1
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Gim J, Rubio PYM, Mohandoss S, Lee YR. Lewis Acid-Catalyzed Benzannulation of Vinyloxiranes with 3-Formylchromones or 1,4-Quinones for Diversely Functionalized 2-Hydroxybenzophenones, 1,4-Naphthoquinones, and Anthraquinones. J Org Chem 2024; 89:2538-2549. [PMID: 38302117 DOI: 10.1021/acs.joc.3c02554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
A facile and convenient protocol for the regioselective construction of functionalized 2-hydroxybenzophenones is described. This protocol involves the Sc(OTf)3/BF3·OEt2-catalyzed benzannulation of 2-vinyloxirans with 3-formylchromone, which involves cascade in situ diene formation, [4 + 2] cycloaddition, elimination, and ring-opening strategies. Moreover, it provides an expedited synthetic pathway to access biologically intriguing 1,4-naphthoquinones and anthraquinones including vitamin K3 and tectoquinone. The synthesized compounds also hold potential for use as UV filters and show promise as chemosensors for Cu2+ and Mg2+ ions.
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Affiliation(s)
- Jihwan Gim
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Peter Yuosef M Rubio
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Sonaimuthu Mohandoss
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Yong Rok Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
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2
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Gordeeva AI, Valueva AA, Rybakova EE, Ershova MO, Shumov ID, Kozlov AF, Ziborov VS, Kozlova AS, Zgoda VG, Ivanov YD, Ilgisonis EV, Kiseleva OI, Ponomarenko EA, Lisitsa AV, Archakov AI, Pleshakova TO. MS Identification of Blood Plasma Proteins Concentrated on a Photocrosslinker-Modified Surface. Int J Mol Sci 2023; 25:409. [PMID: 38203578 PMCID: PMC10778900 DOI: 10.3390/ijms25010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
This work demonstrates the use of a modified mica to concentrate proteins, which is required for proteomic profiling of blood plasma by mass spectrometry (MS). The surface of mica substrates, which are routinely used in atomic force microscopy (AFM), was modified with a photocrosslinker to allow "irreversible" binding of proteins via covalent bond formation. This modified substrate was called the AFM chip. This study aimed to determine the role of the surface and crosslinker in the efficient concentration of various types of proteins in plasma over a wide concentration range. The substrate surface was modified with a 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) photocrosslinker, activated by UV irradiation. AFM chips were incubated with plasma samples from a healthy volunteer at various dilution ratios (102X, 104X, and 106X). Control experiments were performed without UV irradiation to evaluate the contribution of physical protein adsorption to the concentration efficiency. AFM imaging confirmed the presence of protein layers on the chip surface after incubation with the samples. MS analysis of different samples indicated that the proteomic profile of the AFM-visualized layers contained common and unique proteins. In the working series of experiments, 228 proteins were identified on the chip surface for all samples, and 21 proteins were not identified in the control series. In the control series, a total of 220 proteins were identified on the chip surface, seven of which were not found in the working series. In plasma samples at various dilution ratios, a total of 146 proteins were identified without the concentration step, while 17 proteins were not detected in the series using AFM chips. The introduction of a concentration step using AFM chips allowed us to identify more proteins than in plasma samples without this step. We found that AFM chips with a modified surface facilitate the efficient concentration of proteins owing to the adsorption factor and the formation of covalent bonds between the proteins and the chip surface. The results of our study can be applied in the development of highly sensitive analytical systems for determining the complete composition of the plasma proteome.
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Affiliation(s)
| | | | | | | | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (A.I.G.); (A.A.V.); (E.E.R.); (M.O.E.); (A.F.K.); (V.S.Z.); (A.S.K.); (V.G.Z.); (Y.D.I.); (E.V.I.); (O.I.K.); (E.A.P.); (A.V.L.); (A.I.A.); (T.O.P.)
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3
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Schultz C, Farley SE, Tafesse FG. "Flash & Click": Multifunctionalized Lipid Derivatives as Tools To Study Viral Infections. J Am Chem Soc 2022; 144:13987-13995. [PMID: 35900117 PMCID: PMC9377334 DOI: 10.1021/jacs.2c02705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this perspective article, we describe the current status of lipid tools for studying host lipid-virus interactions at the cellular level. We discuss the potential lipidomic changes that viral infections impose on host cells and then outline the tools available and the resulting options to investigate the host cell lipid interactome. The future outcome will reveal new targets for treating virus infections.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Scotland E Farley
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University; 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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4
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Sultana S, Rubio PYM, Khanal HD, Lee YR. Sc(OTf) 3/BF 3·OEt 2-Catalyzed Annulation of 3-Formylchromones with Functionalized Alkenes: Access to Diverse 2-Hydroxybenzophenones. Org Lett 2022; 24:4360-4364. [PMID: 35678709 DOI: 10.1021/acs.orglett.2c01538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Sc(OTf)3/BF3·OEt2-catalyzed annulation of 3-formylchromones with functionalized alkenes for the direct construction of 2-hydroxybenzophenones is described. Sc(OTf)3/BF3·OEt2 acts as a synergistic catalyst, providing rapid synthetic access to diversely and highly functionalized 2-hydroxybenzophenones. This reaction has excellent regio- and chemoselectivities and is suitable for late-stage functionalization. The reaction proceeds via [3 + 3] and [4 + 2] cycloaddition processes, through carbonyl-ene, Diels-Alder, or aldol-type reactions. Furthermore, this protocol tolerates the various functional groups present in natural terpenes and steroids.
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Affiliation(s)
- Sabera Sultana
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Peter Yuosef M Rubio
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Hari Datta Khanal
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Yong Rok Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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5
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Li Y, Xia C, Zhao H, Xie Y, Zhang Y, Zhang W, Yu Y, Wang J, Qin W. A new photolabeling probe for efficient enrichment and deep profiling of cell surface membrane proteome by mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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McKenna SM, Fay EM, McGouran JF. Flipping the Switch: Innovations in Inducible Probes for Protein Profiling. ACS Chem Biol 2021; 16:2719-2730. [PMID: 34779621 PMCID: PMC8689647 DOI: 10.1021/acschembio.1c00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Over the past two
decades, activity-based probes have enabled a
range of discoveries, including the characterization of new enzymes
and drug targets. However, their suitability in some labeling experiments
can be limited by nonspecific reactivity, poor membrane permeability,
or high toxicity. One method for overcoming these issues is through
the development of “inducible” activity-based probes.
These probes are added to samples in an unreactive state and require in situ transformation to their active form before labeling
can occur. In this Review, we discuss a variety of approaches to inducible
activity-based probe design, different means of probe activation,
and the advancements that have resulted from these applications. Additionally,
we highlight recent developments which may provide opportunities for
future inducible activity-based probe innovations.
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Affiliation(s)
- Sean M. McKenna
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
| | - Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
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7
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Covalent Protein Immobilization onto Muscovite Mica Surface with a Photocrosslinker. MINERALS 2020. [DOI: 10.3390/min10050464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Muscovite mica with an amino silane-modified surface is commonly used as a substrate in atomic force microscopy (AFM) studies of biological macromolecules. Herein, the efficiency of two different protein immobilization strategies employing either (N-hydroxysuccinimide ester)-based crosslinker (DSP) or benzophenone-based photoactivatable crosslinker (SuccBB) has been compared using AFM and mass spectrometry analysis. Two proteins with different physicochemical properties—human serum albumin (HSA) and horseradish peroxidase enzyme protein (HRP)—have been used as model objects in the study. In the case of HRP, both crosslinkers exhibited high immobilization efficiency—as opposed to the case with HSA, when sufficient capturing efficiency has only been observed with SuccBB photocrosslinker. The results obtained herein can find their application in commonly employed bioanalytical systems and in the development of novel highly sensitive chip-based diagnostic platforms employing immobilized proteins. The obtained data can also be of interest for other research areas in medicine and biotechnology employing immobilized biomolecules.
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8
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Hassan MM, Olaoye OO. Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors. Molecules 2020; 25:E2285. [PMID: 32414020 PMCID: PMC7288102 DOI: 10.3390/molecules25102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Olasunkanmi O. Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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9
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Sannino A, Gironda-Martínez A, Gorre ÉMD, Prati L, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections. ACS COMBINATORIAL SCIENCE 2020; 22:204-212. [PMID: 32109359 DOI: 10.1021/acscombsci.0c00023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growing importance of DNA-encoded chemical libraries (DECLs) as tools for the discovery of protein binders has sparked an interest for the development of efficient screening methodologies, capable of discriminating between high- and medium-affinity ligands. Here, we present a systematic investigation of selection methodologies, featuring a library displayed on single-stranded DNA, which could be hybridized to a complementary oligonucleotide carrying a diazirine photoreactive group. Model experiments, performed using ligands of different affinity to carbonic anhydrase IX, revealed a recovery of preferential binders up to 10%, which was mainly limited by the highly reactive nature of carbene intermediates generated during the photo-cross-linking process. Ligands featuring acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared to their counterparts based on 3-sulfamoyl benzoic acid, which had a lower affinity toward the target. A systematic evaluation of experimental parameters revealed conditions that were ideally suited for library screening, which were used for the screening of a combinatorial DECL library, featuring 669 240 combinations of two sets of building blocks. Compared to conventional affinity capture procedures on protein immobilized on solid supports, photo-cross-linking provided a better discrimination of low-affinity CAIX ligands over the background signal and therefore can be used as a tandem methodology with the affinity capture procedures.
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Affiliation(s)
| | | | | | - Luca Prati
- Philochem AG, 8112 Otelfingen, Switzerland
| | | | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
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10
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Oukhatar F, Eliseeva SV, Bonnet CS, Placidi M, Logothetis NK, Petoud S, Angelovski G, Tóth É. Toward MRI and Optical Detection of Zwitterionic Neurotransmitters: Near-Infrared Luminescent and Magnetic Properties of Macrocyclic Lanthanide(III) Complexes Appended with a Crown Ether and a Benzophenone Chromophore. Inorg Chem 2019; 58:13619-13630. [DOI: 10.1021/acs.inorgchem.9b00887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Fatima Oukhatar
- Centre de Biophysique Moléculaire, UPR 4301, CNRS, Université d’Orléans, rue Charles Sadron, 45071 Orléans, Cedex 2, France
- Department of Physiology of Cognitive Processes and MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 8, 72076 Tubingen, Germany
| | - Svetlana V. Eliseeva
- Centre de Biophysique Moléculaire, UPR 4301, CNRS, Université d’Orléans, rue Charles Sadron, 45071 Orléans, Cedex 2, France
| | - Célia S. Bonnet
- Centre de Biophysique Moléculaire, UPR 4301, CNRS, Université d’Orléans, rue Charles Sadron, 45071 Orléans, Cedex 2, France
| | - Matteo Placidi
- Department of Physiology of Cognitive Processes and MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 8, 72076 Tubingen, Germany
| | - Nikos K. Logothetis
- Department of Physiology of Cognitive Processes and MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 8, 72076 Tubingen, Germany
- Department of Imaging Science and Biomedical Engineering, University of Manchester, Manchester, M13 9PT, U.K
| | - Stéphane Petoud
- Centre de Biophysique Moléculaire, UPR 4301, CNRS, Université d’Orléans, rue Charles Sadron, 45071 Orléans, Cedex 2, France
| | - Goran Angelovski
- Department of Physiology of Cognitive Processes and MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 8, 72076 Tubingen, Germany
| | - Éva Tóth
- Centre de Biophysique Moléculaire, UPR 4301, CNRS, Université d’Orléans, rue Charles Sadron, 45071 Orléans, Cedex 2, France
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11
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Photoreactive benzophenone as anchor of modifier to construct durable anti-platelets polymer surface. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Halloran MW, Lumb JP. Recent Applications of Diazirines in Chemical Proteomics. Chemistry 2019; 25:4885-4898. [PMID: 30444029 DOI: 10.1002/chem.201805004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.
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Affiliation(s)
- Matthew W Halloran
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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13
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Yuan L, Qu B, Chen J, Lv H, Yang X. Engineering modifiers bearing benzophenone with enhanced reactivity to construct surface microstructures. Polym Chem 2019. [DOI: 10.1039/c9py00764d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strategy is proposed to construct a patterned surface with controllable thickness by designing the chain backbone of BP-capped modifiers.
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Affiliation(s)
- Liguang Yuan
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Baoliu Qu
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Jiayue Chen
- Wego Holding Company Limited
- Weihai 264210
- P.R. China
| | - Hongying Lv
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Xiaoniu Yang
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
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14
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Anti-Hyperuricemic Effect of 2-Hydroxy-4-methoxy-benzophenone-5-sulfonic Acid in Hyperuricemic Mice through XOD. Molecules 2018; 23:molecules23102671. [PMID: 30336599 PMCID: PMC6222621 DOI: 10.3390/molecules23102671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/25/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Conventionally, benzophenone-type molecules are beneficial for alleviating the UV exposure of humans. More importantly, various compounds with this skeleton have demonstrated various biological activities. In this paper, we report the anti-hyperuricemic effect of the benzophenone compound 2-hydroxy-4-methoxybenzophenone-5-sulfonic acid (HMS). Preliminarily, its molecular docking score and xanthine oxidase (XOD) inhibition suggested a good anti-hyperuricemic effect. Then, its anti-hyperuricemic effect, primary mechanisms and general toxicity were examined on a hyperuricemic mouse model which was established using potassium oxonate and hypoxanthine together. HMS demonstrated a remarkable anti- hyperuricemic effect which was near to that of the control drugs, showing promising perspective. General toxicity was assessed and it showed no negative effects on body weight growth and kidney function. Moreover, anti-inflammatory action was observed for HMS via spleen and thymus changes. Its anti-hyperuricemic mechanisms may be ascribed to its inhibition of XOD and its up-regulation of organic anion transporter 1 (OAT1) and down-regulation of glucose transporter 9 (GLUT9).
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15
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Chen Y, Topp EM. Photolytic Labeling and Its Applications in Protein Drug Discovery and Development. J Pharm Sci 2018; 108:791-797. [PMID: 30339867 DOI: 10.1016/j.xphs.2018.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/19/2022]
Abstract
In this mini-review, the major types of photolytic labeling reagents are presented together with their reaction mechanisms. The applications of photolytic labeling in protein drug discovery and development are then discussed; these have expanded from studies of protein-protein interactions in vivo to protein-matrix interactions in lyophilized solids. The mini-review concludes with recommendations for further development of the approach, which include the need for new and more chemically diverse photo-reactive reagents and better understanding of the mechanisms of photolytic labeling reactions in various media.
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Affiliation(s)
- Yuan Chen
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907.
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16
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Coin I. Application of non-canonical crosslinking amino acids to study protein-protein interactions in live cells. Curr Opin Chem Biol 2018; 46:156-163. [PMID: 30077876 DOI: 10.1016/j.cbpa.2018.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
The genetic incorporation of non-canonical amino acids (ncAAs) equipped with photo-crosslinking and chemical crosslinking moieties has found broad application in the study of protein-protein interactions from a unique perspective in live cells. We highlight here applications of photo-activatable ncAAs to map protein interaction surfaces and to capture protein-protein interactions, and we describe recent efforts to efficiently couple photo-crosslinking with mass spectrometric analysis. In addition, we describe recent advances in the development and application of ncAAs for chemical crosslinking, including protein stapling, photo-control of protein conformation, two-dimensional crosslinking, and stabilization of transient and low-affinity protein-protein interactions. We expect that the field will keep growing in the near future and enable the tackling of ambitious biological questions.
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Affiliation(s)
- Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04301 Leipzig, Germany.
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17
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Zhao XZ, Métifiot M, Kiselev E, Kessl JJ, Maddali K, Marchand C, Kvaratskhelia M, Pommier Y, Burke TR. HIV-1 Integrase-Targeted Short Peptides Derived from a Viral Protein R Sequence. Molecules 2018; 23:molecules23081858. [PMID: 30049955 PMCID: PMC6222646 DOI: 10.3390/molecules23081858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 01/28/2023] Open
Abstract
HIV-1 integrase (IN) inhibitors represent a new class of highly effective anti-AIDS therapeutics. Current FDA-approved IN strand transfer inhibitors (INSTIs) share a common mechanism of action that involves chelation of catalytic divalent metal ions. However, the emergence of IN mutants having reduced sensitivity to these inhibitors underlies efforts to derive agents that antagonize IN function by alternate mechanisms. Integrase along with the 96-residue multifunctional accessory protein, viral protein R (Vpr), are both components of the HIV-1 pre-integration complex (PIC). Coordinated interactions within the PIC are important for viral replication. Herein, we report a 7-mer peptide based on the shortened Vpr (69–75) sequence containing a biotin group and a photo-reactive benzoylphenylalanyl residue, and which exhibits low micromolar IN inhibitory potency. Photo-crosslinking experiments have indicated that the peptide directly binds IN. The peptide does not interfere with IN-DNA interactions or induce higher-order, aberrant IN multimerization, suggesting a mode of action for the peptide that is distinct from clinically used INSTIs and developmental allosteric IN inhibitors. This compact Vpr-derived peptide may serve as a valuable pharmacological tool to identify a potential new pharmacologic site.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center of Cancer Research, Frederick, MD 21702, USA.
| | - Mathieu Métifiot
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jacques J Kessl
- College of Pharmacy and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406, USA.
| | - Kasthuraiah Maddali
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Mamuka Kvaratskhelia
- College of Pharmacy and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Terrence R Burke
- Chemical Biology Laboratory, Center of Cancer Research, Frederick, MD 21702, USA.
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18
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Desrochers GF, Cornacchia C, McKay CS, Pezacki JP. Activity-Based Phosphatidylinositol Kinase Probes Detect Changes to Protein-Protein Interactions During Hepatitis C Virus Replication. ACS Infect Dis 2018; 4:752-757. [PMID: 29509402 DOI: 10.1021/acsinfecdis.8b00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions are integral to host-virus interactions and can contribute significantly to enzyme regulation by changing the localization of both host and viral enzymes within the cell, inducing conformational change relevant to enzyme activity or recruiting other additional proteins to form functional complexes. Identifying the interactors of active enzymes using an activity-based protein profiling probe has allowed us to characterize both normal enzyme activation mechanisms and the manner by which these mechanisms are hijacked and altered by the hepatitis C virus (HCV). Here, we report use of a novel activity-based probe, PIKBPyne, which labels phosphatidylinositol kinases (PIKs) in an activity-based manner, to investigate HCV-dependent changes in protein-protein interactions for PI4KB. Herein, we report the synthesis of new variations on PIKBPyne, compare their ability to label the interacting partners of PI4KB, and demonstrate the utility of our approach in characterizing virus-mediated changes to host function.
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Affiliation(s)
- Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Christina Cornacchia
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Craig S. McKay
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd., Ottawa, Ontario K1H 8M5, Canada
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19
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Riga EK, Saar JS, Erath R, Hechenbichler M, Lienkamp K. On the Limits of Benzophenone as Cross-Linker for Surface-Attached Polymer Hydrogels. Polymers (Basel) 2017; 9:E686. [PMID: 30965984 PMCID: PMC6418956 DOI: 10.3390/polym9120686] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022] Open
Abstract
The synthesis of different photo-reactive poly(alkenyl norbornenes) and poly(oxonorbornenes) containing benzophenone (BP) via ring-opening metatheses polymerization (ROMP) is described. These polymers are UV irradiated to form well-defined surface-attached polymer networks and hydrogels. The relative propensity of the polymers to cross-link is evaluated by studying their gel content and its dependency on BP content, irradiation wavelength (254 or 365 nm) and energy dose applied (up to 11 J·cm-²). Analysis of the UV spectra of the polymer networks demonstrates that the poly(oxonorbornenes) show the expected BP-induced crosslinking behavior at 365 nm, although high irradiation energy doses and BP content are needed. However, these polymers undergo chain scission at 254 nm. The poly(alkenyl norbornenes), on the other hand, do not cross-link at 365 nm, whereas moderate to good cross-linking is observed at 254 nm. UV spectra demonstrate that the cross-linking at 254 nm is due to BP cross-linking combined with a [2 + 2] cylcoaddition of the alkenyl double bonds. This indicates limitations of benzophenone as a universally applicable cross-linking for polymer networks and hydrogels.
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Affiliation(s)
- Esther K Riga
- Freiburg Center für Interactive Materials and Bioinspired Technologies (FIT) and Department of Microsystems Engineering (IMTEK), Albert-Ludwigs-Universität, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
| | - Julia S Saar
- Freiburg Center für Interactive Materials and Bioinspired Technologies (FIT) and Department of Microsystems Engineering (IMTEK), Albert-Ludwigs-Universität, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
| | - Roman Erath
- Freiburg Center für Interactive Materials and Bioinspired Technologies (FIT) and Department of Microsystems Engineering (IMTEK), Albert-Ludwigs-Universität, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
| | - Michelle Hechenbichler
- Freiburg Center für Interactive Materials and Bioinspired Technologies (FIT) and Department of Microsystems Engineering (IMTEK), Albert-Ludwigs-Universität, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
| | - Karen Lienkamp
- Freiburg Center für Interactive Materials and Bioinspired Technologies (FIT) and Department of Microsystems Engineering (IMTEK), Albert-Ludwigs-Universität, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
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20
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Hauser M, Qian C, King ST, Kauffman S, Naider F, Hettich RL, Becker JM. Identification of peptide-binding sites within BSA using rapid, laser-induced covalent cross-linking combined with high-performance mass spectrometry. J Mol Recognit 2017; 31. [PMID: 28994207 DOI: 10.1002/jmr.2680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/31/2017] [Accepted: 09/17/2017] [Indexed: 11/07/2022]
Abstract
We are developing a rapid, time-resolved method using laser-activated cross-linking to capture protein-peptide interactions as a means to interrogate the interaction of serum proteins as delivery systems for peptides and other molecules. A model system was established to investigate the interactions between bovine serum albumin (BSA) and 2 peptides, the tridecapeptide budding-yeast mating pheromone (α-factor) and the decapeptide human gonadotropin-releasing hormone (GnRH). Cross-linking of α-factor, using a biotinylated, photoactivatable p-benzoyl-L-phenylalanine (Bpa)-modified analog, was energy-dependent and achieved within seconds of laser irradiation. Protein blotting with an avidin probe was used to detect biotinylated species in the BSA-peptide complex. The cross-linked complex was trypsinized and then interrogated with nano-LC-MS/MS to identify the peptide cross-links. Cross-linking was greatly facilitated by Bpa in the peptide, but some cross-linking occurred at higher laser powers and high concentrations of a non-Bpa-modified α-factor. This was supported by experiments using GnRH, a peptide with sequence homology to α-factor, which was likewise found to be cross-linked to BSA by laser irradiation. Analysis of peptides in the mass spectra showed that the binding site for both α-factor and GnRH was in the BSA pocket defined previously as the site for fatty acid binding. This model system validates the use of laser-activation to facilitate cross-linking of Bpa-containing molecules to proteins. The rapid cross-linking procedure and high performance of MS/MS to identify cross-links provides a method to interrogate protein-peptide interactions in a living cell in a time-resolved manner.
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Affiliation(s)
- Melinda Hauser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Chen Qian
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Steven T King
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Sarah Kauffman
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assemblies Institute, College of Staten Island, CUNY, New York, NY, USA
- Programs in Biochemistry and Chemistry, Graduate Center, The City University of New York, New York, NY, USA
| | - Robert L Hettich
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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21
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Porosa L, Caschera A, Bedard J, Mocella A, Ronan E, Lough AJ, Wolfaardt G, Foucher DA. UV-Curable Contact Active Benzophenone Terminated Quaternary Ammonium Antimicrobials for Applications in Polymer Plastics and Related Devices. ACS APPLIED MATERIALS & INTERFACES 2017; 9:27491-27503. [PMID: 28777541 DOI: 10.1021/acsami.7b07363] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A series of UV active benzophenone ([C6H5COC6H4-O-(CH2)n-N+Me2R][X-]; 4, R = C12H25, n = 3, X- = Br-; 5a-c, R = C18H37, n = 3, X- = Cl-, Br-, I-; 6a-c, R = C18H37, n = 4, X- = Cl-, Br-, I-; 7a-c, R = C18H37, n = 6, X- = Cl-, Br-, I-) terminated C12 and C18 quaternary ammonium salts (QACs) were prepared by thermal or microwave-driven Menshutkin protocols of the appropriate benzophenone alkyl halide (1a-c, 2a-c, 3a-c) with the corresponding dodecyl- or octadecyl N,N-dimethylamine. All new compounds were characterized by NMR spectroscopy, HRMS spectrometry, and, in one instance (4), by single-crystal X-ray crystallography. Representative C12 and C18 benzophenone QACs were formulated into 1% (w/v) water or water/ethanol-based aerosol spray coatings and then UV-cured onto plastic substrates (polypropylene, polyethylene, polystyrene, polyvinyl chloride, and polyether ether ketone) with exposure to low to moderate doses of UV (20-30 J cm-2). Confirmation as to the presence of the coatings was detected by advancing water contact angle measurements, which revealed a more hydrophilic surface after coating. Further confirmation was gained by X-ray photoelectron spectroscopy analysis, time of flight secondary ion mass spectrometry, and bromophenol blue staining, all of which showed the presence of the attached quaternary ammonium molecule. Analysis of surfaces treated with the C18 benzophenone 5b by atomic force microscopy and surface profilometry revealed a coating thickness of ∼350 nm. The treated samples along with controls were then evaluated for their antimicrobial efficacy against Gram-positive (Arthrobacter sp., Listeria monocytogenes) and Gram-negative (Pseudomonas aeruginosa) bacteria at a solid/air interface using the large drop inoculum protocol; this technique gave no evidence for cell adhesion after a 3 h time frame. These antimicrobial materials show promise for their use as coatings on plastic biomedical devices with the aim of preventing biofilm formation and preventing the spread of hospital acquired infections.
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Affiliation(s)
- Lukas Porosa
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Alexander Caschera
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Joseph Bedard
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Amanda Mocella
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Evan Ronan
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Alan J Lough
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Gideon Wolfaardt
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Stellenbosch University Water Institute Secretariat, Faculty of Natural Science, Stellenbosch Central , Stellenbosch 7599, South Africa
| | - Daniel A Foucher
- Department of Chemistry and Biology, Ryerson University , 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
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22
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Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
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Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
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23
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Wrigstedt P, Iashin V, Lagerblom K, Keskiväli J, Chernichenko K, Repo T. Syntheses of C-6 Aryl- and Alkynyl-Substituted Thymidines from Thymidine trans-5,6-Bromohydrins. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Vladimir Iashin
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Kalle Lagerblom
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Juha Keskiväli
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Konstantin Chernichenko
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Timo Repo
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
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24
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Morel E, Poyer F, Vaslin L, Bombard S, Teulade-Fichou MP. Photoactivatable platinum(II) terpyridine derivatives for G-quadruplex DNA double anchoring. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Wrigstedt P, Kavakka J, Heikkinen S, Nieger M, Räisänen M, Repo T. The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues. J Org Chem 2016; 81:3848-59. [PMID: 27080560 DOI: 10.1021/acs.joc.6b00495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This report describes an efficient procedure for the generation and isolation of various thymine and thymidine 5,6-epoxides from the corresponding trans-5,6-bromohydrins by reaction with triethylamine. The quantitative isolation of the epoxides, accomplished by solvent precipitation of triethylamine hydrobromide, enabled their regiospecific ring-opening at C6 position by organometallic nucleophiles. The reaction was amenable to a broad range of alkyl, aryl, alkenyl, and alkynyl organomagnesium, -zinc, -aluminum, or -boron reagents, although the reactivity was strongly affected by the electronic effects of N3 protecting group. Additionally, the reaction featured excellent cis-diastereoselectivity providing access to C6-carbon-functionalized dihydrothymidine cis-alcohols, which are synthetic derivatives of UV-induced DNA lesions, namely, thymidine (6-4) photoproducts.
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Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Jari Kavakka
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Martin Nieger
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Minna Räisänen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Timo Repo
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
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26
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Mihai DM, Hall S, Deng H, Welch CJ, Kawamura A. Benzophenone and its analogs bind to human glyoxalase 1. Bioorg Med Chem Lett 2015; 25:5349-51. [PMID: 26420066 DOI: 10.1016/j.bmcl.2015.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
Abstract
Benzophenone is a popular photophore for photoaffinity-labeling. It is also an important framework for drug development; many drugs contain benzophenone or analogous frameworks. The current work reports that benzophenone and its analogs bind to human glyoxalase 1. The binding, however, has little effect on the catalytic activity of this enzyme. The implications of the finding in terms of both drug development and photoaffinity-labeling are discussed.
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Affiliation(s)
- Doina M Mihai
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
| | - Steven Hall
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Haidian District, Beijing 100084, China
| | - Christopher J Welch
- Department of Process & Analytical Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Akira Kawamura
- Department of Chemistry, Hunter College and The CUNY Graduate Center, 695 Park Avenue, New York, NY 10065, USA
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27
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Xu H, Hett EC, Gopalsamy A, Parikh MD, Geoghegan KF, Kyne RE, Menard CA, Narayanan A, Robinson RP, Johnson DS, Tones MA, Jones LH. A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS. MOLECULAR BIOSYSTEMS 2015; 11:2709-12. [DOI: 10.1039/c5mb00288e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photoaffinity library expedited the discovery of a site-specific DcpS probe.
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Affiliation(s)
- Hua Xu
- Worldwide Medicinal Chemistry
- Pfizer Inc
- Cambridge
- USA
| | - Erik C. Hett
- Worldwide Medicinal Chemistry
- Pfizer Inc
- Cambridge
- USA
| | | | | | - Kieran F. Geoghegan
- Structural Biology and Biophysics
- Worldwide Medicinal Chemistry
- Pfizer Inc
- Groton CT
- USA
| | | | | | | | | | | | | | - Lyn H. Jones
- Worldwide Medicinal Chemistry
- Pfizer Inc
- Cambridge
- USA
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28
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Yang T, Liu Z, Li XD. Developing diazirine-based chemical probes to identify histone modification 'readers' and 'erasers'. Chem Sci 2014; 6:1011-1017. [PMID: 29560188 PMCID: PMC5811097 DOI: 10.1039/c4sc02328e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 10/24/2014] [Indexed: 01/06/2023] Open
Abstract
New chemical tools to ‘trap’ post translational modification (PTM)-mediated protein–protein interactions.
Post translational modifications (PTMs, e.g., phosphorylation, acetylation and methylation) of histone play important roles in regulating many fundamental cellular processes such as gene transcription, DNA replication and damage repair. While ‘writer’ and ‘eraser’ enzymes modify histones by catalyzing the addition and removal of histone PTMs, ‘reader’ proteins recognize these modified histones and ‘translate’ the PTMs by executing distinct cellular programs. Therefore, identification of the regulating enzymes and binding partners of histone PTMs is essential for understanding their regulatory mechanisms and cellular functions. Here we report the development of diazirine-based photoaffinity probes for identification of ‘readers’ and ‘erasers’ of histone PTMs. When compared with previously described benzophenone-based photoaffinity probes, the present probes demonstrate significantly improved photo-cross-linking rates, yields and specificities for capturing proteins that recognize a trimethylation mark on histone H3 lysine 4 (H3K4Me3). Furthermore, we show that the diazirine-based probes can also be used to identify enzymes that catalyse the removal of histone lysine acetylation and malonylation. This study provides new chemical tools for examining PTM-mediated protein–protein interactions and broadens the scope of our photo-cross-linking strategy from finding histone PTM ‘readers’ to identifying dynamic and transient interactions between PTMs and their ‘erasers’.
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Affiliation(s)
- Tangpo Yang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Zheng Liu
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Xiang David Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
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29
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Verga D, Hamon F, Poyer F, Bombard S, Teulade-Fichou MP. Photo-Cross-Linking Probes for Trapping G-Quadruplex DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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30
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Verga D, Hamon F, Poyer F, Bombard S, Teulade-Fichou MP. Photo-Cross-Linking Probes for Trapping G-Quadruplex DNA. Angew Chem Int Ed Engl 2013; 53:994-8. [DOI: 10.1002/anie.201307413] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/14/2013] [Indexed: 01/18/2023]
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31
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Chuang VTG, Otagiri M. Photoaffinity labeling of plasma proteins. Molecules 2013; 18:13831-59. [PMID: 24217326 PMCID: PMC6270137 DOI: 10.3390/molecules181113831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/22/2013] [Accepted: 11/04/2013] [Indexed: 12/20/2022] Open
Abstract
Photoaffinity labeling is a powerful technique for identifying a target protein. A high degree of labeling specificity can be achieved with this method in comparison to chemical labeling. Human serum albumin (HSA) and α1-acid glycoprotein (AGP) are two plasma proteins that bind a variety of endogenous and exogenous substances. The ligand binding mechanism of these two proteins is complex. Fatty acids, which are known to be transported in plasma by HSA, cause conformational changes and participate in allosteric ligand binding to HSA. HSA undergoes an N-B transition, a conformational change at alkaline pH, that has been reported to result in increased ligand binding. Attempts have been made to investigate the impact of fatty acids and the N-B transition on ligand binding in HSA using ketoprofen and flunitrazepam as photolabeling agents. Meanwhile, plasma AGP is a mixture of genetic variants of the protein. The photolabeling of AGP with flunitrazepam has been utilized to shed light on the topology of the protein ligand binding site. Furthermore, a review of photoaffinity labeling performed on other major plasma proteins will also be discussed. Using a photoreactive natural ligand as a photolabeling agent to identify target protein in the plasma would reduce non-specific labeling.
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Affiliation(s)
- Victor Tuan Giam Chuang
- School of Pharmacy, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth 6845, WA, Australia
- Authors to whom correspondence should be addressed; E-Mails: (V.T.G.C.); (M.O.); Tel.: +61-8-9266-1983 (V.T.G.C.); Fax: +61-8-9266-2769 (V.T.G.C.); Tel./Fax: +81-96-326-3887 (M.O.)
| | - Masaki Otagiri
- Graduate School of Pharmaceutical Sciences, DDS Research Institute, Sojo University, Kumamoto 860-0082, Japan
- Authors to whom correspondence should be addressed; E-Mails: (V.T.G.C.); (M.O.); Tel.: +61-8-9266-1983 (V.T.G.C.); Fax: +61-8-9266-2769 (V.T.G.C.); Tel./Fax: +81-96-326-3887 (M.O.)
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32
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Fer MJ, Olatunji S, Bouhss A, Calvet-Vitale S, Gravier-Pelletier C. Toward Analogues of MraY Natural Inhibitors: Synthesis of 5′-Triazole-Substituted-Aminoribosyl Uridines Through a Cu-Catalyzed Azide–Alkyne Cycloaddition. J Org Chem 2013; 78:10088-105. [DOI: 10.1021/jo4014035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mickaël J. Fer
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Samir Olatunji
- Laboratoire
des
Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie
et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 11, UMR 8619 CNRS, Orsay F-91405, France
| | - Ahmed Bouhss
- Laboratoire
des
Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie
et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 11, UMR 8619 CNRS, Orsay F-91405, France
| | - Sandrine Calvet-Vitale
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Christine Gravier-Pelletier
- Laboratoire de
Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601 CNRS, 45 rue des Saints Pères, 75006 Paris, France
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33
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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34
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Yang P, Yang W. Surface Chemoselective Phototransformation of C–H Bonds on Organic Polymeric Materials and Related High-Tech Applications. Chem Rev 2013; 113:5547-94. [PMID: 23614481 DOI: 10.1021/cr300246p] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Peng Yang
- Key Laboratory
of Applied Surface
and Colloid Chemistry, Ministry of Education, College of Chemistry
and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, China
| | - Wantai Yang
- The State Key Laboratory of
Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing
100029, China
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35
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Prats-Alfonso E, Oberhansl S, Lagunas A, Martínez E, Samitier J, Albericio F. Effective and Versatile Strategy for the Total Solid-Phase Synthesis of Alkanethiols for Biological Applications. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Paramelle D, Miralles G, Subra G, Martinez J. Chemical cross-linkers for protein structure studies by mass spectrometry. Proteomics 2013; 13:438-56. [PMID: 23255214 DOI: 10.1002/pmic.201200305] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 12/24/2022]
Abstract
The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, Singapore
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38
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Ueda M. Chemical Biology of Natural Products on the Basis of Identification of Target Proteins. CHEM LETT 2012. [DOI: 10.1246/cl.2012.658] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Dubinsky L, Krom BP, Meijler MM. Diazirine based photoaffinity labeling. Bioorg Med Chem 2011; 20:554-70. [PMID: 21778062 DOI: 10.1016/j.bmc.2011.06.066] [Citation(s) in RCA: 278] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/19/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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40
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Bandyopadhyay S, Bong D. Synthesis of Trifunctional Phosphatidylserine Probes for Identification of Lipid-Binding Proteins. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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A vancomycin photoprobe identifies the histidine kinase VanSsc as a vancomycin receptor. Nat Chem Biol 2010; 6:327-9. [PMID: 20383152 DOI: 10.1038/nchembio.350] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 03/09/2010] [Indexed: 11/08/2022]
Abstract
Inducible resistance to the glycopeptide antibiotic vancomycin requires expression of vanH, vanA and vanX, controlled by a two-component regulatory system consisting of a receptor histidine kinase, VanS, and a response regulator, VanR. The identity of the VanS receptor ligand has been debated. Using a synthesized vancomycin photoaffinity probe, we show that vancomycin directly binds Streptomyces coelicolor VanS (VanSsc) and this binding is correlated with resistance and required for vanH, vanA and vanX gene expression.
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42
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Marcon L, Wang M, Coffinier Y, Le Normand F, Melnyk O, Boukherroub R, Szunerits S. Photochemical immobilization of proteins and peptides on benzophenone-terminated boron-doped diamond surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1075-1080. [PMID: 19821607 DOI: 10.1021/la903012v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The successful covalent linking of green fluorescence protein and streptavidin to patterned benzophenone-modified boron-doped diamond (BDD) electrodes is demonstrated. Photoreactive benzophenone moieties were covalently grafted to oxidized diamond surfaces via an esterification reaction. Patterned BDD surfaces were obtained using a UV/ozone lithographic approach either on hydrogen-terminated BDD or on poly(ethylene)-glycol-modified BDD surfaces. UV light (lambda = 365 nm) irradiation of the patterned BDD surfaces in the presence of green fluorescence protein (GFP) or streptavidin resulted in the covalent immobilization of the proteins. The presence of poly(ethylene) glycol chains reduces significantly the nonspecific adsorption of the proteins. The success of the photoimmobilization of streptavidin was evidenced through biomolecular interaction with avidin. The preservation of the biological activity was furthermore underlined by photoimmobilization of peptides directly onto benzophenone modified BDD using a photomask.
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Affiliation(s)
- Lionel Marcon
- Institut de Recherche Interdisciplinaire (IRI, USR 3078), Parc de la Haute Borne, 50 Avenue de Halley, BP 70478, 59658 Villeneuve d'Ascq, France
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43
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Yin Z, Chen YL, Kondreddi RR, Chan WL, Wang G, Ng RH, Lim JYH, Lee WY, Jeyaraj DA, Niyomrattanakit P, Wen D, Chao A, Glickman JF, Voshol H, Mueller D, Spanka C, Dressler S, Nilar S, Vasudevan SG, Shi PY, Keller TH. N-sulfonylanthranilic acid derivatives as allosteric inhibitors of dengue viral RNA-dependent RNA polymerase. J Med Chem 2010; 52:7934-7. [PMID: 20014868 DOI: 10.1021/jm901044z] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A novel class of compounds containing N-sulfonylanthranilic acid was found to specifically inhibit dengue viral polymerase. The structural requirements for inhibition and a preliminary structure-activity relationship are described. A UV cross-linking experiment was used to map the allosteric binding site of the compound on the viral polymerase.
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Affiliation(s)
- Zheng Yin
- Novartis Institute for Tropical Diseases, Chromos, 138670, Singapore
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44
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Liebes Y, Amir L, Marks RS, Banai M. Immobilization strategies of Brucella particles on optical fibers for use in chemiluminescence immunosensors. Talanta 2009; 80:338-45. [DOI: 10.1016/j.talanta.2009.06.070] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 06/18/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
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45
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Stokes AL, Miyake-Stoner SJ, Peeler JC, Nguyen DP, Hammer RP, Mehl RA. Enhancing the utility of unnatural amino acid synthetases by manipulating broad substrate specificity. MOLECULAR BIOSYSTEMS 2009; 5:1032-8. [DOI: 10.1039/b904032c] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Kawamura A, Hindi S, Mihai DM, James L, Aminova O. Binding is not enough: flexibility is needed for photocrosslinking of Lck kinase by benzophenone photoligands. Bioorg Med Chem 2008; 16:8824-9. [PMID: 18799314 PMCID: PMC2581794 DOI: 10.1016/j.bmc.2008.08.077] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/27/2008] [Accepted: 08/29/2008] [Indexed: 10/21/2022]
Abstract
Benzophenone photophores are employed widely for photoaffinity-labeling studies. Photolabeling with benzophenone, however, is hardly a routine experiment. Even when a photoprobe binds to its target, photocrosslinking does not necessarily occur. This is because photolabeling by benzophenone is affected by many factors other than target-binding, such as conformational flexibility of photoligand. Despite the widespread recognition of such complications, there has been no systematic study to assess the relative importance of individual factors that can affect photolabeling efficiency. In order to gain an insight into this problem, we conducted a structure-activity relationship (SAR) study of benzophenone photoligands for Lck kinase, in which photoligands with varying target-binding affinity and conformational flexibility were compared. The study found that binding-affinity, as indicated by kinase inhibitory potency, did not correlate with photolabeling efficiency. Instead, conformational flexibility was found to be the determining factor for efficient photolabeling by our photoligands. Implication of the current findings, in particular, with regard to selection and optimization of benzophenone photoligands, is discussed.
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Affiliation(s)
- Akira Kawamura
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA.
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47
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Boscá F, Marín ML, Miranda MA. Photoreactivity of the Nonsteroidal Anti-inflammatory 2-Arylpropionic Acids with Photosensitizing Side Effects¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0740637potnai2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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48
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Konry T, Bouhifd M, Cosnier S, Whelan M, Valsesia A, Rossi F, Marks RS. Electrogenerated indium tin oxide-coated glass surface with photosensitive interfaces: Surface analysis. Biosens Bioelectron 2007; 22:2230-6. [PMID: 17156996 DOI: 10.1016/j.bios.2006.10.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2006] [Revised: 10/22/2006] [Accepted: 10/31/2006] [Indexed: 11/26/2022]
Abstract
We present herein a photo-immobilization technique for the localized and specific conjugation of biochip platforms with different proteinaceous bioreceptors, such as antigen or antibodies. This methodology based on a photoactivable electrogenerated polymer film, pyrrole-benzophenone, allows the covalent immobilization of biomolecules through light mediation. The surface-conductive glass platform electropolymerized with poly(pyrrole-benzophenone) thin film may then be used to affinity-coat the chip with molecular recognition probes. This glass chip electroconductive surface modification is done by the deposition of a thin layer of indium tin oxide (ITO). Thereafter, pyrrole-benzophenone monomers are electropolymerized onto the conductive metal oxide surface and then exposed to an antigen Staphylococcal Enterotoxin B (SEB)) solution and illuminated with UV light (wavelength approximately 345 nm) through a mask. As a result of the photochemical reaction, a pattern thin layer of the antigen was covalently bound to the benzophenone-modified surface. Then the sample to be analyzed, along with its specific target antibody (anti-SEB antibodies), is introduced onto the glass surface and left to react with the previously photo-immobilized antigen. When the immuno-reaction is completed, the specifically attached immunoglobulin analytes are detected by using secondary antibodies conjugated with Fluorescein isothiocyanate (FITC). The fluorescence signal emanating from the biochip surface is then quantified by two methods, using a filtered intensified charge-coupled device (CCD) camera and a grating spectrometer.
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Affiliation(s)
- Tania Konry
- The Department of Biotechnology Engineering, Faculty of Engineering Science, Ben Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
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49
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Balakirev MY, Porte S, Vernaz-Gris M, Berger M, Arié JP, Fouqué B, Chatelain F. Photochemical patterning of biological molecules inside a glass capillary. Anal Chem 2007; 77:5474-9. [PMID: 16131055 DOI: 10.1021/ac0504619] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A simple way for photochemical patterning of biological molecules onto the inner wall of fused-silica capillary is described. The method is based on a modification of the inner capillary surface with photoactive benzophenone (BP) derivative. The UV irradiation at 365 nm of the capillary filled with a sample solution results in cross-linking of the solutes to the BP moiety via a stable covalent bond. As a proof of concept, oligonucleotides and proteins were arrayed inside the capillary using an inverted microscope as an irradiation device. We demonstrated that the capillary arrays produced in this way are functional and could be used in different bioassays including DNA hybridization, protein interaction studies, and immunoassays. Having a sensitivity comparable to the fluorophore-based assays in a planar format, the capillary array possesses several advantages including submicroliter sample volume and a short assay time. The capillary format should therefore be considered as a possible alternative to a planar format in a number of low-density array applications such as mutation detection and diagnostic immunoassays.
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Affiliation(s)
- Maxim Y Balakirev
- Laboratoire Biopuces, Département Réponse et Dynamique Cellulaires, and Laboratoire d'Electronique de Technologie de l'Information (LETI), Commissariat à l'Energie Atomique, 17 rue des Martyrs, 38054 Grenoble, France.
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50
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Musial-Siwek M, Rusch SL, Kendall DA. Selective photoaffinity labeling identifies the signal peptide binding domain on SecA. J Mol Biol 2006; 365:637-48. [PMID: 17084862 PMCID: PMC1851904 DOI: 10.1016/j.jmb.2006.10.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 10/02/2006] [Accepted: 10/08/2006] [Indexed: 11/26/2022]
Abstract
SecA, an ATPase crucial to the Sec-dependent translocation machinery in Escherichia coli, recognizes and directly binds the N-terminal signal peptide of an exported preprotein. This interaction plays a central role in the targeting and transport of preproteins via the SecYEG channel. Here we identify the signal peptide binding groove (SPBG) on SecA addressing a key issue regarding the SecA-preprotein interaction. We employ a synthetic signal peptide containing the photoreactive benzoylphenylalanine to efficiently and specifically label SecA containing a unique Factor Xa site. Comparison of the photolabeled fragment from the subsequent proteolysis of several SecAs, which vary only in the location of the Factor Xa site, reveals one 53 residue segment in common with the entire series. The covalently modified SecA segment produced is the same in aqueous solution and in lipid vesicles. This spans amino acid residues 269 to 322 of the E. coli protein, which is distinct from a previously proposed signal peptide binding site, and contributes to a hydrophobic peptide binding groove evident in molecular models of SecA.
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Affiliation(s)
| | | | - Debra A. Kendall
- *Corresponding author. Department of Molecular and Cell Biology, 91 North Eagleville Road, University of Connecticut, Storrs, Connecticut 06269-3125, USA; Tel.: (860) 486-1891; Fax: (860) 486-4331; E-mail: ()
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