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Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
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Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
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2
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Schwickert K, Andrzejewski M, Grabowsky S, Schirmeister T. Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands. J Org Chem 2021; 86:6169-6183. [PMID: 33835801 DOI: 10.1021/acs.joc.0c02993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via 19F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.
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Affiliation(s)
- Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Michał Andrzejewski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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3
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Leyva E, Platz MS, Loredo-Carrillo SE, Aguilar J. Fluoro Aryl Azides: Synthesis, Reactions and Applications. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200608132505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The complex photochemistry of aryl azides has fascinated scientists
for several decades. Spectroscopists have investigated the intermediates formed by
different analytical techniques. Theoretical chemists have explained the intrinsic interplay of
intermediates under different experimental conditions.
Objective & Method:
A complete understanding of the photochemistry of a given fluoro
aryl azide is a basic requisite for its use in chemistry. In this review, we will discuss the
synthesis of several fluoro substituted aryl azides and the reactions and intermediates generated
upon photolysis and thermolysis of these azides and some examples of their applications
in photoaffinity labeling and organic synthesis.
Conclusion:
In spite of the extensive research on the photochemistry of fluoro aryl azides, there are some areas
that remain to be investigated. The application of this reaction in the synthesis of novel heterocyclic compounds
has not been fully studied. Since fluorophenyl azides are known to undergo C-H and N-H insertion reactions,
they could be used to prepare new fluorinated molecules or in the biochemical process known as photoaffinity
labeling.
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Affiliation(s)
- Elisa Leyva
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
| | - Matthew S. Platz
- Department of Chemistry, University of Hawaii, Hilo, 200 West Kawili St. Hilo, HI 96720, United States
| | - Silvia E. Loredo-Carrillo
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
| | - Johana Aguilar
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
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4
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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5
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Pan S, Zhang H, Wang C, Yao SCL, Yao SQ. Target identification of natural products and bioactive compounds using affinity-based probes. Nat Prod Rep 2017; 33:612-20. [PMID: 26580476 DOI: 10.1039/c5np00101c] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Covering: 2010 to 2014.Advances in isolation, synthesis and screening strategies have made many bioactive substances available. However, in most cases their putative biological targets remain unknown. Herein, we highlight recent advances in target identification of natural products and bioactive compounds by using affinity-based probes. Aided by photoaffinity labelling, this strategy can capture potential cellular targets (on and off) of a natural product or bioactive compound in live cells directly, even when the compound-target interaction is reversible with moderate affinity. The knowledge of these targets may help uncover molecular pathways and new therapeutics for currently untreatable diseases. In this highlight, we will introduce the development of various photoactivatable groups, their synthesis and applications in target identification of natural products and bioactive compounds, with a focus on work done in recent years and from our laboratory. We will further discuss the strengths and weaknesses of each group and the outlooks for this novel proteome-wide profiling strategy.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Hailong Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Chenyu Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Samantha C L Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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6
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Seifert T, Malo M, Lengqvist J, Sihlbom C, Jarho EM, Luthman K. Identification of the Binding Site of Chroman-4-one-Based Sirtuin 2-Selective Inhibitors using Photoaffinity Labeling in Combination with Tandem Mass Spectrometry. J Med Chem 2016; 59:10794-10799. [PMID: 27933951 DOI: 10.1021/acs.jmedchem.6b01117] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Photoaffinity labeling (PAL) was used to identify the binding site of chroman-4-one-based SIRT2-selective inhibitors. The photoactive diazirine 4, a potent SIRT2 inhibitor, was subjected to detailed photochemical characterization. In PAL experiments with SIRT2, a tryptic peptide originating from the covalent attachment of photoactivated 4 was identified. The peptide covers both the active site of SIRT2 and the proposed binding site of chroman-4-one-based inhibitors. A high-power LED was used as source for the monochromatic UV light enabling rapid photoactivation.
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Affiliation(s)
- Tina Seifert
- Department of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg , Kemivagen 10, SE-41296 Göteborg, Sweden
| | - Marcus Malo
- Department of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg , Kemivagen 10, SE-41296 Göteborg, Sweden
| | - Johan Lengqvist
- The Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg , SE-41390 Göteborg, Sweden
| | - Carina Sihlbom
- The Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg , SE-41390 Göteborg, Sweden
| | - Elina M Jarho
- School of Pharmacy, University of Eastern Finland , P.O. Box 1627, 70211 Kuopio, Finland
| | - Kristina Luthman
- Department of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg , Kemivagen 10, SE-41296 Göteborg, Sweden
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7
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Glycoarray Technologies: Deciphering Interactions from Proteins to Live Cell Responses. MICROARRAYS 2016; 5:microarrays5010003. [PMID: 27600069 PMCID: PMC5003448 DOI: 10.3390/microarrays5010003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/02/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023]
Abstract
Microarray technologies inspired the development of carbohydrate arrays. Initially, carbohydrate array technology was hindered by the complex structures of glycans and their structural variability. The first designs of glycoarrays focused on the HTP (high throughput) study of protein-glycan binding events, and subsequently more in-depth kinetic analysis of carbohydrate-protein interactions. However, the applications have rapidly expanded and now achieve successful discrimination of selective interactions between carbohydrates and, not only proteins, but also viruses, bacteria and eukaryotic cells, and most recently even live cell responses to immobilized glycans. Combining array technology with other HTP technologies such as mass spectrometry is expected to allow even more accurate and sensitive analysis. This review provides a broad overview of established glycoarray technologies (with a special focus on glycosaminoglycan applications) and their emerging applications to the study of complex interactions between glycans and whole living cells.
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8
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Kanoh N. Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules. Nat Prod Rep 2016; 33:709-18. [DOI: 10.1039/c5np00117j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
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9
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Pourcelle V, Laurent S, Welle A, Vriamont N, Stanicki D, Vander Elst L, Muller RN, Marchand-Brynaert J. Functionalization of the PEG Corona of Nanoparticles by Clip Photochemistry in Water: Application to the Grafting of RGD Ligands on PEGylated USPIO Imaging Agent. Bioconjug Chem 2015; 26:822-9. [DOI: 10.1021/acs.bioconjchem.5b00041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Vincent Pourcelle
- Institute
of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Louis Pasteur 1 bte L4.01.02, 1348 Louvain-La-Neuve, Belgium
| | - Sophie Laurent
- Department
of General, Organic and Biomedical Chemistry, NMR and Molecular Imaging
Laboratory, University of Mons, B-7000 Mons, Belgium
- Center for Microscopy and Molecular Imaging (CMMI), Rue Adrienne Bolland, 8 B-6041 Gosselies, Belgium
| | - Alexandre Welle
- Institute
of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Louis Pasteur 1 bte L4.01.02, 1348 Louvain-La-Neuve, Belgium
| | - Nicolas Vriamont
- Institute
of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Louis Pasteur 1 bte L4.01.02, 1348 Louvain-La-Neuve, Belgium
| | - Dimitri Stanicki
- Department
of General, Organic and Biomedical Chemistry, NMR and Molecular Imaging
Laboratory, University of Mons, B-7000 Mons, Belgium
| | - Luce Vander Elst
- Department
of General, Organic and Biomedical Chemistry, NMR and Molecular Imaging
Laboratory, University of Mons, B-7000 Mons, Belgium
- Center for Microscopy and Molecular Imaging (CMMI), Rue Adrienne Bolland, 8 B-6041 Gosselies, Belgium
| | - Robert N. Muller
- Department
of General, Organic and Biomedical Chemistry, NMR and Molecular Imaging
Laboratory, University of Mons, B-7000 Mons, Belgium
- Center for Microscopy and Molecular Imaging (CMMI), Rue Adrienne Bolland, 8 B-6041 Gosselies, Belgium
| | - Jacqueline Marchand-Brynaert
- Institute
of Condensed Matter and Nanosciences, Université catholique de Louvain, Place Louis Pasteur 1 bte L4.01.02, 1348 Louvain-La-Neuve, Belgium
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10
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Singh V, Nand A, Sarita S. Universal screening platform using three-dimensional small molecule microarray based on surface plasmon resonance imaging. RSC Adv 2015. [DOI: 10.1039/c5ra15637h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we report a potent methodology for drug screening on a three-dimensional (3D) surface using a carbene based photo-cross-linking reaction.
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Affiliation(s)
- Vikramjeet Singh
- Center for Drug Delivery System
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- China
| | - Amita Nand
- National Center for Nanoscience and Technology
- Beijing 100190
- People’s Republic of China
- University of Chinese Academy
- of Sciences
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11
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Preston GW, Wilson AJ. Photo-induced covalent cross-linking for the analysis of biomolecular interactions. Chem Soc Rev 2013; 42:3289-301. [DOI: 10.1039/c3cs35459h] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Kölbel K, Ihling CH, Sinz A. Analysis of Peptide Secondary Structures by Photoactivatable Amino Acid Analogues. Angew Chem Int Ed Engl 2012; 51:12602-5. [DOI: 10.1002/anie.201205308] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 11/09/2022]
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13
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Preston GW, Radford SE, Ashcroft AE, Wilson AJ. Covalent cross-linking within supramolecular peptide structures. Anal Chem 2012; 84:6790-7. [PMID: 22746360 DOI: 10.1021/ac301198c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
β-Sheet peptide nanostructures (e.g., amyloid fibrils) are recognized as important entities in biological systems and as functional materials in their own right. Their unique physical properties and architectural complexity, however, present a challenge for structure determination at atomic resolution. Covalent cross-linking and mass spectrometry are appealing methods for this endeavor because, potentially, a large amount of information can be extracted from a small sample in a single experiment. Previously, we described preliminary studies on the use of a photoreactive diazirine-containing amino acid to cross-link peptide monomers in nanostructures, together with the integrated separation and analysis of the products using ion mobility spectrometry coupled to conventional mass spectrometry. Here, a pH-switchable system (Aβ(16-22), a sequence from the amyloid-β peptide) was used to examine cross-linking chemistry in morphologically distinct supramolecular structures containing, or entirely composed of, diazirine-functionalized peptides. We examine the relationship between cross-linker chemistry, covalent cross-links (identified using chemical derivatization and tandem mass spectrometry), and noncovalent structure, and report differences in the site of cross-linking that can only be explained by supramolecular templating. The results demonstrate the applicability of the approach for obtaining structural restraints in ordered supramolecular assemblies, provided that a considered evaluation of the cross-linked products is undertaken.
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Affiliation(s)
- George W Preston
- School of Chemistry, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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14
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Das J. Aliphatic diazirines as photoaffinity probes for proteins: recent developments. Chem Rev 2011; 111:4405-17. [PMID: 21466226 DOI: 10.1021/cr1002722] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joydip Das
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77204, USA.
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15
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Geurink PP, Prely LM, van der Marel GA, Bischoff R, Overkleeft HS. Photoaffinity labeling in activity-based protein profiling. Top Curr Chem (Cham) 2011; 324:85-113. [PMID: 22028098 DOI: 10.1007/128_2011_286] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Activity-based protein profiling has come to the fore in recent years as a powerful strategy for studying enzyme activities in their natural surroundings. Substrate analogs that bind covalently and irreversibly to an enzyme active site and that are equipped with an identification or affinity tag can be used to unearth new enzyme activities, to establish whether and at what subcellular location the enzymes are active, and to study the inhibitory effects of small compounds. A specific class of activity-based protein probes includes those that employ a photo-activatable group to create the covalent bond. Such probes are targeted to those enzymes that do not employ a catalytic nucleophile that is part of the polypeptide backbone. An overview of the various photo-activatable groups that are available to chemical biology researchers is presented, with a focus on their (photo)chemistry and their application in various research fields. A number of comparative studies are described in which the efficiency of various photo-activatable groups are compared.
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Affiliation(s)
- Paul P Geurink
- Leiden Institute of Chemistry and the Netherlands Proteomics Centre, Leiden University, The Netherlands
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16
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Construction of photo-cross-linked microarrays of small molecules. Methods Mol Biol 2010. [PMID: 20857354 DOI: 10.1007/978-1-60761-845-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Small molecule microarrays are one of the most promising approaches to screen ligand molecules for individual proteins of interest. However, their potential has not been fully realized due to the limited number of methods to introduce small molecules onto the solid surfaces. To expand the compatibility of small molecule microarrays, we have developed a unique photo-cross-linking approach for immobilizing various small molecules, including natural products, on glass slides.
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17
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Ismaili H, Lee S, Workentin MS. Diazirine-modified gold nanoparticle: template for efficient photoinduced interfacial carbene insertion reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14958-14964. [PMID: 20735050 DOI: 10.1021/la102621h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Photolysis of a 3-aryl-3-(trifluoromethyl)diazirine-modified monolayer-protected gold nanoparticles (2-C(12)MPNs), with a core size of 1.8 ± 0.3 nm, in the presence of model carbene trapping reagents leads to efficient, essentially quantitative, modification of the interface via carbene insertion reactions. The utility of carbene insertion reactions as a general approach for the modification of Au-MPNs to provide a breadth of new structures available was demonstrated using acetic acid, methanol, benzyl alcohol, phenol, benzylamine, methyl acrylate, and styrene (10a-g, respectively) as electrophilic carbene trapping agents to form the corresponding modified 3a-g-C(12)MPNs. The 1.8 ± 0.3 nm gold nanoparticles bearing a diazirine group (2-C(12)MPNs) were synthesized using the ligand exchange reaction with the requisite 3-aryl-3-(trifluoromethyl)diazirinealkylthiol. The 2-C(12)MPNs and the resulting products of the reaction on the MPN (3a-g-C(12)MPN) were fully characterized by IR, (1)H NMR, and (19)F NMR spectroscopy and, when applicable, transmission electron microscopy (TEM). Verification for the 3a-g-C(12)MPNs was accomplished by comparison of the spectral data to those of obtained for the photoreactions of 3-(3-methoxyphenyl)-3-(trifluoromethyl)-3H-diazirine as a model with 10a-g.
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Affiliation(s)
- Hossein Ismaili
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7
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18
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Synthesis of bioorthogonal and crosslinking amino acids for use in peptide synthesis. Amino Acids 2010; 39:1381-4. [PMID: 20411286 DOI: 10.1007/s00726-010-0594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022]
Abstract
The ability to incorporate non-canonical amino acids into proteins by genetic or chemical methods allows one to introduce novel chemical properties into a protein at a defined residue. Such a residue may then be modified using common organic transformations. In this way, the structure or function of the peptide may be altered without perturbing any of the other neighbouring amino acids in the peptide chain. Here, we describe the syntheses and potential applications of multiple para-substituted phenylalanine derivatives comprising an isothiocyanate, α-diazoketone, or nitrone functionality. In all, three novel amino acids were synthesized in good overall yields. These non-canonical amino acids permit the further development of in vitro and in vivo chemoselective and regioselective bioconjugate reactions not possible with other reagents.
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19
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Kanoh N. Organic Chemistry at the Interface of Complex Bioactive Natural Product and Chemical Biology. J SYN ORG CHEM JPN 2010. [DOI: 10.5059/yukigoseikyokaishi.68.939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Mackinnon AL, Taunton J. Target Identification by Diazirine Photo-Cross-linking and Click Chemistry. ACTA ACUST UNITED AC 2009; 1:55-73. [PMID: 23667793 DOI: 10.1002/9780470559277.ch090167] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Target identification of biologically active small-molecules is often the rate-determining step in forward chemical genetics. Photo-affinity labeling (PAL) represents a useful biochemical strategy for target identification in complex protein mixtures. This unit describes the use of alkyl diazirine-based photo-affinity probes and Cu(I)-catalyzed click chemistry to covalently label and visualize the targets of biologically active small-molecules. A general method for affinity purification of probe-modified proteins, useful for identification of protein targets, is also described.
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Affiliation(s)
- Andrew L Mackinnon
- Program in Chemistry and Chemical Biology and Department of Cellular and Molecular Pharmacology University of California, San Francisco San Francisco, California 94158-2280, USA
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21
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Miyazaki I, Okumura H, Simizu S, Takahashi Y, Kanoh N, Muraoka Y, Nonomura Y, Osada H. Structure-Affinity Relationship Study of Bleomycins and ShbleProtein by Use of a Chemical Array. Chembiochem 2009; 10:845-52. [DOI: 10.1002/cbic.200800728] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Wang J, Burdzinski G, Kubicki J, Platz MS. Ultrafast UV−Vis and IR Studies of p-Biphenylyl Acetyl and Carbomethoxy Carbenes. J Am Chem Soc 2008; 130:11195-209. [DOI: 10.1021/ja803096p] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jin Wang
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Gotard Burdzinski
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Jacek Kubicki
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Matthew S. Platz
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
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23
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Kanoh N, Nakamura T, Honda K, Yamakoshi H, Iwabuchi Y, Osada H. Distribution of photo-cross-linked products from 3-aryl-3-trifluoromethyldiazirines and alcohols. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Wang J, Kubicki J, Gustafson TL, Platz MS. The Dynamics of Carbene Solvation: An Ultrafast Study of p-Biphenylyltrifluoromethylcarbene. J Am Chem Soc 2008; 130:2304-13. [DOI: 10.1021/ja077705m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jin Wang
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Jacek Kubicki
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Terry L. Gustafson
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
| | - Matthew S. Platz
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, and the Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, 85 Umultowska, Poznan 61-614, Poland
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25
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Vodovozova EL. Photoaffinity labeling and its application in structural biology. BIOCHEMISTRY (MOSCOW) 2007; 72:1-20. [PMID: 17309432 DOI: 10.1134/s0006297907010014] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This review contains a brief consideration of some theoretical aspects of photoaffinity (photoreactive) labeling (PAL), and the most widely used photoreactive groups, such as arylazide, benzophenone, and 3-(trifluoromethyl)-3-phenyldiazirine, are characterized in comparison. Experimental methodology is described, including modern approaches of mass spectrometry for analysis of cross-linking products between the photoreactive probes and biomolecules. Examples of PAL application in diverse fields of structural biology during the last five-ten years are presented. Potential drug targets, transport processes, stereochemistry of interaction of G-protein-coupled receptors with ligands, as well as structural changes in nicotinic acetylcholine receptor are considered. Applications of photoaffinity ganglioside and phospholipid probes for studying biological membranes and of nucleotide probes in investigations of replicative and transcriptional complexes, as well as photoaffinity glycoconjugates for detecting carbohydrate-binding proteins are covered. In combination with modern techniques of instrumental analysis and computer-aided modeling, PAL remains the most important approach in studies on the organization of biological systems.
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Affiliation(s)
- E L Vodovozova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
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26
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Kanoh N, Asami A, Kawatani M, Honda K, Kumashiro S, Takayama H, Simizu S, Amemiya T, Kondoh Y, Hatakeyama S, Tsuganezawa K, Utata R, Tanaka A, Yokoyama S, Tashiro H, Osada H. Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein-ligand interactions. Chem Asian J 2007; 1:789-97. [PMID: 17441122 DOI: 10.1002/asia.200600208] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have developed a unique photo-cross-linking approach for immobilizing a variety of small molecules in a functional-group-independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on-array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo-cross-linked microarrays of about 2000 natural products and drugs were constructed. This photo-cross-linked microarray format was found to be useful not merely for ligand screening but also to study the structure-activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo-cross-linking process.
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Affiliation(s)
- Naoki Kanoh
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Kanoh N, Honda K, Simizu S, Muroi M, Osada H. Photo-cross-linked small-molecule affinity matrix for facilitating forward and reverse chemical genetics. Angew Chem Int Ed Engl 2006; 44:3559-62. [PMID: 15880755 DOI: 10.1002/anie.200462370] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Naoki Kanoh
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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28
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Skorey K, Waddleton D, Therien M, Leriche T. Enzyme occupancy measurement of intracellular protein tyrosine phosphatase 1B using photoaffinity probes. Anal Biochem 2005; 349:49-61. [PMID: 16360107 DOI: 10.1016/j.ab.2005.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 11/07/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is believed to be one of the enzymes involved in down-regulating the insulin receptor and is a drug target for the treatment of type II diabetes. To better understand the in vitro and in vivo behavior of PTP1B inhibitors, a cell-based assay to directly measure enzyme occupancy of PTP1B by inhibitors using photoaffinity labeling was developed. Two photoaffinity probes were synthesized containing the photolabile diazirine moiety. These photoprobes were specific for PTP1B and T-cell protein tyrosine phosphatase over CD45, with the most potent photoprobe having an IC(50) value of 0.2nM for PTP1B. Activation of the photoprobes with a 40-W UV lamp in the presence of purified AspTyrLysAspAspAspAspLys (Flag)-PTP1B formed a 1:1 irreversible adduct with the enzyme. The photolabeling was competed by known PTP1B inhibitors, vanadate, and the peptide inhibitor N-benzoyl-l-glutamyl-[4-phosphono(difluoromethyl)]-l-phenylalanyl-[4-phosphono(difluoromethyl)]l-phenylalanineamide (BzN-EJJ-amide). In HepG2 (human hepatoma cell line) cells, endogenous PTP1B was labeled by the UV-activated photoprobes in both lysed and intact cells. Enzyme occupancy measurements were conducted with a series of PTP1B inhibitors using the photoprobe affinity assay. Several compounds were shown to bind to endogenous PTP1B in the HepG2 intact cells.
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Affiliation(s)
- Kathryn Skorey
- Department of Biochemistry and Molecular Biology, Merck Frosst Centre for Therapeutic Research, Kirkland, Que., Canada H9H 3L1.
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29
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Kanoh N, Honda K, Simizu S, Muroi M, Osada H. Photo-Cross-Linked Small-Molecule Affinity Matrix for Facilitating Forward and Reverse Chemical Genetics. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462370] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Tyagi NK, Kinne RKH. Synthesis of photoaffinity probes [2′-iodo-4′-(3′′-trifluoromethyldiazirinyl)phenoxy]-d-glucopyranoside and [(4′-benzoyl)phenoxy]-d-glucopyranoside for the identification of sugar-binding and phlorizin-binding sites in the sodium/d-glucose cotransporter protein. Anal Biochem 2003; 323:74-83. [PMID: 14622961 DOI: 10.1016/j.ab.2003.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In this paper we describe the synthesis and photochemical and biochemical properties of two new photoaffinity probes designed for studies on the structure-function relationship of the sodium D-glucose cotransporter (SGLT1). The two probes are [2(')-iodo-4(')-(3(")-trifluoromethyldiazirinyl)phenoxy]-D-glucopyranoside (TIPDG), a mimic for the phenyl glucopyranoside arbutin which is transported by SGLT1 with a very high affinity, and [(4(')-benzoyl)phenoxy]-D-glucopyranoside (BzG), a model compound for phlorizin, the most potent competitive inhibitor of sugar translocation by SGLT1. Both photoaffinity probes TIPDG (lambda(max)=358 nm) and BzG (lambda(max)=293 nm) can be activated at 350-360 nm, avoiding protein-damaging wavelengths. In inhibitor studies on sodium-dependent D-glucose uptake into rabbit intestinal brush border membrane vesicles TIPDG and BzG showed a fully competitive inhibition with regard to the sugar with respective K(i) values of 22+/-5 microM for TIPDG and 12+/-2 microM for BzG. These K(i) values are comparable to those of their parent compounds arbutin (25+/-6 microM) and phlorizin (8+/-1 microM). To further test the potential of TIPDG and BzG as photoaffinity probes, truncated loop 13 protein, supposed to be part of the substrate recognition site of SGLT1, was exposed to TIPDG and BzG in solution. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis demonstrated that TIPDG and BzG successfully labeled the protein. These preliminary results suggest that both photoaffinity probes are promising tools for the study of the structure-function relationship of SGLT1 and other SGLT1 family transporter proteins.
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Affiliation(s)
- Navneet Kumar Tyagi
- Department II. Epithelial Cell Physiology, Max-Planck Institute for Molecular Physiology, Otto-Hahn Str. 11, 44227 Dortmund, Germany
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31
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Stéphan E, Affergan T, Weber P, Jaouen G. Boron trifluoride promoted addition of aryllithiums to estrone benzyl ether. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)02185-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Kersey ID, Bhogal N, Donnelly D, Fishwick CW, Findlay JB, Ward P. A Non-peptidic photoactivatable antagonist for mapping the antagonist binding site of the tachykinin NK2 receptor. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00075-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Hatanaka Y, Hashimoto M, Kanaoka Y. A novel biotinylated heterobifunctional cross-linking reagent bearing an aromatic diazirine. Bioorg Med Chem 1994; 2:1367-73. [PMID: 7788299 DOI: 10.1016/s0968-0896(00)82088-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The synthesis of a p-[(3-trifluoromethyl)diazirine-3-yl]benzoic acid derivative is described as a new carbene generating heterobifunctional cross-linking reagent. The cross-linker carries a biotin moiety in order to make use of avidin-biotin technology for specific manipulation of cross-linked components. To evaluate the ability of this reagent, the inter-subunit cross-linking of egg-white avidin tetramer was investigated. As a typical application of avidin-biotin technology for cross-linking experiments, a chemiluminescent detection method was examined to identify photobiotinylated components. A cross-linked dimeric product with an apparent molecular mass of 38 kDa was clearly visualized by the combined use of a horseradish peroxidase-streptavidin conjugate and a luminol-based chemiluminescent system.
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Affiliation(s)
- Y Hatanaka
- Research Institute for Wakan-Yaku, Toyama Medical and Pharmaceutical University, Japan
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35
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An efficient route to S-N-(9-fluorenylmethoxycarbonyl)-4′-(1-azi-2,2,2-trifluoroethyl)phenylalanine. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)60743-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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