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Knaack JIH, Meier C. Out of the Dark, into the Light: Metabolic Fluorescent Labeling of Nucleic Acids. ChemMedChem 2024; 19:e202400160. [PMID: 38712684 DOI: 10.1002/cmdc.202400160] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
This review outlines recent advances in live-cell imaging techniques for nucleic acids. We describe the evolution of these methods, particularly highlighting the development of metabolic labeling approaches compatible with living systems using fluorescence-based labeling.
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Affiliation(s)
- J Iven H Knaack
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Chris Meier
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
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2
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [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: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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3
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Huang W, Laughlin ST. Cell-selective bioorthogonal labeling. Cell Chem Biol 2024; 31:409-427. [PMID: 37837964 DOI: 10.1016/j.chembiol.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/25/2023] [Accepted: 09/19/2023] [Indexed: 10/16/2023]
Abstract
In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Scott T Laughlin
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA.
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4
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Zhang C, Wu J, Zhang Y, Huang Z. Click chemistry and natural products. Chin J Nat Med 2024; 22:97-99. [PMID: 38342571 DOI: 10.1016/s1875-5364(24)60557-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Indexed: 02/13/2024]
Affiliation(s)
- Chen Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Zhangjian Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Key Laboratory of Natural Medicines Active Components and Drug Release Technology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China.
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5
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Rieger L, Pfeuffer B, Wagenknecht HA. Metabolic labelling of DNA in cells by means of the "photoclick" reaction triggered by visible light. RSC Chem Biol 2023; 4:1037-1042. [PMID: 38033731 PMCID: PMC10685802 DOI: 10.1039/d3cb00150d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 12/02/2023] Open
Abstract
Two pyrene-tetrazole conjugates were synthesized as photoreactive chromophores that allow for the first time the combination of metabolic labelling of DNA in cells and subsequent bioorthogonal "photoclick" modification triggered by visible light. Two strained alkenes and three alkene-modified nucleosides were used as reactive counterparts and revealed no major differences in their "photoclick" reactivity. This is a significant advantage because it allows 5-vinyl-2'-deoxyuridine to be applied as the smallest possible alkene-modified nucleoside for metabolic labelling of DNA in cells. Both pyrene-tetrazole conjugates show fluorogenicity during the "photoclick" reactions, which is a second advantage for cellular imaging. Living HeLa cells were incubated with 5-vinyl-2'-deoxyuridine for 48 h to ensure one cell division. After fixation, the newly synthesized genomic DNA was successfully labelled by irradiation with visible light at 405 nm and 450 nm. This method is an attractive tool for the visualization of genomic DNA in cells with full spatiotemporal control by the use of visible light as a reaction trigger.
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Affiliation(s)
- Lisa Rieger
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6 Karlsruhe 76131 Germany
| | - Bastian Pfeuffer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6 Karlsruhe 76131 Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6 Karlsruhe 76131 Germany
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6
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Kumar GS, Lin Q. Seeking Citius: Photochemical Access of Reactive Intermediates for Faster Bioorthogonal Reactions. Chembiochem 2022; 23:e202200175. [PMID: 35612501 PMCID: PMC9488641 DOI: 10.1002/cbic.202200175] [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: 03/29/2022] [Revised: 05/24/2022] [Indexed: 11/08/2022]
Abstract
Fast bioorthogonal reactions are sought after because of their superior performance in labeling low-abundance biomolecules in native cellular environments. An attractive strategy to increase reaction kinetics is to access the reactive intermediates through photochemical activation. To this end, significant progress was made in the last few years in harnessing two highly reactive intermediates-nitrile imine and tetrazine-generated through photoinduced ring rupture and catalytic photooxidation, respectively. The efficient capture of these reactive intermediates by their cognate reaction partners has enabled bioorthogonal fluorescent labeling of biomolecules in live cells.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
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7
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Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
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Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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8
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Melnykov KP, Voloshyna OV, Vashchenko BV, Demchuk OP, Hryshchuk OV, Grygorenko OO. 4,4‐Difluorospiro[2.2]pentan‐1‐yl – A Fluorinated Substituent to Expand the Synthetic and Medicinal Chemists’ Toolbox. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kostiantyn P. Melnykov
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | - Olena V. Voloshyna
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | - Bohdan V. Vashchenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | | | | | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
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9
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Xiong Q, Zheng T, Shen X, Li B, Fu J, Zhao X, Wang C, Yu Z. Expanding the functionality of proteins with genetically encoded dibenzo[ b, f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration. Chem Sci 2022; 13:3571-3581. [PMID: 35432856 PMCID: PMC8943893 DOI: 10.1039/d1sc05710c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair (PylRS/tRNACUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.
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Affiliation(s)
- Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Chunxia Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
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10
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Jemas A, Xie Y, Pigga JE, Caplan JL, am Ende CW, Fox JM. Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light. J Am Chem Soc 2022; 144:1647-1662. [PMID: 35072462 PMCID: PMC9364228 DOI: 10.1021/jacs.1c10390] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
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Affiliation(s)
- Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jessica E. Pigga
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L. Caplan
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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11
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Kumar GS, Racioppi S, Zurek E, Lin Q. Superfast Tetrazole-BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells. J Am Chem Soc 2022; 144:57-62. [PMID: 34964645 PMCID: PMC8982153 DOI: 10.1021/jacs.1c10354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principles computations provide vital insights into the origin of the tetrazole-BCN cycloaddition's superior kinetics compared to the tetrazole-spirohexene cycloaddition. The tetrazole-BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 s.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Stefano Racioppi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Eva Zurek
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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12
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Lewandowski TM, An P, Ramil CP, Fang M, Lin Q. Dual fluorescent labeling of GLP-1R in live cells via enzymatic tagging and bioorthogonal chemistry. RSC Chem Biol 2022; 3:702-706. [PMID: 35755189 PMCID: PMC9175107 DOI: 10.1039/d2cb00107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R. The resulting GLP-1R conformational biosensors permit a FRET-based analysis of the receptor subdomain movement in response to ligand stimulation in live cells. To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R.![]()
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Affiliation(s)
- Tracey M. Lewandowski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Carlo P. Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
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13
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Wang C, Zhang H, Zhang T, Zou X, Wang H, Rosenberger J, Vannam R, Trout WS, Grimm JB, Lavis LD, Thorpe C, Jia X, Li Z, Fox JM. Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts. J Am Chem Soc 2021; 143:10793-10803. [PMID: 34250803 PMCID: PMC8765119 DOI: 10.1021/jacs.1c05547] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of trans-cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by trans-cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and trans-cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.
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Affiliation(s)
- Chuanqi Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - He Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Tao Zhang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xiaoyu Zou
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Hui Wang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Julia Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Raghu Vannam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinqiao Jia
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
- Delaware Biotechnology Institute, Newark, Delaware 19711, USA
| | - Zibo Li
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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14
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Hu Y, Schomaker JM. Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions. Chembiochem 2021; 22:3254-3262. [PMID: 34261195 DOI: 10.1002/cbic.202100164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed 'mutually orthogonal'. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Jennifer M Schomaker
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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15
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Fairbanks BD, Macdougall LJ, Mavila S, Sinha J, Kirkpatrick BE, Anseth KS, Bowman CN. Photoclick Chemistry: A Bright Idea. Chem Rev 2021; 121:6915-6990. [PMID: 33835796 PMCID: PMC9883840 DOI: 10.1021/acs.chemrev.0c01212] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.
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Affiliation(s)
- Benjamin D Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Laura J Macdougall
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Sudheendran Mavila
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Jasmine Sinha
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Bruce E Kirkpatrick
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
- Medical Scientist Training Program, School of Medicine, University of Colorado, Aurora, Coorado 80045, United States
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, Boulder, Colorado 80303, United States
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16
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Abstract
The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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17
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Abstract
Click chemistry has been established rapidly as one of the most valuable methods for the chemical transformation of complex molecules. Due to the rapid rates, clean conversions to the products, and compatibility of the reagents and reaction conditions even in complex settings, it has found applications in many molecule-oriented disciplines. From the vast landscape of click reactions, approaches have emerged in the past decade centered around oxidative processes to generate in situ highly reactive synthons from dormant functionalities. These approaches have led to some of the fastest click reactions know to date. Here, we review the various methods that can be used for such oxidation-induced "one-pot" click chemistry for the transformation of small molecules, materials, and biomolecules. A comprehensive overview is provided of oxidation conditions that induce a click reaction, and oxidation conditions are orthogonal to other click reactions so that sequential "click-oxidation-click" derivatization of molecules can be performed in one pot. Our review of the relevant literature shows that this strategy is emerging as a powerful approach for the preparation of high-performance materials and the generation of complex biomolecules. As such, we expect that oxidation-induced "one-pot" click chemistry will widen in scope substantially in the forthcoming years.
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Affiliation(s)
- Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Floris van Delft
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,Synaffix BV, Industrielaan 63, 5349 AE, Oss, The Netherlands
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18
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Tian Y, Fang M, Lin Q. Intracellular bioorthogonal labeling of glucagon receptor via tetrazine ligation. Bioorg Med Chem 2021; 43:116256. [PMID: 34153838 DOI: 10.1016/j.bmc.2021.116256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/21/2023]
Abstract
The third intracellular loop (ICL3) in the cytosolic face of glucagon receptor (GCGR) experiences significant conformational transition during receptor activation. It thus offers an attractive site for the introduction of organic fluorophores in our efforts to construct fluorescence-based GPCR biosensors. Herein, we report our confocal microscopic study of intracellular fluorescent labeling of ICL3 using a bioorthogonal chemistry strategy. Our approach involves the site-specific introduction of a strained alkene amino acid into the ICL3 through genetic code expansion, followed by a highly specific inverse electron-demand Diels-Alder reaction with the fluorescent tetrazine probes. Among the three strained alkene amino acids examined, both SphK and 2'-aTCOK offered successful fluorescent labeling of GCGR ICL3 with the appropriate tetrazine probes. At the same time, 4'-TCOK gave high background fluorescence due to its intracellular retention. The fluorescent tetrazine probes were designed following a computational model for background-free intracellular fluorescent labeling; however, their performance varied significantly in live-cell imaging as the strong non-specific signals interfered with the specific ones. Among all GCGR ICL3 mutants bearing a strained alkene, the H339SphK/2'-aTCOK mutants provided the best reaction partners for the BODIPY-Tz1/4 reagents in the bioorthogonal labeling reactions. The results from this study highlight the challenges in identifying bioorthogonal reactant pairs suitable for intracellular labeling of low-abundance receptors in live-cell imaging studies.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States; Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States.
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19
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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.
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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
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20
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Fay R, Holland JP. Tuning Tetrazole Photochemistry for Protein Ligation and Molecular Imaging. Chemistry 2021; 27:4893-4897. [PMID: 33427351 DOI: 10.1002/chem.202100061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 02/01/2023]
Abstract
Photochemistry provides a wide range of alternative reagents that hold potential for use in bimolecular functionalisation of proteins. Here, we report the synthesis and characterisation of metal ion binding chelates derivatised with disubstituted tetrazoles for the photoradiochemical labelling of monoclonal antibodies (mAbs). The photophysical properties of tetrazoles featuring extended aromatic systems and auxochromic substituents to tune excitation toward longer wavelengths (365 and 395 nm) were studied. Two photoactivatable chelates based on desferrioxamine B (DFO) and the aza-macrocycle NODAGA were functionalised with a tetrazole and developed for protein labelling with 89 Zr, 64 Cu and 68 Ga radionuclides. DFO-tetrazole (1) was assessed by direct conjugation to formulated trastuzumab and subsequent radiolabelling with 89 Zr. Radiochemical studies and cellular-based binding assays demonstrated that the radiotracer remained stable in vitro retained high immunoreactivity. Positron emission tomography (PET) imaging and biodistribution studies were used to measure the tumour specific uptake and pharmacokinetic profile in mice bearing SK-OV-3 xenografts. Experiments demonstrate that tetrazole-based photochemistry is a viable approach for the light-induced synthesis of PET radiotracers.
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Affiliation(s)
- Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jason P Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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21
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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
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22
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Jiang T, Laughlin ST. Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation. Methods Enzymol 2020; 641:1-34. [PMID: 32713519 DOI: 10.1016/bs.mie.2020.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.
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Affiliation(s)
- Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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23
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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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24
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Wang Y, Weng J, Wen X, Hu Y, Ye D. Recent advances in stimuli-responsive in situ self-assembly of small molecule probes for in vivo imaging of enzymatic activity. Biomater Sci 2020; 9:406-421. [PMID: 32627767 DOI: 10.1039/d0bm00895h] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Stimuli-responsive in situ self-assembly of small molecule probes into nanostructures has been promising for the construction of molecular probes for in vivo imaging. In the past few years, a number of intelligent molecular imaging probes with fluorescence, magnetic resonance imaging (MRI), positron electron tomography (PET) or photoacoustic imaging (PA) modality have been developed based on the in situ self-assembly strategy. In this minireview, we summarize the recent advances in the development of different modality imaging probes through controlling in situ self-assembly for in vivo imaging of enzymatic activity. This review starts from the brief introduction of two different chemical approaches amenable for in situ self-assembly, including (1) stimuli-mediated proteolysis and (2) stimuli-triggered biocompatible reaction. We then discuss their applications in the design of fluorescence, MRI, PET, PA, and bimodality imaging probes for in vivo imaging of different enzymes, such as caspase-3, furin, gelatinase and phosphatase. Finally, we discuss the current and prospective challenges in the stimuli-responsive in situ self-assembly strategy for in vivo imaging.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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25
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Abstract
In this method paper, we describe the protocols for selective labeling of GCGR, a member of the class B GPCR family regulating glucose homeostasis, in live cells. A two-step procedure is presented in which a strained alkene chemical reporter is inserted into any desired location within the GPCR in the first step, followed by a robust bioorthogonal ligation reaction with a fluorophore-conjugated tetrazine or tetrazole reagent in the second step. The amber codon suppression strategy was adopted for site-specific incorporation of the strained alkene reporter, either spirohexene or trans-cyclooctene, in HEK293T cells. Subsequently, the inverse electron-demand Diels-Alder reaction with an AF647-conjugated 3,6-di (2-pyridyl)-S-tetrazine (DpTz) was performed with the alkene-encoded GCGR on live-cell surface. Alternatively, a photo-induced cycloaddition with a Cy5-conjugated, sterically shielded tetrazole was carried out, giving rise to faster fluorescent labeling along with excellent selectivity. Owing to their robust reaction kinetics and excellent chemoselectivity, the bioorthogonal labeling protocols described here could be readily adapted to labeling any accessible protein targets, e.g., membrane proteins, in live cells.
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Affiliation(s)
- Srikanth Kumar Gangam
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, United States.
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26
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Affiliation(s)
- Matteo Zanda
- Loughborough University Centre for Sensing and Imaging Science School of Science Sir David Davies Building, Chemistry Department 113TU Loughborough United Kingdom
- C.N.R.‐SCITEC Via Mancinelli 7 20131 Milano Italy
| | - Raffaella Bucci
- Loughborough University Centre for Sensing and Imaging Science School of Science Sir David Davies Building, Chemistry Department 113TU Loughborough United Kingdom
| | - Nikki L. Sloan
- Loughborough University Centre for Sensing and Imaging Science School of Science Sir David Davies Building, Chemistry Department 113TU Loughborough United Kingdom
| | - Lydia Topping
- Loughborough University Centre for Sensing and Imaging Science School of Science Sir David Davies Building, Chemistry Department 113TU Loughborough United Kingdom
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27
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Li X, Wang Y, Yang H, Yin D, Tian Y. Design of Hydrazone-Modified 1,8-Naphthalimides as Fluorogenic Click Probes Based on Nitrile Imine-Alkyne Cycloaddition. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine; Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation; Institute of Materia Medica; Peking Union Medical College and Chinese Academy of Medical Sciences; 1 Xian Nong Tan Street 100050 Beijing China
| | - Yongcheng Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine; Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation; Institute of Materia Medica; Peking Union Medical College and Chinese Academy of Medical Sciences; 1 Xian Nong Tan Street 100050 Beijing China
| | - Hong Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine; Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation; Institute of Materia Medica; Peking Union Medical College and Chinese Academy of Medical Sciences; 1 Xian Nong Tan Street 100050 Beijing China
| | - Dali Yin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine; Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation; Institute of Materia Medica; Peking Union Medical College and Chinese Academy of Medical Sciences; 1 Xian Nong Tan Street 100050 Beijing China
| | - Yulin Tian
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine; Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation; Institute of Materia Medica; Peking Union Medical College and Chinese Academy of Medical Sciences; 1 Xian Nong Tan Street 100050 Beijing China
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28
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Gao J, Xiong Q, Wu X, Deng J, Zhang X, Zhao X, Deng P, Yu Z. Direct ring-strain loading for visible-light accelerated bioorthogonal ligation via diarylsydnone-dibenzo[b,f ][1,4,5]thiadiazepine photo-click reactions. Commun Chem 2020; 3:29. [PMID: 36703431 PMCID: PMC9814081 DOI: 10.1038/s42004-020-0273-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/07/2020] [Indexed: 01/29/2023] Open
Abstract
Ultra-fast and selective covalent-bond forming reactions with spatiotemporal controllability are foundational for developing a bioorthogonal approach with high manipulability. However, it is challenging to exploit a reporter functional group to achieve these requirements simultaneously. Here, 11H-Dibenzo[c,f][1,2]diazepine and a set of heterocyclic analogues are investigated for both their photo-switching natures and their ability to serve as dipolarophiles in photo-click reactions with diarylsydnone. Sulfur-containing dibenzothiadiazepine (DBTD) is discovered to be an excellent chemical reporter in cycloaddition with visible-light excitation for in-situ ring-strain loading via its (Z) → (E) photo-isomerization. The bioorthogonal utility of the DBTD tag in spatiotemporally controlled ligation for protein modifications on live cells is also demonstrated.
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Affiliation(s)
- Jingshuo Gao
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Qin Xiong
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Xueting Wu
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Jiajie Deng
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Xiaocui Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Xiaohu Zhao
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Pengchi Deng
- grid.13291.380000 0001 0807 1581Analytical and Testing Center, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
| | - Zhipeng Yu
- grid.13291.380000 0001 0807 1581Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, 610064 Chengdu, China
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29
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Jiang S, Wu X, Liu H, Deng J, Zhang X, Yao Z, Zheng Y, Li B, Yu Z. Ring‐Strain‐Promoted Ultrafast Diaryltetrazole–Alkyne Photoclick Reactions Triggered by Visible Light. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.201900290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shichao Jiang
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Xueting Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Hui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Jiajie Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Xiaocui Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Zhuojun Yao
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Yuanqin Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Bo Li
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationSichuan University 29 Wangjiang Road Chengdu 610064 China
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30
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Deng J, Wu X, Guo G, Zhao X, Yu Z. Photoisomerization-enhanced 1,3-dipolar cycloaddition of carbon-bridged octocyclic azobenzene with photo-released nitrile imine for peptide stapling and imaging in live cells. Org Biomol Chem 2020; 18:5602-5607. [DOI: 10.1039/d0ob01027h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel photo-click ligation reaction between nitrile imines and photo-switchable octocyclic azobenzenes was established to both tune the conformation of the NoxaB peptide and conjugate probes with enhanced efficacy in cell apoptosis.
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Affiliation(s)
- Jiajie Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Xueting Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Guiling Guo
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
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31
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Abstract
Bioorthogonal chemistry has offered an invaluable reactivity-based tool to chemical biology owing to its exquisite specificity in tagging a diverse set of biomolecules in their native environment. Despite tremendous progress in the field over the past decade, designing a suitable bioorthogonal chemical probe to investigate a given biological system remains a challenge. In this Perspective, we put forward a series of fitness factors that can be used to assess the performance of bioorthogonal chemical probes. The consideration of these criteria should encourage continuous innovation in bioorthogonal probe development as well as enhance the quality of biological data.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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32
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Livingstone K, Bertrand S, Mowat J, Jamieson C. Metal-free C-C bond formation via coupling of nitrile imines and boronic acids. Chem Sci 2019; 10:10412-10416. [PMID: 32110332 PMCID: PMC6988605 DOI: 10.1039/c9sc03032h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
The challenges of developing sustainable methods of carbon-carbon bond formation remains a topic of considerable importance in synthetic chemistry. Capitalizing on the highly reactive nature of the nitrile imine 1,3-dipole, we have developed a novel metal-free coupling of this species with aryl boronic acids. Photochemical generation of a nitrile imine intermediate and trapping with a palette of boronic acids enabled rapid and facile access to a broad library of more than 25 hydrazone derivatives in up to 92% yield, forming a carbon-carbon bond in a metal free fashion. This represents the first reported example of direct reaction between boronic acids and a 1,3-dipole.
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Affiliation(s)
- Keith Livingstone
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral St , Glasgow G1 1XL , UK .
| | - Sophie Bertrand
- GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage , Hertfordshire SG1 2NY , UK
| | - Jenna Mowat
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral St , Glasgow G1 1XL , UK .
| | - Craig Jamieson
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral St , Glasgow G1 1XL , UK .
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33
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Holland JP, Gut M, Klingler S, Fay R, Guillou A. Photochemical Reactions in the Synthesis of Protein-Drug Conjugates. Chemistry 2019; 26:33-48. [PMID: 31599057 DOI: 10.1002/chem.201904059] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 12/15/2022]
Abstract
The ability to modify biologically active molecules such as antibodies with drug molecules, fluorophores or radionuclides is crucial in drug discovery and target identification. Classic chemistry used for protein functionalisation relies almost exclusively on thermochemically mediated reactions. Our recent experiments have begun to explore the use of photochemistry to effect rapid and efficient protein functionalisation. This article introduces some of the principles and objectives of using photochemically activated reagents for protein ligation. The concept of simultaneous photoradiosynthesis of radiolabelled antibodies for use in molecular imaging is introduced as a working example. Notably, the goal of producing functionalised proteins in the absence of pre-association (non-covalent ligand-protein binding) introduces requirements that are distinct from the more regular use of photoactive groups in photoaffinity labelling. With this in mind, the chemistry of thirteen different classes of photoactivatable reagents that react through the formation of intermediate carbenes, electrophiles, dienes, or radicals, is assessed.
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Affiliation(s)
- Jason P Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Melanie Gut
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Klingler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amaury Guillou
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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34
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Suzuki I, Shimazu JY, Tsunoi S, Shibata I. Diastereoselective Synthesis of Spiro[2.3]hexanes from Methylenecyclopropane and Cyanoalkenes Catalyzed by a Tin-Ate Complex. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Itaru Suzuki
- Research Center for Environmental Preservation; Osaka University; 2-4, Yamadaoka, Suita 565-0871 Osaka Japan
| | - Jun-ya Shimazu
- Research Center for Environmental Preservation; Osaka University; 2-4, Yamadaoka, Suita 565-0871 Osaka Japan
- Division of Applied Chemistry; Graduate School of Engineering; Osaka University; 2-1, Yamadaoka, Suita 565-0871 Osaka Japan
| | - Shinji Tsunoi
- Research Center for Environmental Preservation; Osaka University; 2-4, Yamadaoka, Suita 565-0871 Osaka Japan
| | - Ikuya Shibata
- Research Center for Environmental Preservation; Osaka University; 2-4, Yamadaoka, Suita 565-0871 Osaka Japan
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35
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Kumar P, Zainul O, Camarda FM, Jiang T, Mannone JA, Huang W, Laughlin ST. Caged Cyclopropenes with Improved Tetrazine Ligation Kinetics. Org Lett 2019; 21:3721-3725. [DOI: 10.1021/acs.orglett.9b01177] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Pratik Kumar
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - Omar Zainul
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - Frank M. Camarda
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - John A. Mannone
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - Wei Huang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
| | - Scott T. Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11790, United States
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36
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF-Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019; 58:6987-6992. [PMID: 30888728 DOI: 10.1002/anie.201901760] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Indexed: 01/05/2023]
Abstract
As a typical bioorthogonal reaction, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) has been used for drug design and synthesis. However, for localized drug synthesis, it is important to be able to determine where the CuAAC reaction occurs in living cells. In this study, we constructed a heterogeneous copper catalyst on a metal-organic framework that could preferentially accumulate in the mitochondria of living cells. Our system enabled the localized synthesis of drugs through a site-specific CuAAC reaction in mitochondria with good biocompatibility. Importantly, the subcellular catalytic process for localized drug synthesis avoided the problems of the delivery and distribution of toxic molecules. In vivo tumor therapy experiments indicated that the localized synthesis of resveratrol-derived drugs led to greater antitumor efficacy and minimized side effects usually associated with drug delivery and distribution.
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Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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37
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF–Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901760] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
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38
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An P, Lin Q. Sterically shielded tetrazoles for a fluorogenic photoclick reaction: tuning cycloaddition rate and product fluorescence. Org Biomol Chem 2019; 16:5241-5244. [PMID: 29995029 DOI: 10.1039/c8ob01404c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A panel of sterically shielded tetrazoles with different N-aryl groups were synthesized and subsequently evaluated in the photoinduced tetrazole-alkene cycloaddition reaction. It was found that increase in the HOMO energy of the corresponding nitrile imines leads to a faster cycloaddition reaction along with a red shift in the fluorescence emission of the pyrazoline cycloadduct.
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Affiliation(s)
- Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
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39
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Abstract
The bioorthogonal reaction toolbox contains approximately two-dozen unique chemistries that permit selective tagging and probing of biomolecules. Over the past two decades, significant effort has been devoted to optimizing and discovering bioorthogonal reagents that are faster, fluorogenic, and orthogonal to the already existing bioorthogonal repertoire. Conversely, efforts to explore bioorthogonal reagents whose reactivity can be controlled in space and/or time are limited. The "activatable" bioorthogonal reagents that do exist are often unimodal, meaning that their reagent's activation method cannot be easily modified to enable activation with red-shifted wavelengths, enzymes, or metabolic-byproducts and ions like H2O2 or Fe3+. Here, we summarize the available activatable bioorthogonal reagents with a focus on our recent addition: modular caged cyclopropenes. We designed caged cyclopropenes to be unreactive to their bioorthogonal partner until they are activated through the removal of the cage by light, an enzyme, or another reaction partner. To accomplish this, their structure includes a nitrogen atom at the cyclopropene C3 position that is decorated with the desired caging group through a carbamate linkage. This 3-N cyclopropene system can allow control of cyclopropene reactivity using a multitude of already available photo- and enzyme-caging groups. Additionally, this cyclopropene scaffold can enable metabolic-byproduct or ion activation of bioorthogonal reactions.
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Affiliation(s)
- Pratik Kumar
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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40
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Zhang XY, Yang S, Wei Y, Shi M. Thermally-induced intramolecular [2 + 2] cycloaddition of acrylamide-tethered alkylidenecyclopropanes. Org Biomol Chem 2019; 16:6399-6404. [PMID: 30168557 DOI: 10.1039/c8ob01765d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An efficient and highly regio- and diastereoselective synthetic method to cyclobutane-containing spiro[2.3]hexane fused with six-membered hetero-cycles has been disclosed via a thermally-induced intramolecular [2 + 2] cycloaddition of acrylamide-tethered alkylidenecyclopropanes. The DFT calculations indicate that this intramolecular cycloaddition proceeds in a concerted manner and account for the product selectivity. These reactions exhibited excellent yields and functional group tolerance under metal free conditions.
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Affiliation(s)
- Xiao-Yu Zhang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Meilong Road No. 130, Shanghai, 200237, China
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41
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Kumar P, Jiang T, Li S, Zainul O, Laughlin ST. Caged cyclopropenes for controlling bioorthogonal reactivity. Org Biomol Chem 2019; 16:4081-4085. [PMID: 29790564 DOI: 10.1039/c8ob01076e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bioorthogonal ligations have been designed and optimized to provide new experimental avenues for understanding biological systems. Generally, these optimizations have focused on improving reaction rates and orthogonality to both biology and other members of the bioorthogonal reaction repertoire. Less well explored are reactions that permit control of bioorthogonal reactivity in space and time. Here we describe a strategy that enables modular control of the cyclopropene-tetrazine ligation. We developed 3-N-substituted spirocyclopropenes that are designed to be unreactive towards 1,2,4,5-tetrazines when bulky N-protecting groups sterically prohibit the tetrazine's approach, and reactive once the groups are removed. We describe the synthesis of 3-N spirocyclopropenes with an appended electron withdrawing group to promote stability. Modification of the cyclopropene 3-N with a bulky, light-cleavable caging group was effective at stifling its reaction with tetrazine, and the caged cyclopropene was resistant to reaction with biological nucleophiles. As expected, upon removal of the light-labile group, the 3-N cyclopropene reacted with tetrazine to form the expected ligation product both in solution and on a tetrazine-modified protein. This reactivity caging strategy leverages the popular carbamate protecting group linkage, enabling the use of diverse caging groups to tailor the reaction's activation modality for specific applications.
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Affiliation(s)
- Pratik Kumar
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
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42
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Yao Z, Wu X, Zhang X, Xiong Q, Jiang S, Yu Z. Synthesis and evaluation of photo-activatable β-diarylsydnone-l-alanines for fluorogenic photo-click cyclization of peptides. Org Biomol Chem 2019; 17:6777-6781. [DOI: 10.1039/c9ob00898e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
β-Diarylsydnone-l-alanines were designed and introduced into peptides allowing photo-cyclization only in phosphate containing buffer with concomitant fluorescence generation in live cells.
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Affiliation(s)
- Zhuojun Yao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Xueting Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Xiaocui Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Shichao Jiang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu 610064
- P. R. China
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43
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Lin AE, Lin Q. Rapid Identification of Functional Pyrrolysyl-tRNA Synthetases via Fluorescence-Activated Cell Sorting. Int J Mol Sci 2018; 20:ijms20010029. [PMID: 30577609 PMCID: PMC6337664 DOI: 10.3390/ijms20010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023] Open
Abstract
The orthogonal pyrrolysyl-tRNA synthetase/tRNACUA pair and their variants have provided powerful tools for expanding the genetic code to allow for engineering of proteins with augmented structure and function not present in Nature. To expedite the discovery of novel pyrrolysyl-tRNA synthetase (PylRS) variants that can charge non-natural amino acids into proteins site-specifically, herein we report a streamlined protocol for rapid construction of the pyrrolysyl-tRNA synthetase library, selection of the functional PylRS mutants using fluorescence-activated cell sorting, and subsequent validation of the selected PylRS mutants through direct expression of the fluorescent protein reporter using a single bacterial strain. We expect that this protocol should be generally applicable to rapid identification of the functional PylRS mutants for charging a wide range of non-natural amino acids into proteins.
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Affiliation(s)
- Andrew E Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA.
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA.
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44
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Schart VF, Hassenrück J, Späte AK, Dold JEGA, Fahrner R, Wittmann V. Triple Orthogonal Labeling of Glycans by Applying Photoclick Chemistry. Chembiochem 2018; 20:166-171. [DOI: 10.1002/cbic.201800740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Verena F. Schart
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Jessica Hassenrück
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Anne-Katrin Späte
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Jeremias E. G. A. Dold
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Raphael Fahrner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
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45
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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.
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Affiliation(s)
- Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
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46
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Li J, Kong H, Huang L, Cheng B, Qin K, Zheng M, Yan Z, Zhang Y. Visible Light-Initiated Bioorthogonal Photoclick Cycloaddition. J Am Chem Soc 2018; 140:14542-14546. [DOI: 10.1021/jacs.8b08175] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hao Kong
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Lei Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ke Qin
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mengmeng Zheng
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zheng Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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47
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Zhang L, Zhang X, Yao Z, Jiang S, Deng J, Li B, Yu Z. Discovery of Fluorogenic Diarylsydnone-Alkene Photoligation: Conversion of ortho-Dual-Twisted Diarylsydnones into Planar Pyrazolines. J Am Chem Soc 2018; 140:7390-7394. [DOI: 10.1021/jacs.8b02493] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Linmeng Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Xiaocui Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Zhuojun Yao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Shichao Jiang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Jiajie Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Bo Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, People’s Republic of China
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48
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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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49
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An P, Lewandowski TM, Erbay TG, Liu P, Lin Q. Sterically Shielded, Stabilized Nitrile Imine for Rapid Bioorthogonal Protein Labeling in Live Cells. J Am Chem Soc 2018; 140:4860-4868. [PMID: 29565582 DOI: 10.1021/jacs.8b00126] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In pursuit of fast bioorthogonal reactions, reactive moieties have been increasingly employed for selective labeling of biomolecules in living systems, posing a challenge in attaining reactivity without sacrificing selectivity. To address this challenge, here we report a bioinspired strategy in which molecular shape controls the selectivity of a transient, highly reactive nitrile imine dipole. By tuning the shape of structural pendants attached to the ortho position of the N-aryl ring of diaryltetrazoles-precursors of nitrile imines, we discovered a sterically shielded nitrile imine that favors the 1,3-dipolar cycloaddition over the competing nucleophilic addition. The photogenerated nitrile imine exhibits an extraordinarily long half-life of 102 s in aqueous medium, owing to its unique molecular shape that hinders the approach of a nucleophile as shown by DFT calculations. The utility of this sterically shielded nitrile imine in rapid (∼1 min) bioorthogonal labeling of glucagon receptor in live mammalian cells was demonstrated.
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Affiliation(s)
- Peng An
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
| | - Tracey M Lewandowski
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
| | - Tuğçe G Erbay
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Peng Liu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Qing Lin
- Department of Chemistry , State University of New York at Buffalo , Buffalo , New York 14260-3000 , United States
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Mulks FF, Antoni PW, Rominger F, Hashmi ASK. Cyclopropenylgold(I) Complexes as Aurated Carbenoids or Quasi-Carbenes. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201701526] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Florian F. Mulks
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Patrick W. Antoni
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - A. Stephen K. Hashmi
- Organisch-Chemisches Institut; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Chemistry Department, Faculty of Science; King Abdulaziz University (KAU); Jeddah 21589 Saudi Arabia
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