1
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Kawaguchi M, Furuse Y, Ieda N, Nakagawa H. Development of Nucleoside Diphosphate-Bearing Fragile Histidine Triad-Imaging Fluorescence Probes with Well-Tuned Hydrophobicity for Intracellular Delivery. ACS Sens 2022; 7:2732-2742. [PMID: 35981239 DOI: 10.1021/acssensors.2c01273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Fluorescence-guided cancer surgery can dramatically improve recurrence rates and postoperative quality of life of patients by accurately distinguishing the boundary between normal and cancer tissues during surgery, thereby minimizing excision of normal tissue. One promising target in early stage cancer is fragile histidine triad (FHIT), a cancer suppressor protein with dinucleoside triphosphate hydrolase activity. In this study, we have developed fluorescence probes containing a nucleoside diphosphate moiety, which dramatically improves the reactivity and specificity for FHIT, and a moderately lipophilic ester moiety to increase the membrane permeability. The ester moiety is cleaved by ubiquitous intracellular esterases, and then, FHIT in the cells specifically cleaves nucleoside monophosphate. The remaining phosphate moiety is rapidly cleaved by ubiquitous intracellular phosphatases to release the fluorescent dye. We confirmed that this probe can detect FHIT activity in living cells. A comprehensive evaluation of the effects of various ester moieties revealed that probes with CLogP = 5-7 showed good membrane permeability and were good substrates of the target enzyme; these findings may be helpful in the rational design of other multiple phosphate-containing probes targeting intracellular enzymes.
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Affiliation(s)
- Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Yuri Furuse
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
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2
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Herzog D, Jansen J, Mißun M, Diederichs K, Stengel F, Marx A. Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3A Elucidates Its Inhibitory Action on Translation. J Am Chem Soc 2022; 144:8613-8623. [PMID: 35522782 PMCID: PMC9121386 DOI: 10.1021/jacs.2c00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The tumor suppressor protein fragile histidine triad (Fhit) is known to be associated with genomic instability and apoptosis. The tumor-suppressive function of Fhit depends on the interaction with the alarmone diadenosine triphosphate (Ap3A), a noncanonical nucleotide whose concentration increases upon cellular stress. How the Fhit-Ap3A complex exerts its signaling function is unknown. Here, guided by a chemical proteomics approach employing a synthetic stable Fhit-Ap3A complex, we found that the Fhit-Ap3A complex, but not Fhit or Ap3A alone, impedes translation. Our findings provide a mechanistic model in which Fhit translocates from the nucleolus into the cytosol upon stress to form an Fhit-Ap3A complex. The Fhit-Ap3A complex impedes translation both in vitro and in vivo, resulting in reduced cell viability. Overall, our findings provide a mechanistic model by which the tumor suppressor Fhit collaborates with the alarmone Ap3A to regulate cellular proliferation.
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3
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Krüger L, Albrecht CJ, Schammann HK, Stumpf FM, Niedermeier ML, Yuan Y, Stuber K, Wimmer J, Stengel F, Scheffner M, Marx A. Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate. Nat Commun 2021; 12:5808. [PMID: 34608152 PMCID: PMC8490401 DOI: 10.1038/s41467-021-26075-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/10/2021] [Indexed: 01/14/2023] Open
Abstract
The nucleotides diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) are formed in prokaryotic and eukaryotic cells. Since their concentrations increase significantly upon cellular stress, they are considered to be alarmones triggering stress adaptive processes. However, their cellular roles remain elusive. To elucidate the proteome-wide interactome of Ap3A and Ap4A and thereby gain insights into their cellular roles, we herein report the development of photoaffinity-labeling probes and their employment in chemical proteomics. We demonstrate that the identified ApnA interactors are involved in many fundamental cellular processes including carboxylic acid and nucleotide metabolism, gene expression, various regulatory processes and cellular response mechanisms and only around half of them are known nucleotide interactors. Our results highlight common functions of these ApnAs across the domains of life, but also identify those that are different for Ap3A or Ap4A. This study provides a rich source for further functional studies of these nucleotides and depicts useful tools for characterization of their regulatory mechanisms in cells. Diadenosine polyphosphates (ApAs) are involved in cellular stress signaling but only a few molecular targets have been characterized so far. Here, the authors develop ApnA-based photoaffinity-labeling probes and use them to identify Ap3A and Ap4A binding proteins in human cell lysates.
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Affiliation(s)
- Lena Krüger
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Christoph J Albrecht
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Florian M Stumpf
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Katrin Stuber
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Josua Wimmer
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.
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4
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Bhat A, Li S, Hammler D, Winterhalder MJ, Marx A, Zumbusch A. Live Cell Imaging of Enzymatic Turnover of an Adenosine 5'-Tetraphosphate Analog. Int J Mol Sci 2021; 22:ijms22168616. [PMID: 34445322 PMCID: PMC8395338 DOI: 10.3390/ijms22168616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 01/11/2023] Open
Abstract
The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as a tool to follow enzymatic activity. While a number of fluorescence sensors are known, so far, there are no methods available for the real-time monitoring of ATP hydrolysis inside live cells. We present the synthesis and application of a novel fluorogenic adenosine 5′-tetraphosphate (Ap4) analog suited for this task. Upon enzymatic hydrolysis, the molecule displays an increase in fluorescence intensity, which provides a readout of its turnover. We demonstrate how this can be used for monitoring cellular processes involving Ap4 hydrolysis. To this end, we visualized the enzymatic activity in live cells using confocal fluorescence microscopy of the Ap4 analog. Our results demonstrate that the Ap4 analog is hydrolyzed in lysosomes. We show that this approach is suited to visualize the lysosome distribution profiles within the live cell and discuss how it can be employed to gather information regarding autophagic flux.
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5
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Kawaguchi M, Sekimoto E, Ohta Y, Ieda N, Murakami T, Nakagawa H. Synthesis of Fluorescent Probes Targeting Tumor-Suppressor Protein FHIT and Identification of Apoptosis-Inducing FHIT Inhibitors. J Med Chem 2021; 64:9567-9576. [PMID: 34160227 DOI: 10.1021/acs.jmedchem.1c00874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the early diagnosis of cancer, leading to a better chance of full recovery, marker genes whose expression is already altered in precancerous lesions are desirable, and the tumor-suppressor gene FHIT is one candidate. The gene product, FHIT protein, has a unique dinucleoside triphosphate hydrolase (AP3Aase) activity, and in this study, we designed and synthesized a series of FHIT fluorescent probes utilizing this activity. We optimized the probe structure for high and specific reactivity with FHIT and applied the optimized probe in a screening assay for FHIT inhibitors. Screening of a compound library with this assay identified several hits. Structural development of a hit compound afforded potent FHIT inhibitors. These inhibitors induce apoptosis in FHIT-expressing cancers via caspase activation. Our results support the idea that FHIT binders, no matter whether inhibitors or agonists of AP3Aase activity, might be promising anticancer agents.
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Affiliation(s)
- Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Eriko Sekimoto
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Yuhei Ohta
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.,Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takashi Murakami
- Faculty of Medicine, Saitama Medical University, 38 Moro-hongo, Moroyama, Iruma, Saitama 350-0495, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
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6
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Tanshinones induce tumor cell apoptosis via directly targeting FHIT. Sci Rep 2021; 11:12217. [PMID: 34108553 PMCID: PMC8190080 DOI: 10.1038/s41598-021-91708-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/17/2021] [Indexed: 02/08/2023] Open
Abstract
The liposoluble tanshinones are bioactive components in Salvia miltiorrhiza and are widely investigated as anti-cancer agents, while the molecular mechanism is to be clarified. In the present study, we identified that the human fragile histidine triad (FHIT) protein is a direct binding protein of sodium tanshinone IIA sulfonate (STS), a water-soluble derivative of Tanshinone IIA (TSA), with a Kd value of 268.4 ± 42.59 nM. We also found that STS inhibited the diadenosine triphosphate (Ap3A) hydrolase activity of FHIT through competing for the substrate-binding site with an IC50 value of 2.2 ± 0.05 µM. Notably, near 100 times lower binding affinities were determined between STS and other HIT proteins, including GALT, DCPS, and phosphodiesterase ENPP1, while no direct binding was detected with HINT1. Moreover, TSA, Tanshinone I (TanI), and Cryptotanshinone (CST) exhibited similar inhibitory activity as STS. Finally, we demonstrated that depletion of FHIT significantly blocked TSA's pro-apoptotic function in colorectal cancer HCT116 cells. Taken together, our study sheds new light on the molecular basis of the anti-cancer effects of the tanshinone compounds.
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7
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Wang M, Guo S, He M, Shao X, Feng L, Yu Y, Gong W, Liu Q, Melnikov V, Wang X, He Z, Jiang L, Chen M, Sun J, Cai J, Zhao Y, Li Y, Tritos NA, Hu Z, Zhang Z. High-Performance Liquid Chromatography-Mass Spectrometry-Based Lipid Metabolite Profiling of Acromegaly. J Clin Endocrinol Metab 2020; 105:5701424. [PMID: 31930294 DOI: 10.1210/clinem/dgaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/10/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT Metabolic disorders, especially dysregulated lipid metabolism, increase the risk of cardiovascular mortality in acromegaly. Previous studies measuring plasma macromolecular lipids have yielded conflicting results. PURPOSE To explore the plasma lipid metabolite profiles by metabolomics analysis and identify potential metabolites associated with cardiac function in acromegaly. METHODS Plasma was obtained from 80 newly diagnosed, untreated patients with acromegaly and 80 healthy controls. Echocardiography was performed. Based on the results of an oral glucose tolerance test (OGTT), patients were categorized into 2 groups: normal glucose tolerance (NGT, n = 28) and impaired glucose tolerance or diabetes mellitus (IGT/DM, n = 52). High-performance liquid chromatography-mass spectrometry (HPLC-MS)-based metabolomics analysis was conducted. Data were processed by principal components analysis (PCA), orthogonal partial least square-discriminant analysis (OPLS-DA), and MetaboAnalyst 4.0. Associations between metabolic substances and cardiovascular parameters were also explored. RESULTS Metabolomics uncovered a distinct metabolic pattern between acromegaly and healthy controls, and perturbed pathways mainly include glycerophospholipid metabolism, sphingolipid metabolism, as well as linoleic acid metabolism. Collective analysis showed that phosphatidylethanolamine (PE) (22:6/16:0) was positively correlated with LV mass, while lysophosphatidylcholine (LysoPC) (16:0) was positively correlated with fractional shortening (FS) and left ventricle ejection fraction (LVEF). CONCLUSION Patients with acromegaly have distinct lipid metabolite profiling, while PE (22:6/16:0) and LysoPC (16:0) are correlated with cardiac structure and function, which may contribute to the risk of cardiovascular complications.
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Affiliation(s)
- Meng Wang
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shizhe Guo
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Min He
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoqing Shao
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Feng
- Instrumental Analysis Center of Jiaotong University, Shanghai, China
| | - Yifei Yu
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Gong
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qingfeng Liu
- Department of Pharmacy, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | | | - Xiaoxue Wang
- Instrumental Analysis Center of Jiaotong University, Shanghai, China
| | - Zhian He
- Instrumental Analysis Center of Jiaotong University, Shanghai, China
| | - Lin Jiang
- Healthcare Center of Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Maohua Chen
- Department of Neurosurgery, The Central Hospital of Wenzhou, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Jun Sun
- Department of Neurosurgery, The Central Hospital of Wenzhou, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Jianyong Cai
- Department of Neurosurgery, The Central Hospital of Wenzhou, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Yao Zhao
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiming Li
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nicholas A Tritos
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Zhiyu Hu
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Shanghai Jiao Tong University, Shanghai, China
- Institute of Nano/Micro Energy, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaoyun Zhang
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
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8
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Chrominski M, Baranowski MR, Chmielinski S, Kowalska J, Jemielity J. Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes. J Org Chem 2020; 85:3440-3453. [PMID: 31994393 PMCID: PMC7497640 DOI: 10.1021/acs.joc.9b03198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protected guanosine and adenosine ribonucleosides and guanine nucleotides are readily functionalized with CF3 substituents within the nucleobase. Protected guanosine is trifluoromethylated at the C8 position under radical-generating conditions in up to 95% yield and guanosine 5'-oligophosphates in up to 35% yield. In the case of adenosine, the selectivity of trifluoromethylation depends heavily on the functional group protection strategy and leads to a set of CF3-modified nucleosides with different substitution patterns (C8, C2, or both) in up to 37% yield. Further transformations based on phosphorimidazolide chemistry afford various CF3-substituted mono- and dinucleoside oligophosphates in good yields. The utility of the trifluoromethylated nucleotides as probes for 19F NMR-based real-time enzymatic reaction monitoring is demonstrated with three different human nucleotide hydrolases (Fhit, DcpS, and cNIIIB). Substrate and product(s) resonances were sufficiently separated to enable effective tracking of each enzymatic activity of interest.
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Affiliation(s)
- Mikolaj Chrominski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Sebastian Chmielinski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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9
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Appy L, Chardet C, Peyrottes S, Roy B. Synthetic Strategies for Dinucleotides Synthesis. Molecules 2019; 24:molecules24234334. [PMID: 31783537 PMCID: PMC6930578 DOI: 10.3390/molecules24234334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Dinucleoside 5′,5′-polyphosphates (DNPs) are endogenous substances that play important intra- and extracellular roles in various biological processes, such as cell proliferation, regulation of enzymes, neurotransmission, platelet disaggregation and modulation of vascular tone. Various methodologies have been developed over the past fifty years to access these compounds, involving enzymatic processes or chemical procedures based either on P(III) or P(V) chemistry. Both solution-phase and solid-support strategies have been developed and are reported here. Recently, green chemistry approaches have emerged, offering attracting alternatives. This review outlines the main synthetic pathways for the preparation of dinucleoside 5′,5′-polyphosphates, focusing on pharmacologically relevant compounds, and highlighting recent advances.
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10
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Zheng M, Mex M, Götz KH, Marx A. Synthesis of disaccharide nucleoside analogues as potential poly(ADP-ribose) polymerase-1 inhibitors. Org Biomol Chem 2019; 16:8904-8907. [PMID: 30203829 DOI: 10.1039/c8ob01894d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is an important target in cancer therapy. We present the synthesis of novel disaccharide nucleoside analogues that resemble the central motif of poly(ADP-ribose) and test their inhibitory effects on human PARP-1. Some compounds show inhibition of enzymatic activity in vitro and thus might be interesting for further investigations.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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11
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Hammler D, Marx A, Zumbusch A. Fluorescence-Lifetime-Sensitive Probes for Monitoring ATP Cleavage. Chemistry 2018; 24:15329-15335. [PMID: 30070405 DOI: 10.1002/chem.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes.
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Affiliation(s)
- Daniel Hammler
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied Photonics, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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12
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Wanat P, Kasprzyk R, Kopcial M, Sikorski PJ, Strzelecka D, Jemielity J, Kowalska J. ExciTides: NTP-derived probes for monitoring pyrophosphatase activity based on excimer-to-monomer transitions. Chem Commun (Camb) 2018; 54:9773-9776. [PMID: 30105342 DOI: 10.1039/c8cc04968h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a new type of nucleotide-derived fluorescent probe designed for monitoring pyrophosphatase activity based on excimer-to-monomer transitions, called ExciTide. The nucleotides were designed with two self-interacting dye moieties and synthesised using copper-catalysed azide-alkyne cycloaddition click chemistry. We applied these probes for enzyme activity monitoring and inhibitor evaluation. Some of the probes permeated into living cells, yielding interesting prospects for future applications.
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Affiliation(s)
- Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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13
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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14
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Götz KH, Hacker SM, Mayer D, Dürig JN, Stenger S, Marx A. Inhibitors of the Diadenosine Tetraphosphate Phosphorylase Rv2613c of Mycobacterium tuberculosis. ACS Chem Biol 2017; 12:2682-2689. [PMID: 28892605 DOI: 10.1021/acschembio.7b00653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intracellular concentration of diadenosine tetraphospate (Ap4A) increases upon exposure to stress conditions. Despite being discovered over 50 years ago, the cellular functions of Ap4A are still enigmatic. If and how the varied Ap4A is a signal and involved in the signaling pathways leading to an appropriate cellular response remain to be discovered. Because the turnover of Ap4A by Ap4A cleaving enzymes is rapid, small molecule inhibitors for these enzymes would provide tools for the more detailed study of the role of Ap4A. Here, we describe the development of a high-throughput screening assay based on a fluorogenic Ap4A substrate for the identification and optimization of small molecule inhibitors for Ap4A cleaving enzymes. As proof-of-concept we screened a library of over 42 000 compounds toward their inhibitory activity against the Ap4A phosphorylase (Rv2613c) of Mycobacterium tuberculosis (Mtb). A sulfanylacrylonitril derivative with an IC50 of 260 ± 50 nM in vitro was identified. Multiple derivatives were synthesized to further optimize their properties with respect to their in vitro IC50 values and their cytotoxicity against human cells (HeLa). In addition, we selected two hits to study their antimycobacterial activity against virulent Mtb to show that they might be candidates for further development of antimycobacterial agents against multidrug-resistant Mtb.
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Affiliation(s)
- Kathrin H. Götz
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Stephan M. Hacker
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Daniel Mayer
- Institute
for Medical Microbiology and Hygiene, University Hospital of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - Jan-Niklas Dürig
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Steffen Stenger
- Institute
for Medical Microbiology and Hygiene, University Hospital of Ulm, Albert-Einstein-Allee
11, D-89081 Ulm, Germany
| | - Andreas Marx
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
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15
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Lange S, Hacker SM, Schmid P, Scheffner M, Marx A. Small-Molecule Inhibitors of the Tumor Suppressor Fhit. Chembiochem 2017. [PMID: 28643453 DOI: 10.1002/cbic.201700226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The tumor suppressor Fhit and its substrate diadenosine triphosphate (Ap3 A) are important factors in cancer development and progression. Fhit has Ap3 A hydrolase activity and cleaves Ap3 A into adenosine monophosphate (AMP) and adenosine diphosphate (ADP); this is believed to terminate Fhit-mediated signaling. How the catalytic activity of Fhit is regulated and how the Fhit⋅Ap3 A complex might exert its growth-suppressive function remain to be discovered. Small-molecule inhibitors of the enzymatic activity of Fhit would provide valuable tools for the elucidation of its tumor-suppressive functions. Here we describe the development of a high-throughput screen for the identification of such small-molecule inhibitors of Fhit. Two clusters of inhibitors that decreased the activity of Fhit by at least 90 % were identified. Several derivatives were synthesized and exhibited in vitro IC50 values in the nanomolar range.
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Affiliation(s)
- Sandra Lange
- Department of Chemistry, Konstanz Research School-Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry, Konstanz Research School-Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Philipp Schmid
- Department of Chemistry, Konstanz Research School-Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School-Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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16
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Ermert S, Marx A, Hacker SM. Phosphate-Modified Nucleotides for Monitoring Enzyme Activity. Top Curr Chem (Cham) 2017; 375:28. [PMID: 28251563 DOI: 10.1007/s41061-017-0117-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023]
Abstract
Nucleotides modified at the terminal phosphate position have been proven to be interesting entities to study the activity of a variety of different protein classes. In this chapter, we present various types of modifications that were attached as reporter molecules to the phosphate chain of nucleotides and briefly describe the chemical reactions that are frequently used to synthesize them. Furthermore, we discuss a variety of applications of these molecules. Kinase activity, for instance, was studied by transfer of a phosphate modified with a reporter group to the target proteins. This allows not only studying the activity of kinases, but also identifying their target proteins. Moreover, kinases can also be directly labeled with a reporter at a conserved lysine using acyl-phosphate probes. Another important application for phosphate-modified nucleotides is the study of RNA and DNA polymerases. In this context, single-molecule sequencing is made possible using detection in zero-mode waveguides, nanopores or by a Förster resonance energy transfer (FRET)-based mechanism between the polymerase and a fluorophore-labeled nucleotide. Additionally, fluorogenic nucleotides that utilize an intramolecular interaction between a fluorophore and the nucleobase or an intramolecular FRET effect have been successfully developed to study a variety of different enzymes. Finally, also some novel techniques applying electron paramagnetic resonance (EPR)-based detection of nucleotide cleavage or the detection of the cleavage of fluorophosphates are discussed. Taken together, nucleotides modified at the terminal phosphate position have been applied to study the activity of a large diversity of proteins and are valuable tools to enhance the knowledge of biological systems.
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Affiliation(s)
- Susanne Ermert
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany.
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17
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Hofer A, Marques E, Kieliger N, Gatter SKN, Jordi S, Ferrari E, Hofmann M, Fitzpatrick TB, Hottiger MO, Jessen HJ. Chemoselective Dimerization of Phosphates. Org Lett 2016; 18:3222-5. [PMID: 27308921 DOI: 10.1021/acs.orglett.6b01466] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A methodology for the synthesis of oligophosphate conjugates using phosphordiamidites is described. This strategy facilitates the straightforward preparation of C2-symmetric dinucleoside tri-, penta-, and heptaphosphates. Moreover, unsymmetric compounds such as thiamine adenosine triphosphate and thiamine cytidine triphosphate can be prepared. The material is used to study the inhibitory activity of thiaminylated nucleotides against adenosine diphosphate ribosyltransferases.
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Affiliation(s)
| | | | | | | | | | | | - Manuel Hofmann
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | | | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg , Albertstr. 21, 79104 Freiburg i. B., Germany
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18
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Wallrodt S, Buntz A, Wang Y, Zumbusch A, Marx A. Intrazelluläre Visualisierung der Entstehung von Poly(ADP-Ribose) mit bioorthogonal funktionalisierten NAD+-Analoga. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sarah Wallrodt
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Annette Buntz
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Yan Wang
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Zumbusch
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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19
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Wallrodt S, Buntz A, Wang Y, Zumbusch A, Marx A. Bioorthogonally Functionalized NAD(+) Analogues for In-Cell Visualization of Poly(ADP-Ribose) Formation. Angew Chem Int Ed Engl 2016; 55:7660-4. [PMID: 27080423 DOI: 10.1002/anie.201600464] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/29/2016] [Indexed: 01/11/2023]
Abstract
Poly(ADP-ribos)ylation (PARylation) is a major posttranslational modification and signaling event in most eukaryotes. Fundamental processes like DNA repair and transcription are coordinated by this transient polymer and its binding to proteins. ADP-ribosyltransferases (ARTs) build complex ADP-ribose chains from NAD(+) onto various acceptor proteins. Molecular studies of PARylation thus remain challenging. Herein, we present the development of bioorthogonally functionalized NAD(+) analogues for the imaging of PARylation in vitro and in cells. Our results show that 2-modified NAD(+) analogues perform remarkably well and can be applied to the in-cell visualization of PARylation simultaneously in two colors. This tool gives insight into the substrate scope of ARTs and will help to further elucidate the biological role of PARylation by offering fast optical, multichannel read-outs.
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Affiliation(s)
- Sarah Wallrodt
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Annette Buntz
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Yan Wang
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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20
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Hacker SM, Buntz A, Zumbusch A, Marx A. Direct Monitoring of Nucleotide Turnover in Human Cell Extracts and Cells by Fluorogenic ATP Analogs. ACS Chem Biol 2015; 10:2544-52. [PMID: 26274552 DOI: 10.1021/acschembio.5b00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleotides containing adenosine play pivotal roles in every living cell. Adenosine triphosphate (ATP), for example, is the universal energy currency, and ATP-consuming processes also contribute to posttranslational protein modifications. Nevertheless, detecting the turnover of adenosine nucleotides in the complex setting of a cell remains challenging. Here, we demonstrate the use of fluorogenic analogs of ATP and adenosine tetraphosphate to study nucleotide hydrolysis in lysates of human cell lines and in intact human cells. We found that the adenosine triphosphate analog is completely stable in lysates of human cell lines, whereas the adenosine tetraphosphate analog is rapidly turned over. The observed activity in human cell lysates can be assigned to a single enzyme, namely, the human diadenosine tetraphosphate hydrolase NudT2. Since NudT2 has been shown to be a prognostic factor for breast cancer, the adenosine tetraphosphate analog might contribute to a better understanding of its involvement in cancerogenesis and allow the straightforward screening for inhibitors. Studying hydrolysis of the analogs in intact cells, we found that electroporation is a suitable method to deliver nucleotide analogs into the cytoplasm and show that high FRET efficiencies can be detected directly after internalization. Time-dependent experiments reveal that adenosine triphosphate and tetraphosphate analogs are both processed in the cellular environment. This study demonstrates that these nucleotide analogs indeed bear the potential to be powerful tools for the exploration of nucleotide turnover in the context of whole cells.
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Affiliation(s)
- Stephan M. Hacker
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Annette Buntz
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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21
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Warminski M, Warminska Z, Kowalska J, Jemielity J. mRNA Cap Modification through Carbamate Chemistry: Synthesis of Amino- and Carboxy-Functionalised Cap Analogues Suitable for Labelling and Bioconjugation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Novartis Chemistry Lectureship 2014/2015: R. Sarpong, A. Doyle, M. S. Sigman, F. Glorius, D. Trauner und K. R. Liedl / Karl-Heinz-Beckurts-Preis: A. Marx / Preis der Polymer Networks Group für Nachwuchswissenschaftler: D. Díaz Díaz, J. Groll, F. H. Schach. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Novartis Chemistry Lectureship 2014-2015: R. Sarpong, A. Doyle, M. S. Sigman, F. Glorius, D. Trauner, and K. R. Liedl / Karl Heinz Beckurts Prize: A. Marx / Polymer Networks Group Young Investigator Award: D. Díaz Díaz, J. Groll, F. H. Schacher, and S. Se. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201500425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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