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Strecker C, Peters H, Hackl T, Peters T, Meyer B. Fragment Growing to Design Optimized Inhibitors for Human Blood Group B Galactosyltransferase (GTB). ChemMedChem 2019; 14:1336-1342. [PMID: 31207161 DOI: 10.1002/cmdc.201900296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/13/2019] [Indexed: 12/22/2022]
Abstract
Human blood group B galactosyltransferase (GTB) catalyzes the galactosylation of the H antigen and is responsible for the formation of the blood group antigen of phenotype B. The ABO blood group system is well studied and routinely serotyped before transfusion and transplantation. Blood type subgroups have been repeatedly linked to an increased occurrence of diseases (e.g., a highly increased incidence rate for pancreatic cancer for individuals with blood group phenotype B). 3-Phenyl-5-(piperazin-1-yl)-1,2,4-thiadiazole 1 has previously been described to inhibit GTB with a Ki value of 800 μm. In this work, we describe a computer-guided fragment-growing approach for the optimization of this fragment that was subsequently realized by synthesizing the most promising ligands. Enlarging the phenyl moiety of fragment 1 to a naphthyl moiety resulted in ligand 3-(naphthalene-1-yl)-5-(piperazin-1-yl)-1,2,4-thiadiazole 2 a, which shows a threefold improvement in binding affinity (Ki =271 μm).
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Affiliation(s)
- Claas Strecker
- Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Hannelore Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Thomas Hackl
- Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Bernd Meyer
- Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
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2
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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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3
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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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Zielinski T, Reichman M, Donover PS, Lowery RG. Development and Validation of a Universal High-Throughput UDP-Glycosyltransferase Assay with a Time-Resolved FRET Signal. Assay Drug Dev Technol 2016; 14:240-51. [PMID: 27136323 DOI: 10.1089/adt.2016.711] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Glycosyltransferase enzymes play diverse metabolic and regulatory roles by catalyzing the transfer of sugar molecules to protein, lipid, and carbohydrate acceptors, and they are increasingly of interest as therapeutic targets in a number of diseases, including metabolic disorders, cancer, and infectious diseases. The glycosyltransferases are a challenging target class from an assay development perspective because of the diversity of both donor and acceptor substrates and the lack of suitable glycan detection methods. However, many glycosyltransferases use uridine 5'-diphosphate (UDP) sugars as donor substrates, and detection of the free UDP reaction product provides a generic approach for measuring the activity of those enzymes. To exploit this approach for a broadly applicable high-throughput screening (HTS) assay for discovery of glycosyltransferase inhibitors, we developed a Transcreener(®) assay for immunodetection of UDP with a time-resolved Förster resonance energy transfer (TR-FRET) signal. We optimized the assay for detection of glycosyltransferase activity with nucleotide diphosphate (NDP) sugars at concentrations from 10 μM to 1 mM, achieving Z' values of 0.6 or higher. The assay was validated by orthogonal pooled screening with 8,000 compounds using polypeptide N-acetylgalactosaminyltransferase T3 as the target, and the hits were confirmed using an orthogonal readout. The reagents and signal were both stable for more than 8 h at room temperature, insuring robust performance in automated HTS environments. The TR-FRET-based UDP detection assay provides a broadly applicable approach for screening glycosyltransferases that use a UDP-sugar donor.
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Affiliation(s)
| | - Melvin Reichman
- 2 Lankenau Institute for Medical Research , Wynnewood, Pennsylvania
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5
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Isolation and analysis of sugar nucleotides using solid phase extraction and fluorophore assisted carbohydrate electrophoresis. MethodsX 2016; 3:251-60. [PMID: 27222820 PMCID: PMC4821447 DOI: 10.1016/j.mex.2016.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/11/2016] [Indexed: 11/23/2022] Open
Abstract
The building blocks of simple and complex oligosaccharides, termed sugar nucleotides, are often overlooked for their role in metabolic diseases and may hold the key to the underlying disease pathogenesis. Multiple reasons may account for the lack of analysis and quantitation of these sugar nucleotides, including the difficulty in isolation and purification as well as the required expensive instrumentation such as a high performance liquid chromatography (HPLC), mass spectrometer, or capillary electrophoresis. We have established a simple yet effective way to purify and quantitate sugar nucleotides using solid phase extraction (SPE) chromatography combined with fluorophore assisted carbohydrate electrophoresis (FACE). The simplicity of use, combined with the ability to run multiple samples at one time, give this technique a distinct advantage over the established methods for isolation and analysis of sugar nucleotides from cell culture models. Sugar nucleotides can be easily purified with solid phase extraction chromatography. FACE can be used to analyze multiple nucleotide sugar extracts with a single run. The proposed method is simple, affordable, and uses common everyday research labware.
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Key Words
- AMAC, 2-aminoacridone
- APS, ammonium persulfate
- CMP, cytosine monophosphate
- Carbohydrate
- Electrophoresis
- FACE, fluorophore assisted carbohydrate electrophoresis
- Face
- GDP, guanosine diphosphate
- Gal, galactose
- GalNAc, N-acetylgalactosamine
- GlcNAc, N-acetylglucosamine
- GlcUA, glucuronic acid
- HPLC
- HPLC, high performance liquid chromatography
- Man, Mannose
- NeuAc, sialic acid
- SPE, solid phase extraction
- Sugar nucleotide analysis by SPE and FACE
- Sugar nucleotides
- TEAA, triethylamine acetate
- TEMED, N′,N′,N′N′-tetramethylenediamine
- UDP, uridine diphosphate
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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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7
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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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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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9
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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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