1
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George T, Grant T, Munhoz IS, Do T, Masuda JD. Group 11 complexes of a bulky triazene ligand. Dalton Trans 2024; 53:13107-13118. [PMID: 39041247 DOI: 10.1039/d4dt01561d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
A new triazene ligand was prepared by the reaction of the bulky aryl azide, TerMesN3, (2,6-bis(2,4,6-trimethylphenyl)phenyl azide), with the bulky N-heterocyclic carbene (NHC), SIPr (N,N'-2,6-bis(diisopropylphenyl)-3,4-dihydroimidazol-2-ylidene). The steric bulk of these two groups leads to perpendicular bonding of the NHC-N3 plane and the aryl group which provides immense steric crowding around the triazene core. The corresponding π-conjugated triazene ligand was utilized as a neutral, monodentate ligand which results in monomeric Cu(I)Cl, Ag(I)OTf, and Au(I)Cl complexes. Instability of the π-conjugated triazene Au(I)Cl complex was observed, even under inert conditions. When dissolved and photolyzed in THF with workup in isopropanol, the compound decomposes forming [(SIPrNH)2Au(I)][Au(I)Cl2] a relatively stable compound to light, moisture, and water - alongside the formation of gold nanoparticles which were characterized using scanning electron microscopy with energy dispersive spectroscopy.
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Affiliation(s)
- Tanner George
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
| | - Tamika Grant
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
| | | | - Thai Do
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
| | - Jason D Masuda
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
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2
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Šlachtová V, Motornov V, Beier P, Vrabel M. Bioorthogonal Cycloadditions of C3-Trifluoromethylated 1,2,4-Triazines with trans-Cyclooctenes. Chemistry 2024; 30:e202400839. [PMID: 38739300 DOI: 10.1002/chem.202400839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/14/2024]
Abstract
1,2,4-triazines are a valuable class of heterodienes that can be employed in inverse electron-demand Diels-Alder reactions. However, their broader application in bioorthogonal chemistry is limited due to their low reactivity. This article focuses on 3-(trifluoromethyl)-1,2,4-triazines, which can be efficiently prepared in a one-pot reaction from NH-1,2,3-triazoles. These triazines are highly reactive in reactions with strained cyclooctenes, giving second-order rate constants as high as 230 M-1 s-1. Despite their high reactivity, the compounds remain sufficiently stable under biologically relevant conditions. We show that some of the compounds are fluorogenic, a property of potential use in bioimaging. In addition, we demonstrate the successful application of the triazines in labeling model biomolecules. Our work shows that the reactivity of 1,2,4-triazines can be enhanced by the 3-CF3-substitution, which we consider an important step toward the wider use of this promising class of reagents.
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Affiliation(s)
- Veronika Šlachtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Vladimir Motornov
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
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3
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Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 DOI: 10.1007/s41061-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
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Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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4
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Elantabli FM, Shehata MR, Makhlouf AA, Abdel-Rahman LH. Co(II), Ni(II), and Cu(II) complexes derived from 1,2,4-triazine: synthesis, characterization, anticancer activity, DFT, and molecular docking studies with a COVID-19 protein receptor. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2075742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fatma M. Elantabli
- Chemistry Department, Faculty of Science, Fayoum University, Fayoum, Egypt
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5
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Zhou H, Li Y, Wang S, Wang L, Wang R. Tracking of Nascent Deoxynucleic Acids Enable by Incorporation of Uridine Variant with 2 Prime Azidomethyl Tag and Click Chemistry. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Cao S, Tang T, Li J, He Z. Visible light-driven [3 + 3] annulation reaction of 2 H-azirines with Huisgen zwitterions and synthesis of 1,2,4-triazines. Org Chem Front 2022. [DOI: 10.1039/d2qo00564f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A visible light-driven [3 + 3] annulation reaction of 2H-azirines with Huisgen zwitterions is developed for the first time.
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Affiliation(s)
- Shixuan Cao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tong Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiatian Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhengjie He
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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7
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Zhang FG, Chen Z, Tang X, Ma JA. Triazines: Syntheses and Inverse Electron-demand Diels-Alder Reactions. Chem Rev 2021; 121:14555-14593. [PMID: 34586777 DOI: 10.1021/acs.chemrev.1c00611] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Triazines are an important class of six-membered aromatic heterocycles possessing three nitrogen atoms, resulting in three types of regio-isomers: 1,2,4-triazines (a-triazines), 1,2,3-triazines (v-triazines), and 1,3,5-triazines (s-triazines). Notably, the application of triazines as cyclic aza-dienes in inverse electron-demand Diels-Alder (IEDDA) cycloaddition reactions has been established as a unique and powerful method in N-heterocycle synthesis, natural product preparation, and bioorthogonal chemistry. In this review, we comprehensively summarize the advances in the construction of these triazines via annulation and ring-expansion reactions, especially emphasizing recent developments and challenges. The synthetic transformations of triazines are focused on IEDDA cycloaddition reactions, which have allowed access to a wide scope of heterocycles, including pyridines, carbolines, azepines, pyridazines, pyrazines, and pyrimidines. The utilization of triazine IEDDA reactions as key steps in natural product synthesis is also discussed. More importantly, a particular attention is paid on the bioorthogonal application of triazines in fast click ligation with various strained alkenes and alkynes, which opens a new opportunity for studying biomolecules in chemical biology.
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Affiliation(s)
- Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. China
| | - Zhen Chen
- College of Chemical Engineering, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, Jiangsu 210037, P. R. China
| | - Xiaodong Tang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. China
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8
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Krell K, Pfeuffer B, Rönicke F, Chinoy ZS, Favre C, Friscourt F, Wagenknecht HA. Fast and Efficient Postsynthetic DNA Labeling in Cells by Means of Strain-Promoted Sydnone-Alkyne Cycloadditions. Chemistry 2021; 27:16093-16097. [PMID: 34633713 PMCID: PMC9297951 DOI: 10.1002/chem.202103026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 12/16/2022]
Abstract
Sydnones are highly stable mesoionic 1,3‐dipoles that react with cyclooctynes through strain‐promoted sydnone‐alkyne cycloaddition (SPSAC). Although sydnones have been shown to be valuable bioorthogonal chemical reporters for the labeling of proteins and complex glycans, nucleic acids have not yet been tagged by SPSAC. Evaluation of SPSAC kinetics with model substrates showed fast reactions with cyclooctyne probes (up to k=0.59 M−1 s−1), and two different sydnones were effectively incorporated into both 2’‐deoxyuridines at position 5, and 7‐deaza‐2’‐deoxyadenosines at position 7. These modified nucleosides were synthetically incorporated into single‐stranded DNAs, which were successfully postsynthetically labeled with cyclooctyne probes both in vitro and in cells. These results show that sydnones are versatile bioorthogonal tags and have the premise to become essential tools for tracking DNA and potentially RNA in living cells.
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Affiliation(s)
- Katja Krell
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Bastian Pfeuffer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Zoeisha S Chinoy
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Camille Favre
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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9
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Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:molecules26195925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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10
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Govindarajan A, Gnanasambandam V. Toward Intracellular Bioconjugation Using Transition-Metal-Free Techniques. Bioconjug Chem 2021; 32:1431-1454. [PMID: 34197073 DOI: 10.1021/acs.bioconjchem.1c00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bioconjugation is the chemical strategy of covalent modification of biomolecules, using either an external reagent or other biomolecules. Since its inception in the twentieth century, the technique has grown by leaps and bounds, and has a variety of applications in chemical biology. However, it is yet to reach its full potential in the study of biochemical processes in live cells, mainly because the bioconjugation strategies conflict with cellular processes. This has mostly been overcome by using transition metal catalysts, but the presence of metal centers limit them to in vitro use, or to the cell surface. These hurdles can potentially be circumvented by using metal-free strategies. However, the very modifications that are necessary to make such metal-free reactions proceed effectively may impact their biocompatibility. This is because biological processes are easily perturbed and greatly depend on the prevailing inter- and intracellular environment. With this taken into consideration, this review analyzes the applicability of the transition-metal-free strategies reported in this decade to the study of biochemical processes in vivo.
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Affiliation(s)
- Aaditya Govindarajan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
| | - Vasuki Gnanasambandam
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
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11
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Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 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.
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Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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12
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Zhang F, Chen Z, Cheung CW, Ma J. Aryl Diazonium
Salt‐Triggered
Cyclization and Cycloaddition Reactions: Past, Present, and Future. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000270] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fa‐Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
| | - Zhen Chen
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
| | - Chi Wai Cheung
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
| | - Jun‐An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University Tianjin 300072 China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City Fuzhou 350207 Fujian China
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13
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Synthesis and photolysis of 3-tert-butyl-4-oxy(mercapto)-1,4-dihydropyrazolo[5,1-c][1,2,4]triazines. Russ Chem Bull 2020. [DOI: 10.1007/s11172-020-2825-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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15
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Kozhevnikov VN, Deary ME, Mantso T, Panayiotidis MI, Sims MT. Iridium(iii) complexes of 1,2,4-triazines as potential bioorthogonal reagents: metal coordination facilitates luminogenic reaction with strained cyclooctynes. Chem Commun (Camb) 2019; 55:14283-14286. [PMID: 31709444 DOI: 10.1039/c9cc06828g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this paper we describe unprecedented Ir(iii) complexes of 5-(2-pyridyl)-1,2,4-triazine and their reactivity towards the strained cyclooctyne BCN. The coordination of a 1,2,4-triazine ring to an iridium(iii) ion drastically increases the speed of the reaction, showing the second order rate constant of 8 M-1 s-1, the record value to date for a triazine-BCN reaction.
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Affiliation(s)
- Valery N Kozhevnikov
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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16
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Tu J, Svatunek D, Parvez S, Liu ACG, Levandowski BJ, Eckvahl HJ, Peterson RT, Houk KN, Franzini RM. Stable, Reactive, and Orthogonal Tetrazines: Dispersion Forces Promote the Cycloaddition with Isonitriles. Angew Chem Int Ed Engl 2019; 58:9043-9048. [PMID: 31062496 PMCID: PMC6615965 DOI: 10.1002/anie.201903877] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/25/2019] [Indexed: 12/11/2022]
Abstract
The isocyano group is a structurally compact bioorthogonal functional group that reacts with tetrazines under physiological conditions. Now it is shown that bulky tetrazine substituents accelerate this cycloaddition. Computational studies suggest that dispersion forces between the isocyano group and the tetrazine substituents in the transition state contribute to the atypical structure-activity relationship. Stable asymmetric tetrazines that react with isonitriles at rate constants as high as 57 L mol-1 s-1 were accessible by combining bulky and electron-withdrawing substituents. Sterically encumbered tetrazines react selectively with isonitriles in the presence of strained alkenes/alkynes, which allows for the orthogonal labeling of three proteins. The established principles will open new opportunities for developing tetrazine reactants with improved characteristics for diverse labeling and release applications with isonitriles.
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Affiliation(s)
- Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112 (USA)
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569 (USA)
| | - Saba Parvez
- Department of Pharmacology and Toxicology, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112 (USA)
| | - Albert C. G. Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569 (USA)
| | - Brian J. Levandowski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569 (USA)
| | - Hannah J. Eckvahl
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569 (USA)
| | - Randall T. Peterson
- Department of Pharmacology and Toxicology, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112 (USA)
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569 (USA)
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112 (USA)
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17
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Tu J, Svatunek D, Parvez S, Liu AC, Levandowski BJ, Eckvahl HJ, Peterson RT, Houk KN, Franzini RM. Stable, Reactive, and Orthogonal Tetrazines: Dispersion Forces Promote the Cycloaddition with Isonitriles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Julian Tu
- Department of Medicinal ChemistryUniversity of Utah 30 S 2000 E Salt Lake City UT 84112 USA
| | - Dennis Svatunek
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles Los Angeles CA 90095-1569 USA
| | - Saba Parvez
- Department of Pharmacology and ToxicologyUniversity of Utah 30 S 2000 E Salt Lake City UT 84112 USA
| | - Albert C. Liu
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles Los Angeles CA 90095-1569 USA
| | - Brian J. Levandowski
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles Los Angeles CA 90095-1569 USA
| | - Hannah J. Eckvahl
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles Los Angeles CA 90095-1569 USA
| | - Randall T. Peterson
- Department of Pharmacology and ToxicologyUniversity of Utah 30 S 2000 E Salt Lake City UT 84112 USA
| | - Kendall N. Houk
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles Los Angeles CA 90095-1569 USA
| | - Raphael M. Franzini
- Department of Medicinal ChemistryUniversity of Utah 30 S 2000 E Salt Lake City UT 84112 USA
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18
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Reisacher U, Groitl B, Strasser R, Cserép GB, Kele P, Wagenknecht HA. Triazine-Modified 7-Deaza-2'-deoxyadenosines: Better Suited for Bioorthogonal Labeling of DNA by PCR than 2'-Deoxyuridines. Bioconjug Chem 2019; 30:1773-1780. [PMID: 31117344 DOI: 10.1021/acs.bioconjchem.9b00295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
6-Ethynyl-1,2,4-triazine is a small bioorthogonally reactive group we applied for fluorescent labeling of oligonucleotides by Diels-Alder reactions with inverse electron demand. We synthetically attached this functional group to the 7-position of 7-deaza-2'-deoxyadenosine triphosphate and to the 5-position of 2'-deoxyuridine triphosphate. Both modified nucleotide triphosphates were used in comparison for primer extension experiments (PEX) and PCR amplification to finally yield multilabeled oligonucleotides by the postsynthetic reaction with a highly reactive bicyclo[6.1.0]nonyne-rhodamine conjugate. These experiments show that 6-ethynyl-1,2,4-triazine is much better tolerated by the DNA polymerase when attached to the 7-position of 7-deaza-2'-deoxyadenosine in comparison to the attachment at the 5-position of 2'-deoxyuridine. This became evident both by PAGE analysis of the PCR products and real-time kinetic observation of DNA polymerase activity during primer extension using switchSENSE. Generally, our results imply that bioorthogonal labeling strategies are better suited for 7-deaza-2'-adenosines than conventional and available 2'-deoxyuridines.
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Affiliation(s)
- Ulrike Reisacher
- Karlsruhe Institute of Technology , Institute of Organic Chemistry , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Bastian Groitl
- Dynamic Biosensors GmbH, Lochhamer Straße 15 , 82152 Martinsried , Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH, Lochhamer Straße 15 , 82152 Martinsried , Germany
| | - Gergely B Cserép
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , 1117 Budapest , Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , 1117 Budapest , Hungary
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology , Institute of Organic Chemistry , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
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19
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Baalmann M, Ziegler MJ, Werther P, Wilhelm J, Wombacher R. Enzymatic and Site-Specific Ligation of Minimal-Size Tetrazines and Triazines to Proteins for Bioconjugation and Live-Cell Imaging. Bioconjug Chem 2019; 30:1405-1414. [PMID: 30883100 DOI: 10.1021/acs.bioconjchem.9b00157] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Diels-Alder reactions with inverse electron demand (DAinv) have emerged as an indispensable tool for bioorthogonal labeling and the manipulation of biomolecules. In this context, reactions between tetrazines and strained dienophiles have received attention because of high reaction rates. Current methods for the DAinv-mediated functionalization of proteins suffer from slow reactivity, impaired stability, isomerization, or elimination of the incorporated strained dienophiles. We report here a versatile platform for the posttranslational, highly selective, and quantitative modification of proteins with stable dienes. New synthetic access to minimal size tetrazine and triazine derivatives enabled us to synthesize tailored diene substrates for the lipoic acid protein ligase A (LplA) from Escherichia coli, which we employ for the rapid, mild, and quantitative bioconjugation of proteins by DAinv. The presented method benefits from the minimal tag size for LplA recognition and can be applied to proteins from any source organism. We demonstrate its broad suitability by site-specific in vitro protein labeling and live cell labeling for fluorescence microscopy. With this work we expand the scope of DAinv bioorthogonal chemistry for site-specific protein labeling, providing additional experimental flexibility for preparing well-defined bioconjugates and addressing biological questions in complex biological environments.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Jonas Wilhelm
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
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20
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Chen Z, Ren N, Ma X, Nie J, Zhang FG, Ma JA. Silver-Catalyzed [3 + 3] Dipolar Cycloaddition of Trifluorodiazoethane and Glycine Imines: Access to Highly Functionalized Trifluoromethyl-Substituted Triazines and Pyridines. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00846] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhen Chen
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Nan Ren
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaoxiao Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Jing Nie
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
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21
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Reisacher U, Ploschik D, Rönicke F, Cserép GB, Kele P, Wagenknecht HA. Copper-free dual labeling of DNA by triazines and cyclopropenes as minimal orthogonal and bioorthogonal functions. Chem Sci 2019; 10:4032-4037. [PMID: 31015943 PMCID: PMC6450502 DOI: 10.1039/c8sc05588b] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
Two different and small functions for inverse electron demand Diels–Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2′-deoxyuridine, and the 1-methylcyclopropene to the 7-position of 7-deaza-2′-deoxyadenosine.
Two different and small functions for inverse electron demand Diels–Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2′-deoxyuridine triphosphate, and the 1-methylcyclopropene to the 7-position of 7-deaza-2′-deoxyadenosine triphosphate. These two modified nucleotides were sequence-selectively incorporated into oligonucleotides by DNA polymerases. These products were labeled by two different fluorescent dyes using postsynthetic reactions that are not only bioorthogonal in general, but also mutually orthogonal.
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Affiliation(s)
- Ulrike Reisacher
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Damian Ploschik
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Franziska Rönicke
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Gergely B Cserép
- Chemical Biology Research Group , Institute of Organic Chemistry , Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , H-1117 Budapest , Hungary
| | - Péter Kele
- Chemical Biology Research Group , Institute of Organic Chemistry , Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , H-1117 Budapest , Hungary
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
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22
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Sarac I, Hollenstein M. Terminal Deoxynucleotidyl Transferase in the Synthesis and Modification of Nucleic Acids. Chembiochem 2019; 20:860-871. [PMID: 30451377 DOI: 10.1002/cbic.201800658] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Indexed: 12/26/2022]
Abstract
The terminal deoxynucleotidyl transferase (TdT) belongs to the X family of DNA polymerases. This unusual polymerase catalyzes the template-independent addition of random nucleotides on 3'-overhangs during V(D)J recombination. The biological function and intrinsic biochemical properties of the TdT have spurred the development of numerous oligonucleotide-based tools and methods, especially if combined with modified nucleoside triphosphates. Herein, we summarize the different applications stemming from the incorporation of modified nucleotides by the TdT. The structural, mechanistic, and biochemical properties of this polymerase are also discussed.
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Affiliation(s)
- Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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23
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Ploschik D, Rönicke F, Beike H, Strasser R, Wagenknecht HA. DNA Primer Extension with Cyclopropenylated 7-Deaza-2'-deoxyadenosine and Efficient Bioorthogonal Labeling in Vitro and in Living Cells. Chembiochem 2018; 19:1949-1953. [PMID: 29968274 DOI: 10.1002/cbic.201800354] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 01/06/2023]
Abstract
A deoxyadenosine triphosphate (dATP) analogue for DNA labeling was synthesized with the 1-methylcyclopropene (1MCP) group at the 7-position of 7-deaza-2'-deoxyadenosine and applied for primer extension experiments. The real-time kinetic data reveals that this 1MCP-modified dATP analogue is incorporated into DNA much faster than that of the similarly 1MCP-modified deoxyuridine triphosphate (dUTP) analogue. The postsynthetic fluorescent labeling of these oligonucleotides works efficiently according to PAGE analysis, and can be applied for immobilization of a functional antibody on a surface. Site-specific labeling at two different positions in DNA was achieved and the bioorthogonality of the postsynthetic fluorescent labeling was demonstrated in living HeLa cells.
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Affiliation(s)
- Damian Ploschik
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Hanna Beike
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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24
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Krömer M, Bártová K, Raindlová V, Hocek M. Synthesis of Dihydroxyalkynyl and Dihydroxyalkyl Nucleotides as Building Blocks or Precursors for Introduction of Diol or Aldehyde Groups to DNA for Bioconjugations. Chemistry 2018; 24:11890-11894. [PMID: 29790604 DOI: 10.1002/chem.201802282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 01/18/2023]
Abstract
(3,4-Dihydroxybut-1-ynyl)uracil, -cytosine and -7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs) were prepared by direct aqueous Sonogashira cross-coupling of halogenated dNTPs with dihydroxybut-1-yne and converted to 3,4-dihydroxybutyl dNTPs through catalytic hydrogenation. Sodium periodate oxidative cleavage of dihydroxybutyl-dUTP gave the desired aliphatic aldehyde-linked dUTP, whereas the oxidative cleavage of the corresponding deazaadenine dNTP gave a cyclic aminal. All dihydroxyalkyl or -alkynyl dNTPs and the formylethyl-dUTP were good substrates for DNA polymerases and were used for synthesis of diol- or aldehyde-linked DNA. The aldehyde linked DNA was used for the labelling or bioconjugations through hydrazone formation or reductive aminations.
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Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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25
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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]
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26
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Abstract
Chemical tools are transforming our understanding of biomolecules and living systems. Included in this group are bioorthogonal reagents-functional groups that are inert to most biological species, but can be selectively ligated with complementary probes, even in live cells and whole organisms. Applications of these tools have revealed fundamental new insights into biomolecule structure and function-information often beyond the reach of genetic approaches. In many cases, the knowledge gained from bioorthogonal probes has enabled new questions to be asked and innovative research to be pursued. Thus, the continued development and application of these tools promises to both refine our view of biological systems and facilitate new discoveries. Despite decades of achievements in bioorthogonal chemistry, limitations remain. Several reagents are too large or insufficiently stable for use in cellular environments. Many bioorthogonal groups also cross-react with one another, restricting them to singular tasks. In this Account, we describe our work to address some of the voids in the bioorthogonal toolbox. Our efforts to date have focused on small reagents with a high degree of tunability: cyclopropenes, triazines, and cyclopropenones. These motifs react selectively with complementary reagents, and their unique features are enabling new pursuits in biology. The Account is organized by common themes that emerged in our development of novel bioorthogonal reagents and reactions. First, natural product structures can serve as valuable starting points for probe design. Cyclopropene, triazine, and cyclopropenone motifs are all found in natural products, suggesting that they would be metabolically stable and compatible with a variety of living systems. Second, fine-tuning bioorthogonal reagents is essential for their successful translation to biological systems. Different applications demand different types of probes; thus, generating a collection of tools that span a continuum of reactivities and stabilities remains an important goal. We have used both computational analyses and mechanistic studies to guide the optimization of various cyclopropene and triazine probes. Along the way, we identified reagents that are chemoselective but best suited for in vitro work. Others are selective and robust enough for use in living organisms. The last section of this Account highlights the need for the continued pursuit of new reagents and reactions. Challenges exist when bioorthogonal chemistries must be used in concert, given that many exploit similar mechanisms and cannot be used simultaneously. Such limitations have precluded certain multicomponent labeling studies and other biological applications. We have relied on mechanistic and computational insights to identify mutually orthogonal sets of reactions, in addition to exploring unique genres of reactivity. The continued development of mechanistically distinct, biocompatible reactions will further diversify the bioorthogonal reaction portfolio for examining biomolecules.
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