1
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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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2
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Wei W, Zhang J, Xu Z, Liu Z, Huang C, Cheng K, Meng L, Matsuda Y, Hao Q, Zhang H, Sun H. Universal Strategy to Develop Fluorogenic Probes for Lysine Deacylase/Demethylase Activity and Application in Discriminating Demethylation States. ACS Sens 2023; 8:28-39. [PMID: 36602906 DOI: 10.1021/acssensors.2c01345] [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: 01/06/2023]
Abstract
Dynamically controlling the post-translational modification of the ε-amino groups of lysine residues is critical for regulating many cellular events. Increasing studies have revealed that many important diseases, including cancer and neurological disorders, are associated with the malfunction of lysine deacylases and demethylases. Developing fluorescent probes that are capable of detecting lysine deacylase and demethylase activity is highly useful for interrogating their roles in epigenetic regulation and diseases. Due to the distinct substrate recognition of these epigenetic eraser enzymes, designing a universal strategy for detecting their activity poses substantial difficulty. Moreover, designing activity-based probes for differentiating their demethylation states is even more challenging and still remains largely unexplored. Herein, we report a universal strategy to construct probes that can detect the enzymatic activity of epigenetic "erasers" through NBD-based long-distance intramolecular reactions. The probes can be easily prepared by installing the O-NBD group at the C-terminal residue of specific peptide substrates by click chemistry. Based on this strategy, detecting the activity of lysine deacetylase, desuccinylase, or demethylase with superior sensitivity and selectivity has been successfully achieved through single-step probe development. Furthermore, the demethylase probe based on this strategy is capable of distinguishing different demethylation states by both absorption and fluorescence lifetime readout. We envision that these newly developed probes will provide powerful tools to facilitate drug discovery in epigenetics in the future.
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Affiliation(s)
- Wenyu Wei
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Jie Zhang
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Zhiqiang Xu
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Zhiyang Liu
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Chen Huang
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Ke Cheng
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Lingkuan Meng
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Yudai Matsuda
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China
| | - Quan Hao
- Department of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong999077, China
| | - Huatang Zhang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong510006, China
| | - Hongyan Sun
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
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3
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Kawaguchi M, Nakajima Y, Nakagawa H. Development of Sirtuin Fluorescence Probes and Medicinal Chemistry Research Targeting SIRT Family. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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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] [MESH Headings] [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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5
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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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6
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Roopa, Priya B, Bhalla V, Kumar M, Kumar N. Fluorescent molecular probe-based activity and inhibition monitoring of histone deacetylases. Chem Commun (Camb) 2021; 57:11153-11164. [PMID: 34613324 DOI: 10.1039/d1cc04034k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Extensive studies in recent decades have revealed that gene expression regulation is not limited to genetic mutations but also to processes that do not alter the genetic sequence. Post-translational histone modification is one of these processes in addition to DNA or RNA modifications. Histone modifications are essential in controlling histone functions and play a vital role in cellular gene expression. The reversible histone acetylation, regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is an example of such modifications. HDACs are involved in the deacetylation of histones and lead to the termination of gene expression. Although this cellular process is essential, upregulation of HDACs is found in numerous cancers. Therefore, research related to the activity and inhibition monitoring of HDACs is necessary to gain profound knowledge of these enzymes and evaluate the success of the therapeutic approach. In this perspective, methodology derived from fluorescent molecular probes is one of the preferable methods. Herein, we describe fluorescent probes developed to target HDACs by considering their activity and inhibition characteristics.
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Affiliation(s)
- Roopa
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Bhanu Priya
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Vandana Bhalla
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Manoj Kumar
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Naresh Kumar
- Department of Chemistry, SRM University, Delhi-NCR, Sonepat-131029, Haryana, India.
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7
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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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8
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Xie Y, Yang L, Chen Q, Zhang J, Feng L, Chen JL, Hao Q, Zhang L, Sun H. Single-step fluorescent probes to detect decrotonylation activity of HDACs through intramolecular reactions. Eur J Med Chem 2020; 212:113120. [PMID: 33422982 DOI: 10.1016/j.ejmech.2020.113120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
Lysine crotonylation plays vital roles in gene transcription and cellular metabolism. Nevertheless, methods for dissecting the molecular mechanisms of decrotonyaltion remains limited. So far, there is no single-step fluorescent method developed for enzymatic decrotonylation activity detection. The major difficulty is that the aliphatic crotonylated lysine doesn't allow π-conjugation to a fluorophore and decrotonylation can not modulate the electronic state directly. Herein, we have designed and synthesized two activity-based single-step fluorogenic probes KTcr-I and KTcr-II for detecting enzymatic decrotonylation activity. These two probes can be recognized by histone deacetylases and undergo intramolecular nucleophilic exchange reaction to generate fluorescence signal. Notably, peptide sequence-dependent effect was observed. KTcr-I can be recognized by Sirt2 more effectively, while KTcr-II with LGKcr peptide sequence preferentially reacted with HDAC3. Compared to other methods of studying enzymatic decrotonylation activity, our single-step fluorescent method has a number of advantages, such as facileness, high sensitivity, cheap facility and little material consumed. We envision that the probes developed in this study will provide useful tools to screen inhibitors which suppress the decrotonylation activity of HDACs. Such probes will be useful for further delineating the roles of decrotonylation enzyme and aid in biomarker identification and drug discovery.
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Affiliation(s)
- Yusheng Xie
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Liu Yang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Qingxin Chen
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jie Zhang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Ling Feng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jian Lin Chen
- School of Science and Technology, The Open University of Hong Kong, Hong Kong Special Administrative Region
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China; Department of Biomedical Science, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
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9
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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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10
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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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