1
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Gagestein B, von Hegedus JH, Kwekkeboom JC, Heijink M, Blomberg N, van der Wel T, Florea BI, van den Elst H, Wals K, Overkleeft HS, Giera M, Toes REM, Ioan-Facsinay A, van der Stelt M. Comparative Photoaffinity Profiling of Omega-3 Signaling Lipid Probes Reveals Prostaglandin Reductase 1 as a Metabolic Hub in Human Macrophages. J Am Chem Soc 2022; 144:18938-18947. [PMID: 36197299 PMCID: PMC9585591 DOI: 10.1021/jacs.2c06827] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The fish oil constituent
docosahexaenoic acid (DHA, 22:6
n-3) is
a signaling lipid with anti-inflammatory properties. The molecular
mechanisms underlying the biological effect of DHA are poorly understood.
Here, we report the design, synthesis, and application of a complementary
pair of bio-orthogonal, photoreactive probes based on the polyunsaturated
scaffold DHA and its oxidative metabolite 17-hydroxydocosahexaenoic
acid (17-HDHA). In these probes, an alkyne serves as a handle to introduce
a fluorescent reporter group or a biotin-affinity tag via copper(I)-catalyzed
azide-alkyne cycloaddition. This pair of chemical probes was used
to map specific targets of the omega-3 signaling lipids in primary
human macrophages. Prostaglandin reductase 1 (PTGR1) was identified
as an interaction partner that metabolizes 17-oxo-DHA, an oxidative
metabolite of 17-HDHA. 17-oxo-DHA reduced the formation of pro-inflammatory
lipids 5-HETE and LTB4 in human macrophages and neutrophils. Our results
demonstrate the potential of comparative photoaffinity protein profiling
for the discovery of metabolic enzymes of bioactive lipids and highlight
the power of chemical proteomics to uncover new biological insights.
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Affiliation(s)
- Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Johannes H von Hegedus
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Joanneke C Kwekkeboom
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Marieke Heijink
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Niek Blomberg
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Bogdan I Florea
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Hans van den Elst
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Kim Wals
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Herman S Overkleeft
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Andreea Ioan-Facsinay
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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2
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Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
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Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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3
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Van Vleet TR, Liguori MJ, Lynch JJ, Rao M, Warder S. Screening Strategies and Methods for Better Off-Target Liability Prediction and Identification of Small-Molecule Pharmaceuticals. SLAS DISCOVERY 2018; 24:1-24. [PMID: 30196745 DOI: 10.1177/2472555218799713] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pharmaceutical discovery and development is a long and expensive process that, unfortunately, still results in a low success rate, with drug safety continuing to be a major impedance. Improved safety screening strategies and methods are needed to more effectively fill this critical gap. Recent advances in informatics are now making it possible to manage bigger data sets and integrate multiple sources of screening data in a manner that can potentially improve the selection of higher-quality drug candidates. Integrated screening paradigms have become the norm in Pharma, both in discovery screening and in the identification of off-target toxicity mechanisms during later-stage development. Furthermore, advances in computational methods are making in silico screens more relevant and suggest that they may represent a feasible option for augmenting the current screening paradigm. This paper outlines several fundamental methods of the current drug screening processes across Pharma and emerging techniques/technologies that promise to improve molecule selection. In addition, the authors discuss integrated screening strategies and provide examples of advanced screening paradigms.
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Affiliation(s)
- Terry R Van Vleet
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Michael J Liguori
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - James J Lynch
- 2 Department of Integrated Science and Technology, AbbVie, N Chicago, IL, USA
| | - Mohan Rao
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Scott Warder
- 3 Department of Target Enabling Science and Technology, AbbVie, N Chicago, IL, USA
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4
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Soethoudt M, Stolze SC, Westphal MV, van Stralen L, Martella A, van Rooden EJ, Guba W, Varga ZV, Deng H, van Kasteren SI, Grether U, IJzerman AP, Pacher P, Carreira EM, Overkleeft HS, Ioan-Facsinay A, Heitman LH, van der Stelt M. Selective Photoaffinity Probe That Enables Assessment of Cannabinoid CB 2 Receptor Expression and Ligand Engagement in Human Cells. J Am Chem Soc 2018; 140:6067-6075. [PMID: 29420021 PMCID: PMC5958339 DOI: 10.1021/jacs.7b11281] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 01/09/2023]
Abstract
Chemical tools and methods that report on G protein-coupled receptor (GPCR) expression levels and receptor occupancy by small molecules are highly desirable. We report the development of LEI121 as a photoreactive probe to study the type 2 cannabinoid receptor (CB2R), a promising GPCR to treat tissue injury and inflammatory diseases. LEI121 is the first CB2R-selective bifunctional probe that covalently captures CB2R upon photoactivation. An incorporated alkyne serves as ligation handle for the introduction of reporter groups. LEI121 enables target engagement studies and visualization of endogenously expressed CB2R in HL-60 as well as primary human immune cells using flow cytometry. Our findings show that strategically functionalized probes allow monitoring of endogenous GPCR expression and engagement in human cells using tandem photoclick chemistry and hold promise as biomarkers in translational drug discovery.
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Affiliation(s)
- Marjolein Soethoudt
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Sara C. Stolze
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Matthias V. Westphal
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, Zürich 8093, Switzerland
| | - Luuk van Stralen
- Department
of Rheumatology, Leiden University Medical
Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Andrea Martella
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Eva J. van Rooden
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Wolfgang Guba
- Roche Innovation
Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Zoltan V. Varga
- Laboratory
of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institutes
of Health, 5625 Fishers Lane, Rockville, Maryland 20852, United
States
| | - Hui Deng
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Sander I. van Kasteren
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Uwe Grether
- Roche Innovation
Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Adriaan P. IJzerman
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Pal Pacher
- Laboratory
of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institutes
of Health, 5625 Fishers Lane, Rockville, Maryland 20852, United
States
| | - Erick M. Carreira
- Laboratorium
für Organische Chemie, Eidgenössische
Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, Zürich 8093, Switzerland
| | - Herman S. Overkleeft
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Andreea Ioan-Facsinay
- Department
of Rheumatology, Leiden University Medical
Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Laura H. Heitman
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute
of Chemistry, Research Division
of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, and Bio-Organic Synthesis,
Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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5
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Schlossmann J, Wolfertstetter S. Identification of cCMP and cUMP Substrate Proteins and Cross Talk Between cNMPs. Handb Exp Pharmacol 2017; 238:149-167. [PMID: 26721673 DOI: 10.1007/164_2015_38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
cCMP and cUMP are pyrimidine cyclic nucleotides which are present in several types of cells. These molecules could exert diverse cellular functions and might act as second messengers. In the last years, diverse approaches were performed to analyze possible cellular substrates and signaling pathways of cCMP and cUMP. In this review these approaches are summarized, and probable cross talk of these signaling molecules is described. These analyses might lead to the (patho)physiological and pharmacological relevance of these noncanonical cyclic nucleotides.
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Affiliation(s)
- Jens Schlossmann
- Pharmacology and Toxicology, Institute of Pharmacy, University Regensburg, Universitätsstr. 31, D-93040, Regensburg, Germany.
| | - Stefanie Wolfertstetter
- Pharmacology and Toxicology, Institute of Pharmacy, University Regensburg, Universitätsstr. 31, D-93040, Regensburg, Germany
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6
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Blex C, Michaelis S, Schrey AK, Furkert J, Eichhorst J, Bartho K, Gyapon Quast F, Marais A, Hakelberg M, Gruber U, Niquet S, Popp O, Kroll F, Sefkow M, Schülein R, Dreger M, Köster H. Targeting G Protein-Coupled Receptors by Capture Compound Mass Spectrometry: A Case Study with Sertindole. Chembiochem 2017; 18:1639-1649. [PMID: 28557180 DOI: 10.1002/cbic.201700152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Indexed: 01/06/2023]
Abstract
Unbiased chemoproteomic profiling of small-molecule interactions with endogenous proteins is important for drug discovery. For meaningful results, all protein classes have to be tractable, including G protein-coupled receptors (GPCRs). These receptors are hardly tractable by affinity pulldown from lysates. We report a capture compound (CC)-based strategy to target and identify GPCRs directly from living cells. We synthesized CCs with sertindole attached to the CC scaffold in different orientations to target the dopamine D2 receptor (DRD2) heterologously expressed in HEK 293 cells. The structure-activity relationship of sertindole for DRD2 binding was reflected in the activities of the sertindole CCs in radioligand displacement, cell-based assays, and capture compound mass spectrometry (CCMS). The activity pattern was rationalized by molecular modelling. The most-active CC showed activities very similar to that of unmodified sertindole. A concentration of DRD2 in living cells well below 100 fmol used as an experimental input was sufficient for unambiguous identification of captured DRD2 by mass spectrometry. Our new CCMS workflow broadens the arsenal of chemoproteomic technologies to close a critical gap for the comprehensive characterization of drug-protein interactions.
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Affiliation(s)
- Christian Blex
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Present address: Department of Neurology and Experimental Neurology, Charité, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Simon Michaelis
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Anna K Schrey
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Institute for Physiology/Structural Bioinformatics Group, Charité, University Medicine Berlin, Philippstrasse 12, 10115, Berlin, Germany
| | - Jens Furkert
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jenny Eichhorst
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Kathrin Bartho
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Thermo Fisher Scientific GmbH, Im Steingrund 4-6, 63303, Dreieich, Germany
| | - Frederick Gyapon Quast
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Glycotope GmbH, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anett Marais
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Medical Bioinformatics, Centogene AG, Schillingstrasse 68, 18057, Berlin, Germany
| | | | - Uschi Gruber
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Sylvia Niquet
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Oliver Popp
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Friedrich Kroll
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,YARA International, Hanninghof 35, 48249, Duelmen, Germany
| | - Michael Sefkow
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Celares GmbH, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Ralf Schülein
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Mathias Dreger
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Hubert Köster
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
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7
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Xiao Y, Wang Y. Global discovery of protein kinases and other nucleotide-binding proteins by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:601-19. [PMID: 25376990 PMCID: PMC5609854 DOI: 10.1002/mas.21447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 05/11/2023]
Abstract
Nucleotide-binding proteins, such as protein kinases, ATPases and GTP-binding proteins, are among the most important families of proteins that are involved in a number of pivotal cellular processes. However, global study of the structure, function, and expression level of nucleotide-binding proteins as well as protein-nucleotide interactions can hardly be achieved with the use of conventional approaches owing to enormous diversity of the nucleotide-binding protein family. Recent advances in mass spectrometry (MS) instrumentation, coupled with a variety of nucleotide-binding protein enrichment methods, rendered MS-based proteomics a powerful tool for the comprehensive characterizations of the nucleotide-binding proteome, especially the kinome. Here, we review the recent developments in the use of mass spectrometry, together with general and widely used affinity enrichment approaches, for the proteome-wide capture, identification and quantification of nucleotide-binding proteins, including protein kinases, ATPases, GTPases, and other nucleotide-binding proteins. The working principles, advantages, and limitations of each enrichment platform in identifying nucleotide-binding proteins as well as profiling protein-nucleotide interactions are summarized. The perspectives in developing novel MS-based nucleotide-binding protein detection platform are also discussed. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:601-619, 2016.
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Affiliation(s)
| | - Yinsheng Wang
- Correspondence to: Yinsheng Wang, Department of Chemistry, University of California, Riverside, CA 92521-0403.
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8
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Inhibition of c-Rel DNA binding is critical for the anti-inflammatory effects of novel PIKfyve inhibitor. Eur J Pharmacol 2016; 780:93-105. [DOI: 10.1016/j.ejphar.2016.03.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 01/15/2023]
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9
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Stolze SC, Liu N, Wijdeven RH, Tuin AW, van den Nieuwendijk AMCH, Florea BI, van der Stelt M, van der Marel GA, Neefjes JJ, Overkleeft HS. Photo-crosslinking of clinically relevant kinases using H89-derived photo-affinity probes. MOLECULAR BIOSYSTEMS 2016; 12:1809-17. [PMID: 27138522 DOI: 10.1039/c6mb00257a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The profiling of kinases using established proteomics techniques is hampered by their non-covalent mode-of-action. One way to overcome this caveat is the use of probes featuring photo-labelling groups that can be activated by UV irradiation to generate a reactive species that will establish a covalent bond to the enzyme. In this study we have used the well-known kinase inhibitor H89 as a lead for the development of probes for the affinity-based profiling of clinically relevant kinases. A labelling protocol was established for recombinant kinases and more complex protein mixtures using gel-based techniques. We also show that the probes act in a competitive manner with other kinase inhibitors.
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Affiliation(s)
- Sara C Stolze
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | - Nora Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | - Ruud H Wijdeven
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Adriaan W Tuin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | | | - Bogdan I Florea
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | - Mario van der Stelt
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
| | - Jacques J Neefjes
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
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10
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Donaldson L, Meier S, Gehring C. The arabidopsis cyclic nucleotide interactome. Cell Commun Signal 2016; 14:10. [PMID: 27170143 PMCID: PMC4865018 DOI: 10.1186/s12964-016-0133-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. METHODS An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. RESULTS A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. CONCLUSIONS We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.
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Affiliation(s)
- Lara Donaldson
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag × 3, Rondebosch, 7701, South Africa.
| | - Stuart Meier
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Christoph Gehring
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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11
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von Kleist L, Michaelis S, Bartho K, Graebner O, Schlief M, Dreger M, Schrey AK, Sefkow M, Kroll F, Koester H, Luo Y. Identification of Potential Off-target Toxicity Liabilities of Catechol-O-methyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry. J Med Chem 2016; 59:4664-75. [PMID: 27074629 DOI: 10.1021/acs.jmedchem.5b01970] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Structurally related inhibitors of a shared therapeutic target may differ regarding potential toxicity issues that are caused by different off-target bindings. We devised a differential competition capture compound mass spectrometry (dCCMS) strategy to effectively differentiate off-target profiles. Tolcapone and entacapone are potent inhibitors of catechol-O-methyl transferase (COMT) for the treatment of Parkinson's disease. Tolcapone is also known for its hepatotoxic side effects even though it is therapeutically more potent than entacapone. Here, we identified 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) as a possible toxicity-causing off-target of tolcapone, and this protein is not bound by the less toxic COMT inhibitor entacapone. Moreover, two novel compounds from a focused library synthesized in-house, N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide and 5-(3,4-dihydroxy-5-nitrobenzylidene)-3-ethylthiazolidine-2,4-dione, were utilized to gain insight into the structure-activity relationships in binding to COMT and the novel off-target HIBCH. These compounds, especially N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide, could serve as starting point for the development of improved and more specific COMT inhibitors.
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Affiliation(s)
- Lisa von Kleist
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Simon Michaelis
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Kathrin Bartho
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Olivia Graebner
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Marén Schlief
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Mathias Dreger
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Anna K Schrey
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Sefkow
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Friedrich Kroll
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Hubert Koester
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Yan Luo
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
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12
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Masuda S, Tomohiro T, Yamaguchi S, Morimoto S, Hatanaka Y. Structure-assisted ligand-binding analysis using fluorogenic photoaffinity labeling. Bioorg Med Chem Lett 2015; 25:1675-1678. [DOI: 10.1016/j.bmcl.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
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13
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Tomohiro T, Morimoto S, Shima T, Chiba J, Hatanaka Y. An Isotope-Coded Fluorogenic Cross-Linker for High-Performance Target Identification Based on Photoaffinity Labeling. Angew Chem Int Ed Engl 2014; 53:13502-5. [DOI: 10.1002/anie.201408580] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/02/2014] [Indexed: 12/19/2022]
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14
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Tomohiro T, Morimoto S, Shima T, Chiba J, Hatanaka Y. An Isotope-Coded Fluorogenic Cross-Linker for High-Performance Target Identification Based on Photoaffinity Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408580] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Brown LJ, Baranowski M, Wang Y, Schrey AK, Lenz T, Taverna SD, Cole PA, Sefkow M. Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins. Anal Biochem 2014; 467:14-21. [PMID: 25172130 DOI: 10.1016/j.ab.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022]
Abstract
S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 μM, 6.0 ± 2.9 μM, and 10.06 ± 2.87 μM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.
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Affiliation(s)
- Lindsey J Brown
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Yun Wang
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Thomas Lenz
- Caprotec Bioanalytics, 12489 Berlin, Germany
| | - Sean D Taverna
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Philip A Cole
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
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16
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Park AJ, Havekes R, Choi JH, Luczak V, Nie T, Huang T, Abel T. A presynaptic role for PKA in synaptic tagging and memory. Neurobiol Learn Mem 2014; 114:101-112. [PMID: 24882624 DOI: 10.1016/j.nlm.2014.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/01/2014] [Accepted: 05/04/2014] [Indexed: 12/14/2022]
Abstract
Protein kinase A (PKA) and other signaling molecules are spatially restricted within neurons by A-kinase anchoring proteins (AKAPs). Although studies on compartmentalized PKA signaling have focused on postsynaptic mechanisms, presynaptically anchored PKA may contribute to synaptic plasticity and memory because PKA also regulates presynaptic transmitter release. Here, we examine this issue using genetic and pharmacological application of Ht31, a PKA anchoring disrupting peptide. At the hippocampal Schaffer collateral CA3-CA1 synapse, Ht31 treatment elicits a rapid decay of synaptic responses to repetitive stimuli, indicating a fast depletion of the readily releasable pool of synaptic vesicles. The interaction between PKA and proteins involved in producing this pool of synaptic vesicles is supported by biochemical assays showing that synaptic vesicle protein 2 (SV2), Rim1, and SNAP25 are components of a complex that interacts with cAMP. Moreover, acute treatment with Ht31 reduces the levels of SV2. Finally, experiments with transgenic mouse lines, which express Ht31 in excitatory neurons at the Schaffer collateral CA3-CA1 synapse, highlight a requirement for presynaptically anchored PKA in pathway-specific synaptic tagging and long-term contextual fear memory. These results suggest that a presynaptically compartmentalized PKA is critical for synaptic plasticity and memory by regulating the readily releasable pool of synaptic vesicles.
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Affiliation(s)
- Alan Jung Park
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
| | - Robbert Havekes
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
| | - Jennifer Hk Choi
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
| | - Vince Luczak
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
| | - Ting Nie
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA.,Department of Pediatrics, Emory University, VAMC, 1670 Clairmont Rd Atlanta, GA 30033, USA
| | - Ted Huang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
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17
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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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18
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Morimoto S, Tomohiro T, Maruyama N, Hatanaka Y. Photoaffinity casting of a coumarin flag for rapid identification of ligand-binding sites within protein. Chem Commun (Camb) 2013; 49:1811-3. [PMID: 23349004 DOI: 10.1039/c3cc38594a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
A photo-switchable fluorescent flagging approach has been developed to identify photoaffinity-labeled peptides in target protein. Upon photochemical release of the ligand, the protein was newly modified with a coumarin in place of the previously attached biotin. It allowed us to simplify complex identification processes for labeled sites.
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Affiliation(s)
- Shota Morimoto
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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19
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Donaldson L, Meier S. An affinity pull-down approach to identify the plant cyclic nucleotide interactome. Methods Mol Biol 2013; 1016:155-73. [PMID: 23681578 DOI: 10.1007/978-1-62703-441-8_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry-techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants.
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Affiliation(s)
- Lara Donaldson
- Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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20
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Maurer A, Zeyher C, Amin B, Kalbacher H. A Periodate-Cleavable Linker for Functional Proteomics under Slightly Acidic Conditions: Application for the Analysis of Intracellular Aspartic Proteases. J Proteome Res 2012; 12:199-207. [DOI: 10.1021/pr300758c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andreas Maurer
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Claus Zeyher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Bushra Amin
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
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21
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Zinn N, Hopf C, Drewes G, Bantscheff M. Mass spectrometry approaches to monitor protein-drug interactions. Methods 2012; 57:430-40. [PMID: 22687620 DOI: 10.1016/j.ymeth.2012.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/16/2012] [Accepted: 05/28/2012] [Indexed: 12/16/2022] Open
Abstract
Recent advances in mass spectrometry-based approaches have enabled the investigation of drug-protein interactions in various ways including the direct detection of drug-target complexes, the examination of drug-induced changes in the target protein structure, and the monitoring of enzymatic target activity. Mass spectrometry-based proteomics methods also permit the unbiased analysis of changes in protein abundance and post-translational modifications induced by drug action. Finally, chemoproteomic affinity enrichment studies enable the deconvolution of drug targets under close to physiological conditions. This review provides an overview of current methods for the characterization of drug-target interactions by mass spectrometry and describes a protocol for chemoproteomic target binding studies using immobilized bioactive molecules.
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Affiliation(s)
- Nico Zinn
- Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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22
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Michaelis S, Marais A, Schrey AK, Graebner OY, Schaudt C, Sefkow M, Kroll F, Dreger M, Glinski M, Koester H, Metternich R, Fischer JJ. Dabigatran and Dabigatran Ethyl Ester: Potent Inhibitors of Ribosyldihydronicotinamide Dehydrogenase (NQO2). J Med Chem 2012; 55:3934-44. [DOI: 10.1021/jm3001339] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Michaelis
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Anett Marais
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Anna K. Schrey
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | | | - Cornelia Schaudt
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Michael Sefkow
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Friedrich Kroll
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Mathias Dreger
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Mirko Glinski
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Hubert Koester
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | | | - Jenny J. Fischer
- caprotec bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
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23
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Abstract
The term "chemical proteomics" refers to a research area at the interface of chemistry, biochemistry, and cell biology that focuses on studying the mechanism of action of bioactive small molecule compounds, which comprises the mapping of their target proteins and their impact on protein expression and posttranslational modifications in target cells or tissues of interest on a proteome-wide level. For this purpose, a large arsenal of approaches has emerged in recent years, many of which employing quantitative mass spectrometry. This review briefly summarizes major experiment types employed in current chemical proteomics research.
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24
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Bantscheff M, Drewes G. Chemoproteomic approaches to drug target identification and drug profiling. Bioorg Med Chem 2012; 20:1973-8. [DOI: 10.1016/j.bmc.2011.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/21/2011] [Accepted: 11/02/2011] [Indexed: 12/21/2022]
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25
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Schirle M, Bantscheff M, Kuster B. Mass Spectrometry-Based Proteomics in Preclinical Drug Discovery. ACTA ACUST UNITED AC 2012; 19:72-84. [DOI: 10.1016/j.chembiol.2012.01.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 01/14/2023]
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26
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Lenger J, Kaschani F, Lenz T, Dalhoff C, Villamor JG, Köster H, Sewald N, van der Hoorn RA. Labeling and enrichment of Arabidopsis thaliana matrix metalloproteases using an active-site directed, marimastat-based photoreactive probe. Bioorg Med Chem 2012; 20:592-6. [DOI: 10.1016/j.bmc.2011.06.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 01/12/2023]
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27
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Fischer JJ, Graebner Neé Baessler OY, Dreger M. Proteome-wide identification of staurosporine-binding kinases using capture compound mass spectrometry. Methods Mol Biol 2012; 795:135-47. [PMID: 21960220 DOI: 10.1007/978-1-61779-337-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The enormous diversity of kinases and their pivotal role in cell signaling have set kinases in the focus of biomedical research. Profiling the kinome of tissues of different origin is essential for biomarker discovery. In drug research, it is necessary to comprehend the specificity profile of a given kinase inhibitor. Capture Compound Mass Spectrometry (CCMS) (Koster et al., Assay Drug. Dev. Technol. 5:381-390, 2007) addresses the need for a tool to physically isolate and reliably profile the binders of kinase inhibitors directly in biological samples. Capture Compounds™ are trifunctional probes: a selectivity function consisting of the kinase inhibitor interacts reversibly with the native target proteins in equilibrium, a photoactivatable reactivity function forms an irreversible covalent bond to the target protein upon irradiation, and a sorting function allows the captured protein(s) to be isolated and identified by mass spectrometric analysis in an affinity-driven manner. Capture Compounds™ with any kinase inhibitor as selectivity function can be synthesized. We here used staurosporine as the selectivity function because it targets and, therefore, allows profiling a broad range of kinases (Romano and Giordano, Cell Cycle 7:3364-3668, 2008). Furthermore, we give an example of the application of the staurosporine Capture Compound to isolate kinases from human liver-derived HepG2 cells.
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28
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Probing small molecule–protein interactions: A new perspective for functional proteomics. J Proteomics 2011; 75:100-15. [DOI: 10.1016/j.jprot.2011.07.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/01/2011] [Accepted: 07/13/2011] [Indexed: 11/22/2022]
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29
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Improvement of capture compound mass spectrometry technology (CCMS) for the profiling of human kinases by combination with 2D LC-MS/MS. J Biomed Biotechnol 2011; 2011:850589. [PMID: 21941435 PMCID: PMC3176445 DOI: 10.1155/2011/850589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 06/16/2011] [Indexed: 01/06/2023] Open
Abstract
An increasingly popular and promising field in functional proteomics is the isolation of proteome subsets based on small molecule-protein interactions. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate captured protein conjugates from complex biological samples for direct protein identification by liquid chromatography/mass spectrometry (nLC-MS/MS). In this study we used staurosporine as a selectivity group for analysis in HepG2 cells derived from human liver. In the present study, we combined the functional isolation of kinases with different separation workflows of automated split-free nanoflow liquid chromatography prior to mass spectrometric analysis. Two different CCMS setups, CCMS technology combined with 1D LC-MS and 2D LC-MS, were compared regarding the total number of kinase identifications. By extending the chromatographic separation of the tryptic digested captured proteins from 1D LC linear gradients to 2D LC we were able to identify 97 kinases. This result is similar to the 1D LC setup we previously reported but this time 4 times less input material was needed. This makes CCMS of kinases an even more powerful tool for the proteomic profiling of this important protein family.
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30
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Fischer JJ, Dalhoff C, Schrey AK, Graebner OY, Michaelis S, Andrich K, Glinski M, Kroll F, Sefkow M, Dreger M, Koester H. Dasatinib, imatinib and staurosporine capture compounds - Complementary tools for the profiling of kinases by Capture Compound Mass Spectrometry (CCMS). J Proteomics 2011; 75:160-8. [PMID: 21664307 DOI: 10.1016/j.jprot.2011.05.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/13/2011] [Accepted: 05/20/2011] [Indexed: 01/08/2023]
Abstract
Capture Compound Mass Spectrometry (CCMS) is a platform technology for the functional isolation of subproteomes. Here we report the synthesis of two new kinase Capture Compounds (CCs) based on the tyrosine-kinase specific inhibitors dasatinib and imatinib and compare their interaction profiles to that of our previously reported staurosporine-CCs. CCs are tri-functional molecules: they comprise a sorting function (e.g. the small molecule or drug of interest) which interacts with target proteins, a photo-activatable reactivity function to covalently trap the interacting proteins, and a sorting function to isolate the CC-protein conjugates from complex biological samples for protein identification by liquid chromatography/mass spectrometry (LC-MS/MS). We present data of CCMS experiments from human HepG2 cells and compare the profiles of the kinases isolated with dasatinib, imatinib and staurosporine CC, respectively. Dasatinib and imatinib have a more selective kinase binding profile than staurosporine. Moreover, the new CCs allow isolation and identification of additional kinases, complementing the staurosporine CC. The family of kinase CCs will be a valuable tool for the proteomic profiling of this important protein class. Besides sets of expected kinases we identified additional specific interactors; these off-targets may be of relevance in the view of the pharmacological profile of dasatinib and imatinib.
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31
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Affiliation(s)
- Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA.
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32
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Rotili D, Altun M, Hamed RB, Loenarz C, Thalhammer A, Hopkinson RJ, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ. Photoactivable peptides for identifying enzyme-substrate and protein-protein interactions. Chem Commun (Camb) 2011; 47:1488-90. [PMID: 21152646 DOI: 10.1039/c0cc04457a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Photoactivated cross-linking of peptides to proteins is a useful strategy for identifying enzyme-substrate and protein-protein interactions in cell lysates as demonstrated by studies on the human hypoxia inducible factor system.
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Affiliation(s)
- Dante Rotili
- University of Oxford, Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, United Kingdom
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33
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Hanke SE, Bertinetti D, Badel A, Schweinsberg S, Genieser HG, Herberg FW. Cyclic nucleotides as affinity tools: phosphorothioate cAMP analogues address specific PKA subproteomes. N Biotechnol 2010; 28:294-301. [PMID: 21147280 DOI: 10.1016/j.nbt.2010.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/02/2010] [Accepted: 12/05/2010] [Indexed: 11/29/2022]
Abstract
cAMP (adenosine-3',5'-cyclic monophosphate) is a general second messenger controlling distinct targets in eukaryotic cells. In a (sub)proteomic approach, two classes of phosphorothioate cAMP affinity tools were used to isolate and to identify signalling complexes of the main cAMP target, cAMP dependent protein kinase (PKA). Agonist analogues (here: Sp-cAMPS) bind to the regulatory subunits of PKA (PKA-R), together with their interaction partners, and cause dissociation of a holoenzyme complex comprising PKA-R and catalytic subunits of PKA (PKA-C). Antagonist analogues (here: Rp-cAMPS) bind to the holoenzyme without dissociating the complex and were developed to identify interaction partners that bind to the entire complex or to PKA-C. More than 80 different proteins were isolated from tissue extracts including several PKA isoforms and known as well as potentially new interaction partners. Nevertheless, unspecific binding of general nucleotide binding proteins limited the outcome of this chemical proteomics approach. Surface plasmon resonance (SPR) was employed to optimise the entire workflow of pull down proteomics and to quantify the effects of different nucleotides (ATP, ADP, GTP and NADH) on PKA-R binding to affinity material. We could demonstrate that the addition of NADH to lysates improved specificity in pull down experiments. Using a combination of SPR studies and pull down experiments it was shown unambiguously that it is possible to specifically elute protein complexes with cAMP or cGMP from cAMPS analogue matrices. The side-by-side analysis of the PKA-R interactome and the holoenzyme complexed with interacting proteins will contribute to a further dissection of the multifaceted PKA signalling network.
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Affiliation(s)
- Susanne E Hanke
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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34
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35
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Luo Y, Fischer JJ, Baessler OYGN, Schrey AK, Ungewiss J, Glinski M, Sefkow M, Dreger M, Koester H. GDP-capture compound--a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS). J Proteomics 2009; 73:815-9. [PMID: 20026263 DOI: 10.1016/j.jprot.2009.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/01/2009] [Accepted: 12/02/2009] [Indexed: 12/28/2022]
Abstract
The functional isolation of proteome subsets based on small molecule-protein interactions is an increasingly popular and promising field in functional proteomics. Entire protein families may be profiled on the basis of their common interaction with a metabolite or small molecule inhibitor. This is enabled by novel multifunctional small molecule probes. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate Capture Compound-protein conjugates from complex biological samples for direct trypsinisation and protein identification by liquid chromatography/mass spectrometry (CCMS). We here present the synthesis and application of a novel GDP-Capture Compound for the functional enrichment of GTPases, a pivotal protein family that exerts key functions in signal transduction. We present data from CCMS experiments on two biological lysates from Escherichia coli and from human-derived Hek293 cells. The GDP-Capture Compound robustly captures a wide range of different GTPases from both systems and will be a valuable tool for the proteomic profiling of this important protein family.
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Affiliation(s)
- Yan Luo
- Caprotec Bioanalytics GmbH, Volmerstrasse 5, 12489 Berlin, Germany
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