151
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Eising S, van der Linden NGA, Kleinpenning F, Bonger KM. Vinylboronic Acids as Efficient Bioorthogonal Reactants for Tetrazine Labeling in Living Cells. Bioconjug Chem 2018; 29:982-986. [PMID: 29438611 PMCID: PMC5942871 DOI: 10.1021/acs.bioconjchem.7b00796] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Bioorthogonal chemistry
can be used for the selective modification
of biomolecules without interfering with any other functionality present
in the cell. The tetrazine ligation is very suitable as a bioorthogonal
reaction because of its selectivity and high reaction rates with several
alkenes and alkynes. Recently, we described vinylboronic acids (VBAs)
as novel hydrophilic bioorthogonal moieties that react efficiently
with dipyridyl-s-tetrazines and used them for protein
modification in cell lysate. It is not clear, however, whether VBAs
are suitable for labeling experiments in living cells because of the
possible coordination with, for example, vicinal carbohydrate diols.
Here, we evaluated VBAs as bioorthogonal reactants for labeling of
proteins in living cells using an irreversible inhibitor of the proteasome
and compared the reactivity to that of an inhibitor containing norbornene,
a widely used reactant for the tetrazine ligation. No large differences
were observed between the VBA and norbornene probes in a two-step
labeling approach with a cell-penetrable fluorescent tetrazine, indicating
that the VBA gives little or no side reactions with diols and can
be used efficiently for protein labeling in living cells.
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Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Nicole G A van der Linden
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Fleur Kleinpenning
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Kimberly M Bonger
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
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152
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Oller-Salvia B, Kym G, Chin JW. Rapid and Efficient Generation of Stable Antibody-Drug Conjugates via an Encoded Cyclopropene and an Inverse-Electron-Demand Diels-Alder Reaction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712370] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
| | - Gene Kym
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
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153
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Kekulandara DN, Samarasinghe KTG, Munkanatta Godage DNP, Ahn YH. Clickable glutathione using tetrazine-alkene bioorthogonal chemistry for detecting protein glutathionylation. Org Biomol Chem 2018; 14:10886-10893. [PMID: 27812596 DOI: 10.1039/c6ob02050j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein glutathionylation is one of the major cysteine oxidative modifications in response to reactive oxygen species (ROS). We recently developed a clickable glutathione approach for detecting glutathionylation by using a glutathione synthetase mutant (GS M4) that synthesizes azido-glutathione (γGlu-Cys-azido-Ala) in situ in cells. In order to demonstrate the versatility of clickable glutathione and to increase the chemical tools for detecting glutathionylation, we sought to develop clickable glutathione that uses tetrazine-alkene bioorthogonal chemistry. Here we report two alkene-containing glycine surrogates (allyl-Gly and allyl-Ser) for the biosynthesis of clickable glutathione and their use for detection, enrichment, and identification of glutathionylated proteins. Our results provide chemical tools (allyl-Gly and allyl-Ser for GS M4) for versatile characterization of protein glutathionylation. In addition, we show that the active site of GS can be tuned to introduce a small size chemical tag on glutathione for exploring glutathione function in cells.
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Affiliation(s)
| | | | | | - Young-Hoon Ahn
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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154
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Lambert WD, Scinto SL, Dmitrenko O, Boyd SJ, Magboo R, Mehl RA, Chin JW, Fox JM, Wallace S. Computationally guided discovery of a reactive, hydrophilic trans-5-oxocene dienophile for bioorthogonal labeling. Org Biomol Chem 2018; 15:6640-6644. [PMID: 28752889 PMCID: PMC5708333 DOI: 10.1039/c7ob01707c] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The use of organic chemistry principles and prediction techniques has enabled the development of new bioorthogonal reactions. As this "toolbox" expands to include new reaction manifolds and orthogonal reaction pairings, the continued development of existing reactions remains an important objective. This is particularly important in cellular imaging, where non-specific background fluorescence has been linked to the hydrophobicity of the bioorthogonal moiety. Here we report that trans-5-oxocene (oxoTCO) displays enhanced reactivity and hydrophilicity compared to trans-cyclooctene (TCO) in the tetrazine ligation reaction. Aided by ab initio calculations we show that the insertion of a single oxygen atom into the trans-cyclooctene (TCO) ring system is sufficient to impart aqueous solubility and also results in significant rate acceleration by increasing angle strain. We demonstrate the rapid and quantitative cycloaddition of oxoTCO using a water-soluble tetrazine derivative and a protein substrate containing a site-specific genetically encoded tetrazine moiety both in vitro and in vivo. We anticipate that oxoTCO will find use in studies where hydrophilicity and fast bioconjugation kinetics are paramount.
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Affiliation(s)
- William D Lambert
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samuel L Scinto
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Olga Dmitrenko
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samantha J Boyd
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | | | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Joseph M Fox
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Stephen Wallace
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK and Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, UK
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155
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Xu M, Galindo-Murillo R, Cheatham TE, Franzini RM. Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insights. Org Biomol Chem 2018; 15:9855-9865. [PMID: 29139516 DOI: 10.1039/c7ob02191g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bioorthogonal dissociative reactions boast diverse potential applications in chemical biology and drug delivery. The reaction of benzonorbornadienes with tetrazines to release amines from carbamate leaving groups was recently introduced as a bioorthogonal bond-cleavage reaction. The present study aimed at investigating the scope of leaving groups that are compatible with benzonorbornadienes. Synthesis of several benzonorbornadienes with different releasable groups is reported, and the reaction of these molecules with tetrazine was found to be rapid and afforded high release yields. The tetrazine-induced release of molecules proceeds in a cascade of steps including inverse-electron demand cycloaddition and cycloreversion reactions that form unstable isoindoles/isobenzofuran intermediates and spontaneously eliminate a leaving group of interest. In the case of oxygen-bridged BNBDs at room temperature, we observed the formation of an unproductive byproduct.
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Affiliation(s)
- M Xu
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT-84112, USA.
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156
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Mandal N, Datta A. Dynamical Effects along the Bifurcation Pathway Control Semibullvalene Formation in Deazetization Reactions. J Phys Chem B 2018; 122:1239-1244. [PMID: 29316395 DOI: 10.1021/acs.jpcb.7b09533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Post-transition-state dynamics during the deazetization of 3 resulting in two degenerate semibullvalenes (4 and 5) have been investigated with density functional theory (DFT) and quasi-classical trajectory (QCT) calculations. Removal of N2 from 3 occurs through a synchronous and concerted pathway through an ambimodal transition-state (TS1). In addition to TS2, the exclusively anticipated product from minimum energy pathway (MEP) calculations, trajectories initiated from TS1 produce 4, TS2, and 5 in 1:1:1 ratio. Isotopic substitutions (12C(13C/14C)-H(D) at 1-2 positions) result in purely Newtonian kinetic isotope effects (4:5 ≈ 1.4 for 13C1-13C2), an unequivocal evidence for dynamics controlled product formation.
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Affiliation(s)
- Nilangshu Mandal
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
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157
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Werther P, Möhler JS, Wombacher R. A Bifunctional Fluorogenic Rhodamine Probe for Proximity-Induced Bioorthogonal Chemistry. Chemistry 2017; 23:18216-18224. [DOI: 10.1002/chem.201703607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Jasper S. Möhler
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
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158
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Elliott TS, Bianco A, Townsley FM, Fried SD, Chin JW. Tagging and Enriching Proteins Enables Cell-Specific Proteomics. Cell Chem Biol 2017; 23:805-815. [PMID: 27447048 PMCID: PMC4959846 DOI: 10.1016/j.chembiol.2016.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/23/2016] [Indexed: 01/01/2023]
Abstract
Cell-specific proteomics in multicellular systems and whole animals is a promising approach to understand the differentiated functions of cells and tissues. Here, we extend our stochastic orthogonal recoding of translation (SORT) approach for the co-translational tagging of proteomes with a cyclopropene-containing amino acid in response to diverse codons in genetically targeted cells, and create a tetrazine-biotin probe containing a cleavable linker that offers a way to enrich and identify tagged proteins. We demonstrate that SORT with enrichment, SORT-E, efficiently recovers and enriches SORT tagged proteins and enables specific identification of enriched proteins via mass spectrometry, including low-abundance proteins. We show that tagging at distinct codons enriches overlapping, but distinct sets of proteins, suggesting that tagging at more than one codon enhances proteome coverage. Using SORT-E, we accomplish cell-specific proteomics in the fly. These results suggest that SORT-E will enable the definition of cell-specific proteomes in animals during development, disease progression, and learning and memory. A tetrazine-biotin probe containing a cleavable linker was created Proteomes labeled with cyclopropene amino acids were enriched and identified Proteome coverage is increased by targeting the amino acids to multiple codons Cell-specific proteomics was accomplished in the fly
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Affiliation(s)
- Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ambra Bianco
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Fiona M Townsley
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen D Fried
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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159
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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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160
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Huang LL, Liu K, Zhang Q, Xu J, Zhao D, Zhu H, Xie HY. Integrating Two Efficient and Specific Bioorthogonal Ligation Reactions with Natural Metabolic Incorporation in One Cell for Virus Dual Labeling. Anal Chem 2017; 89:11620-11627. [DOI: 10.1021/acs.analchem.7b03043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Li-Li Huang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Kejiang Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Qianmei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jin Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Dongxu Zhao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Houshun Zhu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hai-Yan Xie
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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161
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Liu K, Enns B, Evans B, Wang N, Shang X, Sittiwong W, Dussault PH, Guo J. A genetically encoded cyclobutene probe for labelling of live cells. Chem Commun (Camb) 2017; 53:10604-10607. [PMID: 28902227 PMCID: PMC5648060 DOI: 10.1039/c7cc05580c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a cyclobutene-containing amino acid into proteins in response to an amber nonsense codon. Fast and fluorescent labeling of purified proteins and intact proteins in live cells was demonstrated using the inverse electron demand Diels-Alder reaction with a tetrazine.
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Affiliation(s)
- K Liu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
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162
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Liu F, Liang Y, Houk KN. Bioorthogonal Cycloadditions: Computational Analysis with the Distortion/Interaction Model and Predictions of Reactivities. Acc Chem Res 2017; 50:2297-2308. [PMID: 28876890 PMCID: PMC5675536 DOI: 10.1021/acs.accounts.7b00265] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bioorthogonal chemistry has had a major impact on the study of biological processes in vivo. Biomolecules of interest can be tracked by using probes and reporters that do not react with cellular components and do not interfere with metabolic processes in living cells. Much time and effort has been devoted to the screening of potential bioorthogonal reagents experimentally. This Account describes how our groups have performed computational screening of reactivity and mutual orthogonality. Our collaborations with experimentalists have led to the development of new and useful reactions. Dozens of bioorthogonal cycloadditions have been reported in the literature in the past few years, but as interest in tracking multiple targets arises, our computational screening has gained importance for the discovery of new mutually orthogonal bioorthogonal cycloaddition pairs. The reactivities of strained alkenes and alkynes with common 1,3-dipoles such as azides, along with mesoionic sydnones and other novel 1,3-dipoles, have been explored. Studies of "inverse-electron-demand" dienes such as triazines and tetrazines that have been used in bioorthogonal Diels-Alder cycloadditions are described. The color graphics we have developed give a snapshot of whether reactions are fast enough for cellular applications (green), adequately reactive for labeling (yellow), or only useful for synthesis or do not occur at all (red). The colors of each box give an instant view of rates, while bar graphs provide an analysis of the factors that control reactivity. This analysis uses the distortion/interaction or activation strain model of cycloaddition reactivity developed independently by our group and that of F. Matthias Bickelhaupt in The Netherlands. The model analyzes activation barriers in terms of the energy required to distort the reactants to the transition state geometry. This energy, called the distortion energy or activation strain, constitutes the major component of the activation energy. The strong bonding interaction between the termini of the two reactants, which we call the interaction energy, overcomes the distortion energy and leads to the new bonds in the products. This Account describes how we have analyzed and predicted bioorthogonal cycloaddition reactivity using the distortion/interaction model and how our experimental collaborators have employed these insights to create new bioorthogonal cycloadditions. The graphics we use document and predict which combinations of cycloadditions will be useful in bioorthogonal chemistry and which pairs of reactions are mutually orthogonal. For example, the fast reaction of 5-phenyl-1,2,4-triazine and a thiacycloheptyne will not interfere with the other fast reaction of 3,6-diphenyl-1,2,4,5-tetrazine and a cyclopropene. No cross reactions will occur, as these are very slow reactions.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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163
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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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164
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Levandowski BJ, Hamlin TA, Bickelhaupt FM, Houk KN. Role of Orbital Interactions and Activation Strain (Distortion Energies) on Reactivities in the Normal and Inverse Electron-Demand Cycloadditions of Strained and Unstrained Cycloalkenes. J Org Chem 2017; 82:8668-8675. [DOI: 10.1021/acs.joc.7b01673] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brian J. Levandowski
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Trevor A. Hamlin
- Department
of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
(ACMM), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - F. Matthias Bickelhaupt
- Department
of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
(ACMM), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Institute
for Molecules and Materials (IMM), Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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165
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Abstract
Posttranslational protein glycosylation is conserved in all kingdoms of life and implicated in the regulation of protein structure, function, and localization. The visualization of glycosylation states of designated proteins within living cells is of great importance for unraveling the biological roles of intracellular protein glycosylation. Our generally applicable approach is based on the incorporation of a glucosamine analog, Ac4GlcNCyoc, into the cellular glycome via metabolic engineering. Ac4GlcNCyoc can be labeled in a second step via inverse-electron-demand Diels-Alder chemistry with fluorophores inside living cells. Additionally, target proteins can be expressed as enhanced green fluorescent protein (EGFP)-fusion proteins. To assess the proximity of the donor EGFP and the glycan-anchored acceptor fluorophore, Förster resonance energy transfer (FRET) is employed and read out with high contrast by fluorescence lifetime imaging (FLIM) microscopy. In this chapter, we present a detailed description of methods required to perform protein-specific imaging of glycosylation inside living cells. These include the complete synthesis of Ac4GlcNCyoc, immunoprecipitation of EGFP-fusion proteins to examine the Ac4GlcNCyoc modification state, and a complete section on basics, performance, as well as data analysis for FLIM-FRET microscopy. We also provide useful notes necessary for reproducibility and point out strengths and limitations of the approach.
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166
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Masuya T, Murai M, Ito T, Aburaya S, Aoki W, Miyoshi H. Pinpoint Chemical Modification of the Quinone-Access Channel of Mitochondrial Complex I via a Two-Step Conjugation Reaction. Biochemistry 2017; 56:4279-4287. [DOI: 10.1021/acs.biochem.7b00612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Takahiro Masuya
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takeshi Ito
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shunsuke Aburaya
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Wataru Aoki
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- Division of Applied
Life
Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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167
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Hudak JE, Alvarez D, Skelly A, von Andrian UH, Kasper DL. Illuminating vital surface molecules of symbionts in health and disease. Nat Microbiol 2017. [PMID: 28650431 PMCID: PMC5546223 DOI: 10.1038/nmicrobiol.2017.99] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The immunomodulatory surface molecules of commensal and pathogenic bacteria are critical to microorganisms' survival and the host's response1,2. Recent studies have highlighted the unique and important responses elicited by commensal-derived surface macromolecules3-5. However, the technology available to track these molecules in host cells and tissues remains primitive. We report, here, an interdisciplinary approach that uses metabolic labelling combined with bioorthogonal click chemistry (that is, reactions performed in living organisms)6 to specifically tag up to three prominent surface immunomodulatory macromolecules-peptidoglycan, lipopolysaccharide and capsular polysaccharide-either simultaneously or individually in live anaerobic commensal bacteria. Importantly, the peptidoglycan labelling enables, for the first time, the specific labelling of live endogenous, anaerobic bacteria within the mammalian host. This approach has allowed us to image and track the path of labelled surface molecules from live, luminal bacteria into specific intestinal immune cells in the living murine host during health and disease. The chemical labelling of three specific macromolecules within a live organism offers the potential for in-depth visualization of host-pathogen interactions.
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Affiliation(s)
- Jason E Hudak
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Alvarez
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ashwin Skelly
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ulrich H von Andrian
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, USA
| | - Dennis L Kasper
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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168
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Burke EG, Gold B, Hoang TT, Raines RT, Schomaker JM. Fine-Tuning Strain and Electronic Activation of Strain-Promoted 1,3-Dipolar Cycloadditions with Endocyclic Sulfamates in SNO-OCTs. J Am Chem Soc 2017; 139:8029-8037. [PMID: 28505435 DOI: 10.1021/jacs.7b03943] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ability to achieve predictable control over the polarization of strained cycloalkynes can influence their behavior in subsequent reactions, providing opportunities to increase both rate and chemoselectivity. A series of new heterocyclic strained cyclooctynes containing a sulfamate backbone (SNO-OCTs) were prepared under mild conditions by employing ring expansions of silylated methyleneaziridines. SNO-OCT derivative 8 outpaced even a difluorinated cyclooctyne in a 1,3-dipolar cycloaddition with benzylazide. The various orbital interactions of the propargylic and homopropargylic heteroatoms in SNO-OCT were explored both experimentally and computationally. The inclusion of these heteroatoms had a positive impact on stability and reactivity, where electronic effects could be utilized to relieve ring strain. The choice of the heteroatom combinations in various SNO-OCTs significantly affected the alkyne geometries, thus illustrating a new strategy for modulating strain via remote substituents. Additionally, this unique heteroatom activation was capable of accelerating the rate of reaction of SNO-OCT with diazoacetamide over azidoacetamide, opening the possibility of further method development in the context of chemoselective, bioorthogonal labeling.
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Affiliation(s)
- Eileen G Burke
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Brian Gold
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Trish T Hoang
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Ronald T Raines
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Jennifer M Schomaker
- Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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169
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Zhu Y, Chen X. Expanding the Scope of Metabolic Glycan Labeling in Arabidopsis thaliana. Chembiochem 2017; 18:1286-1296. [PMID: 28383803 DOI: 10.1002/cbic.201700069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/26/2022]
Abstract
Metabolic glycan labeling (MGL) has gained wide utility and has become a useful tool for probing glycosylation in living systems. For the past three decades, the development and application of MGL have mostly focused on animal glycosylation. Recently, exploiting MGL for studying plant glycosylation has gained interest. Here, we describe a systematic evaluation of MGL for fluorescence imaging of root glycans in Arabidopsis thaliana. Nineteen monosaccharide analogues containing a bioorthogonal group (azide, alkyne, or cyclopropene) were synthesized and evaluated for metabolic incorporation into root glycans. Among these unnatural sugars, 14 (including three new compounds) were evaluated in plants for the first time. Our results showed that five unnatural sugars metabolically labeled root glycans efficiently, and enabled fluorescence imaging by bioorthogonal conjugation with fluorophores. We optimized the experimental procedures for MGL in Arabidopsis. Finally, distinct distribution patterns of the newly synthesized glycans were observed along the root developmental zones, thus indicating regulated biosynthesis of glycans during root development. We envision that MGL will find broad applications in plant glycobiology.
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Affiliation(s)
- Yuntao Zhu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center and, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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170
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Row RD, Shih HW, Alexander AT, Mehl RA, Prescher JA. Cyclopropenones for Metabolic Targeting and Sequential Bioorthogonal Labeling. J Am Chem Soc 2017; 139:7370-7375. [DOI: 10.1021/jacs.7b03010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Austin T. Alexander
- 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
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171
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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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172
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Dold JEGA, Pfotzer J, Späte AK, Wittmann V. Dienophile-Modified Mannosamine Derivatives for Metabolic Labeling of Sialic Acids: A Comparative Study. Chembiochem 2017; 18:1242-1250. [DOI: 10.1002/cbic.201700002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Jeremias E. G. A. Dold
- University of Konstanz; Department of Chemistry and; Konstanz Research School Chemical Biology; KoRS-CB); 78457 Konstanz Germany
| | - Jessica Pfotzer
- University of Konstanz; Department of Chemistry and; Konstanz Research School Chemical Biology; KoRS-CB); 78457 Konstanz Germany
| | - Anne-Katrin Späte
- University of Konstanz; Department of Chemistry and; Konstanz Research School Chemical Biology; KoRS-CB); 78457 Konstanz Germany
| | - Valentin Wittmann
- University of Konstanz; Department of Chemistry and; Konstanz Research School Chemical Biology; KoRS-CB); 78457 Konstanz Germany
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173
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Kozma E, Demeter O, Kele P. Bio-orthogonal Fluorescent Labelling of Biopolymers through Inverse-Electron-Demand Diels-Alder Reactions. Chembiochem 2017; 18:486-501. [PMID: 28070925 PMCID: PMC5363342 DOI: 10.1002/cbic.201600607] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 02/06/2023]
Abstract
Bio-orthogonal labelling schemes based on inverse-electron-demand Diels-Alder (IEDDA) cycloaddition have attracted much attention in chemical biology recently. The appealing features of this reaction, such as the fast reaction kinetics, fully bio-orthogonal nature and high selectivity, have helped chemical biologists gain deeper understanding of biochemical processes at the molecular level. Listing the components and discussing the possibilities and limitations of these reagents, we provide a recent snapshot of the field of IEDDA-based biomolecular manipulation with special focus on fluorescent modulation approaches through the use of bio-orthogonalized building blocks. At the end, we discuss challenges that need to be addressed for further developments in order to overcome recent limitations and to enable researchers to answer biomolecular questions in more detail.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Orsolya Demeter
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Péter Kele
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
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174
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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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175
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Montenegro J, Phipps RJ. Highlights from the 52nd EUCHEM conference on stereochemistry, Bürgenstock, Switzerland, May 2017. Chem Commun (Camb) 2017; 53:9960-9966. [DOI: 10.1039/c7cc90258a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strong wind that was blowing in Brunnen on the 4th of May 2017 was prophetic of the storm of ideas and creativity that would later fall over the participants of the 52nd edition of the Bürgenstock conference.
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Affiliation(s)
- Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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176
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Kumar P, Shukhman D, Laughlin ST. A photocaged, cyclopropene-containing analog of the amino acid neurotransmitter glutamate. Tetrahedron Lett 2016; 57:5750-5752. [PMID: 30245532 PMCID: PMC6150495 DOI: 10.1016/j.tetlet.2016.10.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Substituted cyclopropenes serve as compact biorthogonal appendages that enable analysis of biomolecules in complex systems. Neurotransmitters, a chemically diverse group of biomolecules that control neuron excitation and inhibition, are not among the systems that have been studied using biorthogonal chemistry. Here we describe the synthesis of cyclopropene-containing analogs of the excitatory amino acid neurotransmitter glutamate starting from a Garner's aldehyde-derived alkyne. The deprotected cyclopropene glutamate was stable in solution but decomposed upon concentration. Appending a light-cleavable group improved the stability of the cyclopropene while simultaneously caging the neurotransmitter. This strategy has the potential to permit deployment of cyclopropene-modified glutamate as a bioorthogonal probe of the neurotransmitter glutamate in vivo with spatiotemporal precision.
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Affiliation(s)
- Pratik Kumar
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - David Shukhman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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177
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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178
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Smits AH, Borrmann A, Roosjen M, van Hest JC, Vermeulen M. Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics. ACS Chem Biol 2016; 11:3245-3250. [PMID: 27643597 DOI: 10.1021/acschembio.6b00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Epitope-tagging is an effective tool to facilitate protein enrichment from crude cell extracts. Traditionally, N- or C-terminal fused tags are employed, which, however, can perturb protein function. Unnatural amino acids (UAAs) harboring small reactive handles can be site-specifically incorporated into proteins, thus serving as a potential alternative for conventional protein tags. Here, we introduce Click-MS, which combines the power of site-specific UAA incorporation, bioorthogonal chemistry, and quantitative mass spectrometry-based proteomics to specifically enrich a single protein of interest from crude mammalian cell extracts. By genetic encoding of p-azido-l-phenylalanine, the protein of interest can be selectively captured using copper-free click chemistry. We use Click-MS to enrich proteins that function in different cellular compartments, and we identify protein-protein interactions, showing the great potential of Click-MS for interaction proteomics workflows.
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Affiliation(s)
- Arne H. Smits
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Annika Borrmann
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Mark Roosjen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jan C.M. van Hest
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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179
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Oliveira BL, Guo Z, Boutureira O, Guerreiro A, Jiménez‐Osés G, Bernardes GJL. A Minimal, Unstrained S-Allyl Handle for Pre-Targeting Diels-Alder Bioorthogonal Labeling in Live Cells. Angew Chem Int Ed Engl 2016; 55:14683-14687. [PMID: 27763724 PMCID: PMC5132151 DOI: 10.1002/anie.201608438] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 09/27/2016] [Indexed: 11/12/2022]
Abstract
The unstrained S-allyl cysteine amino acid was site-specifically installed on apoptosis protein biomarkers and was further used as a chemical handle and ligation partner for 1,2,4,5-tetrazines by means of an inverse-electron-demand Diels-Alder reaction. We demonstrate the utility of this minimal handle for the efficient labeling of apoptotic cells using a fluorogenic tetrazine dye in a pre-targeting approach. The small size, easy chemical installation, and selective reactivity of the S-allyl handle towards tetrazines should be readily extendable to other proteins and biomolecules, which could facilitate their labeling within live cells.
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Affiliation(s)
- Bruno L. Oliveira
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Zijian Guo
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Omar Boutureira
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Ana Guerreiro
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Gonzalo Jiménez‐Osés
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química26006LogroñoSpain
- Institute of Biocomputation and Physics of Complex Systems (BIFI)University of ZaragozaBIFI-IQFR (CSIC)ZaragozaSpain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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180
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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181
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Oliveira BL, Guo Z, Boutureira O, Guerreiro A, Jiménez-Osés G, Bernardes GJL. A Minimal, Unstrained S-Allyl Handle for Pre-Targeting Diels-Alder Bioorthogonal Labeling in Live Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Bruno L. Oliveira
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Zijian Guo
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Omar Boutureira
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Ana Guerreiro
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Gonzalo Jiménez-Osés
- Departamento de Química; Universidad de La Rioja; Centro de Investigación en Síntesis Química; 26006 Logroño Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI); University of Zaragoza; BIFI-IQFR (CSIC) Zaragoza Spain
| | - Gonçalo J. L. Bernardes
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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182
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Shang X, Song X, Faller C, Lai R, Li H, Cerny R, Niu W, Guo J. Fluorogenic protein labeling using a genetically encoded unstrained alkene. Chem Sci 2016; 8:1141-1145. [PMID: 28451254 PMCID: PMC5369545 DOI: 10.1039/c6sc03635j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 09/23/2016] [Indexed: 12/26/2022] Open
Abstract
A new fluorogenic bioorthogonal reaction between styrene (an unstrained alkene) and a tetrazine was developed.
We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.
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Affiliation(s)
- X Shang
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - X Song
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - C Faller
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - R Lai
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - H Li
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - R Cerny
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - W Niu
- Department of Chemical & Biomolecular Engineering , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - J Guo
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
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183
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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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184
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Eising S, Lelivelt F, Bonger KM. Vinylboronic Acids as Fast Reacting, Synthetically Accessible, and Stable Bioorthogonal Reactants in the Carboni-Lindsey Reaction. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Francis Lelivelt
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Kimberly M. Bonger
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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185
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Eising S, Lelivelt F, Bonger KM. Vinylboronic Acids as Fast Reacting, Synthetically Accessible, and Stable Bioorthogonal Reactants in the Carboni-Lindsey Reaction. Angew Chem Int Ed Engl 2016; 55:12243-7. [PMID: 27605057 PMCID: PMC5113785 DOI: 10.1002/anie.201605271] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/10/2016] [Indexed: 11/09/2022]
Abstract
Bioorthogonal reactions are widely used for the chemical modification of biomolecules. The application of vinylboronic acids (VBAs) as non‐strained, synthetically accessible and water‐soluble reaction partners in a bioorthogonal inverse electron‐demand Diels–Alder (iEDDA) reaction with 3,6‐dipyridyl‐s‐tetrazines is described. Depending on the substituents, VBA derivatives give second‐order rate constants up to 27 m−1 s−1 in aqueous environments at room temperature, which is suitable for biological labeling applications. The VBAs are shown to be biocompatible, non‐toxic, and highly stable in aqueous media and cell lysate. Furthermore, VBAs can be used orthogonally to the strain‐promoted alkyne–azide cycloaddition for protein modification, making them attractive complements to the bioorthogonal molecular toolbox.
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Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Francis Lelivelt
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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186
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Merkel M, Arndt S, Ploschik D, Cserép GB, Wenge U, Kele P, Wagenknecht HA. Scope and Limitations of Typical Copper-Free Bioorthogonal Reactions with DNA: Reactive 2′-Deoxyuridine Triphosphates for Postsynthetic Labeling. J Org Chem 2016; 81:7527-38. [DOI: 10.1021/acs.joc.6b01205] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Marcus Merkel
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stefanie Arndt
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Damian Ploschik
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Gergely B. Cserép
- Chemical
Biology Research Group, Institute of Organic Chemistry, Research Centre
for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
krt. 2, H-1117 Budapest, Hungary
| | - Ulrike Wenge
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Péter Kele
- Chemical
Biology Research Group, Institute of Organic Chemistry, Research Centre
for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
krt. 2, H-1117 Budapest, Hungary
| | - Hans-Achim Wagenknecht
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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187
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Wratil PR, Horstkorte R, Reutter W. Metabolic Glycoengineering with N-Acyl Side Chain Modified Mannosamines. Angew Chem Int Ed Engl 2016; 55:9482-512. [PMID: 27435524 DOI: 10.1002/anie.201601123] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 12/14/2022]
Abstract
In metabolic glycoengineering (MGE), cells or animals are treated with unnatural derivatives of monosaccharides. After entering the cytosol, these sugar analogues are metabolized and subsequently expressed on newly synthesized glycoconjugates. The feasibility of MGE was first discovered for sialylated glycans, by using N-acyl-modified mannosamines as precursor molecules for unnatural sialic acids. Prerequisite is the promiscuity of the enzymes of the Roseman-Warren biosynthetic pathway. These enzymes were shown to tolerate specific modifications of the N-acyl side chain of mannosamine analogues, for example, elongation by one or more methylene groups (aliphatic modifications) or by insertion of reactive groups (bioorthogonal modifications). Unnatural sialic acids are incorporated into glycoconjugates of cells and organs. MGE has intriguing biological consequences for treated cells (aliphatic MGE) and offers the opportunity to visualize the topography and dynamics of sialylated glycans in vitro, ex vivo, and in vivo (bioorthogonal MGE).
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Affiliation(s)
- Paul R Wratil
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195, Berlin, Germany.
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystrasse 1, 06114, Halle, Germany.
| | - Werner Reutter
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195, Berlin, Germany
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188
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Wratil PR, Horstkorte R, Reutter W. Metabolisches Glykoengineering mitN-Acyl-Seiten- ketten-modifizierten Mannosaminen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601123] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Paul R. Wratil
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie; Charité - Universitätsmedizin Berlin; Arnimallee 22 14195 Berlin Deutschland
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie; Martin-Luther-Universität Halle-Wittenberg; Hollystraße 1 06114 Halle Deutschland
| | - Werner Reutter
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie; Charité - Universitätsmedizin Berlin; Arnimallee 22 14195 Berlin Deutschland
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189
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Gold B, Aronoff MR, Raines RT. Decreasing Distortion Energies without Strain: Diazo-Selective 1,3-Dipolar Cycloadditions. J Org Chem 2016; 81:5998-6006. [PMID: 27332711 PMCID: PMC5141247 DOI: 10.1021/acs.joc.6b00948] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The diazo group has attributes that complement those of the azido group for applications in chemical biology. Here, we use computational analyses to provide insights into the chemoselectivity of the diazo group in 1,3-dipolar cycloadditions. Dipole distortion energies are responsible for ∼80% of the overall energetic barrier for these reactions. Here, we show that diazo compounds, unlike azides, provide an opportunity to decrease that barrier substantially without introducing strain into the dipolarophile. The ensuing rate enhancement is due to the greater nucleophilic character of a diazo group compared to that of an azido group, which can accommodate decreased distortion energies without predistortion. The tuning of distortion energies with substituents in a diazo compound or dipolarophile can enhance reactivity and selectivity in a predictable manner. Notably, these advantages of diazo groups are amplified in water. Our findings provide a theoretical framework that can guide the design and application of both diazo compounds and azides in "orthogonal" contexts, especially for biological investigations.
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Affiliation(s)
- Brian Gold
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Matthew R. Aronoff
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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190
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Yu P, Yang Z, Liang Y, Hong X, Li Y, Houk KN. Distortion-Controlled Reactivity and Molecular Dynamics of Dehydro-Diels–Alder Reactions. J Am Chem Soc 2016; 138:8247-52. [DOI: 10.1021/jacs.6b04113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Peiyuan Yu
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Zhongyue Yang
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yong Liang
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Xin Hong
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yanwei Li
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and
Biochemistry, University of California, Los Angeles, California 90095, United States
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191
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Späte AK, Dold JEGA, Batroff E, Schart VF, Wieland DE, Baudendistel OR, Wittmann V. Exploring the Potential of Norbornene-Modified Mannosamine Derivatives for Metabolic Glycoengineering. Chembiochem 2016; 17:1374-83. [DOI: 10.1002/cbic.201600197] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Anne-Katrin Späte
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Jeremias E. G. A. Dold
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Ellen Batroff
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Verena F. Schart
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Daniel E. Wieland
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Oliver R. Baudendistel
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Valentin Wittmann
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
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192
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Sherratt AR, Chigrinova M, MacKenzie DA, Rastogi NK, Ouattara MTM, Pezacki AT, Pezacki JP. Dual Strain-Promoted Alkyne–Nitrone Cycloadditions for Simultaneous Labeling of Bacterial Peptidoglycans. Bioconjug Chem 2016; 27:1222-6. [DOI: 10.1021/acs.bioconjchem.6b00063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Allison R. Sherratt
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
| | - Mariya Chigrinova
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
| | - Douglas A. MacKenzie
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa K1N 6N5, Canada
| | - Neelabh K. Rastogi
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa K1N 6N5, Canada
| | - Myriam T. M. Ouattara
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
| | - Aidan T. Pezacki
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa K1N 6N5, Canada
| | - John P. Pezacki
- Life
Sciences Division, National Research Council of Canada, 100 Sussex
Drive, Ottawa K1A 0R6, Canada
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa K1N 6N5, Canada
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193
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Nischan N, Kohler JJ. Advances in cell surface glycoengineering reveal biological function. Glycobiology 2016; 26:789-96. [PMID: 27066802 DOI: 10.1093/glycob/cww045] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/04/2016] [Indexed: 12/31/2022] Open
Abstract
Cell surface glycans are critical mediators of cell-cell, cell-ligand, and cell-pathogen interactions. By controlling the set of glycans displayed on the surface of a cell, it is possible to gain insight into the biological functions of glycans. Moreover, control of glycan expression can be used to direct cellular behavior. While genetic approaches to manipulate glycosyltransferase gene expression are available, their utility in glycan engineering has limitations due to the combinatorial nature of glycan biosynthesis and the functional redundancy of glycosyltransferase genes. Biochemical and chemical strategies offer valuable complements to these genetic approaches, notably by enabling introduction of unnatural functionalities, such as fluorophores, into cell surface glycans. Here, we describe some of the most recent developments in glycoengineering of cell surfaces, with an emphasis on strategies that employ novel chemical reagents. We highlight key examples of how these advances in cell surface glycan engineering enable study of cell surface glycans and their function. Exciting new technologies include synthetic lipid-glycans, new chemical reporters for metabolic oligosaccharide engineering to allow tandem and in vivo labeling of glycans, improved chemical and enzymatic methods for glycoproteomics, and metabolic glycosyltransferase inhibitors. Many chemical and biochemical reagents for glycan engineering are commercially available, facilitating their adoption by the biological community.
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Affiliation(s)
- Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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194
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Edwards A, Rubin M. Efficient one-pot synthesis of 1-arylcycloprop-2-ene-1-carboxamides. Org Biomol Chem 2016; 14:2883-90. [PMID: 26864495 DOI: 10.1039/c6ob00156d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An expeditious and cost-efficient method for synthesis of 1-arylcycloprop-2-ene-1-carboxamides was developed. This one-pot protocol involving coupling of amines with acyl chlorides, generated upon treatment of cyclopenylcarboxylic acids with oxalyl chloride, is applicable for the preparation of sensitive products with a reactive, unsubstituted strained double bond.
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Affiliation(s)
- Andrew Edwards
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, KS 66045-7582, USA.
| | - Michael Rubin
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, KS 66045-7582, USA. and Department of Chemistry, North Caucasus State University, 1a Pushkin St., Stavropol 355009, Russian Federation
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195
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Abstract
Over the years, there have been remarkable efforts in the development of selective protein labeling strategies. In this review, we deliver a comprehensive overview of the currently available bioorthogonal and chemoselective reactions. The ability to introduce bioorthogonal handles to proteins is essential to carry out bioorthogonal reactions for protein labeling in living systems. We therefore summarize the techniques that allow for site-specific "installation" of bioorthogonal handles into proteins. We also highlight the biological applications that have been achieved by selective chemical labeling of proteins.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
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196
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Svatunek D, Denk C, Rosecker V, Sohr B, Hametner C, Allmaier G, Fröhlich J, Mikula H. Efficient low-cost preparation of trans-cyclooctenes using a simplified flow setup for photoisomerization. MONATSHEFTE FUR CHEMIE 2016; 147:579-585. [PMID: 27069284 PMCID: PMC4785212 DOI: 10.1007/s00706-016-1668-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Abstract Bioorthogonal ligations have emerged as highly versatile chemical tools for biomedical research. The exceptionally fast reaction between 1,2,4,5-tetrazines and trans-cyclooctenes (TCOs), also known as tetrazine ligation, is frequently used in this regard. Growing numbers of applications for the tetrazine ligation led to an increased demand for TCO compounds, whose commercial availability is still very limited. Reported photochemical procedures for the preparation of TCOs using flow chemistry are straightforward and high yielding but require expensive equipment. Within this contribution, we present the construction and characterization of a low-cost flow photoreactor assembled from readily accessible components. Syntheses of all commonly used trans-cyclooctene derivatives were successfully carried out using the described system. We are convinced that the presented system for photoisomerization will promote access to bioorthogonally reactive TCO derivatives. Graphical abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s00706-016-1668-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria ; Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Christoph Denk
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | | | - Barbara Sohr
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | | | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
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197
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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198
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Lee YJ, Kurra Y, Liu WR. Phospha-Michael Addition as a New Click Reaction for Protein Functionalization. Chembiochem 2016; 17:456-61. [PMID: 26756316 DOI: 10.1002/cbic.201500697] [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: 12/28/2015] [Indexed: 01/01/2023]
Abstract
A new type of click reaction between an alkyl phosphine and acrylamide was developed and applied for site-specific protein labeling in vitro and in live cells. Acrylamide is a small electrophilic olefin that readily undergoes phospha-Michael addition with an alkyl phosphine. Our kinetic study indicated a second-order rate constant of 0.07 m(-1) s(-1) for the reaction between tris(2-carboxyethyl)phosphine and acrylamide at pH 7.4. To demonstrate its application in protein functionalization, we used a dansyl-phosphine conjugate to successfully label proteins that were site-specifically installed with N(ɛ) -acryloyl-l-lysine and employed a biotin-phosphine conjugate to selectively probe human proteins that were metabolically labeled with N-acryloyl-galactosamine.
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Affiliation(s)
- Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
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199
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Yang YF, Liang Y, Liu F, Houk KN. Diels-Alder Reactivities of Benzene, Pyridine, and Di-, Tri-, and Tetrazines: The Roles of Geometrical Distortions and Orbital Interactions. J Am Chem Soc 2016; 138:1660-7. [PMID: 26804318 DOI: 10.1021/jacs.5b12054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cycloadditions of benzene and ten different azabenzenes (pyridine, three diazines, three triazines, and three tetrazines) with the ethylene dienophile have been explored with density functional theory (M06-2X) and analyzed with the distortion/interaction model. Activation barriers correlate closely with both distortion energies and interaction energies over an activation energy range of 45 kcal/mol. The replacement of CH with N increases Diels-Alder reactivity due not only to the more favorable orbital interaction, but also to a decrease in distortion energy. The rates of reactions are greatly influenced by the nature of the bonds being formed: two C-C bonds > one C-C bond, and one C-N bond > two C-N bonds. The activation energy of Diels-Alder reactions correlates very well with reaction energies and with the NICS(0) values of the aromatic dienes. The distortion energy of the Diels-Alder reaction transition states mostly arises from the diene out-of-plane distortion energy.
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Affiliation(s)
- Yun-Fang Yang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Yong Liang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Fang Liu
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
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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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