51
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Mulks FF, Antoni PW, Rominger F, Hashmi ASK. Cyclopropenylgold(I) Complexes as Aurated Carbenoids or Quasi-Carbenes. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201701526] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Florian F. Mulks
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Patrick W. Antoni
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - A. Stephen K. Hashmi
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Chemistry Department, Faculty of Science; King Abdulaziz University (KAU); Jeddah 21589 Saudi Arabia
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52
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Wang Y, An R, Luo Z, Ye D. Firefly Luciferin-Inspired Biocompatible Chemistry for Protein Labeling and In Vivo Imaging. Chemistry 2017; 24:5707-5722. [PMID: 29068109 DOI: 10.1002/chem.201704349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Biocompatible reactions have emerged as versatile tools to build various molecular imaging probes that hold great promise for the detection of biological processes in vitro and/or in vivo. In this Minireview, we describe the recent advances in the development of a firefly luciferin-inspired biocompatible reaction between cyanobenzothiazole (CBT) and cysteine (Cys), and highlight its versatility to label proteins and build multimodality molecular imaging probes. The review starts from the general introduction of biocompatible reactions, which is followed by briefly describing the development of the firefly luciferin-inspired biocompatible chemistry. We then discuss its applications for the specific protein labeling and for the development of multimodality imaging probes (fluorescence, bioluminescence, MRI, PET, photoacoustic, etc.) that enable high sensitivity and spatial resolution imaging of redox environment, furin and caspase-3/7 activity in living cells and mice. Finally, we offer the conclusions and our perspective on the various and potential applications of this reaction. We hope that this review will contribute to the research of biocompatible reactions for their versatile applications in protein labeling and molecular imaging.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Ruibing An
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Zhiliang Luo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Deju Ye
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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53
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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: 21] [Impact Index Per Article: 3.0] [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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54
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Menzel JP, Noble BB, Lauer A, Coote ML, Blinco JP, Barner-Kowollik C. Wavelength Dependence of Light-Induced Cycloadditions. J Am Chem Soc 2017; 139:15812-15820. [DOI: 10.1021/jacs.7b08047] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jan P. Menzel
- School
of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular
Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Benjamin B. Noble
- Australian
Research Council Centre of Excellence for Electromaterials Science,
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Andrea Lauer
- School
of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular
Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
- Institut
für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Michelle L. Coote
- Australian
Research Council Centre of Excellence for Electromaterials Science,
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - James P. Blinco
- School
of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Christopher Barner-Kowollik
- School
of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular
Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
- Institut
für Biologische Grenzflächen, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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55
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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56
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017; 56:14521-14525. [DOI: 10.1002/anie.201708151] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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57
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Ramil CP, Dong M, An P, Lewandowski TM, Yu Z, Miller LJ, Lin Q. Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2017; 139:13376-13386. [PMID: 28876923 DOI: 10.1021/jacs.7b05674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new bioorthogonal reactant pair, spiro[2.3]hex-1-ene (Sph) and 3,6-di(2-pyridyl)-s-tetrazine (DpTz), for the strain-promoted inverse electron-demand Diels-Alder cycloaddition, that is, tetrazine ligation, is reported. As compared to the previously reported strained alkenes such as trans-cyclooctene (TCO) and 1,3-disubstituted cyclopropene, Sph exhibits balanced reactivity and stability in tetrazine ligation with the protein substrates. A lysine derivative of Sph, SphK, was site-selectively incorporated into the extracellular loop regions (ECLs) of GCGR and GLP-1R, two members of class B G protein-coupled receptors (GPCRs) in mammalian cells with the incorporation efficiency dependent on the location. Subsequent bioorthogonal reactions with the fluorophore-conjugated DpTz reagents afforded the fluorescently labeled GCGR and GLP-1R ECL mutants with labeling yield as high as 68%. A multitude of functional assays were performed with these GPCR mutants, including ligand binding, ligand-induced receptor internalization, and ligand-stimulated intracellular cAMP accumulation. Several positions in the ECL3s of GCGR and GLP-1R were identified that tolerate SphK mutagenesis and subsequent bioorthogonal labeling. The generation of functional, fluorescently labeled ECL3 mutants of GCGR and GLP-1R should allow biophysical studies of conformation dynamics of this important class of GPCRs in their native environment in live cells.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
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58
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Owens AE, Grasso KT, Ziegler CA, Fasan R. Two-Tier Screening Platform for Directed Evolution of Aminoacyl-tRNA Synthetases with Enhanced Stop Codon Suppression Efficiency. Chembiochem 2017; 18:1109-1116. [PMID: 28383180 PMCID: PMC5586079 DOI: 10.1002/cbic.201700039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 01/06/2023]
Abstract
Genetic code expansion through amber stop codon suppression provides a powerful tool for introducing non-proteinogenic functionalities into proteins for a broad range of applications. However, ribosomal incorporation of noncanonical amino acids (ncAAs) by means of engineered aminoacyl-tRNA synthetases (aaRSs) often proceeds with significantly reduced efficiency compared to sense codon translation. Here, we report the implementation of a versatile platform for the development of engineered aaRSs with enhanced efficiency in mediating ncAA incorporation by amber stop codon suppression. This system integrates a white/blue colony screen with a plate-based colorimetric assay, thereby combining high-throughput capabilities with reliable and quantitative measurement of aaRS-dependent ncAA incorporation efficiency. This two-tier functional screening system was successfully applied to obtain a pyrrolysyl-tRNA synthetase (PylRS) variant (CrtK-RS(4.1)) with significantly improved efficiency (+250-370 %) for mediating the incorporation of Nϵ -crotonyl-lysine and other lysine analogues of relevance for the study of protein post-translational modifications into a target protein. Interestingly, the beneficial mutations accumulated by CrtK-RS(4.1) were found to localize within the noncatalytic N-terminal domain of the enzyme and could be transferred to another PylRS variant, improving the ability of the variant to incorporate its corresponding ncAA substrate. This work introduces an efficient platform for the improvement of aaRSs that could be readily extended to other members of this enzyme family and/or other target ncAAs.
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Affiliation(s)
- Andrew E Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Katherine T Grasso
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Christine A Ziegler
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
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59
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Siegl SJ, Dzijak R, Vázquez A, Pohl R, Vrabel M. The discovery of pyridinium 1,2,4-triazines with enhanced performance in bioconjugation reactions. Chem Sci 2017; 8:3593-3598. [PMID: 30155204 PMCID: PMC6092722 DOI: 10.1039/c6sc05442k] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/01/2017] [Indexed: 01/06/2023] Open
Abstract
1,2,4-Triazines have recently been identified as versatile dienes participating in the inverse electron-demand Diels-Alder reaction with strained dienophiles. However, their widespread utility in bioconjugation reactions is still limited. Herein, we report a systematic study on the reactivity of various 1,2,4-triazines with trans-cyclooctenes showing that the structure of both the triazine and the dienophile significantly affect the reaction rate. Our kinetic study led to the discovery of novel cationic 1,2,4-triazines with superior properties for bioconjugation reactions. We have developed an efficient method that enables their late-stage functionalization and allows for easy access to various useful heterobifunctional scaffolds. In addition, these charged dienes form unprecedented fluorescent products upon reaction with trans-cyclooctenes and can be used for fluorogenic labeling of subcellular compartments in live cells.
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Affiliation(s)
- Sebastian J Siegl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 , Prague , Czech Republic .
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 , Prague , Czech Republic .
| | - Arcadio Vázquez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 , Prague , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 , Prague , Czech Republic .
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , 16610 , Prague , Czech Republic .
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60
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Ravasco JMJM, Monteiro CM, Trindade AF. Cyclopropenes: a new tool for the study of biological systems. Org Chem Front 2017. [DOI: 10.1039/c7qo00054e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclopropenes have become an important mini-tag tool in chemical biology, participating in fast inverse electron demand Diels–Alder and photoclick reactions in biological settings.
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Affiliation(s)
- João M. J. M. Ravasco
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Carlos M. Monteiro
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Alexandre F. Trindade
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
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61
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Singh MS, Chowdhury S, Koley S. Advances of azide-alkyne cycloaddition-click chemistry over the recent decade. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.044] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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62
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Yang Y, Song H, He D, Zhang S, Dai S, Lin S, Meng R, Wang C, Chen PR. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label. Nat Commun 2016; 7:12299. [PMID: 27460181 PMCID: PMC4974458 DOI: 10.1038/ncomms12299] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Coupling photocrosslinking reagents with mass spectrometry has become a powerful tool for studying protein–protein interactions in living systems, but it still suffers from high rates of false-positive identifications as well as the lack of information on interaction interface due to the challenges in deciphering crosslinking peptides. Here we develop a genetically encoded photo-affinity unnatural amino acid that introduces a mass spectrometry-identifiable label (MS-label) to the captured prey proteins after photocrosslinking and prey–bait separation. This strategy, termed IMAPP (In-situ cleavage and MS-label transfer After Protein Photocrosslinking), enables direct identification of photo-captured substrate peptides that are difficult to uncover by conventional genetically encoded photocrosslinkers. Taking advantage of the MS-label, the IMAPP strategy significantly enhances the confidence for identifying protein–protein interactions and enables simultaneous mapping of the binding interface under living conditions. Mapping protein-protein interaction using crosslinking and mass spectroscopy strategies is hampered by a high rate of false-positive results. Here, the authors develop a genetically encoded photo-affinity probe for accurate identification of protein interaction partners and crosslinking sites.
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Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuai Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shizhong Dai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shixian Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Rong Meng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
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63
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Sequential oxidation/thermal induced intramolecular [2+2] cycloaddition of propynol-vinylidenecyclopropanes: access to novel cyclobutene-containing spiro[2.3]hexenes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.11.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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64
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Herner A, Lin Q. Photo-Triggered Click Chemistry for Biological Applications. Top Curr Chem (Cham) 2016; 374:1. [PMID: 27397964 PMCID: PMC4935935 DOI: 10.1007/s41061-015-0002-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022]
Abstract
In the last decade and a half, numerous bioorthogonal reactions have been developed with a goal to study biological processes in their native environment, i.e., in living cells and animals. Among them, the photo-triggered reactions offer several unique advantages including operational simplicity with the use of light rather than toxic metal catalysts and ligands, and exceptional spatiotemporal control through the application of an appropriate light source with pre-selected wavelength, light intensity and exposure time. While the photoinduced reactions have been studied extensively in materials research, e.g., on macromolecular surface, the adaptation of these reactions for chemical biology applications is still in its infancy. In this chapter, we review the recent efforts in the discovery and optimization the photo-triggered bioorthogonal reactions, with a focus on those that have shown broad utility in biological systems. We discuss in each cases the chemical and mechanistic background, the kinetics of the reactions and the biological applicability together with the limiting factors.
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Affiliation(s)
- András Herner
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
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65
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Narayanam MK, Liang Y, Houk KN, Murphy JM. Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening. Chem Sci 2016; 7:1257-1261. [PMID: 29910881 PMCID: PMC4763938 DOI: 10.1039/c5sc03259h] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/11/2015] [Indexed: 12/22/2022] Open
Abstract
Density functional theory (DFT) calculations and experiments in tandem led to discoveries of new reactivities and selectivities involving bioorthogonal sydnone cycloadditions. Dibenzocyclooctyne derivatives (DIBAC and BARAC) were identified to be especially reactive dipolarophiles, which undergo the (3 + 2) cycloadditions with N-phenyl sydnone with the rate constant of up to 1.46 M-1 s-1. Most significantly, the sydnone-dibenzocyclooctyne and norbornene-tetrazine cycloadditions were predicted to be mutually orthogonal. This was validated experimentally and used for highly selective fluorescence labeling of two proteins simultaneously.
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Affiliation(s)
- Maruthi Kumar Narayanam
- Crump Institute for Molecular Imaging , David Geffen School of Medicine , University of California , Los Angeles , California 90095 , USA .
| | - Yong Liang
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
- Department of Chemical and Biomolecular Engineering , University of California , Los Angeles , California 90095 , USA
| | - Jennifer M Murphy
- Crump Institute for Molecular Imaging , David Geffen School of Medicine , University of California , Los Angeles , California 90095 , USA .
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66
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Xiong DC, Zhu J, Han MJ, Luo HX, Wang C, Yu Y, Ye Y, Tai G, Ye XS. Rapid probing of sialylated glycoproteins in vitro and in vivo via metabolic oligosaccharide engineering of a minimal cyclopropene reporter. Org Biomol Chem 2015; 13:3911-7. [PMID: 25735895 DOI: 10.1039/c5ob00069f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
ManNAc analogues are important chemical tools for probing sialylation dynamically via metabolic oligosaccharide engineering (MOE). The size of N-acyl and the nature of the chemical handle are two determinants of metabolic incorporation efficiency. We demonstrated a minimal, stable, bioorthogonal, and reactive N-Cp (N-(cycloprop-2-ene-1-ylcarbonyl)) group and the imaging of sialylated glycans using Ac4ManNCp in vitro and in vivo. The results revealed that the Cp group can efficiently be incorporated into the cellular sialic acid and detected rapidly by the reaction with FITC-Tz in different cells. The metabolic incorporation efficiency of non-cytotoxic Ac4ManNCp is not only superior to Ac4ManNMCp, but also superior to the widely-used Ac4ManNAz in some cell lines. Moreover, when Ac4ManNCp was administered to mice, a rapid and intense labelling of splenocytes as well as glycoproteins of sera and organs was observed. This is the first reported metabolic labelling of cyclopropene-modified sugars in vivo. Therefore, Ac4ManNCp is a powerful probe for efficient and rapid MOE and it may find wide applications in the labelling of glycans.
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Affiliation(s)
- De-Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Center for Molecular and Translational Medicine, Peking University, Xue Yuan Road No. 38, Beijing 100191, China.
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67
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Patterson DM, Prescher JA. Orthogonal bioorthogonal chemistries. Curr Opin Chem Biol 2015; 28:141-9. [DOI: 10.1016/j.cbpa.2015.07.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/20/2015] [Accepted: 07/17/2015] [Indexed: 01/20/2023]
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68
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Luo HX, Niu YH, Cao XP, Ye XS. Cyclopropenes for the Synthesis of Cyclopropane-Fused Dihydroquinolines and Benzazepines. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500203] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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69
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Shih HW, Prescher JA. A Bioorthogonal Ligation of Cyclopropenones Mediated by Triarylphosphines. J Am Chem Soc 2015; 137:10036-9. [DOI: 10.1021/jacs.5b06969] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hui-Wen Shih
- 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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70
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Cheng G, Lim RKV, Ramil CP, Lin Q. Storable N-phenylcarbamate palladacycles for rapid functionalization of an alkyne-encoded protein. Chem Commun (Camb) 2015; 50:11679-82. [PMID: 25140915 DOI: 10.1039/c4cc02969k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report the synthesis of storable N-phenylcarbamate palladacycles that showed robust reactivity in the cross-coupling reaction with an alkyne-encoded protein with a second-order rate constant approaching 19 770 ± 930 M(-1) s(-1).
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Affiliation(s)
- Gang Cheng
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
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71
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Yang M, Li J, Chen PR. Transition metal-mediated bioorthogonal protein chemistry in living cells. Chem Soc Rev 2015; 43:6511-26. [PMID: 24867400 DOI: 10.1039/c4cs00117f] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Considerable attention has been focused on improving the biocompatibility of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), a hallmark of bioorthogonal reaction, in living cells. Besides creating copper-free versions of click chemistry such as strain promoted azide-alkyne cycloaddition (SPAAC), a central effort has also been made to develop various Cu(I) ligands that can prevent the cytotoxicity of Cu(I) ions while accelerating the CuAAC reaction. Meanwhile, additional transition metals such as palladium have been explored as alternative sources to promote a bioorthogonal conjugation reaction on cell surface, as well as within an intracellular environment. Furthermore, transition metal mediated chemical conversions beyond conjugation have also been utilized to manipulate protein activity within living systems. We highlight these emerging examples that significantly enriched our protein chemistry toolkit, which will likely expand our view on the definition and applications of bioorthogonal chemistry.
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Affiliation(s)
- Maiyun Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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72
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Edwards A, Rubin M. Synthesis of 1-arylcycloprop-2-ene carboxylates with non-substituted double bond via a Rh(II)-catalyzed cyclopropenation of trimethylsilylacetylene with coarsely purified aryldiazoacetates. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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73
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Li N, Ramil CP, Lim RKV, Lin Q. A genetically encoded alkyne directs palladium-mediated protein labeling on live mammalian cell surface. ACS Chem Biol 2015; 10:379-84. [PMID: 25347611 PMCID: PMC4340352 DOI: 10.1021/cb500649q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
The merging of site-specific incorporation
of small bioorthogonal
functional groups into proteins via amber codon suppression with bioorthogonal
chemistry has created exciting opportunities to extend the power of
organic reactions to living systems. Here we show that a new alkyne
amino acid can be site-selectively incorporated into mammalian proteins
via a known orthogonal pyrrolysyl-tRNA synthetase/tRNACUA pair and directs an unprecedented, palladium-mediated cross-coupling
reaction-driven protein labeling on live mammalian cell surface. A
comparison study with the alkyne-encoded proteins in vitro indicated that this terminal alkyne is better suited for the palladium-mediated
cross-coupling reaction than the copper-catalyzed click chemistry.
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Affiliation(s)
- Nan Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Carlo P. Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Reyna K. V. Lim
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
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74
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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75
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Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells. Angew Chem Int Ed Engl 2015; 54:4597-602. [DOI: 10.1002/anie.201410433] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/08/2014] [Indexed: 11/10/2022]
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76
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Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410433] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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77
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Borrmann A, Fatunsin O, Dommerholt J, Jonker AM, Löwik DWPM, van Hest JCM, van Delft FL. Strain-Promoted Oxidation-Controlled Cyclooctyne–1,2-Quinone Cycloaddition (SPOCQ) for Fast and Activatable Protein Conjugation. Bioconjug Chem 2015; 26:257-61. [DOI: 10.1021/bc500534d] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Annika Borrmann
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Olumide Fatunsin
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Jan Dommerholt
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Anika M. Jonker
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Dennis W. P. M. Löwik
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Jan C. M. van Hest
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Floris L. van Delft
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
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78
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Hu C, Chen Y. Chemoselective and fast decarboxylative allylation by photoredox catalysis under mild conditions. Org Chem Front 2015. [DOI: 10.1039/c5qo00187k] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A chemoselective and fast decarboxylative allylation is developed by photoredox catalysis to build C(sp3)–allyl bonds under mild conditions.
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Affiliation(s)
- Chenchen Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Collaborative Innovation Center of Chemistry for Life Sciences
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Collaborative Innovation Center of Chemistry for Life Sciences
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
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79
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Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment - Expanding the chemistry in biology. Chem Sci 2015; 6:50-69. [PMID: 28553457 PMCID: PMC5424465 DOI: 10.1039/c4sc01534g] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022] Open
Abstract
Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of 'non-sense' codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.
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Affiliation(s)
- Anaëlle Dumas
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Lukas Lercher
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher D Spicer
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Benjamin G Davis
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
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80
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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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81
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Espeel P, Du Prez FE. “Click”-Inspired Chemistry in Macromolecular Science: Matching Recent Progress and User Expectations. Macromolecules 2014. [DOI: 10.1021/ma501386v] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pieter Espeel
- Department
of Organic and
Macromolecular Chemistry, Polymer Chemistry Research Group, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
| | - Filip E. Du Prez
- Department
of Organic and
Macromolecular Chemistry, Polymer Chemistry Research Group, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
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82
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Lim RKV, Li N, Ramil CP, Lin Q. Fast and sequence-specific palladium-mediated cross-coupling reaction identified from phage display. ACS Chem Biol 2014; 9:2139-48. [PMID: 25025771 PMCID: PMC4168780 DOI: 10.1021/cb500443x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fast and specific bioorthogonal reactions are highly desirable because they provide efficient tracking of biomolecules that are present in low abundance and/or involved in fast dynamic process in living systems. Toward this end, classic strategy involves the optimization of substrate structures and reaction conditions in test tubes, testing their compatibility with biological systems, devising synthetic biology schemes to introduce the modified substrates into living cells or organisms, and finally validating the superior kinetics for enhanced capacity in tracking biomolecules in vivo--a lengthy process often mired by unexpected results. Here, we report a streamlined approach in which the "microenvironment" of a bioorthogonal chemical reporter is exploited directly in biological systems via phage-assisted interrogation of reactivity (PAIR) to optimize not only reaction kinetics but also specificity. Using the PAIR strategy, we identified a short alkyne-containing peptide sequence showing fast kinetics (k2=13,000±2000 M(-1) s(-1)) in a palladium-mediated cross-coupling reaction. Site-directed mutagenesis studies suggested that the residues surrounding the alkyne moiety facilitate the assembly of a key palladium-alkyne intermediate along the reaction pathway. When this peptide sequence was inserted into the extracellular domain of epidermal growth factor receptor (EGFR), this reactive sequence directed the specific labeling of EGFR in live mammalian cells.
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Affiliation(s)
- Reyna K. V. Lim
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Nan Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Carlo P. Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
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83
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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: 562] [Impact Index Per Article: 56.2] [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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84
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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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85
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Genetic code expansion and bioorthogonal labelling enables cell specific proteomics in an animal. Curr Opin Chem Biol 2014; 21:154-60. [DOI: 10.1016/j.cbpa.2014.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 11/20/2022]
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86
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Shih HW, Kamber DN, Prescher JA. Building better bioorthogonal reactions. Curr Opin Chem Biol 2014; 21:103-11. [DOI: 10.1016/j.cbpa.2014.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/25/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
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87
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Photoclick chemistry: a fluorogenic light-triggered in vivo ligation reaction. Curr Opin Chem Biol 2014; 21:89-95. [PMID: 25022432 DOI: 10.1016/j.cbpa.2014.05.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 12/11/2022]
Abstract
The ability to use chemical reactivity to monitor and control biomolecular processes with a spatial and temporal precision motivated the development of light-triggered in vivo chemistries. To this end, the photoinduced tetrazole-alkene cycloaddition, also termed 'photoclick chemistry' offers a very rapid chemical ligation platform for the manipulation of biomolecules and matrices in vivo. Here we outline the recent developments in the optimization of this chemistry, ranging from the search for substrates that offer two-photon photoactivatability, superior reaction kinetics, and/or genetic encodability, to the study of the reaction mechanism. The applications of the photoclick chemistry in protein labeling in vitro and in vivo as well as in preparing 'smart' hydrogels for 3D cell culture are highlighted.
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88
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Darko A, Wallace S, Dmitrenko O, Machovina MM, Mehl RA, Chin JW, Fox JM. Conformationally Strained trans-Cyclooctene with Improved Stability and Excellent Reactivity in Tetrazine Ligation. Chem Sci 2014; 5:3770-3776. [PMID: 26113970 DOI: 10.1039/c4sc01348d] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Computation has guided the design of conformationally-strained dioxolane-fused trans-cyclooctene (d-TCO) derivatives that display excellent reactivity in the tetrazine ligation. A water soluble derivative of 3,6-dipyridyl-s-tetrazine reacts with d-TCO with a second order rate k2 366,000 (+/- 15,000) M-1s-1 at 25 °C in pure water. Furthermore, d-TCO derivatives can be prepared easily, are accessed through diastereoselective synthesis, and are typically crystalline bench-stable solids that are stable in aqueous solution, blood serum, or in the presence of thiols in buffered solution. GFP with a genetically encoded tetrazine-containing amino acid was site-specifically labelled in vivo by a d-TCO derivative. The fastest bioorthogonal reaction reported to date [k2 3,300,000 (+/- 40,000) M-1s-1 in H2O at 25 °C] is described herein with a cyclopropane-fused trans-cyclooctene. d-TCO derivatives display rates within an order of magnitude of these fastest trans-cyclooctene reagents, and also display enhanced stability and aqueous solubility.
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Affiliation(s)
- Ampofo Darko
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Stephen Wallace
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Olga Dmitrenko
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Melodie M Machovina
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Joseph M Fox
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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89
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Gattner MJ, Ehrlich M, Vrabel M. Sulfonyl azide-mediated norbornene aziridination for orthogonal peptide and protein labeling. Chem Commun (Camb) 2014; 50:12568-71. [DOI: 10.1039/c4cc04117h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we show that electron-deficient sulfonyl azides can be used for selective functionalization of norbornene containing peptides and proteins.
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Affiliation(s)
- Michael J. Gattner
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
| | - Michael Ehrlich
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
| | - Milan Vrabel
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
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