1
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Li J, Cheng M, Zhang H, Wang Y, Guo W, Zheng Y. A Tetrazine Amplification System for Visual Detection of Trace Analytes via Click-Release Reactions. Angew Chem Int Ed Engl 2024:e202414246. [PMID: 39623886 DOI: 10.1002/anie.202414246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 12/02/2024] [Indexed: 12/17/2024]
Abstract
Achieving visual detection of analytes at ultra-low concentrations in complex mixtures remains a persistent challenge. While sophisticated techniques offer single-molecule sensitivity, practical hurdles remain, necessitating tailored signal amplification systems for direct visual detection. In this study, we develop a strategy for the visualized detection of tetrazine through a "click-release-oxidation-cycle" (CROC) cascade amplification process. We systematically describe the construction and synthesis of this system, the kinetic process of click release, the kinetics of oxidation to tetrazine and its cascade amplification effect in trace amounts of tetrazine. This system is capable of amplifying the signal of tetrazine at a concentration as low as 2 nM by 105-fold, thereby providing a clearly visible purple signal. Finally, as proof of concept, we successfully apply this method to visually detect trace β-galactosidase (β-gal) and Pd2+.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Mingxin Cheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Hongbo Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Yichen Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Weiwei Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
- School of Science, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Yueqin Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, 211198, P. R. China
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2
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Song G, Yang Z, Huang Y, Bai H, Lv F, Wang S. Chemically engineered exogenous organic reactions in living cells for in situ fluorescence imaging and biomedical applications. J Mater Chem B 2024; 12:11852-11866. [PMID: 39485083 DOI: 10.1039/d4tb01925c] [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: 11/03/2024]
Abstract
The unique microenvironment within living cells, characterized by high glutathione levels, reactive oxygen species concentrations, and active enzymes, facilitates the execution of chemical reactions. Recent advances in organic chemistry and chemical biology have leveraged living cells as reactors for chemical synthesis. This review summarizes recent reports on key intracellular in situ synthesis processes, including the synthesis of near-infrared fluorescent dyes, intracellular oxidative cross-linking, bioorthogonal reactions, and intracellular polymerization reactions. These methods have been applied to fluorescence imaging, tumor treatment, and the enhancement of biological functions. Finally, we discuss the challenges and opportunities in the field of in situ intracellular synthesis. We aim to guide the design of chemical molecules for in situ synthesis, improving the efficiency and control of artificial reactions in living cells, and ultimately achieving cell factory-like exogenous biological synthesis, biological function enhancement, and biomedical applications.
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Affiliation(s)
- Gang Song
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwen Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Haotian Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Fu Y, Zhang X, Wu L, Wu M, James TD, Zhang R. Bioorthogonally activated probes for precise fluorescence imaging. Chem Soc Rev 2024. [PMID: 39555968 DOI: 10.1039/d3cs00883e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Over the past two decades, bioorthogonal chemistry has undergone a remarkable development, challenging traditional assumptions in biology and medicine. Recent advancements in the design of probes tailored for bioorthogonal applications have met the increasing demand for precise imaging, facilitating the exploration of complex biological systems. These state-of-the-art probes enable highly sensitive, low background, in situ imaging of biological species and events within live organisms, achieving resolutions comparable to the size of the biomolecule under investigation. This review provides a comprehensive examination of various categories of bioorthogonally activated in situ fluorescent labels. It highlights the intricate design and benefits of bioorthogonal chemistry for precise in situ imaging, while also discussing future prospects in this rapidly evolving field.
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Affiliation(s)
- Youxin Fu
- College of Science, Nanjing Forestry University, Nanjing, 210037, P. R. China
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Xing Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, P. R. China
| | - Luling Wu
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK.
| | - Miaomiao Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK.
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.
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4
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Cabanero DC, Rovis T. Low-energy photoredox catalysis. Nat Rev Chem 2024:10.1038/s41570-024-00663-6. [PMID: 39528711 DOI: 10.1038/s41570-024-00663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2024] [Indexed: 11/16/2024]
Abstract
With the advent of photoredox catalysis, new synthetic paradigms have been established with many novel transformations being achieved. Nevertheless, modern photoredox chemistry has several drawbacks, namely, deficiencies in reaction efficiency and scalability. Furthermore, wavelengths of light in excess of the energy required for a chemical reaction are often used. In this Review, we document recent developments of low-energy light-absorbing catalysts and their cognate photochemical methods, advantageously mitigating off-cycle photochemical reactivity of excited-state species in the reaction mixture and improving batch scalability of photochemical reactions. Finally, developments in red-light photoredox catalysis are leading the next-generation applications to polymer science and biochemistry-chemical biology, enabling catalytic reactions within media composites - including mammalian tissue - that are historically recalcitrant with blue-light photoredox catalysis.
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Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, USA.
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5
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Kao WS, Huang W, Zhang Y, Wen K, Meyer A, Escorihuela J, Laughlin ST. Redox-Activated Substrates for Enhancing Activatable Cyclopropene Bioorthogonal Reactions. Chembiochem 2024; 25:e202400304. [PMID: 39183177 DOI: 10.1002/cbic.202400304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/08/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Bioorthogonal chemistry has become a mainstay in chemical biology and is making inroads in the clinic with recent advances in protein targeting and drug release. Since the field's beginning, a major focus has been on designing bioorthogonal reagents with good selectivity, reactivity, and stability in complex biological environments. More recently, chemists have imbued reagents with new functionalities like click-and-release or light/enzyme-controllable reactivity. We have previously developed a controllable cyclopropene-based bioorthogonal ligation, which has excellent stability in physiological conditions and can be triggered to react with tetrazines by exposure to enzymes, biologically significant small molecules, or light spanning the visual spectrum. Here, to improve reactivity and gain a better understanding of this system, we screened diene reaction partners for the cyclopropene. We found that a cyclopropene-quinone pair is 26 times faster than reactions with 1,2,4,5-tetrazines. Additionally, we showed that the reaction of the cyclopropene-quinone pair can be activated by two orthogonal mechanisms: caging group removal on the cyclopropene and oxidation/reduction of the quinone. Finally, we demonstrated that this caged cyclopropene-quinone can be used as an imaging tool to label the membranes of fixed, cultured cells.
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Affiliation(s)
- Wei-Siang Kao
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
| | - Wei Huang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
| | - Yunlei Zhang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
| | - Kangqiao Wen
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
| | - Andrea Meyer
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, Avda. Vicente Andrés Estellés s/n, Burjassot, Valencia, 46100, Spain
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY-11794, USA
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6
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Huang W, Wen K, Laughlin ST, Escorihuela J. Unveiling the reactivity of 2 H-(thio)pyran-2-(thi)ones in cycloaddition reactions with strained alkynes through density functional theory studies. Org Biomol Chem 2024; 22:8285-8292. [PMID: 39302140 DOI: 10.1039/d4ob01263a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Over the past two decades, click chemistry transformations have revolutionized chemical and biological sciences. Among the different strain-promoted cycloadditions, the inverse electron demand Diels-Alder reaction (IEDDA) has been established as a benchmark reaction. We have theoretically investigated the IEDDA reaction of endo-bicyclo[6.1.0]nonyne (endo-BCN) with 2H-pyran-2-one, 2H-thiopyran-2-one, 2H-pyran-2-thione and 2H-thiopyran-2-thione. These 2H-(thio)pyran-2-(thi)ones have displayed different reactivity towards endo-BCN. Density functional theory (DFT) calculations show, in agreement with experiments, that endo-BCN reacts significantly faster with 2H-thiopyran-2-one compared to other 2H-(thio)pyran-2-(thi)one derivatives because of the lower distortion energy. Experimentally determined second-order rate constants for the reaction of a 2H-pyran-2-thione with different strained derivatives, including a 1-methylcyclopropene derivative and several cycloalkynes (exo-BCN, (1R,8S)-bicyclo[6.1.0]non-4-yne-9,9-diyl)dimethanol, dibenzocycylooctyne and a light activatable silacycloheptyne, were used to validate the computational investigations and shed light on this reaction.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Kangqiao Wen
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain.
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7
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Šlachtová V, Bellová S, Vrabel M. Synthesis of C 3-Substituted N1- tert-Butyl 1,2,4-Triazinium Salts via the Liebeskind-Srogl Reaction for Fluorogenic Labeling of Live Cells. J Org Chem 2024; 89:14634-14640. [PMID: 38224304 PMCID: PMC11494656 DOI: 10.1021/acs.joc.3c02454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024]
Abstract
We recently described the development and application of a new bioorthogonal conjugation, the triazinium ligation. To explore the wider application of this reaction, in this work, we introduce a general method for synthesizing C3-substituted triazinium salts based on the Liebeskind-Srogl cross-coupling reaction and catalytic thioether reduction. These methods enabled the synthesis of triazinium derivatives for investigating the effect of different substituents on the ligation kinetics and stability of the compounds under biologically relevant conditions. Finally, we demonstrate that the combination of a coumarin fluorophore attached to position C3 with a C5-(4-methoxyphenyl) substituent yields a fluorogenic triazinium probe suitable for no-wash, live-cell labeling. The developed methodology represents a promising synthetic approach to the late-stage modification of triazinium salts, potentially widening their applications in bioorthogonal reactions.
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Affiliation(s)
- Veronika Šlachtová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Simona Bellová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
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8
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Borade BR, Fang M, Lin Q. Synthesis of Hydrazonyl Sultones via Phosphine-Mediated Cyclodehydration of Vicinal Sulfo-acyl Hydrazides. Org Lett 2024; 26:8239-8243. [PMID: 39311752 DOI: 10.1021/acs.orglett.4c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
We report a phosphine-mediated cyclodehydration procedure for the facile synthesis of N-aryl/alkyl-substituted hydrazonyl sultones, a class of bioorthogonal reagents, from the readily prepared vicinal sulfo-acyl hydrazides in moderate to good yields. The aqueous stability and bioorthogonal reactivity of these hydrazonyl sultones toward bicyclo[6.1.0]non-4-yn-9-ylmethanol were investigated, revealing key structural requirements for hydrazonyl sultones to possess balanced stability and reactivity.
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Affiliation(s)
- Balasaheb R Borade
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Ming Fang
- 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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9
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Li Y, Su Y, Wang H, Xie Y, Wang X, Chang L, Jing Y, Zhang J, Ma JA, Jin H, Lou X, Peng Q, Liu T. Computation-Guided Discovery of Diazole Monosubstituted Tetrazines as Optimal Bioorthogonal Tools. J Am Chem Soc 2024; 146:26884-26896. [PMID: 39164893 DOI: 10.1021/jacs.4c07958] [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: 08/22/2024]
Abstract
Monosubstituted tetrazines are important bioorthogonal reactive tools due to their rapid ligation with trans-cyclooctene. However, their application is limited by the reactivity-stability paradox in biological environments. In this study, we demonstrated that steric effects are crucial in resolving this paradox through theoretical methods and developed a simple synthetic route to validate our computational findings, leading to the discovery of 1,3-azole-4-yl and 1,2-azole-3-yl monosubstituted tetrazines as superior bioorthogonal tools. These new tetrazines surpass previous tetrazines in terms of high reactivities and elevated stabilities. The most stable tetrazine exhibits a reasonable stability (71% remaining after 24 h incubation in cell culture medium) and an exceptionally high reactivity (k2 > 104 M-1 s-1 toward trans-cyclooctene). Due to its good stability in biological systems, a noncanonical amino acid containing such a tetrazine side chain was genetically encoded into proteins site-specifically via an expanded genetic code. The encoded protein can be efficiently labeled using cyclopropane-fused trans-cyclooctene dyes in living mammalian cells with an ultrafast reaction rate exceeding 107 M-1 s-1, making it one of the fastest protein labeling reactions reported to date. Additionally, we showed its superiority through in vivo reactions in living mice, achieving an efficient local anchoring of proteins. These tetrazines are expected to be optimal bioorthogonal reactive tools within living systems.
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Affiliation(s)
- Yuxuan Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yeyu Su
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yuanzhe Xie
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Liying Chang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yanbo Jing
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jiayi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jun-An Ma
- Department of Chemistry, Tianjin University, Tianjin 300072, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qian Peng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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10
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Fu Y, Simeth NA, Szymanski W, Feringa BL. Visible and near-infrared light-induced photoclick reactions. Nat Rev Chem 2024; 8:665-685. [PMID: 39112717 DOI: 10.1038/s41570-024-00633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2024] [Indexed: 09/11/2024]
Abstract
Photoclick reactions combine the advantages offered by light-driven processes, that is, non-invasive and high spatiotemporal control, with classical click chemistry and have found applications ranging from surface functionalization, polymer conjugation, photocrosslinking, protein labelling and bioimaging. Despite these advances, most photoclick reactions typically require near-ultraviolet (UV) and mid-UV light to proceed. UV light can trigger undesirable responses, including cellular apoptosis, and therefore, visible and near-infrared light-induced photoclick reaction systems are highly desirable. Shifting to a longer wavelength can also reduce degradation of the photoclick reagents and products. Several strategies have been used to induce a bathochromic shift in the wavelength of irradiation-initiating photoclick reactions. For instance, the extension of the conjugated π-system, triplet-triplet energy transfer, multi-photon excitation, upconversion technology, photocatalytic and photoinitiation approaches, and designs involving photocages have all been used to achieve this goal. Current design strategies, recent advances and the outlook for long wavelength-driven photoclick reactions are presented.
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Affiliation(s)
- Youxin Fu
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Nadja A Simeth
- Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Göttingen, Germany.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
- Department of Medicinal Chemistry, Photopharmacology and Imaging, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Groningen, The Netherlands.
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11
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Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [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: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
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Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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12
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Zhang Y, Liu S, Guo F, Qin S, Zhou N, Liu Z, Fan X, Chen PR. Bioorthogonal Quinone Methide Decaging Enables Live-Cell Quantification of Tumor-Specific Immune Interactions. J Am Chem Soc 2024; 146:15186-15197. [PMID: 38789930 DOI: 10.1021/jacs.4c02052] [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: 05/26/2024]
Abstract
Effective antitumor immunity hinges on the specific engagement between tumor and cytotoxic immune cells, especially cytotoxic T cells. Although investigating these intercellular interactions is crucial for characterizing immune responses and guiding immunotherapeutic applications, direct and quantitative detection of tumor-T cell interactions within a live-cell context remains challenging. We herein report a photocatalytic live-cell interaction labeling strategy (CAT-Cell) relying on the bioorthogonal decaging of quinone methide moieties for sensitive and selective investigation and quantification of tumor-T cell interactions. By developing quinone methide-derived probes optimized for capturing cell-cell interactions (CCIs), we demonstrated the capacity of CAT-Cell for detecting CCIs directed by various types of receptor-ligand pairs (e.g., CD40-CD40L, TCR-pMHC) and further quantified the strengths of tumor-T cell interactions that are crucial for evaluating the antitumor immune responses. We further applied CAT-Cell for ex vivo quantification of tumor-specific T cell interactions on splenocyte and solid tumor samples from mouse models. Finally, the broad compatibility and utility of CAT-Cell were demonstrated by integrating it with the antigen-specific targeting system as well as for tumor-natural killer cell interaction detection. By leveraging the bioorthogonal photocatalytic decaging chemistry on quinone methide, CAT-Cell provides a sensitive, tunable, universal, and noninvasive toolbox for unraveling and quantifying the crucial but delicate tumor-immune interactions under live-cell settings.
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Affiliation(s)
- Yan Zhang
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shibo Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fuhu Guo
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shan Qin
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Nan Zhou
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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13
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Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 PMCID: PMC11559631 DOI: 10.1007/s41061-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
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Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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14
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Işık M, Kısaçam MA. Readily Accessible and Brightly Fluorogenic BODIPY/NBD-Tetrazines via S NAr Reactions. J Org Chem 2024; 89:6513-6519. [PMID: 38598957 PMCID: PMC11077493 DOI: 10.1021/acs.joc.3c02864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024]
Abstract
We describe SNAr reactions of some commercial amino-tetrazines and halo-dyes, which give efficiently quenched BODIPY/NBD-tetrazines (ΦFl < 0.01) in high yields and, importantly, with high purities affordable via simple silica gel chromatography only. The dyes exhibit large Stokes shifts, moderate environmental sensitivity, and emission enhancements (up to 193-fold) upon Tz ligation with BCN─a strained dienophile. They successfully serve as labels for HSA protein premodified with BCN, resulting in bright blue-green emission upon ligation.
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Affiliation(s)
- Murat Işık
- Department
of Food Engineering, Bingöl University, 12000 Bingöl, Türkiye
| | - Mehmet Ali Kısaçam
- Department
of Biochemistry, Faculty of Veterinary Medicine, Mustafa Kemal University, 31060 Hatay, Türkiye
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15
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Sherstiuk A, Lledós A, Lönnecke P, Hernando J, Sebastián RM, Hey-Hawkins E. Dithienylethene-Based Photoswitchable Phosphines for the Palladium-Catalyzed Stille Coupling Reaction. Inorg Chem 2024; 63:7652-7664. [PMID: 38624066 PMCID: PMC11061837 DOI: 10.1021/acs.inorgchem.3c04423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Homogeneous transition metal catalysis is a constantly developing field in chemical sciences. A growing interest in this area is photoswitchable catalysis, which pursues in situ modulation of catalyst activity through noninvasive light irradiation. Phosphorus ligands are excellent targets to accomplish this goal by introducing photoswitchable moieties; however, only a limited number of examples have been reported so far. In this work, we have developed a series of palladium complexes capable of catalyzing the Stille coupling reaction that contain photoisomerizable phosphine ligands based on dithienylethene switches. Incorporation of electron-withdrawing substituents into these dithienylethene moieties allows variation of the electron density on the phosphorus atom of the ligands upon light irradiation, which in turn leads to a modulation of the catalytic properties of the formed complexes and their activity in a model Stille coupling reaction. These results are supported by theoretical computations, which show that the energy barriers for the rate-determining steps of the catalytic cycle decrease when the photoswitchable phosphine ligands are converted to their closed state.
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Affiliation(s)
- Anastasiia Sherstiuk
- Faculty
of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, D-04103 Leipzig, Germany
- Department
of Chemistry, Universitat Autònoma
de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Agustí Lledós
- Department
of Chemistry, Universitat Autònoma
de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Peter Lönnecke
- Faculty
of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, D-04103 Leipzig, Germany
| | - Jordi Hernando
- Department
of Chemistry, Universitat Autònoma
de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
| | - Rosa María Sebastián
- Department
of Chemistry, Universitat Autònoma
de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona, Spain
- Centro
de Innovación en Química Avanzada (ORFEO−CINQA), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra 08193, Barcelona,Spain
| | - Evamarie Hey-Hawkins
- Faculty
of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, D-04103 Leipzig, Germany
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16
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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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17
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Hillman A, Hyland SN, Wodzanowski KA, Moore DL, Ratna S, Jemas A, Sandles LMD, Chaya T, Ghosh A, Fox JM, Grimes CL. Minimalist Tetrazine N-Acetyl Muramic Acid Probes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion. J Am Chem Soc 2024; 146:6817-6829. [PMID: 38427023 PMCID: PMC10941766 DOI: 10.1021/jacs.3c13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
N-Acetyl muramic acid (NAM) probes containing alkyne or azide groups are commonly used to investigate aspects of cell wall synthesis because of their small size and ability to incorporate into bacterial peptidoglycan (PG). However, copper-catalyzed alkyne-azide cycloaddition (CuAAC) reactions are not compatible with live cells, and strain-promoted alkyne-azide cycloaddition (SPAAC) reaction rates are modest and, therefore, not as desirable for tracking the temporal alterations of bacterial cell growth, remodeling, and division. Alternatively, the tetrazine-trans-cyclooctene ligation (Tz-TCO), which is the fastest known bioorthogonal reaction and not cytotoxic, allows for rapid live-cell labeling of PG at biologically relevant time scales and concentrations. Previous work to increase reaction kinetics on the PG surface by using tetrazine probes was limited because of low incorporation of the probe. Described here are new approaches to construct a minimalist tetrazine (Tz)-NAM probe utilizing recent advancements in asymmetric tetrazine synthesis. This minimalist Tz-NAM probe was successfully incorporated into pathogenic and commensal bacterial PG where fixed and rapid live-cell, no-wash labeling was successful in both free bacterial cultures and in coculture with human macrophages. Overall, this probe allows for expeditious labeling of bacterial PG, thereby making it an exceptional tool for monitoring PG biosynthesis for the development of new antibiotic screens. The versatility and selectivity of this probe will allow for real-time interrogation of the interactions of bacterial pathogens in a human host and will serve a broader utility for studying glycans in multiple complex biological systems.
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Affiliation(s)
- Ashlyn
S. Hillman
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Stephen N. Hyland
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Kimberly A. Wodzanowski
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - DeVonte L. Moore
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Sushanta Ratna
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Andrew Jemas
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Liam-Michael D. Sandles
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Timothy Chaya
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Arit Ghosh
- Delaware
Biotechnology Institute, UDEL Flow Cytometry Core, University of Delaware, Newark, Delaware 19716, United States
| | - Joseph M. Fox
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Catherine L. Grimes
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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18
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Chang M, Dong Y, Xu H, Cruickshank-Taylor AB, Kozora JS, Behpour B, Wang W. Senolysis Enabled by Senescent Cell-Sensitive Bioorthogonal Tetrazine Ligation. Angew Chem Int Ed Engl 2024; 63:e202315425. [PMID: 38233359 PMCID: PMC11226389 DOI: 10.1002/anie.202315425] [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: 10/12/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Although the clearance of senescent cells has been proven to slow down the aging process and promote anti-cancer chemotherapy, the development of senolytics remains challenging. Herein, we report a senolytic strategy enabled by senescent cell-sensitive bioorthogonal tetrazine ligation. Our design is based on linking dihydrotetrazine (Tz) to a galactose (Gal) moiety that serves both as a recognition moiety for senescence-associated β-galactosidase and a caging group for the control of tetrazine activity. Gal-Tz enables efficient click-release of a fluorescent hemicyanine and doxorubicin from a trans-cyclooctene-caged prodrug to detect and eliminate senescent HeLa and A549 cells over non-senescent counterparts with a 16.44 senolytic index. Furthermore, we leverage the strategy for the selective activation and delivery of proteolysis-targeting chimeras (PROTACs) as senolytics. PROTAC prodrug TCO-ARV-771 can be selectively activated by Gal-Tz and delivered into senescent HeLa and A549 cells to induce the degradation of bromodomain-containing protein 4. Senolytic PROTACs may offer an efficient way for intervention on cell senescence thanks to their unique capacity to degrade target proteins in a sub-stoichiometric and catalytic fashion. The results of this study establish the bioorthogonal tetrazine ligation approach as a viable strategy for selective removal of senescent cells.
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Affiliation(s)
- Mengyang Chang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yue Dong
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Hang Xu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, 85721, USA
| | | | - Jacob S Kozora
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Baran Behpour
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, USA
| | - Wei Wang
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona Cancer Center, and BIO5 Institute, University of Arizona, Tucson, Arizona, 85721, USA
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19
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Yu H, Wang S, Fu Y, Wagner M, Weil T, Liu S, Zhao W, Zhong F, Wu Y. Spatiotemporally Controlled Photolabeling of Genetically Unmodified Proteins in Live Cells. Anal Chem 2024; 96:1932-1940. [PMID: 38241704 DOI: 10.1021/acs.analchem.3c04099] [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: 01/21/2024]
Abstract
Selective labeling of the protein of interest (POI) in genetically unmodified live cells is crucial for understanding protein functions and kinetics in their natural habitat. In particular, spatiotemporally controlled installation of the labels on a POI under light control without affecting their original activity is in high demand but is a tremendous challenge. Here, we describe a novel ligand-directed photoclick strategy for spatiotemporally controlled labeling of endogenous proteins in live cells. It was realized with a designer labeling reagent skillfully integrating the photochemistries of 2-nitrophenylpropyloxycarbonyl and 3-hydroxymethyl-2-naphthol with an affinity ligand. Highly electrophilic ortho-naphthoquinone methide was photochemically released and underwent a proximity coupling reaction with nucleophilic amino acid residues on the POI in live cells. With fluorescein as a marker, this photoclick strategy enables time-resolved labeling of carbonic anhydrase subtypes localized either on the cell membrane or in the cytoplasm and a discriminable visualization of their metabolic kinetics. Given the versatility underlined by facilely tethering other functional entities (e.g., biotin, a peptide short chain) via acylation or (in cell) Huisgen cycloaddition, this affinity-driven photoclick chemistry opens up enormous opportunities for discovering dynamic functions and mechanistic interrogation of endogenous proteins in live cells.
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Affiliation(s)
- Huaibin Yu
- School of Medicine and Health, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
- Zhengzhou Research Institute, Harbin Institute of Technology, Zhengzhou, Henan 450000, China
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Shuangshuang Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yu Fu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shaoqin Liu
- School of Medicine and Health, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
- Key Laboratory of Microsystems and Microstructures Manufacturing (Ministry of Education), Harbin Institute of Technology, Harbin 150001, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Fangrui Zhong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yuzhou Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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20
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Eddins AJ, Bednar RM, Jana S, Pung A, Mbengi L, Meyer K, Perona JJ, Cooley RB, Andrew Karplus P, Mehl RA. Truncation-Free Genetic Code Expansion with Tetrazine Amino Acids for Quantitative Protein Ligations. Bioconjug Chem 2023; 34:2243-2254. [PMID: 38047550 PMCID: PMC11641772 DOI: 10.1021/acs.bioconjchem.3c00380] [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] [Indexed: 12/05/2023]
Abstract
Quantitative labeling of biomolecules is necessary to advance areas of antibody-drug conjugation, super-resolution microscopy imaging of molecules in live cells, and determination of the stoichiometry of protein complexes. Bio-orthogonal labeling to genetically encodable noncanonical amino acids (ncAAs) offers an elegant solution; however, their suboptimal reactivity and stability hinder the utility of this method. Previously, we showed that encoding stable 1,2,4,5-tetrazine (Tet)-containing ncAAs enables rapid, complete conjugation, yet some expression conditions greatly limited the quantitative reactivity of the Tet-protein. Here, we demonstrate that reduction of on-protein Tet ncAAs impacts their reactivity, while the leading cause of the unreactive protein is near-cognate suppression (NCS) of UAG codons by endogenous aminoacylated tRNAs. To overcome incomplete conjugation due to NCS, we developed a more catalytically efficient tRNA synthetase and developed a series of new machinery plasmids harboring the aminoacyl tRNA synthetase/tRNA pair (aaRS/tRNA pair). These plasmids enable robust production of homogeneously reactive Tet-protein in truncation-free cell lines, eliminating the contamination caused by NCS and protein truncation. Furthermore, these plasmid systems utilize orthogonal synthetic origins, which render these machinery vectors compatible with any common expression system. Through developing these new machinery plasmids, we established that the aaRS/tRNA pair plasmid copy-number greatly affects the yields and quality of the protein produced. We then produced quantitatively reactive soluble Tet-Fabs, demonstrating the utility of this system for rapid, homogeneous conjugations of biomedically relevant proteins.
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Affiliation(s)
- Alex J. Eddins
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Riley M. Bednar
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Subhashis Jana
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Abigail Pung
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Lea Mbengi
- Portland State University, Department of Chemistry, Portland, OR 97207
| | - Kyle Meyer
- Portland State University, Department of Chemistry, Portland, OR 97207
| | - John J. Perona
- Portland State University, Department of Chemistry, Portland, OR 97207
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
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21
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Zhang H, Fang M, Lin Q. Photo-activatable Reagents for Bioorthogonal Ligation Reactions. Top Curr Chem (Cham) 2023; 382:1. [PMID: 38091203 DOI: 10.1007/s41061-023-00447-4] [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: 10/04/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
Light-induced bioorthogonal reactions offer spatiotemporal control over selective biomolecular labeling. This review covers the recent advances in the design of photo-activatable reagents for bioorthogonal conjugation reactions in living systems. These reagents are stable in the absence of light, but transformed into reactive species upon light illumination, which then undergo rapid ligation reactions. The light wavelength has been tuned from ultraviolet to near infrared to enable efficient photo-activation in reactions in deep tissues. The most prominent photo-activatable reagents are presented, including tetrazoles, tetrazines, 9,10-phenanthrenequinone, diarylsydnones, and others. A particular focus is on the strategies for improving reaction kinetics and biocompatibility accomplished through careful molecular engineering. The utilities of these photo-activatable reagents are illustrated through a broad range of biological applications, including in vivo protein labeling, positron emission tomography (PET) imaging, responsive hydrogels, and fluorescence microscopy. The further development and optimization of these biocompatible photo-activatable reagents should lead to new chemical biology strategies for studying biomolecular structure and function in living systems.
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Affiliation(s)
- Heyang Zhang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260, USA.
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22
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Hu F, Zhang C, Liu Z, Xie X, Zhao X, Luo Y, Fu J, Li B, Hu C, Su Z, Yu Z. Photoswitchable and long-lived seven-membered cyclic singlet diradicals for the bioorthogonal photoclick reaction. Chem Sci 2023; 14:13254-13264. [PMID: 38023496 PMCID: PMC10664533 DOI: 10.1039/d3sc03675h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Annularly 1,3-localized singlet diradicals are energetic and homolytic intermediates, but commonly too short-lived for widespread utilization. Herein, we describe a direct observation of a long-lived and seven-membered singlet diradical, oxepine-3,6-dione-2,7-diyl (OXPID), via spectroscopic experiments and also theoretical evidence from computational studies, which is generated via photo-induced ring-expansion of 2,3-diaryl-1,4-naphthoquinone epoxide (DNQO). The photo-generated OXPID reverts to the thermally stable σ-bonded DNQO with t1/2 in the μs level, thus constituting a novel class of T-type molecular photoswitches with high light-energy conversion efficiency (η = 7.8-33%). Meanwhile, the OXPID is equilibrated to a seven-membered cyclic 1,3-dipole as an electronic tautomer that can be captured by ring-strained dipolarophiles with an ultrafast cycloaddition rate (k2CA up to 109 M-1 s-1). The T-type photoswitchable DNQO is then exploited to be a highly selective and recyclable photoclick reagent, enabling spatiotemporal-resolved bioorthogonal ligation on living cell membranes via a tailored DNQO-Cy3 probe.
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Affiliation(s)
- Fuqiang Hu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Cefei Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhihao Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xinyu Xie
- 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
| | - Yanju Luo
- Analytical & Testing Center, 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
| | - 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
| | - Changwei Hu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhishan Su
- 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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23
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Stone DJ, Macias-Contreras M, Crist SM, Bucag CFT, Seo G, Zhu L. SNAP-tagging live cells via chelation-assisted copper-catalyzed azide-alkyne cycloaddition. Org Biomol Chem 2023; 21:7419-7436. [PMID: 37665276 DOI: 10.1039/d3ob01003a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
SNAP-tag is a single-turnover enzyme that has become a powerful tool, hence a popular choice, of targeted cellular protein labeling. Three SNAP-tag substrates that carry the copper-chelating 2-picolyl azide moiety are prepared, one of which has an unconventional 5-pyridylmethyl-substituted guanine structure, rather than the usual benzylguanine that is optimized to be accepted by SNAP-tag. All three substrates are effective in transferring a 2-picolyl azide moiety to SNAP-tag in live cells under conventional labeling conditions (30-minute incubation of cells with labeling reagents at 37 °C under 5% CO2). Live cells that are decorated with chelating azido groups on the extracellular side of membranes undergo copper-catalyzed azide-alkyne cycloaddition (CuAAC) with an ethynyl-functionalized fluorophore to accomplish membrane protein labeling by a fluorescent dye. The chelation-assisted CuAAC labeling step is rapid (<1 minute) with a relatively low dose of the copper catalyst (20 μM), and consequently exerts no ill effect on the labeled cells. A SNAP-tag substrate that carries a non-chelating azide moiety, on the other hand, fails to produce satisfactory labeling under the same constraints. The rapid, live cell-compatible SNAP-tag/chelation-assisted CuAAC two-step method expands the utility of SNAP-tag in protein labeling applications.
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Affiliation(s)
- Daniel J Stone
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Shaun M Crist
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Christelle F T Bucag
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Gwimoon Seo
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
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24
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Savastano M, López de la Torre MD, Pagliai M, Poggi G, Ridi F, Bazzicalupi C, Melguizo M, Bianchi A. Crystal engineering of high explosives through lone pair-π interactions: Insights for improving thermal safety. iScience 2023; 26:107330. [PMID: 37636051 PMCID: PMC10448033 DOI: 10.1016/j.isci.2023.107330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 08/29/2023] Open
Abstract
In this high-risk/high-reward study, we prepared complexes of a high explosive anion (picrate) with potentially explosive s-tetrazine-based ligands with the sole purpose of advancing the understanding of one of the weakest supramolecular forces: the lone pair-π interaction. This is a proof-of-concept study showing how lone pair-π contacts can be effectively used in crystal engineering, even of high explosives, and how the supramolecular architecture of the resulting crystalline phases influences their experimental thermokinetic properties. Herein we present XRD structures of 4 novel detonating compounds, all showcasing lone pair-π interactions, their thermal characterization (DSC, TGA), including the correlation of experimental thermokinetic parameters with crystal packing, and in silico explosion properties. This last aspect is relevant for improving the safety of high-energy materials.
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Affiliation(s)
- Matteo Savastano
- Department of Human Sciences and Quality of Life Promotion, University San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | | | - Marco Pagliai
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giovanna Poggi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Francesca Ridi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Manuel Melguizo
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071 Jaén, Spain
| | - Antonio Bianchi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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25
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Šlachtová V, Bellová S, La-Venia A, Galeta J, Dračínský M, Chalupský K, Dvořáková A, Mertlíková-Kaiserová H, Rukovanský P, Dzijak R, Vrabel M. Triazinium Ligation: Bioorthogonal Reaction of N1-Alkyl 1,2,4-Triazinium Salts. Angew Chem Int Ed Engl 2023; 62:e202306828. [PMID: 37436086 DOI: 10.1002/anie.202306828] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/13/2023]
Abstract
The development of reagents that can selectively react in complex biological media is an important challenge. Here we show that N1-alkylation of 1,2,4-triazines yields the corresponding triazinium salts, which are three orders of magnitude more reactive in reactions with strained alkynes than the parent 1,2,4-triazines. This powerful bioorthogonal ligation enables efficient modification of peptides and proteins. The positively charged N1-alkyl triazinium salts exhibit favorable cell permeability, which makes them superior for intracellular fluorescent labeling applications when compared to analogous 1,2,4,5-tetrazines. Due to their high reactivity, stability, synthetic accessibility and improved water solubility, the new ionic heterodienes represent a valuable addition to the repertoire of existing modern bioorthogonal reagents.
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Affiliation(s)
- Veronika Šlachtová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Simona Bellová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Agustina La-Venia
- Current address: Instituto de Química Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Juraj Galeta
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Karel Chalupský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Peter Rukovanský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 16000, Prague, Czech Republic
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26
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Saha PC, Das RS, Das S, Sepay N, Chatterjee T, Mukherjee A, Bera T, Kar S, Bhattacharyya M, Sengupta A, Guha S. Live-Cell Mitochondrial Targeted NIR Fluorescent Covalent Labeling of Specific Proteins Using a Dual Localization Effect. Bioconjug Chem 2023; 34:1407-1417. [PMID: 37289994 DOI: 10.1021/acs.bioconjchem.3c00185] [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: 06/10/2023]
Abstract
Here, our designed water-soluble NIR fluorescent unsymmetrical Cy-5-Mal/TPP+ consists of a lipophilic cationic TPP+ subunit that can selectively target and accumulate in a live-cell inner mitochondrial matrix where a maleimide residue of the probe undergoes faster chemoselective and site-specific covalent attachment with the exposed Cys residue of mitochondrion-specific proteins. On the basis of this dual localization effect, Cy-5-Mal/TPP+ molecules remain for a longer time period even after membrane depolarization, enabling long-term live-cell mitochondrial imaging. Due to the adequate concentration of Cy-5-Mal/TPP+ reached in live-cell mitochondria, it facilitates site-selective NIR fluorescent covalent labeling with Cys-exposed proteins, which are identified by the in-gel fluorescence assay and LC-MS/MS-based proteomics and supported by a computational method. This dual targeting approach with admirable photostability, narrow NIR absorption/emission bands, bright emission, long fluorescence lifetime, and insignificant cytotoxicity has been shown to improve real-time live-cell mitochondrial tracking including dynamics and interorganelle crosstalk with multicolor imaging applications.
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Affiliation(s)
- Pranab Chandra Saha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Rabi Sankar Das
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Shreya Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Nayim Sepay
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Tanima Chatterjee
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal 700019, India
| | - Ayan Mukherjee
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Tapas Bera
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Samiran Kar
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal 700019, India
| | - Arunima Sengupta
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal 700032, India
| | - Samit Guha
- Department of Chemistry, Organic Chemistry Section, Jadavpur University, Kolkata, West Bengal 700032, India
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27
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Kozma E, Bojtár M, Kele P. Bioorthogonally Assisted Phototherapy: Recent Advances and Prospects. Angew Chem Int Ed Engl 2023; 62:e202303198. [PMID: 37161824 DOI: 10.1002/anie.202303198] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
Photoresponsive materials offer excellent spatiotemporal control over biological processes and the emerging phototherapeutic methods are expected to have significant effects on targeted cancer therapies. Recent examples show that combination of photoactivatable approaches with bioorthogonal chemistry enhances the precision of targeted phototherapies and profound implications are foreseen particularly in the treatment of disperse/diffuse tumors. The extra level of on-target selectivity and improved spatial/temporal control considerably intensified related bioorthogonally assisted phototherapy research. The anticipated growth of further developments in the field justifies the timeliness of a brief summary of the state of the art.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
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28
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Abstract
As chemical biologists sought methods to modify and study biomolecules in their native environments, the need for bioorthogonal chemical reactions emerged. These fast and selective reactions between otherwise inert, abiotic functional groups have enabled exploration of some of the most intriguing and challenging questions in chemical biology. Further, the ability to perform organic reactions in cells and organisms has led to important applications in clinical spaces, and one reaction is now an integral part of a phase 2 trial for treating solid tumors. Given that bioorthogonal chemistry was a recipient of the 2022 Nobel Prize, we expect this field to be even more energized. Here, we highlight some of the most recent studies in this sphere and how these set the stage for where bioorthogonal chemistry is headed.
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Affiliation(s)
- Kaitlin M. Hartung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ellen M. Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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29
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Dworzak MR, Montone CM, Halaszynski NI, Yap GPA, Kloxin CJ, Bloch ED. Rapid post-synthetic modification of porous coordination cages with copper-catalyzed click chemistry. Chem Commun (Camb) 2023; 59:8977-8980. [PMID: 37387311 PMCID: PMC11552439 DOI: 10.1039/d3cc02015k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Novel cobalt calixarene-capped and zirconium-based porous coordination cages were prepared with alkyne and azide functionality to leverage post-synthetic modification by click chemistry. While the calixarene-capped cages showed impressive stability when exposed to the most straightforward copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction conditions with copper(II) sulfate and sodium ascorbate as the reducing agent, milder reaction conditions were necessary to perform analogous CuAAC reactions on zirconium-based cages. Reaction kinetics were monitored by IR spectroscopy, confirming rapid reaction times (<3 hours).
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Affiliation(s)
- Michael R Dworzak
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Christine M Montone
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Nicole I Halaszynski
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA.
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA.
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Eric D Bloch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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30
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Ligthart NAM, de Geus MAR, van de Plassche MAT, Torres García D, Isendoorn MME, Reinalda L, Ofman D, van Leeuwen T, van Kasteren SI. A Lysosome-Targeted Tetrazine for Organelle-Specific Click-to-Release Chemistry in Antigen Presenting Cells. J Am Chem Soc 2023. [PMID: 37269296 DOI: 10.1021/jacs.3c02139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bioorthogonal deprotections are readily used to control biological function in a cell-specific manner. To further improve the spatial resolution of these reactions, we here present a lysosome-targeted tetrazine for an organelle-specific deprotection reaction. We show that trans-cyclooctene deprotection with this reagent can be used to control the biological activity of ligands for invariant natural killer T cells in the lysosome to shed light on the processing pathway in antigen presenting cells. We then use the lysosome-targeted tetrazine to show that long peptide antigens used for CD8+ T cell activation do not pass through this organelle, suggesting a role for the earlier endosomal compartments for their processing.
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Affiliation(s)
- Nina A M Ligthart
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mark A R de Geus
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Merel A T van de Plassche
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Diana Torres García
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marjolein M E Isendoorn
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Luuk Reinalda
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daniëlle Ofman
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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31
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Fang M, Kumar GS, Racioppi S, Zhang H, Rabb JD, Zurek E, Lin Q. Hydrazonyl Sultones as Stable Tautomers of Highly Reactive Nitrile Imines for Fast Bioorthogonal Ligation Reaction. J Am Chem Soc 2023; 145:9959-9964. [PMID: 37104819 DOI: 10.1021/jacs.2c12325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Here we report the design and synthesis of a new class of bioorthogonal reagents called hydrazonyl sultones (HS) that serve as stable tautomers of highly reactive nitrile imines (NI). Compared to the photogenerated NI, HS display a broad range of aqueous stability and tunable reactivity in a 1,3-dipolar cycloaddition reaction, depending on substituents, sultone ring structure, and solvent conditions. DFT calculations have provided vital insights into the HS → NI tautomerism, including a base-mediated anionic tautomerization pathway and a small activation barrier. Comparative kinetic analysis of tetrazole vs HS-mediated cycloadditions reveals that a tiny fraction of the reactive NI (∼15 ppm) is present in the tautomeric mixture, underpinning the extraordinary stability of the six-membered HS. We further demonstrate the utilities of HS in selective modification of bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN)-lysine-containing nanobodies in phosphate buffered saline and fluorescent labeling of a BCN-lysine-encoded transmembrane glucagon receptor on live cells.
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Affiliation(s)
- Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - 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
| | - Heyang Zhang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Johnathan D Rabb
- 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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32
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Rosenberger JE, Xie Y, Fang Y, Lyu X, Trout WS, Dmitrenko O, Fox JM. Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells. J Am Chem Soc 2023; 145:6067-6078. [PMID: 36881718 PMCID: PMC10589873 DOI: 10.1021/jacs.2c10655] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red light (660 nm) photocatalysis is used to initiate a cascade of DHTz oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially available conjugates of Hoechst dye (SiR-H) and docetaxel (SiR-T) are used to localize SiR to the nucleus and microtubules, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 μM SiR and 40 μM photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate-determining elimination step. In cellular studies, this uncaging process is successful at low concentrations of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as a photocatalyst and the fluorescent reporter for microtubule depolymerization, and with confocal microscopy, it was possible to visualize microtubule depolymerization in real time as the result of photocatalytic uncaging in live cells.
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Affiliation(s)
- Julia E. Rosenberger
- 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
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinyi Lyu
- 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
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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33
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Xie X, Hu F, Zhou Y, Liu Z, Shen X, Fu J, Zhao X, Yu Z. Photoswitchable Oxidopyrylium Ylide for Photoclick Reaction with High Spatiotemporal Precision: A Dynamic Switching Strategy to Compensate for Molecular Diffusion. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202300034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Xinyu Xie
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Sichuan University Chengdu 610064 China
| | - Fuqiang Hu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Sichuan University Chengdu 610064 China
| | - Yuqiao Zhou
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Sichuan University Chengdu 610064 China
| | - Zhihao Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Sichuan University Chengdu 610064 China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education College of Chemistry Sichuan University Chengdu 610064 China
| | - Jielin Fu
- 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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34
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Xie X, Hu F, Zhou Y, Liu Z, Shen X, Fu J, Zhao X, Yu Z. Photoswitchable Oxidopyrylium Ylide for Photoclick Reaction with High Spatiotemporal Precision: A Dynamic Switching Strategy to Compensate for Molecular Diffusion. Angew Chem Int Ed Engl 2023; 62:e202300034. [PMID: 36825842 DOI: 10.1002/anie.202300034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
We describe a novel type of photoclick reaction between 2,3-diaryl indenone epoxide (DIO) and ring-strained dipolarophiles, in which DIO serves as a P-type photoswitch to produce mesoionic oxidopyrylium ylide (PY) to initiate an ultra-fast [5+2] cycloaddition (k2hν =1.9×105 M-1 s-1 ). The photoisomerization between DIO and PY can be tightly controlled by either 365 or 520 nm photo-stimulation, which allows reversion or regeneration of the reactive PY dipole on demand. Thus, this reversible photoactivation was exploited to increase the chemoselectivity of the [5+2] cycloaddition in complex environments via temporal dual-λ stimulation sequences and to recycle the DIO reagent for batch-wise protein conjugation. A dynamic photoswitching strategy is also proposed to compensate for molecular diffusion of PY in aqueous solution, enhancing the spatial resolution of lithographic surface decoration and bioorthogonal labeling on living cells via a spatiotemporal dual-λ photo-modulation.
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Affiliation(s)
- Xinyu Xie
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Fuqiang Hu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuqiao Zhou
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zhihao Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Jielin Fu
- 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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35
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Neighboring Nitrogen Atom-Induced Reactions of Azidoacetyl Hydrazides, including Unexpected Nitrogen-Nitrogen Bond Cleavage of the Hydrazide. ORGANICS 2022. [DOI: 10.3390/org3040035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We studied the hydrazide compounds of the α-azidoacetyl group, which showed specific click reactivity by the intramolecular hydrogen bonding between the azido group and the N-H of the hydrazide moiety. In the competitive click reactions with a general alkyl azide, both traceless and non-traceless Staudinger-Bertozzi ligation occurred azide-site-selectively by the acceleration effect of the hydrogen bonding. However, the product obtained from the traceless reaction was further transformed into heterocyclic compounds. In addition, in an attempt at a synthesis of naphthalimide-possessing azidoacetyl hydrazide, nitrogen-nitrogen bond cleavage of the azidoacetyl hydrazides occurred to give the reduced amine product. These unexpected results could help design molecules for the successful Staudinger-Bertozzi ligation of the hydrazide compounds and develop a new nitrogen-nitrogen bond cleavage method.
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36
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Truong VX, Holloway JO, Barner-Kowollik C. Fluorescence turn-on by photoligation - bright opportunities for soft matter materials. Chem Sci 2022; 13:13280-13290. [PMID: 36507164 PMCID: PMC9682895 DOI: 10.1039/d2sc05403e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
Photochemical ligation has become an indispensable tool for applications that require spatially addressable functionalisation, both in biology and materials science. Interestingly, a number of photochemical ligations result in fluorescent products, enabling a self-reporting function that provides almost instantaneous visual feedback of the reaction's progress and efficiency. Perhaps no other chemical reaction system allows control in space and time to the same extent, while concomitantly providing inherent feedback with regard to reaction success and location. While photoactivable fluorescent properties have been widely used in biology for imaging purposes, the expansion of the array of photochemical reactions has further enabled its utility in soft matter materials. Herein, we concisely summarise the key developments of fluorogenic-forming photoligation systems and their emerging applications in both biology and materials science. We further summarise the current challenges and future opportunities of exploiting fluorescent self-reporting reactions in a wide array of chemical disciplines.
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Affiliation(s)
- Vinh X Truong
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (ASTAR) 2 Fusionopolis Way Singapore 138 634 Singapore
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) Brisbane QLD 4000 Australia
| | - Joshua O Holloway
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) Brisbane QLD 4000 Australia
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT) Brisbane QLD 4000 Australia
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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Knittel CH, Devaraj NK. Bioconjugation Strategies for Revealing the Roles of Lipids in Living Cells. Acc Chem Res 2022; 55:3099-3109. [PMID: 36215688 DOI: 10.1021/acs.accounts.2c00511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The structural boundaries of living cells are composed of numerous membrane-forming lipids. Lipids not only are crucial for the cellular compartmentalization but also are involved in cell signaling as well as energy storage. Abnormal lipid levels have been linked to severe human diseases such as cancer, multiple sclerosis, neurodegenerative diseases, as well as lysosomal storage disorders. Given their biological significance, there is immense interest in studying lipids and their effect on cells. However, limiting factors include the low solubility of lipids, their structural complexity, and the challenge of using genetic techniques to directly manipulate lipid structure. Current methods to study lipids rely mostly on lipidomics, which analyzes the composition of lipid extracts using mass spectrometry. Although, these efforts have successfully catalogued and profiled a great number of lipids in cells, many aspects about their exact functional role and subcellular distribution remain enigmatic.In this Account, we outline how our laboratory developed and applied different bioconjugation strategies to study the role of lipids and lipid modifications in cells. Inspired by our ongoing work on developing lipid bioconjugation strategies to generate artificial cell membranes, we developed a ceramide synthesis method in live cells using a salicylaldehyde ester that readily reacts with sphingosine in form of a traceless ceramide ligation. Our study not only confirmed existing knowledge about the association of ceramides with cell death, but also gave interesting new findings about the structure-function relationship of ceramides in apoptosis. Our initial efforts led us to investigate probes that detect endogenous sphingolipids using live cell imaging. We describe the development of a fluorogenic probe that reacts chemoselectively with sphingosine in living cells, enabling the detection of elevated endogenous levels of this biomarker in human disease. Building on our interest in the fluorescence labeling of lipids, we have also explored the use of bioorthogonal reactions to label chemically synthesized lipid probes. We discuss the development of photocaged dihydrotetrazine lipids, where the initiation of the bioorthogonal reaction can be triggered by visible light, allowing for live cell modification of membranes with spatiotemporal control.Finally, proteins are often post-translationally modified by lipids, which have important effects on protein subcellular localization and function. Controlling lipid modifications with small molecule probes could help reveal the function of lipid post-translational modifications and could potentially inspire novel therapeutic strategies. We describe how our previous studies on synthetic membrane formation inspired us to develop an amphiphilic cysteine derivative that depalmitoylates membrane-bound S-acylated proteins in live cells. Ultimately, we applied this amphiphile mediated depalmitoylation (AMD) in studies investigating the palmitoylation of cancer relevant palmitoylated proteins in healthy and diseased cells.
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Affiliation(s)
- Caroline H Knittel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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Tang L, Bednar RM, Rozanov ND, Hemshorn ML, Mehl RA, Fang C. Rational Design for High Bioorthogonal Fluorogenicity of Tetrazine-Encoded Green Fluorescent Proteins. NATURAL SCIENCES (WEINHEIM, GERMANY) 2022; 2:e20220028. [PMID: 36440454 PMCID: PMC9699285 DOI: 10.1002/ntls.20220028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of bioorthogonal fluorogenic probes constitutes a vital force to advance life sciences. Tetrazine-encoded green fluorescent proteins (GFPs) show high bioorthogonal reaction rate and genetic encodability, but suffer from low fluorogenicity. Here, we unveil the real-time fluorescence mechanisms by investigating two site-specific tetrazine-modified superfolder GFPs via ultrafast spectroscopy and theoretical calculations. Förster resonance energy transfer (FRET) is quantitatively modeled and revealed to govern the fluorescence quenching; for GFP150-Tet with a fluorescence turn-on ratio of ~9, it contains trimodal subpopulations with good (P1), random (P2), and poor (P3) alignments between the transition dipole moments of protein chromophore (donor) and tetrazine tag (Tet-v2.0, acceptor). By rationally designing a more free/tight environment, we created new mutants Y200A/S202Y to introduce more P2/P1 populations and improve the turn-on ratios to ~14/31, making the fluorogenicity of GFP150-Tet-S202Y the highest among all up-to-date tetrazine-encoded GFPs. In live eukaryotic cells, the GFP150-Tet-v3.0-S202Y mutant demonstrates notably increased fluorogenicity, substantiating our generalizable design strategy.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
| | - Riley M. Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Nikita D. Rozanov
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
| | - Marcus L. Hemshorn
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, Oregon 97331-7305, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, USA
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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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Xiao M, Zhang YK, Li R, Li S, Wang D, An P. Photoactivatable Fluorogenic Azide-Alkyne Click Reaction: A Dual-Activation Fluorescent Probe. Chem Asian J 2022; 17:e202200634. [PMID: 35819362 DOI: 10.1002/asia.202200634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/01/2022] [Indexed: 11/12/2022]
Abstract
Aryl azide and diaryl tetrazole are both photoactive molecules, which can form nitrene and nitrile imine intermediates respectively by photolysis. Depending on the new finding that the azide can suppress the photolysis of tetrazole in the azide-tetrazole conjugated system, we developed aryl azide-tetrazole probes for the photoactivatable fluorogenic azide alkyne click (PFAAC) reaction, in which the aryl azide-tetrazole probes were not phoroactivatable fluorogenic itself, but the triazole products after click reaction were prefluorophore that can be activated by light. Therefore, in PFAAC chemistry, the fluorescent probes can be activated by two orthogonal events: azide-alkyne click reaction and light, which leads to spatiotemporal resolution and high signal-to-noise ratio. This PFAAC process was proved in vitro by copper catalyzed or strain-promoted azide-alkyne reactions and in live cells by spatiotemporally controlled organelle imaging. By incorporation a linker to the azide-tetrazole conjugate, this PFAAC chemistry could covalently label extra probes to the biomolecules and spatiotemporally detecting this process by photoinduced fluorescence.
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Affiliation(s)
| | | | | | | | - Di Wang
- Yunnan University, chemistry, CHINA
| | - Peng An
- Yunnan University, school of chemical science and technology, South Outer Ring Road, 650500, Kunming, CHINA
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42
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Kondor CA, Gorantla JN, Leonard GD, Fehl C. Synthesis and mammalian cell compatibility of light-released glycan precursors for controlled metabolic engineering. Bioorg Med Chem 2022; 70:116918. [PMID: 35810714 DOI: 10.1016/j.bmc.2022.116918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022]
Abstract
Sugar additions to biomolecules, or glycans, are some of the most abundant biomolecule modifications in biology because they enable cells to adapt to changing nutrient and stress conditions. An unmet challenge for the field of glycobiology is the study of glycan biosynthetic pathways with chemical control, especially in live cell settings. The objective of this study was to create biocompatible glycan precursors with controlled release properties. Here, we report eleven "caged" sugar probes that release glycan biosynthetic precursor molecules upon light exposure. The specific sugar pathways we target with our probes regulate the addition of the N-acetyl sugars GlcNAc, GalNAc, and sialic acid onto biomolecules in cells, each of which has the potential to alter glycan processes involved in cell morphology, signaling, and behavior. We hypothesized that our glycan precursor probes would remain biologically inert until light-initiated decaging conditions were met, avoiding biological activities including metabolism and cytotoxicity. The photocaged analogs of GlcNAc, GalNAc, and ManNAc (sialic acid precursor) sugars, which we call "photo-sugars," were released within minutes of light exposure at their optimal wavelengths. During the course of the study, we characterized the cell compatibility of these sugars under their respective decaging conditions, and found highly cell compatible GlcNAc, GalNAc, and ManNAc photocaged precursors. Release of GlcNAc-1-phosphate precursors led to altered ATP levels in cells, demonstrating preliminary metabolic engineering. We envision these probes as useful additions to the chemical glycobiology field that will enable spatiotemporal control over glycosylation pathways in living mammalian cells.
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Affiliation(s)
- Courtney A Kondor
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA
| | - Jaggaiah N Gorantla
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA
| | - Garry D Leonard
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202, USA.
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Wang F, Kong H, Meng X, Tian X, Wang C, Xu L, Zhang X, Wang L, Xie R. A light-initiated chemical reporter strategy for spatiotemporal labeling of biomolecules. RSC Chem Biol 2022; 3:539-545. [PMID: 35656482 PMCID: PMC9092362 DOI: 10.1039/d2cb00072e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The emergence of optochemical approaches has had a diverse impact over a broad range of biological research due to spatiotemporal regulation. Herein, we integrate this feature into the bioorthogonal chemical reporter strategy, which enables visible light-controlled spatiotemporal labeling of cell-surface glycans, lipids, and proteins. The metabolic precursors were first incorporated into live cells, and next the bioorthogonal reaction converted the azide/alkyne into a photo-active functional group, which allowed for subsequent photo-click reaction. We demonstrated this strategy by specifically labeling sialome, mucin-type O-glycome, phospholipids and newly-synthesized membrane proteins, respectively. The sequential photoirradiation-orthogonal reporter tagging (SPORT) should facilitate the probing of biomolecules in complex biological systems with high spatiotemporal precision.
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Affiliation(s)
- Feifei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hao Kong
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Lei Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Xiang Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated, Hospital of Nanjing University Medical School Nanjing 210008 China
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Drum Tower, Clinical Medical College of Nanjing Medical University Nanjing 210008 China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
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44
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Liu Z, Xie X, Huang Z, Lin F, Liu S, Chen Z, Qin S, Fan X, Chen PR. Spatially resolved cell tagging and surfaceome labeling via targeted photocatalytic decaging. Chem 2022. [DOI: 10.1016/j.chempr.2022.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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