1
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Crawford CJ, Schultz-Johansen M, Luong P, Vidal-Melgosa S, Hehemann JH, Seeberger PH. Automated Synthesis of Algal Fucoidan Oligosaccharides. J Am Chem Soc 2024; 146:18320-18330. [PMID: 38916244 PMCID: PMC11240576 DOI: 10.1021/jacs.4c02348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Fucoidan, a sulfated polysaccharide found in algae, plays a central role in marine carbon sequestration and exhibits a wide array of bioactivities. However, the molecular diversity and structural complexity of fucoidan hinder precise structure-function studies. To address this, we present an automated method for generating well-defined linear and branched α-fucan oligosaccharides. Our syntheses include oligosaccharides with up to 20 cis-glycosidic linkages, diverse branching patterns, and 11 sulfate monoesters. In this study, we demonstrate the utility of these oligosaccharides by (i) characterizing two endo-acting fucoidan glycoside hydrolases (GH107), (ii) utilizing them as standards for NMR studies to confirm suggested structures of algal fucoidans, and (iii) developing a fucoidan microarray. This microarray enabled the screening of the molecular specificity of four monoclonal antibodies (mAb) targeting fucoidan. It was found that mAb BAM4 has cross-reactivity to β-glucans, while mAb BAM2 has reactivity to fucoidans with 4-O-sulfate esters. Knowledge of the mAb BAM2 epitope specificity provided evidence that a globally abundant marine diatom, Thalassiosira weissflogii, synthesizes a fucoidan with structural homology to those found in brown algae. Automated glycan assembly provides access to fucoidan oligosaccharides. These oligosaccharides provide the basis for molecular level investigations into fucoidan's roles in medicine and carbon sequestration.
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Affiliation(s)
- Conor J Crawford
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mikkel Schultz-Johansen
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Phuong Luong
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Peter H Seeberger
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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2
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Li S, Chen Q, Xu Q, Wei Z, Shen Y, Wang H, Cai H, Gu M, Xiao Y. Hierarchical Self-Assembly Molecular Building Blocks as Intelligent Nanoplatforms for Ovarian Cancer Theranostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309547. [PMID: 38408141 PMCID: PMC11077652 DOI: 10.1002/advs.202309547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/05/2024] [Indexed: 02/28/2024]
Abstract
Hierarchical self-assembly from simple building blocks to complex polymers is a feasible approach to constructing multi-functional smart materials. However, the polymerization process of polymers often involves challenges such as the design of building blocks and the drive of external energy. Here, a hierarchical self-assembly with self-driven and energy conversion capabilities based on p-aminophenol and diethylenetriamine building blocks is reported. Through β-galactosidase (β-Gal) specific activation to the self-assembly, the intelligent assemblies (oligomer and superpolymer) with excellent photothermal and fluorescent properties are dynamically formed in situ, and thus the sensitive multi-mode detection of β-Gal activity is realized. Based on the overexpression of β-Gal in ovarian cancer cells, the self-assembly superpolymer is specifically generated in SKOV-3 cells to achieve fluorescence imaging. The photothermal therapeutic ability of the self-assembly oligomer (synthesized in vitro) is evaluated by a subcutaneous ovarian cancer model, showing satisfactory anti-tumor effects. This work expands the construction of intelligent assemblies through the self-driven cascade assembly of small molecules and provides new methods for the diagnosis and treatment of ovarian cancer.
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Affiliation(s)
- Shuo Li
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Jiangsu Institute of HematologyNational Clinical Research Center for Hematologic DiseasesNHC Key Laboratory of Thrombosis and HemostasisThe First Affiliated Hospital and Collaborative Innovation Center of HematologySoochow UniversitySuzhou215006China
| | - Qingrong Chen
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Qi Xu
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Zhongyu Wei
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Yongjin Shen
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Hua Wang
- Department of Gynecological OncologyZhongnan Hospital of Wuhan UniversityHubei Key Laboratory of Tumor Biological BehaviorsHubei Cancer Clinical Study CenterWuhan430071China
| | - Hongbing Cai
- Department of Gynecological OncologyZhongnan Hospital of Wuhan UniversityHubei Key Laboratory of Tumor Biological BehaviorsHubei Cancer Clinical Study CenterWuhan430071China
| | - Meijia Gu
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Yuxiu Xiao
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityKey Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
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3
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Wu L, Chowdhury A, Zhou Z, Chen K, Wang W, Niu J. Precision Cellulose from Living Cationic Polymerization of Glucose 1,2,4-Orthopivalates. J Am Chem Soc 2024; 146:7963-7970. [PMID: 38483110 DOI: 10.1021/jacs.4c01355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Cellulose serves as a sustainable biomaterial for a wide range of applications in biotechnology and materials science. While chemical and enzymatic glycan assembly methods have been developed to access modest quantities of synthetic cellulose for structure-property studies, chemical polymerization strategies for scalable and well-controlled syntheses of cellulose remain underdeveloped. Here, we report the synthesis of precision cellulose via living cationic ring-opening polymerization (CROP) of glucose 1,2,4-orthopivalates. In the presence of dibutyl phosphate as an initiator and triflic acid as a catalyst, precision cellulose with well-controlled molecular weights, defined chain-end groups, and excellent regio- and stereospecificity was readily prepared. We further demonstrated the utility of this method through the synthesis of precision native d-cellulose and rare precision l-cellulose.
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Affiliation(s)
- Lianqian Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Arjun Chowdhury
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Zefeng Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kuiru Chen
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Wenqi Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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4
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Yadav N, Djalali S, Poveda A, Ricardo MG, Seeberger PH, Jiménez-Barbero J, Delbianco M. Dissecting the Conformational Stability of a Glycan Hairpin. J Am Chem Soc 2024; 146:6369-6376. [PMID: 38377472 PMCID: PMC10921397 DOI: 10.1021/jacs.4c00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan-glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.
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Affiliation(s)
- Nishu Yadav
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Surusch Djalali
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Ana Poveda
- CIC
bioGUNE, Basque Research and Technology Alliance, Derio 48160, Spain
| | - Manuel G. Ricardo
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Peter H. Seeberger
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology Alliance, Derio 48160, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48009, Spain
- Department
of Inorganic & Organic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa 48940, Spain
- Centro de
Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid 28029, Spain
| | - Martina Delbianco
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
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5
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Nybro Dansholm C, Meier S, Beeren SR. Amylose Dimerization in Solution Can Be Studied Using a Model System. Chembiochem 2024; 25:e202300832. [PMID: 38220779 DOI: 10.1002/cbic.202300832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
Amylose, the linear polymer of α-1,4-linked glucopyranose units, is known to crystallize as a parallel double helix, but evidence of this duplex forming in solution has remained elusive for decades. We show how the dimerization of short amylose chains can be detected in solution using NMR spectroscopy when the glucans are labeled at the reducing-end with an aromatic moiety that overcomes chemical shift degeneracy leading to distinct signals for the single-stranded and duplex amylose. A set of α-1,4 glucans with varying lengths of 6, 12, 18, and 22 glucose units and a 4-aminobenzamide label were synthesized, enabling the first systematic thermodynamic study of the association of amylose in solution. The dimerization is enthalpically driven, entropically unfavorable and beyond a minimum length of 12, each additional pair of glucose residues stabilizes the duplex by 0.85 kJ mol-1 . This fundamental knowledge provides a basis for a quantitative understanding of starch structure, gelation and enzymatic digestion, and lays the foundations for the strategic use of α-1,4-glucans in the development of self-assembled materials.
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Affiliation(s)
- Charlotte Nybro Dansholm
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, Kongens Lyngby, DK-2800, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, Kongens Lyngby, DK-2800, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, Kongens Lyngby, DK-2800, Denmark
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6
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Abstract
The structural complexity of glycans poses a serious challenge in the chemical synthesis of glycosides, oligosaccharides and glycoconjugates. Glycan complexity, determined by composition, connectivity, and configuration far exceeds what nature achieves with nucleic acids and proteins. Consequently, glycoside synthesis ranks among the most complex tasks in organic synthesis, despite involving only a simple type of bond-forming reaction. Here, we introduce the fundamental principles of glycoside bond formation and summarize recent advances in glycoside bond formation and oligosaccharide synthesis.
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Affiliation(s)
- Conor J Crawford
- Department of Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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7
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Fittolani G, Tyrikos-Ergas T, Poveda A, Yu Y, Yadav N, Seeberger PH, Jiménez-Barbero J, Delbianco M. Synthesis of a glycan hairpin. Nat Chem 2023; 15:1461-1469. [PMID: 37400598 PMCID: PMC10533408 DOI: 10.1038/s41557-023-01255-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
| | - Yang Yu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Simpson Querrey Institute, Northwestern University, Evanston, IL, USA
| | - Nishu Yadav
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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8
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Seibel J, Fittolani G, Mirhosseini H, Wu X, Rauschenbach S, Anggara K, Seeberger PH, Delbianco M, Kühne TD, Schlickum U, Kern K. Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging. Angew Chem Int Ed Engl 2023; 62:e202305733. [PMID: 37522820 DOI: 10.1002/anie.202305733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/01/2023]
Abstract
Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. Bottom-up engineering of carbohydrate materials demands an atomic-level understanding of their molecular structures and interactions in condensed phases. Here, high-resolution scanning tunneling microscopy (STM) is used to visualize at submolecular resolution the three-dimensional structure of cellulose oligomers assembled on Au(1111) and the interactions that drive their assembly. The STM imaging, supported by ab initio calculations, reveals the orientation of all glycosidic bonds and pyranose rings in the oligomers, as well as details of intermolecular interactions between the oligomers. By comparing the assembly of D- and L-oligomers, these interactions are shown to be enantioselective, capable of driving spontaneous enantioseparation of cellulose chains from its unnatural enantiomer and promoting the formation of engineered carbohydrate assemblies in the condensed phases.
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Affiliation(s)
- Johannes Seibel
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany
- Current address: Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Giulio Fittolani
- Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195, Berlin, Germany
| | - Hossein Mirhosseini
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, 33098, Paderborn, Germany
| | - Xu Wu
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
| | - Stephan Rauschenbach
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
- Department of Chemistry, University of Oxford, OX13TA, Oxford, UK
| | - Kelvin Anggara
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
| | - Peter H Seeberger
- Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195, Berlin, Germany
| | - Martina Delbianco
- Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, 33098, Paderborn, Germany
- Center for Advanced Systems Understanding (CASUS) and Helmholtz Zentrum Dresden-Rossendorf, 02826, Görlitz, Germany
| | - Uta Schlickum
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
- Institut de Physique, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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9
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Dal Colle MCS, Ricardo MG, Hribernik N, Danglad-Flores J, Seeberger PH, Delbianco M. Linker, loading, and reaction scale influence automated glycan assembly. Beilstein J Org Chem 2023; 19:1015-1020. [PMID: 37440787 PMCID: PMC10334207 DOI: 10.3762/bjoc.19.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Automated glycan assembly (AGA) affords collections of well-defined glycans in a short amount of time. We systematically analyzed how parameters connected to the solid support affect the AGA outcome for three different glycan sequences. We showed that, while loading and reaction scale did not significantly influence the AGA outcome, the chemical nature of the linker dramatically altered the isolated yields. We identified that the major determinants of AGA yields are cleavage from the solid support and post-AGA purification steps.
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Affiliation(s)
- Marlene C S Dal Colle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Manuel G Ricardo
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Nives Hribernik
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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10
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Romeo JR, Lucera JD, Jensen D, Davis LM, Bennett CS. Application of Redox-Active Ester Catalysis to the Synthesis of Pyranose Alkyl C-Glycosides. Org Lett 2023; 25:3760-3765. [PMID: 37171292 DOI: 10.1021/acs.orglett.3c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The direct coupling of shelf-stable, tetrachloro-N-hydroxyphthalimide ester (TCNHPI) glycosyl donors with a variety of alkylzinc reagents under redox catalysis is described. Alkyl C-glycosides are formed directly by a decarboxylative, Negishi-type process in 31-73% yields without the need for photocatalytic activation or additional reductants. Extension of this approach to the coupling of TCNHPI donors with stereodefined α-alkoxy furan-containing alkylzinc halides enabled de novo synthesis of methylene-linked exo-C-disaccharides via an Achmatowicz rearrangement.
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Affiliation(s)
- Joseph R Romeo
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jon D Lucera
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Drew Jensen
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Luke M Davis
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Clay S Bennett
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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11
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Quintana JI, Atxabal U, Unione L, Ardá A, Jiménez-Barbero J. Exploring multivalent carbohydrate-protein interactions by NMR. Chem Soc Rev 2023; 52:1591-1613. [PMID: 36753338 PMCID: PMC9987413 DOI: 10.1039/d2cs00983h] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 02/09/2023]
Abstract
Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.
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Affiliation(s)
- Jon I Quintana
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Unai Atxabal
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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12
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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13
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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14
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Giraldo JD, Garrido-Miranda KA, Schoebitz M. Chitin and its derivatives: Functional biopolymers for developing bioproducts for sustainable agriculture-A reality? Carbohydr Polym 2023; 299:120196. [PMID: 36876809 DOI: 10.1016/j.carbpol.2022.120196] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022]
Abstract
Chitinous materials (chitin and its derivatives) are obtained from renewable sources, mainly shellfish waste, having a great potential for the development of bioproducts as alternatives to synthetic agrochemicals. Recent studies have provided evidence that the use of these biopolymers can help control postharvest diseases, increase the content of nutrients available to plants, and elicit positive metabolic changes that lead to higher plant resistance against pathogens. However, agrochemicals are still widely and intensively used in agriculture. This perspective addresses the gap in knowledge and innovation to make bioproducts based on chitinous materials more competitive in the market. It also provides the readers with background to understand why these products are scarcely used and the aspects that need to be considered to increase their use. Finally, information on the development and commercialization of agricultural bioproducts containing chitin or its derivatives in the Chilean market is also provided.
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Affiliation(s)
- Juan D Giraldo
- Escuela de Ingeniería Ambiental, Instituto de Acuicultura, Universidad Austral de Chile, Sede Puerto Montt, Balneario Pelluco, Los Pinos s/n, Chile.
| | - Karla A Garrido-Miranda
- Center of Waste Management and Bioenergy, Scientific and Technological Bioresource Nucleus, BIOREN-UFRO, Universidad de la Frontera, P.O. Box 54-D, Temuco, Chile; Agriaquaculture Nutritional Genomic Center (CGNA), Temuco 4780000, Chile.
| | - Mauricio Schoebitz
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Campus Concepción, Casilla 160-C, Universidad de Concepción, Chile; Laboratory of Biofilms and Environmental Microbiology, Center of Biotechnology, University of Concepción, Barrio Universitario s/n, Concepción, Chile.
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15
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Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
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Affiliation(s)
- Marlene C. S. Dal Colle
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Giulio Fittolani
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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16
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Ricardo MG, Reuber EE, Yao L, Danglad-Flores J, Delbianco M, Seeberger PH. Design, Synthesis, and Characterization of Stapled Oligosaccharides. J Am Chem Soc 2022; 144:18429-18434. [PMID: 36173281 PMCID: PMC9562281 DOI: 10.1021/jacs.2c06882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Stapling short peptides
to lock specific conformations and thereby
obtain superior pharmacological properties is well established. However,
similar concepts have not been applied to oligosaccharides. Here,
we describe the design, synthesis, and characterization of the first
stapled oligosaccharides. Automated assembly of β-(1,6)-glucans
equipped with two alkenyl side chains was followed by on-resin Grubbs
metathesis for efficient ring closure with a variety of cross-linkers
of different sizes. Oligosaccharide stapling increases enzymatic stability
and cell penetration, therefore opening new opportunities for the
use of glycans in medicinal chemistry.
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Affiliation(s)
- Manuel G Ricardo
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Emelie E Reuber
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ling Yao
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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17
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Chemical synthesis of polysaccharides. Curr Opin Chem Biol 2022; 69:102154. [DOI: 10.1016/j.cbpa.2022.102154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/22/2022]
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18
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Mukherjee S, Jana S, Khawas S, Kicuntod J, Marschall M, Ray B, Ray S. Synthesis, molecular features and biological activities of modified plant polysaccharides. Carbohydr Polym 2022; 289:119299. [DOI: 10.1016/j.carbpol.2022.119299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
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19
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Chaube MA, Trattnig N, Lee D, Belkhadir Y, Pfrengle F. Synthesis of Fungal Cell Wall Oligosaccharides and Their Ability to Trigger Plant Immune Responses. European J Org Chem 2022; 2022:e202200313. [PMID: 36035813 PMCID: PMC9401017 DOI: 10.1002/ejoc.202200313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/20/2022] [Indexed: 12/04/2022]
Abstract
Oligosaccharide fragments of fungal cell wall glycans are important molecular probes for studying both the biology of fungi and fungal infections of humans, animals, and plants. The fungal cell wall contains large amounts of various polysaccharides that are ligands for pattern recognition receptors (PRRs), eliciting an immune response upon recognition. Towards the establishment of a glycan array platform for the identification of new ligands of plant PRRs, tri-, penta-, and heptasaccharide fragments of different cell wall polysaccharides were prepared. Chito- and β-(1→6)-gluco-oligosaccharides were synthesized by automated glycan assembly (AGA), and α-(1→3)- and α-(1→4)-gluco-oligosaccharides were synthesized in solution using a recently reported highly α-selective glycosylation methodology. Incubation of plants with the synthesized oligosaccharides revealed i) length dependence for plant activation by chito-oligosaccharides and ii) β-1,6-glucan oligosaccharides as a new class of glycans capable of triggering plant activation.
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Affiliation(s)
- Manishkumar A. Chaube
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Nino Trattnig
- Department of ChemistryUniversity of Natural Resources and Life Sciences,ViennaMuthgasse 181190ViennaAustria
| | - Du‐Hwa Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr Gasse 31030ViennaAustria
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr Gasse 31030ViennaAustria
| | - Fabian Pfrengle
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of ChemistryUniversity of Natural Resources and Life Sciences,ViennaMuthgasse 181190ViennaAustria
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20
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Affiliation(s)
- Xiaona Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - You Yang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
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21
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Greis K, Kirschbaum C, Fittolani G, Mucha E, Chang R, von Helden G, Meijer G, Delbianco M, Seeberger PH, Pagel K. Neighboring Group Participation of Benzoyl Protecting Groups in C3- and C6-Fluorinated Glucose. European J Org Chem 2022; 2022:e202200255. [PMID: 35915640 PMCID: PMC9321577 DOI: 10.1002/ejoc.202200255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/23/2022] [Indexed: 11/17/2022]
Abstract
Fluorination is a potent method to modulate chemical properties of glycans. Here, we study how C3- and C6-fluorination of glucosyl building blocks influence the structure of the intermediate of the glycosylation reaction, the glycosyl cation. Using a combination of gas-phase infrared spectroscopy and first-principles theory, glycosyl cations generated from fluorinated and non-fluorinated monosaccharides are structurally characterized. The results indicate that neighboring group participation of the C2-benzoyl protecting group is the dominant structural motif for all building blocks, correlating with the β-selectivity observed in glycosylation reactions. The infrared signatures indicate that participation of the benzoyl group in enhanced by resonance effects. Participation of remote acyl groups such as Fmoc or benzyl on the other hand is unfavored. The introduction of the less bulky fluorine leads to a change in the conformation of the ring pucker, whereas the structure of the active dioxolenium site remains unchanged.
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Affiliation(s)
- Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Giulio Fittolani
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Eike Mucha
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Rayoon Chang
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Martina Delbianco
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
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22
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Kasdekar N, Walke G, Deshpande K, Hotha S. Glycosyl Vinylogous Carbonates as Glycosyl Donors by Metal-Free Activation. J Org Chem 2022; 87:5472-5484. [PMID: 35414184 DOI: 10.1021/acs.joc.1c02427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthesis of glycoconjugates employs a glycosylation reaction wherein an electrophile and a nucleophile known as a glycosyl donor and an aglycon, respectively, are involved. Glycosyl donors often contain a leaving group at the anomeric carbon that upon reaction with activator(s) results in a highly reactive electrophilic species reported as an oxycarbenium ion contact pair that will then be attacked by the aglycon. Therefore, identification of the correct glycosyl donor and activation protocol is essential for the synthesis of all glycoconjugates. Recently identified [Au]/[Ag]-catalyzed activation of ethynylcyclohexyl glycosyl carbonates is one such versatile method for the synthesis of glycosides, oligosaccharides, and glycoconjugates. In this work, stable glycosyl vinylogous carbonates were identified to undergo glycosidation in the presence of a sub-stoichiometric quantity of TfOH. The reaction is fast and suitable for donors containing both C2-ethers and C2-esters. Donors positioned with C2-ethers resulted in anomeric mixtures with greater selectivity toward 1,2-cis glycosides, whereas those with C2-esters gave 1,2-trans selective glycosides. The versatility of the method is demonstrated by conducting the glycosylation with more than 25 substrates. Furthermore, the utility of the glycosyl vinylogous carbonate donors is demonstrated with the successful synthesis of the branched pentaarabinofuranoside moiety of the Mycobacterium tuberculosis cell wall.
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Affiliation(s)
- Niteshlal Kasdekar
- Department of Chemistry, Indian Institute of Science Education and Research Pune 411 008, India
| | - Gulab Walke
- Department of Chemistry, Indian Institute of Science Education and Research Pune 411 008, India
| | - Kshitij Deshpande
- Department of Chemistry, Indian Institute of Science Education and Research Pune 411 008, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science Education and Research Pune 411 008, India
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23
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Wang J, Feng Y, Sun T, Zhang Q, Chai Y. Photolabile 2-(2-Nitrophenyl)-propyloxycarbonyl (NPPOC) for Stereoselective Glycosylation and Its Application in Consecutive Assembly of Oligosaccharides. J Org Chem 2022; 87:3402-3421. [PMID: 35171610 DOI: 10.1021/acs.joc.1c03006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photolabile protecting group (PPG) 2-(2-nitrophenyl)-propyloxycarbonyl (NPPOC) was explored in glycosylation and applied in the consecutive synthesis of oligosaccharides. NPPOC displays a strong neighboring group participation (NGP) effect to facilitate the construction of 1,2-trans glycosides in excellent yield. Notably, NPPOC could be efficiently removed by photolysis, and the deprotection conditions are friendly to typical protecting groups. A branched and asymmetric oligomannose Man6 was rapidly prepared, and the consecutive assembly of oligosaccharides without intermediate purification was further investigated owing to the compatibility conditions between NPPPOC's photolysis and glycosylation.
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Affiliation(s)
- Jincai Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Yingle Feng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Taotao Sun
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Yonghai Chai
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
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24
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Sletten ET, Danglad-Flores J, Leichnitz S, Abragam Joseph A, Seeberger PH. Expedited synthesis of mannose-6-phosphate containing oligosaccharides. Carbohydr Res 2021; 511:108489. [PMID: 34922155 DOI: 10.1016/j.carres.2021.108489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023]
Abstract
Currently, the reaction toolbox for the functionalization of glycans assembled on solid-phase is quite limited. Automated (1 h) and manual (overnight) phosphorylation protocols that enable the solid-phase synthesis of oligosaccharides containing up to two mannose-6-phosphates are presented. Automated glycan assembly expedited access to substrates and facilitated the screening of experimental conditions.
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Affiliation(s)
- Eric T Sletten
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Sabrina Leichnitz
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476, Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - A Abragam Joseph
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476, Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
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25
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Cord-Landwehr S, Moerschbacher BM. Deciphering the ChitoCode: fungal chitins and chitosans as functional biopolymers. Fungal Biol Biotechnol 2021; 8:19. [PMID: 34893090 PMCID: PMC8665597 DOI: 10.1186/s40694-021-00127-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022] Open
Abstract
Chitins and chitosans are among the most widespread and versatile functional biopolymers, with interesting biological activities and superior material properties. While chitins are evolutionary ancient and present in many eukaryotes except for higher plants and mammals, the natural distribution of chitosans, i.e. extensively deacetylated derivatives of chitin, is more limited. Unequivocal evidence for its presence is only available for fungi where chitosans are produced from chitin by the action of chitin deacetylases. However, neither the structural details such as fraction and pattern of acetylation nor the physiological roles of natural chitosans are known at present. We hypothesise that the chitin deacetylases are generating chitins and chitosans with specific acetylation patterns and that these provide information for the interaction with specific chitin- and chitosan-binding proteins. These may be structural proteins involved in the assembly of the complex chitin- and chitosan-containing matrices such as fungal cell walls and insect cuticles, chitin- and chitosan-modifying and -degrading enzymes such as chitin deacetylases, chitinases, and chitosanases, but also chitin- and chitosan-recognising receptors of the innate immune systems of plants, animals, and humans. The acetylation pattern, thus, may constitute a kind of 'ChitoCode', and we are convinced that new in silico, in vitro, and in situ analytical tools as well as new synthetic methods of enzyme biotechnology and organic synthesis are currently offering an unprecedented opportunity to decipher this code. We anticipate a deeper understanding of the biology of chitin- and chitosan-containing matrices, including their synthesis, assembly, mineralisation, degradation, and perception. This in turn will improve chitin and chitosan biotechnology and the development of reliable chitin- and chitosan-based products and applications, e.g. in medicine and agriculture, food and feed sciences, as well as cosmetics and material sciences.
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Affiliation(s)
- Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany.
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26
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Poveda A, Fittolani G, Seeberger PH, Delbianco M, Jiménez-Barbero J. The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis. Front Mol Biosci 2021; 8:784318. [PMID: 34859057 PMCID: PMC8631391 DOI: 10.3389/fmolb.2021.784318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.
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Affiliation(s)
- Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain.,Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
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27
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Wang L, Lowary TL. Synthesis of structurally-defined polymeric glycosylated phosphoprenols as potential lipopolysaccharide biosynthetic probes. Chem Sci 2021; 12:12192-12200. [PMID: 34667585 PMCID: PMC8457389 DOI: 10.1039/d1sc03852d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022] Open
Abstract
The biosynthesis of lipopolysaccharide (LPS), a key immunomodulatory molecule produced by gram-negative bacteria, has been a topic of long-term interest. To date, the chemical probes used as tools to study LPS biosynthetic pathways have consisted primarily of small fragments of the larger structure (e.g., the O-chain repeating unit). While such compounds have helped to provide significant insight into many aspects of LPS assembly, understanding other aspects will require larger, more complex probes. For example, the molecular interactions between polymeric LPS biosynthetic intermediates and the proteins that transfer them across the inner and outer membrane remain largely unknown. We describe the synthesis of two lipid-linked polysaccharides, containing 11 and 27 monosaccharide residues, that are related to LPS O-chain biosynthesis in Escherichia coli O9a. This work has led not only to multi-milligram quantities of two biosynthetic probes, but also provided insights into challenges that must be overcome in the chemical synthesis of structurally-defined polysaccharides. The synthesis of lipid-linked polysaccharides containing 11 and 27 monosaccharides via a ‘frame-shift’ strategy is described. The work provides biosynthetic probes and highlights challenges in synthesizing structurally-defined polymeric glycans.![]()
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada .,Institute of Biological Chemistry, Academia Sinica Academia Road, Section 2, #128, Nangang Taipei 11529 Taiwan.,Institute of Biochemical Sciences, National Taiwan University Section 4, #1, Roosevelt Road. Taipei 10617 Taiwan
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28
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Malerz S, Mudryk K, Tomaník L, Stemer D, Hergenhahn U, Buttersack T, Trinter F, Seidel R, Quevedo W, Goy C, Wilkinson I, Thürmer S, Slavíček P, Winter B. Following in Emil Fischer's Footsteps: A Site-Selective Probe of Glucose Acid-Base Chemistry. J Phys Chem A 2021; 125:6881-6892. [PMID: 34328745 PMCID: PMC8381351 DOI: 10.1021/acs.jpca.1c04695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/14/2021] [Indexed: 12/27/2022]
Abstract
Liquid-jet photoelectron spectroscopy was applied to determine the first acid dissociation constant (pKa) of aqueous-phase glucose while simultaneously identifying the spectroscopic signature of the respective deprotonation site. Valence spectra from solutions at pH values below and above the first pKa reveal a change in glucose's lowest ionization energy upon the deprotonation of neutral glucose and the subsequent emergence of its anionic counterpart. Site-specific insights into the solution-pH-dependent molecular structure changes are also shown to be accessible via C 1s photoelectron spectroscopy. The spectra reveal a considerably lower C 1s binding energy of the carbon site associated with the deprotonated hydroxyl group. The occurrence of photoelectron spectral fingerprints of cyclic and linear glucose prior to and upon deprotonation are also discussed. The experimental data are interpreted with the aid of electronic structure calculations. Our findings highlight the potential of liquid-jet photoelectron spectroscopy to act as a site-selective probe of the molecular structures that underpin the acid-base chemistry of polyprotic systems with relevance to environmental chemistry and biochemistry.
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Affiliation(s)
- Sebastian Malerz
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Karen Mudryk
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Lukáš Tomaník
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, Prague 6 16628, Czech Republic
| | - Dominik Stemer
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Uwe Hergenhahn
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Tillmann Buttersack
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Florian Trinter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Institut
für Kernphysik, Goethe-Universität, Max-von-Laue-Straße 1, 60438 Frankfurt am Main, Germany
| | - Robert Seidel
- Operando
Interfacial Photochemistry, Helmholtz-Zentrum
Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
- Institut
für Chemie, Humboldt-Universität
zu Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
| | - Wilson Quevedo
- Operando
Interfacial Photochemistry, Helmholtz-Zentrum
Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Claudia Goy
- Centre for
Molecular Water Science (CMWS), Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Iain Wilkinson
- Department
of Locally-Sensitive & Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und
Energie, Hahn-Meitner-Platz
1, 14109 Berlin, Germany
| | - Stephan Thürmer
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, Prague 6 16628, Czech Republic
| | - Bernd Winter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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29
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Selective
13
C‐Labels on Repeating Glycan Oligomers to Reveal Protein Binding Epitopes through NMR: Polylactosamine Binding to Galectins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Moure MJ, Gimeno A, Delgado S, Diercks T, Boons G, Jiménez‐Barbero J, Ardá A. Selective 13 C-Labels on Repeating Glycan Oligomers to Reveal Protein Binding Epitopes through NMR: Polylactosamine Binding to Galectins. Angew Chem Int Ed Engl 2021; 60:18777-18782. [PMID: 34128568 PMCID: PMC8456918 DOI: 10.1002/anie.202106056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/10/2021] [Indexed: 12/12/2022]
Abstract
A combined chemo-enzymatic synthesis/NMR-based methodology is presented to identify, in unambiguous manner, the distinctive binding epitope within repeating sugar oligomers when binding to protein receptors. The concept is based on the incorporation of 13 C-labels at specific monosaccharide units, selected within a repeating glycan oligomeric structure. No new chemical tags are added, and thus the chemical entity remains the same, while the presence of the 13 C-labeled monosaccharide breaks the NMR chemical shift degeneracy that occurs in the non-labeled compound and allows the unique identification of the different components of the oligomer. The approach is demonstrated by a proof-of-concept study dealing with the interaction of a polylactosamine hexasaccharide with five different galectins that display distinct preferences for these entities.
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Affiliation(s)
- María J. Moure
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
| | - Ana Gimeno
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
| | - Sandra Delgado
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
| | - Tammo Diercks
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
| | - Geert‐Jan Boons
- Chemical Biology and Drug DiscoveryUtrecht UniversityUtrechtThe Netherlands
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGeorgiaUSA
- Department of ChemistryUniversity of GeorgiaAthensGeorgiaUSA
| | - Jesús Jiménez‐Barbero
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
- Ikerbasque, Basque Foundation for SciencePlaza Euskadi 548009BilbaoSpain
- Department of Organic & Inorganic ChemistryUniversity of the Basque CountryUPV/EHUSpain
| | - Ana Ardá
- Chemical Glycobiology labCIC bioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048160DerioSpain
- Ikerbasque, Basque Foundation for SciencePlaza Euskadi 548009BilbaoSpain
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31
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Fittolani G, Tyrikos-Ergas T, Vargová D, Chaube MA, Delbianco M. Progress and challenges in the synthesis of sequence controlled polysaccharides. Beilstein J Org Chem 2021; 17:1981-2025. [PMID: 34386106 PMCID: PMC8353590 DOI: 10.3762/bjoc.17.129] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/22/2021] [Indexed: 01/15/2023] Open
Abstract
The sequence, length and substitution of a polysaccharide influence its physical and biological properties. Thus, sequence controlled polysaccharides are important targets to establish structure-properties correlations. Polymerization techniques and enzymatic methods have been optimized to obtain samples with well-defined substitution patterns and narrow molecular weight distribution. Chemical synthesis has granted access to polysaccharides with full control over the length. Here, we review the progress towards the synthesis of well-defined polysaccharides. For each class of polysaccharides, we discuss the available synthetic approaches and their current limitations.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Denisa Vargová
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Manishkumar A Chaube
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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32
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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33
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Abstract
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Polysaccharides are
Nature’s most abundant biomaterials
essential for plant cell wall construction and energy storage. Seemingly
minor structural differences result in entirely different functions:
cellulose, a β (1–4) linked glucose polymer, forms fibrils
that can support large trees, while amylose, an α (1–4)
linked glucose polymer forms soft hollow fibers used for energy storage.
A detailed understanding of polysaccharide structures requires pure
materials that cannot be isolated from natural sources. Automated
Glycan Assembly provides quick access to trans-linked
glycans analogues of cellulose, but the stereoselective installation
of multiple cis-glycosidic linkages present in amylose
has not been possible to date. Here, we identify thioglycoside building
blocks with different protecting group patterns that, in concert with
temperature and solvent control, achieve excellent stereoselectivity
during the synthesis of linear and branched α-glucan polymers
with up to 20 cis-glycosidic linkages. The molecules
prepared with the new method will serve as probes to understand the
biosynthesis and the structure of α-glucans.
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Affiliation(s)
- Yuntao Zhu
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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34
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Abstract
The monomer sequence dictates the structure and properties of natural polymers. Such a structure–property relationship is well known for polypeptides and polynucleotides but not for polysaccharides, the most abundant biopolymers on Earth. Here, we establish the structure–property relationship for a polysaccharide at the atomic level by determining molecular flexibility of carbohydrate chains with defined sequences. The chain flexibility can be engineered one linkage at a time by chemical substitution and conformation change, highlighting how the primary and secondary structures of a carbohydrate dictate its flexibility—a critical observable in the de novo design of carbohydrate materials. Our approach can be extended to establish the structure–property relationship at the atomic level of any molecule that can be electrosprayed. Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, are the most abundant materials found in nature whose structures and properties have been characterized only at the submicrometer level. Here, by imaging single-cellulose chains at the nanoscale, we determine the structure and local flexibility of cellulose as a function of its sequence (primary structure) and conformation (secondary structure). Changing the primary structure by chemical substitutions and geometrical variations in the secondary structure allow the chain flexibility to be engineered at the single-linkage level. Tuning local flexibility opens opportunities for the bottom-up design of carbohydrate materials.
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35
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Fittolani G, Shanina E, Guberman M, Seeberger PH, Rademacher C, Delbianco M. Automatisierte Glykan‐Assemblierung
19
F‐markierter Glykansonden ermöglicht Hochdurchsatz‐NMR‐Untersuchungen von Protein‐Glykan‐Interaktionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Elena Shanina
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Mónica Guberman
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Derzeitige Adresse: Medicinal Chemistry Leibniz-Forschungsinstitut für Molekulare Pharmakologie Robert-Rössle Straße 10 13125 Berlin Deutschland
| | - Peter H. Seeberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
| | - Christoph Rademacher
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Derzeitige Adresse: Department of Pharmaceutical Chemistry University of Vienna Althanstraße 14 1080 Wien Österreich
- Derzeitige Adresse: Department of Microbiology, Immunobiology and Genetics Max F. Perutz Labs Campus Vienna Biocenter 5 1030 Wien Österreich
| | - Martina Delbianco
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Deutschland
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36
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Fittolani G, Shanina E, Guberman M, Seeberger PH, Rademacher C, Delbianco M. Automated Glycan Assembly of 19 F-labeled Glycan Probes Enables High-Throughput NMR Studies of Protein-Glycan Interactions. Angew Chem Int Ed Engl 2021; 60:13302-13309. [PMID: 33784430 PMCID: PMC8252726 DOI: 10.1002/anie.202102690] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Indexed: 12/23/2022]
Abstract
Protein-glycan interactions mediate important biological processes, including pathogen host invasion and cellular communication. Herein, we showcase an expedite approach that integrates automated glycan assembly (AGA) of 19 F-labeled probes and high-throughput NMR methods, enabling the study of protein-glycan interactions. Synthetic Lewis type 2 antigens were screened against seven glycan binding proteins (GBPs), including DC-SIGN and BambL, respectively involved in HIV-1 and lung infections in immunocompromised patients, confirming the preference for fucosylated glycans (Lex , H type 2, Ley ). Previously unknown glycan-lectin weak interactions were detected, and thermodynamic data were obtained. Enzymatic reactions were monitored in real-time, delivering kinetic parameters. These results demonstrate the utility of AGA combined with 19 F NMR for the discovery and characterization of glycan-protein interactions, opening up new perspectives for 19 F-labeled complex glycans.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Elena Shanina
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Mónica Guberman
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare PharmakologieRobert-Rössle Strasse 1013125BerlinGermany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Christoph Rademacher
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Current address: Department of Pharmaceutical ChemistryUniversity of ViennaAlthanstrasse 141080ViennaAustria
- Current address: Department of Microbiology, Immunobiology and GeneticsMax F. Perutz LabsCampus Vienna Biocenter 51030ViennaAustria
| | - Martina Delbianco
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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37
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Kuprov I, Morris LC, Glushka JN, Prestegard JH. Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 323:106891. [PMID: 33445107 PMCID: PMC7873838 DOI: 10.1016/j.jmr.2020.106891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 05/09/2023]
Abstract
Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories - no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.
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Affiliation(s)
- Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton, UK
| | - Laura C Morris
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
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38
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Tyrikos‐Ergas T, Bordoni V, Fittolani G, Chaube MA, Grafmüller A, Seeberger PH, Delbianco M. Systematic Structural Characterization of Chitooligosaccharides Enabled by Automated Glycan Assembly. Chemistry 2021; 27:2321-2325. [PMID: 33290603 PMCID: PMC7898498 DOI: 10.1002/chem.202005228] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 01/01/2023]
Abstract
Chitin, a polymer composed of β(1-4)-linked N-acetyl-glucosamine monomers, and its partially deacetylated analogue chitosan, are abundant biopolymers with outstanding mechanical as well as elastic properties. Their degradation products, chitooligosaccharides (COS), can trigger the innate immune response in humans and plants. Both material and biological properties are dependent on polymer length, acetylation, as well as the pH. Without well-defined samples, a complete molecular description of these factors is still missing. Automated glycan assembly (AGA) enabled rapid access to synthetic well-defined COS. Chitin-cellulose hybrid oligomers were prepared as important tools for a systematic structural analysis. Intramolecular interactions, identified by molecular dynamics simulations and NMR analysis, underscore the importance of the chitosan amino group for the stabilization of specific geometries.
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Affiliation(s)
- Theodore Tyrikos‐Ergas
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Vittorio Bordoni
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Giulio Fittolani
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Manishkumar A. Chaube
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Andrea Grafmüller
- Department of TheoryMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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39
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Anggara K, Zhu Y, Delbianco M, Rauschenbach S, Abb S, Seeberger PH, Kern K. Exploring the Molecular Conformation Space by Soft Molecule-Surface Collision. J Am Chem Soc 2020; 142:21420-21427. [PMID: 33167615 PMCID: PMC7760097 DOI: 10.1021/jacs.0c09933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 01/08/2023]
Abstract
Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is sampled by exciting an initial gas-phase molecular conformer into diverse conformation states, using soft molecule-surface collision (0.5-5.0 eV). The resulting ground and excited molecular conformations, adsorbed on the surface, are imaged at the single-molecule level. This technique permits the exploration of oligosaccharide conformations, until now, limited by the high flexibility of oligosaccharides and ensemble-averaged analytical methods. As a model for cellulose, cellohexaose chains are observed in two conformational extremes, the typical "extended" chain and the atypical "coiled" chain-the latter identified as the gas-phase conformer preserved on the surface. Observing conformations between these two extremes reveals the physical properties of cellohexaose, behaving as a rigid ribbon that becomes flexible when twisted. The conformation space of any molecule that can be electrosprayed can now be explored.
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Affiliation(s)
- Kelvin Anggara
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Yuntao Zhu
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Martina Delbianco
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
| | - Stephan Rauschenbach
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sabine Abb
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Peter H. Seeberger
- Max
Planck Institute of Colloids and Interfaces, Am Muhlenberg 1, Potsdam DE-14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin DE-14195, Germany
| | - Klaus Kern
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Institut
de Physique, École Polytechnique
Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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40
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Serizawa T, Maeda T, Yamaguchi S, Sawada T. Aqueous Suspensions of Cellulose Oligomer Nanoribbons for Growth and Natural Filtration-Based Separation of Cancer Spheroids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13890-13898. [PMID: 33135411 DOI: 10.1021/acs.langmuir.0c02294] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In vitro growth of cancer spheroids (CSs) and the subsequent separation of CSs from a 2D or 3D cell culture system are important for fundamental cancer studies and cancer drug screening. Although biopolymer-based or synthetic hydrogels are suitable candidates to be used as 3D cell culture scaffolds, alternatives with better processing capabilities are still required to set up cell culture microenvironment. In this study, we show that aqueous suspensions of crystalline nanoribbons composed of cellulose oligomers have a potential for CS growth and separation. The nanoribbon suspensions in serum-containing cell culture media fixed single cancer cells and CSs with large sizes in a 3D space, leading to suspension cultures for CS growth corresponding to culture time. Well-grown CSs were easily separated from the suspensions by natural filtration using a mesh filter with a suitable pore size. Cell viability tests revealed negligible cytotoxicity of the nanoribbons. In addition, physical damages to CSs by the separation procedures were negligible. Stable suspensions of biocompatible nanomaterials will thus provide novel microenvironments for growth and separation of diverse cell aggregates.
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Affiliation(s)
- Takeshi Serizawa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tohru Maeda
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Saeko Yamaguchi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Toshiki Sawada
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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41
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Hamagami H, Yamaguchi Y, Tanaka H. Chemical Synthesis of Residue-Selectively 13C and 2H Double-Isotope-Labeled Oligosaccharides as Chemical Probes for the NMR-Based Conformational Analysis of Oligosaccharides. J Org Chem 2020; 85:16115-16127. [PMID: 33107296 DOI: 10.1021/acs.joc.0c01939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The conformational analysis of oligosaccharide is a fundamental issue in glycobiology. NMR measurements of atom-selectively 13C-labeled oligosaccharides have provided valuable information concerning their conformation, which would not be possible using nonlabeled oligosaccharides. The amount of accessible information from an atom-selectively labeled molecule, however, is limited. In this work, we report on the chemical synthesis of residue-selectively 13C- and 2H-labeled oligosaccharides and their use in conformational analysis. 1H NMR measurements of such double isotope-labeled compounds can provide a great deal of information on the dihedral angles across glycosidic linkages. We demonstrated this method in the conformational analyses of some linear and branched β(1,3)-glucan oligosaccharides.
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Affiliation(s)
- Hiroki Hamagami
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H101 Ookayama, Meguro, Tokyo 152-8552, Japan
| | - Yoshiki Yamaguchi
- RIKEN-Max-Planck Joint Research Center for Systems Chemical Biology RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H101 Ookayama, Meguro, Tokyo 152-8552, Japan
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42
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Preparation of Defined Chitosan Oligosaccharides Using Chitin Deacetylases. Int J Mol Sci 2020; 21:ijms21217835. [PMID: 33105791 PMCID: PMC7660110 DOI: 10.3390/ijms21217835] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
During the past decade, detailed studies using well-defined 'second generation' chitosans have amply proved that both their material properties and their biological activities are dependent on their molecular structure, in particular on their degree of polymerisation (DP) and their fraction of acetylation (FA). Recent evidence suggests that the pattern of acetylation (PA), i.e., the sequence of acetylated and non-acetylated residues along the linear polymer, is equally important, but chitosan polymers with defined, non-random PA are not yet available. One way in which the PA will influence the bioactivities of chitosan polymers is their enzymatic degradation by sequence-dependent chitosan hydrolases present in the target tissues. The PA of the polymer substrates in conjunction with the subsite preferences of the hydrolases determine the type of oligomeric products and the kinetics of their production and further degradation. Thus, the bioactivities of chitosan polymers will at least in part be carried by the chitosan oligomers produced from them, possibly through their interaction with pattern recognition receptors in target cells. In contrast to polymers, partially acetylated chitosan oligosaccharides (paCOS) can be fully characterised concerning their DP, FA, and PA, and chitin deacetylases (CDAs) with different and known regio-selectivities are currently emerging as efficient tools to produce fully defined paCOS in quantities sufficient to probe their bioactivities. In this review, we describe the current state of the art on how CDAs can be used in forward and reverse mode to produce all of the possible paCOS dimers, trimers, and tetramers, most of the pentamers and many of the hexamers. In addition, we describe the biotechnological production of the required fully acetylated and fully deacetylated oligomer substrates, as well as the purification and characterisation of the paCOS products.
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43
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Zhu Q, Shen Z, Chiodo F, Nicolardi S, Molinaro A, Silipo A, Yu B. Chemical synthesis of glycans up to a 128-mer relevant to the O-antigen of Bacteroides vulgatus. Nat Commun 2020; 11:4142. [PMID: 32811831 PMCID: PMC7434892 DOI: 10.1038/s41467-020-17992-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Glycans are involved in various life processes and represent critical targets of biomedical developments. Nevertheless, the accessibility to long glycans with precise structures remains challenging. Here we report on the synthesis of glycans consisting of [→4)-α-Rha-(1 → 3)-β-Man-(1 → ] repeating unit, which are relevant to the O-antigen of Bacteroides vulgatus, a common component of gut microbiota. The optimal combination of assembly strategy, protecting group arrangement, and glycosylation reaction has enabled us to synthesize up to a 128-mer glycan. The synthetic glycans are accurately characterized by advanced NMR and MS approaches, the 3D structures are defined, and their potent binding activity with human DC-SIGN, a receptor associated with the gut lymphoid tissue, is disclosed.
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Affiliation(s)
- Qian Zhu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhengnan Shen
- School of Physical Science and Technology, ShanghaiTech University, 393 Huaxia Middle Road, Shanghai, 201210, China
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, De Boelelaan 1108, 1081HZ, Amsterdam, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126, Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126, Napoli, Italy.
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-Lane Xiangshan, Hangzhou, 310024, China.
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44
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Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
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Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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45
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Wu X, Delbianco M, Anggara K, Michnowicz T, Pardo-Vargas A, Bharate P, Sen S, Pristl M, Rauschenbach S, Schlickum U, Abb S, Seeberger PH, Kern K. Imaging single glycans. Nature 2020; 582:375-378. [DOI: 10.1038/s41586-020-2362-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/27/2020] [Indexed: 11/09/2022]
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46
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Sletten ET, Danglad-Flores J, Nuño M, Guthrie D, Seeberger PH. Automated Glycan Assembly in a Variable-Bed Flow Reactor Provides Insights into Oligosaccharide-Resin Interactions. Org Lett 2020; 22:4213-4216. [PMID: 32396006 PMCID: PMC7281783 DOI: 10.1021/acs.orglett.0c01264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A pressure-based variable-bed flow reactor built for peptide synthesis and capable of real-time monitoring of resin swelling was adapted for automated glycan assembly. In the context of the solid-phase synthesis of several oligosaccharides, the coupling efficiencies, resin growth patterns, and saccharide solvation during the synthesis were determined. The presented work provides the first estimation of on-resin oligosaccharide solvation and an alternative technique to UV-vis monitoring.
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Affiliation(s)
- Eric T Sletten
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Manuel Nuño
- Vapourtec, Ltd., Park Farm Business Centre, Fornham St. Genevieve, Bury St. Edmunds, Suffolk IP28 6TS, United Kingdom
| | - Duncan Guthrie
- Vapourtec, Ltd., Park Farm Business Centre, Fornham St. Genevieve, Bury St. Edmunds, Suffolk IP28 6TS, United Kingdom
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimalle 22, 14195 Berlin, Germany
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47
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Cord-Landwehr S, Richter C, Wattjes J, Sreekumar S, Singh R, Basa S, El Gueddari NE, Moerschbacher BM. Patterns matter part 2: Chitosan oligomers with defined patterns of acetylation. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104577] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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48
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Li BH, Ye XS. Recent advances in glycan synthesis. Curr Opin Chem Biol 2020; 58:20-27. [PMID: 32480314 DOI: 10.1016/j.cbpa.2020.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/13/2020] [Indexed: 12/29/2022]
Abstract
Carbohydrates play important roles in life science, but their synthesis is always hampered by their complicated chemical structures. Scientists have never stopped trying to solve the problem of glycan synthesis from various aspects. Here a brief overview of recent progress in glycan synthesis, including chemical approaches, chemoenzymatic approaches, and automated synthesis, will be discussed, focusing on the efficiency of new glycosylation methods, the stereoselectivity of coupled products, and their applications in the assembly of complex glycan chains.
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Affiliation(s)
- Bo-Han Li
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, China.
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49
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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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50
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Nanovesicles displaying functional linear and branched oligomannose self-assembled from sequence-defined Janus glycodendrimers. Proc Natl Acad Sci U S A 2020; 117:11931-11939. [PMID: 32424105 PMCID: PMC7275670 DOI: 10.1073/pnas.2003938117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Synthetic macromolecules that mimic glycolipids, named Janus glycodendrimers (JGDs), have been shown to self-assemble into nanoscale vesicles displaying glycans on their outer surface, similar to the glycocalyx coating of eukaryotic cells, bacteria, and viruses. Specifically, both linear and branched oligosaccharides synthesized by automated glycan assembly, with hydrophobic linkers, have been used to create JGDs via an isothiocyanate–amine coupling reaction. Surprisingly, in spite of the hydrophobic linker, these JGDs self-organize into nanovesicles exhibiting lamellar surface morphologies, which mimic the recognition structures of cell-surface glycans and viral glycoproteins. Therefore, they are likely to be useful in helping elucidate mechanisms of significance for translational medicine such as the camouflage functionality employed by viruses to evade recognition. Cell surfaces are often decorated with glycoconjugates that contain linear and more complex symmetrically and asymmetrically branched carbohydrates essential for cellular recognition and communication processes. Mannose is one of the fundamental building blocks of glycans in many biological membranes. Moreover, oligomannoses are commonly found on the surface of pathogens such as bacteria and viruses as both glycolipids and glycoproteins. However, their mechanism of action is not well understood, even though this is of great potential interest for translational medicine. Sequence-defined amphiphilic Janus glycodendrimers containing simple mono- and disaccharides that mimic glycolipids are known to self-assemble into glycodendrimersomes, which in turn resemble the surface of a cell by encoding carbohydrate activity via supramolecular multivalency. The synthetic challenge of preparing Janus glycodendrimers containing more complex linear and branched glycans has so far prevented access to more realistic cell mimics. However, the present work reports the use of an isothiocyanate-amine “click”-like reaction between isothiocyanate-containing sequence-defined amphiphilic Janus dendrimers and either linear or branched oligosaccharides containing up to six monosaccharide units attached to a hydrophobic amino-pentyl linker, a construct not expected to assemble into glycodendrimersomes. Unexpectedly, these oligoMan-containing dendrimers, which have their hydrophobic linker connected via a thiourea group to the amphiphilic part of Janus glycodendrimers, self-organize into nanoscale glycodendrimersomes. Specifically, the mannose-binding lectins that best agglutinate glycodendrimersomes are those displaying hexamannose. Lamellar “raft-like” nanomorphologies on the surface of glycodendrimersomes, self-organized from these sequence-defined glycans, endow these membrane mimics with high biological activity.
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