1
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Nepravishta R, Ramírez-Cárdenas J, Rocha G, Walpole S, Hicks T, Monaco S, Muñoz-García JC, Angulo J. Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy. J Med Chem 2024; 67:10025-10034. [PMID: 38848103 PMCID: PMC11215723 DOI: 10.1021/acs.jmedchem.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor-ligand interactions enabling binding detection and structural characterization. Comparison of relaxation and exchange matrix calculations with 1H STD NMR experimental data is essential for the validation of 3D structures of protein-ligand complexes. In this work, we present a new approach based on the calculation of a reduced relaxation matrix, in combination with funnel metadynamics MD simulations, that allows a very fast generation of experimentally STD-NMR-validated 3D structures of low-affinity protein-ligand complexes.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Cancer Research Horizons, CRUK Scotland Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, U.K
| | - Jonathan Ramírez-Cárdenas
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Gabriel Rocha
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Juan C Muñoz-García
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
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2
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Yang W, Ramadan S, Zu Y, Sun M, Huang X, Yu B. Chemical synthesis and functional evaluation of glycopeptides and glycoproteins containing rare glycosyl amino acid linkages. Nat Prod Rep 2024. [PMID: 38888170 DOI: 10.1039/d4np00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Covering: 1987 to 2023Naturally existing glycoproteins through post-translational protein glycosylation are highly heterogeneous, which not only impedes the structure-function studies, but also hinders the development of their potential medical usage. Chemical synthesis represents one of the most powerful tools to provide the structurally well-defined glycoforms. Being the key step of glycoprotein synthesis, glycosylation usually takes place at serine, threonine, and asparagine residues, leading to the predominant formation of the O- and N-glycans, respectively. However, other amino acid residues containing oxygen, nitrogen, sulfur, and nucleophilic carbon atoms have also been found to be glycosylated. These diverse glycoprotein linkages, occurring from microorganisms to plants and animals, play also pivotal biological roles, such as in cell-cell recognition and communication. The availability of these homogenous rare glycopeptides and glycoproteins can help decipher the glyco-code for developing therapeutic agents. This review highlights the chemical approaches for assembly of the functional glycopeptides and glycoproteins bearing these "rare" carbohydrate-amino acid linkages between saccharide and canonical amino acid residues and their derivatives.
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Affiliation(s)
- Weizhun Yang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Sherif Ramadan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Yan Zu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Mengxia Sun
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Biao Yu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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3
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Polasky DA, Lu L, Yu F, Li K, Shortreed MR, Smith LM, Nesvizhskii AI. Quantitative proteome-wide O-glycoproteomics analysis with FragPipe. Anal Bioanal Chem 2024:10.1007/s00216-024-05382-x. [PMID: 38877149 DOI: 10.1007/s00216-024-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Identification of O-glycopeptides from tandem mass spectrometry data is complicated by the near complete dissociation of O-glycans from the peptide during collisional activation and by the combinatorial explosion of possible glycoforms when glycans are retained intact in electron-based activation. The recent O-Pair search method provides an elegant solution to these problems, using a collisional activation scan to identify the peptide sequence and total glycan mass, and a follow-up electron-based activation scan to localize the glycosite(s) using a graph-based algorithm in a reduced search space. Our previous O-glycoproteomics methods with MSFragger-Glyco allowed for extremely fast and sensitive identification of O-glycopeptides from collisional activation data but had limited support for site localization of glycans and quantification of glycopeptides. Here, we report an improved pipeline for O-glycoproteomics analysis that provides proteome-wide, site-specific, quantitative results by incorporating the O-Pair method as a module within FragPipe. In addition to improved search speed and sensitivity, we add flexible options for oxonium ion-based filtering of glycans and support for a variety of MS acquisition methods and provide a comparison between all software tools currently capable of O-glycosite localization in proteome-wide searches.
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Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Lei Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pharmaceutical Chemistry, University of San Francisco, San Francisco, CA, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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4
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Zhu Q, Geng D, Li J, Zhang J, Sun H, Fan Z, He J, Hao N, Tian Y, Wen L, Li T, Qin W, Chu X, Wang Y, Yi W. A Computational and Chemical Design Strategy for Manipulating Glycan-Protein Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308522. [PMID: 38582526 PMCID: PMC11199974 DOI: 10.1002/advs.202308522] [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: 11/08/2023] [Revised: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Glycans are complex biomolecules that encode rich information and regulate various biological processes, such as fertilization, host-pathogen binding, and immune recognition, through interactions with glycan-binding proteins. A key driving force for glycan-protein recognition is the interaction between the π electron density of aromatic amino acid side chains and polarized C─H groups of the pyranose (termed the CH-π interaction). However, the relatively weak binding affinity between glycans and proteins has hindered the application of glycan detection and imaging. Here, computational modeling and molecular dynamics simulations are employed to design a chemical strategy that enhances the CH-π interaction between glycans and proteins by genetically incorporating electron-rich tryptophan derivatives into a lectin PhoSL, which specifically recognizes core fucosylated N-linked glycans. This significantly enhances the binding affinity of PhoSL with the core fucose ligand and enables sensitive detection and imaging of core fucosylated glycans in vitro and in xenograft tumors in mice. Further, the study showed that this strategy is applicable to improve the binding affinity of GafD lectin for N-acetylglucosamine-containing glycans. The approach thus provides a general and effective way to manipulate glycan-protein recognition for glycoscience applications.
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Affiliation(s)
- Qiang Zhu
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Didi Geng
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jingchao Li
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jinqiu Zhang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Haofan Sun
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Zhiya Fan
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Jiahui He
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Ninghui Hao
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Yinping Tian
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Liuqing Wen
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Tiehai Li
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Weijie Qin
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Xiakun Chu
- Advanced Materials ThrustFunction HubThe Hong Kong University of Science and TechnologyGuangzhou511400China
| | - Yong Wang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Wen Yi
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- Cancer CentreZhejiang UniversityHangzhou310012China
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5
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Xu Z, Liu Y, Liu J, Ma W, Zhang Z, Chapla DG, Wen L, Moremen KW, Yi W, Li T. Integrated chemoenzymatic synthesis of a comprehensive sulfated ganglioside glycan library to decipher functional sulfoglycomics and sialoglycomics. Nat Chem 2024; 16:881-892. [PMID: 38844638 DOI: 10.1038/s41557-024-01540-x] [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: 08/07/2023] [Accepted: 04/19/2024] [Indexed: 06/12/2024]
Abstract
Ganglioside glycans are ubiquitous and complex biomolecules that are involved in a wide range of biological functions and disease processes. Variations in sialylation and sulfation render the structural complexity and diversity of ganglioside glycans, and influence protein-carbohydrate interactions. Structural and functional insights into the biological roles of these glycans are impeded due to the limited accessibility of well-defined structures. Here we report an integrated chemoenzymatic strategy for expeditious and systematic synthesis of a comprehensive 65-membered ganglioside glycan library covering all possible patterns of sulfation and sialylation. This strategy relies on the streamlined modular assembly of three common sialylated precursors by highly stereoselective iterative sialylation, modular site-specific sulfation through flexible orthogonal protecting-group manipulations and enzymatic-catalysed diversification using three sialyltransferase modules and a galactosidase module. These diverse ganglioside glycans enable exploration into their structure-function relationships using high-throughput glycan microarray technology, which reveals that different patterns of sulfation and sialylation on these glycans mediate their unique binding specificities.
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Affiliation(s)
- Zhuojia Xu
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yating Liu
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jialin Liu
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing Ma
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhumin Zhang
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Liuqing Wen
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Wen Yi
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tiehai Li
- State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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6
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Babulic JL, De León González FV, Capicciotti CJ. Recent advances in photoaffinity labeling strategies to capture Glycan-Protein interactions. Curr Opin Chem Biol 2024; 80:102456. [PMID: 38705088 DOI: 10.1016/j.cbpa.2024.102456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024]
Abstract
Glycans decorate all cells and are critical mediators of cellular processes through recognition by glycan-binding proteins (GBPs). While targeting glycan-protein interactions has great therapeutic potential, these interactions are challenging to study as they are generally transient and exhibit low binding affinities. Glycan-based photo-crosslinkable probes have enabled covalent capture and identification of unknown GBP receptors and glycoconjugate ligands. Here, we review recent progress in photo-crosslinking approaches targeting glycan-mediated interactions. We discuss two prominent emerging strategies: 1) development of photo-crosslinkable oligosaccharide ligands to identify GBP receptors; and 2) cell-surface glyco-engineering to identify glycoconjugate ligands of GBPs. Overall, photoaffinity labeling affords valuable insights into complex glycan-protein networks and is poised to help elucidate the glycan-protein interactome, providing novel targets for therapeutic intervention.
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Affiliation(s)
- Jonathan L Babulic
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | | | - Chantelle J Capicciotti
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada; Department of Chemistry, Queen's University, Kingston, K7L 2S8, Canada; Department of Surgery, Queen's University, Kingston, K7L 2V7, Canada.
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7
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Keisham S, Saito S, Kowashi S, Tateno H. Droplet-Based Glycan and RNA Sequencing for Profiling the Distinct Cellular Glyco-States in Single Cells. SMALL METHODS 2024; 8:e2301338. [PMID: 38164999 DOI: 10.1002/smtd.202301338] [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: 10/02/2023] [Revised: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Plate-based single-cell glycan and RNA sequencing (scGR-seq) is previously developed to realize the integrated analysis of glycome and transcriptome in single cells. However, the sample size is limited to only a few hundred cells. Here, a droplet-based scGR-seq is developed to address this issue by adopting a 10x Chromium platform to simultaneously profile ten thousand cells' glycome and transcriptome in single cells. To establish droplet-based scGR-seq, a comparative analysis of two distinct cell lines is performed: pancreatic ductal adenocarcinoma cells and normal pancreatic duct cells. Droplet-based scGR-seq revealed distinct glycan profiles between the two cell lines that showed a strong correlation with the results obtained by flow cytometry. Next, droplet-based scGR-seq is applied to a more complex sample: peripheral blood mononuclear cells (PBMC) containing various immune cells. The method can systematically map the glycan signature for each immune cell in PBMC as well as glycan alterations by cell lineage. Prediction of the association between the glycan expression and the gene expression using regression analysis ultimately leads to the identification of a glycan epitope that impacts cellular functions. In conclusion, the droplet-based scGR-seq realizes the high-throughput profiling of the distinct cellular glyco-states in single cells.
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Affiliation(s)
- Sunanda Keisham
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sayoko Saito
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Satori Kowashi
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, Multicellular System Regulation Research Group, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, 305-8566, Japan
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8
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De León González FV, Boddington ME, Kofsky JM, Prindl MI, Capicciotti CJ. Glyco-Engineering Cell Surfaces by Exo-Enzymatic Installation of GlcNAz and LacNAz Motifs. ACS Chem Biol 2024; 19:629-640. [PMID: 38394345 DOI: 10.1021/acschembio.3c00542] [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: 02/25/2024]
Abstract
Exo-enzymatic glyco-engineering of cell-surface glycoconjugates enables the selective display of well-defined glyco-motifs bearing bioorthogonal functional groups, which can be used to study glycans and their interactions with glycan-binding proteins. In recent years, strategies to edit cellular glycans by installing monosaccharides and their derivatives using glycosyltransferase enzymes have rapidly expanded. However, analogous methods to introduce chemical reporter-functionalized type 2 LacNAc motifs have not been reported. Herein, we report the chemo-enzymatic synthesis of unnatural UDP-GlcNAc and UDP-GalNAc nucleotide-sugars bearing azide, alkyne, and diazirine functionalities on the C2-acetamido group using the mutant uridylyltransferase AGX1F383A. The unnatural UDP-GlcNAc derivatives were examined as substrates for the human GlcNAc-transferase B3GNT2, where it was found that modified donors were tolerated for transfer, albeit to a lesser extent than the natural UDP-GlcNAc substrate. When the GlcNAc derivatives were examined as acceptor substrates for the human Gal-transferase B4GalT1, all derivatives were well tolerated and the enzyme could successfully form derivatized LacNAcs. B3GNT2 was also used to exo-enzymatically install GlcNAc and unnatural GlcNAc derivatives on cell-surface glycans. GlcNAc- or GlcNAz-engineered cells were further extended by B4GalT1 and UDP-Gal, producing LacNAc- or LacNAz-engineered cells. Our proof-of-concept glyco-engineering labeling strategy is amenable to different cell types and our work expands the exo-enzymatic glycan editing toolbox to selectively introduce unnatural type 2 LacNAc motifs.
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Affiliation(s)
| | - Marie E Boddington
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Joshua M Kofsky
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
| | - Martha I Prindl
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
| | - Chantelle J Capicciotti
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
- Department of Surgery, Queen's University, Kingston K7L 2V7, Canada
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9
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Kofsky JM, Babulic JL, Boddington ME, De León González FV, Capicciotti CJ. Glycosyltransferases as versatile tools to study the biology of glycans. Glycobiology 2023; 33:888-910. [PMID: 37956415 DOI: 10.1093/glycob/cwad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023] Open
Abstract
All cells are decorated with complex carbohydrate structures called glycans that serve as ligands for glycan-binding proteins (GBPs) to mediate a wide range of biological processes. Understanding the specific functions of glycans is key to advancing an understanding of human health and disease. However, the lack of convenient and accessible tools to study glycan-based interactions has been a defining challenge in glycobiology. Thus, the development of chemical and biochemical strategies to address these limitations has been a rapidly growing area of research. In this review, we describe the use of glycosyltransferases (GTs) as versatile tools to facilitate a greater understanding of the biological roles of glycans. We highlight key examples of how GTs have streamlined the preparation of well-defined complex glycan structures through chemoenzymatic synthesis, with an emphasis on synthetic strategies allowing for site- and branch-specific display of glyco-epitopes. We also describe how GTs have facilitated expansion of glyco-engineering strategies, on both glycoproteins and cell surfaces. Coupled with advancements in bioorthogonal chemistry, GTs have enabled selective glyco-epitope editing of glycoproteins and cells, selective glycan subclass labeling, and the introduction of novel biomolecule functionalities onto cells, including defined oligosaccharides, antibodies, and other proteins. Collectively, these approaches have contributed great insight into the fundamental biological roles of glycans and are enabling their application in drug development and cellular therapies, leaving the field poised for rapid expansion.
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Affiliation(s)
- Joshua M Kofsky
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Jonathan L Babulic
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Marie E Boddington
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON K7L 2V7, Canada
| | | | - Chantelle J Capicciotti
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, ON K7L 2V7, Canada
- Department of Surgery, Queen's University, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
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10
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Lossio CF, Osterne VJS, Pinto-Junior VR, Chen S, Oliveira MV, Verduijn J, Verbeke I, Serna S, Reichardt NC, Skirtach A, Cavada BS, Van Damme EJM, Nascimento KS. Structural Analysis and Characterization of an Antiproliferative Lectin from Canavalia villosa Seeds. Int J Mol Sci 2023; 24:15966. [PMID: 37958949 PMCID: PMC10649158 DOI: 10.3390/ijms242115966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Cells use glycans to encode information that modulates processes ranging from cell-cell recognition to programmed cell death. This information is encoded within a glycocode, and its decoding is performed by carbohydrate-binding proteins. Among these, lectins stand out due to their specific and reversible interaction with carbohydrates. Changes in glycosylation patterns are observed in several pathologies, including cancer, where abnormal glycans are found on the surfaces of affected tissues. Given the importance of the bioprospection of promising biomolecules, the current work aimed to determine the structural properties and anticancer potential of the mannose-specific lectin from seeds of Canavalia villosa (Cvill). Experimental elucidation of the primary and 3D structures of the lectin, along with glycan array and molecular docking, facilitated the determination of its fine carbohydrate-binding specificity. These structural insights, coupled with the lectin's specificity, have been combined to explain the antiproliferative effect of Cvill against cancer cell lines. This effect is dependent on the carbohydrate-binding activity of Cvill and its uptake in the cells, with concomitant activation of autophagic and apoptotic pathways.
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Affiliation(s)
- Claudia F. Lossio
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Vinicius J. S. Osterne
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Department of Physics, Federal University of Ceara, Fortaleza 60440-970, Brazil
| | - Simin Chen
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Joost Verduijn
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Isabel Verbeke
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sonia Serna
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Niels C. Reichardt
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
- Centro de Investigación Biomédica en Red (CIBER-BBN), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Andre Skirtach
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
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11
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Hussnaetter KP, Palm P, Pich A, Franzreb M, Rapp E, Elling L. Strategies for Automated Enzymatic Glycan Synthesis (AEGS). Biotechnol Adv 2023; 67:108208. [PMID: 37437855 DOI: 10.1016/j.biotechadv.2023.108208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Glycans are the most abundant biopolymers on earth and are constituents of glycoproteins, glycolipids, and proteoglycans with multiple biological functions. The availability of different complex glycan structures is of major interest in biotechnology and basic research of biological systems. High complexity, establishment of general and ubiquitous synthesis techniques, as well as sophisticated analytics, are major challenges in the development of glycan synthesis strategies. Enzymatic glycan synthesis with Leloir-glycosyltransferases is an attractive alternative to chemical synthesis as it can achieve quantitative regio- and stereoselective glycosylation in a single step. Various strategies for synthesis of a wide variety of different glycan structures has already be established and will exemplarily be discussed in the scope of this review. However, the application of enzymatic glycan synthesis in an automated system has high demands on the equipment, techniques, and methods. Different automation approaches have already been shown. However, while these techniques have been applied for several glycans, only a few strategies are able to conserve the full potential of enzymatic glycan synthesis during the process - economical and enzyme technological recycling of enzymes is still rare. In this review, we show the major challenges towards Automated Enzymatic Glycan Synthesis (AEGS). First, we discuss examples for immobilization of glycans or glycosyltransferases as an important prerequisite for the embedment and implementation in an enzyme reactor. Next, improvement of bioreactors towards automation will be described. Finally, analysis and monitoring of the synthesis process are discussed. Furthermore, automation processes and cycle design are highlighted. Accordingly, the transition of recent approaches towards a universal automated glycan synthesis platform will be projected. To this end, this review aims to describe essential key features for AEGS, evaluate the current state-of-the-art and give thought- encouraging impulses towards future full automated enzymatic glycan synthesis.
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Affiliation(s)
- Kai Philip Hussnaetter
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Philip Palm
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Andrij Pich
- Functional and Interactive Polymers, Institute of Technical and Macromolecular Chemistry and DWI Leibniz-Institute for Interactive Materials e.V., RWTH Aachen University, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Matthias Franzreb
- Karlsruher Institute of Technology (KIT), Institute of Functional Interfaces, Hermann v. Helmholtz, Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestrasse 20 * ZENIT, 39120 Magdeburg, Germany; Max Planck Institute for Dynamics of Complex Technical System, Bioprocess Engineering, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany.
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12
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Lete M, Hoffmann M, Schomann N, Martínez-Castillo A, Peccati F, Konietzny PB, Delgado S, Snyder NL, Jiménez-Oses G, Abrescia NGA, Ardá A, Hartmann L, Jiménez-Barbero J. Molecular Recognition of Glycan-Bearing Glycomacromolecules Presented at Membrane Surfaces by Lectins: An NMR View. ACS OMEGA 2023; 8:16883-16895. [PMID: 37214724 PMCID: PMC10193412 DOI: 10.1021/acsomega.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
Lectin-glycan interactions are at the heart of a multitude of biological events. Glycans are usually presented in a multivalent manner on the cell surface as part of the so-called glycocalyx, where they interact with other entities. This multivalent presentation allows us to overcome the typical low affinities found for individual glycan-lectin interactions. Indeed, the presentation of glycans may drastically impact their binding by lectins, highly affecting the corresponding binding affinity and even selectivity. In this context, we herein present the study of the interaction of a variety of homo- and heteromultivalent lactose-functionalized glycomacromolecules and their lipid conjugates with two human galectins. We have employed as ligands the glycomacromolecules, as well as liposomes decorated with those structures, to evaluate their interactions in a cell-mimicking environment. Key details of the interaction have been unravelled by NMR experiments, both from the ligand and receptor perspectives, complemented by cryo-electron microscopy methods and molecular dynamics simulations.
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Affiliation(s)
- Marta
G. Lete
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Miriam Hoffmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Nils Schomann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Ane Martínez-Castillo
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Francesca Peccati
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Patrick B. Konietzny
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Sandra Delgado
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Nicole L. Snyder
- Department
of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Gonzalo Jiménez-Oses
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Nicola G. A. Abrescia
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas, Instituto de Salud Carlos
III, Madrid 28029, Spain
| | - Ana Ardá
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Laura Hartmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Department
of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid 28029, Spain
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13
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Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
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Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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14
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Diessler ME, Hernández R, Gomez Castro G, Barbeito CG. Decidual cells and decidualization in the carnivoran endotheliochorial placenta. Front Cell Dev Biol 2023; 11:1134874. [PMID: 37009475 PMCID: PMC10060884 DOI: 10.3389/fcell.2023.1134874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Decidualization is considered a distinctive feature of eutherian pregnancy, and has appeared during evolution along with the development of invasive forms of placentation, as the endotheliochorial placenta. Although decidualization is not massive in carnivores, as it is in most species developing hemochorial placentas, isolated or grouped cells regarded as decidual have been documented and characterized, mainly in bitches and queens. For the majority of the remaining species of the order, data in the bibliography are fragmentary. In this article, general morphological aspects of decidual stromal cells (DSCs), their time of appearance and lasting, data about the expression of cytoskeletal proteins and molecules considered as markers of decidualization were reviewed. From the data reviewed, it follows that carnivoran DSCs take part either in the secretion of progesterone, prostaglandins, relaxin, among other substances, or at least in the signaling pathways triggered by them. Beyond their physiological roles, some of those molecules are already being used, or are yet under study, for the non-invasive endocrine monitoring and reproductive control of domestic and wild carnivores. Only insulin-like growth factor binding protein 1, among the main decidual markers, has been undoubtedly demonstrated in both species. Laminin, on the contrary, was found only in feline DSCs, and prolactin was preliminary reported in dogs and cats. Prolactin receptor, on the other hand, was found in both species. While canine DSCs are the only placental cell type expressing the nuclear progesterone receptor (PGR), that receptor has not been demonstrated neither in feline DSCs, nor in any other cell in the queen placenta, although the use of PGR blockers leads to abortion. Against this background, and from the data gathered so far, it is unquestionable that DSCs in carnivorans do play a pivotal role in placental development and health. The knowledge about placental physiology is critical for medical care and breeding management, primarily in domestic carnivores; it is also absolutely crucial for a conservation approach in the management of endangered carnivore species.
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Affiliation(s)
- Mónica Elizabeth Diessler
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), La Plata, Argentina
- *Correspondence: Mónica Elizabeth Diessler,
| | - Rocío Hernández
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), La Plata, Argentina
| | - Gimena Gomez Castro
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), FCV, UNLP, La Plata, Argentina
| | - Claudio Gustavo Barbeito
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), FCV, UNLP, La Plata, Argentina
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15
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HS, an Ancient Molecular Recognition and Information Storage Glycosaminoglycan, Equips HS-Proteoglycans with Diverse Matrix and Cell-Interactive Properties Operative in Tissue Development and Tissue Function in Health and Disease. Int J Mol Sci 2023; 24:ijms24021148. [PMID: 36674659 PMCID: PMC9867265 DOI: 10.3390/ijms24021148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Heparan sulfate is a ubiquitous, variably sulfated interactive glycosaminoglycan that consists of repeating disaccharides of glucuronic acid and glucosamine that are subject to a number of modifications (acetylation, de-acetylation, epimerization, sulfation). Variable heparan sulfate chain lengths and sequences within the heparan sulfate chains provide structural diversity generating interactive oligosaccharide binding motifs with a diverse range of extracellular ligands and cellular receptors providing instructional cues over cellular behaviour and tissue homeostasis through the regulation of essential physiological processes in development, health, and disease. heparan sulfate and heparan sulfate-PGs are integral components of the specialized glycocalyx surrounding cells. Heparan sulfate is the most heterogeneous glycosaminoglycan, in terms of its sequence and biosynthetic modifications making it a difficult molecule to fully characterize, multiple ligands also make an elucidation of heparan sulfate functional properties complicated. Spatio-temporal presentation of heparan sulfate sulfate groups is an important functional determinant in tissue development and in cellular control of wound healing and extracellular remodelling in pathological tissues. The regulatory properties of heparan sulfate are mediated via interactions with chemokines, chemokine receptors, growth factors and morphogens in cell proliferation, differentiation, development, tissue remodelling, wound healing, immune regulation, inflammation, and tumour development. A greater understanding of these HS interactive processes will improve therapeutic procedures and prognoses. Advances in glycosaminoglycan synthesis and sequencing, computational analytical carbohydrate algorithms and advanced software for the evaluation of molecular docking of heparan sulfate with its molecular partners are now available. These advanced analytic techniques and artificial intelligence offer predictive capability in the elucidation of heparan sulfate conformational effects on heparan sulfate-ligand interactions significantly aiding heparan sulfate therapeutics development.
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16
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Doud EH, Yeh ES. Mass Spectrometry-Based Glycoproteomic Workflows for Cancer Biomarker Discovery. Technol Cancer Res Treat 2023; 22:15330338221148811. [PMID: 36740994 PMCID: PMC9903044 DOI: 10.1177/15330338221148811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glycosylation has a clear role in cancer initiation and progression, with numerous studies identifying distinct glycan features or specific glycoproteoforms associated with cancer. Common findings include that aggressive cancers tend to have higher expression levels of enzymes that regulate glycosylation as well as glycoproteins with greater levels of complexity, increased branching, and enhanced chain length1. Research in cancer glycoproteomics over the last 50-plus years has mainly focused on technology development used to observe global changes in glycosylation. Efforts have also been made to connect glycans to their protein carriers as well as to delineate the role of these modifications in intracellular signaling and subsequent cell function. This review discusses currently available techniques utilizing mass spectrometry-based technologies used to study glycosylation and highlights areas for future advancement.
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Affiliation(s)
- Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, USA
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
| | - Elizabeth S. Yeh
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, USA
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17
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Bertuzzi S, Peccati F, Serna S, Artschwager R, Notova S, Thépaut M, Jiménez-Osés G, Fieschi F, Reichardt NC, Jiménez-Barbero J, Ardá A. Immobilization of Biantennary N-Glycans Leads to Branch Specific Epitope Recognition by LSECtin. ACS CENTRAL SCIENCE 2022; 8:1415-1423. [PMID: 36313162 PMCID: PMC9615123 DOI: 10.1021/acscentsci.2c00719] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 05/04/2023]
Abstract
The molecular recognition features of LSECtin toward asymmetric N-glycans have been scrutinized by NMR and compared to those occurring in glycan microarrays. A pair of positional glycan isomers (LDN3 and LDN6), a nonelongated GlcNAc4Man3 N-glycan (G0), and the minimum binding epitope (the GlcNAcβ1-2Man disaccharide) have been used to shed light on the preferred binding modes under both experimental conditions. Strikingly, both asymmetric LDN3 and LDN6 N-glycans are recognized by LSECtin with similar affinities in solution, in sharp contrast to the results obtained when those glycans are presented on microarrays, where only LDN6 was efficiently recognized by the lectin. Thus, different results can be obtained using different experimental approaches, pointing out the tremendous difficulty of translating in vitro results to the in vivo environment.
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Affiliation(s)
- Sara Bertuzzi
- Basque
Research & Technology Alliance (BRTA), Chemical Glycobiology Group, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Francesca Peccati
- Basque Research
& Technology Alliance (BRTA), Computational Chemistry Group, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Sonia Serna
- Glycotechnology
Group, Basque Research and Technology Alliance (BRTA), CIC biomaGUNE, Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Raik Artschwager
- Glycotechnology
Group, Basque Research and Technology Alliance (BRTA), CIC biomaGUNE, Paseo Miramón 182, 20014 San Sebastian, Spain
- Memorial
Sloan Kettering Cancer Center, 417 East 68th Street, New
York, New York 10065, United States
| | - Simona Notova
- CNRS,
CEA, Institut de Biologie Structurale, University
of Grenoble Alpes, 38000 Grenoble, France
| | - Michel Thépaut
- CNRS,
CEA, Institut de Biologie Structurale, University
of Grenoble Alpes, 38000 Grenoble, France
| | - Gonzalo Jiménez-Osés
- Basque Research
& Technology Alliance (BRTA), Computational Chemistry Group, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain
| | - Franck Fieschi
- CNRS,
CEA, Institut de Biologie Structurale, University
of Grenoble Alpes, 38000 Grenoble, France
- E-mail:
| | - Niels C. Reichardt
- Glycotechnology
Group, Basque Research and Technology Alliance (BRTA), CIC biomaGUNE, Paseo Miramón 182, 20014 San Sebastian, Spain
- CIBER-BBN, Paseo Miramón 182, 20009 San Sebastian, Spain
- E-mail:
| | - Jesús Jiménez-Barbero
- Basque
Research & Technology Alliance (BRTA), Chemical Glycobiology Group, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain
- Department
of Organic Chemistry, II Faculty of Science
and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
- E-mail:
| | - Ana Ardá
- Basque
Research & Technology Alliance (BRTA), Chemical Glycobiology Group, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain
- E-mail:
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18
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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