1
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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2
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Zessin M, Meleshin M, Hilscher S, Schiene-Fischer C, Barinka C, Jung M, Schutkowski M. Continuous Fluorescent Sirtuin Activity Assay Based on Fatty Acylated Lysines. Int J Mol Sci 2023; 24:ijms24087416. [PMID: 37108579 PMCID: PMC10138348 DOI: 10.3390/ijms24087416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Lysine deacetylases, like histone deacetylases (HDACs) and sirtuins (SIRTs), are involved in many regulatory processes such as control of metabolic pathways, DNA repair, and stress responses. Besides robust deacetylase activity, sirtuin isoforms SIRT2 and SIRT3 also show demyristoylase activity. Interestingly, most of the inhibitors described so far for SIRT2 are not active if myristoylated substrates are used. Activity assays with myristoylated substrates are either complex because of coupling to enzymatic reactions or time-consuming because of discontinuous assay formats. Here we describe sirtuin substrates enabling direct recording of fluorescence changes in a continuous format. Fluorescence of the fatty acylated substrate is different when compared to the deacylated peptide product. Additionally, the dynamic range of the assay could be improved by the addition of bovine serum albumin, which binds the fatty acylated substrate and quenches its fluorescence. The main advantage of the developed activity assay is the native myristoyl residue at the lysine side chain avoiding artifacts resulting from the modified fatty acyl residues used so far for direct fluorescence-based assays. Due to the extraordinary kinetic constants of the new substrates (KM values in the low nM range, specificity constants between 175,000 and 697,000 M-1s-1) it was possible to reliably determine the IC50 and Ki values for different inhibitors in the presence of only 50 pM of SIRT2 using different microtiter plate formats.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Sebastian Hilscher
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Cyril Barinka
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
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3
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Zessin M, Meleshin M, Sippl W, Schutkowski M. Continuous Histone Deacylase Activity Assays. Methods Mol Biol 2023; 2589:411-428. [PMID: 36255640 DOI: 10.1007/978-1-0716-2788-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein lysine acylation represents one of the most common post-translational modifications. Obviously, highly reactive metabolic intermediates, like thioesters and mixed anhydrides between phosphoric acid and organic acids, modify lysine residues spontaneously. Additionally, enzymes using acyl-CoAs as co-substrates transfer the acyl residue specifically to defined sequences within proteins. The counteracting enzymes are called histone deacetylases (HDACs), releasing the free lysine side chain. Such enzymatic activities are involved in different cellular processes like tumor progression, immune response, regulation of metabolism, and aging. Modulators of such enzymatic activities represent valuable tools in drug discovery. Therefore, direct and continuous assays to monitor enzymatic activity of HDACs are needed. Here we describe different assay formats allowing both monitoring of Zn2+-dependent HDACs via UV-Vis-spectroscopy and NAD+-dependent HDACs (sirtuins) by fluorescence-based assay formats. Additionally, we describe methods enabling efficient screening of HDAC-inhibitors via fluorescence displacement assays.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Saale, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Saale, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Saale, Germany
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Saale, Germany.
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4
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Simon M, Yang J, Gigas J, Earley EJ, Hillpot E, Zhang L, Zagorulya M, Tombline G, Gilbert M, Yuen SL, Pope A, Van Meter M, Emmrich S, Firsanov D, Athreya A, Biashad SA, Han J, Ryu S, Tare A, Zhu Y, Hudgins A, Atzmon G, Barzilai N, Wolfe A, Moody K, Garcia BA, Thomas DD, Robbins PD, Vijg J, Seluanov A, Suh Y, Gorbunova V. A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A. EMBO J 2022; 41:e110393. [PMID: 36215696 PMCID: PMC9627671 DOI: 10.15252/embj.2021110393] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 02/02/2023] Open
Abstract
Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in aging and metabolism regulation. Targeted sequencing of SIRT6 locus in a population of 450 Ashkenazi Jewish (AJ) centenarians and 550 AJ individuals without a family history of exceptional longevity identified enrichment of a SIRT6 allele containing two linked substitutions (N308K/A313S) in centenarians compared with AJ control individuals. Characterization of this SIRT6 allele (centSIRT6) demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double-strand break repair, and more robustly kill cancer cells compared with wild-type SIRT6. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which was correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.
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Affiliation(s)
- Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jiping Yang
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Jonathan Gigas
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Eric J Earley
- Biostatistics and Epidemiology, RTI International, Durham, NC, USA
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Lei Zhang
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Maria Zagorulya
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Greg Tombline
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Michael Gilbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha L Yuen
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Alexis Pope
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | | | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Advait Athreya
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Jeehae Han
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Seungjin Ryu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Archana Tare
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yizhou Zhu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Adam Hudgins
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Paul D Robbins
- Department of Biochemistry, Molecular Biology and Biophysics and Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
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Kalbas D, Meleshin M, Liebscher S, Zessin M, Melesina J, Schiene-Fischer C, Bülbül EF, Bordusa F, Sippl W, Schutkowski M. Small Changes Make the Difference for SIRT2: Two Different Binding Modes for 3-Arylmercapto-Acylated Lysine Derivatives. Biochemistry 2022; 61:1705-1722. [PMID: 35972884 DOI: 10.1021/acs.biochem.2c00211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sirtuins are protein deacylases regulating metabolism and stress responses and implicated in aging-related diseases. Modulators of the human sirtuins 1-7 are sought as chemical tools and potential therapeutics, for example, for treatment of cancer. We were able to show that 3-aryl-mercapto-succinylated- and 3-benzyl-mercapto-succinylated peptide derivatives yield selective Sirt5 inhibitors with low nM Ki values. Here, we synthesized and characterized 3-aryl-mercapto-butyrylated peptide derivatives as effective and selective sirtuin 2 inhibitors with KD values in the low nanomolar range. According to kinetic measurements and microscale thermophoresis/surface plasmon resonance experiments, the respective inhibitors bind with the 3-aryl-mercapto moiety in the selectivity pocket of Sirtuin 2, inducing a rearrangement of the active site. In contrast, 3-aryl-mercapto-nonalyl or palmitoyl derivatives are characterized by a switch in the binding mode blocking both the hydrophobic channel by the fatty acyl chain and the nicotinamide pocket by the 3-aryl-mercapto moiety.
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Affiliation(s)
- Diana Kalbas
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Sandra Liebscher
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Matthes Zessin
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Jelena Melesina
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Emre Fatih Bülbül
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Frank Bordusa
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Wolfgang Sippl
- Department of Medical Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale 06120, Germany
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6
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Zessin M, Meleshin M, Praetorius L, Sippl W, Bařinka C, Schutkowski M. Uncovering Robust Delactoylase and Depyruvoylase Activities of HDAC Isoforms. ACS Chem Biol 2022; 17:1364-1375. [PMID: 35639992 DOI: 10.1021/acschembio.1c00863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Zinc-dependent histone deacetylases (HDACs) and sirtuins (SIRT) represent two different classes of enzymes which are responsible for deacylation of modified lysine side chains. The repertoire of acyl residues on lysine side chains identified in vivo is rapidly growing, and very recently lysine lactoylation was described to be involved in metabolic reprogramming. Additionally, lysine pyruvoylation represents a marker for aging and liver cirrhosis. Here, we report a systematic analysis of acyl-specificity of human zinc-dependent HDAC and sirtuin isoforms. We identified HDAC3 as a robust delactoylase with several-thousand-fold higher activity as compared to SIRT2, which was claimed to be the major in vivo delactoylase. Additionally, we systematically searched for enzymes, capable of removing pyruvoyl residues from lysine side chains. Using model peptides, we uncovered high depyruvoylase activity for HDAC6 and HDAC8. Interestingly, such substrates have extremely low KM values for both HDAC isoforms, pointing to possible in vivo functions.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Lucas Praetorius
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
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7
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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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8
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Wang P, Chen D, An JX, Lin SX, Liu T, Li Y, Chen L, He B. Development of a single-step fluorogenic sirtuin assay and its applications for high-throughput screening. Org Biomol Chem 2022; 20:1243-1252. [PMID: 35050299 DOI: 10.1039/d1ob02347k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sirtuins (SIRTs) are a class of nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases. Since SIRTs have different subcellular locations and different preferences for deacylation activity, SIRTs are not only highly gaining significance in biological functions but also implications in human diseases. Therefore, it is valuable to establish a high-throughput screening method for the rapid and accurate discovery of SIRT modulators. In this study, we designed and synthesized small molecules 4a-d as fluorogenic probes based on the different lysine substrates of SIRTs, which can be recognized and catalyzed by SIRTs and then spontaneous intramolecular transesterification can give the fluorescence. We have undertaken a comprehensive study of these fluorogenic probes with different SIRTs for assay optimization, validation, kinetics, parameters, and applications of high-throughput screening formats. We envision that these probes will provide useful and powerful tools for the highly efficient discovery of more SIRT inhibitors.
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Affiliation(s)
- Pan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Di Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Jian-Xiong An
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Shu-Xian Lin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang, Guizhou 50004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China.
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9
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Zessin M, Meleshin M, Simic Z, Kalbas D, Arbach M, Gebhardt P, Melesina J, Liebscher S, Bordusa F, Sippl W, Barinka C, Schutkowski M. Continuous Sirtuin/HDAC (histone deacetylase) activity assay using thioamides as PET (Photoinduced Electron Transfer)-based fluorescence quencher. Bioorg Chem 2021; 117:105425. [PMID: 34695733 DOI: 10.1016/j.bioorg.2021.105425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 12/28/2022]
Abstract
Histone deacylase 11 and human sirtuins are able to remove fatty acid-derived acyl moieties from the ε-amino group of lysine residues. Specific substrates are needed for investigating the biological functions of these enzymes. Additionally, appropriate screening systems are required for identification of modulators of enzymatic activities of HDAC11 and sirtuins. We designed and synthesized a set of activity probes by incorporation of a thioamide quencher unit into the fatty acid-derived acyl chain and a fluorophore in the peptide sequence. Systematic variation of both fluorophore and quencher position resulted "super-substrates" with catalytic constants of up to 15,000,000 M-1s-1 for human sirtuin 2 (Sirt2) enabling measurements using enzyme concentrations down to 100 pM in microtiter plate-based screening formats. It could be demonstrated that the stalled intermediate formed by the reaction of Sirt2-bound thiomyristoylated peptide and NAD+ has IC50 values below 200 pM.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Marat Meleshin
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Zeljko Simic
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Diana Kalbas
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Miriam Arbach
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Philip Gebhardt
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Jelena Melesina
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Sandra Liebscher
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Frank Bordusa
- Department of Natural Product Biochemistry, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany.
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10
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Nielsen AL, Rajabi N, Kudo N, Lundø K, Moreno-Yruela C, Bæk M, Fontenas M, Lucidi A, Madsen AS, Yoshida M, Olsen CA. Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration. RSC Chem Biol 2021; 2:612-626. [PMID: 34458803 PMCID: PMC8341974 DOI: 10.1039/d0cb00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme. Here, we report a collection of chemical probes that are potent, selective, stable in serum, water-soluble, and inhibit SIRT2-mediated deacetylation and demyristoylation in cells. Compared to the current landscape of SIRT2 inhibitors, this is a unique ensemble of features built into a single compound. We expect the developed chemotypes to find broad application in the interrogation of SIRT2 functions in both healthy and diseased cells, and to provide a foundation for the development of future therapeutics. Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. Here, we developed small peptide-based inhibitors of its activity in living cells in culture.![]()
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Affiliation(s)
- Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Norio Kudo
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Kathrine Lundø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B DK-2200 Copenhagen Denmark
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Alessia Lucidi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
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11
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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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12
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Yuan T, Keijer J, Guo AH, Lombard DB, de Boer VCJ. An optimized desuccinylase activity assay reveals a difference in desuccinylation activity between proliferative and differentiated cells. Sci Rep 2020; 10:17030. [PMID: 33046741 PMCID: PMC7552388 DOI: 10.1038/s41598-020-72833-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/03/2020] [Indexed: 12/21/2022] Open
Abstract
Succinylation is a novel post-translational modification identified on many proteins and is involved in multiple biological processes. Succinylation levels are dynamically regulated, balanced by succinylation and desuccinylation processes, and are closely connected to metabolic state in vivo. Sirtuins have been shown to possess NAD+-dependent desuccinylation activity in vitro and in vivo, among which the desuccinylation activity of SIRT5 is most extensively studied. Our understanding of the response of succinylation levels to different metabolic conditions, is hampered by the lack of a fast NAD+-dependent desuccinylation assay in a physiological context. In the present study, we therefore optimized and validated a fluorescence-based assay for measuring NAD+-dependent desuccinylation activity in cell lysates. Our results demonstrated that shorter and stricter reaction time was critical to approach the initial rate of NAD+-dependent desuccinylation activity in crude cell lysate systems, as compared to the desuccinylation reaction of purified His-SIRT5. Analysis of desuccinylation activity in SIRT5 knockout HEK293T cells confirmed the relevance of SIRT5 in cellular desuccinylation activity, as well as the presence of other NAD+-dependent desuccinylase activities. In addition, we were able to analyse desuccinylation and deacetylation activity in multiple cell lines using this assay. We showed a remarkably higher desuccinylase activity, but not deacetylase activity, in proliferative cultured muscle and adipose cells in comparison with their differentiated counterparts. Our results reveal an alteration in NAD+-dependent desuccinylation activity under different metabolic states.
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Affiliation(s)
- Taolin Yuan
- Human and Animal Physiology, Wageningen University & Research, Wageningen, 6708 WD, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, 6708 WD, The Netherlands
| | - Angela H Guo
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David B Lombard
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vincent C J de Boer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, 6708 WD, The Netherlands.
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13
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Yang LL, Wang HL, Yan YH, Liu S, Yu ZJ, Huang MY, Luo Y, Zheng X, Yu Y, Li GB. Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery. Eur J Med Chem 2020; 192:112201. [DOI: 10.1016/j.ejmech.2020.112201] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/29/2020] [Accepted: 02/29/2020] [Indexed: 01/09/2023]
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14
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Tharp JM, Hampton JT, Reed CA, Ehnbom A, Chen PHC, Morse JS, Kurra Y, Pérez LM, Xu S, Liu WR. An amber obligate active site-directed ligand evolution technique for phage display. Nat Commun 2020; 11:1392. [PMID: 32170178 PMCID: PMC7070036 DOI: 10.1038/s41467-020-15057-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/14/2020] [Indexed: 01/19/2023] Open
Abstract
Although noncanonical amino acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two decades ago, their application for use in drug discovery has been limited due to inherent library bias towards sense-containing phages. Here, we report a technique based on superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias that has hindered incorporation of ncAAs into phage libraries. We then take advantage of this technique for development of active site-directed ligand evolution of peptides, where the ncAA serves as an anchor to direct the binding of its peptides to the target’s active site. To demonstrate this, phage-displayed peptide libraries are developed that contain a genetically encoded butyryl lysine and are subsequently used to select for ligands that bind SIRT2. These ligands are then modified to develop low nanomolar inhibitors of SIRT2. Most epigenetic regulator inhibitors target tunnels of active sites, rather than the peptide binding groove, leading to concerns with low selectivity. Here the authors use an amber obligate phage library to rapidly identify isoform-selective inhibitors of SIRT2.
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Affiliation(s)
- Jeffery M Tharp
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - J Trae Hampton
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Catrina A Reed
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Andreas Ehnbom
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Peng-Hsun Chase Chen
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jared S Morse
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagirri Kurra
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa M Pérez
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA. .,Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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15
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Wang T, Wang Y, Liu L, Jiang Z, Li X, Tong R, He J, Shi J. Research progress on sirtuins family members and cell senescence. Eur J Med Chem 2020; 193:112207. [PMID: 32222662 DOI: 10.1016/j.ejmech.2020.112207] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/13/2020] [Accepted: 03/04/2020] [Indexed: 02/05/2023]
Abstract
Human aging is a phenomenon of gradual decline and loss of cell, tissue, organ and other functions under the action of external environment and internal factors. It is mainly related to genomic instability, telomere wear, mitochondrial dysfunction, protein balance disorder, antioxidant damage, microRNA expression disorder and so on. Sirtuins protein is a kind of deacetylase which can regulate cell metabolism and participate in a variety of cell physiological functions. It has been found that sirtuins family can prolong the lifespan of yeast. Sirtuins can inhibit human aging through many signaling pathways, including apoptosis signaling pathway, mTOR signaling pathway, sirtuins signaling pathway, AMPK signaling pathway, phosphatidylinositol 3 kinase (PI3K) signaling pathway and so on. Based on this, this paper reviews the action principle of anti-aging star members of sirtuins family Sirt1, Sirt3 and Sirt6 on anti-aging related signaling pathways and typical compounds, in order to provide ideas for the screening of anti-aging compounds of sirtuins family members.
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Affiliation(s)
- Ting Wang
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yujue Wang
- Department of Obstetrics and Gynecology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, China
| | - Li Liu
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Zhongliang Jiang
- Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xingxing Li
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Rongsheng Tong
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Jun He
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu, 610041, China.
| | - Jianyou Shi
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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16
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Structural basis for the activation and inhibition of Sirtuin 6 by quercetin and its derivatives. Sci Rep 2019; 9:19176. [PMID: 31844103 PMCID: PMC6914789 DOI: 10.1038/s41598-019-55654-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Mammalian Sirtuin 6 (Sirt6) is an NAD+-dependent protein deacylase regulating metabolism and chromatin homeostasis. Sirt6 activation protects against metabolic and aging-related diseases, and Sirt6 inhibition is considered a cancer therapy. Available Sirt6 modulators show insufficient potency and specificity, and even partially contradictory Sirt6 effects were reported for the plant flavone quercetin. To understand Sirt6 modulation by quercetin-based compounds, we analysed their binding and activity effects on Sirt6 and other Sirtuin isoforms and solved crystal structures of compound complexes with Sirt6 and Sirt2. We find that quercetin activates Sirt6 via the isoform-specific binding site for pyrrolo[1,2-a]quinoxalines. Its inhibitory effect on other isoforms is based on an alternative binding site at the active site entrance. Based on these insights, we identified isoquercetin as a ligand that can discriminate both sites and thus activates Sirt6 with increased specificity. Furthermore, we find that quercetin derivatives that inhibit rather than activate Sirt6 exploit the same general Sirt6 binding site as the activators, identifying it as a versatile allosteric site for Sirt6 modulation. Our results thus provide a structural basis for Sirtuin effects of quercetin-related compounds and helpful insights for Sirt6-targeted drug development.
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17
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Kutil Z, Mikešová J, Zessin M, Meleshin M, Nováková Z, Alquicer G, Kozikowski A, Sippl W, Bařinka C, Schutkowski M. Continuous Activity Assay for HDAC11 Enabling Reevaluation of HDAC Inhibitors. ACS OMEGA 2019; 4:19895-19904. [PMID: 31788622 PMCID: PMC6882135 DOI: 10.1021/acsomega.9b02808] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/18/2019] [Indexed: 05/05/2023]
Abstract
Histone deacetylase 11 (HDAC11) preferentially removes fatty acid residues from lysine side chains in a peptide or protein environment. Here, we report the development and validation of a continuous fluorescence-based activity assay using an internally quenched TNFα-derived peptide derivative as a substrate. The threonine residue in the +1 position was replaced by the quencher amino acid 3'-nitro-l-tyrosine and the fatty acyl moiety substituted by 2-aminobenzoylated 11-aminoundecanoic acid. The resulting peptide substrate enables fluorescence-based direct and continuous readout of HDAC11-mediated amide bond cleavage fully compatible with high-throughput screening formats. The Z'-factor is higher than 0.85 for the 15 μM substrate concentration, and the signal-to-noise ratio exceeds 150 for 384-well plates. In the absence of NAD+, this substrate is specific for HDAC11. Reevaluation of inhibitory data using our novel assay revealed limited potency and selectivity of known HDAC inhibitors, including Elevenostat, a putative HDAC11-specific inhibitor.
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Affiliation(s)
- Zsófia Kutil
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jana Mikešová
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Matthes Zessin
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Marat Meleshin
- Department
of Enzymology, Institute of Biochemistry and Biotechnology, Charles
Tanford Protein Centre, Martin Luther University
Halle-Wittenberg, Kurt-Mothes-Straße
3a, 06120 Halle
(Saale), Germany
| | - Zora Nováková
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Glenda Alquicer
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Alan Kozikowski
- StarWise
Therapeutics LLC, 505
S Rosa Road, Suite 27, Madison, Wisconsin 53719-1235, United States
| | - Wolfgang Sippl
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Cyril Bařinka
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
- E-mail: . Tel.: +420-325-873-777 (C.B.)
| | - Mike Schutkowski
- Department
of Enzymology, Institute of Biochemistry and Biotechnology, Charles
Tanford Protein Centre, Martin Luther University
Halle-Wittenberg, Kurt-Mothes-Straße
3a, 06120 Halle
(Saale), Germany
- E-mail: . Tel.: +49-345-5524-828 (M.S.)
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18
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Zessin M, Kutil Z, Meleshin M, Nováková Z, Ghazy E, Kalbas D, Marek M, Romier C, Sippl W, Bařinka C, Schutkowski M. One-Atom Substitution Enables Direct and Continuous Monitoring of Histone Deacylase Activity. Biochemistry 2019; 58:4777-4789. [PMID: 31682411 DOI: 10.1021/acs.biochem.9b00786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We developed a one-step direct assay for the determination of histone deacylase (HDAC) activity by substituting the carbonyl oxygen of the acyl moiety with sulfur, resulting in thioacylated lysine side chains. This modification is recognized by class I HDACs with different efficiencies ranging from not accepted for HDAC1 to kinetic constants similar to that of the parent oxo substrate for HDAC8. Class II HDACs can hydrolyze thioacylated substrates with approximately 5-10-fold reduced kcat values, which resembles the effect of thioamide substitution in metallo-protease substrates. Class IV HDAC11 accepts thiomyristoyl modification less efficiently with an ∼5-fold reduced specificity constant. On the basis of the unique spectroscopic properties of thioamide bonds (strong absorption in spectral range of 260-280 nm and efficient fluorescence quenching), HDAC-mediated cleavage of thioamides could be followed by ultraviolet-visible and fluorescence spectroscopy in a continuous manner. The HDAC activity assay is compatible with microtiter plate-based screening formats up to 1536-well plates with Z' factors of >0.75 and signal-to-noise ratios of >50. Using thioacylated lysine residues in p53-derived peptides, we optimized substrates for HDAC8 with a catalytic efficiency of >250000 M-1 s-1, which are more than 100-fold more effective than most of the known substrates. We determined inhibition constants of several inhibitors for human HDACs using thioacylated peptidic substrates and found good correlation with the values from the literature. On the other hand, we could introduce N-methylated, N-acylated lysine residues as inhibitors for HDACs with an IC50 value of 1 μM for an N-methylated, N-myristoylated peptide derivative and human HDAC11.
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Affiliation(s)
- Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Zora Nováková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Ehab Ghazy
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Diana Kalbas
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Martin Marek
- Departement de Biologie Structurale Integrative, Institut de Genetique et Biologie Moleculaire et Cellulaire (IGBMC) , Universite de Strasbourg (UDS), CNRS, INSERM , 1 rue Laurent Fries, B.P. 10142 , 67404 Illkirch Cedex IGBMC, France
| | - Christophe Romier
- Departement de Biologie Structurale Integrative, Institut de Genetique et Biologie Moleculaire et Cellulaire (IGBMC) , Universite de Strasbourg (UDS), CNRS, INSERM , 1 rue Laurent Fries, B.P. 10142 , 67404 Illkirch Cedex IGBMC, France
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles-Tanford-Protein Center , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
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19
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Dai Q, Zheng Z, Xia F, Liu P, Li M. A one-step specific assay for continuous detection of sirtuin 2 activity. Acta Pharm Sin B 2019; 9:1183-1192. [PMID: 31867164 PMCID: PMC6900550 DOI: 10.1016/j.apsb.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022] Open
Abstract
Sirtuins (SIRTs) are nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases with diverse physiological functions. A variety of small molecules have been developed to interrogate the physiological function of SIRTs. Therefore, it is desirable to establish efficient and convenient assays to screen SIRTs modulators. In this study, we designed a series of fluorescent nonapeptide probes derived from substrates of SIRT1–SIRT3. Fluorescence increment of these probes is based on SIRT-mediated removal of the acyl side chain with fluorophore, which makes this system free of lysine-recognizing protease. Comparing the reaction of these fluorescent nonapeptide substrates with SIRT1–SIRT3 and SIRT6, it was confirmed that this assessment system was the most suitable for SIRT2 activity detection. Thus, SIRT2 was used to modify substrates by truncating the amino acids or lysine side chain of nonapeptide. Finally, two specific and efficient fluorescent probes for SIRT2, ne-D9 and ne-K4a, were developed. Evaluation of the results revealed that ne-K4a based assay was more suitable for modulators screening in vitro, while the other specific substrate ne-D9 was stable in cell lysate and could detect the activity of SIRT2 in the same. In summary, this study presents a novel strategy for detecting SIRT2 activity in vitro and in cell lysate.
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20
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Hori Y, Kikuchi K. Chemical Tools with Fluorescence Switches for Verifying Epigenetic Modifications. Acc Chem Res 2019; 52:2849-2857. [PMID: 31577127 DOI: 10.1021/acs.accounts.9b00349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Epigenetic DNA and histone modifications alter chromatin conformation and regulate gene expression. A major DNA modification is methylation, which is catalyzed by DNA methyltransferase (Dnmt) and results in gene suppression. Compared to DNA, histones undergo a greater variety of modification types, one of which is the acetylation of lysine. While histone acetyltransferase (HAT) catalyzes acetylation and activates gene expression, histone deacetylase (HDAC) removes the modification and causes gene suppression. As precise regulation of these epigenetic marks on DNA and histones is critical for cellular functions, their dysregulation causes various diseases including cancer, metabolic syndromes, immune diseases, and psychiatric diseases. Therefore, elucidation of the epigenetic phenomena is important not only in the field of biology but also in medical and pharmaceutical sciences. Furthermore, this field is also attracting industrial interest, because small-molecule inhibitors modulate enzymatic activity for epigenetic modification and are used for cancer treatment. Under these circumstances, various methods for detecting epigenetic modifications have been developed. However, most methods require cell lysis, which is not suitable for real-time detection of enzymatic activity. Since fluorescent probes are attractive chemical tools to solve this issue, chemists made considerable efforts to create fluorescent probes for epigenetics. To date, we have particularly focused on HDAC activity and DNA methylation and have developed fluorescent probes for their detection. The first part of this review describes our recent efforts to develop fluorescent probes for detecting HDAC activity. Since the discovery of HDAC activity in the late 1960s, no fluorescent probe has been developed that can detect enzymatic reactions in a simple, one-step procedure despite its biological and medical importance. We designed fluorescent probes to overcome this limitation by devising two different types of fluorescence switching mechanisms, which are based on aggregation-induced emission (AIE) and intramolecular transesterification. Using these probes, we detected HDAC activity simply by mixing the probes and HDAC for the first time. In the second part, a hybrid approach using a protein-labeling system was employed to detect DNA methylation in living cells. So far, live-cell detection of DNA methylation was conducted by imaging the localization of Fluorescent Proteins (FPs) fused to a methylated DNA-binding domain. However, FP lacks a fluorescence switch and emits fluorescence without binding to methylated DNA. We created a hybrid probe that comprises a fluorogen and a protein and enhances fluorescence intensity upon binding to methylated DNA. To create the hybrid probe, we applied our protein labeling system using the PYP-tag that we previously developed. This method successfully visualized methylated DNA in living cells and verified its dynamics during cell division. Both of the above-mentioned fluorescent probes have great potential for use not only in HDAC and DNA methylation but also in other epigenetics-associated modifications. For example, the mechanism of the HDAC probes can be used to detect histone demethylation. The hybrid probe can be converted to a sensor for imaging acetylated or methylated histones. In this review, we mainly describe how we designed the probes using chemical principles and solved the current obstacles with the probe design and discuss the future prospects of these probes.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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21
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Tian X, Firsanov D, Zhang Z, Cheng Y, Luo L, Tombline G, Tan R, Simon M, Henderson S, Steffan J, Goldfarb A, Tam J, Zheng K, Cornwell A, Johnson A, Yang JN, Mao Z, Manta B, Dang W, Zhang Z, Vijg J, Wolfe A, Moody K, Kennedy BK, Bohmann D, Gladyshev VN, Seluanov A, Gorbunova V. SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species. Cell 2019; 177:622-638.e22. [PMID: 31002797 PMCID: PMC6499390 DOI: 10.1016/j.cell.2019.03.043] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/22/2019] [Accepted: 03/21/2019] [Indexed: 01/09/2023]
Abstract
DNA repair has been hypothesized to be a longevity determinant, but the evidence for it is based largely on accelerated aging phenotypes of DNA repair mutants. Here, using a panel of 18 rodent species with diverse lifespans, we show that more robust DNA double-strand break (DSB) repair, but not nucleotide excision repair (NER), coevolves with longevity. Evolution of NER, unlike DSB, is shaped primarily by sunlight exposure. We further show that the capacity of the SIRT6 protein to promote DSB repair accounts for a major part of the variation in DSB repair efficacy between short- and long-lived species. We dissected the molecular differences between a weak (mouse) and a strong (beaver) SIRT6 protein and identified five amino acid residues that are fully responsible for their differential activities. Our findings demonstrate that DSB repair and SIRT6 have been optimized during the evolution of longevity, which provides new targets for anti-aging interventions.
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Affiliation(s)
- Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Cheng
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Lingfeng Luo
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Ruiyue Tan
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Steven Henderson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Janine Steffan
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Audrey Goldfarb
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Jonathan Tam
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Kitty Zheng
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Adam Cornwell
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Adam Johnson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Jiang-Nan Yang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstraße 11, Jena D-07745, Germany
| | - Zhiyong Mao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Bruno Manta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weiwei Dang
- Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aaron Wolfe
- Ichor Therapeutics, 2521 US-11, Lafayette, NY 13084, USA
| | - Kelsey Moody
- Ichor Therapeutics, 2521 US-11, Lafayette, NY 13084, USA
| | - Brian K Kennedy
- Departments of Biochemistry and Physiology, National University Singapore, Singapore; Centre for Healthy Aging, National University Health System, Singapore
| | - Dirk Bohmann
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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22
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A Novel Substrate Radiotracer for Molecular Imaging of SIRT2 Expression and Activity with Positron Emission Tomography. Mol Imaging Biol 2019; 20:594-604. [PMID: 29423902 PMCID: PMC6816246 DOI: 10.1007/s11307-017-1149-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE The purpose of this study was to develop a SIRT2-specific substrate-type radiotracer for non-invasive PET imaging of epigenetic regulatory processes mediated by SIRT2 in normal and disease tissues. PROCEDURES A library of compounds containing tert-butyloxycarbonyl-lysine-aminomethylcoumarin backbone was derivatized with fluoroalkyl chains 3-16 carbons in length. SIRT2 most efficiently cleaved the myristoyl, followed by 12-fluorododecanoic and 10-fluorodecanoic groups (Kcat/Km 716.5 ± 72.8, 615.4 ± 50.5, 269.5 ± 52.1/s mol, respectively). Radiosynthesis of 12- [18F]fluorododecanoic aminohexanoicanilide (12-[18F]DDAHA) was achieved by nucleophilic radiofluorination of 12-iododecanoic-AHA precursor. RESULTS A significantly higher accumulation of 12-[18F]DDAHA was observed in MCF-7 and MDA-MB-435 cells in vitro as compared to U87, MiaPaCa, and MCF10A, which was consistent with levels of SIRT2 expression. Initial in vivo studies using 12-[18F]DDAHA conducted in a 9L glioma-bearing rats were discouraging, due to rapid defluorination of this radiotracer upon intravenous administration, as evidenced by significant accumulation of F-18 radioactivity in the skull and other bones, which confounded the interpretation of images of radiotracer accumulation within the tumor and other regions of the brain. CONCLUSIONS The next generation of SIRT2-specific radiotracers resistant to systemic defluorination should be developed using alternative sites of radiofluorination on the aliphatic chain of DDAHA. A SIRT2-selective radiotracer may provide information about SIRT2 expression and activity in tumors and normal organs and tissues, which may help to better understand the roles of SIRT2 in different diseases.
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23
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Chen D, Yan L, Zheng W. Cyclic Peptide-Based Sirtuin Substrates. Molecules 2019; 24:E424. [PMID: 30682801 PMCID: PMC6384901 DOI: 10.3390/molecules24030424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/17/2022] Open
Abstract
In the current study, four side chain-to-side chain cyclic peptides (three 5-mers and one 4-mer) harboring Nε-acetyl-lysine or Nε-myristoyl-lysine were found to be in vitro substrates of the human SIRT1/2/3-catalyzed deacylation with good substrate activities, as judged by the kcat/KM ratios.
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Affiliation(s)
- Di Chen
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Lingling Yan
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
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24
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You W, Steegborn C. Structural Basis of Sirtuin 6 Inhibition by the Hydroxamate Trichostatin A: Implications for Protein Deacylase Drug Development. J Med Chem 2018; 61:10922-10928. [PMID: 30395713 DOI: 10.1021/acs.jmedchem.8b01455] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein lysine deacylases comprise three zinc-dependent families and the NAD+-dependent sirtuins Sirt1-7, which contribute to aging-related diseases. Few Sirt6-specific inhibitors are available. Trichostatin A, which belongs to the potent, zinc-chelating hydroxamate inhibitors of zinc-dependent deacylases, was recently found to potently and isoform-specifically inhibit Sirt6. We solved a crystal structure of a Sirt6/ADP-ribose/trichostatin A complex, which reveals nicotinamide pocket and acyl channel as binding site and provides interaction details supporting the development of improved deacylase inhibitors.
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Affiliation(s)
- Weijie You
- Department of Biochemistry , University of Bayreuth , Universitätsstraße 30 , 95445 Bayreuth , Germany
| | - Clemens Steegborn
- Department of Biochemistry , University of Bayreuth , Universitätsstraße 30 , 95445 Bayreuth , Germany
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25
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Spinck M, Ecke M, Sievers S, Neumann H. Highly Sensitive Lysine Deacetylase Assay Based on Acetylated Firefly Luciferase. Biochemistry 2018; 57:3552-3555. [DOI: 10.1021/acs.biochem.8b00483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Spinck
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Maria Ecke
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sonja Sievers
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Heinz Neumann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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26
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Dai H, Sinclair DA, Ellis JL, Steegborn C. Sirtuin activators and inhibitors: Promises, achievements, and challenges. Pharmacol Ther 2018; 188:140-154. [PMID: 29577959 DOI: 10.1016/j.pharmthera.2018.03.004] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NAD+-dependent protein lysine deacylases of the Sirtuin family regulate various physiological functions, from energy metabolism to stress responses. The human Sirtuin isoforms, SIRT1-7, are considered attractive therapeutic targets for aging-related diseases, such as type 2 diabetes, inflammatory diseases and neurodegenerative disorders. We review the status of Sirtuin-targeted drug discovery and development. Potent and selective pharmacological Sirt1 activators and inhibitors are available, and initial clinical trials have been carried out. Several promising inhibitors and activators have also been described for other isoforms. Progress in understanding the mechanisms of Sirtuin modulation by such compounds provides a rational basis for further drug development.
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Affiliation(s)
- Han Dai
- GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, PA 19426, USA
| | - David A Sinclair
- Department of Genetics, Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - James L Ellis
- GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, PA 19426, USA
| | - Clemens Steegborn
- Department of Biochemistry and Research Center for Bio-Macromolecules, University of Bayreuth, 95440 Bayreuth, Germany.
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27
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Kutil Z, Novakova Z, Meleshin M, Mikesova J, Schutkowski M, Barinka C. Histone Deacetylase 11 Is a Fatty-Acid Deacylase. ACS Chem Biol 2018; 13:685-693. [PMID: 29336543 DOI: 10.1021/acschembio.7b00942] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Histone deacetylase 11 (HDAC11) is a sole member of the class IV HDAC subfamily with negligible intrinsic deacetylation activity. Here, we report in vitro profiling of HDAC11 deacylase activities, and our data unequivocally show that the enzyme efficiently removes acyl moieties spanning 8-18 carbons from the side chain nitrogen of the lysine residue of a peptidic substrate. Additionally, N-linked lipoic acid and biotin are removed by the enzyme, although with lower efficacy. Catalytic efficiencies toward dodecanoylated and myristoylated peptides were 77 700 and 149 000 M-1 s-1, respectively, making HDAC11 the most proficient fatty-acid deacylase of the HDAC family. Interestingly, HDAC11 is strongly inhibited by free myristic, palmitic, and stearic acids with inhibition constants of 6.5, 0.9, and 1.6 μM, respectively. At the same time, its deacylase activity is stimulated more than 2.5-fold by both palmitoyl-coenzyme A and myristoyl-coenzyme A, pointing toward metabolic control of the enzymatic activity by fatty-acid metabolites. Our data reveal novel enzymatic activity of HDAC11 that can, in turn, facilitate the uncovering of additional biological functions of the enzyme as well as the design of isoform-specific HDAC inhibitors.
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Affiliation(s)
- Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Marat Meleshin
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Jana Mikesova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Mike Schutkowski
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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28
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Kalbas D, Liebscher S, Nowak T, Meleshin M, Pannek M, Popp C, Alhalabi Z, Bordusa F, Sippl W, Steegborn C, Schutkowski M. Potent and Selective Inhibitors of Human Sirtuin 5. J Med Chem 2018; 61:2460-2471. [PMID: 29494161 DOI: 10.1021/acs.jmedchem.7b01648] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sirtuins are protein deacylases that regulate metabolism and stress responses and are implicated in aging-related diseases. Modulators of the human sirtuins Sirt1-7 are sought as chemical tools and potential therapeutics, e.g., for cancer. Selective and potent inhibitors are available for Sirt2, but selective inhibitors for Sirt5 with Ki values in the low nanomolar range are lacking. We synthesized and screened 3-arylthiosuccinylated and 3-benzylthiosuccinylated peptide derivatives yielding Sirt5 inhibitors with low-nanomolar Ki values. A biotinylated derivative with this scaffold represents an affinity probe for human Sirt5 that is able to selectively extract this enzyme out of complex biological samples like cell lysates. Crystal structures of Sirt5/inhibitor complexes reveal that the compounds bind in an unexpected manner to the active site of Sirt5.
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Affiliation(s)
- Diana Kalbas
- Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Sandra Liebscher
- Department of Natural Product Biochemistry, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Theresa Nowak
- Department of Medical Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Martin Pannek
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany
| | - Corinna Popp
- Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Zayan Alhalabi
- Department of Medical Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Frank Bordusa
- Department of Natural Product Biochemistry, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Wolfgang Sippl
- Department of Medical Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
| | - Clemens Steegborn
- Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany
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29
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Rooker DR, Klyubka Y, Gautam R, Tomat E, Buccella D. Peptide-Based Fluorescent Probes for Deacetylase and Decrotonylase Activity: Toward a General Platform for Real-Time Detection of Lysine Deacylation. Chembiochem 2018; 19:496-504. [PMID: 29235227 DOI: 10.1002/cbic.201700582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 12/11/2022]
Abstract
Histone deacetylases regulate the acetylation levels of numerous proteins and play key roles in physiological processes and disease states. In addition to acetyl groups, deacetylases can remove other acyl modifications on lysines, the roles and regulation of which are far less understood. A peptide-based fluorescent probe for single-reagent, real-time detection of deacetylase activity that can be readily adapted for probing broader lysine deacylation, including decrotonylation, is reported. Following cleavage of the lysine modification, the probe undergoes rapid intramolecular imine formation that results in marked optical changes, thus enabling convenient detection of deacylase activity with good statistical Z' factors for both absorption and fluorescence modalities. The peptide-based design offers broader isozyme scope than that of small-molecule analogues, and is suitable for probing both metal- and nicotinamide adenine dinucleotide (NAD+ )-dependent deacetylases. With an effective sirtuin activity assay in hand, it is demonstrated that iron chelation by Sirtinol, a commonly employed sirtuin inhibitor, results in an enhancement in the inhibitory activity of the compound that may affect its performance in vivo.
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Affiliation(s)
- Debra R Rooker
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yuliya Klyubka
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ritika Gautam
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Elisa Tomat
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Daniela Buccella
- Department of Chemistry, New York University, New York, NY, 10003, USA
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30
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Toro TB, Bryant JR, Watt TJ. Lysine Deacetylases Exhibit Distinct Changes in Activity Profiles Due to Fluorophore Conjugation of Substrates. Biochemistry 2017; 56:4549-4558. [PMID: 28749131 PMCID: PMC5937523 DOI: 10.1021/acs.biochem.7b00270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity. Here, we have compared the activity of several KDACs, representing all major classes of KDACs, with substrates in the presence and absence of AMC as well as peptides for which tryptophan has been substituted for AMC. Our results unequivocally demonstrate that AMC has a significant effect on activity for all KDACs tested. Furthermore, in neither the nature of the effect nor the magnitude is consistent across KDACs, making it impossible to predict the effect of AMC on a particular enzyme-substrate pair. AMC did not affect acetyllysine preference in a multiply acetylated substrate. In contrast, AMC significantly enhanced KDAC6 substrate affinity, greatly reduced Sirt1 activity, eliminated the substrate sequence specificity of KDAC4, and had no consistent effect with KDAC8 substrates. These results indicate that profiling of KDAC activity with labeled peptides is unlikely to produce biologically relevant data.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Jenae R. Bryant
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
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31
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Pande S, Kratasyuk VA, Medvedeva NN, Kolenchukova OA, Salmina AB. Nutritional biomarkers: Current view and future perspectives. Crit Rev Food Sci Nutr 2017; 58:3055-3069. [PMID: 28678523 DOI: 10.1080/10408398.2017.1350136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is a poor relationship between nutrient intake and existing nutritional biomarkers due to variety of factors affecting their sensitivity and specificity. To explore the impact of nutrients at molecular level and devising a sensitive biomarker, proteomics is a central technology with sirtuins as one of the most promising nutritional biomarker. Sirtuins (seven mammalian sirtuins reported so far) have been reported to perform protein deacetylases and ADP-ribosyltransferases activity. It is distributed in different cellular compartments thereby controlling several metabolic processes. Sirtuins are oxidized nicotinamide adenine dinucleotide dependent, which implicates a direct effect of the metabolic state of the cell on its activity. Calorie restriction upregulates the mammalian sirtuin protein levels in variety of tissues and organs where it acts upon both histone and nonhistone substrates. Sirtuin senses nutrient availability and impacts gluconeogenesis, glycolysis, and insulin sensitivity. It deacetylates and inhibits the nuclear receptor that activates fat synthesis and adipogenesis in the body, leading to fat loss and bringing favorable cellular and health changes. Sirtuins mediates intracellular response that promotes cell survival, DNA damage repair thereby increasing the cell longitivity. The activation of sirtuins brings a wide spectrum of other health benefits and its activity levels are indicative of nutritional status as well as disease progression in cancer, inflammation, obesity, cardiovascular diseases, and viral infections. There are several foods that activate sirtuin activity and offer significant health benefits by their consumption.
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Affiliation(s)
- Shubhra Pande
- a Laboratory of Bioluminescent Biotechnologies, Department of Biophysics , Institute of Fundamental Biology and Biotechnology, Siberian Federal University , Krasnoyarsk , Russia.,b Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky , Krasnoyarsk , Russia
| | - Valentina A Kratasyuk
- a Laboratory of Bioluminescent Biotechnologies, Department of Biophysics , Institute of Fundamental Biology and Biotechnology, Siberian Federal University , Krasnoyarsk , Russia.,c Federal State Budgetary Scientific Institution "Institute of Biophysics, Siberian Branch of RAS" , Krasnoyarsk , Russia
| | - Nadezhda N Medvedeva
- b Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky , Krasnoyarsk , Russia
| | - Oxana A Kolenchukova
- a Laboratory of Bioluminescent Biotechnologies, Department of Biophysics , Institute of Fundamental Biology and Biotechnology, Siberian Federal University , Krasnoyarsk , Russia.,d Federal State Budgetary Scientific Institution "Scientific Research Institute of medical problems of the North" , Krasnoyarsk , Russia
| | - Alla B Salmina
- b Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky , Krasnoyarsk , Russia
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32
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Kawaguchi M, Ikegawa S, Ieda N, Nakagawa H. A Fluorescent Probe for Imaging Sirtuin Activity in Living Cells, Based on One-Step Cleavage of the Dabcyl Quencher. Chembiochem 2016; 17:1961-1967. [PMID: 27542094 PMCID: PMC5095863 DOI: 10.1002/cbic.201600374] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Indexed: 12/14/2022]
Abstract
Sirtuins (SIRTs) are a family of NAD+‐dependent histone deacetylases. In mammals, dysfunction of SIRTs is associated with age‐related metabolic diseases and cancers, so SIRT modulators are considered attractive therapeutic targets. However, current screening methodologies are problematic, and no tools for imaging endogenous SIRT activity in living cells have been available until now. In this work we present a series of simple and highly sensitive new SIRT activity probes. Fluorescence of these probes is activated by SIRT‐mediated hydrolytic release of a 4‐(4‐dimethylaminophenylazo)benzoyl (Dabcyl)‐based FRET quencher moiety from the ϵ‐amino group of lysine in a nonapeptide derived from histone H3K9 and bearing a C‐terminal fluorophore. The probe SFP3 detected activities of SIRT1, ‐2, ‐3, and ‐6, which exhibit deacylase activities towards long‐chain fatty acyl groups. We then truncated the molecular structure of SFP3 in order to improve both its stability to peptidases and its membrane permeability, and developed probe KST‐F, which showed specificity for SIRT1 over SIRT2 and SIRT3. We show that KST‐F can visualize endogenous SIRT1 activity in living cells.
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Affiliation(s)
- Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Shohei Ikegawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan.
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