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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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52
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Wu H, Alexander SC, Jin S, Devaraj NK. A Bioorthogonal Near-Infrared Fluorogenic Probe for mRNA Detection. J Am Chem Soc 2016; 138:11429-32. [PMID: 27510580 DOI: 10.1021/jacs.6b01625] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is significant interest in developing methods that visualize and detect RNA. Bioorthogonal template-driven tetrazine ligations could be a powerful route to visualizing nucleic acids in native cells, yet past work has been limited with respect to the diversity of fluorogens that can be activated via a tetrazine reaction. Herein we report a novel bioorthogonal tetrazine uncaging reaction that harnesses tetrazine reactivity to unmask vinyl ether caged fluorophores spanning the visible spectrum, including a near-infrared (NIR)-emitting cyanine dye. Vinyl ether caged fluorophores and tetrazine partners are conjugated to high-affinity antisense nucleic acid probes, which show highly selective fluorogenic reactivity when annealed to their respective target RNA sequences. A target sequence in the 3' untranslated region of an expressed mRNA was detected in live cells employing appropriate nucleic acid probes bearing a tetrazine-reactive NIR fluorogen. Given the expansion of tetrazine fluorogenic chemistry to NIR dyes, we believe highly selective proximity-induced fluorogenic tetrazine reactions could find broad uses in illuminating endogenous biomolecules in cells and tissues.
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Affiliation(s)
- Haoxing Wu
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Seth C Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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53
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Yang K, Zhou F, Kuang Z, Gao G, Driver TG, Song Q. Diborane-Mediated Deoxygenation of o-Nitrostyrenes To Form Indoles. Org Lett 2016; 18:4088-91. [PMID: 27499149 DOI: 10.1021/acs.orglett.6b01934] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A mild, transition metal-free, diborane-mediated deoxygenation of nitro groups was discovered that in situ generates nitrosoarene reactive intermediates. This new reactivity mode of B2pin2 was leveraged to construct indoles from o-nitrostyrenes through a reductive-cyclization reaction that exhibits a Hammett ρ-value of +0.97 relative to σpara values. Our new deoxygenation reaction is efficient, practical, and scaleable, enabling access to a broad range of indoles.
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Affiliation(s)
- Kai Yang
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University , 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Fei Zhou
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607-7061, United States
| | - Zhijie Kuang
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University , 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Guoliang Gao
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University , 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Tom G Driver
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University , 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China.,Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607-7061, United States
| | - Qiuling Song
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University , 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
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54
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Basava V, Yang L, Pradhan P, Lakshman MK. A novel bis(pinacolato)diboron-mediated N-O bond deoxygenative route to C6 benzotriazolyl purine nucleoside derivatives. Org Biomol Chem 2016; 14:7069-83. [PMID: 27377367 PMCID: PMC4981646 DOI: 10.1039/c6ob01170e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reaction of amide bonds in t-butyldimethylsilyl-protected inosine, 2'-deoxyinosine, guanosine, 2'-deoxyguanosine, and 2-phenylinosine with commercially available peptide-coupling agents (benzotriazol-1H-yloxy)tris(dimethylaminophosphonium) hexafluorophosphate (BOP), (6-chloro-benzotriazol-1H-yloxy)trispyrrolidinophosphonium hexafluorophosphate (PyClocK), and (7-azabenzotriazol-1H-yloxy)trispyrrolidinophosphonium hexafluorophospate (PyAOP) gave the corresponding O(6)-(benzotriazol-1-yl) nucleoside analogues containing a C-O-N bond. Upon exposure to bis(pinacolato)diboron and base, the O(6)-(benzotriazol-1-yl) and O(6)-(6-chlorobenzotriazol-1-yl) purine nucleoside derivatives obtained from BOP and PyClocK, respectively, underwent N-O bond reduction and C-N bond formation, leading to the corresponding C6 benzotriazolyl purine nucleoside analogues. In contrast, the 7-azabenzotriazolyloxy purine nucleoside derivatives did not undergo efficient deoxygenation, but gave unsymmetrical nucleoside dimers instead. This is consistent with a prior report on the slow reduction of 1-hydroxy-1H-4-aza and 1-hydroxy-1H-7-azabenzotriazoles. Because of the limited number of commercial benzotriazole-based peptide coupling agents, and to show the applicability of the method when such coupling agents are unavailable, 1-hydroxy-1H-5,6-dichlorobenzotriazole was synthesized. Using this compound, silyl-protected inosine and 2'-deoxyinosine were converted to the O(6)-(5,6-dichlorobenzotriazol-1-yl) derivatives via in situ amide activation with PyBroP. The O(6)-(5,6-dichlorobenzotriazol-1-yl) purine nucleosides so obtained also underwent smooth reduction to afford the corresponding C6 5,6-dichlorobenzotriazolyl purine nucleoside derivatives. A total of 13 examples were studied with successful reactions occurring in 11 cases (the azabenzotriazole derivatives, mentioned above, being the only unreactive entities). To understand whether these reactions are intra or intermolecular processes, a crossover experiment was conducted. The results of this experiment as well as those from reactions conducted in the absence of bis(pinacolato)diboron and in the presence of water indicate that detachment of the benzotriazoloxy group from the nucleoside likely occurs, followed by reduction, and reattachment of the ensuing benzotriazole, leading to products.
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Affiliation(s)
- Vikram Basava
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
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55
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Li J, Chen PR. Development and application of bond cleavage reactions in bioorthogonal chemistry. Nat Chem Biol 2016; 12:129-37. [PMID: 26881764 DOI: 10.1038/nchembio.2024] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/07/2016] [Indexed: 01/10/2023]
Abstract
Bioorthogonal chemical reactions are a thriving area of chemical research in recent years as an unprecedented technique to dissect native biological processes through chemistry-enabled strategies. However, current concepts of bioorthogonal chemistry have largely centered on 'bond formation' reactions between two mutually reactive bioorthogonal handles. Recently, in a reverse strategy, a collection of 'bond cleavage' reactions has emerged with excellent biocompatibility. These reactions have expanded our bioorthogonal chemistry repertoire, enabling an array of exciting new biological applications that range from the chemically controlled spatial and temporal activation of intracellular proteins and small-molecule drugs to the direct manipulation of intact cells under physiological conditions. Here we highlight the development and applications of these bioorthogonal cleavage reactions. Furthermore, we lay out challenges and propose future directions along this appealing avenue of research.
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Affiliation(s)
- Jie Li
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
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56
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Zhang G, Li J, Xie R, Fan X, Liu Y, Zheng S, Ge Y, Chen PR. Bioorthogonal Chemical Activation of Kinases in Living Systems. ACS CENTRAL SCIENCE 2016; 2:325-31. [PMID: 27280167 PMCID: PMC4882735 DOI: 10.1021/acscentsci.6b00024] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 05/06/2023]
Abstract
Selective manipulation of protein kinases under living conditions is highly desirable yet extremely challenging, particularly in a gain-of-function fashion. Here we employ our recently developed bioorthogonal cleavage reaction as a general strategy for intracellular activation of individual kinases. Site-specific incorporation of trans-cyclooctene-caged lysine in place of the conserved catalytic lysine, in conjunction with the cleavage partner dimethyl-tetrazine, allowed efficient lysine decaging with the kinase activity chemically rescued in living systems.
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Affiliation(s)
- Gong Zhang
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua
Center for Life Sciences, Beijing, China
| | - Jie Li
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Ran Xie
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Xinyuan Fan
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Yanjun Liu
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Siqi Zheng
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Yun Ge
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Peng R. Chen
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua
Center for Life Sciences, Beijing, China
- E-mail:
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