1
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Radziejewska I. Tumor-associated carbohydrate antigens of MUC1 - Implication in cancer development. Biomed Pharmacother 2024; 174:116619. [PMID: 38643541 DOI: 10.1016/j.biopha.2024.116619] [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: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
Glycosylation of cancerous epithelial MUC1 protein is specifically altered in comparison to that which is presented by healthy cells. One of such changes is appearing tumor-associated carbohydrate antigens (TACAs) which are rare in normal tissues and are highly correlated with poor clinical outcomes and cancer progression. This review summarizes and describes the role of Tn, T antigens, their sialylated forms as well as fucosylated Lewis epitopes in different aspects of tumor development, progression, and metastasis. Finally, applications of MUC1 glycan epitopes as potential targets for therapeutic strategy of cancers are notified. One of the novelties of this review is presentation of TACAs as inherently connected with MUC1 mucin.
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Affiliation(s)
- Iwona Radziejewska
- Department of Medical Chemistry, Medical University of Białystok, ul. Mickiewicza 2, Białystok 15-222, Poland.
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2
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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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3
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Pratap S, Zhao ZJ. Finding new lanes: Chimeric antigen receptor (CAR) T-cells for myeloid leukemia. Cancer Rep (Hoboken) 2020; 3:e1222. [PMID: 32671999 PMCID: PMC7941581 DOI: 10.1002/cnr2.1222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Myeloid leukemia represents a heterogeneous group of cancers of blood and bone marrow which arise from clonal expansion of hematopoietic myeloid lineage cells. Acute myeloid leukemia (AML) has traditionally been treated with multi-agent chemotherapy, but conventional therapies have not improved the long-term survival for decades. Chronic myeloid leukemia (CML) is an indolent disease which requires lifelong treatment, is associated with significant side effects, and carries a risk of progression to potentially lethal blast crises. RECENT FINDINGS Recent advances in molecular biology, virology, and immunology have enabled researchers to grow and modify T lymphocytes ex-vivo. Chimeric antigen receptor (CAR) T-cell therapy has been shown to specifically target cells of lymphoid lineage and induce remission in acute lymphoblastic leukemia (ALL) patients. While the success of CAR T-cells against ALL is considered a defining moment in modern oncology, similar efficacy against myeloid leukemia cells remains elusive. Over the past 10 years, numerous CAR T-cells have been developed that can target novel myeloid antigens, and many clinical trials are finally starting to yield encouraging results. In this review, we present the recent advances in this field and discuss strategies for future development of myeloid targeting CAR T-cell therapy. CONCLUSIONS The field of CAR T-cell therapy has rapidly evolved over the past few years. It represents a radically new approach towards cancers, and with continued refinement it may become a viable therapeutic option for patients of acute and chronic myeloid leukemia.
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Affiliation(s)
- Suraj Pratap
- University of Oklahoma Health Sciences CenterDepartment of Pediatric Hematology‐OncologyOklahoma CityOklahomaUSA
| | - Zhizhuang J. Zhao
- University of Oklahoma Health Sciences CenterDepartment of PathologyOklahoma CityOklahomaUSA
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4
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Paubelle E, Rocher C, Julia E, Thomas X. Chimeric Antigen Receptor-Engineered T Cell Therapy in Acute Myeloid Leukaemia. EUROPEAN MEDICAL JOURNAL 2018. [DOI: 10.33590/emj/10314141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a disease with a very poor outcome and remains an area of significant unmet need, necessitating novel therapeutic strategies. The progress made in the field of immunotherapy, in particular chimeric antigen receptor (CAR)-engineered T cells, has given rise to many hopes for pathologies such as B cell acute lymphoblastic leukaemia and B cell lymphoma, and many studies have attempted to translate these successes to AML. This review summarises the recent advances in, and defines an ideal target for, CAR T cell therapy in AML.
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Affiliation(s)
- Etienne Paubelle
- Department of Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Lyon, France; LBMC, ENS, CNRS UMR5239, Faculté de Médecine Lyon-Sud, Lyon, France
| | - Clément Rocher
- Department of Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Lyon, France
| | - Edith Julia
- Department of Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Lyon, France
| | - Xavier Thomas
- Department of Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Lyon, France
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5
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Lakshminarayanan A, Richard M, Davis BG. Studying glycobiology at the single-molecule level. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0019-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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6
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Alibay I, Burusco KK, Bruce NJ, Bryce RA. Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics. J Phys Chem B 2018; 122:2462-2474. [PMID: 29419301 DOI: 10.1021/acs.jpcb.7b09841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4C1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.
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Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Kepa K Burusco
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , Heidelberg 69118 , Germany
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
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7
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Abstract
Streptococcus pneumoniae is a leading cause of morbidity and mortality globally. The Pilus-1 proteins, RrgA, RrgB and RrgC of S. pneumoniae have been previously assessed for their role in infection, invasive disease and as possible vaccine candidates. In this study we have investigated the glycan binding repertoire of all three Pilus-1 proteins, identifying that the tip adhesin RrgA has the broadest glycan recognition of the three proteins, binding to maltose/cellobiose, α/β linked galactose and blood group A and H antigens. RrgB only bound mannose, while RrgC bound a subset of glycans also recognized by RrgA. Adherence of S. pneumoniae TIGR4 to epithelial cells was tested using four of the oligosaccharides identified through the glycan array analysis as competitive inhibitors. The blood group H trisaccharide provided the best blocking of S. pneumoniae TIGR4 adherence. Adherence is the first step in disease, and host glycoconjugates are a common target for many adhesins. This study has identified Pilus-1 proteins as new lectins involved in the targeting of host glycosylation by S. pneumoniae.
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8
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Dietrich MH, Harprecht C, Stehle T. The bulky and the sweet: How neutralizing antibodies and glycan receptors compete for virus binding. Protein Sci 2017; 26:2342-2354. [PMID: 28986957 PMCID: PMC5699497 DOI: 10.1002/pro.3319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022]
Abstract
Numerous viruses rely on glycan receptor binding as the initial step in host cell infection. Engagement of specific glycan receptors such as sialylated carbohydrates, glycosaminoglycans, or histo-blood group antigens can determine host range, tissue tropism, and pathogenicity. Glycan receptor-binding sites are typically located in exposed regions on viral surfaces-sites that are also generally prone to binding of neutralizing antibodies that directly interfere with virus-glycan receptor interactions. In this review, we examine the locations and architecture of the glycan- and antibody-binding sites in four different viruses with stalk-like attachment proteins (reovirus, influenza virus, norovirus, and coronavirus) and investigate the mechanisms by which antibodies block glycan recognition. Those viruses exemplify that direct molecular mimicking of glycan receptors by antibodies is rare and further demonstrate that antibodies often partly overlap or bind sufficiently close to the receptor-binding region to hinder access to this site, achieving neutralization partially because of the epitope location and partly due to their sheer size.
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Affiliation(s)
- Melanie H. Dietrich
- Interfaculty Institute of BiochemistryUniversity of TuebingenTuebingenGermany
| | - Christina Harprecht
- Interfaculty Institute of BiochemistryUniversity of TuebingenTuebingenGermany
| | - Thilo Stehle
- Interfaculty Institute of BiochemistryUniversity of TuebingenTuebingenGermany
- Department of PediatricsVanderbilt University School of MedicineNashvilleTennesseeUSA
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9
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Fan M, Li M, Gao L, Geng S, Wang J, Wang Y, Yan Z, Yu L. Chimeric antigen receptors for adoptive T cell therapy in acute myeloid leukemia. J Hematol Oncol 2017; 10:151. [PMID: 28851445 PMCID: PMC5576380 DOI: 10.1186/s13045-017-0519-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/17/2017] [Indexed: 12/17/2022] Open
Abstract
Currently, conventional therapies for acute myeloid leukemia (AML) have high failure and relapse rates. Thus, developing new strategies is crucial for improving the treatment of AML. With the clinical success of anti-CD19 chimeric antigen receptor (CAR) T cell therapies against B-lineage malignancies, many studies have attempted to translate the success of CAR T cell therapy to other malignancies, including AML. This review summarizes the current advances in CAR T cell therapy against AML, including preclinical studies and clinical trials, and discusses the potential AML-associated surface markers that could be used for further CAR technology. Finally, we describe strategies that might address the current issues of employing CAR T cell therapy in AML.
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Affiliation(s)
- Mingxue Fan
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China
| | - Minghao Li
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China
| | - Lipeng Gao
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China
| | - Sicong Geng
- China Novartis Institutes for Biomedical Research Co., Ltd., GDD/TRD/Chemical and Pharmaceutical Profiling, 5F, Building 3, Novartis Campus 4218 Jinke Rd, Zhangjiang Hi-Tech Park Pudong District, Shanghai, 201203, China
| | - Jing Wang
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China
| | - Yiting Wang
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China
| | - Zhiqiang Yan
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China.
| | - Lei Yu
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, NO. 3663 Zhongshan Road, Shanghai, 200062, People's Republic of China.
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10
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Dingjan T, Imberty A, Pérez S, Yuriev E, Ramsland PA. Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. Front Pharmacol 2017; 8:393. [PMID: 28680402 PMCID: PMC5478714 DOI: 10.3389/fphar.2017.00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.
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Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Anne Imberty
- Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble AlpesGrenoble, France
| | - Serge Pérez
- Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble AlpesGrenoble, France
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT UniversityMelbourne, VIC, Australia.,Department of Surgery Austin Health, University of MelbourneMelbourne, VIC, Australia.,Department of Immunology, Central Clinical School, Monash UniversityMelbourne, VIC, Australia.,Burnet InstituteMelbourne, VIC, Australia
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11
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Orlowski RJ, Porter DL, Frey NV. The promise of chimeric antigen receptor T cells (CARTs) in leukaemia. Br J Haematol 2016; 177:13-26. [PMID: 27977050 DOI: 10.1111/bjh.14475] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The success of genetically engineered T cells that express chimeric antigen receptors (CARTs) has been a momentous step forward in harnessing the potent cancer fighting abilities of the immune system. The efficacy seen in relapsed/refractory (r/r) acute lymphoblastic leukaemia (ALL), not only by inducing remission, but also in maintaining long-term disease control, has been unprecedented. While the foundation for this approach has been firmly set in place, continued development will improve the efficacy, toxicity and applicability to other malignancies of this new class of 'living drugs'. In this review, we provide a comprehensive overview of the most current clinical trial data in both acute and chronic leukaemias, and discuss some of the potential ways to enhance the activity and safety of CART therapy going forward.
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Affiliation(s)
- Robert J Orlowski
- Department of Hematology-Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - David L Porter
- Department of Hematology-Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Noelle V Frey
- Department of Hematology-Oncology, University of Pennsylvania, Philadelphia, PA, USA
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12
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Marianski M, Supady A, Ingram T, Schneider M, Baldauf C. Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose. J Chem Theory Comput 2016; 12:6157-6168. [DOI: 10.1021/acs.jctc.6b00876] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Teresa Ingram
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Markus Schneider
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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13
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Antibody recognition of aberrant glycosylation on the surface of cancer cells. Curr Opin Struct Biol 2016; 44:1-8. [PMID: 27821276 DOI: 10.1016/j.sbi.2016.10.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/13/2016] [Indexed: 11/23/2022]
Abstract
Carbohydrate-binding antibodies and carbohydrate-based vaccines are being actively pursued as targeted immunotherapies for a broad range of cancers. Recognition of tumor-associated carbohydrates (glycans) by antibodies is predominantly towards terminal epitopes on glycoproteins and glycolipids on the surface of cancer cells. Crystallography along with complementary experimental and computational methods have been extensively used to dissect antibody recognition of glycan epitopes commonly found in cancer. We provide an overview of the structural biology of antibody recognition of tumor-associated glycans and propose potential rearrangements of these targets in the membrane that could dictate the complex biological activities of these antibodies against cancer cells.
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14
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The Promise of Chimeric Antigen Receptor Engineered T Cells in the Treatment of Hematologic Malignancies. Cancer J 2016; 22:27-33. [PMID: 26841014 DOI: 10.1097/ppo.0000000000000166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Relapsed and refractory hematologic malignancies have a very poor prognosis. Chimeric antigen receptor T cells are emerging as a powerful therapy in this setting. Early clinical trials of genetically modified T cells for the treatment of non-Hodgkin lymphoma, chronic lymphocytic leukemia, and acute lymphoblastic leukemia have shown high complete response rates in patients with few therapeutic options. Exploration is ongoing for other hematologic malignancies including multiple myeloma, acute myeloid leukemia, and Hodgkin lymphoma (HL). At the same time, the design and production of chimeric antigen receptor T cells are being advanced so that this therapy can be more widely utilized. Cytokine release syndrome and neurotoxicity are common, but they are treatable and fully reversible. This review will review available data as well as future developments and challenges in the field.
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15
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Sterner E, Flanagan N, Gildersleeve JC. Perspectives on Anti-Glycan Antibodies Gleaned from Development of a Community Resource Database. ACS Chem Biol 2016; 11:1773-83. [PMID: 27220698 PMCID: PMC4949583 DOI: 10.1021/acschembio.6b00244] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Antibodies are used
extensively for a wide range of basic research
and clinical applications. While an abundant and diverse collection
of antibodies to protein antigens have been developed, good monoclonal
antibodies to carbohydrates are much less common. Moreover, it can
be difficult to determine if a particular antibody has the appropriate
specificity, which antibody is best suited for a given application,
and where to obtain that antibody. Herein, we provide an overview
of the current state of the field, discuss challenges for selecting
and using antiglycan antibodies, and summarize deficiencies in the
existing repertoire of antiglycan antibodies. This perspective was
enabled by collecting information from publications, databases, and
commercial entities and assembling it into a single database, referred
to as the Database of Anti-Glycan Reagents (DAGR). DAGR is a publicly
available, comprehensive resource for anticarbohydrate antibodies,
their applications, availability, and quality.
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Affiliation(s)
- Eric Sterner
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Natalie Flanagan
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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16
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Topin J, Lelimousin M, Arnaud J, Audfray A, Pérez S, Varrot A, Imberty A. The Hidden Conformation of Lewis x, a Human Histo-Blood Group Antigen, Is a Determinant for Recognition by Pathogen Lectins. ACS Chem Biol 2016; 11:2011-20. [PMID: 27198630 DOI: 10.1021/acschembio.6b00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histo-blood group epitopes are fucosylated branched oligosaccharides with well-defined conformations in solution that are recognized by receptors, such as lectins from pathogens. We report here the results of a series of experimental and computational endeavors revealing the unusual distortion of histo-blood group antigens by bacterial and fungal lectins. The Lewis x trisaccharide adopts a rigid closed conformation in solution, while crystallography and molecular dynamics reveal several higher energy open conformations when bound to the Ralstonia solanacearum lectin, which is in agreement with thermodynamic and kinetic measurements. Extensive molecular dynamics simulations confirm rare transient Le(x) openings in solution, frequently assisted by distortion of the central N-acetyl-glucosamine ring. Additional directed molecular dynamic trajectories revealed the role of a conserved tryptophan residue in guiding the fucose into the binding site. Our findings show that conformational adaptation of oligosaccharides is of paramount importance in cell recognition and should be considered when designing anti-infective glyco-compounds.
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Affiliation(s)
- Jérémie Topin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Mickaël Lelimousin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Julie Arnaud
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Aymeric Audfray
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Serge Pérez
- DPM UMR5063, Université Grenoble Alpes, and CNRS, BP 53, 38041 Grenoble cedex 9, France
| | - Annabelle Varrot
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Anne Imberty
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
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17
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Dingjan T, Agostino M, Ramsland PA, Yuriev E. Antibody-Carbohydrate Recognition from Docked Ensembles Using the AutoMap Procedure. Methods Mol Biol 2016; 1331:41-55. [PMID: 26169734 DOI: 10.1007/978-1-4939-2874-3_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Carbohydrate-protein recognition is vital to many processes in health and disease. In particular, elucidation of the structural basis of carbohydrate binding is important to the development of oligosaccharides and oligosaccharide mimetics as vaccines for infectious diseases and cancer. Computational structural techniques are valuable for the study of carbohydrate-protein recognition due to the challenges associated with experimental determination of carbohydrate-protein complexes. AutoMap is a computer program that we have developed to study protein-ligand recognition. AutoMap determines the interactions taking place in a set of highly ranked poses obtained from molecular docking and processes these to identify the protein residues most likely to be involved in interactions. In this protocol, we describe the use of AutoMap and illustrate its suitability for studying antibody recognition of the Lewis Y tetrasaccharide, which is a potential cancer vaccine antigen.
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Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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18
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Vasconcelos-Dos-Santos A, Oliveira IA, Lucena MC, Mantuano NR, Whelan SA, Dias WB, Todeschini AR. Biosynthetic Machinery Involved in Aberrant Glycosylation: Promising Targets for Developing of Drugs Against Cancer. Front Oncol 2015; 5:138. [PMID: 26161361 PMCID: PMC4479729 DOI: 10.3389/fonc.2015.00138] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/02/2015] [Indexed: 12/22/2022] Open
Abstract
Cancer cells depend on altered metabolism and nutrient uptake to generate and keep the malignant phenotype. The hexosamine biosynthetic pathway is a branch of glucose metabolism that produces UDP-GlcNAc and its derivatives, UDP-GalNAc and CMP-Neu5Ac and donor substrates used in the production of glycoproteins and glycolipids. Growing evidence demonstrates that alteration of the pool of activated substrates might lead to different glycosylation and cell signaling. It is already well established that aberrant glycosylation can modulate tumor growth and malignant transformation in different cancer types. Therefore, biosynthetic machinery involved in the assembly of aberrant glycans are becoming prominent targets for anti-tumor drugs. This review describes three classes of glycosylation, O-GlcNAcylation, N-linked, and mucin type O-linked glycosylation, involved in tumor progression, their biosynthesis and highlights the available inhibitors as potential anti-tumor drugs.
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Affiliation(s)
| | - Isadora A Oliveira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Miguel Clodomiro Lucena
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Natalia Rodrigues Mantuano
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Stephen A Whelan
- Department of Biochemistry, Cardiovascular Proteomics Center, Boston University School of Medicine , Boston, MA , USA
| | - Wagner Barbosa Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Adriane Regina Todeschini
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
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19
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Dingjan T, Spendlove I, Durrant LG, Scott AM, Yuriev E, Ramsland PA. Structural biology of antibody recognition of carbohydrate epitopes and potential uses for targeted cancer immunotherapies. Mol Immunol 2015; 67:75-88. [PMID: 25757815 DOI: 10.1016/j.molimm.2015.02.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 11/18/2022]
Abstract
Monoclonal antibodies represent the most successful class of biopharmaceuticals for the treatment of cancer. Mechanisms of action of therapeutic antibodies are very diverse and reflect their ability to engage in antibody-dependent effector mechanisms, internalize to deliver cytotoxic payloads, and display direct effects on cells by lysis or by modulating the biological pathways of their target antigens. Importantly, one of the universal changes in cancer is glycosylation and carbohydrate-binding antibodies can be produced to selectively recognize tumor cells over normal tissues. A promising group of cell surface antibody targets consists of carbohydrates presented as glycolipids or glycoproteins. In this review, we outline the basic principles of antibody-based targeting of carbohydrate antigens in cancer. We also present a detailed structural view of antibody recognition and the conformational properties of a series of related tissue-blood group (Lewis) carbohydrates that are being pursued as potential targets of cancer immunotherapy.
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Affiliation(s)
- Tamir Dingjan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ian Spendlove
- Academic Department of Clinical Oncology, Division of Cancer and Stem cells, University of Nottingham, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Lindy G Durrant
- Academic Department of Clinical Oncology, Division of Cancer and Stem cells, University of Nottingham, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Andrew M Scott
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia; Faculty of Medicine, University of Melbourne, Melbourne, VIC, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia.
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20
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The cholesterol-dependent cytolysins pneumolysin and streptolysin O require binding to red blood cell glycans for hemolytic activity. Proc Natl Acad Sci U S A 2014; 111:E5312-20. [PMID: 25422425 DOI: 10.1073/pnas.1412703111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cholesterol-dependent cytolysin (CDC) pneumolysin (Ply) is a key virulence factor of Streptococcus pneumoniae. Membrane cholesterol is required for the cytolytic activity of this toxin, but it is not clear whether cholesterol is the only cellular receptor. Analysis of Ply binding to a glycan microarray revealed that Ply has lectin activity and binds glycans, including the Lewis histo-blood group antigens. Surface plasmon resonance analysis showed that Ply has the highest affinity for the sialyl LewisX (sLeX) structure, with a K(d) of 1.88 × 10(-5) M. Ply hemolytic activity against human RBCs showed dose-dependent inhibition by sLeX. Flow cytometric analysis and Western blots showed that blocking binding of Ply to the sLeX glycolipid on RBCs prevents deposition of the toxin in the membrane. The lectin domain responsible for sLeX binding is in domain 4 of Ply, which contains candidate carbohydrate-binding sites. Mutagenesis of these predicted carbohydrate-binding residues of Ply resulted in a decrease in hemolytic activity and a reduced affinity for sLeX. This study reveals that this archetypal CDC requires interaction with the sLeX glycolipid cellular receptor as an essential step before membrane insertion. A similar analysis conducted on streptolysin O from Streptococcus pyogenes revealed that this CDC also has glycan-binding properties and that hemolytic activity against RBCs can be blocked with the glycan lacto-N-neotetraose by inhibiting binding to the cell surface. Together, these data support the emerging paradigm shift that pore-forming toxins, including CDCs, have cellular receptors other than cholesterol that define target cell tropism.
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21
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Agostino M, Velkov T, Dingjan T, Williams SJ, Yuriev E, Ramsland PA. The carbohydrate-binding promiscuity of Euonymus europaeus lectin is predicted to involve a single binding site. Glycobiology 2014; 25:101-14. [PMID: 25209582 DOI: 10.1093/glycob/cwu095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Euonymus europaeus lectin (EEL) is a carbohydrate-binding protein derived from the fruit of the European spindle tree. EEL was first identified for its erythrocyte agglutinating properties and specificity for B and H blood groups. However, a detailed molecular picture of the structural basis of carbohydrate recognition by EEL remains to be developed. In this study, we performed fluorescence titrations of a range of carbohydrates against EEL. Binding of EEL to a wide range of carbohydrates was observed, including a series of blood group-related carbohydrates, mannosides, chitotriose and sialic acid. Affinity was strongest for carbohydrates with H-related structures and the B trisaccharide. A homology model of EEL was produced from templates identified using the HHPred server, which employs hidden Markov models (HMMs) to identify templates. The HMM approach identified that the best templates for EEL were proteins featuring a ricin B-like (R-type) fold. Separate templates were used to model the core and binding site regions of the lectin. Through the use of constrained docking and spatial comparison with a template ligand, binding modes for the carbohydrate ligands were predicted. A relationship between the experimental binding energies and the computed binding energies of the selected docked poses was determined and optimized. Collectively, our results suggest that EEL utilizes a single site for recognition of carbohydrates terminating in a variety of monosaccharides.
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Affiliation(s)
- Mark Agostino
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Centre, Barcelona 08034, Spain Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Tony Velkov
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Tamir Dingjan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Paul A Ramsland
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia Department of Immunology, Alfred Medical Research and Education Precinct, Monash University, Melbourne, VIC 3004, Australia
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22
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Kapaev RR, Egorova KS, Toukach PV. Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts. J Chem Inf Model 2014; 54:2594-611. [DOI: 10.1021/ci500267u] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Roman R. Kapaev
- Higher
Chemical College of the Russian Academy of Sciences, Miusskaya
sq. 9, Moscow 125047, Russia
| | - Ksenia S. Egorova
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
| | - Philip V. Toukach
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
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23
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Pederson K, Mitchell DA, Prestegard JH. Structural characterization of the DC-SIGN-Lewis(X) complex. Biochemistry 2014; 53:5700-9. [PMID: 25121780 PMCID: PMC4159204 DOI: 10.1021/bi5005014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) is a C-type lectin highly expressed on the surface of antigen-presenting dendritic cells. DC-SIGN mediates interactions among dendritic cells, pathogens, and a variety of epithelia, myeloid cells, and endothelia by binding to high mannose residues on pathogenic invaders or fucosylated residues on the membranes of other immune cells. Although these interactions are normally beneficial, they can also contribute to disease. The structural characterization of binding geometries is therefore of interest as a basis for the construction of mimetics that can mediate the effects of abnormal immune response. Here, we report the structural characteristics of the interaction of the DC-SIGN carbohydrate recognition domain (CRD) with a common fucosylated entity, the Lewis(X) trisaccharide (Le(X)), using NMR methods. Titration of the monomeric DC-SIGN CRD with Le(X) monitored by 2D NMR revealed significant perturbations of DC-SIGN cross-peak positions in (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra and identified residues near the binding site. Additionally, saturation transfer difference (STD) and transferred nuclear Overhauser effect (trNOE) NMR experiments, using a tetrameric form of DC-SIGN, identified binding epitopes and bound conformations of the Le(X) ligand. The restraints derived from these multiple experiments were used to generate models for the binding of Le(X) to the DC-SIGN CRD. Ranking of the models based on the fit of model-based simulations of the trNOE data and STD buildup curves suggested conformations distinct from those seen in previous crystal structures. The new conformations offer insight into how differences between binding of Lewis(X) and mannose-terminated saccharides may be propagated.
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Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
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24
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Agostino M, Gandhi NS, Mancera RL. Development and application of site mapping methods for the design of glycosaminoglycans. Glycobiology 2014; 24:840-51. [DOI: 10.1093/glycob/cwu045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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25
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Vasile F, Reina JJ, Potenza D, Heggelund JE, Mackenzie A, Krengel U, Bernardi A. Comprehensive analysis of blood group antigen binding to classical and El Tor cholera toxin B-pentamers by NMR. Glycobiology 2014; 24:766-78. [PMID: 24829308 DOI: 10.1093/glycob/cwu040] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cholera is a diarrheal disease responsible for the deaths of thousands, possibly even hundreds of thousands of people every year, and its impact is predicted to further increase with climate change. It has been known for decades that blood group O individuals suffer more severe symptoms of cholera compared with individuals with other blood groups (A, B and AB). The observed blood group dependence is likely to be caused by the major virulence factor of Vibrio cholerae, the cholera toxin (CT). Here, we investigate the binding of ABH blood group determinants to both classical and El Tor CTB-pentamers using saturation transfer difference NMR and show that all three blood group determinants bind to both toxin variants. Although the details of the interactions differ, we see no large differences between the two toxin genotypes and observe very similar binding constants. We also show that the blood group determinants bind to a site distinct from that of the primary receptor, GM1. Transferred NOESY data confirm that the conformations of the blood group determinants in complex with both toxin variants are similar to those of reported X-ray and solution structures. Taken together, this detailed analysis provides a framework for the interpretation of the epidemiological data linking the severity of cholera infection and an individual's blood group, and brings us one step closer to understanding the molecular basis of cholera blood group dependence.
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Affiliation(s)
- Francesca Vasile
- Dipartimento di Chimica, Universita' degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - José J Reina
- Dipartimento di Chimica, Universita' degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Donatella Potenza
- Dipartimento di Chimica, Universita' degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Julie E Heggelund
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern NO-0315, Norway
| | - Alasdair Mackenzie
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern NO-0315, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern NO-0315, Norway
| | - Anna Bernardi
- Dipartimento di Chimica, Universita' degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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26
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Cohen M, Varki A. Modulation of glycan recognition by clustered saccharide patches. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:75-125. [PMID: 24411170 DOI: 10.1016/b978-0-12-800097-7.00003-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
All cells in nature are covered with a dense and complex array of glycan chains. Specific recognition and binding of glycans is a critical aspect of cellular interactions, both within and between species. Glycan-protein interactions tend to be of low affinity but high specificity, typically utilizing multivalency to generate the affinity required for biologically relevant binding. This review focuses on a higher level of glycan organization, the formation of clustered saccharide patches (CSPs), which can constitute unique ligands for highly specific interactions. Due to technical challenges, this aspect of glycan recognition remains poorly understood. We present a wealth of evidence for CSPs-mediated interactions, and discuss recent advances in experimental tools that are beginning to provide new insights into the composition and organization of CSPs. The examples presented here are likely the tip of the iceberg, and much further work is needed to elucidate fully this higher level of glycan organization.
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Affiliation(s)
- Miriam Cohen
- Department Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, California, USA.
| | - Ajit Varki
- Department of Medicine, University of California, San Diego, California, USA; Department Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, California, USA.
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27
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Sattelle BM, Almond A. Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans. Carbohydr Res 2013; 383:34-42. [PMID: 24252626 PMCID: PMC3909462 DOI: 10.1016/j.carres.2013.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/28/2022]
Abstract
Aqueous 10 μs simulations of N-linked mannosyl cores and sialyl Lewis (sLe) antennae are validated. Sequence dependent glycosidic linkage and pyranose ring μs motions are implicated in bioactivity. Stacked pyranoses in sLea and sLex are predicted to be atypically rigid on μs timescales. In a 25 μs simulation of sLex, all known conformers were sampled within the initial 10 μs of dynamics. Unbiased 10 μs simulations are proposed as a route to systematic and accurate glycomic 3D-analysis.
The human glycome comprises a vast untapped repository of 3D-structural information that holds the key to glycan recognition and a new era of rationally designed mimetic chemical probes, drugs, and biomaterials. Toward routine prediction of oligosaccharide conformational populations and exchange rates at thermodynamic equilibrium, we apply hardware-accelerated aqueous molecular dynamics to model μs motions in N-glycans that underpin inflammation and immunity. In 10 μs simulations, conformational equilibria of mannosyl cores, sialyl Lewis (sLe) antennae, and constituent sub-sequences agreed with prior refinements (X-ray and NMR). Glycosidic linkage and pyranose ring flexing were affected by branching, linkage position, and secondary structure, implicating sequence dependent motions in glycomic functional diversity. Linkage and ring conformational transitions that have eluded precise quantification by experiment and conventional (ns) simulations were predicted to occur on μs timescales. All rings populated non-chair shapes and the stacked galactose and fucose pyranoses of sLea and sLex were rigidified, suggesting an exploitable 3D-signature of cell adhesion protein binding. Analyses of sLex dynamics over 25 μs revealed that only 10 μs were sufficient to explore all aqueous conformers. This simulation protocol, which yields conformational ensembles that are independent of initial 3D-structure, is proposed as a route to understanding oligosaccharide recognition and structure–activity relationships, toward development of carbohydrate-based novel chemical entities.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew Almond
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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28
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Mishra SK, Kara M, Zacharias M, Koca J. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation. Glycobiology 2013; 24:70-84. [PMID: 24134878 DOI: 10.1093/glycob/cwt093] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.
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Affiliation(s)
- Sushil Kumar Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 61137 Brno, Czech Republic
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29
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Topin J, Arnaud J, Sarkar A, Audfray A, Gillon E, Perez S, Jamet H, Varrot A, Imberty A, Thomas A. Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PLoS One 2013; 8:e71149. [PMID: 23976992 PMCID: PMC3747263 DOI: 10.1371/journal.pone.0071149] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
Recent advances in glycobiology revealed the essential role of lectins for deciphering the glycocode by specific recognition of carbohydrates. Integrated multiscale approaches are needed for characterizing lectin specificity: combining on one hand high-throughput analysis by glycan array experiments and systematic molecular docking of oligosaccharide libraries and on the other hand detailed analysis of the lectin/oligosaccharide interaction by x-ray crystallography, microcalorimetry and free energy calculations. The lectins LecB from Pseudomonas aeruginosa and BambL from Burkholderia ambifaria are part of the virulence factors used by the pathogenic bacteria to invade the targeted host. These two lectins are not related but both recognize fucosylated oligosaccharides such as the histo-blood group oligosaccharides of the ABH(O) and Lewis epitopes. The specificities were characterized using semi-quantitative data from glycan array and analyzed by molecular docking with the Glide software. Reliable prediction of protein/oligosaccharide structures could be obtained as validated by existing crystal structures of complexes. Additionally, the crystal structure of BambL/Lewis x was determined at 1.6 Å resolution, which confirms that Lewis x has to adopt a high-energy conformation so as to bind to this lectin. Free energies of binding were calculated using a procedure combining the Glide docking protocol followed by free energy rescoring with the Prime/Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method. The calculated data were in reasonable agreement with experimental free energies of binding obtained by titration microcalorimetry. The established predictive protocol is proposed to rationalize large sets of data such as glycan arrays and to help in lead discovery projects based on such high throughput technology.
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Affiliation(s)
- Jeremie Topin
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Julie Arnaud
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anita Sarkar
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Aymeric Audfray
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Emilie Gillon
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Serge Perez
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Helene Jamet
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Annabelle Varrot
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anne Imberty
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- * E-mail:
| | - Aline Thomas
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
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30
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Lawrence SL, Feil SC, Holien JK, Kuiper MJ, Doughty L, Dolezal O, Mulhern TD, Tweten RK, Parker MW. Manipulating the Lewis antigen specificity of the cholesterol-dependent cytolysin lectinolysin. Front Immunol 2012. [PMID: 23181061 PMCID: PMC3500998 DOI: 10.3389/fimmu.2012.00330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The cholesterol-dependent cytolysins (CDCs) attack cells by punching large holes in their membranes. Lectinolysin from Streptococcus mitis is unique among CDCs due to the presence of an N-terminal lectin domain that enhances the pore-forming activity of the toxin. We recently determined the crystal structures of the lectin domain in complex with various glycans. These structures revealed the molecular basis for the Lewis antigen specificity of the toxin. Based on this information we have used in silico molecular modeling to design a mutant toxin, which we predicted would increase its specificity for Lewis y, an antigen found on the surface of cancer cells. Surprisingly, we found by surface plasmon resonance binding experiments that the resultant mutant lectin domain exhibited higher specificity for Lewis b antigens instead. We then undertook comparative crystallographic and molecular dynamics simulation studies of the wild-type and mutant lectin domains to understand the molecular basis for the disparity between the theoretical and experimental results. The crystallographic results revealed that the net number of interactions between Lewis y and wild-type versus mutant was unchanged whereas there was a loss of a hydrogen bond between mutant and Lewis b compared to wild-type. In contrast, the molecular dynamics studies revealed that the Lewis b antigen spent more time in the binding pocket of the mutant compared to wild-type and the reverse was true for Lewis y. The results of these simulation studies are consistent with the conclusions drawn from the surface plasmon resonance studies. This work is part of a program to engineer lectinolysin so that it will target and kill specific cells in human diseases.
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Affiliation(s)
- Sara L Lawrence
- Biota Structural Biology Laboratory and Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research Fitzroy, VIC, Australia
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Auzanneau FI, Jackson TA, Liao L. Stochastic searches and NMR experiments on four Lewis A analogues: NMR experiments support some flexibility around the fucosidic bond. Bioorg Med Chem 2012; 20:5085-93. [PMID: 22867708 DOI: 10.1016/j.bmc.2012.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/04/2012] [Accepted: 07/10/2012] [Indexed: 11/29/2022]
Abstract
We have compared the conformational behavior of three Le(a) analogues with that of Le(a) using stochastic searches (MOE2005) and selective ROESY experiments. In the analogues either or both the β-d-Gal and α-l-Fuc residues were replaced by β-d-Glc and α-l-Rha units, respectively. All compounds showed similar behavior and even though four conformational families were identified, the calculations and NMR experiments support that the 'stacked conformation' known for Le(a) is predominant for all analogues. Interestingly, ROESY showed a correlation between H-1 Fuc/Rha and H-3 GlcNAc which, although small, could be seen in all analogues. For two compounds, the corresponding distance was measured and found to be shorter (∼3.7Å) than that found in the global minimum (4.5Å). While one published study suggests some motion around the fucosidic bond, this constitutes the first experimental evidence supporting such flexibility. Our MD simulation (Amber10/Glycam06) on Le(a) was in full agreement with previous studies which described a rigid conformation for this branched trisaccharide. Thus, NMR seems to indicate that these dynamic studies are underestimating flexibility around the fucosidic bond.
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Abstract
An exposed F-type lectin domain fused to the N-terminus of a cholesterol-dependent cytolysin scaffold allows Streptococcus mitis lectinolysin to cluster at fucose-rich sites on target cell membranes, thereby leading to increased pore-forming toxin activity. In this issue of Structure, Feil and coworkers define the structural basis for lectinolysin glycan-binding specificity.
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Affiliation(s)
- Samuel Bouyain
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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Feil SC, Lawrence S, Mulhern TD, Holien JK, Hotze EM, Farrand S, Tweten RK, Parker MW. Structure of the lectin regulatory domain of the cholesterol-dependent cytolysin lectinolysin reveals the basis for its lewis antigen specificity. Structure 2012; 20:248-58. [PMID: 22325774 PMCID: PMC3682648 DOI: 10.1016/j.str.2011.11.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/25/2011] [Accepted: 11/03/2011] [Indexed: 10/14/2022]
Abstract
The cholesterol-dependent cytolysins (CDCs) punch holes in target cell membranes through a highly regulated process. Streptococcus mitis lectinolysin (LLY) exhibits another layer of regulation with a lectin domain that enhances the pore-forming activity of the toxin. We have determined the crystal structures of the lectin domain by itself and in complex with various glycans that reveal the molecular basis for the Lewis antigen specificity of LLY. A small-angle X-ray scattering study of intact LLY reveals the molecule is flat and elongated with the lectin domain oriented so that the Lewis antigen-binding site is exposed. We suggest that the lectin domain enhances the pore-forming activity of LLY by concentrating toxin molecules at fucose-rich sites on membranes, thus promoting the formation of prepore oligomers on the surface of susceptible cells.
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Affiliation(s)
- Susanne C. Feil
- Biota Structural Biology Laboratory, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Sara Lawrence
- Biota Structural Biology Laboratory, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Terrence D. Mulhern
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jessica K. Holien
- Biota Structural Biology Laboratory, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Eileen M. Hotze
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Stephen Farrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Rodney K. Tweten
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Michael W. Parker
- Biota Structural Biology Laboratory, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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Heimburg-Molinaro J, Lum M, Vijay G, Jain M, Almogren A, Rittenhouse-Olson K. Cancer vaccines and carbohydrate epitopes. Vaccine 2011; 29:8802-26. [PMID: 21964054 PMCID: PMC3208265 DOI: 10.1016/j.vaccine.2011.09.009] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/18/2011] [Accepted: 09/06/2011] [Indexed: 12/17/2022]
Abstract
Tumor-associated carbohydrate antigens (TACA) result from the aberrant glycosylation that is seen with transformation to a tumor cell. The carbohydrate antigens that have been found to be tumor-associated include the mucin related Tn, Sialyl Tn, and Thomsen-Friedenreich antigens, the blood group Lewis related Lewis(Y), Sialyl Lewis(X) and Sialyl Lewis(A), and Lewis(X) (also known as stage-specific embryonic antigen-1, SSEA-1), the glycosphingolipids Globo H and stage-specific embryonic antigen-3 (SSEA-3), the sialic acid containing glycosphingolipids, the gangliosides GD2, GD3, GM2, fucosyl GM1, and Neu5GcGM3, and polysialic acid. Recent developments have furthered our understanding of the T-independent type II response that is seen in response to carbohydrate antigens. The selection of a vaccine target antigen is based on not only the presence of the antigen in a variety of tumor tissues but also on the role this antigen plays in tumor growth and metastasis. These roles for TACAs are being elucidated. Newly acquired knowledge in understanding the T-independent immune response and in understanding the key roles that carbohydrates play in metastasis are being applied in attempts to develop an effective vaccine response to TACAs. The role of each of the above mentioned carbohydrate antigens in cancer growth and metastasis and vaccine attempts using these antigens will be described.
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Affiliation(s)
| | - Michelle Lum
- Department of Cellular and Molecular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Geraldine Vijay
- University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Miten Jain
- Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064
| | - Adel Almogren
- Department Of Pathology, College of Medicine, King Saud University, Riyadh, 11461 Saudi Arabia
| | - Kate Rittenhouse-Olson
- Department Of Pathology, College of Medicine, King Saud University, Riyadh, 11461 Saudi Arabia
- Department of Biotechnical and Clinical Laboratory Sciences, University at Buffalo, Buffalo, NY 14214
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY 14263
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Agostino M, Sandrin MS, Thompson PE, Ramsland PA, Yuriev E. Peptide inhibitors of xenoreactive antibodies mimic the interaction profile of the native carbohydrate antigens. Biopolymers 2011; 96:193-206. [PMID: 20564023 DOI: 10.1002/bip.21427] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Carbohydrate-antibody interactions mediate many cellular processes and immune responses. Carbohydrates expressed on the surface of cells serve as recognition elements for particular cell types, for example, in the ABO(H) blood group system. Antibodies that recognize host-incompatible ABO(H) system antigens exist in the bloodstream of all individuals (except AB individuals), preventing blood transfusion and organ transplantation between incompatible donors and recipients. A similar barrier exists for cross-species transplantation (xenotransplantation), in particular for pig-to-human transplantation. All humans express antibodies against the major carbohydrate xenoantigen, Galalpha (1,3)Gal (alphaGal), preventing successful xenotransplantation. Although antibody binding sites are precisely organized so as to selectively bind a specific antigen, many antibodies recognize molecules other than their native antigen. A range of peptides have been identified that can mimic carbohydrates and inhibit anti-alphaGal antibodies. However, the structural basis of how the peptides achieved this was not known. Previously, we developed an in silico method which we used to investigate carbohydrate recognition by a panel of anti-alphaGal antibodies. The method involves molecular docking of carbohydrates to antibodies and uses the docked carbohydrate poses to generate maps of th antibody binding sites in terms of prevalent hydrogen bonding and van der Waals interactions. We have applied this method to investigate peptide recognition by the anti-alphaGal antibodies. It was found that the site maps of the peptides and the carbohydrates were similar, indicating that the peptides interact with the same residues as those involved in carbohydrate recognition. This study demonstrates the potential for "design by mapping" of anti-carbohydrate antibody inhibitors.
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Affiliation(s)
- Mark Agostino
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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36
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Abstract
Glycans as Biomarkers: Status and PerspectivesProtein glycosylation is a ubiquitous and complex co- and post-translational modification leading to glycan formation, i.e. oligosaccharide chains covalently attached to peptide backbones. The significance of changes in glycosylation for the beginning, progress and outcome of different human diseases is widely recognized. Thus, glycans are considered as unique structures to diagnose, predict susceptibility to and monitor the progression of disease. In the »omics« era, the glycome, a glycan analogue of the proteome and genome, holds considerable promise as a source of new biomarkers. In the design of a strategy for biomarker discovery, new principles and platforms for the analysis of relatively small amounts of numerous glycoproteins are needed. Emerging glycomics technologies comprising different types of mass spectrometry and affinity-based arrays are next in line to deliver new analytical procedures in the field of biomarkers. Screening different types of glycomolecules, selection of differentially expressed components, their enrichment and purification or identification are the most challenging parts of experimental and clinical glycoproteomics. This requires large-scale technologies enabling high sensitivity, proper standardization and validation of the methods to be used. Further progress in the field of applied glycoscience requires an integrated systematic approach in order to explore properly all opportunities for disease diagnosis.
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Agostino M, Yuriev E, Ramsland PA. A computational approach for exploring carbohydrate recognition by lectins in innate immunity. Front Immunol 2011; 2:23. [PMID: 22566813 PMCID: PMC3342079 DOI: 10.3389/fimmu.2011.00023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 06/14/2011] [Indexed: 11/13/2022] Open
Abstract
Recognition of pathogen-associated carbohydrates by a broad range of carbohydrate-binding proteins is central to both adaptive and innate immunity. A large functionally diverse group of mammalian carbohydrate-binding proteins are lectins, which often display calcium-dependent carbohydrate interactions mediated by one or more carbohydrate recognition domains. We report here the application of molecular docking and site mapping to study carbohydrate recognition by several lectins involved in innate immunity or in modulating adaptive immune responses. It was found that molecular docking programs can identify the correct carbohydrate-binding mode, but often have difficulty in ranking it as the best pose. This is largely attributed to the broad and shallow nature of lectin binding sites, and the high flexibility of carbohydrates. Site mapping is very effective at identifying lectin residues involved in carbohydrate recognition, especially with cases that were found to be particularly difficult to characterize via molecular docking. This study highlights the need for alternative strategies to examine carbohydrate–lectin interactions, and specifically demonstrates the potential for mapping methods to extract additional and relevant information from the ensembles of binding poses generated by molecular docking.
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Affiliation(s)
- Mark Agostino
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University Parkville, VIC, Australia
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38
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Theillet FX, Frank M, Vulliez-Le Normand B, Simenel C, Hoos S, Chaffotte A, Bélot F, Guerreiro C, Nato F, Phalipon A, Mulard LA, Delepierre M. Dynamic aspects of antibody:oligosaccharide complexes characterized by molecular dynamics simulations and saturation transfer difference nuclear magnetic resonance. Glycobiology 2011; 21:1570-9. [PMID: 21610193 DOI: 10.1093/glycob/cwr059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Carbohydrates are likely to maintain significant conformational flexibility in antibody (Ab):carbohydrate complexes. As demonstrated herein for the protective monoclonal Ab (mAb) F22-4 recognizing the Shigella flexneri 2a O-antigen (O-Ag) and numerous synthetic oligosaccharide fragments thereof, the combination of molecular dynamics simulations and nuclear magnetic resonance saturation transfer difference experiments, supported by physicochemical analysis, allows us to determine the binding epitope and its various contributions to affinity without using any modified oligosaccharides. Moreover, the methods used provide insights into ligand flexibility in the complex, thus enabling a better understanding of the Ab affinities observed for a representative set of synthetic O-Ag fragments. Additionally, these complementary pieces of information give evidence to the ability of the studied mAb to recognize internal as well as terminal epitopes of its cognate polysaccharide antigen. Hence, we show that an appropriate combination of computational and experimental methods provides a basis to explore carbohydrate functional mimicry and receptor binding. The strategy may facilitate the design of either ligands or carbohydrate recognition domains, according to needed improvements of the natural carbohydrate:receptor properties.
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Guzzi C, Angulo J, Doro F, Reina JJ, Thépaut M, Fieschi F, Bernardi A, Rojo J, Nieto PM. Insights into molecular recognition of LewisX mimics by DC-SIGN using NMR and molecular modelling. Org Biomol Chem 2011; 9:7705-12. [DOI: 10.1039/c1ob05938f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Andreini M, Doknic D, Sutkeviciute I, Reina JJ, Duan J, Chabrol E, Thepaut M, Moroni E, Doro F, Belvisi L, Weiser J, Rojo J, Fieschi F, Bernardi A. Second generation of fucose-based DC-SIGN ligands : affinity improvement and specificity versus Langerin. Org Biomol Chem 2011; 9:5778-86. [DOI: 10.1039/c1ob05573a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Theillet FX, Simenel C, Guerreiro C, Phalipon A, Mulard LA, Delepierre M. Effects of backbone substitutions on the conformational behavior of Shigella flexneri O-antigens: implications for vaccine strategy. Glycobiology 2010; 21:109-21. [DOI: 10.1093/glycob/cwq136] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Agostino M, Jene C, Boyle T, Ramsland PA, Yuriev E. Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures. J Chem Inf Model 2010; 49:2749-60. [PMID: 19994843 DOI: 10.1021/ci900388a] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been implicated in the development of autoimmune diseases and impact areas such as xenotransplantation and cancer treatment. Understanding the nature of antibody-carbohydrate interactions and the method by which saccharides fit into antibody binding sites is important in understanding the recognition process. In silico techniques offer attractive alternatives to experimental methods (X-ray crystallography and NMR) for the study of antibody-carbohydrate complexes. In particular, molecular docking provides information about protein-ligand interactions in systems that are difficult to study with experimental techniques. Before molecular docking can be used to investigate antibody-carbohydrate complexes, validation of an appropriate docking method is required. In this study, four popular docking programs, Glide, AutoDock, GOLD, and FlexX, were assessed for their ability to accurately dock carbohydrates to antibodies. Comparison of top ranking poses with crystal structures highlighted the strengths and weaknesses of these programs. Rigid docking, in which the protein conformation remains static, and flexible docking, where both the protein and ligand are treated as flexible, were compared. This study has revealed that generally molecular docking of carbohydrates to antibodies has been performed best by Glide.
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Affiliation(s)
- Mark Agostino
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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43
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Agostino M, Sandrin MS, Thompson PE, Yuriev E, Ramsland PA. Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps. Glycobiology 2010; 20:724-35. [PMID: 20176856 DOI: 10.1093/glycob/cwq022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbohydrates are notoriously flexible molecules. However, they have an important role in many biochemical processes as specific ligands. Understanding how carbohydrates are recognized by other biological macromolecules (usually proteins) is therefore of considerable scientific value. Interfering with carbohydrate-protein interactions is a potentially useful strategy in combating a range of disease states, as well as being of critical importance in facilitating allo- and xenotransplantation. We have devised an in silico protocol for analyzing carbohydrate-protein interactions. In this study, we have applied the protocol to determine the structures of alphaGal-terminating carbohydrate antigens in complex with a panel of xenoreactive antibodies. The most important feature of the binding modes is the fixed conformation of the Galbeta(1,4)Glc/GlcNAc linkage across all of the binding modes. The preferred conformation of the terminal Galalpha(1,3)Gal linkage varies depending on the antibody binding site topography, although it is possible that some of the antibodies studied recognize more than one Galalpha(1,3)Gal conformation. The binding modes obtained indicate that each antibody uses distinct mechanisms in recognizing the target antigens.
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Affiliation(s)
- Mark Agostino
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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Koti M, Farrugia W, Nagy E, Ramsland PA, Kaushik AK. Construction of single-chain Fv with two possible CDR3H conformations but similar inter-molecular forces that neutralize bovine herpesvirus 1. Mol Immunol 2009; 47:953-60. [PMID: 20006385 DOI: 10.1016/j.molimm.2009.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 11/13/2009] [Accepted: 11/14/2009] [Indexed: 11/26/2022]
Abstract
Bovine herpesvirus 1 (BoHV-1) causes respiratory and genital diseases in cattle for which available vaccines do not confer adequate protection. Since passive immunization with antibodies permits disease prevention, single-chain fragment variable (scFv), originating from a monoclonal bovine IgG1 antibody against BoHV-1, were constructed and expressed in Pichia pastoris in V(lambda)-V(H) orientation via a flexible seven-amino acid linker. Similar to the intact IgG, the purified recombinant scFv neutralized BoHV-1 in vitro and recognized viral antigens in BoHV-1 infected MDBK cells by immunofluorescence. Homology modeling of the Fv predicts two distinct conformations for CDR3H. Firstly, a long protruding CDR3H conformation where no disulfide linkage occurred between two "non-canonical" Cys residues resulted in a large binding cavity between V(lambda) and V(H). Secondly, a smaller potential antigen-binding cavity is predicted with a disulfide linkage between the two Cys residues of CDR3H creating a six-membered loop in the ascending polypeptide, which fitted into the space between V(lambda) and V(H). Despite such potential configurational diversity of the antigen-binding site, the electrostatic surface potentials that would interact with the BoHV-1 epitope are largely similar for both the topographies where salt-bridge type electrostatic interactions likely occur at the edges of the binding site. Given that IgG1 antibody against BoHV-1 is clonally selected, it is likely that disulfide-stabilized broader and flatter surface topography is specifically generated to accommodate the predicted carbohydrate neutralizing B-epitope on BoHV-1. The specificity and neutralizing capacity for BoHV-1 of the scFv should make this bovine antibody fragment a useful diagnostic and potential therapeutic candidate for an important viral pathogen in cattle.
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Affiliation(s)
- Madhuri Koti
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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45
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A possible role for metallic ions in the carbohydrate cluster recognition displayed by a Lewis Y specific antibody. PLoS One 2009; 4:e7777. [PMID: 19901987 PMCID: PMC2770121 DOI: 10.1371/journal.pone.0007777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 10/20/2009] [Indexed: 11/22/2022] Open
Abstract
Background Lewis Y (Ley) is a blood group-related carbohydrate that is expressed at high surface densities on the majority of epithelial carcinomas and is a promising target for antibody-based immunotherapy. A humanized Ley-specific antibody (hu3S193) has shown encouraging safety, pharmacokinetic and tumor-targeting properties in recently completed Phase I clinical trials. Methodology/Principal Findings We report the three-dimensional structures for both the free (unliganded) and bound (Ley tetrasaccharide) hu3S193 Fab from the same crystal grown in the presence of divalent zinc ions. There is no evidence of significant conformational changes occurring in either the Ley carbohydrate antigen or the hu3S193 binding site, which suggests a rigid fit binding mechanism. In the crystal, the hu3S193 Fab molecules are coordinated at their protein-protein interface by two zinc ions and in solution aggregation of Fab can be initiated by zinc, but not magnesium ions. Dynamic light scattering revealed that zinc ions could initiate a sharp transition from hu3S193 Fab monomers to large multimeric aggregates in solution. Conclusions/Significance Zinc ions can mediate interactions between hu3S193 Fab in crystals and in solution. Whether metallic ion mediated aggregation of antibody occurs in vivo is not known, but the present results suggest that similar clustering mechanisms could occur when hu3S193 binds to Ley on cells, particularly given the high surface densities of antigen on the target tumor cells.
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Yuriev E, Agostino M, Farrugia W, Christiansen D, Sandrin MS, Ramsland PA. Structural biology of carbohydrate xenoantigens. Expert Opin Biol Ther 2009; 9:1017-29. [PMID: 19591628 DOI: 10.1517/14712590903066703] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Transplantation of organs across species (xenotransplantation) is being considered to overcome the shortage of human donor organs. However, unmodified pig organs undergo an antibody-mediated hyperacute rejection that is brought about by the presence of natural antibodies to Galalpha(1,3)Gal, which is the major carbohydrate xenoantigen. Genetic modification of pig organs to remove most of the Galalpha(1,3)Gal epitopes has been achieved, but the human immune system may still recognize residual lipid-linked Galalpha(1,3)Gal carbohydrates, new (cryptic) carbohydrates or additional non-Galalpha(1,3)Gal carbohydrate xenoantigens. The structural basis for lectin and antibody recognition of Galalpha(1,3)Gal carbohydrates is starting to be understood and is discussed in this review. Antibody binding to Galalpha(1,3)Gal carbohydrates is predicted to primarily involve end-on insertion of the terminal alphaGal residue, but it is possible that groove-type binding can occur, as for some lectins. It is likely that similar antibody and lectin recognition will occur with other non-Galalpha(1,3)Gal xenoantigens, which potentially represent new barriers for pig-to-human xenotransplantation.
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Affiliation(s)
- Elizabeth Yuriev
- Monash University, Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry and Drug Action, Victoria, Australia
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47
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Agostino M, Sandrin MS, Thompson PE, Yuriev E, Ramsland PA. In silico analysis of antibody-carbohydrate interactions and its application to xenoreactive antibodies. Mol Immunol 2009; 47:233-46. [PMID: 19828202 DOI: 10.1016/j.molimm.2009.09.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 09/11/2009] [Accepted: 09/17/2009] [Indexed: 11/26/2022]
Abstract
Antibody-carbohydrate interactions play central roles in stimulating adverse immune reactions. The most familiar example of such a process is the reaction observed in ABO-incompatible blood transfusion and organ transplantation. The ABO blood groups are defined by the presence of specific carbohydrates expressed on the surface of red blood cells. Preformed antibodies in the incompatible recipient (i.e., different blood groups) recognize cells exhibiting host-incompatible ABO system antigens and proceed to initiate lysis of the incompatible cells. Pig-to-human xenotransplantation presents a similar immunological barrier. Antibodies present in humans recognize carbohydrate antigens on the surface of pig organs as foreign and proceed to initiate hyperacute xenograft rejection. The major carbohydrate xenoantigens all bear terminal Gal alpha(1,3)Gal epitopes (or alphaGal). In this study, we have developed and validated a site mapping technique to investigate protein-ligand recognition and applied it to antibody-carbohydrate systems. This site mapping technique involves the use of molecular docking to generate a series of antibody-carbohydrate complexes, followed by analysis of the hydrogen bonding and van der Waals interactions occurring in each complex. The technique was validated by application to a series of antibody-carbohydrate crystal structures. In each case, the majority of interactions made in the crystal structure complex were able to be reproduced. The technique was then applied to investigate xenoantigen recognition by a panel of monoclonal anti-alphaGal antibodies. The results indicate that there is a significant overlap of the antibody regions engaging the xenoantigens across the panel. Likewise, similar regions of the xenoantigens interact with the antibodies.
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Affiliation(s)
- Mark Agostino
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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48
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Chemoenzymatic synthesis of GDP-L-fucose and the Lewis X glycan derivatives. Proc Natl Acad Sci U S A 2009; 106:16096-101. [PMID: 19805264 DOI: 10.1073/pnas.0908248106] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Lewis X (Le(x))-containing glycans play important roles in numerous cellular processes. However, the absence of robust, facile, and cost-effective methods for the synthesis of Le(x) and its structurally related analogs has severely hampered the elucidation of the specific functions of these glycan epitopes. Here we demonstrate that chemically defined guanidine 5'-diphosphate-beta-l-fucose (GDP-fucose), the universal fucosyl donor, the Le(x) trisaccharide, and their C-5 substituted derivatives can be synthesized on preparative scales, using a chemoenzymatic approach. This method exploits l-fucokinase/GDP-fucose pyrophosphorylase (FKP), a bifunctional enzyme isolated from Bacteroides fragilis 9343, which converts l-fucose into GDP-fucose via a fucose-1-phosphate (Fuc-1-P) intermediate. Combining the activities of FKP and a Helicobacter pylori alpha1,3 fucosyltransferase, we prepared a library of Le(x) trisaccharide glycans bearing a wide variety of functional groups at the fucose C-5 position. These neoglycoconjugates will be invaluable tools for studying Le(x)-mediated biological processes.
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49
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Su Z, Wagner B, Cocinero EJ, Ernst B, Simons JP. The intrinsic conformation of a Lewis antigen: The Lewis×trisaccharide. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Higgins MA, Whitworth GE, El Warry N, Randriantsoa M, Samain E, Burke RD, Vocadlo DJ, Boraston AB. Differential recognition and hydrolysis of host carbohydrate antigens by Streptococcus pneumoniae family 98 glycoside hydrolases. J Biol Chem 2009; 284:26161-73. [PMID: 19608744 DOI: 10.1074/jbc.m109.024067] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The presence of a fucose utilization operon in the Streptococcus pneumoniae genome and its established importance in virulence indicates a reliance of this bacterium on the harvesting of host fucose-containing glycans. The identities of these glycans, however, and how they are harvested is presently unknown. The biochemical and high resolution x-ray crystallographic analysis of two family 98 glycoside hydrolases (GH98s) from distinctive forms of the fucose utilization operon that originate from different S. pneumoniae strains reveal that one enzyme, the predominant type among pneumococcal isolates, has a unique endo-beta-galactosidase activity on the LewisY antigen. Altered active site topography in the other species of GH98 enzyme tune its endo-beta-galactosidase activity to the blood group A and B antigens. Despite their different specificities, these enzymes, and by extension all family 98 glycoside hydrolases, use an inverting catalytic mechanism. Many bacterial and viral pathogens exploit host carbohydrate antigens for adherence as a precursor to colonization or infection. However, this is the first evidence of bacterial endoglycosidase enzymes that are known to play a role in virulence and are specific for distinct host carbohydrate antigens. The strain-specific distribution of two distinct types of GH98 enzymes further suggests that S. pneumoniae strains may specialize to exploit host-specific antigens that vary from host to host, a factor that may feature in whether a strain is capable of colonizing a host or establishing an invasive infection.
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Affiliation(s)
- Melanie A Higgins
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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