51
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Tomohiro T, Hatanaka Y. Diazirine-Based Multifunctional Photo-Probes for Affinity-Based Elucidation of Protein-Ligand Interaction. HETEROCYCLES 2014. [DOI: 10.3987/rev-14-803] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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52
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Ahad AM, Jensen SM, Jewett JC. A traceless Staudinger reagent to deliver diazirines. Org Lett 2013; 15:5060-3. [PMID: 24059816 DOI: 10.1021/ol402404n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A triarylphosphine reagent that reacts with organic azides to install amide-linked diazirines is reported. This traceless Staudinger reagent reacts with complex organic azides to yield amide-linked diazirines, thus expanding the scope of the utility of both azide and diazirine chemistry.
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Affiliation(s)
- Ali M Ahad
- University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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53
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Tan E, Almaraz RT, Khanna HS, Du J, Yarema KJ. Experimental Design Considerations for In Vitro Non-Natural Glycan Display via Metabolic Oligosaccharide Engineering. ACTA ACUST UNITED AC 2013; 2:171-94. [PMID: 23839968 DOI: 10.1002/9780470559277.ch100059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metabolic oligosaccharide engineering (MOE) refers to a technique where non-natural monosaccharide analogs are introduced into living biological systems. Once inside a cell, these compounds intercept a targeted biosynthetic glycosylation pathway and in turn are metabolically incorporated into cell-surface-displayed oligosaccharides where they can modulate a host of biological activities or be exploited as "tags" for bio-orthogonal and chemoselective ligation reactions. Undertaking a MOE experiment can be a daunting task based on the growing repertoire of analogs now available and the ever increasing number of metabolic pathways that can be targeted; therefore, a major emphasis of this article is to describe a general approach for analog design and selection and then provide protocols to ensure safe and efficacious analog usage by cells. Once cell-surface glycans have been successfully remodeled by MOE methodology, the stage is set for probing changes to the myriad cellular responses modulated by these versatile molecules. Curr. Protoc. Chem. Biol. 2:171-194 © 2010 by John Wiley & Sons, Inc.
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Affiliation(s)
- Elaine Tan
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland
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54
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Zou C, Loka RS, Zhang Y, Cairo CW. Glycoform remodeling generates a synthetic T cell phenotype. Bioconjug Chem 2013; 24:907-14. [PMID: 23742724 DOI: 10.1021/bc300599w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The glycan of specific proteins can dictate the response of cells to stimuli, and thus their phenotype. We describe a chemical strategy to modify the cellular glycoform of T cells, which resulted in a modified cellular response. Our data indicate that chemical modification of the phosphatase CD45 is responsible for the observed differences in response to receptor cross-linking. By increasing the content of galactose epitopes in the glycocalyx of a lymphoma cell line, we were able to increase the response of the cell to lectin stimulation through the glycoprotein receptor, CD45. The method described here exploits metabolic labeling of a cell to reprogram the cellular response to external stimuli though changes in the number of lectin binding sites on the cell surface.
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Affiliation(s)
- Chunxia Zou
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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55
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Feng L, Hong S, Rong J, You Q, Dai P, Huang R, Tan Y, Hong W, Xie C, Zhao J, Chen X. Bifunctional Unnatural Sialic Acids for Dual Metabolic Labeling of Cell-Surface Sialylated Glycans. J Am Chem Soc 2013; 135:9244-7. [DOI: 10.1021/ja402326z] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lianshun Feng
- School of Chemical Biology and
Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | | | - Jie Rong
- School of Chemical Biology and
Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | | | | | | | | | | | | | - Jing Zhao
- School of Chemical Biology and
Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
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56
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Deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics. Curr Opin Chem Biol 2012; 17:41-8. [PMID: 23276734 DOI: 10.1016/j.cbpa.2012.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 12/02/2012] [Indexed: 01/27/2023]
Abstract
Bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. Despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. This review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor bacterial glycoprotein dynamics, crosslinking sugars to assess the roles of bacterial glycoproteins, and harnessing bacterial glycosylation systems for the efficient production of industrially important glycoproteins.
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57
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Photocrosslinking approaches to interactome mapping. Curr Opin Chem Biol 2012; 17:90-101. [PMID: 23149092 DOI: 10.1016/j.cbpa.2012.10.034] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/22/2012] [Indexed: 11/21/2022]
Abstract
Photocrosslinking approaches can be used to map interactome networks within the context of living cells. Photocrosslinking methods rely on use of metabolic engineering or genetic code expansion to incorporate photocrosslinking analogs of amino acids or sugars into cellular biomolecules. Immunological and mass spectrometry techniques are used to analyze crosslinked complexes, thereby defining specific interactomes. Because photocrosslinking can be conducted in native, cellular settings, it can be used to define context-dependent interactions. Photocrosslinking methods are also ideally suited for determining interactome dynamics, mapping interaction interfaces, and identifying transient interactions in which intrinsically disordered proteins and glycoproteins engage. Here we discuss the application of cell-based photocrosslinking to the study of specific problems in immune cell signaling, transcription, membrane protein dynamics, nucleocytoplasmic transport, and chaperone-assisted protein folding.
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58
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Billing P, Brinker UH. Solvent dependency of the yield of an N-monosubstituted diaziridine: a GC–MS study. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.03.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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59
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Vendrell M, Zhai D, Er JC, Chang YT. Combinatorial strategies in fluorescent probe development. Chem Rev 2012; 112:4391-420. [PMID: 22616565 DOI: 10.1021/cr200355j] [Citation(s) in RCA: 458] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Marc Vendrell
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, 138667 Singapore.
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60
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Almaraz RT, Aich U, Khanna HS, Tan E, Bhattacharya R, Shah S, Yarema KJ. Metabolic oligosaccharide engineering with N-Acyl functionalized ManNAc analogs: cytotoxicity, metabolic flux, and glycan-display considerations. Biotechnol Bioeng 2011; 109:992-1006. [PMID: 22068462 DOI: 10.1002/bit.24363] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 10/19/2011] [Accepted: 10/24/2011] [Indexed: 12/25/2022]
Abstract
Metabolic oligosaccharide engineering (MOE) is a maturing technology capable of modifying cell surface sugars in living cells and animals through the biosynthetic installation of non-natural monosaccharides into the glycocalyx. A particularly robust area of investigation involves the incorporation of azide functional groups onto the cell surface, which can then be further derivatized using "click chemistry." While considerable effort has gone into optimizing the reagents used for the azide ligation reactions, less optimization of the monosaccharide analogs used in the preceding metabolic incorporation steps has been done. This study fills this void by reporting novel butanoylated ManNAc analogs that are used by cells with greater efficiency and less cytotoxicity than the current "gold standard," which are peracetylated compounds such as Ac₄ ManNAz. In particular, tributanoylated, N-acetyl, N-azido, and N-levulinoyl ManNAc analogs with the high flux 1,3,4-O-hydroxyl pattern of butanoylation were compared with their counterparts having the pro-apoptotic 3,4,6-O-butanoylation pattern. The results reveal that the ketone-bearing N-levulinoyl analog 3,4,6-O-Bu₃ ManNLev is highly apoptotic, and thus is a promising anti-cancer drug candidate. By contrast, the azide-bearing analog 1,3,4-O-Bu₃ ManNAz effectively labeled cellular sialoglycans at concentrations ∼3- to 5-fold lower (e.g., at 12.5-25 µM) than Ac₄ ManNAz (50-150 µM) and exhibited no indications of apoptosis even at concentrations up to 400 µM. In summary, this work extends emerging structure activity relationships that predict the effects of short chain fatty acid modified monosaccharides on mammalian cells and also provides a tangible advance in efforts to make MOE a practical technology for the medical and biotechnology communities.
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Affiliation(s)
- Ruben T Almaraz
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, 5029 Robert H. & Clarice Smith Building, 400 North Broadway, Baltimore, Maryland 21231, USA
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61
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Bond MR, Zhang H, Kim J, Yu SH, Yang F, Patrie SM, Kohler JJ. Metabolism of diazirine-modified N-acetylmannosamine analogues to photo-cross-linking sialosides. Bioconjug Chem 2011; 22:1811-23. [PMID: 21838313 DOI: 10.1021/bc2002117] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Terminal sialic acid residues often mediate the interactions of cell surface glycoconjugates. Sialic acid-dependent interactions typically exhibit rapid dissociation rates, precluding the use of traditional biological techniques for complex isolation. To stabilize these transient interactions, we employ a targeted photo-cross-linking approach in which a diazirine photo-cross-linker is incorporated into cell surface sialylated glycoconjugates through the use of metabolic oligosaccharide engineering. We describe three diazirine-modified N-acetylmannosamine (ManNAc) analogues in which the length of the linker between the pyranose ring and the diazirine was varied. These analogues were each metabolized to their respective sialic acid counterparts, which were added to both glycoproteins and glycolipids. Diazirine-modified sialic acid analogues could be incorporated into both α2-3 and α2-6 linkages. Upon exposure to UV irradiation, diazirine-modified glycoconjugates were covalently cross-linked to their interaction partners. We demonstrate that all three diazirine-modified analogues were capable of competing with endogeneous sialic acid, albeit to varying degrees. We found that larger analogues were less efficiently metabolized, yet could still function as effective cross-linkers. Notably, the addition of the diazirine substituent interferes with metabolism of ManNAc analogues to glycans other than sialosides, providing fidelity to selectively incorporate the cross-linker into sialylated molecules. These compounds are nontoxic and display only minimal growth inhibition at the concentrations required for cross-linking studies. This report provides essential information for the deployment of photo-cross-linking analogues to capture and study ephemeral, yet essential, sialic acid-mediated interactions.
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Affiliation(s)
- Michelle R Bond
- Department of Chemistry, Stanford University , Stanford, CA 94305, United States
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62
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Dubinsky L, Krom BP, Meijler MM. Diazirine based photoaffinity labeling. Bioorg Med Chem 2011; 20:554-70. [PMID: 21778062 DOI: 10.1016/j.bmc.2011.06.066] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/19/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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63
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Das J. Aliphatic diazirines as photoaffinity probes for proteins: recent developments. Chem Rev 2011; 111:4405-17. [PMID: 21466226 DOI: 10.1021/cr1002722] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joydip Das
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77204, USA.
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64
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Chou C, Uprety R, Davis L, Chin JW, Deiters A. Genetically encoding an aliphatic diazirine for protein photocrosslinking. Chem Sci 2011. [DOI: 10.1039/c0sc00373e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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65
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Synthesis of bioorthogonal and crosslinking amino acids for use in peptide synthesis. Amino Acids 2010; 39:1381-4. [PMID: 20411286 DOI: 10.1007/s00726-010-0594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022]
Abstract
The ability to incorporate non-canonical amino acids into proteins by genetic or chemical methods allows one to introduce novel chemical properties into a protein at a defined residue. Such a residue may then be modified using common organic transformations. In this way, the structure or function of the peptide may be altered without perturbing any of the other neighbouring amino acids in the peptide chain. Here, we describe the syntheses and potential applications of multiple para-substituted phenylalanine derivatives comprising an isothiocyanate, α-diazoketone, or nitrone functionality. In all, three novel amino acids were synthesized in good overall yields. These non-canonical amino acids permit the further development of in vitro and in vivo chemoselective and regioselective bioconjugate reactions not possible with other reagents.
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66
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Yu SH, Bond MR, Whitman CM, Kohler JJ. Metabolic labeling of glycoconjugates with photocrosslinking sugars. Methods Enzymol 2010; 478:541-62. [PMID: 20816498 DOI: 10.1016/s0076-6879(10)78026-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein-carbohydrate interactions play essential roles in a variety of biological processes. This class of interactions is particularly important in development, immunology, infection, and carcinogenesis. However, the transient nature of glycan-dependent interactions hampers efforts to detect and characterize these complexes. Photocrosslinking is emerging as a powerful tool to discover and study glycan-dependent complexes. Through the use of photocrosslinking groups, UV irradiation can be employed to introduce a covalent bond between two transiently interacting molecules. Here we describe the use of metabolic oligosaccharide engineering to incorporate a photocrosslinkable sugar into cellular glycoconjugates and the use of this photocrosslinker to covalently capture glycan-mediated interactions.
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Affiliation(s)
- Seok-Ho Yu
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, USA
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67
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Mackinnon AL, Taunton J. Target Identification by Diazirine Photo-Cross-linking and Click Chemistry. ACTA ACUST UNITED AC 2009; 1:55-73. [PMID: 23667793 DOI: 10.1002/9780470559277.ch090167] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Target identification of biologically active small-molecules is often the rate-determining step in forward chemical genetics. Photo-affinity labeling (PAL) represents a useful biochemical strategy for target identification in complex protein mixtures. This unit describes the use of alkyl diazirine-based photo-affinity probes and Cu(I)-catalyzed click chemistry to covalently label and visualize the targets of biologically active small-molecules. A general method for affinity purification of probe-modified proteins, useful for identification of protein targets, is also described.
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Affiliation(s)
- Andrew L Mackinnon
- Program in Chemistry and Chemical Biology and Department of Cellular and Molecular Pharmacology University of California, San Francisco San Francisco, California 94158-2280, USA
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68
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Du J, Meledeo MA, Wang Z, Khanna HS, Paruchuri VDP, Yarema KJ. Metabolic glycoengineering: sialic acid and beyond. Glycobiology 2009; 19:1382-401. [PMID: 19675091 DOI: 10.1093/glycob/cwp115] [Citation(s) in RCA: 229] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This report provides a perspective on metabolic glycoengineering methodology developed over the past two decades that allows natural sialic acids to be replaced with chemical variants in living cells and animals. Examples are given demonstrating how this technology provides the glycoscientist with chemical tools that are beginning to reproduce Mother Nature's control over complex biological systems - such as the human brain - through subtle modifications in sialic acid chemistry. Several metabolic substrates (e.g., ManNAc, Neu5Ac, and CMP-Neu5Ac analogs) can be used to feed flux into the sialic acid biosynthetic pathway resulting in numerous - and sometime quite unexpected - biological repercussions upon nonnatural sialoside display in cellular glycans. Once on the cell surface, ketone-, azide-, thiol-, or alkyne-modified glycans can be transformed with numerous ligands via bioorthogonal chemoselective ligation reactions, greatly increasing the versatility and potential application of this technology. Recently, sialic acid glycoengineering methodology has been extended to other pathways with analog incorporation now possible in surface-displayed GalNAc and fucose residues as well as nucleocytoplasmic O-GlcNAc-modified proteins. Finally, recent efforts to increase the "druggability" of sugar analogs used in metabolic glycoengineering, which have resulted in unanticipated "scaffold-dependent" activities, are summarized.
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Affiliation(s)
- Jian Du
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
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