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Luu T, Gristwood K, Knight JC, Jörg M. Click Chemistry: Reaction Rates and Their Suitability for Biomedical Applications. Bioconjug Chem 2024; 35:715-731. [PMID: 38775705 PMCID: PMC11191409 DOI: 10.1021/acs.bioconjchem.4c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Click chemistry has become a commonly used synthetic method due to the simplicity, efficiency, and high selectivity of this class of chemical reactions. Since their initial discovery, further click chemistry methods have been identified and added to the toolbox of click chemistry reactions for biomedical applications. However, selecting the most suitable reaction for a specific application is often challenging, as multiple factors must be considered, including selectivity, reactivity, biocompatibility, and stability. Thus, this review provides an overview of the benefits and limitations of well-established click chemistry reactions with a particular focus on the importance of considering reaction rates, an often overlooked criterion with little available guidance. The importance of understanding each click chemistry reaction beyond simply the reaction speed is discussed comprehensively with reference to recent biomedical research which utilized click chemistry. This review aims to provide a practical resource for researchers to guide the selection of click chemistry classes for different biomedical applications.
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Affiliation(s)
- Tracey Luu
- Medicinal
Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Katie Gristwood
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
| | - James C. Knight
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
| | - Manuela Jörg
- Medicinal
Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
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2
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Noël N, Martinez A, Massicot F, Vasse JL, Behr JB. Kinetics of Strain-Promoted Alkyne-Nitrone Cycloadditions (SPANC) with Unprotected Carbohydrate Scaffolded Nitrones. Org Lett 2024; 26:3917-3922. [PMID: 38690807 DOI: 10.1021/acs.orglett.4c01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The use of unprotected carbohydrate-derived nitrones as partners in strain-promoted alkyne-nitrone cycloadditions was investigated as a new tool for bioconjugation. The observed second-order reactions displayed rate constants of 3.4 × 10-4-5.8 × 10-2 M-1 s-1, which is the common order of magnitude of reaction kinetics with other simple aliphatic or aromatic nitrones. Applicability of this method to aqueous media was demonstrated by performing a one-pot protocol, which combines sequential formation of the nitrone and cycloaddition with cyclooctyne in water.
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Affiliation(s)
- Nathan Noël
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Agathe Martinez
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Fabien Massicot
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Luc Vasse
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne, CNRS UMR 7312, ICMR, 51687 Reims, France
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3
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Bilodeau DA, Margison KD, Masoud SS, Nakajima M, Pezacki JP. Mechanistic Analysis of Bioorthogonal Double Strain-Promoted Alkyne-Nitrone Cycloadditions Involving Dibenzocyclooctadiyne. ACS Chem Biol 2023; 18:2430-2438. [PMID: 37852229 DOI: 10.1021/acschembio.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The reactions of nitrones with cyclooctadiynes were studied to establish the relative rates of sequential reactions and to determine the limits and scope of this bioorthogonal chemistry. We have established the second-order rate constants for the consecutive additions of a variety of nitrones onto diyne and studied the structure-activity relationships via Hammett plots. Results show that the addition of the second nitrone to the monointermediate occurs significantly faster than the first, with both reactions being faster than analogous reactions with azides. Computational chemistry supports these observations. The rate of second addition increases with electron-deficient nitrones, as demonstrated by a large rho value of 2.08, suggesting that the reaction rate can be controlled by nitrone selectivity. To further investigate the kinetic parameters of the reaction, dinitrone monomers containing cyclic and diaryl-nitrones were designed for use in oligomerization applications. Oligomerization was used as a probe to test the limits of the reactivity and attempt to isolate monocycloaddition products. The oligomer formed from a cyclic nitrone reacts faster, and detailed MALDI mass spectrometry analysis shows that monoaddition products exist only transiently and are not isolatable. These studies inform on the scope and limits of this chemistry in a variety of applications. We successfully demonstrated bacterial cell wall labeling using heterogeneous dual cycloadditions involving nitrone and azide dipoles, where the nitrone was the faster reacting partner on the bacterial cell surface.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Shadi Sedghi Masoud
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Masaya Nakajima
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
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4
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Hu Y, Schomaker JM. Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions. Chembiochem 2021; 22:3254-3262. [PMID: 34261195 DOI: 10.1002/cbic.202100164] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed 'mutually orthogonal'. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Jennifer M Schomaker
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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5
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Bilodeau DA, Margison KD, Serhan M, Pezacki JP. Bioorthogonal Reactions Utilizing Nitrones as Versatile Dipoles in Cycloaddition Reactions. Chem Rev 2021; 121:6699-6717. [PMID: 33464040 DOI: 10.1021/acs.chemrev.0c00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemical reactions have emerged as convenient and rapid methods for incorporating unnatural functionality into living systems. Different prototype reactions have been optimized for use in biological settings. Optimization of 3 + 2 dipolar cycloadditions involving nitrones has resulted in highly efficient reaction conditions for bioorthogonal chemistry. Through substitution at the nitrone carbon or nitrogen atom, stereoelectronic tuning of the reactivity of the dipole has assisted in optimizing reactivity. Nitrones have been shown to react rapidly with cyclooctynes with bimolecular rate constants approaching k2 = 102 M-1 s-1, which are among the fastest bioorthogonal reactions reported (McKay et al. Org. Biomol. Chem. 2012, 10, 3066-3070). Nitrones have also been shown to react with trans-cyclooctenes (TCO) in strain-promoted TCO-nitrone cycloadditions reactions. Copper catalyzed reactions involving alkynes and nitrones have also been optimized for applications in biology. This review provides a comprehensive accounting of the different bioorthogonal reactions that have been developed using nitrones as versatile reactants, and provides some recent examples of applications for probing biological systems.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Mariam Serhan
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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6
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Click chemistry strategies for the accelerated synthesis of functional macromolecules. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210126] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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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: 193] [Impact Index Per Article: 64.3] [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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8
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Zou N, Qin X, Wang Z, Shi W, Mo D. Advances on the Synthesis and Application of α,β-Unsaturated Nitrones. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202109007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Nakajima M, Bilodeau DA, Pezacki JP. Predicting reactivity for bioorthogonal cycloadditions involving nitrones. RSC Adv 2020; 10:29306-29310. [PMID: 35521144 PMCID: PMC9055992 DOI: 10.1039/d0ra05092j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/23/2020] [Indexed: 01/20/2023] Open
Abstract
Nitrones are useful dipoles in both synthesis and in bioorthogonal transformations to report on biological phenomena. In bioorthogonal reactions, nitrones are both small and relatively easy to incorporate into biomolecules, while providing versatility in their ability to harbor different substituents that tune their reactivity. Herein, we examine the reactivities of some common and useful nitrone cycloadditions using density functional theory (DFT) and the distortion/interaction (D/I) model. The data show that relative reactivities can be predicted using these approaches, and useful insights gained further enchancing reactivities of both nitrones and their dipolarophile reaction partners. We find that D/I is a useful guide to understanding and predicting reactivities of cycloadditions involving nitrones.
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Affiliation(s)
- Masaya Nakajima
- Graduate School of Pharmaceutical Sciences, Chiba University 1-8-1 Inohana Chuo-ku Chiba 260-8675 Japan
| | - Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 150 Louis-Pasteur Ottawa Ontario K1N 6N5 Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 150 Louis-Pasteur Ottawa Ontario K1N 6N5 Canada
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10
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Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.
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Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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11
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Margison KD, Bilodeau DA, Mahmoudi F, Pezacki JP. Cycloadditions of
Trans
‐Cyclooctenes and Nitrones as Tools for Bioorthogonal Labelling. Chembiochem 2020; 21:948-951. [DOI: 10.1002/cbic.201900627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Kaitlyn D. Margison
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - Farnaz Mahmoudi
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa 150 Louis-Pasteur Ottawa ON K1N 6N5 Canada
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12
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Bilodeau DA, Margison KD, Ahmed N, Strmiskova M, Sherratt AR, Pezacki JP. Optimized aqueous Kinugasa reactions for bioorthogonal chemistry applications. Chem Commun (Camb) 2020; 56:1988-1991. [PMID: 31960852 DOI: 10.1039/c9cc09473c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Kinugasa reactions hold potential for bioorthogonal chemistry in that the reagents can be biocompatible. Unlike other bioorthogonal reaction products, β-lactams are potentially reactive, which can be useful for synthesizing new biomaterials. A limiting factor for applications consists of slow reaction rates. Herein, we report an optimized aqueous copper(i)-catalyzed alkyne-nitrone cycloaddition involving rearrangement (CuANCR) with rate accelerations made possible by the use of surfactant micelles. We have investigated the factors that accelerate the aqueous CuANCR reaction and demonstrate enhanced modification of a model membrane-associated peptide. We discovered that lipids/surfactants and alkyne structure have a significant impact on the reaction rate, with biological lipids and electron-poor alkynes showing greater reactivity. These new findings have implications for the use of CuANCR for modifying integral membrane proteins as well as live cell labelling and other bioorthogonal applications.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5, Canada.
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13
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Lo KKW. Molecular Design of Bioorthogonal Probes and Imaging Reagents Derived from Photofunctional Transition Metal Complexes. Acc Chem Res 2020; 53:32-44. [PMID: 31916746 DOI: 10.1021/acs.accounts.9b00416] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For more than 15 years, bioorthogonal chemistry has received increasing attention due to its successful applications in the detection and imaging of biomolecules in their native biological environments. The method typically proceeds with the incorporation of a biological substrate appended with a bioorthogonal functional group (chemical reporter), followed by the introduction of the substrate to biological systems. Biomolecules containing the substrate are then recognized by an exogenously delivered bioorthogonal probe. Despite the fact that many useful chemical reporters and bioorthogonal reactions have been developed, most of the bioorthogonal probes reported thus far are fluorescent dyes. A limitation is that stringent washing is required due to the interference caused by the background fluorescence of unreacted probes. Thus, fluorogenic probes with turn-on emission properties upon bioorthogonal labeling have been designed as an alternative strategy. These probes are highly appealing because excellent images can be obtained without the need for washing steps. Nearly all fluorogenic bioorthogonal probes designed are essentially organic dyes, their emission is limited to fluorescence, and the utilization of the probes is confined to bioimaging applications. Recently, there has been a growing interest in the bioimaging and therapeutic applications of luminescent inorganic and organometallic transition metal complexes due to their intriguing photophysical and photochemical properties, high membrane permeability, controllable cellular uptake, intracellular localization, and cytotoxicity. We anticipate that photofunctional transition metal complexes can be exploited as valuable bioorthogonal probes due to these appealing advantages. In this Account, we introduce the molecular design, photophysical and photochemical properties, and biological applications of various bioorthogonal probes and imaging reagents based on photofunctional transition metal complexes. The presence of a cationic metal center significantly enhances the bioorthogonal reactivity of the probes, yet their stability in aqueous solutions can be maintained. Interestingly, some of these metal complexes are strategically modified to display phosphorogenic properties, that is, phosphorescence turn-on upon bioorthogonal labeling reactions. Importantly, these probes not only exhibit favorable photophysical properties after bioorthogonal labeling, but also efficient photoinduced singlet oxygen (1O2) generation. This interesting bioorthogonal reaction-triggered photosensitization capability allows the modulation of 1O2 generation efficiency and contributes to the development of controllable photocytotoxic agents. The exploration of transition metal complex-based probes not only significantly widens the scope of bioorthogonal labeling but also further highlights the unique advantages of these complexes in the design of theranostic reagents. The development of these innovative reagents is expected to contribute to the basic understanding of biological processes in living systems and provide exciting opportunities for new diagnostic and therapeutic applications.
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Affiliation(s)
- Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
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14
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Said AI, El-Emary TI. Diastereoselective synthesis of atropisomeric pyrazolyl pyrrolo[3,4- d]isoxazolidines via pyrazolyl nitrone cycloaddition to facially divergent maleimides: intensive NMR and DFT studies. RSC Adv 2020; 10:845-850. [PMID: 35494462 PMCID: PMC9047523 DOI: 10.1039/c9ra10039c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/16/2019] [Indexed: 11/21/2022] Open
Abstract
A pyrazolyl nitrone (2) underwent 1,3-dipolar cycloadditions to afford some N-substituted maleimides (3a-o). An atropisomeric character was introduced into the formed cycloadducts by using maleimides that have a restricted rotation around the C-N bond. Also, facial selectivity of both endo and exo cycloaddition was observed where the major atropisomer was one that is formed by attacking the nitrone from the less hindered face of the dipolarophile. On the other hand, maleimides with free rotation around the C-N bond led to endo and exo cycloadducts without atropisomerism. The presence of atropisomerism in the formed cycloadducts was confirmed by extensive NMR studies and DFT calculations.
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Affiliation(s)
- Awad I Said
- Chemistry Department, Faculty of Science, Assiut University Assiut Egypt 71516 +20-1012991716
| | - Talaat I El-Emary
- Chemistry Department, Faculty of Science, Assiut University Assiut Egypt 71516 +20-1012991716
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15
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Headley CA, Hoffman CN, Freisen JM, Han Y, Macklin JM, Zweier JL, Rockenbauer A, Kuret J, Villamena FA. Membrane-specific spin trap, 5-dodecylcarbamoyl-5-N-dodecylacetamide-1-pyroline-N-oxide (diC 12PO): theoretical, bioorthogonal fluorescence imaging and EPR studies. Org Biomol Chem 2019; 17:7694-7705. [PMID: 31328213 PMCID: PMC6703941 DOI: 10.1039/c9ob01334b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membranous organelles are major endogenous sources of reactive oxygen and nitrogen species. When present at high levels, these species can cause macromolecular damage and disease. To better detect and scavenge free radical forms of the reactive species at their sources, we investigated whether nitrone spin traps could be selectively targeted to intracellular membranes using a bioorthogonal imaging approach. Electron paramagnetic resonance imaging demonstrated that the novel cyclic nitrone 5-dodecylcarbamoyl-5-N-dodecylacetamide-1-pyroline-N-oxide (diC12PO) could be used to target the nitrone moiety to liposomes composed of phosphatidyl choline. To test localization with authentic membranes in living cells, fluorophores were introduced via strain-promoted alkyne-nitrone cycloaddition (SPANC). Two fluorophore-conjugated alkynes were investigated: hexynamide-fluoresceine (HYA-FL) and dibenzylcyclooctyne-PEG4-5/6-sulforhodamine B (DBCO-Rhod). Computational and mass spectrometry experiments confirmed the cycloadduct formation of DBCO-Rhod (but not HYA-FL) with diC12PO in cell-free solution. Confocal microscopy of bovine aortic endothelial cells treated sequentially with diC12PO and DBCO-Rhod demonstrated clear localization of fluorescence with intracellular membranes. These results indicate that targeting of nitrone spin traps to cellular membranes is feasible, and that a bioorthogonal approach can aid the interrogation of their intracellular compartmentalization properties.
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Affiliation(s)
- Colwyn A Headley
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Claire N Hoffman
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Juliana M Freisen
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Yongbin Han
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Joseph M Macklin
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Jay L Zweier
- Davis Heart and Lung Research Institute, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences, and Department of Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Jeff Kuret
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Frederick A Villamena
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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16
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Strmiskova M, Bilodeau DA, Chigrinova M, Pezacki JP. Phenanthridine-based nitrones as substrates for strain-promoted alkyne-nitrone cycloadditions. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past decade, bioorthogonal chemistry that facilitates the efficient conjugation of biomolecules has expanded from the copper-catalyzed alkyne-azide cycloadditions to a multitude of diverse reactions, varying additives and reactional partners, and most often offering better alternatives with faster rates and lower toxicity of employed reactants. Among these, the copper-free strain-promoted cycloaddition reactions have been demonstrated to be more promising, offering a reaction without toxic metal catalysts and with faster inherent kinetic rate constants. The strain-promoted alkyne-nitrone cycloadditions are easily tunable from both the (strained) alkyne and nitrone perspective, both compounds giving the opportunity to modulate the rate of reaction by substituting various positions. Previously, acyclic nitrones have been evaluated in the strain-promoted alkyne-nitrone reactions; however, they were notably prone to hydrolysis. Some five-membered ring endocyclic nitrones developed concomitantly offered the advantage of relatively fast kinetics and better resistance to degradation in aqueous conditions and have been successfully used for labelling of biomolecules in living systems. Herein, we have prepared and studied nitrones inspired by the phenanthridine scaffold that efficiently undergo strain-promoted alkyne-nitrone reactions. Phenanthridine nitrones react fast with strained cyclooctynes with large bimolecular rate constants while maintaining bioorthogonality and resistance to hydrolysis.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - Mariya Chigrinova
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
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17
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Click chemistry in sphingolipid research. Chem Phys Lipids 2018; 215:71-83. [DOI: 10.1016/j.chemphyslip.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
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18
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Braun AC, Gutmann M, Lühmann T, Meinel L. Bioorthogonal strategies for site-directed decoration of biomaterials with therapeutic proteins. J Control Release 2018; 273:68-85. [PMID: 29360478 DOI: 10.1016/j.jconrel.2018.01.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
Abstract
Emerging strategies targeting site-specific protein modifications allow for unprecedented selectivity, fast kinetics and mild reaction conditions with high yield. These advances open exciting novel possibilities for the effective bioorthogonal decoration of biomaterials with therapeutic proteins. Site-specificity is particularly important to the therapeutics' end and translated by targeting specific functional groups or introducing new functional groups into the therapeutic at predefined positions. Biomimetic strategies are designed for modification of therapeutics emulating enzymatic strategies found in Nature. These strategies are suitable for a diverse range of applications - not only for protein-polymer conjugation, particle decoration and surface immobilization, but also for the decoration of complex biomaterials and the synthesis of bioresponsive drug delivery systems. This article reviews latest chemical and enzymatic strategies for the biorthogonal decoration of biomaterials with therapeutic proteins and inter-positioned linker structures. Finally, the numerous reports at the interface of biomaterials, linkers, and therapeutic protein decoration are integrated into practical advice for design considerations intended to support the selection of productive ligation strategies.
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Affiliation(s)
- Alexandra C Braun
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Marcus Gutmann
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Tessa Lühmann
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany.
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19
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Fisher SA, Baker AEG, Shoichet MS. Designing Peptide and Protein Modified Hydrogels: Selecting the Optimal Conjugation Strategy. J Am Chem Soc 2017; 139:7416-7427. [PMID: 28481537 DOI: 10.1021/jacs.7b00513] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hydrogels are used in a wide variety of biomedical applications including tissue engineering, biomolecule delivery, cell delivery, and cell culture. These hydrogels are often designed with a specific biological function in mind, requiring the chemical incorporation of bioactive factors to either mimic extracellular matrix or to deliver a payload to diseased tissue. Appropriate synthetic techniques to ligate bioactive factors, such as peptides and proteins, onto hydrogels are critical in designing materials with biological function. Here, we outline strategies for peptide and protein immobilization. We specifically focus on click chemistry, enzymatic ligation, and affinity binding for transient immobilization. Protein modification strategies have shifted toward site-specific modification using unnatural amino acids and engineered site-selective amino acid sequences to preserve both activity and structure. The selection of appropriate protein immobilization strategies is vital to engineering functional hydrogels. We provide insight into chemistry that balances the need for facile reactions while maintaining protein bioactivity or desired release.
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Affiliation(s)
- Stephanie A Fisher
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Alexander E G Baker
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Molly S Shoichet
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
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20
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Sminia TJ, Zuilhof H, Wennekes T. Getting a grip on glycans: A current overview of the metabolic oligosaccharide engineering toolbox. Carbohydr Res 2016; 435:121-141. [PMID: 27750120 DOI: 10.1016/j.carres.2016.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022]
Abstract
This review discusses the advances in metabolic oligosaccharide engineering (MOE) from 2010 to 2016 with a focus on the structure, preparation, and reactivity of its chemical probes. A brief historical overview of MOE is followed by a comprehensive overview of the chemical probes currently available in the MOE molecular toolbox and the bioconjugation techniques they enable. The final part of the review focusses on the synthesis of a selection of probes and finishes with an outlook on recent and potential upcoming advances in the field of MOE.
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Affiliation(s)
- Tjerk J Sminia
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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21
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Tang TSM, Liu HW, Lo KKW. Structural Manipulation of Ruthenium(II) Polypyridine Nitrone Complexes to Generate Phosphorogenic Bioorthogonal Reagents for Selective Cellular Labeling. Chemistry 2016; 22:9649-59. [DOI: 10.1002/chem.201601332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Tommy Siu-Ming Tang
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Hua-Wei Liu
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Kenneth Kam-Wing Lo
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
- State Key Laboratory of Millimeter Waves; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
- Center for Functional Photonics; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
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22
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Xiao ZF, Ding TH, Mao SW, Ning XS, Kang YB. Zinc Iodide-Mediated Direct Synthesis of 2,3-Dihydroisoxazoles from Alkynes and Nitrones. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Bioorthogonal Chemistry—Introduction and Overview [corrected]. Top Curr Chem (Cham) 2016; 374:9. [PMID: 27572992 DOI: 10.1007/s41061-016-0010-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/15/2016] [Indexed: 01/25/2023]
Abstract
Bioorthogonal chemistry has emerged as a new powerful tool that facilitates the study of structure and function of biomolecules in their native environment. A wide variety of bioorthogonal reactions that can proceed selectively and efficiently under physiologically relevant conditions are now available. The common features of these chemical reactions include: fast kinetics, tolerance to aqueous environment, high selectivity and compatibility with naturally occurring functional groups. The design and development of new chemical transformations in this direction is an important step to meet the growing demands of chemical biology. This chapter aims to introduce the reader to the field by providing an overview on general principles and strategies used in bioorthogonal chemistry. Special emphasis is given to cycloaddition reactions, namely to 1,3-dipolar cycloadditions and Diels-Alder reactions, as chemical transformations that play a predominant role in modern bioconjugation chemistry. The recent advances have established these reactions as an invaluable tool in modern bioorthogonal chemistry. The key aspects of the methodology as well as future outlooks in the field are discussed.
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24
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Spears RJ, Fascione MA. Site-selective incorporation and ligation of protein aldehydes. Org Biomol Chem 2016; 14:7622-38. [DOI: 10.1039/c6ob00778c] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The incorporation of aldehyde handles into proteins, and subsequent chemical reactions thereof, is rapidly proving to be an effective way of generating homogeneous, covalently linked protein constructs that can display a vast array of functionality.
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25
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Abstract
Various vinyl ketonitrones are prepared using new strategies and were applied to synthesize heterocycles in organic synthesis.
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Affiliation(s)
- Wei-Min Shi
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Ministry of Education of China and School of Chemistry & Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- China
| | - Xiao-Pan Ma
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Ministry of Education of China and School of Chemistry & Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- China
| | - Gui-Fa Su
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Ministry of Education of China and School of Chemistry & Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- China
| | - Dong-Liang Mo
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Ministry of Education of China and School of Chemistry & Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- China
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26
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Lee LCC, Lau JCW, Liu HW, Lo KKW. Conferring Phosphorogenic Properties on Iridium(III)-Based Bioorthogonal Probes through Modification with a Nitrone Unit. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Lawrence Cho-Cheung Lee
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Jonathan Chun-Wai Lau
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Hua-Wei Liu
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Kenneth Kam-Wing Lo
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
- State Key Laboratory of Millimeter Waves; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong (P.R. China
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27
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Lee LCC, Lau JCW, Liu HW, Lo KKW. Conferring Phosphorogenic Properties on Iridium(III)-Based Bioorthogonal Probes through Modification with a Nitrone Unit. Angew Chem Int Ed Engl 2015; 55:1046-9. [DOI: 10.1002/anie.201509396] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Lawrence Cho-Cheung Lee
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Jonathan Chun-Wai Lau
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Hua-Wei Liu
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
| | - Kenneth Kam-Wing Lo
- Department of Biology and Chemistry; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong P.R. China
- State Key Laboratory of Millimeter Waves; City University of Hong Kong; Tat Chee Avenue, Kowloon Hong Kong (P.R. China
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28
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Chigrinova M, MacKenzie DA, Sherratt AR, Cheung LLW, Pezacki JP. Kinugasa reactions in water: from green chemistry to bioorthogonal labelling. Molecules 2015; 20:6959-69. [PMID: 25913933 PMCID: PMC6272444 DOI: 10.3390/molecules20046959] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 11/16/2022] Open
Abstract
The Kinugasa reaction has become an efficient method for the direct synthesis of β-lactams from substituted nitrones and copper(I) acetylides. In recent years, the reaction scope has been expanded to include the use of water as the solvent, and with micelle-promoted [3+2] cycloadditions followed by rearrangement furnishing high yields of β-lactams. The high yields of stable products under aqueous conditions render the modified Kinugasa reaction amenable to metabolic labelling and bioorthogonal applications. Herein, the development of methods for use of the Kinugasa reaction in aqueous media is reviewed, with emphasis on its potential use as a bioorthogonal coupling strategy.
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Affiliation(s)
- Mariya Chigrinova
- Life Sciences Division, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Douglas A. MacKenzie
- Life Sciences Division, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allison R. Sherratt
- Life Sciences Division, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Lawrence L. W. Cheung
- Life Sciences Division, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +1-613-993-7253; Fax: +1-613-941-8447
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29
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MacKenzie DA, Sherratt AR, Chigrinova M, Kell AJ, Pezacki JP. Bioorthogonal labelling of living bacteria using unnatural amino acids containing nitrones and a nitrone derivative of vancomycin. Chem Commun (Camb) 2015; 51:12501-4. [DOI: 10.1039/c5cc04901f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Unnaturald-amino acids bearing endocyclic nitrones were developed for live-cell labelling of the bacterial peptidoglycan layer.
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Affiliation(s)
- Douglas A. MacKenzie
- Life Sciences Division
- National Research Council of Canada
- Ottawa
- Canada
- Department of Chemistry
| | | | - Mariya Chigrinova
- Life Sciences Division
- National Research Council of Canada
- Ottawa
- Canada
| | - Arnold J. Kell
- Life Sciences Division
- National Research Council of Canada
- Ottawa
- Canada
| | - John Paul Pezacki
- Life Sciences Division
- National Research Council of Canada
- Ottawa
- Canada
- Department of Chemistry
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30
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McKay CS, Finn MG. Click chemistry in complex mixtures: bioorthogonal bioconjugation. CHEMISTRY & BIOLOGY 2014; 21:1075-101. [PMID: 25237856 PMCID: PMC4331201 DOI: 10.1016/j.chembiol.2014.09.002] [Citation(s) in RCA: 565] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/18/2023]
Abstract
The selective chemical modification of biological molecules drives a good portion of modern drug development and fundamental biological research. While a few early examples of reactions that engage amine and thiol groups on proteins helped establish the value of such processes, the development of reactions that avoid most biological molecules so as to achieve selectivity in desired bond-forming events has revolutionized the field. We provide an update on recent developments in bioorthogonal chemistry that highlights key advances in reaction rates, biocompatibility, and applications. While not exhaustive, we hope this summary allows the reader to appreciate the rich continuing development of good chemistry that operates in the biological setting.
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Affiliation(s)
- Craig S McKay
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M G Finn
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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31
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MacKenzie DA, Sherratt AR, Chigrinova M, Cheung LLW, Pezacki JP. Strain-promoted cycloadditions involving nitrones and alkynes—rapid tunable reactions for bioorthogonal labeling. Curr Opin Chem Biol 2014; 21:81-8. [DOI: 10.1016/j.cbpa.2014.05.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
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32
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MacKenzie DA, Pezacki JP. Kinetics studies of rapid strain-promoted [3+2] cycloadditions of nitrones with bicyclo[6.1.0]nonyne. CAN J CHEM 2014. [DOI: 10.1139/cjc-2013-0577] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strain-promoted alkyne−nitrone cycloaddition (SPANC) reactions represent a bioorthogonal labeling strategy that is both very rapid and at the same time efficient and selective. Nitrones provide increased reaction rates as well as greater susceptibility toward stereoelectronic modification when compared with organic azides. We find that strain-promoted cycloadditions of cyclic nitrones with bicyclo[6.1.0]nonyne react with second-order rate constants as large as 1.49 L mol−1 s−1 at 25 °C. These reactions display rate constants that are up to 37-fold greater than those of the analogous reactions of benzyl azide with bicyclo[6.1.0]nonyne. We observed that reactions of nitrones with bicyclo[6.1.0]nonyne showed a stronger dependence on substituent effect for the reaction, as evidenced by a larger Hammett ρ value, than that for biaryl-aza-cyclooctanone. We demonstrate the ability to stereoelectronically tune the reactivity of nitrones towards different cyclooctynes in SPANC reactions. This ability to introduce selectivity into different SPANC reactions through substituent provides the opportunity to perform multiple SPANC reactions in one reaction vessel and opens up potential applications in multiplex labeling.
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Affiliation(s)
- Douglas A. MacKenzie
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada; Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
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33
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 801] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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34
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Patterson DM, Nazarova LA, Prescher JA. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014; 9:592-605. [PMID: 24437719 DOI: 10.1021/cb400828a] [Citation(s) in RCA: 531] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.
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Affiliation(s)
- David M. Patterson
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Lidia A. Nazarova
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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35
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Wang XS, Lee YJ, Liu WR. The nitrilimine-alkene cycloaddition is an ultra rapid click reaction. Chem Commun (Camb) 2014; 50:3176-9. [PMID: 24519550 DOI: 10.1039/c3cc48682f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The transient formation of nitrilimine in aqueous conditions is greatly influenced by pH and chloride. In basic conditions (pH 10) with no chloride, a diarylnitrilimine precursor readily ionizes to form diarylnitrilimine that reacts almost instantly with an acrylamide-containing protein and fluorescently labels it.
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36
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Sherratt AR, Chigrinova M, McKay CS, Beaulieu LPB, Rouleau Y, Pezacki JP. Copper-catalysed cycloaddition reactions of nitrones and alkynes for bioorthogonal labelling of living cells. RSC Adv 2014. [DOI: 10.1039/c4ra07851a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An adapted biocompatible version of the Kinugasa reaction, the copper-catalysed alkyne-nitrone cycloaddition followed by rearrangement (CuANCR), was developed for live-cell labelling.
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Affiliation(s)
| | - Mariya Chigrinova
- Life Sciences Division
- National Research Council of Canada
- Ottawa, Canada
| | - Craig S. McKay
- Life Sciences Division
- National Research Council of Canada
- Ottawa, Canada
- Department of Chemistry
- University of Ottawa
| | - Louis-Philippe B. Beaulieu
- Life Sciences Division
- National Research Council of Canada
- Ottawa, Canada
- Department of Chemistry
- University of Ottawa
| | - Yanouchka Rouleau
- Life Sciences Division
- National Research Council of Canada
- Ottawa, Canada
| | - John Paul Pezacki
- Life Sciences Division
- National Research Council of Canada
- Ottawa, Canada
- Department of Chemistry
- University of Ottawa
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37
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Abstract
The use of covalent chemistry to track biomolecules in their native environment-a focus of bioorthogonal chemistry-has received considerable interest recently among chemical biologists and organic chemists alike. To facilitate wider adoption of bioorthogonal chemistry in biomedical research, a central effort in the last few years has been focused on the optimization of a few known bioorthogonal reactions, particularly with respect to reaction kinetics improvement, novel genetic encoding systems, and fluorogenic reactions for bioimaging. During these optimizations, three strategies have emerged, including the use of ring strain for substrate activation in the cycloaddition reactions, the discovery of new ligands and privileged substrates for accelerated metal-catalysed reactions, and the design of substrates with pre-fluorophore structures for rapid "turn-on" fluorescence after selective bioorthogonal reactions. In addition, new bioorthogonal reactions based on either modified or completely unprecedented reactant pairs have been reported. Finally, increasing attention has been directed toward the development of mutually exclusive bioorthogonal reactions and their applications in multiple labeling of a biomolecule in cell culture. In this feature article, we wish to present the recent progress in bioorthogonal reactions through the selected examples that highlight the above-mentioned strategies. Considering increasing sophistication in bioorthogonal chemistry development, we strive to project several exciting opportunities where bioorthogonal chemistry can make a unique contribution to biology in the near future.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.
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Chigrinova M, McKay CS, Beaulieu LPB, Udachin KA, Beauchemin AM, Pezacki JP. Rearrangements and addition reactions of biarylazacyclooctynones and the implications to copper-free click chemistry. Org Biomol Chem 2013; 11:3436-41. [DOI: 10.1039/c3ob40683k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Debets MF, van Hest JCM, Rutjes FPJT. Bioorthogonal labelling of biomolecules: new functional handles and ligation methods. Org Biomol Chem 2013; 11:6439-55. [PMID: 23969529 DOI: 10.1039/c3ob41329b] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marjoke F Debets
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands.
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Lang K, Davis L, Wallace S, Mahesh M, Cox DJ, Blackman ML, Fox JM, Chin JW. Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions. J Am Chem Soc 2012; 134:10317-20. [PMID: 22694658 PMCID: PMC3687367 DOI: 10.1021/ja302832g] [Citation(s) in RCA: 421] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Rapid, site-specific labeling of proteins with diverse
probes remains
an outstanding challenge for chemical biologists. Enzyme-mediated
labeling approaches may be rapid but use protein or peptide fusions
that introduce perturbations into the protein under study and may
limit the sites that can be labeled, while many “bioorthogonal”
reactions for which a component can be genetically encoded are too
slow to effect quantitative site-specific labeling of proteins on
a time scale that is useful for studying many biological processes.
We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol
(BCN) and tetrazines that is 3–7 orders of magnitude faster
than many bioorthogonal reactions. Unlike the reactions of strained
alkenes, including trans-cyclooctenes and norbornenes,
with tetrazines, the BCN–tetrazine reaction gives a
single product of defined stereochemistry. We have discovered aminoacyl-tRNA
synthetase/tRNA pairs for the efficient site-specific incorporation
of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts
extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate
the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli, and in live mammalian cells. These approaches may be extended to
site-specific protein labeling in animals, and we anticipate that
they will have a broad impact on labeling and imaging studies.
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Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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Flores M, García-García P, Garrido NM, Marcos IS, Sanz F, Díez D. From isoxazolidines to tetrahydro-1,3-oxazines for the synthesis of chiral pyrrolidines. RSC Adv 2012. [DOI: 10.1039/c2ra22110a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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