Bioorganic Chemistry Highlights and New Aspects

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Edition: 1st
Format: Paperback
Pub. Date: 1999-12-16
Publisher(s): Wiley-VCH
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Summary

The understanding of (patho)physiological processes - the biosynthesis of biomolecules such as enzymes, nucleic acids, and secondary metabolites; the pathways of signaltransduction; or the function of pharmaceutical agents - is of increasing importance not only for drug research but also for the development of new synthetic methods in organic chemistry and biochemistry. In a truly interdisciplinary way bioorganic chemistry unites the central questions of biochemistry, medicinal chemistry, organic chemistry, and spectroscopy. This book fills a void in this rapidly growing field of chemistry and gives a thorough yet understandable introduction for advanced students and researchers alike. Contributions of more than sixty scientists provide a topical overview of recent advances in: drug development based on natural products; the biosynthesis, activity, and application of enzymes; carbohydrates; peptides; nucleic acids; analytical methods in bioorganic chemistry. This book will be an appetizer for all - students and researchers alike - seeking orientation in this fascinating field of chemistry.

Author Biography

>Ulf Diederichsen studied Chemistry in Freiburg, Germany, with a diploma work in organic synthesis and completed his Ph.D. in 1993 under the supervision of Albert Eschenmoser at the ETH Zürich working on homo- and glucose-DNA. Following postdoctoral work on radical chemistry at the University of Pittsburgh, USA, in the group of Dennis Curran, he gained his habilitation at the Technical University Munich, Germany, with Horst Kessler as mentor. In 1999, he was appointed professor of Organic Chemistry at the University Würzburg, Germany, until joining the Georg-August-University in Göttingen, Germany, in 2001 as full professor of Organic Chemistry. He was visiting professor at the LMU Munich and Goering Visiting Professor at the University of Wisconsin, USA. In 1999 he got the Karl Winnacker stipend and Hellmut-Bredereck award and is an ordinary member of Göttingen Academy of Sciences and Humanities since 2012

Table of Contents

Natural Products and Drug Research
1(78)
Structural diversity of surface lipids from spiders
1(7)
Stefan Schulz
Chemistry of marine pyrrole-imidazole alkaloids
8(10)
Thomas Lindel
Holger Hoffmann
Matthias Hochgurtel
Synthesis of non-cyclized pyrrole-imidazole alkaloids
9(4)
Synthesis of the cyclized oroidin skeleton
13(5)
Natural products and their role in pesticide discovery
18(10)
Robert Velten
Hubert Dyker
Matthias Gehling
Oliver Gutbrod
Folker Lieb
Andreas Schoop
Cripowellin--microderivatization
18(2)
Rocaglamide -- synthesis towards new analogs
20(2)
Pyrenocine -- total synthesis of analogs
22(2)
PF 1022A -- synthesis of an aza analog of the cyclodepsipeptide
24(4)
Common principles in marginolactone (macrolactone) biosynthesis
28(10)
Marion Zerlin
Ralf Thiericke
Biosynthetic building blocks
28(3)
Biosynthetic relationships
31(2)
Common principles
33(3)
Manipulation of the metabolite pattern
36(2)
Synthesis and biological activity of leukotriene derivatives
38(5)
Stefan Jaroch
Bernd Buchmann
Werner Skuballa
Diazoketones - versatile starting materials for the diastereoselective synthesis of β-lactams
43(5)
Joachim Podlech
Michael R. Linder
Preparation of β-lactams
43(3)
Mechanistic Considerations
46(2)
Selenium compounds in chemical and biochemical oxidation reactions
48(5)
Gianfranco Fragale
Sara Hauptli
Michele Leuenberger
Thomas Wirth
Synthetic routes to oligo-tetrahydrofurans and oligo-pyrrolidines
53(7)
Ulrich Koert
Glycosphingolipids of myelin: Potential target antigens of demyelinating antibody activity in multiple sclerosis
60(6)
Eckhard Kirschning
Rudolf Dernick
Binding of human mAbs to surface antigens of cultured brain cells
61(1)
Reaction pattern of autoantibody DS1F8 with intracellular antigens
62(1)
Reaction pattern of mAb DS1F8 with purified lipids in ELISA
62(1)
Conclusions
63(3)
Combinatorial chemistry for the identification of novel bioactive compounds
66(6)
Andreas L. Marzinzik
Eduard R. Felder
Combinatorial chemistry in drug discovery
66(1)
Molecular diversity on rigid scaffolds
67(1)
Solid-phase synthesis toward multiple core structures
68(4)
Supramolecular polymer chemistry based on multiple hydrogen bonding
72(7)
Ronald F.M. Lange
E.W. Meijer
Enzymatic Synthesis and Biotransformation
79(54)
Enzymatic C--C coupling: The development of aromatic prenylation for organic synthesis
79(10)
Ludger Wessjohann
Bernd Sontag
Marco-Aurelio Dessoy
Prenyl transferases
80(2)
Production, stability and substrate specificity of `ubiA-prenyltransferase'
82(2)
Parametrization and scale-up
84(2)
Conclusion and Outlook
86(3)
Are there enzyme-catalyzed Diels--Alder reactions? An investigation into the polyketide-synthase system required for the biosynthesis of cytochalasans
89(6)
Alfons Hadener
Gilles Ritter
Patrick M. Schaeffer
N. Patrick J. Stamford
Screening of blocked mutants of Zygosporium masonii
89(1)
Synthesis of derivatives of putative early polyketide intermediates and incorporation experiments
90(2)
Towards the characterization of the PKS gene cluster associated with cytochalasin D biosynthesis in Z. masonii
92(3)
The truth about enzymatic halogenation in bacteria
95(7)
Karl-Heinz van Pee
Haloperoxidases
95(3)
Haloperoxidases and halometabolite biosynthesis
98(1)
The search for new, specific halogenases
98(4)
Enzymatic Baeyer--Villiger oxidation with cyclohexanone monooxygenase: A new system of cofactor regeneration
102(9)
Marina Vogel
Ulrich Schwarz-Linek
Cyclohexanone monooxygenase
103(1)
A new method of NADPH regeneration
103(2)
Baeyer--Villiger oxidation with the system cyclohexanone monooxygenase/formate dehydrogenase
105(1)
Optimization of the reaction conditions
105(1)
Application of the new coupled enzyme system
106(5)
The synthesis of optically active [2.2]paracyclophanes by biotransformations
111(10)
Markus Pietzsch
Henning Hopf
Preparation of optically active planar chiral paracyclophanes
111(1)
Biocatalysis in the enantioselective preparation of cyclophanes
111(2)
Biotransformation of monosubstituted [2.2]paracyclophanes
113(1)
Bioreduction of 4-formyl[2.2]paracyclophane 1
113(1)
Synthesis of 4-hydroxy[2.2]paracyclophane 3 using hydrolases
114(3)
Synthesis of optically active disubstituted [2.2]paracyclophanes
117(1)
Screening for bioreduction and hydrolytic activity
118(1)
Chemoenzymatic synthesis of 5-formyl-4-hydroxy[2.2]paracyclophane (6)
119(2)
Multivariate analysis of biotransformations for a more effective strain selection (Intelligent screening)
121(6)
Wolf-Rainer Abraham
Oxidation of eugenol
123(1)
Enantiomer separation
123(1)
Hydration of trans-nerolidol
124(1)
Epoxidation of trans-nerolidol
124(1)
Hydroxylation of aristolenepoxide
125(1)
Monoterpene alcohols
125(2)
Extending the applicability of lipases and esterases for organic synthesis
127(6)
Uwe T. Bornscheuer
Results
127(1)
Resolution of a Bryostatin 1 building block
127(1)
Directed evolution of an esterase
128(5)
Carbohydrate Chemistry and Glycobiology
133(52)
Multivalent neoglycoconjugates for the inhibition of mannose-sensitive carbohydrate-protein interactions
133(18)
Thisbe K. Lindhorst
Multivalency in carbohydrate-protein interactions
133(1)
Synthesis of multivalent neoglycoconjugates
134(1)
Chemistries for glycocluster synthesis
134(1)
Core molecules for glycocluster and glycodendrimer synthesis
135(5)
Synthesis of mannose-containing glycoclusters and glycodendrimers
140(3)
Testing of the antiadhesive properties of synthetic α-mannosyl clusters
143(6)
Conclusion
149(2)
Octyl O- and S-glycosides related to the GPI anchor of Trypanosoma brucei as probes for in vitro galactosylation by trypanosomal α-galactosyltransferases
151(9)
Thomas Ziegler
Ralf Dettmann
Michael Duszenko
Results and discussion
152(1)
Synthesis of acceptors
152(2)
Enzymatic α-galactosylation
154(3)
Preparation of trypanosome membrane fractions
157(3)
Convenient synthesis of C-branched carbohydrates from glycals
160(6)
Thomas Sommermann
Michael Maurer
Torsten Linker
Manganese(III) acetate-mediated additions
160(1)
Ceric(IV) ammonium nitrate (CAN)-mediated additions
161(1)
Mechanistic considerations
161(2)
Addition of malonates in the presence of nucleophiles
163(1)
Conclusion
164(2)
Enzymatic tools for the synthesis of nucleotide (deoxy)sugars
166(6)
Lothar Elling
Enzymatic synthesis of nucleotide (deoxy)sugars from sucrose
166(1)
In situ regeneration of UDP-D-galactose from sucrose
167(2)
Enzymatic synthesis of GDP-D-mannose from d-mannose
169(3)
The enzyme dTDP-glucose-4, 6-dehydratase as a tool for the synthesis of deoxy sugars
172(13)
Werner Klaffke
Syntheses
174(7)
Synthesis of dTDP-ascarylose
181(2)
Conclusion
183(2)
Peptide Chemistry and Applications
185(48)
α,α-Disubstituted amino acids and bicyclic lactams: Potential building blocks for the synthesis of peptide mimics
185(8)
Bernhard Westermann
Nicole Diedrichs
Ina Gedrath
Armin Walter
Synthesis of enantiomerically pure β-ketoesters and derivatives via enzyme-catalyzed kinetic resolutions
186(1)
Synthesis of α,α-disubstituted amino acids
187(1)
Synthesis of bicyclic turn mimetics
188(1)
Synthesis of bicyclic lactams
188(1)
Synthesis of bridged tetrapeptides
189(4)
β-Amino acids as building blocks for peptide modification
193(8)
Norbert Sewald
β-Amino acids in medicinal chemistry - a brief survey
193(1)
Do β-amino acids induce secondary structure elements?
194(1)
Synthesis of enantiomerically pure β-amino acids
195(2)
Cyclic RGD peptides containing β-amino acids
197(4)
Reactions of chelated amino acid ester enolates and their application to natural product synthesis
201(6)
Uli Kazmaier
Asymmetric aldol reactions
202(1)
Asymmetric chelate Claisen rearrangements
203(1)
Chelate Claisen rearrangements of chiral esters
203(1)
Chelate Claisen rearrangements in the presence of chiral ligands
204(3)
Cyclodepsipeptides: From natural product to anthelmin-tically active synthetic enniatins
207(8)
Peter Jeschke
Winfried Etzel
Achim Harder
Michael Schindler
Axel Gohrt
Ulrich Pleiβ
Horst Kleinkauf
Rainer Zocher
Gerhard Thielking
Wolfgang Gau
Gerhard Bonse
Total synthesis of enniatins
207(1)
Optimization strategy of enniatins
208(4)
NMR spectroscopic investigations of enniatins
212(1)
Synthesis of a tritium labeled enniatin
212(1)
Enzymatic biosynthesis of (R)-lactic acid containing enniatins
213(1)
Conclusions and outlook
213(2)
Artificial biomimetic receptor molecules
215(10)
Thomas Schrader
Michael Herm
Christian Kirsten
Synthetic adrenaline receptors
215(1)
Recognition of amino alcohols
215(2)
Recognition of the catechole
217(2)
Biomimetic and chiral recognition of adrenaline
219(1)
Conclusions and perspectives
220(1)
Synthetic peptide receptors
221(1)
Intermolecular β-sheet stabilization
221(2)
Conclusions and perspectives
223(2)
Design and synthesis of modulators of sphingolipid biosynthesis
225(8)
Christoph Arenz
Athanassios Giannis
The need for synthetic modulators of sphingolipid biosynthesis
225(2)
The concept
227(1)
Results and discussion
227(1)
Results
227(3)
Discussion
230(3)
Nucleic Acid Chemistry: Mechanisms and Mimetics
233(58)
Structural alterations of the isopolar phosphonate bond in nucleotide and oligonucleotide analogs
233(9)
Magdalena Endova
Sarka Kralikova
Radek Liboska
Miroslav Otmar
Dominik Rejman
Zdenek Tocik
Ivan Rosenberg
5-(Adenin-9-yl)pentofuranosylphosphonates and 2-(adenin-9-yl)cycloalkyloxymethanephosphonates
233(2)
O-Phosphonomethylnucleosides
235(1)
O-Phosphonoalkylidenenucleosides
236(1)
5'-C and 3'-C-phosphorylnucleosides
237(1)
5'-Deoxy-4'-phoshonomethoxynucleosides
237(1)
O-Phosphonomethyl group in oligonucleotides
238(2)
Conclusions
240(2)
DNA Repair: From model compounds to artificial enzymes
242(13)
Thomas Carell
Lars Burgdorf
Jens Butenandt
Robert Epple
Anja Schwogler
The degradation and repair of the genetic information
242(1)
DNA Photolyase Repair Enzymes
242(3)
Mechanistic investigations with model compounds
245(1)
General aspects and cleavage assay
245(2)
pH-Dependency of the cleavage reaction
247(1)
Solvent dependency of the cleavage reaction
248(1)
The role of the second cofactor
249(1)
Bis-deazaflavin model systems
249(1)
Mixed flavin and deazaflavin model systems
250(1)
Future directions
251(1)
The third generation model compounds
251(1)
Towards artificial DNA photolyases
252(3)
Alanyl-PNA: A model system for DNA using a linear peptide backbone as scaffold
255(7)
Ulf Diederichsen
Alanyl pepeptide nucleic acid (PNA): constitution and model for duplex formation
255(1)
Pairing properties of analyl-PNA
256(2)
Analyl-PNA: A DNA i-motif analog
258(1)
Intercalation to alanyl-PNA
259(1)
Amino acid side chain-nucleobase interactions
260(2)
New PNA buildings block for antisense research
262(10)
Stephan Jordan
Christoph Schwemler
Synthesis of new PNAs
263(2)
Properties of the new homo-oligomers
265(1)
Synthesis and properties of hetero-oligomers
266(3)
Future improvements
269(3)
RNAse active site model systems
272(9)
Markus Kalesse
Thorsten Oost
Studies on hairpin ribozymes
281(10)
Sabine Muller
Design of the HpH5 ribozyme and its substrate
283(1)
Preparation of ribozymes
284(1)
Synthesis of substrate RNAs
285(1)
Quantitative assay of ribozyme activity
286(1)
Kinetic analysis of HpH5 ribozyme cleavage
287(4)
Biosynthetic Pathways and Biochemistry
291(67)
Neuropeptide Y: A molecule for hunger, stress and memory
291(7)
Annette G. Beck-Sickinger
Chiara Cabrele
Richard Soll
What is neuropeptide Y?
291(1)
What are the molecular targets of neuropeptide Y?
292(1)
What can we learn from structure-activity studies?
293(1)
Analogues of neuropeptide Y: Which amino acids are essential?
294(1)
Segments of the peptide - how do we get them active as well?
294(1)
Centrally truncated peptides: NPY analogs that miss the middle segment
295(1)
Why do we work with neuropeptide Y?
296(2)
Biosynthetic studies on deoxysugars: Implications for enzyme-mediated synthesis of deoxyoligosaccharides
298(7)
Andreas Kirschning
Carsten Oelkers
Monika Ries
Andreas Schonberger
Sven-Eric Wohlert
Jurgen Rohr
Background
298(1)
Synthesis of deuterated deoxysugars
299(2)
Biosynthetic studies
301(1)
Conclusions
302(3)
Investigations on the biosynthesis of landomycin A
305(8)
Sven-Eric Wohlert
Andreas Bechthold
Claus Beninga
Thomas Henkel
Meike Holzenkampfer
Andreas Kirschning
Carsten Oelkers
Monika Ries
Susanne Weber
Ulrike Weiβbach
Lucia Westrich
Jurgen Rohr
Landomycins - an introduction
305(1)
Biosynthetic studies on the aglycone moiety
305(2)
Biosynthetic studies on the deoxyoligosaccharide chain
307(1)
Biosynthetic studies on the single deoxysugar building blocks
308(5)
Oligosacharide antibiotics: Perspective for combinatorial biosynthesis
313(9)
Andreas Bechthold
Jurgen Rohr
Avilamycin A
313(1)
Landomycin and urdamycins
313(3)
Results of investigations
316(1)
Preparation and screening of cosmid libraries
316(1)
Gene function
316(4)
Perspectives
320(2)
Biosynthesis of plant xanthones
322(7)
Ludger Beerhues
Wagner Barillas
Stefan Peters
Werner Schmidt
Xanthone biosynthesis in Centaurium erythraea
322(2)
Xanthone biosynthesis in Hypericum androsaemum
324(5)
Screening of peptide libraries for the identification of mimotopes which crossreact with antibody epitopes
329(8)
Christoph Seidel
Michael Grol
Hans-Georg Batz
Jens Schneider-Mergener
Ricardo Cortese
Rob Meloen
Peptide libraries
329(1)
Materials and methods
330(1)
Monoclonal antibody anti-Troponin T M7
330(1)
Monoclonal antibody anti-CK-MB M-6.12.47
330(1)
Monoclonal antibody anti-CK-MB M-7.4.5
330(1)
Free peptide model libraries for iterative and positional scanning processes [2,4]
330(1)
Cellulose membrane bound peptide libraries [3]
331(1)
Phage display library
331(1)
Screening methods
332(1)
Biosensor experiments [8]
332(1)
Results
332(3)
Discussion
335(2)
Probes for DNA base flipping by DNA methyltransferases
337(9)
Birgit Holz
Elmar Weinhold
DNA methyltransferases and the biological role of DNA methylation
337(1)
DNA base flipping as observed in X-ray structures of DNA methyltransferases
338(1)
2-Aminopurine in DNA as fluorescent probe for DNA base flipping
338(1)
Detection of DNA base flipping
339(1)
Kinetics of DNA base flipping
340(2)
Tighter binding of modified DNA to DNA methyltransferases
342(1)
Binding of duplex ODNs containing a mismatched target base
342(1)
Binding of duplex ODNs containing an abasic site
342(1)
Chemical detection of extrahelical bases in DNA---Mtase complexes
343(1)
Other DNA-modifying enzymes using a DNA base flipping mechanism
344(2)
Manipulating intracellular signal transduction
346(12)
Carsten Schultz
Andrew Schnaars
Marco T. Rudolf
Methodology
346(1)
Confirming known messenger functions
347(2)
New messenger functions
349(4)
Drug development
353(2)
Conclusions, questions, and perspectives
355(3)
Physical and Analytical Methods
358(73)
Adventures with atomic force microscopy
358(7)
Chris Abell
Rachel McKendry
Trevor Rayment
Atomic force microscopy (AFM)
359(1)
Biological imaging
360(1)
Chemical force microscopy (CFM)
361(1)
Chiral discrimination by chemical force microscopy
362(1)
Future directions
363(2)
Marine natural products: New ways in the constitutional assignment
365(14)
Matthias Kock
Jochen Junker
Constitutional assignment by NMR spectroscopy
365(3)
ADEQUATE - New NMR experiments for the constitutional assignment
368(3)
COCON - Translation of NMR correlation data into moelcular constitutions
371(1)
Constitutional assignment of marine natural products
371(4)
Summary and outlook
375(4)
Structural studies of intermolecular interactions by NMR spectroscopy
379(9)
Gerd Gemmecker
Binding site mapping
379(1)
The bacterial phosphotransferase system
380(3)
Mapping protein-protein interactions by NMR
383(2)
SAR-by-NMR
385(3)
Tailor-made experimental building blocks for NMR studies of bioorganic compounds
388(8)
Steffen J. Glaser
Computer-aided design of NMR experiments
388(1)
Tailor-made experiments for the correlation of resonances
389(1)
Tailor-made experiments for the determination of coupling constants
390(3)
A new criterion for optimal senistivity
393(3)
NMR Techniques for the investigation of carbohydrate-protein interactions
396(13)
Thomas Weimar
Carbohydrate-protein complexes
396(1)
Carbohydrate NMR
396(1)
NMR experiments of carbohydrate-protein complexes - Transferred NOEs
397(2)
Using transferred NOE experiments to solve the bound conformation of a Streptococcus Group A trisaccharide-antigen [17]
399(1)
T1p-filtered trNOE experiments
400(1)
Spin diffusion in trNOE spectra
400(4)
An investigation of the complex of glucoamylase with a maltose heteroanalog inhibitor [27]
404(2)
Conclusions
406(3)
Access to structural diversity via chemical screening
409(9)
Susanne Grabley
Ralf Thiericke
The chemical screening method
409(2)
New secondary metabolites from chemical screening
411(1)
Hydrophilic-chemical screening
411(1)
Biomolecular-chemical screening
412(1)
Classification of microbial strain collections
413(1)
Biological activities
414(2)
Discussion
416(2)
Carbohydrate - protein interaction studies by various NMR methods and computational calculations
418(13)
Hans-Christian Siebert
Unbound oligosaccharides
418(4)
Ligand-lectin complexes
422(1)
CIDNP experiments
422(6)
Conclusion
428(3)
Subject Index 431

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