1
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Jin S, He Z, Du Y, Jin G, Wang K, Yang F, Zhang J. An overview of cyclopropenone derivatives as promising bioactive molecules. Bioorg Med Chem Lett 2024; 109:129845. [PMID: 38852789 DOI: 10.1016/j.bmcl.2024.129845] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Cyclopropenone is a valuable electrophilic reagent that can react with electrophilic reagents, nucleophilic reagents, free radicals, organic metals, etc. Furthermore, cyclopropenone derivatives have shown significant biological activity in various diseases, such as triple-negative breast cancer (TNBC), melanoma, and alopecia areata (AA). The cyclopropenone analogue diphenylcyclopropenone (DPCP) has been approved for the treatment of AA. Given the potential therapeutic benefits of cyclopropenone derivatives, this review aims to systematically summarize the structures, synthesis routes, and potential pharmacological functions of cyclopropenone analogues in the hope of offering novel insights for further rational design of more drugs based on the cyclopropenone skeleton for the treatment of human diseases.
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Affiliation(s)
- Sasa Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Yuanbing Du
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Gang Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Kaiyue Wang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Feifei Yang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Jingyu Zhang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
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2
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Knaack JIH, Meier C. Out of the Dark, into the Light: Metabolic Fluorescent Labeling of Nucleic Acids. ChemMedChem 2024; 19:e202400160. [PMID: 38712684 DOI: 10.1002/cmdc.202400160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
This review outlines recent advances in live-cell imaging techniques for nucleic acids. We describe the evolution of these methods, particularly highlighting the development of metabolic labeling approaches compatible with living systems using fluorescence-based labeling.
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Affiliation(s)
- J Iven H Knaack
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Chris Meier
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
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3
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Chandankar SS, Kondhare D, Deshmukh S, Yang H, Leonard P, Seela F. 7-Deazapurine and Pyrimidine Nucleoside and Oligonucleotide Cycloadducts Formed by Inverse Diels-Alder Reactions with 3,6-Di(pyrid-2-yl)-1,2,4,5-tetrazine: Ethynylated and Vinylated Nucleobases for Functionalization and Impact of Pyridazine Adducts on DNA Base Pair Stability and Mismatch Discrimination. J Org Chem 2024. [PMID: 39052894 DOI: 10.1021/acs.joc.4c00982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
The manuscript reports on 7-deazapurine and pyrimidine nucleoside and oligonucleotide cycloadducts formed by the inverse electron demand Diels-Alder (iEDDA) reaction with 3,6-di(pyrid-2-yl)-1,2,4,5-tetrazine. Cycloadducts were constructed from ethynylated and vinylated nucleobases. Oligonucleotides were synthesized containing iEDDA modifications, and the impact on duplex stability was investigated. iEDDA reactions were performed on nucleoside triple bond side chains. Oxidation was not required in these cases as dihydropyridazine intermediates are not formed. In contrast, oxidation is necessary for reactions performed on alkenyl compounds. This was verified on 5-vinyl-2'-deoxyuridine. A diastereomeric mixture of 1,2-dihydropyridazine cycloadduct intermediates was isolated, characterized, and later oxidized. 12-mer oligonucleotides containing 1,2-pyridazine inverse Diels-Alder cycloadducts and their precursors were hybridized to short DNA duplexes. For that, a series of phosphoramidites was prepared. DNA duplexes with 7-functionalized 7-deazaadenines and 5-functionalized pyrimidines display high duplex stability when spacer units are present between nucleobases and pyridazine cycloadducts. A direct connectivity of the pyridazine moiety to nucleobases as reported for metabolic labeling of vinyl nucleosides reduced duplex stability strongly. Oligonucleotides bearing linkers with and without pyridazine cycloadducts attached to the 7-deazaadenine nucleobase significantly reduced mismatch formation with dC and dG.
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Affiliation(s)
- Somnath Shivaji Chandankar
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Sushma Deshmukh
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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4
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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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5
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Auger SA, Venkatachalapathy S, Suazo KFG, Wang Y, Sarkis AW, Bernhagen K, Justyna K, Schaefer JV, Wollack JW, Plückthun A, Li L, Distefano MD. Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry. Bioconjug Chem 2024; 35:922-933. [PMID: 38654427 DOI: 10.1021/acs.bioconjchem.4c00072] [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: 04/26/2024]
Abstract
Bioorthogonal chemistry has gained widespread use in the study of many biological systems of interest, including protein prenylation. Prenylation is a post-translational modification, in which one or two 15- or 20-carbon isoprenoid chains are transferred onto cysteine residues near the C-terminus of a target protein. The three main enzymes─protein farnesyltransferase (FTase), geranylgeranyl transferase I (GGTase I), and geranylgeranyl transferase II (GGTase II)─that catalyze this process have been shown to tolerate numerous structural modifications in the isoprenoid substrate. This feature has previously been exploited to transfer an array of farnesyl diphosphate analogues with a range of functionalities, including an alkyne-containing analogue for copper-catalyzed bioconjugation reactions. Reported here is the synthesis of an analogue of the isoprenoid substrate embedded with norbornene functionality (C10NorOPP) that can be used for an array of applications, ranging from metabolic labeling to selective protein modification. The probe was synthesized in seven steps with an overall yield of 7% and underwent an inverse electron demand Diels-Alder (IEDDA) reaction with tetrazine-containing tags, allowing for copper-free labeling of proteins. The use of C10NorOPP for the study of prenylation was explored in the metabolic labeling of prenylated proteins in HeLa, COS-7, and astrocyte cells. Furthermore, in HeLa cells, these modified prenylated proteins were identified and quantified using label-free quantification (LFQ) proteomics with 25 enriched prenylated proteins. Additionally, the unique chemistry of C10NorOPP was utilized for the construction of a multiprotein-polymer conjugate for the targeted labeling of cancer cells. That construct was prepared using a combination of norbornene-tetrazine conjugation and azide-alkyne cycloaddition, highlighting the utility of the additional degree of orthogonality for the facile assembly of new protein conjugates with novel structures and functions.
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Affiliation(s)
- Shelby A Auger
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Sneha Venkatachalapathy
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kiall Francis G Suazo
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Yiao Wang
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Alexander W Sarkis
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kaitlyn Bernhagen
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - James W Wollack
- Department of Chemistry and Biochemistry, St. Catherine University, 2004 Randolph Avenue, St. Paul, Minnesota 55105, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota─Twin Cities, 2001 6th Street SE, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
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6
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Bao M, Łuczak K, Chaładaj W, Baird M, Gryko D, Doyle MP. Photo-cycloaddition reactions of vinyldiazo compounds. Nat Commun 2024; 15:4574. [PMID: 38811537 PMCID: PMC11137122 DOI: 10.1038/s41467-024-48274-5] [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: 10/18/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Heterocyclic rings are important structural scaffolds encountered in both natural and synthetic compounds, and their biological activity often depends on these motifs. They are predominantly accessible via cycloaddition reactions, realized by either thermal, photochemical, or catalytic means. Various starting materials are utilized for this purpose, and, among them, diazo compounds are often encountered, especially vinyldiazo compounds that give access to donor-acceptor cyclopropenes which engage in [2+n] cycloaddition reactions. Herein, we describe the development of photochemical processes that produce diverse heterocyclic scaffolds from multisubstituted oximidovinyldiazo compounds. High chemoselectivity, good functional group tolerance, and excellent scalability characterize this methodology, thus predisposing it for broader applications. Experimental and computational studies reveal that under light irradiation these diazo reagents selectively transform into cyclopropenes which engage in cycloaddition reactions with various dipoles, while under thermal conditions the formation of pyrazole from vinyldiazo compounds is favored.
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Affiliation(s)
- Ming Bao
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Klaudia Łuczak
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Wojciech Chaładaj
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland.
| | - Marriah Baird
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Dorota Gryko
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland.
| | - Michael P Doyle
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas, USA.
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7
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Seul N, Lamade D, Stoychev P, Mijic M, Michenfelder RT, Rieger L, Geng P, Wagenknecht HA. Cyclopropenes as Chemical Reporters for Dual Bioorthogonal and Orthogonal Metabolic Labeling of DNA. Angew Chem Int Ed Engl 2024; 63:e202403044. [PMID: 38517205 DOI: 10.1002/anie.202403044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
Dual bioorthogonal labeling enables the investigation and understanding of interactions in the biological environment that are not accessible by a single label. However, applying two bioorthogonal reactions in the same environment remains challenging due to cross-reactivity. We developed a pair of differently modified 2'-deoxynucleosides that solved this issue for dual and orthogonal labeling of DNA. Inverse-electron demand Diels-Alder and photoclick reactions were combined to attach two different fluorogenic labels to genomic DNA in cells. Using a small synthetic library of 1- and 3-methylcyclopropenyl-modified 2'-deoxynucleosides, two 2'-deoxyuridines were identified to be the fastest-reacting ones for each of the two bioorthogonal reactions. Their orthogonal reactivity could be evidenced in vitro. Primer extension experiments were performed with both 2'-deoxyuridines investigating their replication properties as substitutes for thymidine and evaluating subsequent labeling reactions on the DNA level. Finally, dual, orthogonal and metabolic fluorescent labeling of genomic DNA was demonstrated in HeLa cells. An experimental procedure was developed combining intracellular transport and metabolic DNA incorporation of the two 2'-deoxyuridines with the subsequent dual bioorthogonal labeling using a fluorogenic cyanine-styryl tetrazine and a fluorogenic pyrene-tetrazole. These results are fundamental for advanced metabolic labeling strategies for nucleic acids in the future, especially for live cell experiments.
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Affiliation(s)
- Nicola Seul
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Dennis Lamade
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Petko Stoychev
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Michaela Mijic
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Rita T Michenfelder
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Lisa Rieger
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Philipp Geng
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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8
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Kufleitner M, Haiber LM, Li S, Surendran H, Mayer TU, Zumbusch A, Wittmann V. Next-Generation Metabolic Glycosylation Reporters Enable Detection of Protein O-GlcNAcylation in Living Cells without S-Glyco Modification. Angew Chem Int Ed Engl 2024; 63:e202320247. [PMID: 38501674 DOI: 10.1002/anie.202320247] [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: 12/30/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
Protein O-GlcNAcylation is a ubiquitous posttranslational modification of cytosolic and nuclear proteins involved in numerous fundamental regulation processes. Investigation of O-GlcNAcylation by metabolic glycoengineering (MGE) has been carried out for two decades with peracetylated N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine derivatives modified with varying reporter groups. Recently, it has been shown that these derivatives can result in non-specific protein labeling termed S-glyco modification. Here, we report norbornene-modified GlcNAc derivatives with a protected phosphate at the anomeric position and their application in MGE. These derivatives overcome two limitations of previously used O-GlcNAc reporters. They do not lead to detectable S-glyco modification, and they efficiently react in the inverse-electron-demand Diels-Alder (IEDDA) reaction, which can be carried out even within living cells. Using a derivative with an S-acetyl-2-thioethyl-protected phosphate, we demonstrate the protein-specific detection of O-GlcNAcylation of several proteins and the protein-specific imaging of O-GlcNAcylation inside living cells by Förster resonance energy transfer (FRET) visualized by confocal fluorescence lifetime imaging microscopy (FLIM).
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Affiliation(s)
- Markus Kufleitner
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Lisa Maria Haiber
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Shuang Li
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Harsha Surendran
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Thomas U Mayer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Valentin Wittmann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
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9
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Sminia TJ, Aalvink S, de Jong H, Tempelaars MH, Zuilhof H, Abee T, de Vos WM, Tytgat HLP, Wennekes T. Probing Peptidoglycan Synthesis in the Gut Commensal Akkermansia Muciniphila with Bioorthogonal Chemical Reporters. Chembiochem 2024:e202400037. [PMID: 38688858 DOI: 10.1002/cbic.202400037] [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: 01/16/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/02/2024]
Abstract
Our gut microbiota directly influences human physiology in health and disease. The myriad of surface glycoconjugates in both the bacterial cell envelope and our gut cells dominate the microbiota-host interface and play a critical role in host response and microbiota homeostasis. Among these, peptidoglycan is the basic glycan polymer offering the cell rigidity and a basis on which many other glycoconjugates are anchored. To directly study peptidoglycan in gut commensals and obtain the molecular insight required to understand their functional activities we need effective techniques like chemical probes to label peptidoglycan in live bacteria. Here we report a chemically guided approach to study peptidoglycan in a key mucin-degrading gut microbiota member of the Verrucomicrobia phylum, Akkermansia muciniphila. Two novel non-toxic tetrazine click-compatible peptidoglycan probes with either a cyclopropene or isonitrile handle allowed for the detection and imaging of peptidoglycan synthesis in this intestinal species.
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Affiliation(s)
- Tjerk J Sminia
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The, Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The, Netherlands
| | - Hanna de Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The, Netherlands
| | - Marcel H Tempelaars
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The, Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The, Netherlands
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The, Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The, Netherlands
- Current address: Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The, Netherlands
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The, Netherlands
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10
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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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11
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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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12
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Svatunek D, Murnauer A, Tan Z, Houk KN, Lang K. How cycloalkane fusion enhances the cycloaddition reactivity of dibenzocyclooctynes. Chem Sci 2024; 15:2229-2235. [PMID: 38332832 PMCID: PMC10848739 DOI: 10.1039/d3sc05789e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Dibenzoannulated cyclooctynes have emerged as valuable compounds for bioorthogonal reactions. They are commonly used in combination with azides in strain-promoted 1,3-dipolar cycloadditions. They are typically, however, unreactive towards 3,6-disubstituted tetrazines in inverse electron-demand Diels-Alder cycloadditions. Recently a dibenzoannulated bicyclo[6.1.0]nonyne derivative (DMBO) with a cyclopropane fused to the cyclooctyne core was described, which showed surprising reactivity towards tetrazines. To elucidate the unusual reactivity of DMBO, we performed density functional theory calculations and revealed that a tub-like structure in the transition state results in a much lower activation barrier than in the absence of cyclopropane fusion. The same transition state geometry is found for different cycloalkanes fused to the cyclooctyne core albeit higher activation barriers are observed for increased ring sizes. This conformation is energetically unfavored for previously known dibenzoannulated cyclooctynes and allows tetrazines and azides to approach DMBO from the face rather than the edge, a trajectory that was hitherto not observed for this class of activated dieno- and dipolarophiles.
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Affiliation(s)
- Dennis Svatunek
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095-1569 USA
- Institute of Applied Synthetic Chemistry, TU Wien Getreidemarkt 9 1060 Vienna Austria
| | - Anton Murnauer
- Department of Chemistry and Applied Biosciences, ETH Zurich 8093 Zurich Switzerland
| | - Zhuoting Tan
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095-1569 USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095-1569 USA
| | - Kathrin Lang
- Department of Chemistry and Applied Biosciences, ETH Zurich 8093 Zurich Switzerland
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13
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Huang W, Gunawardhana N, Zhang Y, Escorihuela J, Laughlin ST. Pyranthiones/Pyrones: "Click and Release" Donors for Subcellular Hydrogen Sulfide Delivery and Labeling. Chemistry 2024; 30:e202303465. [PMID: 37985373 DOI: 10.1002/chem.202303465] [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: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
Hydrogen sulfide (H2 S), one of the most important gasotransmitters, plays a critical role in endogenous signaling pathways of many diseases. However, developing H2 S donors with both tunable release kinetics and high release efficiency for subcellular delivery has been challenging. Here, we describe a click and release reaction between pyrone/pyranthiones and bicyclononyne (BCN). This reaction features a release of CO2 /COS with second-order rate constants comparable to Strain-Promoted Azide-Alkyne Cycloaddition reactions (SPAACs). Interestingly, pyranthiones showed enhanced reaction rates compared to their pyrone counterparts. We investigated pyrone biorthogonality and demonstrated their utility in protein labeling applications. Moreover, we synthesized substituted pyranthiones with H2 S release kinetics that can address the range of physiologically relevant H2 S dynamics in cells and achieved quantitative H2 S release efficiency in vitro. Finally, we explored the potential of pyranthiones as H2 S/COS donors for mitochondrial-targeted H2 S delivery in living cells.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, United States
| | - Nipuni Gunawardhana
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, United States
| | - Yunlei Zhang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, United States
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100, Valencia, Spain
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, United States
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14
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Kang D, Kim J. Enamine N-oxides: Design, Synthesis, and Function in Bioorthogonal Reactions. Synlett 2024; 35:145-154. [PMID: 38947226 PMCID: PMC11210832 DOI: 10.1055/a-2127-1086] [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] [Indexed: 07/02/2024]
Abstract
Enamine N-oxides act as a chemical linchpin bridging two bioorthogonal associative and dissociative reactions. This article describes the design of enamine N-oxides; their synthesis through the retro-Cope elimination reaction; the use of solvent, hyperconjugation, strain, and rehybridization effects to achieve bioorthogonal reactivity; and their rapid reductive cleavage with diboron reagents. The coordinated assembly and disassembly of the enamine N-oxide motif constitutes a powerful chemical operation that enables the attachment and detachment of small molecules from biomacromolecules in a biological setting.
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Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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15
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Chaudhuri R, Bhattacharya S, Dash J. Bioorthogonal Chemistry in Translational Research: Advances and Opportunities. Chembiochem 2023; 24:e202300474. [PMID: 37800582 DOI: 10.1002/cbic.202300474] [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: 06/24/2023] [Revised: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Bioorthogonal chemistry is a rapidly expanding field of research that involves the use of small molecules that can react selectively with biomolecules in living cells and organisms, without causing any harm or interference with native biochemical processes. It has made significant contributions to the field of biology and medicine by enabling selective labeling, imaging, drug targeting, and manipulation of bio-macromolecules in living systems. This approach offers numerous advantages over traditional chemistry-based methods, including high specificity, compatibility with biological systems, and minimal interference with biological processes. In this review, we provide an overview of the recent advancements in bioorthogonal chemistry and their current and potential applications in translational research. We present an update on this innovative chemical approach that has been utilized in cells and living systems during the last five years for biomedical applications. We also highlight the nucleic acid-templated synthesis of small molecules by using bioorthogonal chemistry. Overall, bioorthogonal chemistry provides a powerful toolset for studying and manipulating complex biological systems, and holds great potential for advancing translational research.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Semantee Bhattacharya
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Jyotirmayee Dash
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
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16
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Finkelstein DS, Du Bois J. Trifunctional Saxitoxin Conjugates for Covalent Labeling of Voltage-Gated Sodium Channels. Chembiochem 2023; 24:e202300493. [PMID: 37746898 PMCID: PMC10863845 DOI: 10.1002/cbic.202300493] [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: 07/04/2023] [Revised: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Voltage-gated sodium ion channels (NaV s) are integral membrane protein complexes responsible for electrical signal conduction in excitable cells. Methods that enable selective labeling of NaV s hold potential value for understanding how channel regulation and post-translational modification are influenced during development and in response to diseases and disorders of the nervous system. We have developed chemical reagents patterned after (+)-saxitoxin (STX) - a potent and reversible inhibitor of multiple NaV isoforms - and affixed with a reactive electrophile and either a biotin cofactor, fluorophore, or 'click' functional group for labeling wild-type channels. Our studies reveal enigmatic structural effects of the probes on the potency and efficiency of covalent protein modification. Among the compounds analyzed, a STX-maleimide-coumarin derivative is most effective at irreversibly blocking Na+ conductance when applied to recombinant NaV s and endogenous channels expressed in hippocampal neurons. Mechanistic analysis supports the conclusion that high-affinity toxin binding is a prerequisite for covalent protein modification. Results from these studies are guiding the development of next-generation tool compounds for selective modification of NaV s expressed in the plasma membranes of cells.
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Affiliation(s)
- Darren S Finkelstein
- Department of Chemistry, Stanford University, 337 Campus Dr., Stanford, CA 94305, USA
- Present address: Pliant Therapeutics, 260 Littlefield Avenue, South San Francisco, CA 94080, USA
| | - J Du Bois
- Department of Chemistry, Stanford University, 337 Campus Dr., Stanford, CA 94305, USA
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17
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Paliya BS, Sharma VK, Tuohy MG, Singh HB, Koffas M, Benhida R, Tiwari BK, Kalaskar DM, Singh BN, Gupta VK. Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans. Biotechnol Adv 2023; 67:108180. [PMID: 37236328 DOI: 10.1016/j.biotechadv.2023.108180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023]
Abstract
The recent advancement in the human glycome and progress in the development of an inclusive network of glycosylation pathways allow the incorporation of suitable machinery for protein modification in non-natural hosts and explore novel opportunities for constructing next-generation tailored glycans and glycoconjugates. Fortunately, the emerging field of bacterial metabolic engineering has enabled the production of tailored biopolymers by harnessing living microbial factories (prokaryotes) as whole-cell biocatalysts. Microbial catalysts offer sophisticated means to develop a variety of valuable polysaccharides in bulk quantities for practical clinical applications. Glycans production through this technique is highly efficient and cost-effective, as it does not involve expensive initial materials. Metabolic glycoengineering primarily focuses on utilizing small metabolite molecules to alter biosynthetic pathways, optimization of cellular processes for glycan and glycoconjugate production, characteristic to a specific organism to produce interest tailored glycans in microbes, using preferably cheap and simple substrate. However, metabolic engineering faces one of the unique challenges, such as the need for an enzyme to catalyze desired substrate conversion when natural native substrates are already present. So, in metabolic engineering, such challenges are evaluated, and different strategies have been developed to overcome them. The generation of glycans and glycoconjugates via metabolic intermediate pathways can still be supported by glycol modeling achieved through metabolic engineering. It is evident that modern glycans engineering requires adoption of improved strain engineering strategies for creating competent glycoprotein expression platforms in bacterial hosts, in the future. These strategies include logically designing and introducing orthogonal glycosylation pathways, identifying metabolic engineering targets at the genome level, and strategically improving pathway performance (for example, through genetic modification of pathway enzymes). Here, we highlight current strategies, applications, and recent progress in metabolic engineering for producing high-value tailored glycans and their applications in biotherapeutics and diagnostics.
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Affiliation(s)
- Balwant S Paliya
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Vivek K Sharma
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Maria G Tuohy
- Biochemistry, School of Biological and Chemical Sciences, College of Science & Engineering, University of Galway (Ollscoil na Gaillimhe), University Road, Galway City, Ireland
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rachid Benhida
- Institut de Chimie de Nice, UMR7272, Université Côte d'Azur, Nice, France; Mohamed VI Polytechnic University, Lot 660, Hay Moulay Rachid 43150, Benguerir, Morocco
| | | | - Deepak M Kalaskar
- UCL Division of Surgery and Interventional Science, Royal Free Hospital Campus, University College London, Rowland Hill Street, NW3 2PF, UK
| | - Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India.
| | - Vijai K Gupta
- Biorefining and Advanced Materials Research Centre, SRUC, Barony Campus, Parkgate, Dumfries DG1 3NE, United Kingdom.
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18
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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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19
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Tu HF, Jeandin A, Bon C, Brocklehurst C, Lima F, Suero MG. Late-Stage Aryl C-H Bond Cyclopropenylation with Cyclopropenium Cations. Angew Chem Int Ed Engl 2023; 62:e202308379. [PMID: 37459194 DOI: 10.1002/anie.202308379] [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: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Herein, we disclose the first regio-, site- and chemoselective late-stage (hetero)aryl C-H bond cyclopropenylation with cyclopropenium cations (CPCs). The process is fast, operationally simple and shows an excellent functional group tolerance in densely-functionalized drug molecules, natural products, agrochemicals and fluorescent dyes. Moreover, we discovered that the installation of the cyclopropene ring in drug molecules could not only be used to shield against metabolic instability but also as a synthetic tool to reach medicinally-relevant sp3 -rich scaffolds exploiting the highly-strained nature of the cyclopropene ring with known transformations.
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Affiliation(s)
- Hang-Fei Tu
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
| | - Aliénor Jeandin
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
- Departament de Química Analítica i Química Orgánica, Universitat Rovira i Virgili, Calle Marcel.lí Domingo, 1, 43007, Tarragona, Spain
| | - Corentin Bon
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Cara Brocklehurst
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Fabio Lima
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Marcos G Suero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
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20
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Svatunek D, Chojnacki K, Deb T, Eckvahl H, Houk KN, Franzini RM. Orthogonal Inverse-Electron-Demand Cycloaddition Reactions Controlled by Frontier Molecular Orbital Interactions. Org Lett 2023; 25:6340-6345. [PMID: 37591496 PMCID: PMC10476241 DOI: 10.1021/acs.orglett.3c02265] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Chemoselective pairs of bioorthogonal reactants enable the simultaneous labeling of several biomolecules. Here, we access orthogonal click reactions by exploiting differences in frontier molecular orbital interaction energies in transition states. We establish that five-membered cyclic dienes are inert to isonitriles but readily react with strained alkynes, while tetrazines with bulky substituents readily react with isonitriles. Strained alkynes show an opposite reactivity pattern. The approach was demonstrated by orthogonally labeling two proteins with different fluorophores.
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Affiliation(s)
- Dennis Svatunek
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Institute
of Applied Synthetic Chemistry, TU Wien, 1060 Vienna, Austria
| | - Konrad Chojnacki
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Titas Deb
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Hannah Eckvahl
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Raphael M. Franzini
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Huntsman
Cancer Institute, Salt Lake City, Utah 84112, United States
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21
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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22
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Auvray M, Naud-Martin D, Fontaine G, Bolze F, Clavier G, Mahuteau-Betzer F. Ultrabright two-photon excitable red-emissive fluorogenic probes for fast and wash-free bioorthogonal labelling in live cells. Chem Sci 2023; 14:8119-8128. [PMID: 37538830 PMCID: PMC10395273 DOI: 10.1039/d3sc01754k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
Fluorogenic bioorthogonal reactions are promising tools for tracking small molecules or biomolecules in living organisms. Two-photon excitation, by shifting absorption towards the red, significantly increases the signal-to-noise ratio and decreases photodamage, while allowing imaging about 10 times deeper than with a confocal microscope. However, efficient two-photon excitable fluorogenic probes are currently lacking. We report here the design and synthesis of fluorogenic probes based on a two-photon excitable fluorophore and a tetrazine quenching moiety. These probes react with bicyclo[6.1.0]no-4-yn-9ylmethanol (BCN) with a good to impressive kinetic rate constant (up to 1.1 × 103 M-1 s-1) and emit in the red window with moderate to high turn-on ratios. TDDFT allowed the rationalization of both the kinetic and fluorogenic performance of the different probes. The best candidate displays a 13.8-fold turn-on measured by quantifying fluorescence intensities in live cells under one-photon excitation, whereas a value of 3 is sufficient for high contrast live-cell imaging. In addition, live-cell imaging under two-photon excitation confirmed that there was no need for washing to monitor the reaction between BCN and this probe since an 8.0-fold turn-on was measured under two-photon excitation. Finally, the high two-photon brightness of the clicked adduct (>300 GM) allows the use of a weak laser power compatible with in vivo imaging.
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Affiliation(s)
- Marie Auvray
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Delphine Naud-Martin
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Gaëlle Fontaine
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Frédéric Bolze
- UMR7199, Faculté de Pharmacie 67401 Illkirch-Graffenstaden France
| | | | - Florence Mahuteau-Betzer
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
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23
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Mattheisen JM, Limberakis C, Ruggeri RB, Dowling MS, Am Ende CW, Ceraudo E, Huber T, McClendon CL, Sakmar TP. Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2023; 145:11173-11184. [PMID: 37116188 DOI: 10.1021/jacs.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures, the discovery of allosteric modulators remains challenging due to the dynamic nature of GPCRs in native membranes. We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems. We employed genetic code expansion to site-specifically introduce noncanonical amino acids with reactive groups in C-C chemokine receptor 5 (CCR5) near an allosteric binding site for the drug maraviroc. We then used molecular dynamics simulations to design heterobifunctional maraviroc analogues consisting of a drug fragment connected by a flexible linker to a reactive moiety capable of undergoing a bioorthogonal coupling reaction. We synthesized a library of these analogues and employed the bioorthogonal inverse electron demand Diels-Alder reaction to couple the analogues to the engineered CCR5 in live cells, which were then assayed using cell-based signaling assays. Tetherable low-affinity maraviroc fragments displayed an increase in potency for CCR5 engineered with reactive unnatural amino acids that were adjacent to the maraviroc binding site. The strategy we describe to tether novel drug fragments to GPCRs should prove useful to probe allosteric or cryptic binding site functionality in fragment-based GPCR-targeted drug discovery.
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Affiliation(s)
- Jordan M Mattheisen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
| | - Chris Limberakis
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Christopher L McClendon
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
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24
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Ma B, Niu W, Guo J. Proximity-enhanced protein crosslinking through an alkene-tetrazine reaction. Bioorg Chem 2023; 132:106359. [PMID: 36642019 PMCID: PMC9957846 DOI: 10.1016/j.bioorg.2023.106359] [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: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023]
Abstract
The inverse electron demand Diels-Alder (iEDDA) reaction between a tetrazine and a strained alkene has been widely explored as useful bioorthogonal chemistry for selective labeling of biomolecules. In this work, we exploit the slow reaction between a non-conjugated terminal alkene and a tetrazine, and apply this reaction to achieving a proximity-enhanced protein crosslinking. In one protein subunit, a terminal alkene-containing amino acid was site-specifically incorporated in response to an amber nonsense codon. In another protein subunit, a tetrazine moiety was introduced through the attachment to a cysteine residue. Fast protein crosslinking was achieved due to a large increase in effective molarity of the two reactants that were brought to close proximity by the two interacting protein subunits. Such a proximity-enhanced protein crosslinking is useful for the study of protein-protein interactions.
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Affiliation(s)
- Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
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25
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Kufleitner M, Haiber LM, Wittmann V. Metabolic glycoengineering - exploring glycosylation with bioorthogonal chemistry. Chem Soc Rev 2023; 52:510-535. [PMID: 36537135 DOI: 10.1039/d2cs00764a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glycans are involved in numerous biological recognition events. Being secondary gene products, their labeling by genetic methods - comparable to GFP labeling of proteins - is not possible. To overcome this limitation, metabolic glycoengineering (MGE, also known as metabolic oligosaccharide engineering, MOE) has been developed. In this approach, cells or organisms are treated with synthetic carbohydrate derivatives that are modified with a chemical reporter group. In the cytosol, the compounds are metabolized and incorporated into newly synthesized glycoconjugates. Subsequently, the reporter groups can be further derivatized in a bioorthogonal ligation reaction. In this way, glycans can be visualized or isolated. Furthermore, diverse targeting strategies have been developed to direct drugs, nanoparticles, or whole cells to a desired location. This review summarizes research in the field of MGE carried out in recent years. After an introduction to the bioorthogonal ligation reactions that have been used in in connection with MGE, an overview on carbohydrate derivatives for MGE is given. The last part of the review focuses on the many applications of MGE starting from mammalian cells to experiments with animals and other organisms.
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Affiliation(s)
- Markus Kufleitner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Lisa Maria Haiber
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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26
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Kang D, Wahl C, Kim J. Synthesis of push-pull-activated ynol ethers and their evaluation in the bioorthogonal hydroamination reaction. Org Biomol Chem 2022; 20:9217-9221. [PMID: 36367436 PMCID: PMC9769999 DOI: 10.1039/d2ob01917e] [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: 12/02/2023]
Abstract
A new class of push-pull-activated alkynes featuring di- and trifluorinated ynol ethers was synthesized. The difluorinated ynol ether exhibited an optimal balance of stability and reactivity, displaying a substantially improved half-life in the presence of aqueous thiols over the previously reported 1-haloalkyne analogs while reacting just as fast in the hydroamination reaction with N,N-diethylhydroxylamine. The trifluorinated ynol ether reacted significantly faster, exhibiting a second order rate constant of 0.56 M-1 s-1 in methanol, but it proved too unstable toward thiols. These fluorinated ynol ethers further demonstrate the importance of the hyperconjugation-rehybridization effect in activating alkynes and demonstrate how substituent effects can both activate and stabilize alkynes for bioorthogonal reactivity.
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Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Conrad Wahl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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27
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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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28
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Gupta M, Levine SR, Spitale RC. Probing Nascent RNA with Metabolic Incorporation of Modified Nucleosides. Acc Chem Res 2022; 55:2647-2659. [PMID: 36073807 DOI: 10.1021/acs.accounts.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The discovery of previously unknown functional roles of RNA in biological systems has led to increased interest in revealing novel RNA molecules as therapeutic targets and the development of tools to better understand the role of RNA in cells. RNA metabolic labeling broadens the scope of studying RNA by incorporating of unnatural nucleobases and nucleosides with bioorthogonal handles that can be utilized for chemical modification of newly synthesized cellular RNA. Such labeling of RNA provides access to applications including measurement of the rates of synthesis and decay of RNA, cellular imaging for RNA localization, and selective enrichment of nascent RNA from the total RNA pool. Several unnatural nucleosides and nucleobases have been shown to be incorporated into RNA by endogenous RNA synthesis machinery of the cells. RNA metabolic labeling can also be performed in a cell-specific manner, where only cells expressing an essential enzyme incorporate the unnatural nucleobase into their RNA. Although several discoveries have been enabled by the current RNA metabolic labeling methods, some key challenges still exist: (i) toxicity of unnatural analogues, (ii) lack of RNA-compatible conjugation chemistries, and (iii) background incorporation of modified analogues in cell-specific RNA metabolic labeling. In this Account, we showcase work done in our laboratory to overcome these challenges faced by RNA metabolic labeling.To begin, we discuss the cellular pathways that have been utilized to perform RNA metabolic labeling and study the interaction between nucleosides and nucleoside kinases. Then we discuss the use of vinyl nucleosides for metabolic labeling and demonstrate the low toxicity of 5-vinyluridine (5-VUrd) compared to other widely used nucleosides. Next, we discuss cell-specific RNA metabolic labeling with unnatural nucleobases, which requires the expression of a specific phosphoribosyl transferase (PRT) enzyme for incorporation of the nucleobase into RNA. In the course of this work, we discovered the enzyme uridine monophosphate synthase (UMPS), which is responsible for nonspecific labeling with modified uracil nucleobases. We were able to overcome this background labeling by discovering a mutant uracil PRT (UPRT) that demonstrates highly specific RNA metabolic labeling with 5-vinyluracil (5-VU). Furthermore, we discuss the optimization of inverse-electron-demand Diels-Alder (IEDDA) reactions for performing chemical modification of vinyl nucleosides to achieve covalent conjugation of RNA without transcript degradation. Finally, we highlight our latest endeavor: the development of mutually orthogonal chemical reactions for selective labeling of 5-VUrd and 2-vinyladenosine (2-VAdo), which allows for potential use of multiple vinyl nucleosides for simultaneous investigation of multiple cellular processes involving RNA. We hope that our methods and discoveries encourage scientists studying biological systems to include RNA metabolic labeling in their toolkit for studying RNA and its role in biological systems.
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29
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJC, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid—a Naturally Occurring 1,2‐Cyclopropene Fatty Acid—by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates**. Angew Chem Int Ed Engl 2022; 61:e202207640. [PMID: 35838324 PMCID: PMC9546306 DOI: 10.1002/anie.202207640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Indexed: 12/25/2022]
Abstract
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2‐cyclopropene‐containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron‐demand Diels–Alder reaction with quenched tetrazine‐fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper‐catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging.
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Affiliation(s)
- Kristine Bertheussen
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Merel van de Plassche
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Iakovia Ttofi
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sander I. van Kasteren
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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30
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Parle D, Bulat F, Fouad S, Zecchini H, Brindle KM, Neves AA, Leeper FJ. Metabolic Glycan Labeling of Cancer Cells Using Variably Acetylated Monosaccharides. Bioconjug Chem 2022; 33:1467-1473. [PMID: 35876696 PMCID: PMC9389531 DOI: 10.1021/acs.bioconjchem.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/06/2022] [Indexed: 11/30/2022]
Abstract
Methylcyclopropene (Cyoc)-tagged tetra-acetylated monosaccharides, and in particular mannosamine derivatives, are promising tools for medical imaging of cancer using metabolic oligosaccharide engineering and the extremely fast inverse electron-demand Diels-Alder bioorthogonal reaction. However, the in vivo potential of these monosaccharide derivatives has yet to be fully explored due to their low aqueous solubility. To address this issue, we sought to vary the extent of acetylation of Cyoc-tagged monosaccharides and probe its effect on the extent of glycan labeling in various cancer cell lines. We demonstrate that, in the case of AcxManNCyoc, tri- and diacetylated derivatives generated significantly enhanced cell labeling compared to the tetra-acetylated monosaccharide. In contrast, for the more readily soluble azide-tagged sugars, a decrease in acetylation led to decreased glycan labeling. Ac3ManNCyoc gave better labeling than the azido-tagged Ac4ManNAz and has significant potential for in vitro and in vivo imaging of glycosylated cancer biomarkers.
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Affiliation(s)
- Daniel
R. Parle
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Flaviu Bulat
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Shahd Fouad
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Heather Zecchini
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Kevin M. Brindle
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - André A. Neves
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Finian J. Leeper
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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31
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Xie F, Jiang H, Jia X, Zhang J, Zhu Z, Du J, Tang Y. Bridgehead Alkene-Enabled Strain-Driven Bioorthogonal Reaction. Org Lett 2022; 24:5304-5308. [PMID: 35849354 DOI: 10.1021/acs.orglett.2c01895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Herein, we report a novel bioorthogonal reaction that hinges on a bridgehead alkene (BHA)-enabled inverse-electron-demand Diels-Alder (IEDDA) cycloaddition. Readily accessible from natural product β-caryophyllene, the strained BHA displays high reactivity toward the IEDDA reaction while maintaining excellent biocompatibility. The developed IEDDA reaction has been applied to in vitro protein labeling and pretargeted live cell imaging.
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Affiliation(s)
- Fayang Xie
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Haolin Jiang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiangqian Jia
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jingyang Zhang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Zhu Zhu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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32
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJ, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid – a Naturally Occurring 1,2‐Cyclopropene Fatty Acid – by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Bertheussen
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | | | - Thomas Bakkum
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Berend Gagestein
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Iakovia Ttofi
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Alexi J.C. Sarris
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Herman S. Overkleeft
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Mario van der Stelt
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Sander Izaak van Kasteren
- Leiden University Leiden Institute of Chemistry Gorlaeus LaboratoryEinsteinweg 55 2333 CC Leiden NETHERLANDS
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33
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Xu W, Shao Z, Tang C, Zhang C, Chen Y, Liang Y. Fluorogenic sydnonimine probes for orthogonal labeling. Org Biomol Chem 2022; 20:5953-5957. [PMID: 35311845 DOI: 10.1039/d2ob00159d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A FRET-based fluorescence turn-on probe is designed, which employs a sydnonimine as the linker to match specific fluorophore and quencher pairs and releases the fluorescence after the "click-and-release" reaction. Furthermore, we realized selective fluorescence labeling by exploiting the mutual orthogonality between sydnonimine-DIBAC and tetrazine-1,3-Cp cycloaddition pairs.
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Affiliation(s)
- Wenyuan Xu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Zhuzhou Shao
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Cheng Tang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Chun Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China.
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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34
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Kumar GS, Racioppi S, Zurek E, Lin Q. Superfast Tetrazole-BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells. J Am Chem Soc 2022; 144:57-62. [PMID: 34964645 PMCID: PMC8982153 DOI: 10.1021/jacs.1c10354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principles computations provide vital insights into the origin of the tetrazole-BCN cycloaddition's superior kinetics compared to the tetrazole-spirohexene cycloaddition. The tetrazole-BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 s.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Stefano Racioppi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Eva Zurek
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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35
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Lee J, Kim J, Heo I, Kim SJ, Lee HY, Jang S, Jang KS, Yang CS, Lee Y, Yoo WC, Min SJ. One-Pot Bifunctionalization of Silica Nanoparticles Conjugated with Bioorthogonal Linkers: Application in Dual-modal Imaging. Biomater Sci 2022; 10:3540-3546. [DOI: 10.1039/d2bm00258b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent surface modification of silica nanoparticles (SNPs) offers great potential for the development of multimodal nanomaterials for biomedical applications. Herein, we report the synthesis of covalently conjugated bifunctional SNPs and...
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36
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Sun H, Xue Q, Zhang C, Wu H, Feng P. Derivatization based on tetrazine scaffolds: synthesis of tetrazine derivatives and their biomedical applications. Org Chem Front 2022. [DOI: 10.1039/d1qo01324f] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The recent advances in tetrazine scaffold-based derivatizations have been summarized. The advantages and limitations of derivatization methods and applications of the developed tetrazine derivatives in bioorthogonal chemistry have been highlighted.
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Affiliation(s)
- Hongbao Sun
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qinghe Xue
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chang Zhang
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center (HMRRC), Department of Radiology, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Feng
- Clinical Trial Center, West China Hospital of Sichuan University, Chengdu 610041, China
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37
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Zhang X, Xu H, Li J, Su D, Mao W, Shen G, Li L, Wu H. Isonitrile induced bioorthogonal activation of fluorophores and mutually orthogonal cleavage in live cells. Chem Commun (Camb) 2021; 58:573-576. [PMID: 34913446 DOI: 10.1039/d1cc05774j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fluorophores with different emission wavelengths were efficiently quenched by a tert-butyl terminated tetrazylmethyl group and activated by an isonitrile-tetrazine click-to-release reaction. Nucleic acid templated chemistry significantly accelerated this bioorthogonal cleavage. Moreover, two mutually orthogonal fluorogenic cleavage reactions were simultaneously conducted in live cells for the first time.
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Affiliation(s)
- Xiaoyang Zhang
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hui Xu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jie Li
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Dunyan Su
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Wuyu Mao
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Guohua Shen
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lin Li
- Laboratory of Clinical Nuclear Medicine, Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
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38
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Kataki-Anastasakou A, Hernandez S, Sletten EM. Cell-surface Labeling via Bioorthogonal Host-Guest Chemistry. ACS Chem Biol 2021; 16:2124-2129. [PMID: 34669367 DOI: 10.1021/acschembio.1c00494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The widespread adoption of the bioorthogonal chemical reporter strategy revolutionized chemical biology. However, its translation to living mammals has been challenging, due to the size/stability properties of the chemical reporter group and/or the reaction kinetics of the labeling step. While developing new bioorthogonal reactions has been the traditional approach to optimizing the bioorthogonal chemical reporter strategy, here we present a different avenue, leveraging intermolecular interactions, to create bioorthogonal host-guest pairs. This approach, deemed "bioorthogonal complexation, does not rely on activated functional groups or second-order rate constants. We utilize the cucurbit[7]uril (CB[7]) scaffold to showcase bioorthogonal complexation and determine that medium-affinity (Ka ≈ 108-109 M-1) guests efficiently label cell surfaces and outperform the strain-promoted azide-alkyne cycloaddition. Finally, we implement bioorthogonal complexation in the chemical reporter strategy through the metabolic incorporation of ortho-carborane into cell-surface glycans and detection with a CB[7]-fluorescein conjugate.
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Affiliation(s)
- Anna Kataki-Anastasakou
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Selena Hernandez
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Ellen M. Sletten
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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39
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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40
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Saha A, Bello D, Fernández-Tejada A. Advances in chemical probing of protein O-GlcNAc glycosylation: structural role and molecular mechanisms. Chem Soc Rev 2021; 50:10451-10485. [PMID: 34338261 PMCID: PMC8451060 DOI: 10.1039/d0cs01275k] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Indexed: 12/11/2022]
Abstract
The addition of O-linked-β-D-N-acetylglucosamine (O-GlcNAc) onto serine and threonine residues of nuclear and cytoplasmic proteins is an abundant, unique post-translational modification governing important biological processes. O-GlcNAc dysregulation underlies several metabolic disorders leading to human diseases, including cancer, neurodegeneration and diabetes. This review provides an extensive summary of the recent progress in probing O-GlcNAcylation using mainly chemical methods, with a special focus on discussing mechanistic insights and the structural role of O-GlcNAc at the molecular level. We highlight key aspects of the O-GlcNAc enzymes, including development of OGT and OGA small-molecule inhibitors, and describe a variety of chemoenzymatic and chemical biology approaches for the study of O-GlcNAcylation. Special emphasis is placed on the power of chemistry in the form of synthetic glycopeptide and glycoprotein tools for investigating the site-specific functional consequences of the modification. Finally, we discuss in detail the conformational effects of O-GlcNAc glycosylation on protein structure and stability, relevant O-GlcNAc-mediated protein interactions and its molecular recognition features by biological receptors. Future research in this field will provide novel, more effective chemical strategies and probes for the molecular interrogation of O-GlcNAcylation, elucidating new mechanisms and functional roles of O-GlcNAc with potential therapeutic applications in human health.
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Affiliation(s)
- Abhijit Saha
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
| | - Davide Bello
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
| | - Alberto Fernández-Tejada
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain
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41
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Nellinger S, Rapp MA, Southan A, Wittmann V, Kluger PJ. An Advanced 'clickECM' That Can be Modified by the Inverse-Electron-Demand Diels-Alder Reaction. Chembiochem 2021; 23:e202100266. [PMID: 34343379 PMCID: PMC9291553 DOI: 10.1002/cbic.202100266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/02/2021] [Indexed: 11/11/2022]
Abstract
The extracellular matrix (ECM) represents the natural environment of cells in tissue and therefore is a promising biomaterial in a variety of applications. Depending on the purpose, it is necessary to equip the ECM with specific addressable functional groups for further modification with bioactive molecules, for controllable cross-linking and/or covalent binding to surfaces. Metabolic glycoengineering (MGE) enables the specific modification of the ECM with such functional groups without affecting the native structure of the ECM. In a previous approach (S. M. Ruff, S. Keller, D. E. Wieland, V. Wittmann, G. E. M. Tovar, M. Bach, P. J. Kluger, Acta Biomater. 2017, 52, 159-170), we demonstrated the modification of an ECM with azido groups, which can be addressed by bioorthogonal copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here, we demonstrate the modification of an ECM with dienophiles (terminal alkenes, cyclopropene), which can be addressed by an inverse-electron-demand Diels-Alder (IEDDA) reaction. This reaction is cell friendly as there are no cytotoxic catalysts needed. We show the equipment of the ECM with a bioactive molecule (enzyme) and prove that the functional groups do not influence cellular behavior. Thus, this new material has great potential for use as a biomaterial, which can be individually modified in a wide range of applications.
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Affiliation(s)
- Svenja Nellinger
- Reutlingen Research Institute, Reutlingen University, School of Applied Chemistry, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Mareike A Rapp
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Alexander Southan
- Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Petra J Kluger
- Reutlingen Research Institute, Reutlingen University, School of Applied Chemistry, Alteburgstr. 150, 72762, Reutlingen, Germany
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42
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Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push-Pull-Activated Linear Alkynes. Angew Chem Int Ed Engl 2021; 60:16947-16952. [PMID: 34019705 DOI: 10.1002/anie.202104863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/16/2021] [Indexed: 01/14/2023]
Abstract
A bioorthogonal reaction between N,N-dialkylhydroxylamines and push-pull-activated halogenated alkynes is described. We explore the use of rehybridization effects in activating alkynes, and we show that electronic effects, when competing stereoelectronic and inductive factors are properly balanced, sufficiently activate a linear alkyne in the uncatalyzed conjugative retro-Cope elimination reaction while adequately protecting it against cellular nucleophiles. This design preserves the low steric profile of an alkyne and pairs it with a comparably unobtrusive hydroxylamine. The kinetics are on par with those of the fastest strain-promoted azide-alkyne cycloaddition reactions, the products regioselectively formed, the components sufficiently stable and easily installed, and the reaction suitable for cellular labeling.
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Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheldon T Cheung
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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43
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Hu Y, Schomaker JM. Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions. Chembiochem 2021; 22:3254-3262. [PMID: 34261195 DOI: 10.1002/cbic.202100164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed 'mutually orthogonal'. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Jennifer M Schomaker
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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44
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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45
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Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push–Pull‐Activated Linear Alkynes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Sheldon T. Cheung
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Justin Kim
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
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46
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Bilodeau DA, Margison KD, Serhan M, Pezacki JP. Bioorthogonal Reactions Utilizing Nitrones as Versatile Dipoles in Cycloaddition Reactions. Chem Rev 2021; 121:6699-6717. [PMID: 33464040 DOI: 10.1021/acs.chemrev.0c00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemical reactions have emerged as convenient and rapid methods for incorporating unnatural functionality into living systems. Different prototype reactions have been optimized for use in biological settings. Optimization of 3 + 2 dipolar cycloadditions involving nitrones has resulted in highly efficient reaction conditions for bioorthogonal chemistry. Through substitution at the nitrone carbon or nitrogen atom, stereoelectronic tuning of the reactivity of the dipole has assisted in optimizing reactivity. Nitrones have been shown to react rapidly with cyclooctynes with bimolecular rate constants approaching k2 = 102 M-1 s-1, which are among the fastest bioorthogonal reactions reported (McKay et al. Org. Biomol. Chem. 2012, 10, 3066-3070). Nitrones have also been shown to react with trans-cyclooctenes (TCO) in strain-promoted TCO-nitrone cycloadditions reactions. Copper catalyzed reactions involving alkynes and nitrones have also been optimized for applications in biology. This review provides a comprehensive accounting of the different bioorthogonal reactions that have been developed using nitrones as versatile reactants, and provides some recent examples of applications for probing biological systems.
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Affiliation(s)
- Didier A Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Kaitlyn D Margison
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Mariam Serhan
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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47
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Kim EJ. Advances in Strategies and Tools Available for Interrogation of Protein O-GlcNAcylation. Chembiochem 2021; 22:3010-3026. [PMID: 34101962 DOI: 10.1002/cbic.202100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/08/2021] [Indexed: 11/08/2022]
Abstract
The attachment of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine and threonine residues of numerous proteins in the nucleus, cytoplasm, and mitochondria is a reversible post-translational modification (PTM) and plays an important role as a regulator of various cellular processes in both healthy and disease states. Advances in strategies and tools that allow for the detection of dynamic O-GlcNAcylation on cellular proteins have helped to enhance our initial and ongoing understanding of its dynamic effects on cellular stimuli and given insights into its link to the pathogenesis of several chronic diseases. Furthermore, chemical genetic strategies and related tools have been successfully applied to a myriad of biological systems with a new level of spatiotemporal and molecular precision. These strategies have started to be used in studying and controlling O-GlcNAcylation both in vivo and in vitro. In this minireview, overviews of recent advances in molecular tools being applied to the detection and identification of O-GlcNAcylation on cellular proteins as well as on individual proteins are provided. In addition, chemical genetic strategies that have already been applied or are potentially usable in O-GlcNAc functional are also discussed.
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Affiliation(s)
- Eun Ju Kim
- Daegu University, Gyeongsan-Si, Gyeongsangbuk-do, Republic of Korea
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48
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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49
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Tharp JM, Vargas-Rodriguez O, Schepartz A, Söll D. Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons. ACS Chem Biol 2021; 16:766-774. [PMID: 33723984 DOI: 10.1021/acschembio.1c00120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We recently described an orthogonal initiator tRNA (itRNATy2) that can initiate protein synthesis with noncanonical amino acids (ncAAs) in response to the UAG nonsense codon. Here, we report that a mutant of itRNATy2 (itRNATy2AUA) can efficiently initiate translation in response to the UAU tyrosine codon, giving rise to proteins with an ncAA at their N-terminus. We show that, in cells expressing itRNATy2AUA, UAU can function as a dual-use codon that selectively encodes ncAAs at the initiating position and predominantly tyrosine at elongating positions. Using itRNATy2AUA, in conjunction with its cognate tyrosyl-tRNA synthetase and two mutually orthogonal pyrrolysyl-tRNA synthetases, we demonstrate that UAU can be reassigned along with UAG or UAA to encode two distinct ncAAs in the same protein. Furthermore, by engineering the substrate specificity of one of the pyrrolysyl-tRNA synthetases, we developed a triply orthogonal system that enables simultaneous reassignment of UAU, UAG, and UAA to produce proteins containing three distinct ncAAs at precisely defined sites. To showcase the utility of this system, we produced proteins containing two or three ncAAs, with unique bioorthogonal functional groups, and demonstrate that these proteins can be separately modified with multiple fluorescent probes.
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50
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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