1
|
Su C, Dallaston MA, Watson RD, Fahrenhorst-Jones T, Cameron JP, Pierens GK, Bernhardt PV, Savage GP, Williams CM. The (±)-5-Aza[1.0]triblattane Skeleton via Azetine Cycloaddition. Org Lett 2024; 26:2827-2831. [PMID: 38253345 DOI: 10.1021/acs.orglett.3c03655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The first synthesis of the 5-aza[1.0]triblattane skeleton was achieved through a [4 + 2] cycloaddition approach using a suitably protected azetine and cyclopentadiene. A series of azetines were synthesized to explore both stability and suitable N-protection. The key step following cycloaddition utilized a noninitiated protonated aminyl radical cyclization to install the final 5-azatriblattane bond, but it was found to be considerably more unstable than the 6-aza isomer under acidic conditions.
Collapse
Affiliation(s)
- Chuyi Su
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Madeleine A Dallaston
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Renée D Watson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Jacob P Cameron
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| | - G Paul Savage
- CSIRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168 Victoria, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland Australia
| |
Collapse
|
2
|
Timmers M, Peeters W, Hauwert NJ, Rijcken CJF, Vermonden T, Dijkgraaf I, Liskamp RMJ. Specific N-terminal attachment of TMTHSI linkers to native peptides and proteins for strain-promoted azide alkyne cycloaddition. Chem Commun (Camb) 2023; 59:11397-11400. [PMID: 37668179 DOI: 10.1039/d3cc03397j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The site specific attachment of the reactive TMTHSI-click handle to the N-terminus of peptides and proteins is described. The resulting molecular constructs can be used in strain-promoted azide alkyne cycloaddition (SPAAC) for reaction with azide containing proteins e.g., antibodies, peptides, nanoparticles, fluorescent dyes, chelators for radioactive isotopes and SPR-chips etc.
Collapse
Affiliation(s)
- Matt Timmers
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Cristal Therapeutics, Maastricht 6229 EV, The Netherlands
| | - Wouter Peeters
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht 6229 ER, The Netherlands
| | | | | | - Tina Vermonden
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Ingrid Dijkgraaf
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht 6229 ER, The Netherlands
| | - Rob M J Liskamp
- Cristal Therapeutics, Maastricht 6229 EV, The Netherlands
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht 6229 ER, The Netherlands
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK.
| |
Collapse
|
3
|
Mitry MMA, Greco F, Osborn HMI. In Vivo Applications of Bioorthogonal Reactions: Chemistry and Targeting Mechanisms. Chemistry 2023; 29:e202203942. [PMID: 36656616 DOI: 10.1002/chem.202203942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Bioorthogonal chemistry involves selective biocompatible reactions between functional groups that are not normally present in biology. It has been used to probe biomolecules in living systems, and has advanced biomedical strategies such as diagnostics and therapeutics. In this review, the challenges and opportunities encountered when translating in vitro bioorthogonal approaches to in vivo settings are presented, with a focus on methods to deliver the bioorthogonal reaction components. These methods include metabolic bioengineering, active targeting, passive targeting, and simultaneously used strategies. The suitability of bioorthogonal ligation reactions and bond cleavage reactions for in vivo applications is critically appraised, and practical considerations such as the optimum scheduling regimen in pretargeting approaches are discussed. Finally, we present our own perspectives for this area and identify what, in our view, are the key challenges that must be overcome to maximise the impact of these approaches.
Collapse
Affiliation(s)
- Madonna M A Mitry
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK.,Department of Pharmaceutical Chemistry Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Francesca Greco
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| |
Collapse
|
4
|
Xie F, Jiang H, Jia X, Zhang J, Zhu Z, Du J, Tang Y. Bridgehead Alkene-Enabled Strain-Driven Bioorthogonal Reaction. Org Lett 2022; 24:5304-5308. [PMID: 35849354 DOI: 10.1021/acs.orglett.2c01895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Herein, we report a novel bioorthogonal reaction that hinges on a bridgehead alkene (BHA)-enabled inverse-electron-demand Diels-Alder (IEDDA) cycloaddition. Readily accessible from natural product β-caryophyllene, the strained BHA displays high reactivity toward the IEDDA reaction while maintaining excellent biocompatibility. The developed IEDDA reaction has been applied to in vitro protein labeling and pretargeted live cell imaging.
Collapse
Affiliation(s)
- Fayang Xie
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Haolin Jiang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiangqian Jia
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jingyang Zhang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Zhu Zhu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
5
|
Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
Collapse
|
6
|
Yuan SP, Dou PH, Jia YQ, Zhao JQ, You Y, Wang ZH, Zhou MQ, Yuan WC. Catalytic asymmetric aromatizing inverse electron-demand [4+2] cycloaddition of 1-thioaurones and 1-azaaurones. Chem Commun (Camb) 2021; 58:553-556. [PMID: 34908046 DOI: 10.1039/d1cc06357j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using 1-thioaurones and 1-azaaurones as electron-deficient oxa-dienes, an organocatalytic asymmetric aromatizing inverse electron-demand [4+2] cycloaddition with γ-deconjugated butenolides and azlactones was developed. A wide range of optically active benzothiophene-fused δ-lactones and indole-fused δ-lactones were obtained with desirable outcomes (up to 94% yield, >99 : 1 dr and 99% ee).
Collapse
Affiliation(s)
- Shu-Pei Yuan
- National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China. .,Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Hao Dou
- National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China. .,Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Qing Jia
- National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China. .,Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Qiang Zhao
- Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Yong You
- Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Zhen-Hua Wang
- Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Ming-Qiang Zhou
- National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Wei-Cheng Yuan
- National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China. .,Innovation Research Center of Chiral Drugs, Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| |
Collapse
|
7
|
Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
Collapse
Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| |
Collapse
|
8
|
Bilodeau DA, Margison KD, Serhan M, Pezacki JP. Bioorthogonal Reactions Utilizing Nitrones as Versatile Dipoles in Cycloaddition Reactions. Chem Rev 2021; 121:6699-6717. [PMID: 33464040 DOI: 10.1021/acs.chemrev.0c00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemical reactions have emerged as convenient and rapid methods for incorporating unnatural functionality into living systems. Different prototype reactions have been optimized for use in biological settings. Optimization of 3 + 2 dipolar cycloadditions involving nitrones has resulted in highly efficient reaction conditions for bioorthogonal chemistry. Through substitution at the nitrone carbon or nitrogen atom, stereoelectronic tuning of the reactivity of the dipole has assisted in optimizing reactivity. Nitrones have been shown to react rapidly with cyclooctynes with bimolecular rate constants approaching k2 = 102 M-1 s-1, which are among the fastest bioorthogonal reactions reported (McKay et al. Org. Biomol. Chem. 2012, 10, 3066-3070). Nitrones have also been shown to react with trans-cyclooctenes (TCO) in strain-promoted TCO-nitrone cycloadditions reactions. Copper catalyzed reactions involving alkynes and nitrones have also been optimized for applications in biology. This review provides a comprehensive accounting of the different bioorthogonal reactions that have been developed using nitrones as versatile reactants, and provides some recent examples of applications for probing biological systems.
Collapse
Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Mariam Serhan
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| |
Collapse
|
9
|
Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
Collapse
Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| |
Collapse
|
10
|
Sun J, Li J, Sun H, Li C, Wu H. Concise Synthesis of Functionalized Cyclobutene Analogues for Bioorthogonal Tetrazine Ligation. Molecules 2021; 26:E276. [PMID: 33429851 PMCID: PMC7827859 DOI: 10.3390/molecules26020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 02/05/2023] Open
Abstract
Novel bioorthogonal tools enable the development of new biomedical applications. Here we report the concise synthesis of a series of aryl-functionalized cyclobutene analogues using commercially available starting materials. Our study demonstrates that cyclobutene acts as a small, strained dienophile to generate stable substrates suitable for bioorthogonal tetrazine ligation.
Collapse
Affiliation(s)
- Jiayu Sun
- Department of Radiology, West China Hospital, Sichuan University, Guo Xue Xiang 37, Chengdu 610041, China; (J.S.); (J.L.); (H.S.)
| | - Jie Li
- Department of Radiology, West China Hospital, Sichuan University, Guo Xue Xiang 37, Chengdu 610041, China; (J.S.); (J.L.); (H.S.)
| | - Hongbao Sun
- Department of Radiology, West China Hospital, Sichuan University, Guo Xue Xiang 37, Chengdu 610041, China; (J.S.); (J.L.); (H.S.)
| | - Chunling Li
- Department of Neurosurgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Haoxing Wu
- Department of Radiology, West China Hospital, Sichuan University, Guo Xue Xiang 37, Chengdu 610041, China; (J.S.); (J.L.); (H.S.)
| |
Collapse
|
11
|
Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| |
Collapse
|
12
|
Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
Collapse
Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
13
|
Smeenk MLWJ, Agramunt J, Bonger KM. Recent developments in bioorthogonal chemistry and the orthogonality within. Curr Opin Chem Biol 2020; 60:79-88. [PMID: 33152604 DOI: 10.1016/j.cbpa.2020.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/09/2023]
Abstract
The emergence of bioorthogonal reactions has greatly advanced research in the fields of biology and medicine. They are not only valuable for labeling, tracking, and understanding biomolecules within living organisms, but also important for constructing advanced bioengineering and drug delivery systems. As the systems studied are increasingly complex, the simultaneous use of multiple bioorthogonal reactions is equally desirable. In this review, we take a look at the different bioorthogonal reactions that have recently been developed, the methods of cellular incorporation and the strategies to create orthogonality within the bioorthogonal landscape.
Collapse
Affiliation(s)
- Mike L W J Smeenk
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jordi Agramunt
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Kimberly M Bonger
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
| |
Collapse
|
14
|
Weterings J, Rijcken CJF, Veldhuis H, Meulemans T, Hadavi D, Timmers M, Honing M, Ippel H, Liskamp RMJ. TMTHSI, a superior 7-membered ring alkyne containing reagent for strain-promoted azide-alkyne cycloaddition reactions. Chem Sci 2020; 11:9011-9016. [PMID: 34123155 PMCID: PMC8163418 DOI: 10.1039/d0sc03477k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/08/2020] [Indexed: 12/25/2022] Open
Abstract
We describe the development of TMTH-SulfoxImine (TMTHSI) as a superior click reagent. This reagent combines a great reactivity, with small size and low hydrophobicity and compares outstandingly with existing click reagents. TMTHSI can be conveniently functionalized with a variety of linkers allowing attachment of a diversity of small molecules and (peptide, nucleic acid) biologics.
Collapse
Affiliation(s)
- Jimmy Weterings
- Cristal Therapeutics Oxfordlaan 55 6229 EV Maastricht The Netherlands
| | | | | | | | - Darya Hadavi
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | - Matt Timmers
- Cristal Therapeutics Oxfordlaan 55 6229 EV Maastricht The Netherlands
| | - Maarten Honing
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | - Hans Ippel
- Department of Biochemistry, CARIM, Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | - Rob M J Liskamp
- Cristal Therapeutics Oxfordlaan 55 6229 EV Maastricht The Netherlands
- Department of Biochemistry, CARIM, Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
- School of Chemistry, Joseph Black Building, University of Glasgow University Avenue Glasgow G12 8QQ UK
- Chemical Biology and Drug Discovery, Department of Pharmaceutics, Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| |
Collapse
|
15
|
Li Y, Fu H. Bioorthogonal Ligations and Cleavages in Chemical Biology. ChemistryOpen 2020; 9:835-853. [PMID: 32817809 PMCID: PMC7426781 DOI: 10.1002/open.202000128] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Bioorthogonal reactions including the bioorthogonal ligations and cleavages have become an active field of research in chemical biology, and they play important roles in chemical modification and functional regulation of biomolecules. This review summarizes the developments and applications of the representative bioorthogonal reactions including the Staudinger reactions, the metal-mediated bioorthogonal reactions, the strain-promoted cycloadditions, the inverse electron demand Diels-Alder reactions, the light-triggered bioorthogonal reactions, and the reactions of chloroquinoxalines and ortho-dithiophenols.
Collapse
Affiliation(s)
- Youshan Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
| | - Hua Fu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
| |
Collapse
|
16
|
Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.
Collapse
Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| |
Collapse
|
17
|
Wang L, Zhang J, Zhao J, Yu P, Wang S, Hu H, Wang R. Recent synthesis of functionalized s-tetrazines and their application in ligation reactions under physiological conditions: a concise overview. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1726009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Li Wang
- Huazhong University of Science and Technology Wuhan City, China
| | - Jingwen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhong Zhao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Yu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmei Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
18
|
Xiong H, Gu Y, Zhang S, Lu F, Ji Q, Liu L, Ma P, Yang G, Hou W, Xu H. Iridium-catalyzed C–H amidation of s-tetrazines. Chem Commun (Camb) 2020; 56:4692-4695. [DOI: 10.1039/d0cc01647k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Synthesis of ortho-amino substituted s-tetrazines by iridium-catalyzed C–H activation for bioconjugation and DNA-encoded library.
Collapse
Affiliation(s)
- Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
- School of Life Science and Technology
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
- School of Life Science and Technology
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| | - Wei Hou
- College of Pharmaceutical Science, and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology
- Hangzhou
- China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- China
| |
Collapse
|
19
|
Kamber DN, Nguyen SS, Liu F, Briggs JS, Shih HW, Row RD, Long ZG, Houk KN, Liang Y, Prescher JA. Isomeric triazines exhibit unique profiles of bioorthogonal reactivity. Chem Sci 2019; 10:9109-9114. [PMID: 31908754 PMCID: PMC6910137 DOI: 10.1039/c9sc01427f] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/11/2019] [Indexed: 11/29/2022] Open
Abstract
Expanding the scope of bioorthogonal reactivity requires access to new and mutually compatible reagents. We report here that 1,2,4-triazines can be tuned to exhibit unique reaction profiles with biocompatible strained alkenes and alkynes. Computational analyses were used to identify candidate orthogonal reactions, and the predictions were experimentally verified. Notably, 5-substituted triazines, unlike their 6-substituted counterparts, undergo rapid [4 + 2] cycloadditions with a sterically encumbered strained alkyne. This unique, sterically controlled reactivity was exploited for dual bioorthogonal labeling. Mutually orthogonal triazines and cycloaddition chemistries will enable new multi-component imaging applications.
Collapse
Affiliation(s)
- David N Kamber
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - Sean S Nguyen
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - Fang Liu
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA
- State Key Laboratory of Coordination Chemistry , Jiangsu Key Laboratory of Advanced Organic Materials , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China .
| | - Jeffrey S Briggs
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - Hui-Wen Shih
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - R David Row
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - Zane G Long
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry , Jiangsu Key Laboratory of Advanced Organic Materials , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China .
| | - Jennifer A Prescher
- Department of Chemistry , University of California , Irvine , California 92697 , USA .
- Department of Molecular Biology & Biochemistry , University of California , Irvine , California 92697 , USA
- Department of Pharmaceutical Sciences , University of California , Irvine , California 92697 , USA
| |
Collapse
|
20
|
Takayama Y, Kusamori K, Nishikawa M. Click Chemistry as a Tool for Cell Engineering and Drug Delivery. Molecules 2019; 24:molecules24010172. [PMID: 30621193 PMCID: PMC6337375 DOI: 10.3390/molecules24010172] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/14/2023] Open
Abstract
Click chemistry has great potential for use in binding between nucleic acids, lipids, proteins, and other molecules, and has been used in many research fields because of its beneficial characteristics, including high yield, high specificity, and simplicity. The recent development of copper-free and less cytotoxic click chemistry reactions has allowed for the application of click chemistry to the field of medicine. Moreover, metabolic glycoengineering allows for the direct modification of living cells with substrates for click chemistry either in vitro or in vivo. As such, click chemistry has become a powerful tool for cell transplantation and drug delivery. In this review, we describe some applications of click chemistry for cell engineering in cell transplantation and for drug delivery in the diagnosis and treatment of diseases.
Collapse
Affiliation(s)
- Yukiya Takayama
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Kosuke Kusamori
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Makiya Nishikawa
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| |
Collapse
|
21
|
Feskov IO, Chernykh AV, Kuchkovska YO, Daniliuc CG, Kondratov IS, Grygorenko OO. 3-((Hetera)cyclobutyl)azetidines, “Stretched” Analogues of Piperidine, Piperazine, and Morpholine: Advanced Building Blocks for Drug Discovery. J Org Chem 2018; 84:1363-1371. [DOI: 10.1021/acs.joc.8b02822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Illia O. Feskov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | | | - Yuliya O. Kuchkovska
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | - Ivan S. Kondratov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| |
Collapse
|
22
|
An P, Wu HY, Lewandowski TM, Lin Q. Hydrophilic azaspiroalkenes as robust bioorthogonal reporters. Chem Commun (Camb) 2018; 54:14005-14008. [PMID: 30483687 DOI: 10.1039/c8cc07432a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two hydrophilic spiroalkenes, azaspiro[2.3]hex-1-ene and azaspiro[2.4]hept-1-ene, were designed and synthesized. Compared to the previously reported spiro[2.3]hex-1-ene, the azaspiroalkenes exhibited greater water solubility and reactivity as dipolarophiles in the photoinduced tetrazole-alkene cycloaddition reaction. In addition, an azaspiro[2.3]hex-1-ene-containing amino acid, AsphK, was found to be charged by an engineered pyrrolysyl-tRNA synthetase into proteins via amber codon suppression in E. coli as well as in mammalian cells.
Collapse
Affiliation(s)
- Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
| | | | | | | |
Collapse
|
23
|
Didier D, Baumann AN, Eisold M. Unsaturated four-membered N-heterocycles: From synthesis to applications. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
24
|
Click chemistry in sphingolipid research. Chem Phys Lipids 2018; 215:71-83. [DOI: 10.1016/j.chemphyslip.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
|
25
|
Wu Y, Hu J, Sun C, Cao Y, Li Y, Xie F, Zeng T, Zhou B, Du J, Tang Y. Nature-Inspired Bioorthogonal Reaction: Development of β-Caryophyllene as a Chemical Reporter in Tetrazine Ligation. Bioconjug Chem 2018; 29:2287-2295. [PMID: 29851464 DOI: 10.1021/acs.bioconjchem.8b00283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A nature-inspired bioorthogonal reaction has been developed, hinging on an inverse-electron-demand Diels-Alder reaction of tetrazine with β-caryophyllene. Readily accessible from the cheap starting material through a scalable synthesis, the newly developed β-caryophyllene chemical reporter displays appealing reaction kinetics and excellent biocompatibility, which renders it applicable to both in vitro protein labeling and live cell imaging. Moreover, it can be used orthogonally to the strain-promoted alkyne-azide cycloaddition for dual protein labeling. This work not only provides an alternative to the existing bioorthogonal reaction toolbox, but also opens a new avenue to utilize naturally occurring scaffolds as bioorthogonal chemical reporters.
Collapse
Affiliation(s)
- Yunfei Wu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China.,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School , Sichuan University , Chengdu 610041 , China
| | - Jiulong Hu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China.,State Key Laboratory of Membrane Biology, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Chen Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yuanhe Li
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Fayang Xie
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Tianyin Zeng
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Bing Zhou
- State Key Laboratory of Membrane Biology, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China.,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School , Sichuan University , Chengdu 610041 , China
| |
Collapse
|
26
|
Qin LH, Hu W, Long YQ. Bioorthogonal chemistry: Optimization and application updates during 2013–2017. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
27
|
Engelsma SB, van den Ende TC, Overkleeft HS, van der Marel GA, Filippov DV. Reaction Rates of Various N
-Acylenamines in the Inverse-Electron-Demand Diels-Alder Reaction. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry; Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas C. van den Ende
- Leiden Institute of Chemistry; Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry; Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry; Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry; Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
28
|
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.
Collapse
Affiliation(s)
- M Xu
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT-84112, USA.
| | | | | | | |
Collapse
|
29
|
Baumann AN, Eisold M, Music A, Haas G, Kiw YM, Didier D. Methods for the Synthesis of Substituted Azetines. Org Lett 2017; 19:5681-5684. [DOI: 10.1021/acs.orglett.7b02847] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas N. Baumann
- Department
of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Michael Eisold
- Department
of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Arif Music
- Department
of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Geoffrey Haas
- Pierre and Marie Curie University, 4 place Jussieu, Paris 75252 Cedex 05, France
| | - Yu Min Kiw
- Ecole Nationale Supérieure de Chimie de Rennes, 11 allée de Beaulieu, Rennes 35708 Cedex 7, France
| | - Dorian Didier
- Department
of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| |
Collapse
|
30
|
Png ZM, Zeng H, Ye Q, Xu J. Inverse-Electron-Demand Diels-Alder Reactions: Principles and Applications. Chem Asian J 2017; 12:2142-2159. [DOI: 10.1002/asia.201700442] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/06/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Zhuang Mao Png
- Institute of Materials Research and Engineering; Agency for Science, Technology and Research (A*STAR); 2 Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Huining Zeng
- Institute of Materials Research and Engineering; Agency for Science, Technology and Research (A*STAR); 2 Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Qun Ye
- Institute of Materials Research and Engineering; Agency for Science, Technology and Research (A*STAR); 2 Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Jianwei Xu
- Institute of Materials Research and Engineering; Agency for Science, Technology and Research (A*STAR); 2 Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
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
| |
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
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
| |
Collapse
|
36
|
Freidel C, Kaloyanova S, Peneva K. Chemical tags for site-specific fluorescent labeling of biomolecules. Amino Acids 2016; 48:1357-72. [DOI: 10.1007/s00726-016-2204-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/18/2016] [Indexed: 01/24/2023]
|
37
|
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.
Collapse
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | | |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
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.
Collapse
|
40
|
Narayanam MK, Liang Y, Houk KN, Murphy JM. Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening. Chem Sci 2016; 7:1257-1261. [PMID: 29910881 PMCID: PMC4763938 DOI: 10.1039/c5sc03259h] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/11/2015] [Indexed: 12/22/2022] Open
Abstract
Density functional theory (DFT) calculations and experiments in tandem led to discoveries of new reactivities and selectivities involving bioorthogonal sydnone cycloadditions. Dibenzocyclooctyne derivatives (DIBAC and BARAC) were identified to be especially reactive dipolarophiles, which undergo the (3 + 2) cycloadditions with N-phenyl sydnone with the rate constant of up to 1.46 M-1 s-1. Most significantly, the sydnone-dibenzocyclooctyne and norbornene-tetrazine cycloadditions were predicted to be mutually orthogonal. This was validated experimentally and used for highly selective fluorescence labeling of two proteins simultaneously.
Collapse
Affiliation(s)
- Maruthi Kumar Narayanam
- Crump Institute for Molecular Imaging , David Geffen School of Medicine , University of California , Los Angeles , California 90095 , USA .
| | - Yong Liang
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
- Department of Chemical and Biomolecular Engineering , University of California , Los Angeles , California 90095 , USA
| | - Jennifer M Murphy
- Crump Institute for Molecular Imaging , David Geffen School of Medicine , University of California , Los Angeles , California 90095 , USA .
| |
Collapse
|
41
|
Wu H, Devaraj NK. Inverse Electron-Demand Diels-Alder Bioorthogonal Reactions. Top Curr Chem (Cham) 2015; 374:3. [PMID: 27572986 DOI: 10.1007/s41061-015-0005-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/01/2015] [Indexed: 12/13/2022]
Abstract
Bioorthogonal reactions have been widely used over the last 10 years for imaging, detection, diagnostics, drug delivery, and biomaterials. Tetrazine reactions are a recently developed class of inverse electron-demand Diels-Alder reactions used in bioorthogonal applications. Given their rapid tunable reaction rate and highly fluorogenic properties, tetrazine bioorthogonal reactions have come to be considered highly attractive tools for elucidating biological functions and messages in vitro and in vivo. In this chapter, we present recent advances expanding the scope of precursor reactivity and we introduce new biomedical methodology based on bioorthogonal tetrazine chemistry. We specifically highlight novel applications for different kinds of biomolecules, including nucleic acid, protein, antibodies, lipids, glycans, and bioactive small molecules, in the areas of imaging, detection, and diagnostics. We also briefly present other recently developed inverse electron-demand Diels-Alder bioorthogonal reactions. Lastly, we consider future directions and potential roles that inverse electron-demand Diels-Alder reactions may play in the fields of bioorthogonal and biomedical chemistry.
Collapse
Affiliation(s)
- Haoxing Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Urey Hall 4120, La Jolla, CA, 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Urey Hall 4120, La Jolla, CA, 92093, USA.
| |
Collapse
|
42
|
Patterson DM, Prescher JA. Orthogonal bioorthogonal chemistries. Curr Opin Chem Biol 2015; 28:141-9. [DOI: 10.1016/j.cbpa.2015.07.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/20/2015] [Accepted: 07/17/2015] [Indexed: 01/20/2023]
|
43
|
Yang K, Yang Z, Dang Q, Bai X. Hydrazones as Productive Dienophiles in the Inverse Electron Demand Diels-Alder Reactions of 1,3,5-Triazines. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
44
|
Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | | |
Collapse
|
45
|
Hörner S, Uth C, Avrutina O, Frauendorf H, Wiessler M, Kolmar H. Combination of inverse electron-demand Diels–Alder reaction with highly efficient oxime ligation expands the toolbox of site-selective peptide conjugations. Chem Commun (Camb) 2015; 51:11130-3. [DOI: 10.1039/c5cc03434e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modular bioconjugation strategy based on stepwise oxime ligation and inverse electron-demand Diels–Alder reaction.
Collapse
Affiliation(s)
- S. Hörner
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - C. Uth
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - O. Avrutina
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - H. Frauendorf
- Georg-August-Universität Göttingen
- Institut für Organische und Biomolekulare Chemie
- Zentrale Analytik/Massenspektrometrie
- 37077 Göttingen
- Germany
| | - M. Wiessler
- Deutsches Krebsforschungszentrum
- Medizinische Physik in der Radiologie
- 69120 Heidelberg
- Germany
| | - H. Kolmar
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| |
Collapse
|
46
|
Holstein JM, Stummer D, Rentmeister A. Enzymatic modification of 5'-capped RNA with a 4-vinylbenzyl group provides a platform for photoclick and inverse electron-demand Diels-Alder reaction. Chem Sci 2014; 6:1362-1369. [PMID: 29560223 PMCID: PMC5811123 DOI: 10.1039/c4sc03182b] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 11/26/2014] [Indexed: 01/20/2023] Open
Abstract
Enzymatic transfer of 4-vinylbenzyl to the mRNA 5′-cap gives access to the fluorogenic photoclick and the inverse electron-demand Diels–Alder reaction.
Chemo-enzymatic strategies provide a highly selective means to label different classes of biomolecules in vitro, but also in vivo. In the field of RNA, efficient labeling of eukaryotic mRNA with small organic reporter molecules would provide a way to detect endogenous mRNA and is therefore highly attractive. Although more and more bioorthogonal reactions are being reported, they can only be applied to chemo-enzymatic strategies if a suitable (i.e., click compatible) modification can be introduced into the RNA of interest. We report enzymatic site-specific transfer of a 4-vinylbenzyl group to the 5′-cap typical of eukaryotic mRNAs. The 4-vinylbenzyl group gives access to mRNA labeling using the inverse electron-demand Diels–Alder reaction, which does not work with an enzymatically transferred allyl group. The 4-vinylbenzyl-modified 5′-cap can also be converted in a photoclick reaction generating a “turn-on” fluorophore. Both click reactions are bioorthogonal and the two step approach also works in eukaryotic cell lysate. Enzymatic transfer of the 4-vinylbenzyl group addresses the lack of flexibility often attributed to biotransformations and thus advances the potential of chemo-enzymatic approaches for labeling.
Collapse
Affiliation(s)
- Josephin Marie Holstein
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany .
| | - Daniela Stummer
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany . .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM) , University of Muenster , 48149 Muenster , Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany . .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM) , University of Muenster , 48149 Muenster , Germany
| |
Collapse
|
47
|
Späte AK, Schart VF, Schöllkopf S, Niederwieser A, Wittmann V. Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering. Chemistry 2014; 20:16502-8. [DOI: 10.1002/chem.201404716] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Indexed: 11/07/2022]
|
48
|
McKay CS, Finn MG. Click chemistry in complex mixtures: bioorthogonal bioconjugation. CHEMISTRY & BIOLOGY 2014; 21:1075-101. [PMID: 25237856 PMCID: PMC4331201 DOI: 10.1016/j.chembiol.2014.09.002] [Citation(s) in RCA: 551] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/18/2023]
Abstract
The selective chemical modification of biological molecules drives a good portion of modern drug development and fundamental biological research. While a few early examples of reactions that engage amine and thiol groups on proteins helped establish the value of such processes, the development of reactions that avoid most biological molecules so as to achieve selectivity in desired bond-forming events has revolutionized the field. We provide an update on recent developments in bioorthogonal chemistry that highlights key advances in reaction rates, biocompatibility, and applications. While not exhaustive, we hope this summary allows the reader to appreciate the rich continuing development of good chemistry that operates in the biological setting.
Collapse
Affiliation(s)
- Craig S McKay
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M G Finn
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| |
Collapse
|
49
|
Liu F, Liang Y, Houk KN. Theoretical elucidation of the origins of substituent and strain effects on the rates of Diels-Alder reactions of 1,2,4,5-tetrazines. J Am Chem Soc 2014; 136:11483-93. [PMID: 25041719 DOI: 10.1021/ja505569a] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Diels-Alder reactions of seven 1,2,4,5-tetrazines with unstrained and strained alkenes and alkynes were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The higher reactivities of alkenes compared to alkynes in the Diels-Alder reactions with tetrazines arise from the differences in both interaction and distortion energies. Alkenes have HOMO energies higher than those of alkynes and therefore stronger interaction energies in inverse-electron-demand Diels-Alder reactions with tetrazines. We have also found that the energies to distort alkenes into the Diels-Alder transition-state geometries are smaller than for alkynes in these reactions. The strained dienophiles, trans-cyclooctene and cyclooctyne, are much more reactive than unstrained trans-2-butene and 2-butyne, because they are predistorted toward the Diels-Alder transition structures. The reactivities of substituted tetrazines correlate with the electron-withdrawing abilities of the substituents. Electron-withdrawing groups lower the LUMO+1 of tetrazines, resulting in stronger interactions with the HOMO of dienophiles. Moreover, electron-withdrawing substituents destabilize the tetrazines, and this leads to smaller distortion energies in the Diels-Alder transition states.
Collapse
Affiliation(s)
- Fang Liu
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
| | | | | |
Collapse
|
50
|
Lopez SA, Houk KN. Substituent Effects on Rates and Torquoselectivities of Electrocyclic Ring-Openings of N-Substituted 2-Azetines. J Org Chem 2014; 79:6189-95. [PMID: 24885772 DOI: 10.1021/jo500919s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Steven A. Lopez
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K. N. Houk
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| |
Collapse
|