1
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Guo J, Balić P, Borodkin VS, Filippov DV, Codée JDC. Synthesis of Unsymmetrical Difluoromethylene Bisphosphonates. Org Lett 2024; 26:739-744. [PMID: 38215221 PMCID: PMC10825822 DOI: 10.1021/acs.orglett.3c04211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/14/2024]
Abstract
We demonstrate the use of the symmetrical diethyl(dimethyl)difluoromethylene bisphosphonate reagent for the synthesis of terminal and unsymmetrical difluoromethylene bisphosphonates, close analogues of biologically important molecules. The difference in reactivity of the methyl and ethyl groups in the symmetrical diethyl(dimthyl)difluoromethylene bisphosphonate is exploited in a stepwise demethylation-condensation sequence to functionalize either side of the reagent to allow the generation of a series of close bioisosteres of natural pyrophosphate molecules, including ADPr, CDP-glycerol and CDP-ribitol.
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Affiliation(s)
- Jianyun Guo
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Pascal Balić
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Vladimir S. Borodkin
- Division
of Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH Dundee, U.K.
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
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2
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Pathak S, Alonso J, Schimpl M, Rafie K, Blair DE, Borodkin VS, Schüttelkopf AW, Albarbarawi O, van Aalten DMF. Author Correction: The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nat Struct Mol Biol 2023; 30:564. [PMID: 36869195 DOI: 10.1038/s41594-023-00945-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Shalini Pathak
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Jana Alonso
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Marianne Schimpl
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Karim Rafie
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - David E Blair
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Vladimir S Borodkin
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Alexander W Schüttelkopf
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Osama Albarbarawi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.,Department of Chemistry, Faculty of Science, Taibah University, Al Madenah Al Monwarah, Saudi Arabia
| | - Daan M F van Aalten
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK. .,Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.
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3
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Gorelik A, Bartual SG, Borodkin VS, Varghese J, Ferenbach AT, van Aalten DMF. Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation. Nat Struct Mol Biol 2019; 26:1071-1077. [PMID: 31695185 PMCID: PMC6858883 DOI: 10.1038/s41594-019-0325-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
Modification of specific Ser and Thr residues of nucleocytoplasmic proteins with O-GlcNAc, catalyzed by O-GlcNAc transferase (OGT), is an abundant posttranslational event essential for proper animal development and is dysregulated in various diseases. Due to the rapid concurrent removal by the single O-GlcNAcase (OGA), precise functional dissection of site-specific O-GlcNAc modification in vivo is currently not possible without affecting the entire O-GlcNAc proteome. Exploiting the fortuitous promiscuity of OGT, we show that S-GlcNAc is a hydrolytically stable and accurate structural mimic of O-GlcNAc that can be encoded in mammalian systems with CRISPR-Cas9 in an otherwise unperturbed O-GlcNAcome. Using this approach, we target an elusive Ser 405 O-GlcNAc site on OGA, showing that this site-specific modification affects OGA stability.
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Affiliation(s)
- Andrii Gorelik
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sergio Galan Bartual
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vladimir S Borodkin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joby Varghese
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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4
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Rafie K, Raimi O, Ferenbach AT, Borodkin VS, Kapuria V, van Aalten DMF. Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats. Open Biol 2018; 7:rsob.170078. [PMID: 28659383 PMCID: PMC5493779 DOI: 10.1098/rsob.170078] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 12/23/2022] Open
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is an essential and dynamic post-translational modification found on hundreds of nucleocytoplasmic proteins in metazoa. Although a single enzyme, O-GlcNAc transferase (OGT), generates the entire cytosolic O-GlcNAc proteome, it is not understood how it recognizes its protein substrates, targeting only a fraction of serines/threonines in the metazoan proteome for glycosylation. We describe a trapped complex of human OGT with the C-terminal domain of TAB1, a key innate immunity-signalling O-GlcNAc protein, revealing extensive interactions with the tetratricopeptide repeats of OGT. Confirmed by mutagenesis, this interaction suggests that glycosylation substrate specificity is achieved by recognition of a degenerate sequon in the active site combined with an extended conformation C-terminal of the O-GlcNAc target site.
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Affiliation(s)
- Karim Rafie
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Olawale Raimi
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vladimir S Borodkin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vaibhav Kapuria
- Center for Integrative Genomics, University of Lausanne 1015, Switzerland
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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5
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Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W. The conserved threonine-rich region of the HCF-1 PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities. J Biol Chem 2018; 293:17754-17768. [PMID: 30224358 PMCID: PMC6240873 DOI: 10.1074/jbc.ra118.004185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/05/2018] [Indexed: 12/28/2022] Open
Abstract
O-Linked GlcNAc transferase (OGT) possesses dual glycosyltransferase–protease activities. OGT thereby stably glycosylates serines and threonines of numerous proteins and, via a transient glutamate glycosylation, cleaves a single known substrate—the so-called HCF-1PRO repeat of the transcriptional co-regulator host-cell factor 1 (HCF-1). Here, we probed the relationship between these distinct glycosylation and proteolytic activities. For proteolysis, the HCF-1PRO repeat possesses an important extended threonine-rich region that is tightly bound by the OGT tetratricopeptide-repeat (TPR) region. We report that linkage of this HCF-1PRO-repeat, threonine-rich region to heterologous substrate sequences also potentiates robust serine glycosylation with the otherwise poor Rp-αS-UDP-GlcNAc diastereomer phosphorothioate and UDP-5S-GlcNAc OGT co-substrates. Furthermore, it potentiated proteolysis of a non-HCF-1PRO-repeat cleavage sequence, provided it contained an appropriately positioned glutamate residue. Using serine- or glutamate-containing HCF-1PRO-repeat sequences, we show that proposed OGT-based or UDP-GlcNAc–based serine-acceptor residue activation mechanisms can be circumvented independently, but not when disrupted together. In contrast, disruption of both proposed activation mechanisms even in combination did not inhibit OGT-mediated proteolysis. These results reveal a multiplicity of OGT glycosylation strategies, some leading to proteolysis, which could be targets of alternative molecular regulatory strategies.
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Affiliation(s)
- Vaibhav Kapuria
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fabienne Lammers
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vladimir S Borodkin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Vincent Zoete
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Fundamental Oncology, Ludwig Lausanne Branch, Faculty of Biology and Medicine, University of Lausanne, 1066 Epalinges, Switzerland
| | - Winship Herr
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
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6
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Borodkin VS, Rafie K, Selvan N, Aristotelous T, Navratilova I, Ferenbach AT, van Aalten DMF. O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry. ACS Chem Biol 2018; 13:1353-1360. [PMID: 29641181 DOI: 10.1021/acschembio.8b00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The attachment of the sugar N-acetyl-D-glucosamine (GlcNAc) to specific serine and threonine residues on proteins is referred to as protein O-GlcNAcylation. O-GlcNAc transferase (OGT) is the enzyme responsible for carrying out the modification, while O-GlcNAcase (OGA) reverses it. Protein O-GlcNAcylation has been implicated in a wide range of cellular processes including transcription, proteostasis, and stress response. Dysregulation of O-GlcNAc has been linked to diabetes, cancer, and neurodegenerative and cardiovascular disease. OGA has been proposed to be a drug target for the treatment of Alzheimer's and cardiovascular disease given that increased O-GlcNAc levels appear to exert a protective effect. The search for specific, potent, and drug-like OGA inhibitors with bioavailability in the brain is therefore a field of active research, requiring orthogonal high-throughput assay platforms. Here, we describe the synthesis of a novel probe for use in a fluorescence polarization based assay for the discovery of inhibitors of OGA. We show that the probe is suitable for use with both human OGA, as well as the orthologous bacterial counterpart from Clostridium perfringens, CpOGA, and the lysosomal hexosaminidases HexA/B. We structurally characterize CpOGA in complex with a ligand identified from a fragment library screen using this assay. The versatile synthesis procedure could be adapted for making fluorescent probes for the assay of other glycoside hydrolases.
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7
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Abstract
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O-GlcNAc
transferase (OGT) is an essential glycosyltransferase
that installs the O-GlcNAc post-translational modification on the
nucleocytoplasmic proteome. We report the development of S-linked
UDP–peptide conjugates as potent bisubstrate OGT inhibitors.
These compounds were assembled in a modular fashion by photoinitiated
thiol–ene conjugation of allyl-UDP and optimal acceptor peptides
in which the acceptor serine was replaced with cysteine. The conjugate
VTPVC(S-propyl-UDP)TA (Ki = 1.3 μM)
inhibits the OGT activity in HeLa cell lysates. Linear fusions of
this conjugate with cell penetrating peptides were explored as prototypes
of cell-penetrant OGT inhibitors. A crystal structure of human OGT
with the inhibitor revealed mimicry of the interactions seen in the
pseudo-Michaelis complex. Furthermore, a fluorophore-tagged derivative
of the inhibitor works as a high affinity probe in a fluorescence
polarimetry hOGT assay.
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Affiliation(s)
- Karim Rafie
- Division of Gene Regulation and Expression, School of Life Sciences , University of Dundee , DD1 5EH Dundee , U.K
| | - Andrii Gorelik
- Division of Gene Regulation and Expression, School of Life Sciences , University of Dundee , DD1 5EH Dundee , U.K
| | - Riccardo Trapannone
- Division of Gene Regulation and Expression, School of Life Sciences , University of Dundee , DD1 5EH Dundee , U.K
| | - Vladimir S Borodkin
- Division of Gene Regulation and Expression, School of Life Sciences , University of Dundee , DD1 5EH Dundee , U.K
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences , University of Dundee , DD1 5EH Dundee , U.K
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8
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Kapuria V, Röhrig UF, Bhuiyan T, Borodkin VS, van Aalten DMF, Zoete V, Herr W. Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes. Genes Dev 2016; 30:960-72. [PMID: 27056667 PMCID: PMC4840301 DOI: 10.1101/gad.275925.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/10/2016] [Indexed: 12/12/2022]
Abstract
In this study, Kapuria et al. investigate the dual glycosyltransferase–protease activity (which occurs in the same active site) of OGT. They show that glycosylation and proteolysis occur through separable mechanisms and present a model for the evolution of HCF-1 proteolysis by OGT. In complex with the cosubstrate UDP-N-acetylglucosamine (UDP-GlcNAc), O-linked-GlcNAc transferase (OGT) catalyzes Ser/Thr O-GlcNAcylation of many cellular proteins and proteolysis of the transcriptional coregulator HCF-1. Such a dual glycosyltransferase–protease activity, which occurs in the same active site, is unprecedented and integrates both reversible and irreversible forms of protein post-translational modification within one enzyme. Although occurring within the same active site, we show here that glycosylation and proteolysis occur through separable mechanisms. OGT consists of tetratricopeptide repeat (TPR) and catalytic domains, which, together with UDP-GlcNAc, are required for both glycosylation and proteolysis. Nevertheless, a specific TPR domain contact with the HCF-1 substrate is critical for proteolysis but not Ser/Thr glycosylation. In contrast, key catalytic domain residues and even a UDP-GlcNAc oxygen important for Ser/Thr glycosylation are irrelevant for proteolysis. Thus, from a dual glycosyltransferase–protease, essentially single-activity enzymes can be engineered both in vitro and in vivo. Curiously, whereas OGT-mediated HCF-1 proteolysis is limited to vertebrate species, invertebrate OGTs can cleave human HCF-1. We present a model for the evolution of HCF-1 proteolysis by OGT.
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Affiliation(s)
- Vaibhav Kapuria
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tanja Bhuiyan
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Vladimir S Borodkin
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Winship Herr
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
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9
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Abstract
Chitin synthases (CHS) produce chitin, an essential component of the fungal cell wall. The molecular mechanism of processive chitin synthesis is not understood, limiting the discovery of new inhibitors of this enzyme class. We identified the bacterial glycosyltransferase NodC as an appropriate model system to study the general structure and reaction mechanism of CHS. A high throughput screening-compatible novel assay demonstrates that a known inhibitor of fungal CHS also inhibit NodC. A structural model of NodC, on the basis of the recently published BcsA cellulose synthase structure, enabled probing of the catalytic mechanism by mutagenesis, demonstrating the essential roles of the DD and QXXRW catalytic motifs. The NodC membrane topology was mapped, validating the structural model. Together, these approaches give insight into the CHS structure and mechanism and provide a platform for the discovery of inhibitors for this antifungal target.
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Affiliation(s)
- Helge C Dorfmueller
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Andrew T Ferenbach
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Vladimir S Borodkin
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Daan M F van Aalten
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
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10
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Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DMF, Agnew B, Kuster B. Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry. J Proteome Res 2013; 12:927-36. [PMID: 23301498 DOI: 10.1021/pr300967y] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The post-translational modification of proteins with N-acetylglucosamine (O-GlcNAc) is involved in the regulation of a wide variety of cellular processes and associated with a number of chronic diseases. Despite its emerging biological significance, the systematic identification of O-GlcNAc proteins is still challenging. In the present study, we demonstrate a significantly improved O-GlcNAc protein enrichment procedure, which exploits metabolic labeling of cells by azide-modified GlcNAc and copper-mediated Click chemistry for purification of modified proteins on an alkyne-resin. On-resin proteolysis using trypsin followed by LC-MS/MS afforded the identification of around 1500 O-GlcNAc proteins from a single cell line. Subsequent elution of covalently resin bound O-GlcNAc peptides using selective β-elimination enabled the identification of 185 O-GlcNAc modification sites on 80 proteins. To demonstrate the practical utility of the developed approach, we studied the global effects of the O-GlcNAcase inhibitor GlcNAcstatin G on the level of O-GlcNAc modification of cellular proteins. About 200 proteins including several key players involved in the hexosamine signaling pathway showed significantly increased O-GlcNAcylation levels in response to the drug, which further strengthens the link of O-GlcNAc protein modification to cellular nutrient sensing and response.
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Affiliation(s)
- Hannes Hahne
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences, Weihenstephan, Technische Universität München, Freising, Germany
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11
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Schimpl M, Zheng X, Borodkin VS, Blair DE, Ferenbach AT, Schüttelkopf AW, Navratilova I, Aristotelous T, Albarbarawi O, Robinson DA, Macnaughtan MA, van Aalten DM. O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis. Nat Chem Biol 2012; 8:969-74. [PMID: 23103942 PMCID: PMC3509171 DOI: 10.1038/nchembio.1108] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/28/2012] [Indexed: 02/03/2023]
Abstract
Protein O-GlcNAcylation is an essential post-translational modification on hundreds of intracellular proteins in metazoa, catalyzed by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) using unknown mechanisms of transfer and substrate recognition. Through crystallographic snapshots and mechanism-inspired chemical probes, we define how human OGT recognizes the sugar donor and acceptor peptide and uses a new catalytic mechanism of glycosyl transfer, involving the sugar donor α-phosphate as the catalytic base as well as an essential lysine. This mechanism seems to be a unique evolutionary solution to the spatial constraints imposed by a bulky protein acceptor substrate and explains the unexpected specificity of a recently reported metabolic OGT inhibitor.
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Affiliation(s)
| | - Xiaowei Zheng
- College of Life Sciences, University of Dundee, Dundee, UK
| | | | - David E. Blair
- College of Life Sciences, University of Dundee, Dundee, UK
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12
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Schimpl M, Borodkin VS, Gray LJ, van Aalten DMF. Synergy of peptide and sugar in O-GlcNAcase substrate recognition. ACTA ACUST UNITED AC 2012; 19:173-8. [PMID: 22365600 PMCID: PMC3476531 DOI: 10.1016/j.chembiol.2012.01.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 12/14/2011] [Accepted: 01/12/2012] [Indexed: 01/17/2023]
Abstract
Protein O-GlcNAcylation is an essential reversible posttranslational modification in higher eukaryotes. O-GlcNAc addition and removal is catalyzed by O-GlcNAc transferase and O-GlcNAcase, respectively. We report the molecular details of the interaction of a bacterial O-GlcNAcase homolog with three different synthetic glycopeptides derived from characterized O-GlcNAc sites in the human proteome. Strikingly, the peptides bind a conserved O-GlcNAcase substrate binding groove with similar orientation and conformation. In addition to extensive contacts with the sugar, O-GlcNAcase recognizes the peptide backbone through hydrophobic interactions and intramolecular hydrogen bonds, while avoiding interactions with the glycopeptide side chains. These findings elucidate the molecular basis of O-GlcNAcase substrate specificity, explaining how a single enzyme achieves cycling of the complete O-GlcNAc proteome. In addition, this work will aid development of O-GlcNAcase inhibitors that target the peptide binding site.
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Affiliation(s)
- Marianne Schimpl
- Division of Cell Signalling & Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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13
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Sizova OV, Ross AJ, Ivanova IA, Borodkin VS, Ferguson MAJ, Nikolaev AV. Probing elongating and branching β-D-galactosyltransferase activities in Leishmania parasites by making use of synthetic phosphoglycans. ACS Chem Biol 2011; 6:648-57. [PMID: 21425873 DOI: 10.1021/cb100416j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protozoan parasites of the genus Leishmania synthesize lipophosphoglycans (LPGs), phosphoglycans and proteophosphoglycans that contain phosphosaccharide repeat units of [-6)Gal(β1-4)Man(α1-OPO(3)H-]. The repeat structures are assembled by sequential addition of Manα1-OPO(3)H and β-Gal. In this study, an UDP-Gal-dependent activity was detected in L. donovani and L. major membranes using synthetic phospho-oligosaccharide fragments of lipophosphoglycan as acceptor substrates. Incubation of a microsomal preparation from L. donovani or L. major parasites with synthetic substrates and UDP-[6-(3)H]Gal resulted in incorporation of radiolabel into these exogenous acceptors. The [(3)H]galactose-labeled products were characterized by degradation into radioactive, low molecular mass fragments upon hydrolysis with mild acid and treatment with β-galactosidases. We showed that the activity detected with L. donovani membranes is the elongating β-d-galactosyltransferase associated with LPG phosphosaccharide backbone biosynthesis (eGalT). The eGalT activity showed a requirement for the presence of at least one phosphodiester group in the substrate and it was enhanced dramatically when two or three phosphodiester groups were present. Using the same substrates we detected two types of galactosyltransferase activity in L. major membranes: the elongating β-d-galactosyltransferase and a branching β-d-galactosyltransferase (bGalT). Both L. major enzymes required a minimum of one phosphodiester group present in the substrate, but acceptors with two or three phosphodiester groups were found to be superior.
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Affiliation(s)
- Olga V. Sizova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrew J. Ross
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K
| | - Irina A. Ivanova
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K
| | - Vladimir S. Borodkin
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K
| | - Michael A. J. Ferguson
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K
| | - Andrei V. Nikolaev
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K
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Dorfmueller HC, Borodkin VS, Schimpl M, Zheng X, Kime R, Read KD, van Aalten DMF. Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases. ACTA ACUST UNITED AC 2011; 17:1250-5. [PMID: 21095575 PMCID: PMC3032886 DOI: 10.1016/j.chembiol.2010.09.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/24/2010] [Accepted: 09/01/2010] [Indexed: 11/16/2022]
Abstract
Posttranslational modification of metazoan nucleocytoplasmic proteins with N-acetylglucosamine (O-GlcNAc) is essential, dynamic, and inducible and can compete with protein phosphorylation in signal transduction. Inhibitors of O-GlcNAcase, the enzyme removing O-GlcNAc, are useful tools for studying the role of O-GlcNAc in a range of cellular processes. We report the discovery of nanomolar OGA inhibitors that are up to 900,000-fold selective over the related lysosomal hexosaminidases. When applied at nanomolar concentrations on live cells, these cell-penetrant molecules shift the O-GlcNAc equilibrium toward hyper-O-GlcNAcylation with EC₅₀ values down to 3 nM and are thus invaluable tools for the study of O-GlcNAc cell biology.
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Affiliation(s)
- Helge C Dorfmueller
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD15EH, Scotland
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Borodkin VS, van Aalten DM. An efficient and versatile synthesis of GlcNAcstatins-potent and selective O-GlcNAcase inhibitors built on the tetrahydroimidazo[1,2-a]pyridine scaffold. Tetrahedron 2010; 66:7838-7849. [PMID: 20976183 PMCID: PMC2956484 DOI: 10.1016/j.tet.2010.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/24/2010] [Accepted: 07/15/2010] [Indexed: 11/24/2022]
Abstract
We report a novel approach to the synthesis of GlcNAcstatins—members of an emerging family of potent and selective inhibitors of peptidyl O-GlcNAc hydrolase build upon tetrahydroimidazo[1,2-a]pyridine scaffold. Making use of a streamlined synthetic sequence featuring de novo synthesis of imidazoles from glyoxal, ammonia and aldehydes, a properly functionalised linear GlcNAcstatin precursor has been efficiently prepared starting from methyl 3,4-O-(2′,3′-dimethoxybutane-2′,3′-diyl)-α-d-mannopyranoside. Subsequent ring closure of the linear precursor in an intramolecular SN2 process furnished the key fused d-mannose-imidazole GlcNAcstatin precursor in excellent yield. Finally, a sequence of transformations of this key intermediate granted expeditious access to a variety of the target compounds bearing a C(2)-phenethyl group and a range of N(8) acyl substituents. The versatility of the new approach stems from an appropriate choice of a set of acid labile permanent protecting groups on the monosaccharide starting material. Application was demonstrated by the synthesis of GlcNAcstatins containing polyunsaturated and thiol-containing amido substituents.
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Dorfmueller HC, Borodkin VS, Blair DE, Pathak S, Navratilova I, van Aalten DMF. Substrate and product analogues as human O-GlcNAc transferase inhibitors. Amino Acids 2010; 40:781-92. [PMID: 20640461 PMCID: PMC3040809 DOI: 10.1007/s00726-010-0688-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 07/01/2010] [Indexed: 11/03/2022]
Abstract
Protein glycosylation on serine/threonine residues with N-acetylglucosamine (O-GlcNAc) is a dynamic, inducible and abundant post-translational modification. It is thought to regulate many cellular processes and there are examples of interplay between O-GlcNAc and protein phosphorylation. In metazoa, a single, highly conserved and essential gene encodes the O-GlcNAc transferase (OGT) that transfers GlcNAc onto substrate proteins using UDP-GlcNAc as the sugar donor. Specific inhibitors of human OGT would be useful tools to probe the role of this post-translational modification in regulating processes in the living cell. Here, we describe the synthesis of novel UDP-GlcNAc/UDP analogues and evaluate their inhibitory properties and structural binding modes in vitro alongside alloxan, a previously reported weak OGT inhibitor. While the novel analogues are not active on living cells, they inhibit the enzyme in the micromolar range and together with the structural data provide useful templates for further optimisation.
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Affiliation(s)
- Helge C Dorfmueller
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, Scotland, UK
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Pathak S, Dorfmueller HC, Borodkin VS, van Aalten DMF. Chemical dissection of the link between streptozotocin, O-GlcNAc, and pancreatic cell death. ACTA ACUST UNITED AC 2008; 15:799-807. [PMID: 18721751 PMCID: PMC2568864 DOI: 10.1016/j.chembiol.2008.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2008] [Revised: 06/11/2008] [Accepted: 06/23/2008] [Indexed: 01/09/2023]
Abstract
Streptozotocin is a natural product that selectively kills insulin-secreting β cells, and is widely used to generate mouse models of diabetes or treat pancreatic tumors. Several studies suggest that streptozotocin toxicity stems from its N-nitrosourea moiety releasing nitric oxide and possessing DNA alkylating activity. However, it has also been proposed that streptozotocin induces apoptosis by inhibiting O-GlcNAcase, an enzyme that, together with O-GlcNAc transferase, is important for dynamic intracellular protein O-glycosylation. We have used galacto-streptozotocin to chemically dissect the link between O-GlcNAcase inhibition and apoptosis. Using X-ray crystallography, enzymology, and cell biological studies on an insulinoma cell line, we show that, whereas streptozotocin competitively inhibits O-GlcNAcase and induces apoptosis, its galacto-configured derivative no longer inhibits O-GlcNAcase, yet still induces apoptosis. This supports a general chemical poison mode of action for streptozotocin, suggesting the need for using more specific inhibitors to study protein O-GlcNAcylation.
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Affiliation(s)
- Shalini Pathak
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, Scotland
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Dorfmueller HC, Borodkin VS, Schimpl M, Shepherd SM, Shpiro NA, van Aalten DMF. GlcNAcstatin: a picomolar, selective O-GlcNAcase inhibitor that modulates intracellular O-glcNAcylation levels. J Am Chem Soc 2007; 128:16484-5. [PMID: 17177381 PMCID: PMC7116141 DOI: 10.1021/ja066743n] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many phosphorylation signal transduction pathways in the eukaryotic cell are modulated by posttranslational modification of specific serines/threonines with N-acetylglucosamine (O-GlcNAc). Levels of O-GlcNAc on key proteins regulate biological processes as diverse as the cell cycle, insulin signaling, and protein degradation. The two enzymes involved in this dynamic and abundant modification are the O-GlcNAc transferase and O-GlcNAcase. Structural data have recently revealed that the O-GlcNAcase possesses an active site with significant structural similarity to that of the human lysosomal hexosaminidases HexA/HexB. PUGNAc, an O-GlcNAcase inhibitor widely used to raise levels of O-GlcNAc in human cell lines, also inhibits these hexosaminidases. Here, we have exploited recent structural information of an O-GlcNAcase-PUGNAc complex to design and synthesize a glucoimidazole-based inhibitor, GlcNAcstatin, which is a 5 pM competitive inhibitor of enzymes of the O-GlcNAcase family, shows 100000-fold selectivity over HexA/B, and binds to the O-GlcNAcase active site by mimicking the transition state as revealed by X-ray crystallography. This compound is able to raise O-GlcNAc levels in human HEK 293 and SH-SY5Y neuroblastoma cell lines and thus provides a novel, potent tool for the study of the role of O-GlcNAc in intracellular signal transduction pathways.
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Yashunsky DV, Borodkin VS, Ferguson MAJ, Nikolaev AV. The chemical synthesis of bioactive glycosylphosphatidylinositols from Trypanosoma cruzi containing an unsaturated fatty acid in the lipid. Angew Chem Int Ed Engl 2006; 45:468-74. [PMID: 16342127 DOI: 10.1002/anie.200502779] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dmitry V Yashunsky
- Faculty of Life Sciences, Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Carnelley Building, Dundee DD1 4HN, UK
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Yashunsky DV, Borodkin VS, Ferguson MAJ, Nikolaev AV. The Chemical Synthesis of Bioactive Glycosylphosphatidylinositols fromTrypanosoma cruzi Containing an Unsaturated Fatty Acid in the Lipid. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502779] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Borodkin VS, Shpiro NA, Azov VA, Kochetkov NK. Substrate dependent intramolecular Pauson-Khand reaction of carbohydrate exo-methylene derivatives. Unexpected formation of fused “[4.1.0] bicycloheptene - pyranose” tricyclic product. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)00046-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Savadian ES, Borodkin VS. [A protective device for treatment using external transosseous fixation equipment]. Ortop Travmatol Protez 1990:36-7. [PMID: 2348994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Morozov BP, Borodkin VS, Karpacheva LI. [Splint for skeletal traction in the treatment of injuries of the lower extremities]. Ortop Travmatol Protez 1987:39-40. [PMID: 3670821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Borodkin VS, Sherepo KM, Morozov BP. [Fractures of the femoral component of a hip endoprosthesis]. Ortop Travmatol Protez 1986:63. [PMID: 3822416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Sivash KM, Kaz'min AI, Sherepo KM, Borodkin VS, Parshutin GE. [Sivash-Kaz'min transportation splint for the hip]. Ortop Travmatol Protez 1985:57-8. [PMID: 3991146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sivash KM, Borodkin VS. [Needle drill]. Ortop Travmatol Protez 1974; 35:82-3. [PMID: 4839681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Sivash KM, Borodkin VS, Kozhin NP. [CITO longitudinal frame for orthopedic bed]. Ortop Travmatol Protez 1973; 34:76-7. [PMID: 4776612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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