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Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database. Biomolecules 2021; 11:biom11040486. [PMID: 33804966 PMCID: PMC8063959 DOI: 10.3390/biom11040486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/20/2022] Open
Abstract
Natural products (NPs), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand–target interactions, and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NPs, and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NPs. In this work, we report and describe the presence of circular, linear, terminal, and non-terminal glycosidic units in NPs, together with their importance in drug discovery.
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2
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MAIT cell-directed therapy of Mycobacterium tuberculosis infection. Mucosal Immunol 2021; 14:199-208. [PMID: 32811991 PMCID: PMC7790750 DOI: 10.1038/s41385-020-0332-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/04/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are potential targets of vaccination and host-directed therapeutics for tuberculosis, but the role of MAIT cells during Mycobacterium tuberculosis (Mtb) infection in vivo is not well understood. Here we find that following Mtb infection MAIT cells mount minimal responses, and MAIT cell-deficient MR1-/- mice display normal survival. Preinfection expansion of MAIT cells through 5-OP-RU vaccination fails to protect against subsequent Mtb challenge. In fact, 5-OP-RU vaccination delays Mtb-specific CD4 T cell priming in lung-draining lymph nodes, and conversely MR1 deficiency or blockade accelerates T cell priming. The MAIT cell-mediated delay in T cell priming is partly dependent on TGF-β. Surprisingly, 5-OP-RU treatment during chronic infection drives MAIT cell expansion and an IL-17A-dependent reduction in bacterial loads. Thus, during early infection MAIT cells directly contribute to the notoriously slow priming of CD4 T cells, but later during infection MAIT cell stimulation may be an effective host-directed therapy for tuberculosis.
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3
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Braganza CD, Shibata K, Fujiwara A, Motozono C, Sonoda KH, Yamasaki S, Stocker BL, Timmer MSM. The effect of MR1 ligand glyco-analogues on mucosal-associated invariant T (MAIT) cell activation. Org Biomol Chem 2019; 17:8992-9000. [DOI: 10.1039/c9ob01436e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glyco-analogues of MR1 ligands can bind MR1 and activate MAIT cells at levels similar to 5-OP-RU.
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Affiliation(s)
- Chriselle D. Braganza
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- Wellington
- New Zealand
| | - Kensuke Shibata
- Department of Ocular Pathology and Imaging Science
- Graduate School of Medical Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Aisa Fujiwara
- Department of Ocular Pathology and Imaging Science
- Graduate School of Medical Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Chihiro Motozono
- Department of Ocular Pathology and Imaging Science
- Graduate School of Medical Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Koh-Hei Sonoda
- Department of Ocular Pathology and Imaging Science
- Graduate School of Medical Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Sho Yamasaki
- Department of Molecular Immunology
- Research Institute for Microbial Diseases
- Osaka University
- Osaka
- Japan
| | - Bridget L. Stocker
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- Wellington
- New Zealand
| | - Mattie S. M. Timmer
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- Wellington
- New Zealand
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4
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Li K, Vorkas CK, Chaudhry A, Bell DL, Willis RA, Rudensky A, Altman JD, Glickman MS, Aubé J. Synthesis, stabilization, and characterization of the MR1 ligand precursor 5-amino-6-D-ribitylaminouracil (5-A-RU). PLoS One 2018; 13:e0191837. [PMID: 29401462 PMCID: PMC5798775 DOI: 10.1371/journal.pone.0191837] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are an abundant class of innate T cells restricted by the MHC I-related molecule MR1. MAIT cells can recognize bacterially-derived metabolic intermediates from the riboflavin pathway presented by MR1 and are postulated to play a role in innate antibacterial immunity through production of cytokines and direct bacterial killing. MR1 tetramers, typically stabilized by the adduct of 5-amino-6-D-ribitylaminouracil (5-A-RU) and methylglyoxal (MeG), are important tools for the study of MAIT cells. A long-standing problem with 5-A-RU is that it is unstable upon storage. Herein we report an efficient synthetic approach to the HCl salt of this ligand, which has improved stability during storage. We also show that synthetic 5-A-RU•HCl produced by this method may be used in protocols for the stimulation of human MAIT cells and production of both human and mouse MR1 tetramers for MAIT cell identification.
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Affiliation(s)
- Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles K. Vorkas
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Ashutosh Chaudhry
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Donielle L. Bell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard A. Willis
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Alexander Rudensky
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - John D. Altman
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Michael S. Glickman
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
- Immunology Program, Sloan Kettering Institute, New York, New York, United States of America
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
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5
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Merino P, Delso I, Tejero T, Ghirardello M, Juste-Navarro V. Nucleoside Diphosphate Sugar Analogues that Target Glycosyltransferases. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pedro Merino
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Ignacio Delso
- NMR Service, Center of Chemistry and Materials of Aragon (CEQMA); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Tomás Tejero
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Mattia Ghirardello
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Verónica Juste-Navarro
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
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6
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Ghirardello M, de Las Rivas M, Lacetera A, Delso I, Lira-Navarrete E, Tejero T, Martín-Santamaría S, Hurtado-Guerrero R, Merino P. Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Chemistry 2016; 22:7215-24. [PMID: 27071848 DOI: 10.1002/chem.201600467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 12/11/2022]
Abstract
The Leloir donors are nucleotide sugars essential for a variety of glycosyltransferases (GTs) involved in the transfer of a carbohydrate to an acceptor substrate, typically a protein or an oligosaccharide. A series of less-polar nucleotide sugar analogues derived from uridine have been prepared by replacing one phosphate unit with an alkyl chain. The methodology is based on the radical hydrophosphonylation of alkenes, which allows coupling of allyl glycosyl compounds with a phosphate unit suitable for conjugation to uridine. Two of these compounds, the GalNAc and galactose derivatives, were further tested on a model GT, such as GalNAc-T2 (an important GT widely distributed in human tissues), to probe that both compounds bound in the medium-high micromolar range. The crystal structure of GalNAc-T2 with the galactose derivative traps the enzyme in an inactive form; this suggests that compounds only containing the β-phosphate could be efficient ligands for the enzyme. Computational studies with GalNAc-T2 corroborate these findings and provide further insights into the mechanism of the catalytic cycle of this family of enzymes.
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Affiliation(s)
- Mattia Ghirardello
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Matilde de Las Rivas
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Alessandra Lacetera
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Ignacio Delso
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
- Servicio de Resonancia Magnética Nuclear, Centro de Química y Materiales de Aragón (CEQMA), Universidad de Zaragoza, CSIC, Campus San Francisco, 50009, Zaragoza, Spain
| | - Erandi Lira-Navarrete
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Tomás Tejero
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain
| | - Sonsoles Martín-Santamaría
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain.
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009, Zaragoza, Spain.
- Fundación ARAID, 50018, Zaragoza, Spain.
- Instituto de Investigaciones Sanitarias de Aragón (IIS-A), Zaragoza, 50009, Spain.
| | - Pedro Merino
- Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain.
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7
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Mechanism-based candidate inhibitors of uridine diphosphate galactopyranose mutase (UGM). Carbohydr Res 2015; 419:1-7. [PMID: 26595659 DOI: 10.1016/j.carres.2015.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 01/07/2023]
Abstract
Uridine diphosphate-galactopyranose mutase (UGM), an enzyme found in many eukaryotic and prokaryotic human pathogens, catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf), the latter being used as the biosynthetic precursor of the galactofuranose polymer portion of the mycobacterium cell wall. We report here the synthesis of a sulfonium and selenonium ion with an appended polyhydroxylated side chain. These compounds were designed as transition state mimics of the UGM-catalyzed reaction, where the head groups carrying a permanent positive charge were designed to mimic both the shape and positive charge of the proposed galactopyranosyl cation-like transition state. An HPLC-based UGM inhibition assay indicated that the compounds inhibited about 25% of UGM activity at 500 µM concentration.
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8
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Wang S, Cuesta-Seijo JA, Striebeck A, Lafont D, Palcic MM, Vidal S. Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates? Chempluschem 2015; 80:1525-1532. [DOI: 10.1002/cplu.201500282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Shuai Wang
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Laboratoire de Chimie Organique 2-Glycochimie, UMR 5246; CNRS and Université Claude Bernard Lyon 1; 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | | | | | - Dominique Lafont
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Laboratoire de Chimie Organique 2-Glycochimie, UMR 5246; CNRS and Université Claude Bernard Lyon 1; 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | - Monica M. Palcic
- Carlsberg Laboratory; Gamle Carlsberg Vej 10 1799 Copenhagen V Denmark
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC V8W 3P6 Canada
| | - Sébastien Vidal
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Laboratoire de Chimie Organique 2-Glycochimie, UMR 5246; CNRS and Université Claude Bernard Lyon 1; 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
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9
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Kuppala R, Borrelli S, Slowski K, Sanders DAR, Ravindranathan Kartha KP, Pinto BM. Synthesis and biological evaluation of nonionic substrate mimics of UDP-Galp as candidate inhibitors of UDP galactopyranose mutase (UGM). Bioorg Med Chem Lett 2015; 25:1995-7. [PMID: 25819094 DOI: 10.1016/j.bmcl.2015.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
Abstract
The synthesis of 1-[5-O-(α-D-galactopyranosyl)-D-glucityl]pyrimidine-2,4(3H)-dione and 1-[(5-O-(β-D-galactopyranosyl)-D-glucityl]pyrimidine-2,4(3H)-dione as non-ionic substrate mimics of UDP-Galp are described. UDP-Galp is a precursor of Galf, which is a primary component of the cell-wall glycans of several microorganisms. The interconversion of UDP-Galp and UDP-Galf is catalyzed by UDP galactopyranose mutase (UGM); its inhibition comprises a mode of compromising the microorganisms. The nonionic polyhydroxylated chain was intended to mimic the ionic pyrophosphate group and the ribose moiety in UDP-Galp and increase the bioavailabilities of the candidate inhibitors. Inhibition assays with UGM of Mycobacterium tuberculosis showed only weak inhibition of the enzyme by these compounds.
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Affiliation(s)
- Ramakrishna Kuppala
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Silvia Borrelli
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Kathryn Slowski
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - K P Ravindranathan Kartha
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - B Mario Pinto
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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10
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Brockhausen I. Crossroads between Bacterial and Mammalian Glycosyltransferases. Front Immunol 2014; 5:492. [PMID: 25368613 PMCID: PMC4202792 DOI: 10.3389/fimmu.2014.00492] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/23/2014] [Indexed: 11/26/2022] Open
Abstract
Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures.
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Affiliation(s)
- Inka Brockhausen
- Department of Medicine, Queen's University , Kingston, ON , Canada ; Department of Biomedical and Molecular Sciences, Queen's University , Kingston, ON , Canada
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11
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Tedaldi L, Wagner GK. Beyond substrate analogues: new inhibitor chemotypes for glycosyltransferases. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00086b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
New inhibitor chemotypes for glycosyltransferases, which are not structurally derived from either donor or acceptor substrate, are being reviewed.
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Affiliation(s)
- Lauren Tedaldi
- Institute of Pharmaceutical Science
- School of Biomedical Sciences
- King's College London
- London
- UK
| | - Gerd K. Wagner
- Institute of Pharmaceutical Science
- School of Biomedical Sciences
- King's College London
- London
- UK
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12
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Wang S, Cuesta-Seijo JA, Lafont D, Palcic MM, Vidal S. Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate. Chemistry 2013; 19:15346-57. [PMID: 24108680 DOI: 10.1002/chem.201301871] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/25/2013] [Indexed: 12/12/2022]
Abstract
A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger-Vilarrasa amide-bond formation, and azide-alkyne click chemistry. The compounds were evaluated as inhibitors of five metal-dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn(2+) ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)-Gal substrate with little interaction with the enzyme.
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Affiliation(s)
- Shuai Wang
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Laboratoire de Chimie Organique 2, Glycochimie, UMR 5246, CNRS and Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 6922 Villeurbanne (France), Fax: (+33) 472-448-109
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13
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Kötzler MP, Blank S, Bantleon FI, Wienke M, Spillner E, Meyer B. Donor assists acceptor binding and catalysis of human α1,6-fucosyltransferase. ACS Chem Biol 2013; 8:1830-40. [PMID: 23730796 DOI: 10.1021/cb400140u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
α1,6-Core-fucosyltransferase (FUT8) is a vital enzyme in mammalian physiological and pathophysiological processes such as tumorigenesis and progress of, among others, non-small cell lung cancer and colon carcinoma. It was also shown that therapeutic antibodies have a dramatically higher efficacy if the α1,6-fucosyl residue is absent. However, specific and potent inhibitors for FUT8 and related enzymes are lacking. Hence, it is crucial to elucidate the structural basis of acceptor binding and the catalytic mechanism. We present here the first structural model of FUT8 in complex with its acceptor and donor molecules. An unusually large acceptor, i.e., a hexasaccharide from the core of N-glycans, is required as minimal structure. Acceptor substrate binding of FUT8 is being dissected experimentally by STD NMR and SPR and theoretically by molecular dynamics simulations. The acceptor binding site forms an unusually large and shallow binding site. Binding of the acceptor to the enzyme is much faster and stronger if the donor is present. This is due to strong hydrogen bonding between O6 of the proximal N-acetylglucosamine and an oxygen atom of the β-phosphate of GDP-fucose. Therefore, we propose an ordered Bi Bi mechanism for FUT8 where the donor molecule binds first. No specific amino acid is present that could act as base during catalysis. Our results indicate a donor-assisted mechanism, where an oxygen of the β-phosphate deprotonates the acceptor. Knowledge of the mechanism of FUT8 is now being used for rational design of targeted inhibitors to address metastasis and prognosis of carcinomas.
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Affiliation(s)
- Miriam P. Kötzler
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Simon Blank
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Frank I. Bantleon
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Martin Wienke
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Edzard Spillner
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Bernd Meyer
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
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14
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Wang S, Lafont D, Rahkila J, Picod B, Leino R, Vidal S. Glycosylation of ‘basic’ alcohols: methyl 6-(hydroxymethyl)picolinate as a case study. Carbohydr Res 2013; 372:35-46. [DOI: 10.1016/j.carres.2013.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 11/28/2022]
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15
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Lundborg M, Ali E, Widmalm G. An in silico virtual screening study for the design of norovirus inhibitors: fragment-based molecular docking and binding free energy calculations. Carbohydr Res 2013; 378:133-8. [PMID: 23582100 DOI: 10.1016/j.carres.2013.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/12/2013] [Accepted: 03/15/2013] [Indexed: 11/18/2022]
Abstract
Gastrointestinal infections caused by noroviruses may be prevented by the inhibition of their binding to histo-blood group carbohydrate antigens. A fragment-based virtual screening approach was used, employing docking followed by molecular dynamics simulations in order to enable binding free energy calculations using the linear interaction energy method. The resulting structures, composed of high-affinity fragments, can be a good starting point for lead optimizations and four molecules that pass both REOS and SYLVIA filters, which can remove known toxic features and assess the synthetic accessibility, respectively, are proposed as inhibitors.
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Affiliation(s)
- Magnus Lundborg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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16
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Schaefer K, Sindhuwinata N, Hackl T, Kötzler MP, Niemeyer FC, Palcic MM, Peters T, Meyer B. A nonionic inhibitor with high specificity for the UDP-Gal donor binding site of human blood group B galactosyltransferase: design, synthesis, and characterization. J Med Chem 2013; 56:2150-4. [PMID: 23406460 DOI: 10.1021/jm300642a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
9-(5-O-α-D-galactopyranosyl)-D-arabinityl-1,3,7-trihydropurine-2,6,8-trione (1) was designed and synthesized as a nonionic inhibitor for the donor binding site of human blood group B galactosyltransferase (GTB). Enzymatic characterization showed 1 to be extremely specific, as the highly homologous human N-acetylgalactosaminyltransferase (GTA) is not inhibited. The binding epitope of 1 demonstrates a high involvement of the arabinityl linker, whereas the galactose residue is only making contact to the protein via its C-2 site, which is very important for the discrimination between galactose and N-acetylgalactosamine, the substrate transferred by GTA. The approach can generate highly specific glycosyltransferase inhibitors.
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Affiliation(s)
- Katrin Schaefer
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany
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Development of inhibitors as research tools for carbohydrate-processing enzymes. Biochem Soc Trans 2012; 40:913-28. [DOI: 10.1042/bst20120201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.
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Kötzler MP, Blank S, Bantleon FI, Spillner E, Meyer B. Donor substrate binding and enzymatic mechanism of human core α1,6-fucosyltransferase (FUT8). Biochim Biophys Acta Gen Subj 2012; 1820:1915-25. [PMID: 22982178 DOI: 10.1016/j.bbagen.2012.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND Fucosylation is essential for various biological processes including tumorigenesis, inflammation, cell-cell recognition and host-pathogen interactions. Biosynthesis of fucosylated glycans is accomplished by fucosyltransferases. The enzymatic product of core α1,6-fucosyltransferase (FUT8) plays a major role in a plethora of pathological conditions, e.g. in prognosis of hepatocellular carcinoma and in colon cancer. Detailed knowledge of the binding mode of its substrates is required for the design of molecules that can modulate the activity of the enzyme. METHODS We provide a detailed description of binding interactions of human FUT8 with its natural donor substrate GDP-fucose and related compounds. GDP-Fuc was placed in FUT8 by structural analogy to the structure of protein-O-fucosyltransferase (cePOFUT) co-crystallized with GDP-Fuc. The epitope of the donor substrate bound to FUT8 was determined by STD NMR. The in silico model is further supported by experimental data from SPR binding assays. The complex was optimized by molecular dynamics simulations. RESULTS Guanine is specifically recognized by His363 and Asp453. Furthermore, the pyrophosphate is tightly bound via numerous hydrogen bonds and contributes affinity to a major part. Arg365 was found to bind both the β-phosphate and the fucose moiety at the same time. CONCLUSIONS Discovery of a novel structural analogy between cePOFUT and FUT8 allows the placement of the donor substrate GDP-Fuc. The positioning was confirmed by various experimental and computational techniques. GENERAL SIGNIFICANCE The model illustrates details of the molecular basis of substrate recognition for a human fucosyltransferase for the first time and, thus, provides a basis for structure-based design of inhibitors.
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Breton C, Fournel-Gigleux S, Palcic MM. Recent structures, evolution and mechanisms of glycosyltransferases. Curr Opin Struct Biol 2012; 22:540-9. [PMID: 22819665 DOI: 10.1016/j.sbi.2012.06.007] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/30/2012] [Accepted: 06/27/2012] [Indexed: 12/19/2022]
Abstract
Cellular glycome assembly requires the coordinated action of a large number of glycosyltransferases that catalyse the transfer of a sugar residue from a donor to specific acceptor molecules. This enzyme family is very ancient, encompassing all three domains of life. There has been considerable recent progress in structural glycobiology with the determination of crystal structures of several important glycosyltransferase members, showing novel folds and variations around a common α/β scaffold. Structural, kinetic and inhibitor data have led to the emergence of various scenarios with respect to their evolutionary history and reaction mechanisms thus highlighting the different solutions that nature has selected to catalyse glycosyl transfer.
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Affiliation(s)
- Christelle Breton
- CERMAV-CNRS, University of Grenoble 1, BP 53, 38041 Grenoble, France.
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