1
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Liu P, Zhou Q, Li J. Integrated Multi-Omics Data Analysis Reveals Associations Between Glycosylation and Stemness in Hepatocellular Carcinoma. Front Oncol 2022; 12:913432. [PMID: 35814473 PMCID: PMC9259879 DOI: 10.3389/fonc.2022.913432] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022] Open
Abstract
Background Glycosylation plays an essential role in driving the progression and treatment resistance of hepatocellular carcinoma (HCC). However, its function in regulating the acquisition and maintenance of the cancer stemness-like phenotype in HCC remains largely unknown. There is also very little known about how CAD and other potential glycosylation regulators may influence stemness. This study explores the relationship between glycosylation and stemness in HCC. Methods Gene set variance analysis (GSVA) was used to assess the TCGA pan-cancer enrichment in glycosylation-related pathways. Univariate, LASSO, and multivariate COX regression were then used to identify prognostic genes in the TCGA-LIHC and construct a prognostic signature. HCC patients were classified into high- and low-risk subgroups based on the signature. The relationship between gene expression profiles and stemness was confirmed using bulk and single-cell RNA-sequencing data. The role of CAD and other genes in regulating the stemness of HCC was also validated by RT-qPCR, CCK-8, and colony formation assay. Copy number variation (CNV), immune infiltration, and clinical features were further analyzed in different subgroups and subsequent gene expression profiles. Sensitive drugs were also screened. Results In the pan-cancer analysis, HCC was shown to have specific glycosylation alterations. Five genes, CAD, SLC51B, LGALS3, B3GAT3, and MT3, identified from 572 glycosylation-related genes, were used to construct a gene signature and predict HCC patient survival in the TCGA cohort. The results demonstrated a significant positive correlation between patients in the high-risk group and both elevated gene expression and HCC dedifferentiation status. A significant reduction in the stemness-related markers, CD24, CD44, CD20, FOXM1, and EpCAM, was found after the knockdown of CAD and other genes in HepG2 and Huh7 cells. Frequent mutations increased CNVs, immune-suppressive responses, and poor prognosis were also associated with the high-risk profile. The ICGC-LIRI-JP cohort confirmed a similar relationship between glycosylation-related subtypes and stemness. Finally, 84 sensitive drugs were screened for abnormal glycosylation of HCC, and carfilzomib was most highly correlated with CAD. Conclusions Glycosylation-related molecular subtypes are associated with HCC stemness and disease prognosis. These results provide new directions for further research on the relationship between glycosylation and stemness phenotypes.
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Affiliation(s)
- Peiyan Liu
- Department of Hepatology, Second People’s Clinical College of Tianjin Medical University, Tianjin, China
- Department of Hepatology, Tianjin Second People’s Hospital, Tianjin, China
| | - Qi Zhou
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China
| | - Jia Li
- Department of Hepatology, Second People’s Clinical College of Tianjin Medical University, Tianjin, China
- Department of Hepatology, Tianjin Second People’s Hospital, Tianjin, China
- *Correspondence: Jia Li,
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2
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Ryan P, Shi Y, von Itzstein M, Rudrawar S. Novel bisubstrate uridine-peptide analogues bearing a pyrophosphate bioisostere as inhibitors of human O-GlcNAc transferase. Bioorg Chem 2021; 110:104738. [PMID: 33667901 DOI: 10.1016/j.bioorg.2021.104738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022]
Abstract
Protein O-linked β-D-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), an essential post-translational as well as cotranslational modification, is the attachment of β-D-N-acetylglucosamine to serine and threonine residues of nucleocytoplasmic proteins. An aberrant O-GlcNAc profile on certain proteins has been implicated in metabolic diseases such as diabetes and cancer. Inhibitors of O-GlcNAc transferase (OGT) are valuable tools to study the cell biology of protein O-GlcNAc modification. In this study we report novel uridine-peptide conjugate molecules composed of an acceptor peptide covalently linked to a catalytically inactive donor substrate analogue that bears a pyrophosphate bioisostere and explore their inhibitory activities against OGT by a radioactive hOGT assay. Further, we investigate the structural basis of their activities via molecular modelling, explaining their lack of potency towards OGT inhibition.
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Affiliation(s)
- Philip Ryan
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia; School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia; School of Chemistry, The University of Sydney, NSW 2006, Australia.
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3
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Brzuska G, Pastuch-Gawolek G, Krawczyk M, Szewczyk B, Krol E. Anti-Tick-Borne Encephalitis Virus Activity of Novel Uridine Glycoconjugates Containing Amide or/and 1,2,3-Triazole Moiety in the Linker Structure. Pharmaceuticals (Basel) 2020; 13:ph13120460. [PMID: 33322151 PMCID: PMC7764612 DOI: 10.3390/ph13120460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) transmitted by ticks is a pathogen of great medical importance. As still no effective antiviral treatment is available, in the present study, a series of uridine glycoconjugates containing amide or/and 1,2,3-triazole moiety in the linker structure was synthesized and evaluated for the antiviral activity against two strains of TBEV: a highly virulent Hypr strain and less virulent Neudoerfl strain, using standardized previously in vitro assays. Our data have shown that four compounds from the series (18–21) possess strong activity against both TBEV strains. The half maximal inhibitory concentration (IC50) values of compounds 18–21 were between 15.1 and 3.7 μM depending on the virus strain, which along with low cytotoxicity resulted in high values of the selectivity index (SI). The obtained results suggest that these compounds may be promising candidates for further development of new therapies against flaviviruses.
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Affiliation(s)
- Gabriela Brzuska
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (G.B.); (B.S.)
| | - Gabriela Pastuch-Gawolek
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland; (G.P.-G.); (M.K.)
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Monika Krawczyk
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland; (G.P.-G.); (M.K.)
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Boguslaw Szewczyk
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (G.B.); (B.S.)
| | - Ewelina Krol
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (G.B.); (B.S.)
- Correspondence: ; Tel.: +48-58-523-63-83
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4
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Makwana V, Ryan P, Malde AK, Anoopkumar-Dukie S, Rudrawar S. Bisubstrate Ether-Linked Uridine-Peptide Conjugates as O-GlcNAc Transferase Inhibitors. ChemMedChem 2020; 16:477-483. [PMID: 32991074 DOI: 10.1002/cmdc.202000582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/24/2020] [Indexed: 12/22/2022]
Abstract
The O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is a master regulator of installing O-GlcNAc onto serine or threonine residues on a multitude of target proteins. Numerous nuclear and cytosolic proteins of varying functional classes, including translational factors, transcription factors, signaling proteins, and kinases are OGT substrates. Aberrant O-GlcNAcylation of proteins is implicated in signaling in metabolic diseases such as diabetes and cancer. Selective and potent OGT inhibitors are valuable tools to study the role of OGT in modulating a wide range of effects on cellular functions. We report linear bisubstrate ether-linked uridine-peptide conjugates as OGT inhibitors with micromolar affinity. In vitro evaluation of the compounds revealed the importance of donor substrate, linker and acceptor substrate in the rational design of bisubstrate analogue inhibitors. Molecular dynamics simulations shed light on the binding of this novel class of inhibitors and rationalized the effect of amino acid truncation of acceptor peptide on OGT inhibition.
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Affiliation(s)
- Vivek Makwana
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Philip Ryan
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia.,MaldE Scientific, Australia
| | - Shailendra Anoopkumar-Dukie
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
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5
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Synthesis, NMR and X-ray studies on novel heteroaromatic aldoxime O-ether 2- and 2,3-unsaturated glycosides. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Lafuente L, Santiago CC, Rojas AH, Piro OE, Echeverría GA, Ponzinibbio A. Selective Synthesis and Molecular Structure of Novel Aminooxyglycosyl Derivatives Bearing Hydroxyphenyl Moieties. ChemistrySelect 2020. [DOI: 10.1002/slct.201903727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Leticia Lafuente
- Centro de Estudio de Compuestos Orgánicos (CEDECOR-UNLP-CIC). Universidad Nacional de La Plata. 47 y 115 1900 La Plata Argentina
| | - Cintia C. Santiago
- Departamento de Química, Facultad de Ciencias Exactas. Universidad Nacional de La Plata. 47 y 115 1900 La Plata Argentina
| | - Agustín H. Rojas
- Centro de Estudio de Compuestos Orgánicos (CEDECOR-UNLP-CIC). Universidad Nacional de La Plata. 47 y 115 1900 La Plata Argentina
| | - Oscar E. Piro
- LANADI e IFLP (CCT-La Plata), Departamento de Física, Facultad de Ciencias Exactas Universidad Nacional de La Plata. CC 67 1900 La Plata Argentina
| | - Gustavo A. Echeverría
- LANADI e IFLP (CCT-La Plata), Departamento de Física, Facultad de Ciencias Exactas Universidad Nacional de La Plata. CC 67 1900 La Plata Argentina
| | - Agustín Ponzinibbio
- Centro de Estudio de Compuestos Orgánicos (CEDECOR-UNLP-CIC). Universidad Nacional de La Plata. 47 y 115 1900 La Plata Argentina
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7
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Moukha-Chafiq O, Reynolds RC, Wilson JC, Snowden TS. Parallel Solution Phase Synthesis and Preliminary Biological Activity of a 5'-Substituted Cytidine Analog Library. ACS COMBINATORIAL SCIENCE 2019; 21:628-634. [PMID: 31365223 DOI: 10.1021/acscombsci.9b00072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A 109-membered library of 5'-substituted cytidine analogs was synthesized, via funding through the NIH Roadmap Initiative and the Pilot Scale Library (PSL) Program. Reaction core compounds contained -NH2 (2) and -COOH (44 and 93) groups that were coupled to a diversity of reactants in a parallel, solution phase format to produce the target library. The assorted reactants included -NH2, -CHO, -SO2Cl, and -COOH functional groups, and condensation with the intermediate core materials 2 and 44 followed by acidic hydrolysis produced 3-91 in good yields and high purity. Linkage of the amino terminus of d-phenylalanine methyl ester to the free 5'-COOH of 44 and NaOH treatment led to core library -COOH precursor 93. In a libraries from libraries approach, compound 93 served as the vital building block for our unique library of dipeptidyl cytidine analogs 94-114 through amide coupling of the -COOH group with numerous commercial amines followed by acidic deprotection. Initial screening of the complete final library through the MLPCN program revealed a modest number of hits over diverse biological processes. These hits might be considered as starting points for hit-to-lead optimization and development studies.
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Affiliation(s)
- Omar Moukha-Chafiq
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Jacob C. Wilson
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
| | - Timothy S. Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
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8
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Affiliation(s)
- Xue-Long Sun
- Department of Chemistry, Chemical and Biomedical Engineering and Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University
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9
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Madec AGE, Schocker NS, Sanchini S, Myratgeldiyev G, Das D, Imperiali B. Facile Solid-Phase Synthesis and Assessment of Nucleoside Analogs as Inhibitors of Bacterial UDP-Sugar Processing Enzymes. ACS Chem Biol 2018; 13:2542-2550. [PMID: 30080379 DOI: 10.1021/acschembio.8b00477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The privileged uptake of nucleosides into cells has generated interest in the development of nucleoside-analog libraries for mining new inhibitors. Of particular interest are applications in the discovery of substrate mimetic inhibitors for the growing number of identified glycan-processing enzymes in bacterial pathogens. However, the high polarity and the need for appropriate protecting group strategies for nucleosides challenges the development of synthetic approaches. Here, we report an accessible, user-friendly synthesis that branches from a common solid phase-immobilized uridinyl-amine intermediate, which can be used as a starting point for diversity-oriented synthesis. We demonstrate the generation of five series of uridinyl nucleoside analogs for investigating inhibitor structure-activity relationships. This library was screened for inhibition of representative enzymes from three functional families including a phosphoglycosyl transferase, a UDP-aminosugar acetyltransferase, and a glycosyltransferase. These candidates were taken from the Gram-negative bacteria Campylobacter concisus and Campylobacter jejuni and the Gram-positive bacterium Clostridium difficile, respectively. Inhibition studies show that specific compound series preferentially inhibit selected enzymes, with IC50 values ranging from 35 ± 7 μM to 174 ± 21 μM. Insights from the screen provide a strong foundation for further structural elaboration, to improve potency, which will be enabled by the same synthetic strategy. The solid-phase strategy was also used to synthesize pseudouridine analogs of lead compounds. Finally, the compounds were found to be nontoxic to mammalian cells, further supporting the opportunities for future development.
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Affiliation(s)
- Amaël G. E. Madec
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nathaniel S. Schocker
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Silvano Sanchini
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gadam Myratgeldiyev
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Debasis Das
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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10
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Palladium-catalyzed site-selective hydrogen isotope exchange (HIE) reaction of arylsulfonamides using amino acid auxiliary. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Zappa F, Failli M, De Matteis MA. The Golgi complex in disease and therapy. Curr Opin Cell Biol 2018; 50:102-116. [PMID: 29614425 DOI: 10.1016/j.ceb.2018.03.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/02/2018] [Accepted: 03/11/2018] [Indexed: 10/17/2022]
Abstract
The Golgi complex occupies a strategic position in the endomembrane system and acts not only as a key trafficking and sorting station and a vital biosynthetic center for glycoproteins and lipids, but also as an active signaling hub. As such, the Golgi complex participates in the establishment and maintenance of cell compartmentalization and in general, cell processes such as cell growth and apoptosis. The different functions of the Golgi complex are executed by composite molecular machineries that have been exhaustively dissected over the last three decades. These machineries can become dysfunctional as a result of mutations in the respective encoding genes or may be hijacked by infectious agents or misregulated in the course of multifactorial diseases such as neurodegeneration and cancer. Small molecules targeting components of these machineries have been instrumental in dissecting their functions in in vitro studies and some of them have been developed or are currently under development for clinical use.
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Affiliation(s)
- Francesca Zappa
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy
| | - Mario Failli
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy; Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy.
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12
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Abstract
Nucleic acids and carbohydrates are essential biomolecules involved in numerous biological and pathological processes. Development of multifunctional building blocks based on nucleosides and sugars is in high demand for the generation of novel oligonucleotide mimics and glycoconjugates for biomedical applications. Recently, aminooxyl-functionalized compounds have attracted increasing research interest because of their easy derivatization through oxime ligation or N-oxyamide formation reactions. Various biological applications have been reported for O-amino carbohydrate- and nucleoside-derived compounds. Here, we report our efforts in the design and synthesis of glyco-, glycosyl, nucleoside- and nucleo-aminooxy acid derivatives from readily available sugars and amino acids, and their use for the generation of N-oxyamide-linked oligosaccharides, glycopeptides, glycolipids, oligonucleosides and nucleopeptides as novel glycoconjugates or oligonucleotide mimics. Delicate and key points in the synthesis will be emphasized.
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13
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Malkowski SN, Dishuck CF, Lamanilao GG, Embry CP, Grubb CS, Cafiero M, Peterson LW. Design, Modeling and Synthesis of 1,2,3-Triazole-Linked Nucleoside-Amino Acid Conjugates as Potential Antibacterial Agents. Molecules 2017; 22:molecules22101682. [PMID: 28994722 PMCID: PMC6151744 DOI: 10.3390/molecules22101682] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 09/27/2017] [Accepted: 10/03/2017] [Indexed: 02/01/2023] Open
Abstract
Copper-catalyzed azide-alkyne cycloadditions (CuAAC or click chemistry) are convenient methods to easily couple various pharmacophores or bioactive molecules. A new series of 1,2,3-triazole-linked nucleoside-amino acid conjugates have been designed and synthesized in 57–76% yields using CuAAC. The azido group was introduced on the 5′-position of uridine or the acyclic analogue using the tosyl-azide exchange method and alkylated serine or proparylglycine was the alkyne. Modeling studies of the conjugates in the active site of LpxC indicate they have promise as antibacterial agents.
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Affiliation(s)
- Sarah N Malkowski
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Carolyn F Dishuck
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Gene G Lamanilao
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Carter P Embry
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Christopher S Grubb
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Mauricio Cafiero
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN 38112, USA.
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14
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Denisov MS, Gorbunov AA, Nebogatikov VO, Pavlogradskaya LV, Glushkov VA. Two-step synthesis of ferrocenyl esters of vanillic acid. RUSS J GEN CHEM+ 2017. [DOI: 10.1134/s107036321703015x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Ghiselli G. Drug-Mediated Regulation of Glycosaminoglycan Biosynthesis. Med Res Rev 2016; 37:1051-1094. [DOI: 10.1002/med.21429] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Giancarlo Ghiselli
- Glyconova Srl; Parco Scientifico Silvano Fumero; Via Ribes 5 Colleretto Giacosa, (TO) Italy
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16
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Bartee D, Morris F, Al-Khouja A, Freel Meyers CL. Hydroxybenzaldoximes Are D-GAP-Competitive Inhibitors of E. coli 1-Deoxy-D-Xylulose-5-Phosphate Synthase. Chembiochem 2015; 16:1771-81. [PMID: 26174207 PMCID: PMC4609000 DOI: 10.1002/cbic.201500119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/05/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase is the first enzyme in the methylerythritol phosphate pathway to essential isoprenoids in pathogenic bacteria and apicomplexan parasites. In bacterial pathogens, DXP lies at a metabolic branch point, serving also as a precursor in the biosynthesis of vitamins B1 and B6, which are critical for central metabolism. In an effort to identify new bisubstrate analogue inhibitors that exploit the large active site and distinct mechanism of DXP synthase, a library of aryl mixed oximes was prepared and evaluated. Trihydroxybenzaldoximes emerged as reversible, low-micromolar inhibitors, competitive against D-glyceraldehyde 3-phosphate (D-GAP) and either uncompetitive or noncompetitive against pyruvate. Hydroxybenzaldoximes are the first class of D-GAP-competitive DXP synthase inhibitors, offering new tools for mechanistic studies of DXP synthase and a new direction for the development of antimicrobial agents targeting isoprenoid biosynthesis.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Francine Morris
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
- Present address: Albert Einstein College of Medicine, Department of Biochemistry, 1301 Morris Park Avenue, Bronx, NY 10461 (USA)
| | - Amer Al-Khouja
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA).
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17
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Vasconcelos-Dos-Santos A, Oliveira IA, Lucena MC, Mantuano NR, Whelan SA, Dias WB, Todeschini AR. Biosynthetic Machinery Involved in Aberrant Glycosylation: Promising Targets for Developing of Drugs Against Cancer. Front Oncol 2015; 5:138. [PMID: 26161361 PMCID: PMC4479729 DOI: 10.3389/fonc.2015.00138] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/02/2015] [Indexed: 12/22/2022] Open
Abstract
Cancer cells depend on altered metabolism and nutrient uptake to generate and keep the malignant phenotype. The hexosamine biosynthetic pathway is a branch of glucose metabolism that produces UDP-GlcNAc and its derivatives, UDP-GalNAc and CMP-Neu5Ac and donor substrates used in the production of glycoproteins and glycolipids. Growing evidence demonstrates that alteration of the pool of activated substrates might lead to different glycosylation and cell signaling. It is already well established that aberrant glycosylation can modulate tumor growth and malignant transformation in different cancer types. Therefore, biosynthetic machinery involved in the assembly of aberrant glycans are becoming prominent targets for anti-tumor drugs. This review describes three classes of glycosylation, O-GlcNAcylation, N-linked, and mucin type O-linked glycosylation, involved in tumor progression, their biosynthesis and highlights the available inhibitors as potential anti-tumor drugs.
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Affiliation(s)
| | - Isadora A Oliveira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Miguel Clodomiro Lucena
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Natalia Rodrigues Mantuano
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Stephen A Whelan
- Department of Biochemistry, Cardiovascular Proteomics Center, Boston University School of Medicine , Boston, MA , USA
| | - Wagner Barbosa Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
| | - Adriane Regina Todeschini
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brasil
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18
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Moukha-Chafiq O, Reynolds RC. Synthesis and general biological activity of a small adenosine-5'-(carboxamide and sulfanilamide) library. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:709-29. [PMID: 25295748 DOI: 10.1080/15257770.2014.931588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A small library of fifty-five adenosine peptide analogs was synthesized, under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative, from 2',3'-O-isopropylideneadenosine-5'-carboxylic acid 2. The coupling of amine or sulfanilamide reactants to the free 5'-carboxylic acid moiety of 2, in automated solution-phase fashion, led after acid-mediated hydrolysis to target compounds 3-57 in good yields and high purity. No marked anticancer or antimalarial activity was noted on preliminary cellular testing. Initial screening through the MLPCN program, however, indicates that these analogs may show diverse and interesting biological activities.
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Affiliation(s)
- Omar Moukha-Chafiq
- a Southern Research Institute , Drug Discovery Division , Birmingham , Alabama , USA
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19
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Moukha-Chafiq O, Reynolds RC. Synthesis of novel peptidyl adenosine antibiotic analogs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 33:53-63. [PMID: 24660880 DOI: 10.1080/15257770.2013.866243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A small library of peptidyl adenosine antibiotic analogs was synthesized, under the Pilot Scale Library Program of the NIH Roadmap initiative, from 2',3'-O-isoproylideneadenosine-5'-carboxylic acid 2 in excellent yield. The coupling of the amino terminus of L-2-aminophenylbutyric methyl ester to a free 5'-carboxylic acid moiety of 2 followed by sodium hydroxide treatment led to carboxylic acid analog 4. Hydrolysis of this latter gave unprotected nucleoside analog 5. Intermediate 4 served as the precursor for the preparation of novel peptidyl adenosine analogs 6-18 in good yields and high purity through peptide coupling reactions to diverse amine derivatives. No marked anticancer and antimalaria activity was noted on preliminary cellular testing; however these analogs should be useful candidates for other types of biological activity.
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Affiliation(s)
- Omar Moukha-Chafiq
- a Southern Research Institute, Drug Discovery Division , Birmingham , AL 35205 , USA
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20
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Conway LP, Delley RJ, Neville J, Freeman GR, Maple HJ, Chan V, Hall AJ, Hodgson DRW. The aqueous N-phosphorylation and N-thiophosphorylation of aminonucleosides. RSC Adv 2014. [DOI: 10.1039/c4ra08317b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Moukha-chafiq O, Reynolds RC. Parallel solution-phase synthesis and general biological activity of a uridine antibiotic analog library. ACS COMBINATORIAL SCIENCE 2014; 16:232-7. [PMID: 24661222 PMCID: PMC4025591 DOI: 10.1021/co4001452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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A small library of ninety four uridine antibiotic analogs was synthesized,
under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative,
from amine 2 and carboxylic acids 33 and 77 in solution-phase fashion. Diverse aldehyde, sulfonyl chloride,
and carboxylic acid reactant sets were condensed to 2, leading after acid-mediated hydrolysis, to the targeted compounds 3–32 in good yields and high purity. Similarly,
treatment of 33 with diverse amines and sulfonamides
gave 34–75. The coupling of the amino
terminus of d-phenylalanine methyl ester to the free 5′-carboxylic
acid moiety of 33 followed by sodium hydroxide treatment
led to carboxylic acid analog 77. Hydrolysis of this
material gave analog 78. The intermediate 77 served as the precursor for the preparation of novel dipeptidyl
uridine analogs 79–99 through peptide
coupling reactions to diverse amine reactants. None of the described
compounds show significant anticancer or antimalarial acivity. A number
of samples exhibited a variety of promising inhibitory, agonist, antagonist,
or activator properties with enzymes and receptors in primary screens
supplied and reported through the NIH MLPCN program.
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Affiliation(s)
- Omar Moukha-chafiq
- Southern Research Institute, Drug Discovery Division, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Southern Research Institute, Drug Discovery Division, Birmingham, Alabama 35205, United States
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22
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The endoplasmic reticulum-resident chaperone heat shock protein 47 protects the Golgi apparatus from the effects of O-glycosylation inhibition. PLoS One 2013; 8:e69732. [PMID: 23922785 PMCID: PMC3726774 DOI: 10.1371/journal.pone.0069732] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 06/11/2013] [Indexed: 02/07/2023] Open
Abstract
The Golgi apparatus is important for the transport of secretory cargo. Glycosylation is a major post-translational event. Recognition of O-glycans on proteins is necessary for glycoprotein trafficking. In this study, specific inhibition of O-glycosylation (Golgi stress) induced the expression of endoplasmic reticulum (ER)-resident heat shock protein (HSP) 47 in NIH3T3 cells, although cell death was not induced by Golgi stress alone. When HSP47 expression was downregulated by siRNA, inhibition of O-glycosylation caused cell death. Three days after the induction of Golgi stress, the Golgi apparatus was disassembled, many vacuoles appeared near the Golgi apparatus and extended into the cytoplasm, the nuclei had split, and cell death assay-positive cells appeared. Six hours after the induction of Golgi stress, HSP47-knockdown cells exhibited increased cleavage of Golgi-resident caspase-2. Furthermore, activation of mitochondrial caspase-9 and ER-resident unfolded protein response (UPR)-related molecules and efflux of cytochrome c from the mitochondria to the cytoplasm was observed in HSP47-knockdown cells 24 h after the induction of Golgi stress. These findings indicate that (i) the ER-resident chaperon HSP47 protected cells from Golgi stress, and (ii) Golgi stress-induced cell death caused by the inhibition of HSP47 expression resulted from caspase-2 activation in the Golgi apparatus, extending to the ER and mitochondria.
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23
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McCorvie TJ, Timson DJ. In silico prediction of the effects of mutations in the human UDP-galactose 4'-epimerase gene: towards a predictive framework for type III galactosemia. Gene 2013; 524:95-104. [PMID: 23644136 DOI: 10.1016/j.gene.2013.04.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/30/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
The enzyme UDP-galactose 4'-epimerase (GALE) catalyses the reversible epimerisation of both UDP-galactose and UDP-N-acetyl-galactosamine. Deficiency of the human enzyme (hGALE) is associated with type III galactosemia. The majority of known mutations in hGALE are missense and private thus making clinical guidance difficult. In this study a bioinformatics approach was employed to analyse the structural effects due to each mutation using both the UDP-glucose and UDP-N-acetylglucosamine bound structures of the wild-type protein. Changes to the enzyme's overall stability, substrate/cofactor binding and propensity to aggregate were also predicted. These predictions were found to be in good agreement with previous in vitro and in vivo studies when data was available and allowed for the differentiation of those mutants that severely impair the enzyme's activity against UDP-galactose. Next this combination of techniques were applied to another twenty-six reported variants from the NCBI dbSNP database that have yet to be studied to predict their effects. This identified p.I14T, p.R184H and p.G302R as likely severely impairing mutations. Although severely impaired mutants were predicted to decrease the protein's stability, overall predicted stability changes only weakly correlated with residual activity against UDP-galactose. This suggests other protein functions such as changes in cofactor and substrate binding may also contribute to the mechanism of impairment. Finally this investigation shows that this combination of different in silico approaches is useful in predicting the effects of mutations and that it could be the basis of an initial prediction of likely clinical severity when new hGALE mutants are discovered.
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Affiliation(s)
- Thomas J McCorvie
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
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24
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Moukha-chafiq O, Reynolds RC. Parallel solution-phase synthesis of an adenosine antibiotic analog library. ACS COMBINATORIAL SCIENCE 2013; 15:147-52. [PMID: 23398694 DOI: 10.1021/co300127z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A library of eighty one adenosine antibiotic analogs was prepared under the Pilot Scale Library Program of the NIH Roadmap initiative from 5'-amino-5'-deoxy-2',3'-O-isopropylidene-adenosine 3. Diverse aldehyde, sulfonyl chloride and carboxylic acid reactant sets were condensed to 3, in solution-phase fashion, leading after acid-mediated hydrolysis to the targeted compounds in good yields and high purity. No marked antituberculosis or anticancer activity was noted on preliminary cellular testing, but these nucleoside analogs should be useful candidates for other types of biological activity.
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Affiliation(s)
- Omar Moukha-chafiq
- Southern Research Institute, Drug Discovery Division,
Birmingham, Al 35205
| | - Robert C. Reynolds
- Southern Research Institute, Drug Discovery Division,
Birmingham, Al 35205
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25
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Duan X, Cai L, Lee LA, Chen H, Wang Q. Incorporation of azide sugar analogue decreases tumorigenic potential of breast cancer cells by reducing cancer stem cell population. Sci China Chem 2013. [DOI: 10.1007/s11426-012-4806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Gong W, Desaulniers JP. Synthesis and properties of RNAs that contain a PNA-RNA dimer. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:389-400. [PMID: 22497254 DOI: 10.1080/15257770.2012.666609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A practical synthesis of a peptide nucleic acid unit combined with an RNA nucleoside (PNA-RNA dimer) is reported. The dimer unit was placed within an RNA oligonucleotide via phosphoramidite chemistry and melting temperature data indicate destabilization relative to a native RNA duplex. Circular dichroism indicates that the overall shape of the duplex remains intact. This PNA-RNA dimer unit will permit future investigations within RNA-based systems, such as RNA interference.
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Affiliation(s)
- Wei Gong
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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27
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da Rocha DR, Santos WC, Lima ES, Ferreira VF. Synthesis of 1,2,3-triazole glycoconjugates as inhibitors of α-glucosidases. Carbohydr Res 2012; 350:14-9. [DOI: 10.1016/j.carres.2011.12.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/22/2011] [Accepted: 12/25/2011] [Indexed: 10/14/2022]
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28
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M. Takacs J, C. Thacker N, Molnár-Tóth J, L. Miska J, G. Barletta R. Preparation of D-Cycloserine and 13C-Labeled D-Cycloserine. HETEROCYCLES 2012. [DOI: 10.3987/com-12-12553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Suchý M, Milne M, Li AX, McVicar N, Dodd DW, Bartha R, Hudson RHE. Mono- and Tetraalkyne Modified Ligands and Their Eu3+ Complexes - Utilizing “Click” Chemistry to Expand the Scope of Conjugation Chemistry. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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30
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Shen F, Li X, Zhang X, Qin Z, Yin Q, Chen H, Zhang J. Synthesis of 1-Aryl-1H
-indazoles via a Ligand-Free Copper- Catalyzed Intramolecular Amination Reaction. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Zhang W, Ntai I, Bolla ML, Malcolmson SJ, Kahne D, Kelleher NL, Walsh CT. Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics. J Am Chem Soc 2011; 133:5240-3. [PMID: 21417270 DOI: 10.1021/ja2011109] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pacidamycins are a family of uridyl peptide antibiotics that inhibit the translocase MraY, an essential enzyme in bacterial cell wall biosynthesis that to date has not been clinically targeted. The pacidamycin structural skeleton contains a doubly inverted peptidyl chain with a β-peptide and a ureido linkage as well as a 3'-deoxyuridine nucleoside attached to DABA(3) of the peptidyl chain via an enamide linkage. Although the biosynthetic gene cluster for pacidamycins was identified recently, the assembly line of this group of peptidyl nucleoside antibiotics remained poorly understood because of the highly dissociated nature of the encoded nonribosomal peptide synthetase (NRPS) domains and modules. This work has identified a minimum set of enzymes needed for generation of the pacidamycin scaffold from amino acid and nucleoside monomers, highlighting a freestanding thiolation (T) domain (PacH) as a key carrier component in the peptidyl chain assembly as well as a freestanding condensation (C) domain (PacI) catalyzing the release of the assembled peptide by a nucleoside moiety. On the basis of the substrate promiscuity of this enzymatic assembly line, several pacidamycin analogues were produced using in vitro total biosynthesis.
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Affiliation(s)
- Wenjun Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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32
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Shen F, Li X, Zhang X, Yin Q, Qin Z, Chen H, Zhang J, Ma Z. Microwave-assisted synthesis of dinucleoside analogues containing a thiazolidin-4-one linkage via one-pot tandem Staudinger/aza-Wittig/cyclization. Org Biomol Chem 2011; 9:5766-72. [DOI: 10.1039/c1ob05675a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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33
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Niewiadomski S, Beebeejaun Z, Denton H, Smith TK, Morris RJ, Wagner GK. Rationally designed squaryldiamides - a novel class of sugar-nucleotide mimics? Org Biomol Chem 2010; 8:3488-99. [PMID: 20532300 DOI: 10.1039/c004165c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar-nucleotides such as GDP-mannose, GDP-fucose and UDP-glucose are important biomolecules with a central role in carbohydrate and glycoconjugate biosynthesis, metabolism and cell signalling. Analogues and mimics of naturally occurring sugar-nucleotides are sought after as chemical tools and inhibitor candidates for sugar-nucleotide-dependent enzymes including glycosyltransferases. Many sugar-nucleotides bind to their target glycosyltransferases via coordination of the diphosphate group to a divalent metal cofactor in the active site. The identification of uncharged, chemically stable surrogates for the diphosphate group, with the ability to coordinate to a divalent metal, is therefore an important design criteria for the development of sugar-nucleotide mimics. Here, we describe the rational design and synthesis of a novel class of sugar-nucleotide mimics based on a squaryldiamide scaffold, an uncharged phosphate isostere. We demonstrate by comprehensive NMR titration experiments that the new sugar-nucleotide mimics coordinate efficiently to Mg(2+), and provide results from biological studies with a therapeutically relevant mannosyltransferase from Trypanosoma brucei. Our findings suggest that squaryldiamides are a promising template for the development of sugar-nucleotide mimics, and illustrate the considerable potential of the squarylamide group as a fragment for inhibitor design.
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34
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Trunkfield AE, Gurcha SS, Besra GS, Bugg TD. Inhibition of Escherichia coli glycosyltransferase MurG and Mycobacterium tuberculosis Gal transferase by uridine-linked transition state mimics. Bioorg Med Chem 2010; 18:2651-63. [PMID: 20226679 PMCID: PMC3034214 DOI: 10.1016/j.bmc.2010.02.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 01/07/2010] [Accepted: 02/16/2010] [Indexed: 11/01/2022]
Abstract
Glycosyltransferase MurG catalyses the transfer of N-acetyl-d-glucosamine to lipid intermediate I on the bacterial peptidoglycan biosynthesis pathway, and is a target for development of new antibacterial agents. A transition state mimic was designed for MurG, containing a functionalised proline, linked through the alpha-carboxylic acid, via a spacer, to a uridine nucleoside. A set of 15 functionalised prolines were synthesised, using a convergent dipolar cycloaddition reaction, which were coupled via either a glycine, proline, sarcosine, or diester linkage to the 5'-position of uridine. The library of 18 final compounds were tested as inhibitors of Escherichia coli glycosyltransferase MurG. Ten compounds showed inhibition of MurG at 1mM concentration, the most active with IC(50) 400microM. The library was also tested against Mycobacterium tuberculosis galactosyltransferase GlfT2, and one compound showed effective inhibition at 1mM concentration.
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Affiliation(s)
- Amy E. Trunkfield
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sudagar S. Gurcha
- Department of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Gurdyal S. Besra
- Department of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Timothy D.H. Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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35
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Thirumalairajan S, Mahaney B, Bearne SL. Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6. Chem Commun (Camb) 2010; 46:3158-60. [PMID: 20424759 DOI: 10.1039/b926894d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An analogue of orotidine 5'-monophosphate (OMP), 6-phosphonouridine 5'-monophosphate is a competitive inhibitor of OMP decarboxylase from E. coli, binding with an affinity similar to that of OMP. Hence the active site is capable of stabilizing negative charge distributed out of the plane of the pyrimidine ring, consistent with the notion of ground state destabilization.
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Affiliation(s)
- Srinath Thirumalairajan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
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36
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Tóth M, Somsák L. 5'-Uridyl derivatives of N-glycosyl allophanic acid and biuret. Carbohydr Res 2010; 345:163-7. [PMID: 19896644 DOI: 10.1016/j.carres.2009.08.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/24/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
Abstract
(2',3'-O-Isopropylidene-5'-uridyl) 4-(2,3,4,6-tetra-O-acetyl-beta-d-glycopyranosyl)allophanates were obtained in the reactions of 2',3'-O-isopropylidene-uridine and O-peracetylated beta-d-gluco-, galacto- and xylopyranosylamines, and OCNCOCl. 2,3,4,6-Tetra-O-acetyl-beta-d-glucopyranosyl isocyanate and N-(2',3'-O-isopropylidene-5'-uridyl)urea gave 1-(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)-5-(2',3'-O-isopropylidene-5'-uridyl)biuret. Deprotection of the beta-d-gluco configured allophanate and biuret was carried out by standard methods.
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Affiliation(s)
- Marietta Tóth
- Department of Organic Chemistry, University of Debrecen, POB 20, H-4010 Debrecen, Hungary
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37
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Patsos G, Corfield A. Management of the human mucosal defensive barrier: evidence for glycan legislation. Biol Chem 2009; 390:581-90. [DOI: 10.1515/bc.2009.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractThe human gastrointestinal barrier comprises several layers which enable protection against the external environment. The mucosal epithelium, lamina propria, glycocalyx and secreted mucus each make a contribution to barrier protection. Glycocalyx and secreted mucins constitute a glycosylated environment which interacts with the enteric microflora. Turnover of the mucus layer and the creation of binding ligands for bacteria are significant factors in gut homeostasis. The gut microbiota is composed of many bacterial species, but improved technology has allowed detection of populations present at different stages of development and in disease. Interaction of the microflora with the gut occurs from birth onwards and enables maturation of gut angiogenesis and glycosylation as demonstrated in mouse models. Glycan legislation regulates the ongoing interaction between the microflora and the host mucosa. This accounts for host glycosylation mechanisms providing a dynamic response to fluctuations in the gut microflora. Evidence for glycan legislation is based on a surgical model where intact mucosa can be compared with and without contact to the faecal microflora. In addition, mucosal cell glycosylation is assessed using inhibitors of O-glycan synthesis. These inhibitors lead to growth arrest in cultured colorectal cancer cell lines through the induction of apoptosis and downregulation of proliferation.
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38
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Seo S, Lewin HA. Reconstruction of metabolic pathways for the cattle genome. BMC SYSTEMS BIOLOGY 2009; 3:33. [PMID: 19284618 PMCID: PMC2669051 DOI: 10.1186/1752-0509-3-33] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/12/2009] [Indexed: 01/21/2023]
Abstract
Background Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement. Results An amalgamated cattle genome database was created using the NCBI and Ensembl cattle genome databases (based on build 3.1) as data sources. PathwayTools was used to create a cattle-specific pathway genome database, which was followed by comprehensive manual curation for the reconstruction of metabolic pathways. The curated database, CattleCyc 1.0, consists of 217 metabolic pathways. A total of 64 mammalian-specific metabolic pathways were modified from the reference pathways in MetaCyc, and two pathways previously identified but missing from MetaCyc were added. Comparative analysis of metabolic pathways revealed the absence of mammalian genes for 22 metabolic enzymes whose activity was reported in the literature. We also identified six human metabolic protein-coding genes for which the cattle ortholog is missing from the sequence assembly. Conclusion CattleCyc is a powerful tool for understanding the biology of ruminants and other cetartiodactyl species. In addition, the approach used to develop CattleCyc provides a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. It is clear that metabolic pathway analysis strongly reflects the quality of the underlying genome annotations. Thus, having well-annotated genomes from many mammalian species hosted in BioCyc will facilitate the comparative analysis of metabolic pathways among different species and a systems approach to comparative physiology.
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Affiliation(s)
- Seongwon Seo
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA.
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39
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Yeoh KK, Butters TD, Wilkinson BL, Fairbanks AJ. Probing replacement of pyrophosphate via click chemistry; synthesis of UDP-sugar analogues as potential glycosyl transferase inhibitors. Carbohydr Res 2009; 344:586-91. [PMID: 19233348 DOI: 10.1016/j.carres.2009.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 12/11/2008] [Accepted: 01/06/2009] [Indexed: 11/17/2022]
Abstract
A series of potential UDP-sugar mimics were readily synthesised by copper(I) catalysed modified Huisgen cycloaddition of the corresponding alpha-propargyl glycosides with 5-azido uridine in aqueous solution. None of the compounds accessed displayed significant inhibitory activity at concentrations of up to 4.5mM in an assay against bovine milk beta-1,4-galactosyltransferase.
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Affiliation(s)
- Kar Kheng Yeoh
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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40
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Patsos G, Hebbe-Viton V, Robbe-Masselot C, Masselot D, San Martin R, Greenwood R, Paraskeva C, Klein A, Graessmann M, Michalski JC, Gallagher T, Corfield A. O-glycan inhibitors generate aryl-glycans, induce apoptosis and lead to growth inhibition in colorectal cancer cell lines. Glycobiology 2009; 19:382-98. [PMID: 19122213 DOI: 10.1093/glycob/cwn149] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Our studies provide direct evidence that O-glycosylation pathways play a role in the regulation of cell growth through apoptosis and proliferation pathways. A series of small molecular weight analogs of the GalNAc-alpha-1-O-serine/threonine structure based on 1-benzyl-2-acetamido-2-deoxy-alpha-O-d-galactopyranoside have been synthesized and tested in the human colorectal cancer cell lines PC/AA/C1/SB10C and HCA7/C29. Three inhibitors, 1-benzyl-2-acetamido-2-deoxy-alpha-O-D-galactopyranoside, and the corresponding 2-azido- and C-glycoside analogs were screened in these colorectal cancer cell lines at 0.5 mM and showed induction of apoptosis and downregulation of proliferation. Treatment of both cell lines with inhibitors led to changes in glycosylation detected with peanut lectin. The inhibition of glycosyltransferase activity in cell homogenates from human colorectal mucosal cells and cultured cell lines could be shown. The competitive action of the inhibitors resulted in the intracellular formation of 28 aryl-glycan products which were identified by MALDI and electrospray mass spectroscopy. The structures showed a differential pattern for each of the inhibitors in both cell lines. Gene array analysis of the glycogenes illustrated a pattern of glycosyltransferases that matched the glycan structures found in glycoproteins and aryl-glycans formed in the PC/AA/C1/SB10C cells; however, there was no action of the three inhibitors on glycogene transcript levels. The inhibitors act at both intermediary metabolic and genomic levels, resulting in altered protein glycosylation and aryl-glycan formation. These events may play a part in growth arrest.
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Affiliation(s)
- Georgios Patsos
- Department of Clinical Science, University of Bristol, Bristol BS8 1TH, UK
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41
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Chiang LW, Pei K, Chen SW, Huang HL, Lin KJ, Yen TC, Yu CS. Combining a Solution-Phase Derived Library with In-Situ Cellular Bioassay: Prompt Screening of Amide-Forming Minilibraries Using MTT Assay. Chem Pharm Bull (Tokyo) 2009; 57:714-8. [DOI: 10.1248/cpb.57.714] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Li-Wu Chiang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University
| | - Kai Pei
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University
| | - Shao-Wei Chen
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University
| | - Ho-Lien Huang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University
| | - Kun-Ju Lin
- Department of Nuclear Medicine, Chang-Gung Memorial Hospital
| | - Tzu-Chen Yen
- Department of Nuclear Medicine, Chang-Gung Memorial Hospital
| | - Chung-Shan Yu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University
- Institute of Nuclear Engineering and Science, National Tsing-Hua University
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42
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Copper catalyzed 1,3-dipolar cycloaddition reaction of azides with N-(2-trifluoroacetylaryl)propargylamines. J Fluor Chem 2008. [DOI: 10.1016/j.jfluchem.2008.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Babič A, Gobec S, Gravier-Pelletier C, Le Merrer Y, Pečar S. Synthesis of 1-C-linked diphosphate analogues of UDP-N-Ac-glucosamine and UDP-N-Ac-muramic acid. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Brown JR, Crawford BE, Esko JD. Glycan antagonists and inhibitors: a fount for drug discovery. Crit Rev Biochem Mol Biol 2008; 42:481-515. [PMID: 18066955 DOI: 10.1080/10409230701751611] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycans, the carbohydrate chains of glycoproteins, proteoglycans, and glycolipids, represent a relatively unexploited area for drug development compared with other macromolecules. This review describes the major classes of glycans synthesized by animal cells, their mode of assembly, and available inhibitors for blocking their biosynthesis and function. Many of these agents have proven useful for studying the biological activities of glycans in isolated cells, during embryological development, and in physiology. Some are being used to develop drugs for treating metabolic disorders, cancer, and infection, suggesting that glycans are excellent targets for future drug development.
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45
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The role of GlcNAc in formation and function of extracellular matrices. Comp Biochem Physiol B Biochem Mol Biol 2008; 149:215-26. [DOI: 10.1016/j.cbpb.2007.10.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 10/17/2007] [Accepted: 10/17/2007] [Indexed: 01/27/2023]
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46
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Williams AH, Raetz CRH. Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase. Proc Natl Acad Sci U S A 2007; 104:13543-50. [PMID: 17698807 PMCID: PMC1959417 DOI: 10.1073/pnas.0705833104] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
UDP-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes the first step of lipid A biosynthesis, the reversible transfer of the R-3-hydroxyacyl chain from R-3-hydroxyacyl acyl carrier protein to the glucosamine 3-OH group of UDP-GlcNAc. Escherichia coli LpxA is highly selective for R-3-hydroxymyristate. The crystal structure of the E. coli LpxA homotrimer, determined previously in the absence of lipid substrates or products, revealed that LpxA contains an unusual, left-handed parallel beta-helix fold. We have now solved the crystal structures of E. coli LpxA with the bound product UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc at a resolution of 1.74 A and with bound UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc at 1.85 A. The structures of these complexes are consistent with the catalytic mechanism deduced by mutagenesis and with a recent 3.0-A structure of LpxA with bound UDP-GlcNAc. Our structures show how LpxA selects for 14-carbon R-3-hydroxyacyl chains and reveal two modes of UDP binding.
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Affiliation(s)
- Allison H. Williams
- Department of Biochemistry, Duke University Medical Center, Box 3711 DUMC, Durham, NC 27710
| | - Christian R. H. Raetz
- Department of Biochemistry, Duke University Medical Center, Box 3711 DUMC, Durham, NC 27710
- *To whom correspondence should be addressed. E-mail:
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47
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Sivapriya K, Suguna P, Shubashree S, Sridhar PR, Chandrasekaran S. Novel chalcogenides of thymidine and uridine: synthesis, properties and applications. Carbohydr Res 2007; 342:1151-8. [PMID: 17397814 DOI: 10.1016/j.carres.2007.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 02/19/2007] [Accepted: 03/10/2007] [Indexed: 11/27/2022]
Abstract
A facile and efficient methodology has been developed for the synthesis of dithymidine and di-uridine derived disulfides using benzyltriethylammonium tetrathiomolybdate as a sulfur transfer reagent. However, a similar reaction of thymidine derivative with tetraethylammonium tetraselenotungstate as a selenium transfer reagent resulted in the formation of an unexpected cyclic diselenide. The disulfide derivatives of nucleosides have been used as precursors in a tandem disulfide cleavage-Michael addition/ring opening reactions to construct aminoacid and carbocyclic derivatives of nucleosides.
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Affiliation(s)
- Kirubakaran Sivapriya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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48
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Chung R, Anderson KS. Alternative synthetic routes to 2′,3′-didehydro-2′,3′-dideoxy-5-hydroxymethyluridine. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Urbaniak MD, Tabudravu JN, Msaki A, Matera KM, Brenk R, Jaspars M, Ferguson MAJ. Identification of novel inhibitors of UDP-Glc 4′-epimerase, a validated drug target for african sleeping sickness. Bioorg Med Chem Lett 2006; 16:5744-7. [PMID: 16962325 DOI: 10.1016/j.bmcl.2006.08.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Revised: 08/22/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
Novel inhibitors of Trypanosoma brucei and mammalian UDP-Glc 4'-epimerase were identified by screening a small library of natural products and commercially available drug-like molecules. The inhibitors possess low micromolar potency against the T. brucei and human enzymes in vitro, display a degree of selectivity between the two enzymes, and are cytotoxic to cultured T. brucei and mammalian cells.
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Affiliation(s)
- Michael D Urbaniak
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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50
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Vidal S, Bruyère I, Malleron A, Augé C, Praly JP. Non-isosteric C-glycosyl analogues of natural nucleotide diphosphate sugars as glycosyltransferase inhibitors. Bioorg Med Chem 2006; 14:7293-301. [PMID: 16843664 DOI: 10.1016/j.bmc.2006.06.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 06/13/2006] [Accepted: 06/23/2006] [Indexed: 11/26/2022]
Abstract
A series of C-glycosyl ethylphosphonophosphate analogues of UDP-Glc, UDP-Gal, UDP-GlcNAc and GDP-Fuc were synthesized from the corresponding C-glycosyl ethylphosphonic acids. Analogues were obtained as alpha-anomers through either diastereoselective photo-induced radical addition of glycosyl bromides (D-Glc, D-Gal and L-Fuc) to diethyl vinylphosphonate, or a multi-step sequence (D-GlcNAc), with subsequent coupling with morpholidate-activated nucleotide monophosphates. The in vitro inhibitory activity of UDP-Gal, GDP-Fuc and UDP-GlcNAc analogues towards glycosyltransferases (beta-1,4-GalT, FUT3 and LgtA) was evaluated through a competition fluorescence assay and IC(50) values of 40 microM, 2 mM and 3.5 mM were obtained, respectively.
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Affiliation(s)
- Sébastien Vidal
- Laboratoire de Chimie Organique 2, UMR-CNRS 5181, Université Claude Bernard Lyon 1, CPE-Lyon Bâtiment 308, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France
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