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Ma P, Svatunek D, Zhu Z, Boger DL, Duan XH, Houk KN. Computational Studies of Reactions of 1,2,4,5-Tetrazines with Enamines in MeOH and HFIP. J Am Chem Soc 2024; 146:18706-18713. [PMID: 38941192 DOI: 10.1021/jacs.4c06067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The reaction between 1,2,4,5-tetrazines and alkenes in polar solvents proceeds through a Diels-Alder cycloaddition along the C-C axis (C3/C6 cycloaddition) of the tetrazine, followed by dinitrogen loss. By contrast, the reactions of 1,2,4,5-tetrazines with enamines in hexafluoroisopropanol (HFIP) give 1,2,4-triazine products stemming from a formal Diels-Alder addition across the N-N axis (N1/N4 cycloaddition). We explored the mechanism of this interesting solvent effect through DFT calculations in detail and revealed a novel reaction pathway characterized by C-N bond formation, deprotonation, and a 3,3-sigmatropic rearrangement. The participation of an HFIP molecule was found to be crucial to the N1/N4 selectivity over C3/C6 due to the more favored initial C-N bond formation than C-C bond formation.
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Affiliation(s)
- Pengchen Ma
- Department of Chemistry, School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Material Chemistry and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - 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
| | - Zixi Zhu
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dale L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xin-Hua Duan
- Department of Chemistry, School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Material Chemistry and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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2
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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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3
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Colombano A, Dalponte L, Dall'Angelo S, Clemente C, Idress M, Ghazal A, Houssen WE. Chemoenzymatic Late-Stage Modifications Enable Downstream Click-Mediated Fluorescent Tagging of Peptides. Angew Chem Int Ed Engl 2023; 62:e202215979. [PMID: 36815722 PMCID: PMC10946513 DOI: 10.1002/anie.202215979] [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: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/24/2023]
Abstract
Aromatic prenyltransferases from cyanobactin biosynthetic pathways catalyse the chemoselective and regioselective intramolecular transfer of prenyl/geranyl groups from isoprene donors to an electron-rich position in these macrocyclic and linear peptides. These enzymes often demonstrate relaxed substrate specificity and are considered useful biocatalysts for structural diversification of peptides. Herein, we assess the isoprene donor specificity of the N1-tryptophan prenyltransferase AcyF from the anacyclamide A8P pathway using a library of 22 synthetic alkyl pyrophosphate analogues, of which many display reactive groups that are amenable to additional functionalization. We further used AcyF to introduce a reactive moiety into a tryptophan-containing cyclic peptide and subsequently used click chemistry to fluorescently label the enzymatically modified peptide. This chemoenzymatic strategy allows late-stage modification of peptides and is useful for many applications.
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Affiliation(s)
- Alessandro Colombano
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Luca Dalponte
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Sergio Dall'Angelo
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Claudia Clemente
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Mohannad Idress
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
- Abzena, Babraham Research CampusCambridgeUK
| | - Ahmad Ghazal
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Wael E. Houssen
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
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4
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Meyvacı E, Öztürk T. Modification of Poly(Styrene‐co‐Acrylonitrile) with Tetrazine by Inverse Electron Demand Diels‐Alder Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202200668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ergül Meyvacı
- Giresun University Department of Chemistry 28200 Giresun Turkey
| | - Temel Öztürk
- Giresun University Department of Chemistry 28200 Giresun Turkey
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5
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Briou B, Améduri B, Boutevin B. Trends in the Diels-Alder reaction in polymer chemistry. Chem Soc Rev 2021; 50:11055-11097. [PMID: 34605835 DOI: 10.1039/d0cs01382j] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Diels-Alder (DA) reaction is regarded as quite a useful strategy in organic and macromolecular syntheses. The reversibility of this reaction and the advent of self-repair technology, as well as other applications in controlled macromolecular architectures and crosslinking, have strongly boosted the research activity, which is still attracting a huge interest in both academic and industrial research. The DA reaction is a simple and scalable toolbox. Though it is well-established that furan/maleimide is the most studied diene/dienophile couple, this perspective article reports strategies using other reversible systems with deeper features on other types of diene/dienophile pairs being either petro-sourced (cyclopentadiene, anthracene) or bio-sourced (muconic and sorbic acids, myrcene and farnesene derivatives, eugenol, cardanol). This review is composed of four sections. The first one briefly recalls the background on the DA reactions involving cyclodimerizations, dienes, and dienophiles, parameters affecting the reaction, while the second part deals with the furan/maleimide reaction. The third one deals with petro-sourced and bio-sourced (or products becoming bio-sourced) reactants involved in DA reactions are also listed and discussed. Finally, the authors' opinion is given on the potential future of the crosslinking-decrosslinking reaction, especially regarding the process (e.g., key temperatures of decrosslinking) or possibly monocomponents. It presents both fundamental and applied research on the DA reaction and its applications.
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Affiliation(s)
- Benoit Briou
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
| | - Bruno Améduri
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
| | - Bernard Boutevin
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
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6
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Mende M, Bordoni V, Tsouka A, Loeffler FF, Delbianco M, Seeberger PH. Multivalent glycan arrays. Faraday Discuss 2020; 219:9-32. [PMID: 31298252 DOI: 10.1039/c9fd00080a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glycan microarrays have become a powerful technology to study biological processes, such as cell-cell interaction, inflammation, and infections. Yet, several challenges, especially in multivalent display, remain. In this introductory lecture we discuss the state-of-the-art glycan microarray technology, with emphasis on novel approaches to access collections of pure glycans and their immobilization on surfaces. Future directions to mimic the natural glycan presentation on an array format, as well as in situ generation of combinatorial glycan collections, are discussed.
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Affiliation(s)
- Marco Mende
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
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7
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Agramunt J, Ginesi R, Pedroso E, Grandas A. Inverse Electron-Demand Diels–Alder Bioconjugation Reactions Using 7-Oxanorbornenes as Dienophiles. J Org Chem 2020; 85:6593-6604. [DOI: 10.1021/acs.joc.0c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jordi Agramunt
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Rebecca Ginesi
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Enrique Pedroso
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- IBUB, Facultat de Quı́mica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Anna Grandas
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- IBUB, Facultat de Quı́mica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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8
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Pagel M. Inverse electron demand Diels-Alder (IEDDA) reactions in peptide chemistry. J Pept Sci 2019; 25:e3141. [PMID: 30585397 DOI: 10.1002/psc.3141] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 01/05/2023]
Abstract
Click chemistry is applied to selectively modify, lable and ligate peptides for their use as therapeutics, in biomaterials or analytical investigations. The inverse electron demand Diels-Alder (IEDDA) reaction is a catalyst-free click reaction with pronounced chemoselectivity and fast reaction rates. Applications and achievements of the IEDDA reaction in peptide chemistry since 2008 are described in this review.
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Affiliation(s)
- Mareen Pagel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Leipzig, Germany
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9
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Abstract
The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.
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Affiliation(s)
- Christopher D. Spicer
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
| | - E. Thomas Pashuck
- NJ
Centre for Biomaterials, Rutgers University, 145 Bevier Road, Piscataway, New Jersey United States
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London, United Kingdom
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10
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Stéen EJL, Edem PE, Nørregaard K, Jørgensen JT, Shalgunov V, Kjaer A, Herth MM. Pretargeting in nuclear imaging and radionuclide therapy: Improving efficacy of theranostics and nanomedicines. Biomaterials 2018; 179:209-245. [PMID: 30007471 DOI: 10.1016/j.biomaterials.2018.06.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 01/18/2023]
Abstract
Pretargeted nuclear imaging and radiotherapy have recently attracted increasing attention for diagnosis and treatment of cancer with nanomedicines. This is because it conceptually offers better imaging contrast and therapeutic efficiency while reducing the dose to radiosensitive tissues compared to conventional strategies. In conventional imaging and radiotherapy, a directly radiolabeled nano-sized vector is administered and allowed to accumulate in the tumor, typically on a timescale of several days. In contrast, pretargeting is based on a two-step approach. First, a tumor-accumulating vector carrying a tag is administered followed by injection of a fast clearing radiolabeled agent that rapidly recognizes the tag of the tumor-bound vector in vivo. Therefore, pretargeting circumvents the use of long-lived radionuclides that is a necessity for sufficient tumor accumulation and target-to-background ratios using conventional approaches. In this review, we give an overview of recent advances in pretargeted imaging strategies. We will critically reflect on the advantages and disadvantages of current state-of-the-art conventional imaging approaches and compare them to pretargeted strategies. We will discuss the pretargeted imaging concept and the involved chemistry. Finally, we will discuss the steps forward in respect to clinical translation, and how pretargeted strategies could be applied to improve state-of-the-art radiotherapeutic approaches.
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Affiliation(s)
- E Johanna L Stéen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Patricia E Edem
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100 Copenhagen, Denmark
| | - Kamilla Nørregaard
- Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100 Copenhagen, Denmark
| | - Jesper T Jørgensen
- Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100 Copenhagen, Denmark
| | - Vladimir Shalgunov
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100 Copenhagen, Denmark
| | - Matthias M Herth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.
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11
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Zhu J, Hiltz J, Tefashe UM, Mauzeroll J, Lennox RB. Microcontact Printing Patterning of an HOPG Surface by an Inverse Electron Demand Diels-Alder Reaction. Chemistry 2018; 24:8904-8909. [PMID: 29873118 DOI: 10.1002/chem.201801326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 11/08/2022]
Abstract
The chemical modification of an sp2 hybridized carbon surface in a controllable manner is very challenging but also crucial for many applications. An inverse electron demand Diels-Alder (IEDDA) reaction using microcontact printing technique is introduced to spatially control the modification of a highly ordered pyrolytic graphite (HOPG) surface under ambient conditions. The covalent modification was characterized by Raman spectroscopy, XPS, and SECM. Tetrazine derivatives can effectively react with an HOPG surface and with microcontact printing methods resulting in spatially patterned surfaces being produced with micrometer-scale resolution.
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Affiliation(s)
- Jun Zhu
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
| | - Jonathan Hiltz
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
| | - Ushula M Tefashe
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
| | - R Bruce Lennox
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 2K6, Canada
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12
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Bojarová P, Křen V. Sugared biomaterial binding lectins: achievements and perspectives. Biomater Sci 2018; 4:1142-60. [PMID: 27075026 DOI: 10.1039/c6bm00088f] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lectins, a distinct group of glycan-binding proteins, play a prominent role in the immune system ranging from pathogen recognition and tuning of inflammation to cell adhesion or cellular signalling. The possibilities of their detailed study expanded along with the rapid development of biomaterials in the last decade. The immense knowledge of all aspects of glycan-lectin interactions both in vitro and in vivo may be efficiently used in bioimaging, targeted drug delivery, diagnostic and analytic biological methods. Practically applicable examples comprise photoluminescence and optical biosensors, ingenious three-dimensional carbohydrate microarrays for high-throughput screening, matrices for magnetic resonance imaging, targeted hyperthermal treatment of cancer tissues, selective inhibitors of bacterial toxins and pathogen-recognising lectin receptors, and many others. This review aims to present an up-to-date systematic overview of glycan-decorated biomaterials promising for interactions with lectins, especially those applicable in biology, biotechnology or medicine. The lectins of interest include galectin-1, -3 and -7 participating in tumour progression, bacterial lectins from Pseudomonas aeruginosa (PA-IL), E. coli (Fim-H) and Clostridium botulinum (HA33) or DC-SIGN, receptors of macrophages and dendritic cells. The spectrum of lectin-binding biomaterials covered herein ranges from glycosylated organic structures, calixarene and fullerene cores over glycopeptides and glycoproteins, functionalised carbohydrate scaffolds of cyclodextrin or chitin to self-assembling glycopolymer clusters, gels, micelles and liposomes. Glyconanoparticles, glycan arrays, and other biomaterials with a solid core are described in detail, including inorganic matrices like hydroxyapatite or stainless steel for bioimplants.
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Affiliation(s)
- P Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
| | - V Křen
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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13
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Sen R, Gahtory D, Escorihuela J, Firet J, Pujari SP, Zuilhof H. Approach Matters: The Kinetics of Interfacial Inverse-Electron Demand Diels-Alder Reactions. Chemistry 2017; 23:13015-13022. [PMID: 28703436 PMCID: PMC5637934 DOI: 10.1002/chem.201703103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 11/11/2022]
Abstract
Rapid and quantitative click functionalization of surfaces remains an interesting challenge in surface chemistry. In this regard, inverse electron demand Diels-Alder (IEDDA) reactions represent a promising metal-free candidate. Herein, we reveal quantitative surface functionalization within 15 min. Furthermore, we report the comprehensive effects of substrate stereochemistry, surrounding microenvironment and substrate order on the reaction kinetics as obtained by surface-bound mass spectrometry (DART-HRMS).
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Affiliation(s)
- Rickdeb Sen
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Digvijay Gahtory
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jorge Escorihuela
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Judith Firet
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Sidharam P Pujari
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin, P.R. China.,Department of Chemical and Materials Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
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14
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Abstract
Not only are glycan-mediated binding processes in cells and organisms essential for a wide range of physiological processes, but they are also implicated in various pathological processes. As a result, elucidation of glycan-associated biomolecular interactions and their consequences is of great importance in basic biological research and biomedical applications. In 2002, we and others were the first to utilize glycan microarrays in efforts aimed at the rapid analysis of glycan-associated recognition events. Because they contain a number of glycans immobilized in a dense and orderly manner on a solid surface, glycan microarrays enable multiple parallel analyses of glycan-protein binding events while utilizing only small amounts of glycan samples. Therefore, this microarray technology has become a leading edge tool in studies aimed at elucidating roles played by glycans and glycan binding proteins in biological systems. In this Account, we summarize our efforts on the construction of glycan microarrays and their applications in studies of glycan-associated interactions. Immobilization strategies of functionalized and unmodified glycans on derivatized glass surfaces are described. Although others have developed immobilization techniques, our efforts have focused on improving the efficiencies and operational simplicity of microarray construction. The microarray-based technology has been most extensively used for rapid analysis of the glycan binding properties of proteins. In addition, glycan microarrays have been employed to determine glycan-protein interactions quantitatively, detect pathogens, and rapidly assess substrate specificities of carbohydrate-processing enzymes. More recently, the microarrays have been employed to identify functional glycans that elicit cell surface lectin-mediated cellular responses. Owing to these efforts, it is now possible to use glycan microarrays to expand the understanding of roles played by glycans and glycan binding proteins in biological systems.
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Affiliation(s)
- Ji Young Hyun
- National Creative Research Initiative Center
for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Jaeyoung Pai
- National Creative Research Initiative Center
for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Injae Shin
- National Creative Research Initiative Center
for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 03722, Korea
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15
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Buhl M, Traboni S, Körsgen M, Lamping S, Arlinghaus HF, Ravoo BJ. On surface O-glycosylation by catalytic microcontact printing. Chem Commun (Camb) 2017; 53:6203-6206. [DOI: 10.1039/c7cc02505j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbohydrate microarrays are made by microcontact printing of glycosyl donors on hydroxyl terminated substrates.
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Affiliation(s)
- Moritz Buhl
- Organic Chemistry Institute and Center for Soft Nanoscience
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Serena Traboni
- Department of Chemical Sciences
- University of Naples Federico II
- I-80126 Naples
- Italy
| | - Martin Körsgen
- Physics Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Sebastian Lamping
- Organic Chemistry Institute and Center for Soft Nanoscience
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | | | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
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16
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Petrelli A, Samain E, Pradeau S, Halila S, Fort S. Efficient Conjugation of Oligosaccharides to Polymer Particles through Furan/Maleimide Diels-Alder Reaction: Application to the Capture of Carbohydrate-Binding Proteins. Chembiochem 2016; 18:206-212. [DOI: 10.1002/cbic.201600509] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Antoine Petrelli
- Université Grenoble Alpes; CERMAV; 38000 Grenoble France
- CNRS; CERMAV; 38000 Grenoble France
| | - Eric Samain
- Université Grenoble Alpes; CERMAV; 38000 Grenoble France
- CNRS; CERMAV; 38000 Grenoble France
| | - Stéphanie Pradeau
- Université Grenoble Alpes; CERMAV; 38000 Grenoble France
- CNRS; CERMAV; 38000 Grenoble France
| | - Sami Halila
- Université Grenoble Alpes; CERMAV; 38000 Grenoble France
- CNRS; CERMAV; 38000 Grenoble France
| | - Sébastien Fort
- Université Grenoble Alpes; CERMAV; 38000 Grenoble France
- CNRS; CERMAV; 38000 Grenoble France
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17
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Sminia TJ, Zuilhof H, Wennekes T. Getting a grip on glycans: A current overview of the metabolic oligosaccharide engineering toolbox. Carbohydr Res 2016; 435:121-141. [PMID: 27750120 DOI: 10.1016/j.carres.2016.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022]
Abstract
This review discusses the advances in metabolic oligosaccharide engineering (MOE) from 2010 to 2016 with a focus on the structure, preparation, and reactivity of its chemical probes. A brief historical overview of MOE is followed by a comprehensive overview of the chemical probes currently available in the MOE molecular toolbox and the bioconjugation techniques they enable. The final part of the review focusses on the synthesis of a selection of probes and finishes with an outlook on recent and potential upcoming advances in the field of MOE.
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Affiliation(s)
- Tjerk J Sminia
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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18
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Späte AK, Dold JEGA, Batroff E, Schart VF, Wieland DE, Baudendistel OR, Wittmann V. Exploring the Potential of Norbornene-Modified Mannosamine Derivatives for Metabolic Glycoengineering. Chembiochem 2016; 17:1374-83. [DOI: 10.1002/cbic.201600197] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Anne-Katrin Späte
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Jeremias E. G. A. Dold
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Ellen Batroff
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Verena F. Schart
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Daniel E. Wieland
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Oliver R. Baudendistel
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
| | - Valentin Wittmann
- University of Konstanz; Department of Chemistry; and Konstanz Research School Chemical Biology (KoRS-CB); 78457 Konstanz Germany
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19
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Freidel C, Kaloyanova S, Peneva K. Chemical tags for site-specific fluorescent labeling of biomolecules. Amino Acids 2016; 48:1357-72. [DOI: 10.1007/s00726-016-2204-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/18/2016] [Indexed: 01/24/2023]
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20
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Svatunek D, Denk C, Rosecker V, Sohr B, Hametner C, Allmaier G, Fröhlich J, Mikula H. Efficient low-cost preparation of trans-cyclooctenes using a simplified flow setup for photoisomerization. MONATSHEFTE FUR CHEMIE 2016; 147:579-585. [PMID: 27069284 PMCID: PMC4785212 DOI: 10.1007/s00706-016-1668-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Abstract Bioorthogonal ligations have emerged as highly versatile chemical tools for biomedical research. The exceptionally fast reaction between 1,2,4,5-tetrazines and trans-cyclooctenes (TCOs), also known as tetrazine ligation, is frequently used in this regard. Growing numbers of applications for the tetrazine ligation led to an increased demand for TCO compounds, whose commercial availability is still very limited. Reported photochemical procedures for the preparation of TCOs using flow chemistry are straightforward and high yielding but require expensive equipment. Within this contribution, we present the construction and characterization of a low-cost flow photoreactor assembled from readily accessible components. Syntheses of all commonly used trans-cyclooctene derivatives were successfully carried out using the described system. We are convinced that the presented system for photoisomerization will promote access to bioorthogonally reactive TCO derivatives. Graphical abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s00706-016-1668-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria ; Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Christoph Denk
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | | | - Barbara Sohr
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | | | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
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21
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Yang YF, Liang Y, Liu F, Houk KN. Diels-Alder Reactivities of Benzene, Pyridine, and Di-, Tri-, and Tetrazines: The Roles of Geometrical Distortions and Orbital Interactions. J Am Chem Soc 2016; 138:1660-7. [PMID: 26804318 DOI: 10.1021/jacs.5b12054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cycloadditions of benzene and ten different azabenzenes (pyridine, three diazines, three triazines, and three tetrazines) with the ethylene dienophile have been explored with density functional theory (M06-2X) and analyzed with the distortion/interaction model. Activation barriers correlate closely with both distortion energies and interaction energies over an activation energy range of 45 kcal/mol. The replacement of CH with N increases Diels-Alder reactivity due not only to the more favorable orbital interaction, but also to a decrease in distortion energy. The rates of reactions are greatly influenced by the nature of the bonds being formed: two C-C bonds > one C-C bond, and one C-N bond > two C-N bonds. The activation energy of Diels-Alder reactions correlates very well with reaction energies and with the NICS(0) values of the aromatic dienes. The distortion energy of the Diels-Alder reaction transition states mostly arises from the diene out-of-plane distortion energy.
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Affiliation(s)
- Yun-Fang Yang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Yong Liang
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Fang Liu
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, ‡Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
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22
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Pagel M, Meier R, Braun K, Wiessler M, Beck-Sickinger AG. On-resin Diels–Alder reaction with inverse electron demand: an efficient ligation method for complex peptides with a varying spacer to optimize cell adhesion. Org Biomol Chem 2016; 14:4809-16. [DOI: 10.1039/c6ob00314a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The DARinvon resin is a new orthogonal reaction in peptide synthesis and the benefits for cell adhesion are discussed.
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Affiliation(s)
- Mareen Pagel
- Institute of Biochemistry
- Faculty of Biosciences
- Pharmacy and Psychology
- Leipzig
- Germany
| | - René Meier
- Institute of Biochemistry
- Faculty of Biosciences
- Pharmacy and Psychology
- Leipzig
- Germany
| | - Klaus Braun
- Deutsches Krebsforschungszentrum
- 69120 Heidelberg
- Germany
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23
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Wu X, Su L, Chen G, Jiang M. Deprotection-Induced Micellization of Glycopolymers: Control of Kinetics and Morphologies. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00572] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Xiulong Wu
- The State
Key Laboratory of Molecular Engineering of Polymers, Collaborative
Innovation Center of Polymers and Polymer Composite Materials and
Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Lu Su
- The State
Key Laboratory of Molecular Engineering of Polymers, Collaborative
Innovation Center of Polymers and Polymer Composite Materials and
Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Guosong Chen
- The State
Key Laboratory of Molecular Engineering of Polymers, Collaborative
Innovation Center of Polymers and Polymer Composite Materials and
Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Ming Jiang
- The State
Key Laboratory of Molecular Engineering of Polymers, Collaborative
Innovation Center of Polymers and Polymer Composite Materials and
Department of Macromolecular Science, Fudan University, Shanghai 200433, China
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24
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Busskamp H, Batroff E, Niederwieser A, Abdel-Rahman OS, Winter RF, Wittmann V, Marx A. Efficient labelling of enzymatically synthesized vinyl-modified DNA by an inverse-electron-demand Diels-Alder reaction. Chem Commun (Camb) 2015; 50:10827-9. [PMID: 25089682 DOI: 10.1039/c4cc04332d] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many applications in biotechnology and molecular biology rely on modified nucleotides. Here, we present an approach for the postsynthetic labelling of enzymatically synthesized vinyl-modified DNA by Diels-Alder reaction with inverse electron demand using a tetrazine. Labelling proceeds very efficiently and supersedes several known approaches.
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Affiliation(s)
- Holger Busskamp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
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25
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Best M, Degen A, Baalmann M, Schmidt TT, Wombacher R. Two-step protein labeling by using lipoic acid ligase with norbornene substrates and subsequent inverse-electron demand Diels-Alder reaction. Chembiochem 2015; 16:1158-62. [PMID: 25900689 DOI: 10.1002/cbic.201500042] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 12/24/2022]
Abstract
Inverse-electron-demand Diels-Alder cycloaddition (DAinv ) between strained alkenes and tetrazines is a highly bio-orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two-step labeling protocol for the site-specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA(W37V) ), followed by the covalent attachment of tetrazine-modified fluorophores to the norbornene moiety through the bio-orthogonal DAinv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13-residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two-step labeling strategy to label proteins in cell lysates in a site-specific manner and performed cell-surface labeling on living cells.
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Affiliation(s)
- Marcel Best
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Anna Degen
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Mathis Baalmann
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Tobias T Schmidt
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Richard Wombacher
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany).
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26
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Hörner S, Uth C, Avrutina O, Frauendorf H, Wiessler M, Kolmar H. Combination of inverse electron-demand Diels–Alder reaction with highly efficient oxime ligation expands the toolbox of site-selective peptide conjugations. Chem Commun (Camb) 2015; 51:11130-3. [DOI: 10.1039/c5cc03434e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modular bioconjugation strategy based on stepwise oxime ligation and inverse electron-demand Diels–Alder reaction.
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Affiliation(s)
- S. Hörner
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - C. Uth
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - O. Avrutina
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
| | - H. Frauendorf
- Georg-August-Universität Göttingen
- Institut für Organische und Biomolekulare Chemie
- Zentrale Analytik/Massenspektrometrie
- 37077 Göttingen
- Germany
| | - M. Wiessler
- Deutsches Krebsforschungszentrum
- Medizinische Physik in der Radiologie
- 69120 Heidelberg
- Germany
| | - H. Kolmar
- Technische Universität Darmstadt
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- 64287 Darmstadt
- Germany
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27
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Späte AK, Schart VF, Schöllkopf S, Niederwieser A, Wittmann V. Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering. Chemistry 2014; 20:16502-8. [DOI: 10.1002/chem.201404716] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Indexed: 11/07/2022]
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28
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Späte AK, Schart VF, Häfner J, Niederwieser A, Mayer TU, Wittmann V. Expanding the scope of cyclopropene reporters for the detection of metabolically engineered glycoproteins by Diels-Alder reactions. Beilstein J Org Chem 2014; 10:2235-42. [PMID: 25298790 PMCID: PMC4187077 DOI: 10.3762/bjoc.10.232] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Monitoring glycoconjugates has been tremendously facilitated by the development of metabolic oligosaccharide engineering. Recently, the inverse-electron-demand Diels-Alder reaction between methylcyclopropene tags and tetrazines has become a popular ligation reaction due to the small size and high reactivity of cyclopropene tags. Attaching the cyclopropene tag to mannosamine via a carbamate linkage has made the reaction even more efficient. Here, we expand the application of cyclopropene tags to N-acylgalactosamine and N-acylglucosamine derivatives enabling the visualization of mucin-type O-glycoproteins and O-GlcNAcylated proteins through Diels-Alder chemistry. Whereas the previously reported cyclopropene-labeled N-acylmannosamine derivative leads to significantly higher fluorescence staining of cell-surface glycoconjugates, the glucosamine derivative gave higher labeling efficiency with protein preparations containing also intracellular proteins.
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Affiliation(s)
- Anne-Katrin Späte
- University of Konstanz, Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Verena F Schart
- University of Konstanz, Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Häfner
- University of Konstanz, Department of Biology and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andrea Niederwieser
- University of Konstanz, Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Thomas U Mayer
- University of Konstanz, Department of Biology and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Valentin Wittmann
- University of Konstanz, Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
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29
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Bakalova SM, Gil Santos A. Diels-Alder reactions of chiral isoimidium salts: a computational study. J Org Chem 2014; 79:8202-11. [PMID: 25090582 DOI: 10.1021/jo501407z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recently, important efforts have been devoted to asymmetric Diels-Alder (DA) cycloadditions. Several chiral auxiliaries and catalysts were tested, originating a multitude of selectivities. Here, we study the ability of the isoimidium group as a dienophile activator in DA reactions, as well as its behavior in the induction of selectivity, when incorporated in chiral auxiliary units. We study dienophiles attached to isoimidium auxiliaries derived from (2R,5R)-2,5-diphenylpyrrolidine and from (R)-bis((R)-1-phenylethyl)amine, and show that they lead to low activation energies in DA additions to different dienes. Reported experimental regio- and endo/exo selectitivites are also fully rationalized. While diastereoselectivities originated by (2R,5R)-2,5-diphenylpyrrolidine based dienophiles can easily be rationalized by a C2 symmetric transition state, several transition states have to be simultaneously accounted for the rationalization of the selectivity obtained with dienophiles based on (R)-bis((R)-1-phenylethyl)amine. In this case, the C2 symmetric structure leads to opposite selectivities to those experimentally observed. Thus, while the structures of the dienophiles derived from these two amines seem similar, their behavior in the induction of stereoselectivity in DA reactions is quite different. Our models, which substantially differ from those previously proposed in the literature, can also be adapted to other reactions in which this type of chiral auxiliaries is used.
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Affiliation(s)
- Snezhana M Bakalova
- REQUIMTE, CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova Lisboa , 2829-516 Caparica, Portugal
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30
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Liu F, Liang Y, Houk KN. Theoretical elucidation of the origins of substituent and strain effects on the rates of Diels-Alder reactions of 1,2,4,5-tetrazines. J Am Chem Soc 2014; 136:11483-93. [PMID: 25041719 DOI: 10.1021/ja505569a] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Diels-Alder reactions of seven 1,2,4,5-tetrazines with unstrained and strained alkenes and alkynes were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The higher reactivities of alkenes compared to alkynes in the Diels-Alder reactions with tetrazines arise from the differences in both interaction and distortion energies. Alkenes have HOMO energies higher than those of alkynes and therefore stronger interaction energies in inverse-electron-demand Diels-Alder reactions with tetrazines. We have also found that the energies to distort alkenes into the Diels-Alder transition-state geometries are smaller than for alkynes in these reactions. The strained dienophiles, trans-cyclooctene and cyclooctyne, are much more reactive than unstrained trans-2-butene and 2-butyne, because they are predistorted toward the Diels-Alder transition structures. The reactivities of substituted tetrazines correlate with the electron-withdrawing abilities of the substituents. Electron-withdrawing groups lower the LUMO+1 of tetrazines, resulting in stronger interactions with the HOMO of dienophiles. Moreover, electron-withdrawing substituents destabilize the tetrazines, and this leads to smaller distortion energies in the Diels-Alder transition states.
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Affiliation(s)
- Fang Liu
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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31
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Arraying the post-translational glycoproteome (PTG). Curr Opin Chem Biol 2014; 18:62-9. [DOI: 10.1016/j.cbpa.2014.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 11/30/2022]
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32
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Roling O, Mardyukov A, Lamping S, Vonhören B, Rinnen S, Arlinghaus HF, Studer A, Ravoo BJ. Surface patterning with natural and synthetic polymers via an inverse electron demand Diels–Alder reaction employing microcontact chemistry. Org Biomol Chem 2014; 12:7828-35. [DOI: 10.1039/c4ob01379d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bioorthogonal ligation methods are the focus of current research due to their versatile applications in biotechnology and materials science for post-functionalization and immobilization of biomolecules.
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Affiliation(s)
- Oliver Roling
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Artur Mardyukov
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Sebastian Lamping
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Benjamin Vonhören
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Stefan Rinnen
- Physikalisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | | | - Armido Studer
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
| | - Bart Jan Ravoo
- Organisch-Chemisches Institut and Graduate School of Chemistry
- Westfälische Wilhelms-Universität Münster
- 48149 Münster, Germany
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33
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Späte AK, Bußkamp H, Niederwieser A, Schart VF, Marx A, Wittmann V. Rapid Labeling of Metabolically Engineered Cell-Surface Glycoconjugates with a Carbamate-Linked Cyclopropene Reporter. Bioconjug Chem 2013; 25:147-54. [DOI: 10.1021/bc4004487] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anne-Katrin Späte
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Holger Bußkamp
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andrea Niederwieser
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Verena F. Schart
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
| | - Valentin Wittmann
- University of Konstanz, Department of Chemistry and Konstanz Research School
Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457 Konstanz, Germany
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Sun H, Chen GYJ, Yao SQ. Recent advances in microarray technologies for proteomics. ACTA ACUST UNITED AC 2013; 20:685-99. [PMID: 23706635 DOI: 10.1016/j.chembiol.2013.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/01/2013] [Accepted: 04/14/2013] [Indexed: 01/04/2023]
Abstract
Proteins are fundamental components of all living systems and critical drivers of biological functions. The large-scale study of proteins, their structures and functions, is defined as proteomics. This systems-wide analysis leads to a more comprehensive view of the intricate signaling transduction pathways that proteins engage in and improves the overall understanding of the complex processes supporting the living systems. Over the last two decades, the development of high-throughput analytical tools, such as microarray technologies, capable of rapidly analyzing thousands of protein-functioning and protein-interacting events, has fueled the growth of this important field. Herein, we review the most recent advancements in microarray technologies, with a special focus on peptide microarray, small molecule microarray, and protein microarray. These technologies have become prominent players in proteomics and have made significant changes to the landscape of life science and biomedical research. We will elaborate on their performance, advantages, challenges, and future directions.
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Affiliation(s)
- Hongyan Sun
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PRC.
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Zhang CJ, Tan CYJ, Ge J, Na Z, Chen GYJ, Uttamchandani M, Sun H, Yao SQ. Preparation of Small-Molecule Microarrays bytrans-Cyclooctene Tetrazine Ligation and Their Application in the High-Throughput Screening of Protein-Protein Interaction Inhibitors of Bromodomains. Angew Chem Int Ed Engl 2013; 52:14060-4. [DOI: 10.1002/anie.201307803] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 09/30/2013] [Indexed: 01/29/2023]
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Zhang CJ, Tan CYJ, Ge J, Na Z, Chen GYJ, Uttamchandani M, Sun H, Yao SQ. Preparation of Small-Molecule Microarrays bytrans-Cyclooctene Tetrazine Ligation and Their Application in the High-Throughput Screening of Protein-Protein Interaction Inhibitors of Bromodomains. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307803] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Protein arrays as tool for studies at the host-pathogen interface. J Proteomics 2013; 94:387-400. [PMID: 24140974 DOI: 10.1016/j.jprot.2013.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 01/10/2023]
Abstract
Pathogens and parasites encode a wide spectrum of multifunctional proteins interacting to and modifying proteins in host cells. However, the current lack of a reliable method to unveil the protein-protein interactions (PPI) at the host-pathogen interface is retarding our understanding of many important pathogenic processes. Thus, the identification of proteins involved in host-pathogen interactions is important for the elucidation of virulence determinants, mechanisms of infection, host susceptibility and/or disease resistance. In this sense, proteomic technologies have experienced major improvements in recent years and protein arrays are a powerful and modern method for studying PPI in a high-throughput format. This review focuses on these techniques analyzing the state-of-the-art of proteomic technologies and their possibilities to diagnose and explore host-pathogen interactions. Major technical advancements, applications and protocol concerns are presented, so readers can appreciate the immense progress achieved and the current technical options available for studying the host-pathogen interface. Finally, future uses of this kind of array-based proteomic tools in the fight against infectious and parasitic diseases are discussed.
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Bakalova SM, Santos AG. Can Diels-Alder Reactions Lead to trans-Fused Products? A Computational Study of the Competitive [4+2] and [2+4] Cycloaddition of Dienes to α-Aryl-Substituted Cyclohexenones. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Abstract
In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research.
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Affiliation(s)
- Sungjin Park
- National Creative Research Initiative Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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Niederwieser A, Späte AK, Nguyen LD, Jüngst C, Reutter W, Wittmann V. Two-Color Glycan Labeling of Live Cells by a Combination of Diels-Alder and Click Chemistry. Angew Chem Int Ed Engl 2013; 52:4265-8. [DOI: 10.1002/anie.201208991] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/24/2012] [Indexed: 12/24/2022]
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Niederwieser A, Späte AK, Nguyen LD, Jüngst C, Reutter W, Wittmann V. Zweifarbenmarkierung von Glycanen lebender Zellen durch Kombination von Diels-Alder- und Klick-Chemie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208991] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Knall AC, Slugovc C. Inverse electron demand Diels–Alder (iEDDA)-initiated conjugation: a (high) potential click chemistry scheme. Chem Soc Rev 2013; 42:5131-42. [DOI: 10.1039/c3cs60049a] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Hassert R, Pagel M, Ming Z, Häupl T, Abel B, Braun K, Wiessler M, Beck-Sickinger AG. Biocompatible silicon surfaces through orthogonal click chemistries and a high affinity silicon oxide binding peptide. Bioconjug Chem 2012; 23:2129-37. [PMID: 22989005 DOI: 10.1021/bc3003875] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multifunctionality is gaining more and more importance in the field of improved biomaterials. Especially peptides feature a broad chemical variability and are versatile mediators between inorganic surfaces and living cells. Here, we synthesized a unique peptide that binds to SiO(2) with nM affinity. We equipped the peptide with the bioactive integrin binding c[RGDfK]-ligand and a fluorescent probe by stepwise Diels-Alder reaction with inverse electron demand and copper(I) catalyzed azide-alkyne cycloaddition. For the first time, we report the generation of a multifunctional peptide by combining these innovative coupling reactions. The resulting peptide displayed an outstanding binding to silicon oxide and induced a significant increase in cell spreading and cell viability of osteoblasts on the oxidized silicon surface.
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Affiliation(s)
- Rayk Hassert
- Institut für Biochemie, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany
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Grabosch C, Kolbe K, Lindhorst TK. Glycoarrays by a New Tandem Noncovalent-Covalent Modification of Polystyrene Microtiter Plates and their Interrogation with Live Cells. Chembiochem 2012; 13:1874-9. [DOI: 10.1002/cbic.201200365] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Indexed: 01/11/2023]
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Wehner JW, Weissenborn MJ, Hartmann M, Gray CJ, Šardzík R, Eyers CE, Flitsch SL, Lindhorst TK. Dual purpose S-trityl-linkers for glycoarray fabrication on both polystyrene and gold. Org Biomol Chem 2012; 10:8919-26. [DOI: 10.1039/c2ob26118a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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