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Zhang D, Lu M, Chen C, Xu Y, Peng T. Fatty Acyl Sulfonyl Fluoride as an Activity-Based Probe for Profiling Fatty Acid-Associated Proteins in Living Cells. Chembiochem 2021; 23:e202100628. [PMID: 34918441 DOI: 10.1002/cbic.202100628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/16/2021] [Indexed: 11/09/2022]
Abstract
Fatty acids play fundamental structural, metabolic, functional, and signaling roles in all biological systems. Altered fatty acid levels and metabolism have been associated with many pathological conditions. Chemical probes have greatly facilitated biological studies on fatty acids. Herein, we report the development and characterization of an alkynyl-functionalized long-chain fatty acid-based sulfonyl fluoride probe for covalent labelling, enrichment, and identification of fatty acid-associated proteins in living cells. Our quantitative chemical proteomics show that this sulfonyl fluoride probe targets diverse classes of fatty acid-associated proteins including many metabolic serine hydrolases that are known to be involved in fatty acid metabolism and modification. We further validate that the probe covalently modifies the catalytically or functionally essential serine or tyrosine residues of its target proteins and enables evaluation of their inhibitors. The sulfonyl fluoride-based chemical probe thus represents a new tool for profiling the expression and activity of fatty acid-associated proteins in living cells.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Minghao Lu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Chengjie Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Yaxin Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
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2
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Qian Y, Schürmann M, Janning P, Hedberg C, Waldmann H. Activity-Based Proteome Profiling Probes Based on Woodward's Reagent K with Distinct Target Selectivity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yong Qian
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Marc Schürmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Christian Hedberg
- Department of Chemistry, Chemical Biology Centre (KBC); Umeå University; 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
- Technical University Dortmund; Department of Chemistry and Chemical Biology; Otto-Hahn-Strasse 6 Dortmund Germany
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3
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Qian Y, Schürmann M, Janning P, Hedberg C, Waldmann H. Activity-Based Proteome Profiling Probes Based on Woodward's Reagent K with Distinct Target Selectivity. Angew Chem Int Ed Engl 2016; 55:7766-71. [DOI: 10.1002/anie.201602666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Qian
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Marc Schürmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Christian Hedberg
- Department of Chemistry, Chemical Biology Centre (KBC); Umeå University; 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
- Technical University Dortmund; Department of Chemistry and Chemical Biology; Otto-Hahn-Strasse 6 Dortmund Germany
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4
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Wei L, Wang Q, Wu H, Ji C, Zhao J. Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure. J Proteomics 2015; 112:83-94. [DOI: 10.1016/j.jprot.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
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5
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List A, Zeiler E, Gallastegui N, Rusch M, Hedberg C, Sieber SA, Groll M. Omuralid und Vibralacton: Unterschiede im Proteasom-β-Lacton-γ-Lactamgerüst verändern die Zielmolekülpräferenz. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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6
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List A, Zeiler E, Gallastegui N, Rusch M, Hedberg C, Sieber SA, Groll M. Omuralide and vibralactone: differences in the proteasome- β-lactone-γ-lactam binding scaffold alter target preferences. Angew Chem Int Ed Engl 2013; 53:571-4. [PMID: 24285701 DOI: 10.1002/anie.201308567] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Indexed: 02/05/2023]
Abstract
Despite their structural similarity, the natural products omuralide and vibralactone have different biological targets. While omuralide blocks the chymotryptic activity of the proteasome with an IC50 value of 47 nM, vibralactone does not have any effect at this protease up to a concentration of 1 mM. Activity-based protein profiling in HeLa cells revealed that the major targets of vibralactone are APT1 and APT2.
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Affiliation(s)
- Anja List
- Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
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7
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Baggelaar MP, Janssen FJ, van Esbroeck ACM, den Dulk H, Allarà M, Hoogendoorn S, McGuire R, Florea BI, Meeuwenoord N, van den Elst H, van der Marel GA, Brouwer J, Di Marzo V, Overkleeft HS, van der Stelt M. Development of an Activity-Based Probe and In Silico Design Reveal Highly Selective Inhibitors for Diacylglycerol Lipase-α in Brain. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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8
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Baggelaar MP, Janssen FJ, van Esbroeck ACM, den Dulk H, Allarà M, Hoogendoorn S, McGuire R, Florea BI, Meeuwenoord N, van den Elst H, van der Marel GA, Brouwer J, Di Marzo V, Overkleeft HS, van der Stelt M. Development of an activity-based probe and in silico design reveal highly selective inhibitors for diacylglycerol lipase-α in brain. Angew Chem Int Ed Engl 2013; 52:12081-5. [PMID: 24173880 DOI: 10.1002/anie.201306295] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/11/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Marc P Baggelaar
- Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands)
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9
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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11
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. The mechanism of caseinolytic protease (ClpP) inhibition. Angew Chem Int Ed Engl 2013; 52:3009-14. [PMID: 23361916 DOI: 10.1002/anie.201204690] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 10/29/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Malte Gersch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Institute of Advanced Studies, Lichtenbergstrasse 4, 85747 Garching, Germany
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12
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. Der Inhibitionsmechanismus der caseinolytischen Protease (ClpP). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204690] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Zimmermann TJ, Bürger M, Tashiro E, Kondoh Y, Martinez NE, Görmer K, Rosin-Steiner S, Shimizu T, Ozaki S, Mikoshiba K, Watanabe N, Hall D, Vetter IR, Osada H, Hedberg C, Waldmann H. Boron-Based Inhibitors of Acyl Protein Thioesterases 1 and 2. Chembiochem 2012; 14:115-22. [DOI: 10.1002/cbic.201200571] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Indexed: 11/08/2022]
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14
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Yang P, Wang M, Liu K, Ngai MH, Sheriff O, Lear MJ, Sze SK, He CY, Yao SQ. Parasite‐Based Screening and Proteome Profiling Reveal Orlistat, an FDA‐Approved Drug, as a Potential Anti
Trypanosoma brucei
Agent
[
]. Chemistry 2012; 18:8403-13. [DOI: 10.1002/chem.201200482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/22/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Peng‐Yu Yang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), Fax: (+65) 6779‐1691
| | - Min Wang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)
| | - Kai Liu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)
| | - Mun Hong Ngai
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), Fax: (+65) 6779‐1691
| | - Omar Sheriff
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)
| | - Martin J. Lear
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), Fax: (+65) 6779‐1691
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Cynthia Y. He
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)
| | - Shao Q. Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), Fax: (+65) 6779‐1691
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15
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Görmer K, Bürger M, Kruijtzer JAW, Vetter I, Vartak N, Brunsveld L, Bastiaens PIH, Liskamp RMJ, Triola G, Waldmann H. Chemical-biological exploration of the limits of the Ras de- and repalmitoylating machinery. Chembiochem 2012; 13:1017-23. [PMID: 22488913 DOI: 10.1002/cbic.201200078] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 11/12/2022]
Abstract
A dynamic de-/repalmitoylation cycle determines localization and activity of H- and N-Ras. This combined cellular de- and repalmitoylation machinery has been shown to be substrate tolerant--it accepts variation of amino acid sequence, structure and configuration. Here, semisynthetic Ras-proteins in which the C-terminal amino acids are replaced by peptoid residues are used to reveal the first limitations of substrate recognition by the de- and repalmitoylating machinery.
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Affiliation(s)
- Kristina Görmer
- Abteilung Chemische Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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