laboratory for the Structure of Matter, Code 6030, U.S. Naval Research Laboratory, Washington, DC 20375, and Departments of Cell Biology and Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
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43
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Kiviranta PH, Suuronen T, Wallén EAA, Leppänen J, Tervonen J, Kyrylenko S, Salminen A, Poso A, Jarho EM. N(epsilon)-thioacetyl-lysine-containing tri-, tetra-, and pentapeptides as SIRT1 and SIRT2 inhibitors. J Med Chem 2009; 52:2153-6. [PMID: 19296597 DOI: 10.1021/jm801401k] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
N()-Thioacetyl-lysine-containing tri-, tetra-, and pentapeptides, based on the alpha-tubulin and p53 protein sequences, were studied as SIRT1 and SIRT2 inhibitors. The potency of the pentapeptides depended on the selection of the side chains. The removal of N- and C-terminal residues of the pentapeptides yielded tripeptides with retained SIRT1 inhibitory activity but decreased SIRT2 inhibitory activity. The most potent SIRT1 inhibitors were equipotent with the reference compound (6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide) with the IC(50) values of 180-330 nM.
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Affiliation(s)
- Päivi H Kiviranta
- Department of Pharmaceutical Chemistry, Institute of Clinical Medicine, University of Kuopio, Kuopio, Finland
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44
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9-Fluorenylmethoxycarbonyl-labeled peptides as substrates in a capillary electrophoresis-based assay for sirtuin enzymes. Anal Biochem 2009; 387:243-8. [DOI: 10.1016/j.ab.2009.01.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 01/27/2009] [Accepted: 01/27/2009] [Indexed: 11/22/2022]
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45
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Wooderchak WL, Zang T, Zhou ZS, Acuña M, Tahara SM, Hevel JM. Substrate Profiling of PRMT1 Reveals Amino Acid Sequences That Extend Beyond the “RGG” Paradigm. Biochemistry 2008; 47:9456-66. [DOI: 10.1021/bi800984s] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Whitney L. Wooderchak
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Tianzhu Zang
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Zhaohui Sunny Zhou
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Marcela Acuña
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Stanley M. Tahara
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Joan M. Hevel
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
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46
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Abstract
Histone modifications modulate chromatin structure and function. A posttranslational modification-randomized, combinatorial library based on the first 21 residues of histone H4 was designed for systematic examination of proteins that interpret a histone code. The 800-member library represented all permutations of most known modifications within the N-terminal tail of histone H4. To determine its utility in a protein binding assay, the on-bead library was screened with an antibody directed against phosphoserine 1 of H4. Among the hits, 59 of 60 sequences were phosphorylated at S1, while 30 of 30 of those selected from the nonhits were unphosphorylated. A 512-member version of the library was then used to determine the binding specificity of the double tudor domain of hJMJD2A, a histone demethylase involved in transcriptional repression. Global linear least-squares fitting of modifications from the identified peptides (40 hits and 34 nonhits) indicated that methylation of K20 was the primary determinant for binding, but that phosphorylation and acetylation of neighboring sites attenuated the interaction. To validate the on-bead screen, isothermal titration calorimetry was performed with 13 H4 peptides. Dissociation constants ranged from 1 mM to 1 microM and corroborated the screening results. The general approach should be useful for probing the specificity of any histone-binding protein.
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Affiliation(s)
- Adam L Garske
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1532, USA
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47
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Gurard-Levin ZA, Mrksich M. The activity of HDAC8 depends on local and distal sequences of its peptide substrates. Biochemistry 2008; 47:6242-50. [PMID: 18470998 PMCID: PMC2605276 DOI: 10.1021/bi800053v] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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This paper introduces a flexible assay for characterizing the activities of the histone deacetylase enzymes. The approach combines mass spectrometry with self-assembled monolayers that present acetylated peptides and enables a label-free and one-step assay of this biochemical activity. The assay was used to characterize the activity of HDAC8 toward peptides taken from the N-terminal tail of the H4 histone and reveals that a distal region of the peptide substrate interacts with the deacetylase at an exosite and contributes to the activity of the substrate. Specifically, a peptide corresponding to residues 8−19 of H4 and having lysine 12 acetylated is an active substrate, but removal of the KRHR (residues 16−19) sequence abolishes activity. Mutation of glycine 11 to arginine in the peptide lacking the KRHR sequence restores activity, demonstrating that both local and distal sequences act synergistically to regulate the activity of the HDAC. Assays with peptides bearing multiply acetylated residues, but in which each acetyl group is isotopically labeled, permit studies of the processive deacetylation of peptides. Peptide substrates having an extended sequence that includes K20 were used to demonstrate that methylation of this residue directly affects HDAC8 activity at K12. This work provides a mechanistic basis for the regulation of HDAC activities by distal sequences and may contribute to studies aimed at evaluating the role of the histone code in regulating gene expression.
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Affiliation(s)
- Zachary A Gurard-Levin
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street,Chicago, Illinois 60521, USA
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48
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Turk BE. Understanding and exploiting substrate recognition by protein kinases. Curr Opin Chem Biol 2008; 12:4-10. [PMID: 18282484 DOI: 10.1016/j.cbpa.2008.01.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
Abstract
Protein kinases play a virtually universal role in cellular regulation and are emerging as an important class of new drug targets, yet the cellular functions of most human kinases largely remain obscure. Aspects of substrate recognition common to all kinases in the ATP nucleotide binding site have been exploited in the generation of analog-specific mutants for exploring kinase function and discovering novel protein substrates. Likewise, understanding interactions with the protein substrate, which differ substantially between kinases, can also help to identify substrates and to produce tools for studying kinase pathways, including fluorescent biosensors. Principles of kinase substrate recognition are particularly valuable in guiding bioinformatics and phosphoproteomics approaches that impact our understanding of signaling pathways and networks on a global scale.
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Affiliation(s)
- Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, P.O. Box 208066, 333 Cedar Street, New Haven, CT 06520, United States.
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49
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Substituting N(epsilon)-thioacetyl-lysine for N(epsilon)-acetyl-lysine in peptide substrates as a general approach to inhibiting human NAD(+)-dependent protein deacetylases. Int J Mol Sci 2008; 9:1-11. [PMID: 19325715 PMCID: PMC2635597 DOI: 10.3390/ijms9010001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 12/21/2007] [Accepted: 01/02/2008] [Indexed: 12/13/2022] Open
Abstract
Inhibitors of human NAD+-dependent protein deacetylases possess great value for deciphering the biology of these enzymes and as potential therapeutics for metabolic and age-related diseases and cancer. In the current study, we have experimentally demonstrated that, the potent inhibition we obtained previously for one of these enzymes (i.e. sirtuin type 1 (SIRT1)) by simply replacing Nε-thioacetyl-lysine for Nε-acetyl-lysine in its peptide substrate, represented a general and efficient strategy to develop potent and selective inhibitors of human NAD+-dependent protein deacetylase enzymes. Indeed, by using this simple inhibition strategy, potent (low-micromolar) and selective (≤40-fold) SIRT2 and SIRT3 inhibitors, which were either comparable or superior to currently existing inhibitors, have also been quickly identified in the current study. These inhibitors could be used as chemical biological tools or as lead compounds for further focused structure-activity optimization.
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50
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