Chemical biology: learning through case studies
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| Format: | Book |
| Language: | English |
| Published: |
Weinheim
WILEY-VCH
2009
|
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XXXIII, 271 S. Ill., graph. Darst. 240 mm x 170 mm |
| ISBN: | 9783527323302 |
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| 245 | 1 | 0 | |a Chemical biology |b learning through case studies |c ed. by Herbert Waldmann ... |
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Contents
Introduction
and Preface
XIII
List of Contributors
XVII
Abbreviations
XXI
List of Boxes and Definitions
XXXI
1
Yeast-Based Chemical Genomic Approaches
1
Katja Hübel
1.1
Introduction
1
1.2
The Biological Problem
1
1.2.1
Interplay between Organic Chemistry and Biology
1
1.2.2
Chemical Genomics
4
1.2.3
Small Molecules in Chemical Genomics
6
1.2.4
Cell-based Genomic Approaches
6
1.2.5
Yeast-Based Chemical Genomic Approaches
7
1.3
The Chemical Approach
11
1.4
Chemical Biological Research/Evaluation-Chemogenomic Profiling:
Elucidating the Mode of Action of Small Molecules
12
1.4.1
Assay Principle
12
1.4.2
The Yeast Deletion Strain Collection
14
1.4.2.1
Homozygous Deletion Strains
14
1.4.2.2
Heterozygous Deletion Strains
14
1.4.3
Advantages and Disadvantages
16
1.4.4
Case Studies
16
1.5
Conclusions
19
References
19
2
Microarray-Based Strategies to Identify Unknown Protein
Interactions
21
Sabine Borgmann
and
Christof
M.
Niemeyer
2.1
Introduction
21
2.2
The Biological Problem
21
2.3
The Chemical Approach
25
2.3.1
Introduction to Microarray Technology
25
Chemical Biology: Learning through Case Studies. Edited by H. Waldmann and P. Janning
Copyright
© 2009
WILEYVCH
Verlag
GmbH
&
Co. KGaA, Weinheim
ISBN:
978-3-527-32330-2
VI Contents
2.3.2
Antibody Microarray for Protein Profiling
28
2.3.3
Self-Assembled Protein Microarrays
29
2.3.4
Self-Assembled Small-Molecule Microarrays
30
2.4
Chemical Biological Research /Evaluation
33
2.4.1
Antibody Microarray for Protein Profiling
33
2.4.2
Self-Assembled Protein Microarrays
35
2.4.3
Self-Assembled Small-Molecule Microarrays
36
2.5
Conclusions
37
References
37
3
Compound Collection Synthesis for Chemical Biology
39
Kama! Kumar
3.1
Introduction
39
3.2
Chemical Probes
-а
Chemical Question with Biological
Consequences
39
3.3
Diversity Oriented Synthesis (DOS)
40
3.3.1
Aims of Diversity Oriented Synthesis
40
3.3.2
DOS Based Library Synthesis and Evaluation
42
3.4
Biology Oriented Synthesis (BIOS)
46
3.4.1
Aims of Biology Oriented Synthesis
46
3.4.2
BIOS-Based Library Synthesis and Evaluation
47
3.5
Conclusions
52
References
52
4
Target Identification and Validation of
a
WNT/ß-Catenin
Pathway
Modulator
55
Petra
Jarming
4.1
Introduction
55
4.2
The Biological Problem
55
4.2.1
Target Identification and Validation
55
4.2.2 WNT/ß-Catenin
Pathway
56
4.2.3
Modulation of the
WNT/ß-Catenin
Pathway by Small Molecules
57
4.3
The Chemical Approach
59
4.3.1
High Throughput Screens
59
4.3.2
Synthesis of QS11, QS11-NC and Coupling to Solid Support
60
4.4
Chemical Biological Research/Evaluation
62
4.4.1
Target Identification
62
4.4.2
Target Validation
64
4.4.3
Mechanism of Action
65
4.5
Conclusions
66
References
66
5
Activity-Based Protein Profiling of Cys Proteases
69
Renier
van
der Hoorn
5.1
Introduction
69
52
The Biological Problem
69
Contents
VII
5.3
The Chemical Approach
70
5.3.1
Epoxide
Probes for Papain-Like Cys Proteases
71
5.3.2
Acyloxymethylketones for Caspase-like Proteases
72
5.3.3
Vinyl Sulfones for Ubiquitin-Specific Proteases
74
5.4
Chemical Biological Research/Evaluation
75
5.5
Conclusions
78
References
78
6
The Use of Photoaffinity Labeling for the Identification of the Binding
Site of the Antibiotic Linezolid
79
Rolf Breinbauer and Matthias
Mentei
6.1
Introduction
79
6.2
The Biological Problem
79
6.3
The Chemical Approach
81
6.3.1
Synthesis of Oxazolidinone Antibiotics
82
6.3.2
Synthesis of Photoaffinity-Labeled Probes
83
6.4
Chemical Biological Research/Evaluation
86
6.5
Conclusions
87
References
88
7
Surgical Strikes: Uses of Analog Sensitive Technologies to Target
Kinases of Interest
89
Matthias Rabiller and Daniel
Rauh
7.1
Introduction
89
7.2
The Biological Problem
89
7.3
The Chemical Genetic Approach
91
7.3.1
Aim of the Chemical Genetic Approach
91
7.3.2
Engineering
ASKA Ligand-Kinase
Pairs
95
7.4
Chemical Biological Research/Evaluation:
ASKA
Technology-
Applications in Molecular Biology
99
7.4.1
Kinase Substrate Identification
99
7.4.2
Kinase Inhibition Studies
101
7.5
Conclusions
102
References
102
8
Modulation of Protein-Protein Interactions by Small Molecules
105
Stefanie
Bovens
and Christian
Ottmann
8.1
Introduction
105
8.2
The Biological Problem
105
8.3
The Chemical Approach 111
8.4
Chemical Biological Research/Evaluation
114
8.4.1
Homodimerization
114
8.4.2
Heterodimerization
116
8.4.3
Engineering the Protein-Iigand Interaction
117
8.5
Conclusions
118
References
119
VIII
I Contents
9
Targeted Protein Degradation in Live Cells
121
Markus
Kaiser
9.1
Introduction
121
9.2
The Biological Problem
121
9.3
The Chemical Approach
124
9.3.1
The PROTAC Approach
124
9.3.2
Conditional Control of Engineered Protein Stability
127
9.4
Chemical Biological Research/Evaluation
129
9.4.1
in Vivo Targeted Protein Degradation by PROTACs
129
9.4.2
in Vivo Evaluation of Shld-l-ControUed Degradation of DD-POI Fusion
Proteins
130
9.5
Conclusions
131
References
132
10
Trapoxin B: From Total Synthesis to Epigenetics
135
Bruno
Bulíc
10.1
Introduction
135
10.2
The Biological Problem
135
10.3
The Chemical Approach
138
10.3.1
Properties of Trapoxin
В
138
10.3.2
Synthesis of the K-trap Affinity Matrix
139
10.4
Chemical Biological Research/Evaluation
140
10.5
Conclusions
143
References
144
11
Native Chemical Ligation-A Tool for Chemical Protein Synthesis
145
Christian F.W. Becker
11.1
Introduction
145
11.2
The Synthetic Challenge
145
11.3
The Chemical Approach-Native Chemical Ligation
148
11.3.1
Principles of Native Chemical Ligation
148
11.3.2
Challenges and Limitations
149
11.4
Chemical Biological Research/Evaluation-The Ras-RBD System
150
11.4.1
Chemical Synthesis of the
Ras
Protein and Its
EfTector RBD
152
11.4.2
In Vitro Analysis of Synthetic
Ras
and RBD 15J
11.5
Conclusions
156
References
156
12
Using Split Inteins to Prepare Semi-synthetic Proteins and to Study the
Mechanism of Protein trans-Splicing
159
Henning
D.
Mootz
12.1
Introduction
159
12.2
The Biological Problem
159
12.3
The Chemical Approach
160
12.3.1
Traditional Protein Bioconjugation
160
12.3.2
Reprogramming Protein Biosynthesis
161
Contents
IX
12.3.3 Chemical Ligation
Methods for
Protein
Semi-synthesis
161
12.3.4
Chemoenzymatic Ways to
Lígate
Two Polypeptides
163
12.4
Chemical Biological Research/Evaluation
164
12.4.1
Mechanism and Structure of Inteins and Split Inteins
164
12.4.2
Semi-synthesis Mediated by Protein traws-Splicing
166
12.4.3
Investigation of the Mechanism of Protein Splicing Using a
Semi-synthetic Intein
171
12.5
Conclusions
172
Acknowledgements
173
References
173
13
Elucidation of the
Ras
Cycle with Semi-synthetic Proteins
175
Luc Brunsveld
13.1
Introduction
175
13.2
The Biological Problem
275
13.3
The Chemical Approach
178
13.3.1
Synthesis of Lipidated Ras-peptides
178
13.3.2
Synthesis of Ras-proteins
181
13.4
Chemical Biological Research/Evaluation
183
13.5
Conclusions
186
References
186
14
The Study of
Rab
CTPase Recycling Using Semi-synthetic Prenylated
Proteins
189
Kirill Alexandrov, Roger Goody, Herbert
Waldmann,
and Yaowen Wu
14.1
Introduction
189
14.2
The Biological Problem
189
14.3
The Chemical Approach
192
14.3.1
Expressed Protein Ligation
192
14.3.2
Synthesis of Prenylated Peptides
192
14.3.3
Semi-synthesis of Soluble Prenylated
Rab
Proteins
194
14.4
Biological Research/Evaluation
197
14.4.1
Structure of Mono- and Di-geranylgeranylated Yptl
:
GDI
Complexes
197
14.4.2
Quantitative Analysis of the Interaction between Prenylated
Rab
and
REP/GDI
200
14.4.3
Mechanistic Model of REP/GDI-Mediated Membrane Extraction of
Rab
Proteins
201
14.5
Conclusions
204
References
205
15
Development of a Model Cancer Vaccine Candidate Based on the
MUCI
Cellular Surface Clycopeptide Epitope
207
Christian
Hedberg
and
Ulrika Westerlind
15.1
Introduction
207
15.2
The Biological Problem
207
Χ Ι
Contents
15.2.1
Carbohydrates in General
207
15.2.2
Mucin
1
and Aberrant Glycosylation in Cancer
208
15.2.3
Immunology
210
15.3
The Chemical Approach
210
15.3.1
Synthesis of Glycosylated
Amino
Acid Building Blocks
212
15.3.2
Synthesis of
MUCI
Glycopeptides Conjugated to
a
Peptide
О
Т
-Cell
Epitope
214
15.3.3
Synthesis of
MUCI
Glycopeptides Conjugated to BSA Carrier Protein
for
ELISA
214
15.4
Chemical Biological Research/Evaluation
217
15.5
Conclusions
217
References
219
16
The Introduction of Chemical Reporter Croups by
Bioorthogonal
Ligation Reactions for the Imaging of Cell-Surface Clycans
221
Rolf Breinbauer and Matthias
Mentei
16.1
Introduction
221
16.2
The Biological Problem
221
16.3
The Chemical Approach
222
16.3.1
Preparation of Cell-Surface Glycans Exhibiting an Azide
Moiety
222
16.3.2
Synthesis of Alkyne-Tagged Fluorescent Probes
225
16.4
Chemical Biological Research/Evaluation
228
16.5
Conclusions
229
References
232
17
Sequence Specific DNA-Binding Small Molecules for Protein
Recruitment and Modulation of Transcription
233
Harts-Dieter
Arndt
and
Sascha Baumann
17.1
Introduction
233
17.2
The Biological Problem-Targeting
DNA
with Small Molecules
233
17.3
The Chemical Approach: The
Polyamide
Rationale
234
17.4
Chemical Biological Research/Evaluation
-Polyamides in
Biological
Applications
237
17.4.1
Hypoxia Inducible Factor
237
17.4.2
Artificial Activators
240
17.5
Conclusions
243
References
243
18
C-Quadruplex Ligands as Tools for Elucidating c-MYC Transnational
Regulation
247
Barbora
Sacca
and
Markus
Kaiser
18.1
Introduction
247
18.2
The Biological Problem
247
18.3
The Chemical Approach
251
Contents
XI
18.4 Chemical
Biological
Research/Evaluation 254
18.5
Conclusion
258
References
258
Index 261 |
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| indexdate | 2024-07-20T10:06:09Z |
| institution | BVB |
| isbn | 9783527323302 |
| language | English |
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| publisher | WILEY-VCH |
| record_format | marc |
| spelling | Chemical biology learning through case studies ed. by Herbert Waldmann ... Weinheim WILEY-VCH 2009 XXXIII, 271 S. Ill., graph. Darst. 240 mm x 170 mm txt rdacontent n rdamedia nc rdacarrier Bioactive compounds Synthesis Biochemistry Experiments Combinatorial chemistry Chemische Biologie (DE-588)7657972-4 gnd rswk-swf Chemische Biologie (DE-588)7657972-4 s DE-604 Waldmann, Herbert 1957- (DE-588)1036301192 edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3191926&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017308229&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Chemical biology learning through case studies Bioactive compounds Synthesis Biochemistry Experiments Combinatorial chemistry Chemische Biologie (DE-588)7657972-4 gnd |
| subject_GND | (DE-588)7657972-4 |
| title | Chemical biology learning through case studies |
| title_auth | Chemical biology learning through case studies |
| title_exact_search | Chemical biology learning through case studies |
| title_full | Chemical biology learning through case studies ed. by Herbert Waldmann ... |
| title_fullStr | Chemical biology learning through case studies ed. by Herbert Waldmann ... |
| title_full_unstemmed | Chemical biology learning through case studies ed. by Herbert Waldmann ... |
| title_short | Chemical biology |
| title_sort | chemical biology learning through case studies |
| title_sub | learning through case studies |
| topic | Bioactive compounds Synthesis Biochemistry Experiments Combinatorial chemistry Chemische Biologie (DE-588)7657972-4 gnd |
| topic_facet | Bioactive compounds Synthesis Biochemistry Experiments Combinatorial chemistry Chemische Biologie |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=3191926&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017308229&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT waldmannherbert chemicalbiologylearningthroughcasestudies |