1
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [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: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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2
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Vidyakina AA, Shtyrov AA, Ryazantsev MN, Khlebnikov AF, Kolesnikov IE, Sharoyko VV, Spiridonova DV, Balova IA, Bräse S, Danilkina NA. Development of Fluorescent Isocoumarin-Fused Oxacyclononyne - 1,2,3-Triazole Pairs. Chemistry 2023; 29:e202300540. [PMID: 37293937 DOI: 10.1002/chem.202300540] [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: 02/18/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent isocoumarin-fused cycloalkynes, which are reactive in SPAAC and give fluorescent triazoles regardless of the azide nature, have been developed. The key structural feature that converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart is the pi-acceptor group (COOMe, CN) at the C6 position of the isocoumarin ring. The design of the fluorescent cycloalkyne/triazole pairs is based on the theoretical study of the S1 state deactivation mechanism of the non-fluorescent isocoumarin-fused cycloalkyne IC9O using multi-configurational ab initio and DFT methodologies. The calculations revealed that deactivation proceeds through the electrocyclic ring opening of the α-pyrone cycle and is accompanied by a redistribution of electron density in the fused benzene ring. We proposed that the S1 excited state deactivation barrier could be increased by introducing a pi-acceptor group into a position that is in direct conjugation with the formed C=O group and has a reduced electron density in the transition state. As a proof of concept, we designed and synthesized two fluorescent isocoumarin-fused cycloalkynes IC9O-COOMe and IC9O-CN bearing pi-acceptors at the C6 position. The importance of the nature of a pi-acceptor group was shown by the example of much less fluorescent CF3 -substituted cycloalkyne IC9O-CF3 .
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Affiliation(s)
- Aleksandra A Vidyakina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Alexander F Khlebnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Ilya E Kolesnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Vladimir V Sharoyko
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Dar'ya V Spiridonova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems-, Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
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3
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Miao Y, Peng L, Chen Z, Hu Y, Tao L, Yao Y, Wu Y, Yang D, Xu T. Recent advances of Phosphodiesterase 4B in cancer. Expert Opin Ther Targets 2023; 27:121-132. [PMID: 36803246 DOI: 10.1080/14728222.2023.2183496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
INTRODUCTION Phosphodiesterase 4B (PDE4B) is a crucial enzyme in the phosphodiesterases (PDEs), acting as a regulator of cyclic adenosine monophosphate (cAMP). It is involved in cancer process through PDE4B/cAMP signaling pathway. Cancer occurs and develops with the regulation of PDE4B in the body, suggesting that PDE4B is a promising therapeutic target. AREAS COVERED This review covereed the function and mechanism of PDE4B in cancer. We summarized the possible clinical applications of PDE4B, and highlighted the possible ways to develop clinical applications of PDE4B inhibitors. We also discussed some common PDEs inhibitors, and expected the development of combined targeting PDE4B and other PDEs drugs in the future. EXPERT OPINION The existing research and clinical data can strongly prove the role of PDE4B in cancer. PDE4B inhibition can effectively increase cell apoptosis, inhibit cell proliferation, transformation, migration, etc., indicating that PDE4B inhibition can effectively inhibit the development of cancer. Other PDEs may antagonize or coordinate this effect. As for the further study on the relationship between PDE4B and other PDEs in cancer, it is still a challenge to develop multi-targeted PDEs inhibitors.
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Affiliation(s)
- Yu Miao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Li Peng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Zhaolin Chen
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, Anhui Province, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Liangsong Tao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Yan Yao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Yincui Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Dashuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, China.,Anhui Key Laboratory of Bioactivity of Natural Products, Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, Anhui Province, China
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4
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Chinoy ZS, Friscourt F. Expanding the Strain‐Promoted 1,3‐Dipolar Cycloaddition Arsenal for a More Selective Bioorthogonal Labeling in Living Cells. Isr J Chem 2022. [DOI: 10.1002/ijch.202200055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zoeisha S. Chinoy
- Institut Européen de Chimie et Biologie Université de Bordeaux 2 rue Robert Escarpit 33607 Pessac France
- Institut des Sciences Moléculaires CNRS UMR5255 33405 Talence France
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie Université de Bordeaux 2 rue Robert Escarpit 33607 Pessac France
- Institut des Sciences Moléculaires CNRS UMR5255 33405 Talence France
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5
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Gulledge ZZ, Duda DP, Dixon DA, Carrick JD. Microwave-Assisted, Metal- and Azide-Free Synthesis of Functionalized Heteroaryl-1,2,3-triazoles via Oxidative Cyclization of N-Tosylhydrazones and Anilines. J Org Chem 2022; 87:12632-12643. [PMID: 36126149 DOI: 10.1021/acs.joc.2c01042] [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
As the search for competent soft-Lewis basic complexants for separations continues to evolve toward identification of a chemoselective moiety for speciation of the minor actinides from the electronically similar lanthanides, synthetic methods must congruently evolve. Synthetic options to convergently construct unsymmetric heteroaryl donor complexants incorporating a 1,2,3-triazole from accessible starting materials for evaluation in separation assays necessitated the development of the described methodology. In this report, metal- and azide-free synthesis of diversely functionalized pyridyl-1,2,3-triazole derivatives facilitated by microwave irradiation was leveraged to prepare a novel class of tridentate ligands. The described work negates the incorporation of thermally sensitive and toxic organoazides by using N-tosylhydrazones and anilines as viable synthetic equivalents in an efficient 12 min reaction time. Adaptation to alternative synthons useful for drug discovery was also realized. Method discovery, optimization, N-tosylhydrazone and aniline substrate scope, as well as a preliminary mechanistic hypotheses supported by DFT calculations are reported herein.
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Affiliation(s)
- Zachary Z Gulledge
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
| | - Damian P Duda
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Jesse D Carrick
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
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6
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Liu L, Zhang D, Johnson M, Devaraj NK. Light-activated tetrazines enable precision live-cell bioorthogonal chemistry. Nat Chem 2022; 14:1078-1085. [PMID: 35788560 PMCID: PMC10198265 DOI: 10.1038/s41557-022-00963-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Bioorthogonal cycloaddition reactions between tetrazines and strained dienophiles are widely used for protein, lipid and glycan labelling because of their extremely rapid kinetics. However, controlling this chemistry in the presence of living mammalian cells with a high degree of spatial and temporal precision remains a challenge. Here we demonstrate a versatile approach to light-activated formation of tetrazines from photocaged dihydrotetrazines. Photouncaging, followed by spontaneous transformation to reactive tetrazine, enables live-cell spatiotemporal control of rapid bioorthogonal cycloaddition with dienophiles such as trans-cyclooctenes. Photocaged dihydrotetrazines are stable in conditions that normally degrade tetrazines, enabling efficient early-stage incorporation of bioorthogonal handles into biomolecules such as peptides. Photocaged dihydrotetrazines allow the use of non-toxic light to trigger tetrazine ligations on living mammalian cells. By tagging reactive phospholipids with fluorophores, we demonstrate modification of HeLa cell membranes with single-cell spatial resolution. Finally, we show that photo-triggered therapy is possible by coupling tetrazine photoactivation with strategies that release prodrugs in response to tetrazine ligation.
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Affiliation(s)
- Luping Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Mai Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
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7
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Ooi JMF, Fairhall JM, Spangler B, Chong DJW, Feng BY, Gamble AB, Hook S. Development of a bioorthogonal fluorescence-based assay for assessing drug uptake and delivery in bacteria. RSC Adv 2022; 12:15631-15642. [PMID: 35685699 PMCID: PMC9126673 DOI: 10.1039/d2ra02272a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
Bioorthogonal chemistry can facilitate the development of fluorescent probes that can be used to sensitively and specifically detect the presence of biological targets. In this study, such an assay was developed to evaluate the uptake and delivery of antimicrobials into Escherichia coli, building on and extending previous work which utilised more resource intensive LCMS detection. The bacteria were genetically engineered to express streptavidin in the periplasmic or cytoplasmic compartments, which was used to localise a bioorthogonal probe (BCN-biotin). Azido-compounds which are delivered to these compartments react with the localised BCN-biotin–streptavidin in a concentration-dependent manner via a strain-promoted alkyne–azide cycloaddition. The amount of azido-compound taken up by bacteria was determined by quantifying unreacted BCN-biotin–streptavidin via an inverse electron demand Diels–Alder reaction between remaining BCN-biotin and a tetrazine-containing fluorescent dye. Following optimisation and validation, the assay was used to assess uptake of liposome-formulated azide-functionalised luciferin and cefoxitin. The results demonstrated that formulation into cationic liposomes improved the uptake of azide-functionalised compounds into the periplasm of E. coli, providing insight on the uptake mechanism of liposomes in the bacteria. This newly developed bioorthogonal fluorescence plate-reader based assay provides a bioactivity-independent, medium-to-high throughput tool for screening compound uptake/delivery. Bioorthogonal alkyne–azide and alkyne–tetrazine chemistries were used to assess drug uptake in bacteria. Azido-drug reacts with streptavidin bound alkyne-biotin within bacteria, the remaining unreacted alkyne is then quantified with a tetrazine-dye.![]()
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Affiliation(s)
| | | | - Benjamin Spangler
- Novartis Institutes for BioMedical Research (NIBR) in Emeryville California USA
| | | | - Brian Y Feng
- Novartis Institutes for BioMedical Research (NIBR) in Emeryville California USA
| | - Allan B Gamble
- School of Pharmacy, University of Otago Dunedin New Zealand
| | - Sarah Hook
- School of Pharmacy, University of Otago Dunedin New Zealand
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8
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Synthesis and Fluorescent Properties of Aminopyridines and the Application in "Click and Probing". Molecules 2022; 27:molecules27051596. [PMID: 35268697 PMCID: PMC8912075 DOI: 10.3390/molecules27051596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Unsubstituted pyridin-2-amine has a high quantum yield and is a potential scaffold for a fluorescent probe. However, the facile access to conjugated highly substituted aminopyridines and the study of their fluorescent properties is scarce. In this paper, synthesis and fluorescent properties of multisubstituted aminopyridines were studied based on a recently developed Rh-catalyzed coupling of vinyl azide with isonitrile to form a vinyl carbodiimide intermediate, following tandem cyclization with an alkyne. An aminopyridine substituted with an azide group as a potential probe was further designed, synthesized, and evaluated. The “clicking-and-probing” experiment of it on BSA protein showed the potential of aminopyridine as a scaffold of a biological probe.
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9
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Platts K, Michel R, Green E, Gillam T, Ghetia M, O'Brien-Simpson N, Li W, Blencowe C, Blencowe A. Pentafulvene-Maleimide Cycloaddition for Bioorthogonal Ligation. Bioconjug Chem 2021; 32:1845-1851. [PMID: 34254789 DOI: 10.1021/acs.bioconjchem.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The applications of bioconjugation chemistry are rapidly expanding, and the addition of new strategies to the bioconjugation and ligation toolbox will further advance progress in this field. Herein, we present a detailed study of the Diels-Alder cycloaddition (DAC) reaction between pentafulvenes and maleimides in aqueous solutions and investigate the reaction as an emerging bioconjugation strategy. The DAC reactions were found to proceed efficiently, quantitatively yielding cycloadducts with reaction rates ranging up to ∼0.7 M-1 s-1 for a series of maleimides, including maleimide-derivatized peptides and proteins. The absence of cross-reactivity of the pentafulvene with a large panel of functional (bio)molecules and biological media further demonstrated the bioorthogonality of this approach. The utility of the DAC reaction for bioorthogonal bioconjugation applications was further demonstrated in the presence of biological media and proteins, as well as through protein derivatization and labeling, which was comparable to the widely employed sulfhydryl-maleimide coupling chemistry.
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Affiliation(s)
- Kirsten Platts
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Robert Michel
- Fleet Bioprocessing, Ltd., Pale Lane, Hartley Whitney, Hampshire RG27 8DH, United Kingdom
| | - Elise Green
- Fleet Bioprocessing, Ltd., Pale Lane, Hartley Whitney, Hampshire RG27 8DH, United Kingdom
| | - Todd Gillam
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia.,Surface Interactions and Soft Matter (SISM) Group, Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Maulik Ghetia
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Neil O'Brien-Simpson
- Centre for Oral Health Research, The Melbourne Dental School and the Bio21 Institute, The University of Melbourne, 720 Swanston Street, Carlton, Melbourne, Victoria 3010, Australia
| | - Wenyi Li
- Centre for Oral Health Research, The Melbourne Dental School and the Bio21 Institute, The University of Melbourne, 720 Swanston Street, Carlton, Melbourne, Victoria 3010, Australia
| | - Christopher Blencowe
- Fleet Bioprocessing, Ltd., Pale Lane, Hartley Whitney, Hampshire RG27 8DH, United Kingdom
| | - Anton Blencowe
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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10
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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11
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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12
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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13
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Zhao Q, Guo G, Zhu W, Zhu L, Da Y, Han Y, Xu H, Wu S, Cheng Y, Zhou Y, Cai X, Jiang X. Suzuki Cross-Coupling Reaction with Genetically Encoded Fluorosulfates for Fluorogenic Protein Labeling. Chemistry 2020; 26:15938-15943. [PMID: 32776653 DOI: 10.1002/chem.202002037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/24/2020] [Indexed: 11/09/2022]
Abstract
A palladium-catalyzed cross-coupling reaction with aryl halide functionalities has recently emerged as a valuable tool for protein modification. Herein, a new fluorogenic modification methodology for proteins, with genetically encoded fluorosulfate-l-tyrosine, which exhibits high efficiency and biocompatibility in bacterial cells as well as in aqueous medium, is described. Furthermore, the cross-coupling of 4-cyanophenylboronic acid on green fluorescent protein was shown to possess a unique fluorogenic property, which could open up the possibility of a responsive "off/on" switch with great potential to enable spectroscopic imaging of proteins with minimal background noise. Taken together, a convenient and efficient catalytic system has been developed that may provide broad utilities in protein visualization and live-cell imaging.
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Affiliation(s)
- Qian Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Guoying Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Weiwei Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Liping Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P.R. China
| | - Yifan Da
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Ying Han
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Hongjiao Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Shuohan Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yaping Cheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yani Zhou
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, P.R. China
| | - Xiaoqing Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Xianxing Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
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14
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15
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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16
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Jiang T, Laughlin ST. Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation. Methods Enzymol 2020; 641:1-34. [PMID: 32713519 DOI: 10.1016/bs.mie.2020.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.
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Affiliation(s)
- Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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17
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Tsao KK, Lee AC, Racine KÉ, Keillor JW. Site-Specific Fluorogenic Protein Labelling Agent for Bioconjugation. Biomolecules 2020; 10:biom10030369. [PMID: 32121143 PMCID: PMC7175205 DOI: 10.3390/biom10030369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 01/29/2023] Open
Abstract
Many clinically relevant therapeutic agents are formed from the conjugation of small molecules to biomolecules through conjugating linkers. In this study, two novel conjugating linkers were prepared, comprising a central coumarin core, functionalized with a dimaleimide moiety at one end and a terminal alkyne at the other. In our first design, we developed a protein labelling method that site-specifically introduces an alkyne functional group to a dicysteine target peptide tag that was genetically fused to a protein of interest. This method allows for the subsequent attachment of azide-functionalized cargo in the facile synthesis of novel protein-cargo conjugates. However, the fluorogenic aspect of the reaction between the linker and the target peptide was less than we desired. To address this shortcoming, a second linker reagent was prepared. This new design also allowed for the site-specific introduction of an alkyne functional group onto the target peptide, but in a highly fluorogenic and rapid manner. The site-specific addition of an alkyne group to a protein of interest was thus monitored in situ by fluorescence increase, prior to the attachment of azide-functionalized cargo. Finally, we also demonstrated that the cargo can also be attached first, in an azide/alkyne cycloaddition reaction, prior to fluorogenic conjugation with the target peptide-fused protein.
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18
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Ghiassian S, Yu L, Gobbo P, Nazemi A, Romagnoli T, Luo W, Luyt LG, Workentin MS. Nitrone-Modified Gold Nanoparticles: Synthesis, Characterization, and Their Potential as 18F-Labeled Positron Emission Tomography Probes via I-SPANC. ACS OMEGA 2019; 4:19106-19115. [PMID: 31763533 PMCID: PMC6868604 DOI: 10.1021/acsomega.9b02322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/28/2019] [Indexed: 05/11/2023]
Abstract
A novel bioorthogonal gold nanoparticle (AuNP) template displaying interfacial nitrone functional groups for bioorthogonal interfacial strain-promoted alkyne-nitrone cycloaddition reactions has been synthesized. These nitrone-AuNPs were characterized in detail using 1H nuclear magnetic resonance spectroscopy, transmission electron microscopy, thermogravimetric analysis, and X-ray photoelectron spectroscopy, and a nanoparticle raw formula was calculated. The ability to control the conjugation of molecules of interest at the molecular level onto the nitrone-AuNP template allowed us to create a novel methodology for the synthesis of AuNP-based radiolabeled probes.
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Affiliation(s)
- Sara Ghiassian
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
| | - Lihai Yu
- London
Regional Cancer Program, 800 Commissioners Rd. E., London N6A 5W9, Ontario, Canada
| | - Pierangelo Gobbo
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
| | - Ali Nazemi
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
| | - Tommaso Romagnoli
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
| | - Wilson Luo
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
| | - Leonard G. Luyt
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
- London
Regional Cancer Program, 800 Commissioners Rd. E., London N6A 5W9, Ontario, Canada
| | - Mark S. Workentin
- Department
of Chemistry and the Center for Materials and Biomaterials
Research and Department of Oncology, The University
of Western Ontario, London N6A 5B7, Ontario, Canada
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19
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Kovacs D, Kiraev SR, Phipps D, Orthaber A, Borbas KE. Eu(III) and Tb(III) Complexes of Octa- and Nonadentate Macrocyclic Ligands Carrying Azide, Alkyne, and Ester Reactive Groups. Inorg Chem 2019; 59:106-117. [DOI: 10.1021/acs.inorgchem.9b01576] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120, Uppsala, Sweden
| | - Salauat R. Kiraev
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120, Uppsala, Sweden
| | - Dulcie Phipps
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120, Uppsala, Sweden
| | - Andreas Orthaber
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120, Uppsala, Sweden
| | - K. Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University, 75120, Uppsala, Sweden
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20
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Recent Advances in Bioorthogonal Click Chemistry for Efficient Synthesis of Radiotracers and Radiopharmaceuticals. Molecules 2019; 24:molecules24193567. [PMID: 31581645 PMCID: PMC6803924 DOI: 10.3390/molecules24193567] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 12/17/2022] Open
Abstract
In recent years, several catalyst-free site-specific reactions have been investigated for the efficient conjugation of biomolecules, nanomaterials, and living cells. Representative functional group pairs for these reactions include the following: (1) azide and cyclooctyne for strain-promoted cycloaddition reaction, (2) tetrazine and trans-alkene for inverse-electron-demand-Diels–Alder reaction, and (3) electrophilic heterocycles and cysteine for rapid condensation/addition reaction. Due to their excellent specificities and high reaction rates, these conjugation methods have been utilized for the labeling of radioisotopes (e.g., radiohalogens, radiometals) to various target molecules. The radiolabeled products prepared by these methods have been applied to preclinical research, such as in vivo molecular imaging, pharmacokinetic studies, and radiation therapy of cancer cells. In this review, we explain the basics of these chemical reactions and introduce their recent applications in the field of radiopharmacy and chemical biology. In addition, we discuss the significance, current challenges, and prospects of using bioorthogonal conjugation reactions.
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21
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Li B, Zhou X, Yang P, Zhu L, Zhong Y, Cai Z, Jiang B, Cai X, Liu J, Jiang X. Photoactivatable Fluorogenic Labeling via Turn-On "Click-Like" Nitroso-Diene Bioorthogonal Reaction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802039. [PMID: 31380178 PMCID: PMC6662066 DOI: 10.1002/advs.201802039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/27/2019] [Indexed: 06/10/2023]
Abstract
Fluorogenic labeling enables imaging cellular molecules of interest with minimal background. This process is accompanied with the notable increase of the quantum yield of fluorophore, thus minimizing the background signals from unactivated profluorophores. Herein, the development of a highly efficient and bioorthogonal nitroso-based Diels-Alder fluorogenic reaction is presented and its usefulness is validated as effective and controllable in fluorescent probes and live-cell labeling strategies for dynamic cellular imaging. It is demonstrated that nitroso-based cycloaddition is an efficient fluorogenic labeling tool through experiments of further UV-activatable fluorescent labeling on proteins and live cells. The ability of tuning the fluorescence of labeled proteins by UV-irradiation enables selective activation of proteins of interest in a particular cell compartment at a given time point, while leaving the remaining labeled molecules untouched.
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Affiliation(s)
- Bai Li
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Xian‐Hao Zhou
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201210China
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Peng‐Yu Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Liping Zhu
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Yuan Zhong
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Zhengjun Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xiaoqing Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Xianxing Jiang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
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22
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Noda H, Asada Y, Shibasaki M, Kumagai N. A fluorogenic C4N4 probe for azide-based labelling. Org Biomol Chem 2019; 17:1813-1816. [DOI: 10.1039/c8ob02695e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A new fluorogenic probe based on the recently identified 2,5-diaminopyrimidine (C4N4) fluorophore is introduced for azide-specific labelling.
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Affiliation(s)
- Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN)
- Tokyo 141-0021
- Japan
| | - Yasuko Asada
- Institute of Microbial Chemistry (BIKAKEN)
- Tokyo 141-0021
- Japan
| | | | - Naoya Kumagai
- Institute of Microbial Chemistry (BIKAKEN)
- Tokyo 141-0021
- Japan
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23
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Yoshida S. Controlled Reactive Intermediates Enabling Facile Molecular Conjugation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180104] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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24
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Liu G, Hu J, Liu S. Emerging Applications of Fluorogenic and Non-fluorogenic Bifunctional Linkers. Chemistry 2018; 24:16484-16505. [PMID: 29893499 DOI: 10.1002/chem.201801290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Indexed: 01/06/2023]
Abstract
Homo- and hetero-bifunctional linkers play vital roles in constructing a variety of functional systems, ranging from protein bioconjugates with drugs and functional agents, to surface modification of nanoparticles and living cells, and to the cyclization/dimerization of synthetic polymers and biomolecules. Conventional approaches for assaying conjugation extents typically rely on ex situ techniques, such as mass spectrometry, gel electrophoresis, and size-exclusion chromatography. If the conjugation process involving bifunctional linkers was rendered fluorogenic, then in situ monitoring, quantification, and optical tracking/visualization of relevant processes would be achieved. In this review, conventional non-fluorogenic linkers are first discussed. Then the focus is on the evolution and emerging applications of fluorogenic bifunctional linkers, which are categorized into hetero-bifunctional single-caging fluorogenic linkers, homo-bifunctional double-caging fluorogenic linkers, and hetero-bifunctional double-caging fluorogenic linkers. In addition, stimuli-cleavable bifunctional linkers designed for both conjugation and subsequent site-specific triggered release are also summarized.
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Affiliation(s)
- Guhuan Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Jinming Hu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Shiyong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the MicroscaleiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
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25
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Favre C, Friscourt F. Fluorogenic Sydnone-Modified Coumarins Switched-On by Copper-Free Click Chemistry. Org Lett 2018; 20:4213-4217. [PMID: 29995429 DOI: 10.1021/acs.orglett.8b01587] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis, photophysical characterization, and biochemical application of sydnone-modified coumarins, a novel class of fluorogenic clickable reagents, are reported. The sydnone moiety, a stable aromatic 1,3-dipole, efficiently quenched the fluorescence of coumarin, which could be restored, with a 132-fold enhancement, upon cycloadditions with cyclooctynes, thereby expanding the fluorogenic click toolbox. TD-DFT calculations suggest that the fluorescence quenching of the sydnone-modified coumarins is likely due to the presence of an energetically low-lying nonemissive charge-separated state.
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Affiliation(s)
- Camille Favre
- Institut Européen de Chimie et Biologie , Université de Bordeaux , 2 rue Robert Escarpit , 33607 Pessac , France.,Institut de Neurosciences Cognitives et Intégratives d'Aquitaine , CNRS UMR5287 , Bordeaux , France
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie , Université de Bordeaux , 2 rue Robert Escarpit , 33607 Pessac , France.,Institut de Neurosciences Cognitives et Intégratives d'Aquitaine , CNRS UMR5287 , Bordeaux , France
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26
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Chupakhin EG, Krasavin MY. Achievements in the synthesis of cyclooctynes for ring strain-promoted [3+2] azide-alkyne cycloaddition. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2295-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 634] [Impact Index Per Article: 105.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
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Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
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28
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Favre C, de Cremoux L, Badaut J, Friscourt F. Sydnone Reporters for Highly Fluorogenic Copper-Free Click Ligations. J Org Chem 2018; 83:2058-2066. [DOI: 10.1021/acs.joc.7b03004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Camille Favre
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Lucie de Cremoux
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Jerome Badaut
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
- Basic
Science Department, Loma Linda University, Loma Linda, California 92350, United States
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
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29
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Decuypère E, Riomet M, Sallustrau A, Bregant S, Thai R, Pieters G, Clavier G, Audisio D, Taran F. Sydnone-coumarins as clickable turn-on fluorescent sensors for molecular imaging. Chem Commun (Camb) 2018; 54:10758-10761. [DOI: 10.1039/c8cc06070c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sydnone-coumarin compounds are interesting turn-on fluorogenic probes for protein labeling.
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Affiliation(s)
- Elodie Decuypère
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Margaux Riomet
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Antoine Sallustrau
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Sarah Bregant
- Service d'Ingénierie Moléculaire des Protéines DRF-JOLIOT-SIMOPRO, CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Robert Thai
- Service d'Ingénierie Moléculaire des Protéines DRF-JOLIOT-SIMOPRO, CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Grégory Pieters
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Gilles Clavier
- PPSM, ENS Cachan
- CNRS
- Université Paris-Saclay
- 94235 Cachan
- France
| | - Davide Audisio
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Frédéric Taran
- Service de Chimie Bio-organique et Marquage DRF-JOLIOT-SCBM
- CEA
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
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30
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Shang X, Lai R, Song X, Li H, Niu W, Guo J. Improved Photoinduced Fluorogenic Alkene-Tetrazole Reaction for Protein Labeling. Bioconjug Chem 2017; 28:2859-2864. [PMID: 29022697 DOI: 10.1021/acs.bioconjchem.7b00562] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The 1,3-dipolar cycloaddition reaction between an alkene and a tetrazole represents one elegant and rare example of fluorophore-forming bioorthogonal chemistry. This is an attractive reaction for imaging applications in live cells that requires less intensive washing steps and/or needs spatiotemporal resolutions. In the present work, as an effort to improve the fluorogenic property of the alkene-tetrazole reaction, an aromatic alkene (styrene) was investigated as the dipolarophile. Over 30-fold improvement in quantum yield of the reaction product was achieved in aqueous solution. According to our mechanistic studies, the observed improvement is likely due to an insufficient protonation of the styrene-tetrazole reaction product. This finding provides useful guidance to the future design of alkene-tetrazole reactions for biological studies. Fluorogenic protein labeling using the styrene-tetrazole reaction was demonstrated both in vitro and in vivo. This was realized by the genetic incorporation of an unnatural amino acid containing the styrene moiety. It is anticipated that the combination of styrene with different tetrazole derivatives can generally improve and broaden the application of alkene-tetrazole chemistry in real-time imaging in live cells.
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Affiliation(s)
- Xin Shang
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Rui Lai
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Xi Song
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Hui Li
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, ‡Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, and §Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
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31
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Ghandiyar S, Hamzehloueian M, Hosseinzadeh R. Mechanism study on the copper-free click reaction of a coumarin-conjugated cyclooctyne. Struct Chem 2017. [DOI: 10.1007/s11224-017-0991-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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32
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Lopchuk JM, Fjelbye K, Kawamata Y, Malins LR, Pan CM, Gianatassio R, Wang J, Prieto L, Bradow J, Brandt TA, Collins MR, Elleraas J, Ewanicki J, Farrell W, Fadeyi OO, Gallego GM, Mousseau JJ, Oliver R, Sach NW, Smith JK, Spangler JE, Zhu H, Zhu J, Baran PS. Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity. J Am Chem Soc 2017; 139:3209-3226. [PMID: 28140573 PMCID: PMC5334783 DOI: 10.1021/jacs.6b13229] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Driven by the ever-increasing pace
of drug discovery and the need
to push the boundaries of unexplored chemical space, medicinal chemists
are routinely turning to unusual strained bioisosteres such
as bicyclo[1.1.1]pentane, azetidine, and cyclobutane to modify their
lead compounds. Too often, however, the difficulty of installing these
fragments surpasses the challenges posed even by the construction
of the parent drug scaffold. This full account describes the development
and application of a general strategy where spring-loaded, strained
C–C and C–N bonds react with amines to allow for the
“any-stage” installation of small, strained ring systems.
In addition to the functionalization of small building blocks and
late-stage intermediates, the methodology has been applied to bioconjugation
and peptide labeling. For the first time, the stereospecific strain-release
“cyclopentylation” of amines, alcohols, thiols,
carboxylic acids, and other heteroatoms is introduced. This report
describes the development, synthesis, scope of reaction, bioconjugation,
and synthetic comparisons of four new chiral “cyclopentylation”
reagents.
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Affiliation(s)
- Justin M Lopchuk
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kasper Fjelbye
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Kawamata
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lara R Malins
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chung-Mao Pan
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan Gianatassio
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jie Wang
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Liher Prieto
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Bradow
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Thomas A Brandt
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael R Collins
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jeff Elleraas
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jason Ewanicki
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - William Farrell
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Olugbeminiyi O Fadeyi
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gary M Gallego
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - James J Mousseau
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert Oliver
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Neal W Sach
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jason K Smith
- Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jillian E Spangler
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Huichin Zhu
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jinjiang Zhu
- Department of Chemistry, La Jolla Laboratories, Pfizer Inc. , 10770 Science Center Drive, San Diego, California 92121, United States
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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33
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Ji X, Ji K, Chittavong V, Aghoghovbia RE, Zhu M, Wang B. Click and Fluoresce: A Bioorthogonally Activated Smart Probe for Wash-Free Fluorescent Labeling of Biomolecules. J Org Chem 2017; 82:1471-1476. [PMID: 28067514 DOI: 10.1021/acs.joc.6b02654] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bioorthogonally activated smart probes greatly facilitate the selective labeling of biomolecules in living system. Herein, we described a novel type of smart probes with tunable reaction rates, high fluorescence turn-on ratio, and easy access. The practicality of such probes was demonstrated by selective labeling of lipid and hCAII in Hela cells.
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Affiliation(s)
- Xingyue Ji
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Kaili Ji
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Vayou Chittavong
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Robert E Aghoghovbia
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Mengyuan Zhu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
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34
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Holstein JM, Muttach F, Schiefelbein SHH, Rentmeister A. Dual 5′ Cap Labeling Based on Regioselective RNA Methyltransferases and Bioorthogonal Reactions. Chemistry 2017; 23:6165-6173. [DOI: 10.1002/chem.201604816] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Josephin M. Holstein
- University of Muenster; Department of Chemistry; Institute of Biochemistry; Wilhelm-Klemm-Straße 2 48149 Muenster Germany
| | - Fabian Muttach
- University of Muenster; Department of Chemistry; Institute of Biochemistry; Wilhelm-Klemm-Straße 2 48149 Muenster Germany
| | - Stephan H. H. Schiefelbein
- University of Muenster; Department of Chemistry; Institute of Biochemistry; Wilhelm-Klemm-Straße 2 48149 Muenster Germany
| | - Andrea Rentmeister
- University of Muenster; Department of Chemistry; Institute of Biochemistry; Wilhelm-Klemm-Straße 2 48149 Muenster Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003-CiM); University of Münster; Germany
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35
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Shie JJ, Liu YC, Hsiao JC, Fang JM, Wong CH. A cell-permeable and triazole-forming fluorescent probe for glycoconjugate imaging in live cells. Chem Commun (Camb) 2017; 53:1490-1493. [DOI: 10.1039/c6cc08805h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A new fluorescence-forming probe, coumOCT, designed by fusing cyclooctyne with a coumarin fluorophore was successfully used for the imaging of azido-glycoconjugates in living HeLa cells.
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Affiliation(s)
| | - Ying-Chih Liu
- Genomics Research Center
- Academia Sinica
- Nankang
- Taiwan
| | | | - Jim-Min Fang
- Genomics Research Center
- Academia Sinica
- Nankang
- Taiwan
- Department of Chemistry
| | - Chi-Huey Wong
- Genomics Research Center
- Academia Sinica
- Nankang
- Taiwan
- Department of Chemistry
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36
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Clark EL, Emmadi M, Krupp KL, Podilapu AR, Helble JD, Kulkarni SS, Dube DH. Development of Rare Bacterial Monosaccharide Analogs for Metabolic Glycan Labeling in Pathogenic Bacteria. ACS Chem Biol 2016; 11:3365-3373. [PMID: 27766829 DOI: 10.1021/acschembio.6b00790] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial glycans contain rare, exclusively bacterial monosaccharides that are frequently linked to pathogenesis and essentially absent from human cells. Therefore, bacterial glycans are intriguing molecular targets. However, systematic discovery of bacterial glycoproteins is hampered by the presence of rare deoxy amino sugars, which are refractory to traditional glycan-binding reagents. Thus, the development of chemical tools that label bacterial glycans is a crucial step toward discovering and targeting these biomolecules. Here, we explore the extent to which metabolic glycan labeling facilitates the studying and targeting of glycoproteins in a range of pathogenic and symbiotic bacterial strains. We began with an azide-containing analog of the naturally abundant monosaccharide N-acetylglucosamine and discovered that it is not broadly incorporated into bacterial glycans, thus revealing a need for additional azidosugar substrates to broaden the utility of metabolic glycan labeling in bacteria. Therefore, we designed and synthesized analogs of the rare deoxy amino d-sugars N-acetylfucosamine, bacillosamine, and 2,4-diacetamido-2,4,6-trideoxygalactose and established that these analogs are differentially incorporated into glycan-containing structures in a range of pathogenic and symbiotic bacterial species. Further application of these analogs will refine our knowledge of the glycan repertoire in diverse bacteria and may find utility in treating a variety of infectious diseases with selectivity.
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Affiliation(s)
- Emily L. Clark
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Madhu Emmadi
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Katharine L. Krupp
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Ananda R. Podilapu
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Jennifer D. Helble
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
| | - Suvarn S. Kulkarni
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Danielle H. Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011, United States
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37
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Renault K, Jouanno LA, Lizzul-Jurse A, Renard PY, Sabot C. Fluorogenic Behaviour of the Hetero-Diels-Alder Ligation of 5-Alkoxyoxazoles with Maleimides and their Applications. Chemistry 2016; 22:18522-18531. [DOI: 10.1002/chem.201603617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Kévin Renault
- Normandie University; CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014); 76000 Rouen France
| | - Laurie-Anne Jouanno
- Department of Chemistry and Biomolecular Sciences; University of Ottawa; 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
| | - Antoine Lizzul-Jurse
- Normandie University; CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014); 76000 Rouen France
| | - Pierre-Yves Renard
- Normandie University; CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014); 76000 Rouen France
| | - Cyrille Sabot
- Normandie University; CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014); 76000 Rouen France
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38
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Nazir R, Stasyuk AJ, Gryko DT. Vertically π-Expanded Coumarins: The Synthesis and Optical Properties. J Org Chem 2016; 81:11104-11114. [DOI: 10.1021/acs.joc.6b02094] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rashid Nazir
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Anton J. Stasyuk
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Daniel T. Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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39
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Zhu HZ, Wang G, Wei HL, Chu HJ, Zhu J. Click synthesis of hydrogels by metal-free 1,3-dipolar cycloaddition reaction between maleimide and azide functionalized polymers. Macromol Res 2016. [DOI: 10.1007/s13233-016-4120-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Knorr G, Kozma E, Herner A, Lemke EA, Kele P. New Red-Emitting Tetrazine-Phenoxazine Fluorogenic Labels for Live-Cell Intracellular Bioorthogonal Labeling Schemes. Chemistry 2016; 22:8972-9. [PMID: 27218228 DOI: 10.1002/chem.201600590] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Indexed: 11/09/2022]
Abstract
The synthesis of a set of tetrazine-bearing fluorogenic dyes suitable for intracellular labeling of proteins in live cells is presented. The red excitability and emission properties ensure minimal autofluorescence, while through-bond energy-transfer-based fluorogenicity reduces nonspecific background fluorescence of unreacted dyes. The tetrazine motif efficiently quenches fluorescence of the phenoxazine core, which can be selectively turned on chemically upon bioorthogonal inverse-electron-demand Diels-Alder reaction with proteins modified genetically with strained trans-cyclooctenes.
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Affiliation(s)
- Gergely Knorr
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Eszter Kozma
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - András Herner
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Péter Kele
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary.
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41
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Dommerholt J, Rutjes FPJT, van Delft FL. Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides. Top Curr Chem (Cham) 2016; 374:16. [PMID: 27573141 PMCID: PMC5480410 DOI: 10.1007/s41061-016-0016-4] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/17/2016] [Indexed: 11/24/2022]
Abstract
A nearly forgotten reaction discovered more than 60 years ago-the cycloaddition of a cyclic alkyne and an organic azide, leading to an aromatic triazole-enjoys a remarkable popularity. Originally discovered out of pure chemical curiosity, and dusted off early this century as an efficient and clean bioconjugation tool, the usefulness of cyclooctyne-azide cycloaddition is now adopted in a wide range of fields of chemical science and beyond. Its ease of operation, broad solvent compatibility, 100 % atom efficiency, and the high stability of the resulting triazole product, just to name a few aspects, have catapulted this so-called strain-promoted azide-alkyne cycloaddition (SPAAC) right into the top-shelf of the toolbox of chemical biologists, material scientists, biotechnologists, medicinal chemists, and more. In this chapter, a brief historic overview of cycloalkynes is provided first, along with the main synthetic strategies to prepare cycloalkynes and their chemical reactivities. Core aspects of the strain-promoted reaction of cycloalkynes with azides are covered, as well as tools to achieve further reaction acceleration by means of modulation of cycloalkyne structure, nature of azide, and choice of solvent.
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42
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Freidel C, Kaloyanova S, Peneva K. Chemical tags for site-specific fluorescent labeling of biomolecules. Amino Acids 2016; 48:1357-72. [DOI: 10.1007/s00726-016-2204-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/18/2016] [Indexed: 01/24/2023]
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43
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Cserép GB, Herner A, Kele P. Bioorthogonal fluorescent labels: a review on combined forces. Methods Appl Fluoresc 2015; 3:042001. [DOI: 10.1088/2050-6120/3/4/042001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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44
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Friscourt F, Fahrni CJ, Boons GJ. Fluorogenic Strain-Promoted Alkyne-Diazo Cycloadditions. Chemistry 2015; 21:13996-4001. [PMID: 26330090 DOI: 10.1002/chem.201502242] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 01/04/2023]
Abstract
Fluorogenic reactions, in which non- or weakly fluorescent reagents produce highly fluorescent products, are attractive for detecting a broad range of compounds in the fields of bioconjugation and material sciences. Herein, we report that a dibenzocyclooctyne derivative modified with a cyclopropenone moiety (Fl-DIBO) can undergo fast strain-promoted cycloaddition reactions under catalyst-free conditions with azides, nitrones, nitrile oxides, as well as mono- and disubstituted diazo-derivatives. Although the reaction with nitrile oxides, nitrones, and disubstituted diazo compounds gave cycloadducts with low quantum yield, monosubstituted diazo reagents produced 1H-pyrazole derivatives that exhibited an approximately 160-fold fluorescence enhancement over Fl-DIBO combined with a greater than 10,000-fold increase in brightness. Concluding from quantum chemical calculations, fluorescence quenching of 3H-pyrazoles, which are formed by reaction with disubstituted diazo-derivatives, is likely due to the presence of energetically low-lying (n,π*) states. The fluorogenic probe Fl-DIBO was successfully employed for the labeling of diazo-tagged proteins without detectable background signal. Diazo-derivatives are emerging as attractive reporters for the labeling of biomolecules, and the studies presented herein demonstrate that Fl-DIBO can be employed for visualizing such biomolecules without the need for probe washout.
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Affiliation(s)
- Frédéric Friscourt
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA), Fax: (+1) 706-542-4412.,Present address: Institut Européen de Chimie et Biologie, Université de Bordeaux, INCIA, CNRS UMR 5287, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Christoph J Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332 (USA)
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA), Fax: (+1) 706-542-4412.
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45
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Debets MF, Prins JS, Merkx D, van Berkel SS, van Delft FL, van Hest JCM, Rutjes FPJT. Synthesis of DIBAC analogues with excellent SPAAC rate constants. Org Biomol Chem 2015; 12:5031-7. [PMID: 24899166 DOI: 10.1039/c4ob00694a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In search for increased reactivity in strain-promoted azide alkyne cycloadditions (SPAAC), the synthesis of new and more reactive cyclooctynes is of pivotal importance. To identify cyclooctynes with enhanced reactivity, without loss of stability, the synthesis and kinetic analysis of new dibenzoazacyclooctyne (DIBAC) analogues were conducted. Starting from iodobenzyl alcohol analogues and ortho-ethynylaniline various substituted dihydrodibenzo[b,f]azocines were produced. Subsequent bromination and elimination proved to be difficult depending on the aromatic substitution pattern, yielding chloro-, bromo-, and methoxy-substituted DIBACs in moderate yield. In the elimination reaction towards nitro- and Br,Cl-DIBAC, the corresponding cyclooctene was obtained instead of the cyclooctyne. Additionally, a dimethoxy-substituted DIBAC analogue was prepared following an alternative route involving light-induced deprotection of a cyclopropenone derivative. In total, four DIBAC analogues were successfully prepared showing excellent rate constants in the SPAAC reaction ranging from 0.45 to 0.9 M(-1) s(-1), which makes them comparable to the fastest cyclooctynes currently known.
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Affiliation(s)
- Marjoke F Debets
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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46
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Chemistry-enabled methods for the visualization of cell-surface glycoproteins in Metazoans. Glycoconj J 2015; 32:443-54. [PMID: 25913724 DOI: 10.1007/s10719-015-9589-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/01/2015] [Accepted: 04/05/2015] [Indexed: 01/20/2023]
Abstract
The majority of cell-surface and secreted proteins are glycosylated, which can directly affect their macromolecular interactions, stability, and localization. Investigating these effects is critical to developing a complete understanding of the role of glycoproteins in fundamental biology and human disease. The development of selective and unique chemical reactions have revolutionized the visualization, identification, and characterization of glycoproteins. Here, we review the chemical methods that have been created to enable the visualization of the major types of cell-surface glycoproteins in living systems, from mammalian cells to whole animals.
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47
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Abstract
Bioorthogonal chemistry has enabled the selective labeling and detection of biomolecules in living systems. Bioorthogonal smart probes, which become fluorescent or deliver imaging or therapeutic agents upon reaction, allow for the visualization of biomolecules or targeted delivery even in the presence of excess unreacted probe. This review discusses the strategies used in the development of bioorthogonal smart probes and highlights the potential of these probes to further our understanding of biology.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
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48
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Xu L, Zolotarskaya OY, Yeudall WA, Yang H. Click hybridization of immune cells and polyamidoamine dendrimers. Adv Healthc Mater 2014; 3:1430-8. [PMID: 24574321 DOI: 10.1002/adhm.201300515] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/25/2014] [Indexed: 11/06/2022]
Abstract
Immobilizing highly branched polyamidoamine (PAMAM) dendrimers to the cell surface represents an innovative method of enhancing cell surface loading capacity to deliver therapeutic and imaging agents. In this work, hybridized immune cells, that is, macrophage RAW264.7 (RAW), with PAMAM dendrimer G4.0 (DEN) on the basis of bioorthogonal chemistry are clicked. Efficient and selective cell surface immobilization of dendrimers is confirmed by confocal microscopy. Viability and motility of RAW-DEN hybrids remain the same as untreated RAW cells according to WST-1 assay and wound closure assay. Furthermore, Western blot analysis reveals that there are no significant alterations in the expression levels of signaling molecules AKT, p38, and NFκB (p65) and their corresponding activated (phosphorylated) forms in RAW cells treated with azido sugar and dendrimer, indicating that the hybridization process neither induced cell stress response nor altered normal signaling pathways. Taken together, this work shows the feasibility of applying bioorthogonal chemistry to create cell-nanoparticle hybrids and demonstrates the noninvasiveness of this cell surface engineering approach.
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Affiliation(s)
- Leyuan Xu
- Department of Biomedical Engineering; Virginia Commonwealth University; Richmond VA 23284 USA
| | - Olga Yu. Zolotarskaya
- Department of Biomedical Engineering; Virginia Commonwealth University; Richmond VA 23284 USA
| | - W. Andrew Yeudall
- Philips Institute of Oral and Craniofacial Molecular Biology; Virginia Commonwealth University; Richmond VA 23298 USA
- Massey Cancer Center; Virginia Commonwealth University; Richmond VA 23298 USA
| | - Hu Yang
- Department of Biomedical Engineering; Virginia Commonwealth University; Richmond VA 23284 USA
- Massey Cancer Center; Virginia Commonwealth University; Richmond VA 23298 USA
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Herner A, Estrada Girona G, Nikić I, Kállay M, Lemke EA, Kele P. New generation of bioorthogonally applicable fluorogenic dyes with visible excitations and large Stokes shifts. Bioconjug Chem 2014; 25:1370-4. [PMID: 24932756 DOI: 10.1021/bc500235p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthesis of a set of new, azide bearing, biorthogonally applicable fluorogenic dyes with large Stokes shifts is presented herein. To assess the fluorogenic performance of these new dyes we have labeled a genetically modulated, cyclooctyne-bearing protein in lysate medium. Studies showed that the labels produce specific signal with minimal background fluorescence. We also provide theoretical insights into the design of such fluorogenic labels.
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Affiliation(s)
- András Herner
- "Lendület" Chemical Biology Research Group, Research Centre for Natural Sciences, Institute of Organic Chemistry, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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50
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Gold B, Batsomboon P, Dudley GB, Alabugin IV. Alkynyl Crown Ethers as a Scaffold for Hyperconjugative Assistance in Noncatalyzed Azide–Alkyne Click Reactions: Ion Sensing through Enhanced Transition-State Stabilization. J Org Chem 2014; 79:6221-32. [DOI: 10.1021/jo500958n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Brian Gold
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Paratchata Batsomboon
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Gregory B. Dudley
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Igor V. Alabugin
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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