Volume 1
Preface xxv
List of Contributors xxvii
1 Synthetic Methodologies 1
Chikako Saotome and
Osamu Kanie
1.1 Introduction 1
1.2 Tactical Analysis for Overall Synthetic Efficiency 1
1.3 Methodological Improvements 2
1.4 Accessibility 11
1.5 Concluding Remarks 32
1.6 References 33
2 Complex Carbohydrate Synthesis 37
Makoto
Kiso, Hideharu Ishida, and Hiromune Ando
2.1 Introduction 37
2.2 Synthetic Gangliosides 38
2.3 Toxin Receptor 50
2.4 Summary and Perspectives 52
2.5 References 52
3 The Chemistry of Sialic Acid 55
Geert-Jan
Boons and Alexei V. Demchenko
3.1 Introduction 55
3.2 Chemical and Enzymatic Synthesis of Sialic Acids 56
3.3 Chemical Glycosidation of Sialic Acids 59
3.4 Enzymatic Glycosidations of Sialic Acids 83
3.5 Synthesis of C- and S-Glycosides of Sialic Acid 91
3.6 Modifications at N-5 94
3.7 References 95
4 Solid-Phase Oligosaccharide Synthesis
103
Peter H. Seeberger
4.1 Introduction 103
4.2 Pioneering Efforts in Solid-Phase Oligosaccharide Synthesis 104
4.3 Synthetic Strategies 105
4.4 Support Materials 107
4.5 Linkers 108
4.6 Synthesis of Oligosaccharides on Solid Support by Use of Different Glycosylating Agents 112
4.7 Automated Solid-Phase Oligosaccharide Synthesis 118
4.8 Conclusion and Outlook 124
4.9 References 125
5 Solution and Polymer-Supported Synthesis of
Carbohydrates 129
Shin-Ichiro Nishimura
5.1 Introduction 129
5.2 Mimicking Glycoprotein Biosynthetic Systems 130
5.3 References 136
6 Enzymatic Synthesis of Oligosaccharides
Jianbo
Zhang, Jun Shao, Prezemk Kowal, and Peng George Wang
6.1 Introduction 137
6.2 Sugar Nucleotide Biosynthetic Pathways 140
6.3 Enzymatic Oligosaccharide Synthesis Processes 151
6.4 Future Directions 162
6.5 References 162
7 Glycopeptides and Glycoproteins: Synthetic Chemistry and
Biology 169
Oliver Seitz
7.1 Introduction 169
7.2 The Glycosidic Linkage 169
7.3 The Challenges of Glycopeptide Synthesis 171
7.4 Synthesis of Preformed Glycosyl Amino Acids 173
7.5 Synthesis of Glycopeptides 181
7.6 Biological and Biophysical Studies 200
7.7 Summary and Outlook 208
7.8 References 209
8 Synthesis of Complex Carbohydrates: Everninomicin
13,384-1 215
K. C. Nicolaou, Helen J. Mitchell, and
Scott A. Snyder
8.1 Introduction 215
8.2 Retrosynthetic Analysis and Strategy 218
8.3 Total Synthesis of Everninomicin 13,384-1 (1) 223
8.4 Conclusion 249
8.5 References 250
9 Chemical Synthesis of Asparagine-Linked Glycoprotein
Oligosaccharides: Recent Examples 253
Yukishige Ito
and Ichiro Matsuo
9.1 Introduction 253
9.2 Synthesis of Asn-Linked Oligosaccharides: Basic Principles 257
9.3 Chemical Synthesis of Complex Oligosaccharides 261
9.4 References 278
10 Chemistry and Biochemistry of Asparagine-Linked Protein
Glycosylation 281
Barbara Imperiali and Vincent W.-F.
Tai
10.1 Protein Glycosylation 281
10.2 Small-Molecule Probes of the Biochemistry of Oligosaccharyl Transferase 283
10.3 Conclusions 301
10.4 References 301
11 Conformational Analysis of C-Glycosides and Related
Compounds: Programming Conformational Profiles of C- and
O-Glycosides 305
Peter G. Goekjian, Alexander Wei,
and Yoshito Kishi
11.1 Introduction 305
11.2 Stereoelectronic Effects and te exo-Anomeric Conformation 306
11.3 Conformational Analysis of C-Glycosides: C-Monoglycosides 309
11.4 1,4-Linked C-Disaccharides: the Importance of syn-Pentane Interactions 314
11.5 Prediction of Conformational Preference and Experimental Validation 318
11.6 Programming Oligosaccharide Conformation 322
11.7 Conformational Design of C-Trisaccharides based on a Human Blood Group Antigen 323
11.8 Conformational Design: Relationship to Biological Activity 330
11.9 Concluding Remarks 336
11.10 Acknowledgements 337
11.11 References 337
12 Synthetic Lipid A Antagonists for Sepsis Treatment
341
William J. Christ, Lynn D. Hawkins, Michael D. Lewis,
and Yoshito Kishi
12.1 Background 341
12.2 Hypothesis and Approach 342
12.3 Conclusion 351
12.4 Acknowledgement 353
12.5 References 353
13 Polysialic Acid Vaccines 357
Harold J.
Jennings
13.1 Introduction 357
13.2 Group C Meningococcal Vaccines 358
13.3 Group B Meningococcal Vaccines 362
13.4 Chemically Modified Group B Meningococcal Vaccines 366
13.5 Cancer Vaccines 371
13.6 Acknowledgements 375
13.7 References 375
14 Synthetic Carbohydrate-Based Vaccines
381
Stacy J. Keding and Samuel J. Danishefsky
14.1 Introduction 381
14.2 Cancer Vaccines 382
14.3 Bacterial Polysaccharide Vaccines 397
14.4 Synthetic Parasitic Polysaccharide Conjugate Vaccine 402
14.5 Conclusions 403
14.6 References 403
15 Chemistry, Biochemistry, and Pharmaceutical Potentials of
Glycosaminoglycans and Related Saccharides
407
Tasneem Islam and Robert J. Linhardt
15.1 Introduction 407
15.2 Dermatan and Chondroitin Sulfates 417
15.3 Hyaluronan 419
15.4 Keratan Sulfate 423
15.5 Other Acidic Polysaccharides 425
15.6 Pharmaceutical Potential and Challenges 430
15.7 Conclusion 432
15.8 References 433
16 A New Generation of Antithrombotics Based on Synthetic
Oligosaccharides 441
Maurice Petitou and Jean-Marc
Herbert
16.1 Introduction 441
16.2 Heparin and Its Mechanism of Action as an Antithrombotic Agent 442
16.3 Synthetic Pentasaccharides, Selective Factor Xa Inhibitors, are Antithrombotic Agents 446
16.4 Synthetic Thrombin-Inhibiting Oligosaccharides: The Next Generation? 452
16.5 The Mechanism of Antithrombin Activation by Synthetic Oligosaccharides 456
16.6 Conclusion and Perspectives 456
16.7 References 457
Volume 2
17 Sequencing of Oligosaccharides and Glycoproteins
461
Stuart M. Haslam, Kay-Hooi Khoo, and Anne Dell
17.1 Mass Spectrometry 462
17.2 MS-Based Sequencing Strategies 466
17.3 Glycan Sequencing and Structural Determination – A Case Study 470
17.4 Mammalian Glycomics 475
17.5 Some Special Case Strategies 477
17.6 References 481
18 Preparation of Heterocyclic 2-Deoxystreptamine
Aminoglycoside Analogues and Characterization of their Interaction
with RNAs by Use of Electrospray Ionization Mass Spectrometry
483
Richard H. Griffey, Steven A. Hofstadler, and Eric E.
Swayze
18.1 Introduction 483
18.2 ESI-MS for Characterization of Aminoglycoside-RNA Interactions 484
18.3 Preparation of Heterocyclic 2-Deoxystreptamines and Binding to a 16S A Site RNA Model 490
18.4 Preparation, Binding, and Biological Activity of Substituted Paromomycin Derivatives 495
18.5 Future Prospects 498
18.6 Acknowledgements 498
18.7 References 498
19 Glycosylation Analysis of a Recombinant P-Selectin
Antagonist by High-pH Anion-Exchange Chromatography with Pulsed
Electrochemical Detection (HPAEC/PED) 501
Mark R.
Hardy and Richard J. Cornell
19.1 Introduction 501
19.2 Use of HPAEC/PED in the Development of Biopharmaceuticals 502
19.3 Biology of P-Selectin 503
19.4 HPAEC/PED as an Adjunct to rPSGL-Ig Process Development 504
19.5 Results and Discussion 508
19.6 Summary 515
19.7 Acknowledgements 516
19.8 References 516
20 Analytical Techniques for the Characterization and
Sequencing of Glycosaminoglycans 517
Ram
Sasisekharan, Zachary Shriver, Mallik Sundaram, and Ganesh
Venkataraman
20.1 Introduction to GAG Linear Complex Polysaccharides 517
20.2 Depolymerization of Nascent GAG Chains 521
20.4 Analytical Tools Used in the Structural Characterization of GAGs 527
20.5 Future Directions 536
20.6 Acknowledgements 537
20.7 References 537
21 Thermodynamic Models of the Multivalency Effect
541
Pavel I. Kitov and David R. Bundle
21.1 Introduction 541
21.2 Concept of Distribution Free Energy 542
21.3 Multivalent Receptor vs. Monovalent Ligand 546
21.4 Multivalent Receptor vs. Multivalent Ligand 551
21.5 Topological Classification of Multivalent Systems 553
21.6 Determination of Microscopic Binding Parameters by Molecular Modeling 555
21.7 Determination of Microscopic Binding Parameters from Binding Data 561
21.8 Thermodynamic Analysis of Multivalent Interaction 562
21.9 Conclusions 570
21.10 Mathematical Appendix 570
21.10.1 Calculation of Statistical Coefficients 570
21.10.2 Multivalent Receptor and Monovalent Ligand 571
21.10.3 Multivalent Binding with Linear and Circular Topology 571
21.10.4 Multivalent Binding with Radial Topology 572
21.10.5 Derivation of Eq. (24) 572
21.11 References 573
22 Synthetic Multivalent Carbohydrate Ligands as Effectors or
Inhibitors of Biological Processes 575
Laura L.
Kiessling, Jason K. Pontrello, and Michael C. Schuster
22.1 Introduction 575
22.2 Multivalent Carbohydrate Ligands as Inhibitors 581
22.3 Multivalent Carbohydrate Ligands as Effectors 596
22.4 Conclusions 605
22.5 References 605
23 Glycosyltransferase Inhibitors
609
Karl-Heinz Jung and Richard R. Schmidt
23.1 Introduction 609
23.2 Glycosyltransferases Utilizing NDP-Sugar Donors 610
23.3 Glycosyltransferases Utilizing NMP-Sugar Donors 641
23.4 Bisubstrate Analogues as Inhibitors 648
23.5 Conclusion 653
23.6 References 654
24 RNA-Aminoglycoside Interactions 661
Haim
Weizman and Yitzhak Tor
24.1 RNA as an Emerging Therapeutic Target 661
24.2 Aminoglycoside Antibiotics: Past and Present 664
24.3 Aminoglycosides as RNA Binders 666
24.4 Identifying RNA Targets and Developing Binding Assays 670
24.5 Dimeric Aminoglycosides 673
24.6 Aminoglycoside-Intercalator Conjugates 675
24.7 Guanidinoglycosides 677
24.8 Summary and Outlook 679
24.9 Acknowledgements 680
24.10 References 680
25 Glycosylated Natural Products 685
Jon S.
Thorson and Thomas Vogt
25.1 Introduction 685
25.2 A Summary of Bioactive Glycosylated Secondary Metabolites 686
25.3 Conclusions 707
25.4 References 707
26 Novel Enzymatic Mechanisms in the Biosynthesis of Unusual
Sugars 713
Alexander Wong, Xuemei He, and Hung-Wen
Liu
26.1 Introduction 713
26.2 Biosynthesis of Deoxysugars 714
26.3 Biosynthesis of Aminosugars 725
26.4 Biosynthesis of Branched-Chain Sugars 730
26.5 Epimerization Reactions 734
26.6 Rearrangement of Hexose Skeletons: UDP-Galactopyranose Mutase-Catalyzed Biosynthesis of Galactofuranose 738
26.7 Summary 740
26.8 Acknowledgements 741
26.9 References 741
27 Neoglycolipids: Identification of Functional Carbohydrate
Epitopes 747
Ten Feizi, Alexander M. Lawson, and
Wengang Chai
27.1 Rationale for Developing Neoglycolipids as Oligosaccharide Probes 747
27.2 The First and Second Generation Neoglycolipids 749
27.3 Mass Spectrometry of Neoglycolipids 750
27.4 Scope of the Neoglycolipid Technology 752
27.5 Oligosaccharide Microarrays 755
27.6 Summary and Perspectives 757
27.7 Acknowledgement 757
27.8 References 757
28 A Preamble to Aglycone Reconstruction for
Membrane-Presented Glycolipid Mimics
761
Murugesapillai Mylvaganam and Clifford A.
Lingwood
28.1 Introduction 761
28.2 The Role of Ceramide Subtype Composition 762
28.3 Effects of Ceramide Subtype Composition in the Binding of Gb3Cer to Verotoxins 764
28.4 Hypothesis Regarding Lipid Replacement Structural Motifs (LRSMs) 766
28.5 Effect of Replacement of GSL Fatty Acyl Chains with Rigid, Non-Planar Hydrophobic Groups 768
28.6 Ada-Gb3Cer, a Functional Mimic of Membrane Presented Gb3Cer for VT Binding 769
28.7 Ceramide Subtype-Dependent Binding of Heat Shock Protein Hsp70 to Sulfogalactosyl Ceramide 772
28.8 Adamantyl-Acyl Ceramide is a Functional Replacement for a Ceramide-Cholesterol Composition: A Study with HIV Coat Protein gp120 775
28.9 Acknowledgement 777
28.10 References 777
29 Small Molecule Inhibitors of the Sulfotransferases
781
Dawn E. Verdugo, Lars C. Pedersen, and Carolyn R.
Bertozzi
29.1 Introduction: Sulfotransferases and the Biology of Sulfation 781
29.2 EST as a Model ST for Inhibitor Design 783
29.3 Inhibition of Representative Golgi-Resident Sulfotransferases: GST-2, GST-3, and TPST-2 792
29.4 Assays for High-Throughput Screening of STs 794
29.5 New Directions in Inhibitor Discovery 796
29.6 Conclusions 796
29.7 Acknowledgements 796
29.8 References 797
30 Carbohydrate-Based Treatment of Cancer Metastasis
803
Reiji Kannagi
30.1 Implication of Carbohydrate Determinants in Cancer Metastasis 803
30.2 Tumor Angiogenesis and Cancer-Endothelial Interaction 808
30.3 Use of Monoclonal Antibodies for Inhibition of Cancer Cell-Endothelial Interaction 809
30.4 Inhibitors of Selectin-Mediated Cell Adhesion 812
30.5 Regulation of Selectin Expression on Endothelial Cells 814
30.6 Enhanced Expression of Sialyl Lex and Sialyl Lea in Malignant Cells and its Modulation 816
30.7 References 824
31 N-Acetylneuraminic Acid Derivatives and Mimetics as
Anti-Influenza Agents 831
Robin Thomson and Mark von
Itzstein
31.1 Introduction 831
31.2 Structure-Based Design of Inhibitors of Influenza Virus Sialidase 836
31.3 Structure/Activity Relationship Studies of N-Acetylneuraminic Acid-Based Influenza Virus Sialidase Inhibitors 840
31.4 Concluding Remarks 856
31.5 Acknowledgements 856
31.6 References 857
32 Modified and Modifying Sugars as a New Tool for the
Development of Therapeutic Agents – The Biochemically Engineered
N-Acyl Side Chain of Sialic Acid: Biological Implications and
Possible Uses in Medicine 863
Rüdiger Horstkorte,
Oliver T. Keppler, and Werner Reutter
32.1 Introduction 863
32.2 N-Acyl Side Chain-Modified Precursors of Sialic Acid 865
32.3 Outlook 871
32.4 Acknowledgements 872
32.5 Abbreviations 872
32.6 References 872
33 Modified and Modifying Sugars as a New Tool for the
Development of Therapeutic Agents – Glycosidated Phospholipids as a
New Type of Antiproliferative Agents 875
Kerstin
Danker, Annette Fischer, and Werner Reutter
33.1 Introduction 875
33.2 Structures of Synthetic Glycosidated Phospholipid Analogues 876
33.3 Antiproliferative Effect and Cytotoxicity of Glycosidated Phospholipid Analogues in Cell Culture Systems 876
33.4 Effect of Glycosidated Phospholipid Analogues on Cell Matrix Adhesion 878
33.5 Mechanisms of Action 879
33.6 Outlook and New Developments 880
33.7 Acknowledgements 881
33.8 References 881
34 Glycoside Primers and Inhibitors of Glycosylation
883
Jillian R. Brown, Mark M. Fuster, and Jeffrey D.
Esko
34.1 Introduction 883
34.2 Glycoside-Based Substrates 883
34.3 Glycoside Primers – Xylosides 884
34.4 Other Types of Primers 885
34.5 Glycosides as Metabolic Decoys 888
34.6 Analogues 890
34.7 References 892
35 Carbohydrate-Based Drug Discovery in the Battle Against
Bacterial Infections: New Opportunities Arising from Programmable
One-Pot Oligosaccharide Synthesis 899
Thomas K.
Ritter and Chi-Huey Wong
35.1 Introduction 899
35.2 Cell-Surface Carbohydrates 900
35.3 Peptidoglycan 904
35.4 Macrolide Antibiotics 913
35.5 Aminoglycosides 917
35.6 Programmable One-Pot Oligosaccharide Synthesis 922
35.7 Summary 927
35.8 References 928
Subject Index 933
Professor Chi-Huey Wong received his B.S. and M.S. degrees from
National Taiwan University, and Ph.D. in Chemistry (with George
Whitesides) from Massachusetts Institute of Technology in 1982. He
started his independent career as Assistant Professor of Chemistry
at Texas A&M University in 1983, where he became Full Professor
in 1987. He has been Professor and Ernest W. Hahn Chair in
Chemistry at the Scripps Research Institute since 1989 and is also
a member of the Skaggs Institute for Chemical Biology since
1996.
Professor Wong is a member of the U.S. National Academy of Sciences
and the American Academy of Arts and Sciences. He is a recipient of
The Searle Scholar Award in Biomedical Sciences (1985), the
Presidential Young Investigator Award in Chemistry (1986), the
American Chemical Society A.C. Cope Scholar Award (1993), the Roy
Whistler Award of the International Carbohydrate Organization
(1994), the American Chemical Society Harrison Howe Award in
Chemistry (1998) and the Claude S. Hudson Award in Carbohydrate
Chemistry (1999), the International Enzyme Engineering Award (1999)
and the Presidential Green Chemistry Challenge Award (2000). He is
a member of Academia Sinica, Taipei (1994), the American Academy of
Arts and Sciences (1996) and the US National Academy of Sciences
(2002). He serves as editor-in-chief of Bioorganic and Medicinal
Chemistry and is an executive board member of the Tetrahedron
Publications. He was head of the Frontier Research Program on
Glycotechnology at RIKEN (Institute of Physical and Chemical
Research, Japan) (1991-1999) and is currently a scientific advisor
of the Max-Planck Institute, a board member of the U.S. National
Research Council on Chemical Sciences and Technology, and is a
founding scientist of Optimer Pharmaceuticals, Inc. He is author
and co-author of over 450 publications, 60 patents and several
books.
His current interests are in the areas of bioorganic and synthetic
chemistry and biocatalysis, including development of new synthetic
chemistry based on enzymatic and chemo-enzymatic reactions,
synthetic approach to carbohydrate-mediated biological recognition,
design and synthesis of mechanism-based inhibitors of enzymes, RNA
and carbohydrate receptors, development of oligosaccharide and
aminoglycoside microarrays for high-throughput screening and the
study of reaction mechanisms.
"In summary, Carbohydrate-Based Drug Discovery Vols. 1 and 2
provide an appropriate and useful look at the current state of the
art in this relevant and rapidly advancing field. I recommend the
book to both experts and less expert readers."
Francesco Nicotra, Universita di Milano-Bicocca (Italy)
ChemBioChem 4/2004
"To summarize, the work provides a comprehensive and excellent
survey of the present situation in carbohydrate research, in which
many interesting details can be spotted. Because of the wide range
of topics covered, the reader will refer to it again and again. It
is likely to become a standard work on the subject, not exclusively
for carbohydrate chemistry enthusiasts."
Oliver Plettenburg, Ulrich Stilz
Angewandte Chemie + IE 2004-43/31
"Leser mit soliden organisch-chemischen Kenntnissen werden ihre
wahre Freude an diesem spannenden Einblick in die moderne
Zuckerchemie haben."
BioTec März/April 2004
"Zusammenfassend stellt dieses Werk einerseits eine nahezu
unerschöpfliche Quelle für den Chemiker und Forscher/Entwickler in
der Pharmazeutischen Industrie dar. Andererseits zeigt es aber auch
dem Mediziner, Pharmazeuten und Naturwissenschaftler neue,
innovative Wege und Tendenzen...auf."
A. Schmidt
Der Mikrobiologe
"Insgesamt ist das vorliegende Werk eine umfassende und sehr
gelungene Zusammenstellung des aktuellen Standes der
Kohlenhydratforschung, in der es viel zu entdecken gibt. Der
Facettenreichtum des diskutierten Stoffes wird den Leser immer
wieder zu den beiden Bänden greifen lassen. Nicht nur für Freunde
der Zuckerchemie sollte Carbohydrate-based Drug Discovery zu einem
Standardwerk werden."
Oliver Plettenburg, Ulrich Stilz
Angewandte Chemie + IE 2004-43/31
"Professionalität und ein gutes wissenschaftliches Netzwerk zahlen
sich für die Qualität eines derartig innovativen Werkes einer noch
etwas stiefmütterlich behandelten Richtung der Wissenschaft
nachhaltig aus."
A. Schmidt
Arzneimittel-Forschung / Drug Research 8/04
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