1
|
Wei Y, Zhang Y, Wang Z, Yang Z, Wang Z, Hao Y, Li G, Gao F, Ye G, Wang J, Liu J. New insight into molecular mechanisms of different polyphenols affecting Sirtuin 3 deacetylation activity. Int J Biol Macromol 2024; 270:132026. [PMID: 38704074 DOI: 10.1016/j.ijbiomac.2024.132026] [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: 02/21/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Multiple phenolic substances have been shown to promote SIRT3 expression, however, few studies have focused on the effects of these phenolics on SIRT3 enzyme activity. This study constructed a variety of reaction systems to elucidate the mechanisms by which different polyphenols affect SIRT3 enzyme activity. The results showed that acP53317-320 was the most suitable substrate among the five acetylated peptide substrates (Kcat/Km = 74.85 ± 1.86 M-1•s-1). All the phenolic compounds involved in the experiment inhibited the enzymatic activity of SIRT3, and the lowest IC50 among them was quercetin (0.12 ± 0.01 mM) and the highest was piceatannol (1.29 ± 0.08 mM). Their inhibition types were mainly competitive and mixed. In addition, piceatannol was found to be a natural SIRT3 agonist by enzyme kinetic analysis and validation of deacetylation efficiency. This study will provide a useful reference for polyphenol modulation of SIRT3 dosage, as well as the development and application of polyphenol-based SIRT3 activators and agonists.
Collapse
Affiliation(s)
- Yulong Wei
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Yiman Zhang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Ziyuan Wang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Zihui Yang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Zongwei Wang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Yiming Hao
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Genying Li
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Fei Gao
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Gaoqi Ye
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China
| | - Jing Wang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China.
| | - Jie Liu
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; National Center of Technology Innovation for Grain Industry (Comprehensive Utilization of Edible by-products), Beijing Technology and Business University, Beijing 100048, China.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Tan S, Li X. Small-Molecule Fluorescent Probes for Detecting HDAC Activity. Chem Asian J 2022; 17:e202200835. [PMID: 36117388 DOI: 10.1002/asia.202200835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Indexed: 11/05/2022]
Abstract
Histone deacetylases (HDACs) play critical roles in epigenetic modification. These enzymes can remove acetyl groups from the N-terminal lysine residues of histones, thereby regulating gene expression. Because of their great relevance to various diseases, numerous HDAC inhibitors have been developed. In this context, assays for HDAC activity are prerequisite. Due to the advantages of small-molecule fluorescent probes, researchers have developed many probes to detect HDAC activity for developing HDAC inhibitors. Based on the mechanism of action, two main types of small-molecule fluorescent probes are known. One type is based on binding affinity that are generally HDAC inhibitor-fluorophore conjugates. The other one is enzyme-activated probes, which act as HDAC substrates and show fluorogenic or ratiometric response after being deacetylated by HDACs.
Collapse
Affiliation(s)
- Shuyu Tan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| |
Collapse
|
4
|
Zähringer S, Rumpf T, Melesina J, Lang AE, Aktories K, Sippl W, Jung M, Wagner GK. Defined stereoisomers of 2″-amino NAD + and their activity against human sirtuins and a bacterial (ADP-ribosyl) transferase. Bioorg Med Chem 2022; 68:116875. [PMID: 35716588 DOI: 10.1016/j.bmc.2022.116875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an important biomolecule with essential roles at the intersection of energy metabolism, epigenetic regulation and cell signalling. Synthetic analogues of NAD+ are therefore of great interest as chemical tools for medicinal chemistry, chemical biology and drug discovery. Herein, we report the chemical synthesis and full analytical characterisation of three stereoisomers of 2″-amino NAD+, and their biochemical evaluation against two classes of NAD+-consuming enzymes: the human sirtuins 1-3, and the bacterial toxin TccC3. To rationalise the observed activities, molecular docking experiments were carried out with SIRT1 and SIRT2, which identified the correct orientation of the pyrophosphate linkage as a major determinant for activity in this series. These results, together with results from stability tests and a conformational analysis, allow, for the first time, a side-by-side comparison of the chemical and biochemical features, and analytical properties, of different 2″-amino NAD+ stereoisomers. Our findings provide insight into the recognition of co-substrate analogues by sirtuins, and will greatly facilitate the application of these important NAD+ analogues as chemical tool compounds for mechanistic studies with these as well as other NAD+-dependent enyzmes.
Collapse
Affiliation(s)
- Sarah Zähringer
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom; Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Jelena Melesina
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Alexander E Lang
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Albertstr 25, 79104 Freiburg, Germany
| | - Klaus Aktories
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Albertstr 25, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Roshdy E, Mustafa M, Shaltout AER, Radwan MO, Ibrahim MAA, Soliman ME, Fujita M, Otsuka M, Ali TFS. Selective SIRT2 inhibitors as promising anticancer therapeutics: An update from 2016 to 2020. Eur J Med Chem 2021; 224:113709. [PMID: 34303869 DOI: 10.1016/j.ejmech.2021.113709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022]
Abstract
Sirtuin 2 (SIRT2) is a member of the human sirtuins, which regulates various biological processes and is deemed as a novel biomarker for different cancers. Depending on the tumor type, SIRT2 knockout leads to a controversial role in tumorigenesis, however, pharmacological inhibition of SIRT2 results exclusively in growth inhibition of various cancer cells. In this respect, selective SIRT2 inhibitors hold therapeutic promise in a wide range of tumors. The literature has a batch of successful stories of SIRT2 modulators discovery. This review presents our perspective on the up-to-date selective SIRT2 inhibitors and their antiproliferative activity.
Collapse
Affiliation(s)
- Eslam Roshdy
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Muhamad Mustafa
- Medicinal Chemistry Department, Faculty of Pharmacy, Deraya University, Minia, Egypt.
| | | | - Mohamed O Radwan
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, School of Pharmacy, Kumamoto University, Kumamoto, 862-0973, Japan; Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto, 862-0976, Japan; Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, 12622, Cairo, Egypt
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mahmoud E Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, School of Pharmacy, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, School of Pharmacy, Kumamoto University, Kumamoto, 862-0973, Japan; Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto, 862-0976, Japan
| | - Taha F S Ali
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt; Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, School of Pharmacy, Kumamoto University, Kumamoto, 862-0973, Japan.
| |
Collapse
|
7
|
Patnaik D, Pao PC, Zhao WN, Silva MC, Hylton NK, Chindavong PS, Pan L, Tsai LH, Haggarty SJ. Exifone Is a Potent HDAC1 Activator with Neuroprotective Activity in Human Neuronal Models of Neurodegeneration. ACS Chem Neurosci 2021; 12:271-284. [PMID: 33417763 DOI: 10.1021/acschemneuro.0c00308] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genomic instability caused by a deficiency in the DNA damage response and repair has been linked to age-related cognitive decline and neurodegenerative diseases. Preventing genomic instability that ultimately leads to neuronal death may provide a broadly effective strategy to protect against multiple potential genotoxic stressors. Recently, the zinc-dependent class I histone deacetylase (HDAC1) has been identified as a critical factor for protecting neurons from deleterious effects of DNA damage in Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Translating these observations to a novel neuroprotective therapy for AD, ALS, and FTD may be advanced by the identification of small molecules capable of increasing the deacetylase activity of HDAC1 selectively over other structurally similar HDACs. Here, we demonstrate that exifone, a drug previously shown to be effective in treating cognitive deficits associated with AD and Parkinson's disease, the molecular mechanism of which has remained poorly understood, potently activates the deacetylase activity of HDAC1. We show that exifone acts as a mixed, nonessential activator of HDAC1 that is capable of binding to both free and substrate-bound enzyme, resulting in an increased relative maximal rate of HDAC1-catalyzed deacetylation. Exifone can directly bind to HDAC1 based upon biolayer interferometry assays with kinetic and selectivity profiling, suggesting that HDAC1 is preferentially targeted compared to other class I HDACs and the kinase CDK5, which have also been implicated in neurodegeneration. Consistent with a mechanism of deacetylase activation intracellularly, the treatment of human induced pluripotent stem cell (iPSC)-derived neuronal cells resulted in globally decreased histone acetylation. Moreover, exifone treatment was neuroprotective in a tauopathy patient iPSC-derived neuronal model subject to oxidative stress. Taken together, these findings reveal exifone as a potent activator of HDAC1-mediated deacetylation, thereby offering a lead for novel therapeutic development aiming to protect genomic integrity in the context of neurodegeneration and aging.
Collapse
Affiliation(s)
- Debasis Patnaik
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ping-Chieh Pao
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - M. Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Norma K. Hylton
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Peter S. Chindavong
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ling Pan
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| |
Collapse
|
8
|
The Lifespan Extension Ability of Nicotinic Acid Depends on Whether the Intracellular NAD + Level Is Lower than the Sirtuin-Saturating Concentrations. Int J Mol Sci 2019; 21:ijms21010142. [PMID: 31878234 PMCID: PMC6982340 DOI: 10.3390/ijms21010142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023] Open
Abstract
Calorie restriction can extend lifespan by increasing intracellular nicotinamide adenine dinucleotide (NAD+), thereby upregulating the activity of sirtuins (Caenorhabditis elegans Sir-2.1; human SIRT1). Nicotinic acid (NA) can be metabolized to NAD+; however, the calorie restriction mimetic (CRM) potential of NA is unclear. This study explored the ability and mechanism of NA to extend the lifespan of human Hs68 cells and C. elegans. We found that NA can efficiently increase the intracellular NAD+ levels in Hs68 cells and C. elegans; however, NA was only able to extend the lifespan of C. elegans. The steady-state NAD+ level in C. elegans was approximately 55 μM. When intracellular NAD+ was increased by a mutation of pme-1 (poly (ADP-ribose) metabolism enzyme 1) or by pretreatment with NAD+ in the medium, the lifespan extension ability of NA disappeared. Additionally, the saturating concentration of NAD+ required by SIRT1 was approximately 200 μM; however, the steady-state concentration of NAD+ in Hs68 cells reached up to 460 μM. These results demonstrate that the lifespan extension ability of NA depends on whether the intracellular level of NAD+ is lower than the sirtuin-saturating concentration in Hs68 cells and in C. elegans. Thus, the CRM potential of NA should be limited to individuals with lower intracellular NAD+.
Collapse
|
9
|
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.
Collapse
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.)
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Bretschneider T, Ozbal C, Holstein M, Winter M, Buettner FH, Thamm S, Bischoff D, Luippold AH. RapidFire BLAZE-Mode Is Boosting ESI-MS Toward High-Throughput-Screening. SLAS Technol 2019; 24:386-393. [PMID: 30698995 DOI: 10.1177/2472630318822449] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Label-free in vitro potency assays are an emerging field in drug discovery to enable more physiological conditions, to improve the readout quality, and to save time. For this approach mass spectrometry (MS) is a powerful technology to directly follow physiological processes. The speed of this methodology, however, was for a long time not compatible with chemiluminescence- or fluorescence-based assays. Recent advances in matrix-assisted laser desorption/ionization (MALDI) instrumentation paved the way for high-throughput MS analysis of label-free assays for large compound libraries, whereas electrospray ionization (ESI)-based mass spectrometers equipped with RapidFire autosamplers were limited to medium throughput. Here we present a technological advancement of the RapidFire device to enable cycle times of 2.5 s per sample. This newly developed BLAZE-mode substantially boosted the ESI-MS analysis speed, providing an alternative technology for label-free high-throughput screening.
Collapse
Affiliation(s)
- Tom Bretschneider
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Can Ozbal
- 2 PureHoney Technologies, Billerica, MA, USA
| | - Markus Holstein
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Martin Winter
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Frank H Buettner
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Sven Thamm
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Daniel Bischoff
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| | - Andreas H Luippold
- 1 Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Biberach an der Riß, Germany
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Ouimet CM, D’Amico CI, Kennedy RT. Advances in capillary electrophoresis and the implications for drug discovery. Expert Opin Drug Discov 2017; 12:213-224. [PMID: 27911223 PMCID: PMC5521262 DOI: 10.1080/17460441.2017.1268121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Many screening platforms are prone to assay interferences that can be avoided by directly measuring the target or enzymatic product. Capillary electrophoresis (CE) and microchip electrophoresis (MCE) have been applied in a variety of formats to drug discovery. CE provides direct detection of the product allowing for the identification of some forms of assay interference. The high efficiency, rapid separations, and low volume requirements make CE amenable to drug discovery. Areas covered: This article describes advances in capillary electrophoresis throughput, sample introduction, and target assays as they pertain to drug discovery and screening. Instrumental advances discussed include integrated droplet microfluidics platforms and multiplexed arrays. Applications of CE to assays of diverse drug discovery targets, including enzymes and affinity interactions are also described. Expert opinion: Current screening with CE does not fully take advantage of the throughputs or low sample volumes possible with CE and is most suitable as a secondary screening method or for screens that are inaccessible with more common platforms. With further development, droplet microfluidics coupled to MCE could take advantage of the low sample requirements by performing assays on the nanoliter scale at high throughput.
Collapse
Affiliation(s)
- Claire M. Ouimet
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
| | - Cara I. D’Amico
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
| |
Collapse
|
14
|
Abstract
Mass spectrometry is a generic technique for the structural and functional analysis of purified proteins. Instrument capabilities and the possibilities of intact protein, peptide fragmentation and native analyses are discussed. Detailed experimental protocols are described for the most commonly applied techniques of protein identification, posttranslational modification (PTM) characterization, PTM mapping, native mass spectrometry, and analysis of membrane proteins using electrospray mass spectrometry.
Collapse
Affiliation(s)
- Rod Chalk
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| |
Collapse
|
15
|
Schuster S, Roessler C, Meleshin M, Zimmermann P, Simic Z, Kambach C, Schiene-Fischer C, Steegborn C, Hottiger MO, Schutkowski M. A continuous sirtuin activity assay without any coupling to enzymatic or chemical reactions. Sci Rep 2016; 6:22643. [PMID: 26940860 PMCID: PMC4778124 DOI: 10.1038/srep22643] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 02/16/2016] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are NAD(+) dependent lysine deacylases involved in many regulatory processes such as control of metabolic pathways, DNA repair and stress response. Modulators of sirtuin activity are required as tools for uncovering the biological function of these enzymes and as potential therapeutic agents. Systematic discovery of such modulators is hampered by the lack of direct and continuous activity assays. The present study describes a novel continuous assay based on the increase of a fluorescence signal subsequent to sirtuin mediated removal of a fluorescent acyl chain from a modified TNFα-derived peptide. This substrate is well recognized by human sirtuins 1-6 and represents the best sirtuin 2 substrate described so far with a kcat/KM-value of 176 000 M(-1)s(-1). These extraordinary substrate properties allow the first determination of Ki-values for the specific Sirt2 inhibitory peptide S2iL5 (600 nM) and for the quasi-universal sirtuin inhibitor peptide thioxo myristoyl TNFα (80 nM).
Collapse
Affiliation(s)
- Sabine Schuster
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Claudia Roessler
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Philipp Zimmermann
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Christian Kambach
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, joint research project gFP5, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Michael O Hottiger
- IVBMB, University of Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| |
Collapse
|
16
|
Abstract
Sirtuins are NAD-dependent lysine deacylases that play critical roles in cellular regulation and are implicated in human diseases. Modulators of sirtuins are needed as tools for investigating their biological functions and possible therapeutic applications. However, the discovery of sirtuin modulators is hampered by the lack of efficient sirtuin assays. Here we report an improved fluorogenic assay for SIRT1, SIRT2, and SIRT3 using a new substrate, a myristoyl peptide with a C-terminal aminocoumarin. The new assay has several advantages, including significantly lower substrate concentration needed, increased signal-to-background ratio, and improved Z'-factor. The novel assay thus will expedite high-throughput screening of SIRT1, SIRT2, and SIRT3 modulators.
Collapse
Affiliation(s)
- Ying-Ling Chiang
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853, USA
- Howard Hughes Medical Institute, Tel: +1 607-255-4650
| |
Collapse
|
17
|
Liang P, Li Q, Wu Z, Jiang JH, Yu RQ. Graphene oxide–peptide nanoassembly as a general approach for monitoring the activity of histone deacetylases. Analyst 2016; 141:3989-92. [DOI: 10.1039/c6an00902f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A novel fluorescent sensor using graphene oxide (GO)–peptide nanoassembly is developed for histone deacetylases (HDACs) based on deacetylation mediated cleavage of substrate peptides, which provides a simple, cost-effective platform for monitoring the activity of HDACs.
Collapse
Affiliation(s)
- Ping Liang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Qing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Zhan Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| |
Collapse
|
18
|
Li Y, Liu T, Liao S, Li Y, Lan Y, Wang A, Wang Y, He B. A mini-review on Sirtuin activity assays. Biochem Biophys Res Commun 2015; 467:459-66. [DOI: 10.1016/j.bbrc.2015.09.172] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
|
19
|
Wang Y, Chen Y, Wang H, Cheng Y, Zhao X. Specific Turn-On Fluorescent Probe with Aggregation-Induced Emission Characteristics for SIRT1 Modulator Screening and Living-Cell Imaging. Anal Chem 2015; 87:5046-9. [DOI: 10.1021/acs.analchem.5b01069] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yi Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Yaqi Chen
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Haibo Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Yiyu Cheng
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang China
| | - Xiaoping Zhao
- College
of Preclinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang China
| |
Collapse
|
20
|
Rye PT, LaMarr WA. Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study. Anal Biochem 2015; 482:40-7. [PMID: 25849585 DOI: 10.1016/j.ab.2015.03.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 02/26/2015] [Accepted: 03/28/2015] [Indexed: 01/28/2023]
Abstract
Glycolysis is a 10-step metabolic pathway involved in producing cellular energy. Many tumors exhibit accelerated glycolytic rates, and enzymes that participate in this pathway are focal points of cancer research. Here, a novel method for the measurement of glycolysis reactants from in vitro samples is presented. Fast and direct measurement is achieved by an automated system that couples on-line solid phase extraction (SPE) with tandem mass spectrometry (MS/MS). The single analytical method enables multiple reactants to be measured concurrently, sustains a cycle time of 8s, and permits the measurement of up to 10,000 samples per day. Concentration-response curves were conducted using standards for 10 metabolic intermediates, and the results demonstrate that the detection strategy has excellent sensitivity (average limit of detection = 5.4 nM), dynamic range (nanomolar to micromolar), and linear response (average R(2) = 0.998). To test the analysis method on reactions, pyrophosphate-dependent phosphofructokinase (PPi-PFK) was used as a model system. Data that corroborate the activation and inhibition of PPi-PFK are presented, and the ways in which SPE-MS/MS simplifies experimental design and interpretation are highlighted. In summary, the method for measuring metabolic intermediates described here demonstrates unprecedented speed, performance, and versatility.
Collapse
Affiliation(s)
- Peter T Rye
- Agilent Technologies, Wakefield, MA 01880, USA.
| | | |
Collapse
|
21
|
Guan X, Lin P, Knoll E, Chakrabarti R. Mechanism of inhibition of the human sirtuin enzyme SIRT3 by nicotinamide: computational and experimental studies. PLoS One 2014; 9:e107729. [PMID: 25221980 PMCID: PMC4164625 DOI: 10.1371/journal.pone.0107729] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/14/2014] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are key regulators of many cellular functions including cell growth, apoptosis, metabolism, and genetic control of age-related diseases. Sirtuins are themselves regulated by their cofactor nicotinamide adenine dinucleotide (NAD+) as well as their reaction product nicotinamide (NAM), the physiological concentrations of which vary during the process of aging. Nicotinamide inhibits sirtuins through the so-called base exchange pathway, wherein rebinding of the reaction product to the enzyme accelerates the reverse reaction. We investigated the mechanism of nicotinamide inhibition of human SIRT3, the major mitochondrial sirtuin deacetylase, in vitro and in silico using experimental kinetic analysis and Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB(GB)SA) binding affinity calculations with molecular dynamics sampling. Through experimental kinetic studies, we demonstrate that NAM inhibition of SIRT3 involves apparent competition between the inhibitor and the enzyme cofactor NAD+, contrary to the traditional characterization of base exchange as noncompetitive inhibition. We report a model for base exchange inhibition that relates such kinetic properties to physicochemical properties, including the free energies of enzyme-ligand binding, and estimate the latter through the first reported computational binding affinity calculations for SIRT3:NAD+, SIRT3:NAM, and analogous complexes for Sir2. The computational results support our kinetic model, establishing foundations for quantitative modeling of NAD+/NAM regulation of mammalian sirtuins during aging and the computational design of sirtuin activators that operate through alleviation of base exchange inhibition.
Collapse
Affiliation(s)
- Xiangying Guan
- Division of Fundamental Research, PMC Advanced Technology, LLC, Mount Laurel, New Jersey, United States of America
| | - Ping Lin
- Division of Fundamental Research, PMC Advanced Technology, LLC, Mount Laurel, New Jersey, United States of America
| | - Eric Knoll
- Division of Fundamental Research, PMC Advanced Technology, LLC, Mount Laurel, New Jersey, United States of America
| | - Raj Chakrabarti
- Division of Fundamental Research, PMC Advanced Technology, LLC, Mount Laurel, New Jersey, United States of America
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|
22
|
Schutkowski M, Fischer F, Roessler C, Steegborn C. New assays and approaches for discovery and design of Sirtuin modulators. Expert Opin Drug Discov 2014; 9:183-99. [DOI: 10.1517/17460441.2014.875526] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
23
|
SPE–MS analysis of absorption, distribution, metabolism and excretion assays: a tool to increase throughput and steamline workflow. Bioanalysis 2012; 4:1111-21. [DOI: 10.4155/bio.12.86] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In an effort to create faster and more efficient bioanalytical methods for drug development, many investigators have evaluated a variety of SPE–MS systems. Over the past 15 years online systems have evolved from run times of >1.5 min/sample to <10 s/sample. High-throughput SPE–MS methods for in vitro absorption, distribution, metabolism and excretion screening assays have been described by several laboratories and shown to produce results comparable to conventional LC–MS/MS systems. While quantitative analysis of small molecules in biological matrixes holds many challenges, for several applications SPE–MS methods have achieved comparable results to LC–MS/MS with the benefit of 10–30-times the throughput. Based on its distinct advantages of throughput and streamlined workflow efficiencies, SPE–MS is a useful tool for the analysis of many in vitro absorption, distribution, metabolism and excretion assays and in vivo bioanalytical studies. Further development of SPE–MS methods and analysis workflows has the potential to expand the capabilities of this technology for other challenging bioanalytical applications.
Collapse
|
24
|
Ralser M, Michel S, Breitenbach M. Sirtuins as regulators of the yeast metabolic network. Front Pharmacol 2012; 3:32. [PMID: 22408620 PMCID: PMC3296958 DOI: 10.3389/fphar.2012.00032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/17/2012] [Indexed: 11/29/2022] Open
Abstract
There is growing evidence that the metabolic network is an integral regulator of cellular physiology. Dynamic changes in metabolite concentrations, metabolic flux, or network topology act as reporters of biological or environmental signals, and are required for the cell to trigger an appropriate biological reaction. Changes in the metabolic network are recognized by specific sensory macromolecules and translated into a transcriptional or translational response. The protein family of sirtuins, discovered more than 30 years ago as regulators of silent chromatin, seems to fulfill the role of a metabolic sensor during aging and conditions of caloric restriction. The archetypal sirtuin, yeast silentinformationregulator2 (SIR2), is an NAD+ dependent protein deacetylase that interacts with metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase and alcohol dehydrogenase, as well as enzymes involved in NAD(H) synthesis, that provide or deprive NAD+ in its close proximity. This influences sirtuin activity, and facilitates a dynamic response of the metabolic network to changes in metabolism with effects on physiology and aging. The molecular network downstream Sir2, however, is complex. In just two orders, Sir2’s metabolism related interactions span half of the yeast proteome, and are connected with virtually every physiological process. Thus, although it is fundamental to analyze single molecular mechanisms, it is at the same time crucial to consider this genome-scale complexity when correlating single molecular events with complex phenotypes such as aging, cell growth, or stress resistance.
Collapse
Affiliation(s)
- Markus Ralser
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
| | | | | |
Collapse
|