Chemogenomics and chemical genetics: a user's introduction for biologists, chemists and informaticians
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| Format: | Book |
| Language: | English |
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Berlin [u.a.]
Springer
2011
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| Series: | Grenoble sciences
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| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XI, 256 S. Ill., graph. Darst. |
| ISBN: | 9783642196140 3642196144 |
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IMAGE 1
CONTENTS
PREFACE 1
INTRODUCTION 3
FIRST PART AUTOMATED PHARMACOLOGICAL SCREENING
CHAPTER 1 - THE PHARMACOLOGICAL SCREENING PROCESS: THE SMALL MOLECULE,
THE BIOLOGICAL SCREEN, THE ROBOT, THE SIGNAL AND THE INFORMATION 7 ERIC
MARECHAL - SYLVAINE ROY - LAURENCE L.AFANECHERE 1.1. INTRODUCTION 7
1.2. THE SCREENING PROCESS: TECHNOLOGICAL OUTLINE 8
1.2.1. MULTI-WELL PLATES, ROBOTS AND DETECTORS 8
1.2.2. CONSUMABLES, COPIES OF CHEMICAL LIBRARIES AND STORAGE 10 1.2.3.
TEST DESIGN, PRIMARY SCREENING, HIT-PICKING, SECONDARY SCREENING 10 1.3.
THE SMALL MOLECULE: OVERVIEW OF THE DIFFERENT TYPES OF CHEMICAL LIBRARY
12 1.3.1. THE SMALL MOLECULE 12
1.3.2. DMSO, THE SOLVENT FOR CHEMICAL LIBRARIES 12
1.3.3. COLLECTIONS OF NATURAL SUBSTANCES 12
1.3.4. COMMERCIAL AND ACADEMIC CHEMICAL LIBRARIES 14
1.4. THE TARGET, AN ONTOLOGY TO BE CONSTRUCTED 14
1.4.1. THE DEFINITION OF A TARGET DEPENDS ON THAT OF A BIOACTIVITY 14
1.4.2. DUALITY OF THE TARGET: MOLECULAR ENTITY AND BIOLOGICAL FUNCTION
15 1.4.3. AN ONTOLOGY TO BE CONSTRUCTED 16
1.5. CONTROLS 17
1.6. A NEW DISCIPLINE AT THE INTERFACE OF BIOLOGY, CHEMISTRY AND
INFORMATICS: CHEMOGENOMICS 17
1.7. CONCLUSION 18
1.8. REFERENCES 19
CHAPTER2- COLLECTIONS OF MOLECULES FOR SCREENING: EXAMPLE OF THE FRENCH
NATIONAL CHEMICAL LIBRARY 23
MARCEL HIBERT 2.1. INTRODUCTION 23
2.2. WHERE ARE THE MOLECULES TO BE FOUND? 25
2.3. STATE OF PROGRESS WITH THE EUROPEAN CHEMICAL LIBRARY 27
2.4. PERSPECTIVES 28
2.5. REFERENCES 28
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/1009990470
DIGITALISIERT DURCH
IMAGE 2
VI CHEMOGENOMICS AND CHEMICAL GENETICS
CHAPTER 3 - THE MINIATURISED BIOLOGICAL ASSAY: CONSTRAINTS AND
LIMITATIONS 29
MARTINE KNIBIEHLER 3.1. INTRODUCTION 29
3.2. GENERAL PROCEDURE FOR THE DESIGN AND VALIDATION OF AN ASSAY 30
3.2.1. CHOICE OF ASSAY 31
3.2.2. SETTING UP THE ASSAY 33
3.2.3. VALIDATION OF THE ASSAY AND AUTOMATION 35
3.3. THE CLASSIC DETECTION METHODS 36
3.4. THE RESULTS 36
3.4.1. THE SIGNAL MEASURED: INCREASE OR DECREASE? 36
3.4.2. THE INFORMATION FROM SCREENING IS MANAGED ON THREE LEVELS 37
3.4.3. PHARMACOLOGICAL VALIDATION 40
3.5. DISCUSSION AND CONCLUSION 40
3.6. REFERENCES 41
CHAPTER 4 - THE SIGNAL: STATISTICAL ASPECTS, NORMALISATION, ELEMENTARY
ANALYSIS 43 SAMUEL WLECZOREK 4.1. INTRODUCTION 43
4.2. NORMALISATION OF THE SIGNALS BASED ON CONTROLS 44
4.2.1. NORMALISATION BY THE PERCENTAGE INHIBITION 44
4.2.2. NORMALISATION RESOLUTION 44
4.2.3. ABERRANT VALUES 46
4.3. DETECTION AND CORRECTION OF MEASUREMENT ERRORS 48
4.4. AUTOMATIC IDENTIFICATION OF POTENTIAL ARTEFACTS 49
4.4.1. SINGULARITIES 49
4.4.2. AUTOMATIC DETECTION OF POTENTIAL ARTEFACTS 50
4.5. CONCLUSION 52
4.6. REFERENCES 52
CHAPTER S - MEASURING BIOACTIVITY: KI, IC50 AND EC50 55
ERIC MARECHAL 5.1. INTRODUCTION 55
5.2. PREREQUISITE FOR ASSAYING THE POSSIBLE BIOACTIVITY OF A MOLECULE:
THE TARGET MUST BE A LIMITING FACTOR 55
5.3. ASSAYING THE ACTION OF AN INHIBITOR ON AN ENZYME UNDER MICHAELIAN
CONDITIONS: KI 56 5.3.1. AN ENZYME IS A BIOLOGICAL CATALYST 57
5.3.2. ENZYMATIC CATALYSIS IS REVERSIBLE 57
5.3.3. THE INITIAL RATE, A MEANS TO CHARACTERISE A REACTION 59
5.3.4. MICHAELIAN CONDITIONS 59
5.3.5. THE SIGNIFICANCE OF KM AND VMAX IN QUALIFYING THE FUNCTION OF AN
ENZYME. 60 5.3.6. THE INHIBITED ENZYME: KI 60
5.4. ASSAYING THE ACTION OF A COMPETITIVE INHIBITOR UPON A RECEPTOR:
IC50 62 5.5. RELATIONSHIP BETWEEN KI AND IC50: THE CHENG-PRUSOFF
EQUATION 63 5.6. EC50: A GENERALISATION FOR ALL MOLECULES GENERATING A
BIOLOGICAL EFFECT (BIOACTIVITY) 64 5.7. CONCLUSION 64
5.8. REFERENCES 65
IMAGE 3
CONTENTS VIL
CHAPTER 6 - MODELLING THE PHARMACOLOGICAL SCREENING:
CONTROLLING THE PROCESSES AND THE CHEMICAL, BIOLOGICAL AND EXPERIMENTAL
INFORMATION 67 SYLVAINE ROY 6.1. INTRODUCTION 67
6.2. NEEDS ANALYSIS BY MODELLING 68
6.3. CAPTURE OF THE NEEDS 69
6.4. DEFINITION OF THE NEEDS AND NECESSITY OF A VOCABULARY COMMON TO
BIOLOGISTS, CHEMISTS AND INFORMATICIANS 69
6.5. SPECIFICATION OF THE NEEDS 69
6.5.1. USE CASES AND THEIR DIAGRAMS 70
6.5.2. ACTIVITY DIAGRAMS 72
6.5.3. CLASS DIAGRAMS AND THE DOMAIN MODEL 73
6.6. CONCLUSION 78
6.7. REFERENCES 78
CHAPTER 7 - QUALITY PROCEDURES IN AUTOMATED SCREENING 79
CAROLINE BARETTE 7.1. INTRODUCTION 79
7.2. THE CHALLENGES OF QUALITY PROCEDURES 79
7.3. A REFERENCE GUIDE: THE ISO 9001 STANDARD 80
7.4. QUALITY PROCEDURES IN FIVE STEPS 82
7.4.1. ASSESSMENT 82
7.4.2. ACTION PLAN - PLANNING 83
7.4.3. PREPARATION 83
7.4.4. IMPLEMENTATION 83
7.4.5. MONITORING 83
7.5. CONCLUSION 84
7.6. REFERENCES 84
SECOND PART HIGH-CONTENT SCREENING AND STRATEGIES IN CHEMICAL GENETICS
CHAPTER 8 - PHENOTYPIC SCREENING WITH CELLS AND FORWARD CHEMICAL
GENETICS STRATEGIES. 87 LAURENCE LAFANECHERE 8.1. INTRODUCTION 87
8.2. THE TRADITIONAL GENETICS APPROACH: FROM PHENOTYPE TO GENE AND FROM
GENE TO PHENOTYPE 88
8.2.1. PHENOTYPE 88
8.2.2. FORWARD AND REVERSE GENETICS 89
8.3. CHEMICAL GENETICS 89
8.4. CHEMICAL LIBRARIES FOR CHEMICAL GENETICS 90
8.4.1. CHEMICAL LIBRARY SIZE 91
8.4.2. CONCENTRATION OF MOLECULES 91
8.4.3. CHEMICAL STRUCTURE DIVERSITY 91
8.4.4. COMPLEXITY OF MOLECULES 93
IMAGE 4
VIII CHEMOGENOMICS AND CHEMICAL GENETICS
8.4.5. ACCESSIBILITY OF MOLECULES TO CELLULAR COMPARTMENTS 93
8.4.6. THE ABUNDANCE OF MOLECULES 94
8.4.7. THE POSSIBILITY OF FUNCTIONALIZING THE MOLECULES 94
8.5. PHENOTYPIC TESTS WITH CELLS 94
8.6. METHODS TO IDENTIFY THE TARGET 96
8.7. CONCLUSIONS 99
8.8. REFERENCES 99
CHAPTER 9 - HIGH-CONTENT SCREENING IN FORWARD (PHENOTYPIC SCREENING WITH
ORGANISMS) AND REVERSE (STRUCTURAL SCREENING BY NMR) CHEMICAL GENETICS
103
BENOIT DEPREZ 9.1. INTRODUCTION 103
9.2. BENEFITS OF HIGH-CONTENT SCREENING 104
9.2.1. SUMMARISED COMPARISON OF HIGH-THROUGHPUT SCREENING AND
HIGH-CONTENT SCREENING 104
9.2.2. ADVANTAGES OF HIGH-CONTENT SCREENING FOR THE DISCOVERY OF NOVEL
THERAPEUTIC TARGETS 104
9.2.3. THE NEMATODE CAENORHABDITIS ELEGANS: A MODEL ORGANISM FOR
HIGH-CONTENT SCREENING 105
9.2.4. ADVANTAGES OF HIGH-CONTENT SCREENING FOR REVERSE CHEMICAL
GENETICS AND THE DISCOVERY OF NOVEL BIOACTIVE MOLECULES 108
9.3. CONSTRAINTS LINKED TO THROUGHPUT AND TO THE LARGE NUMBERS 110
9.3.1. KNOW-HOW 110
9.3.2. MINIATURISATION, RATE AND ROBUSTNESS OF THE ASSAYS 110
9.3.3. NUMBER, CONCENTRATION AND PHYSICOCHEMICAL PROPERTIES OF SMALL
MOLECULES. I LL 9.4. TYPES OF MEASUREMENT FOR HIGH-CONTENT SCREENING 111
9.4.1. THE CRITICAL INFORMATION NEEDED FOR SCREENING I LL
9.4.2. RAW, NUMERICAL RESULTS 111
9.4.3. RESULTS ARISING FROM EXPERT ANALYSES 112
9.5. CONCLUSION 112
9.6. REFERENCES 112
CHAPTER 10 - SOME PRINCIPLES OF DIVERSITY-ORIENTED SYNTHESIS 113
YUNG-SING WONG 10.1. INTRODUCTION 113
10.2. PORTRAIT OF THE SMALL MOLECULE IN DOS 114
10.3. DEFINITION OF THE DEGREE OF DIVERSITY (DD) 116
10.3.1. DEGREE OF DIVERSITY OF THE BUILDING BLOCK 116
10.3.2. DEGREE OF STEREOCHEMICAL DIVERSITY 118
10.3.3. DEGREE OF REGIOCHEMICAL DIVERSITY 119
10.3.4. DEGREE OF SKELETAL DIVERSITY 121
10.4. DIVERGENT MULTI-STEP DOS BY COMBINING ELEMENTS OF DIVERSITY 124
10.5. CONVERGENT DOS: CONDENSATION BETWEEN DISTINCT SMALL MOLECULES 127
10.6. CONCLUSION 130
10.7. REFERENCES 130
IMAGE 5
CONTENTS IX
THIRD PART
TOWARDS AN IN SILICO EXPLORATION OF CHEMICAL AND BIOLOGICAL SPACES
CHAPTER 11 - MOLECULAR DESCRIPTORS AND SIMILARITY INDICES 735
SAMIA ACI 11.1. INTRODUCTION 135
11.2. CHEMICAL FORMULAE AND COMPUTATIONAL REPRESENTATION 136
11.2.1. THE CHEMICAL FORMULA: A REPRESENTATION IN SEVERAL DIMENSIONS 137
11.2.2. MOLECULAR INFORMATION CONTENT 137
11.2.3. MOLECULAR GRAPH AND CONNECTIVITY MATRIX 139
11.3. MOLECULAR DESCRIPTORS 140
11.3.1. ID DESCRIPTORS 141
11.3.2. 2D DESCRIPTORS 141
11.3.3. 3D DESCRIPTORS 144
11.3.4. 3D VERSUS 2D DESCRIPTORS? 146
11.4. MOLECULAR SIMILARITY 147
11.4.1. A BRIEF HISTORY 147
11.4.2. PROPERTIES OF SIMILARITY COEFFICIENTS AND DISTANCE INDICES 147
11.4.3. A FEW SIMILARITY COEFFICIENTS 148
11.5. CONCLUSION 148
11.6. REFERENCES 150
CHAPTER 12 - MOLECULAR LIPOPHILICITY: A PREDOMINANT DESCRIPTOR FOR QSAR
153 GERARD GRASSY - ALAIN CHAVANIEU
12.1. INTRODUCTION 153
12.2. HISTORY 153
12.3. THEORETICAL FOUNDATIONS AND PRINCIPLES OF THE RELATIONSHIP BETWEEN
THE STRUCTURE OF A SMALL MOLECULE AND ITS BIOACTIVITY 154
12.3.1. QSAR, QPAR AND QSPR 154
12.3.2. BASIC EQUATION OF A QSAR STUDY 155
12.4. GENERALITIES ABOUT LIPOPHILICITY DESCRIPTORS 155
12.4.1. SOLUBILITY IN WATER AND IN LIPID PHASES: CONDITIONS FOR
BIOAVAILABILITY 155 12.4.2. PARTITION COEFFICIENTS 156
12.4.3. THE PARTITION COEFFICIENT IS LINKED TO THE CHEMICAL POTENTIAL
156 12.4.4. THERMODYNAMIC ASPECTS OF LIPOPHILICITY 157
12.5. MEASUREMENT AND ESTIMATION OF THE OCTANOL/WATER PARTITION
COEFFICIENT 158 12.5.1. MEASUREMENT METHODS 158
12.5.2. PREDICTION METHODS 160
12.5.3. RELATIONSHIP BETWEEN LIPOPHILICITY AND SOLVATION ENERGY: LSER
163 12.5.4. INDIRECT ESTIMATION OF PARTITION COEFFICIENTS FROM VALUES
CORRELATED WITH MOLECULAR LIPOPHILICITY 163
12.5.5. THREE-DIMENSIONAL APPROACH TO LIPOPHILICITY 165
12.6. SOLVENT SYSTEMS OTHER THAN OCTANOL/WATER 166
12.7. ELECTRONIC PARAMETERS 167
12.7.1. THE HAMMETT PARAMETER, O 167
12.7.2. SWAIN AND LUPTON PARAMETERS 168
IMAGE 6
X CHEMOGENOMICS AND CHEMICAL GENETICS
12.8. STERIC DESCRIPTORS 169
12.9. CONCLUSION 169
12.10. REFERENCES 169
CHAPTER 13 - ANNOTATION AND CLASSIFICATION OF CHEMICAL SPACE IN
CHEMOGENOMICS 171 DRAGOS HORVATH 13.1. INTRODUCTION 171
13.2. FROM THE MEDICINAL CHEMIST'S INTUITION TO A FORMAL TREATMENT OF
STRUCTURAL INFORMATION 171
13.3. MAPPING STRUCTURAL SPACE: PREDICTIVE MODELS 174
13.3.1. MAPPING STRUCTURAL SPACE 174
13.3.2. NEIGHBOURHOOD (SIMILARITY) MODELS 175
13.3.3. LINEAR AND NON-LINEAR EMPIRICAL MODELS 178
13.4. EMPIRICAL FILTERING OF DRUG CANDIDATES 180
13.5. CONCLUSION 181
13.6. REFERENCES 181
CHAPTER 14 - ANNOTATION AND CLASSIFICATION OF BIOLOGICAL SPACE IN
CHEMOGENOMICS 185 JORDI MESTRES 14.1. INTRODUCTION 185
14.2. RECEPTORS 186
14.2.1. DEFINITIONS 186
14.2.2. ESTABLISHING THE ' RC NOMENCLATURE 187
14.2.3. ION-CHANNEL RECEPTORS 188
14.2.4. G PROTEIN-COUPLED RECEPTORS 189
14.2.5. ENZYME RECEPTORS 190
14.2.6. NUCLEAR RECEPTORS 190
14.3. ENZYMES 191
14.3.1. DEFINITIONS 191
14.3.2. THE ' EC NOMENCLATURE 192
14.3.3. SPECIALISED NOMENCLATURE 193
14.4. CONCLUSION 193
14.5. REFERENCES 194
CHAPTER 15 - MACHINE LEARNING AND SCREENING DATA 197
GILLES BLSSON 15.1. INTRODUCTION 197
15.2. MACHINE LEARNING AND SCREENING 199
15.3. STEPS IN THE MACHINE-LEARNING PROCESS 202
15.3.1. REPRESENTATION LANGUAGES 203
15.3.2. DEVELOPING A TRAINING SET 205
15.3.3. MODEL BUILDING 206
15.3.4. VALIDATION AND REVISION 207
15.4. CONCLUSION 209
15.5. REFERENCES AND INTERNET SITES 209
IMAGE 7
CONTENTS XI
CHAPTER 16 * VIRTUAL SCREENING BY MOLECULAR DOCKING 213
DIDIER ROGNAN 16.1. INTRODUCTION 213
16.2. THE 3 STEPS IN VIRTUAL SCREENING 213
16.2.1. PREPARATION OF A CHEMICAL LIBRARY 213
16.2.2. SCREENING BY HIGH-THROUGHPUT DOCKING 216
16.2.3. POST-PROCESSING OF THE DATA 218
16.3. SOME SUCCESSES WITH VIRTUAL SCREENING BY DOCKING 220
16.4. CONCLUSION 221
16.5. REFERENCES 222
APPENDIX BRIDGING PAST AND FUTURE?
CHAPTER 17 - BIODIVERSITY AS A SOURCE OF SMALL MOLECULES FOR
PHARMACOLOGICAL SCREENING: LIBRARIES OF PLANT EXTRACTS 227
FRANCOISE GUERITTE, THIERRY SEVENET, MARC LLTAUDON, VINCENT DUMONTET
17.1. INTRODUCTION 227
17.2. PLANT BIODIVERSITY AND NORTH-SOUTH CO-DEVELOPMENT 229
17.3. PLANT COLLECTION: GUIDELINES 230
17.4. DEVELOPMENT OF A NATURAL-EXTRACT LIBRARY 231
17.4.1. FROM THE PLANT TO THE PLATE 231
17.4.2. MANAGEMENT OF THE EXTRACT LIBRARY 231
17.5. STRATEGY FOR FRACTIONATION, EVALUATION AND DEREPLICATION 233
17.5.1. FRACTIONATION AND DEREPLICATION PROCESS 233
17.5.2. SCREENING FOR BIOACTIVITIES 235
17.5.3. SOME RESULTS OBTAINED WITH SPECIFIC TARGETS 236
17.5.4. POTENTIAL AND LIMITATIONS 239
17.6. CONCLUSION 240
17.7. REFERENCES 240
GLOSSARY 241
THE AUTHORS 253 |
| any_adam_object | 1 |
| author2 | Maréchal, Eric |
| author2_role | edt |
| author2_variant | e m em |
| author_facet | Maréchal, Eric |
| building | Verbundindex |
| bvnumber | BV039593350 |
| classification_rvk | VC 6250 WC 4460 |
| ctrlnum | (OCoLC)724923420 (DE-599)DNB1009990470 |
| dewey-full | 572.8028 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.8028 |
| dewey-search | 572.8028 |
| dewey-sort | 3572.8028 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Biologie Medizin |
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| id | DE-604.BV039593350 |
| illustrated | Illustrated |
| indexdate | 2024-09-06T00:20:10Z |
| institution | BVB |
| isbn | 9783642196140 3642196144 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-024444406 |
| oclc_num | 724923420 |
| open_access_boolean | |
| owner | DE-11 DE-355 DE-BY-UBR DE-19 DE-BY-UBM |
| owner_facet | DE-11 DE-355 DE-BY-UBR DE-19 DE-BY-UBM |
| physical | XI, 256 S. Ill., graph. Darst. |
| publishDate | 2011 |
| publishDateSearch | 2011 |
| publishDateSort | 2011 |
| publisher | Springer |
| record_format | marc |
| series2 | Grenoble sciences |
| spelling | Chemogénomique Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians Eric Maréchal ... eds. Berlin [u.a.] Springer 2011 XI, 256 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Grenoble sciences Literaturangaben Screening (DE-588)4054045-5 gnd rswk-swf Chemische Genetik (DE-588)7688784-4 gnd rswk-swf Chemische Genetik (DE-588)7688784-4 s Screening (DE-588)4054045-5 s DE-604 Maréchal, Eric edt X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3669444&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024444406&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians Screening (DE-588)4054045-5 gnd Chemische Genetik (DE-588)7688784-4 gnd |
| subject_GND | (DE-588)4054045-5 (DE-588)7688784-4 |
| title | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians |
| title_alt | Chemogénomique |
| title_auth | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians |
| title_exact_search | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians |
| title_full | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians Eric Maréchal ... eds. |
| title_fullStr | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians Eric Maréchal ... eds. |
| title_full_unstemmed | Chemogenomics and chemical genetics a user's introduction for biologists, chemists and informaticians Eric Maréchal ... eds. |
| title_short | Chemogenomics and chemical genetics |
| title_sort | chemogenomics and chemical genetics a user s introduction for biologists chemists and informaticians |
| title_sub | a user's introduction for biologists, chemists and informaticians |
| topic | Screening (DE-588)4054045-5 gnd Chemische Genetik (DE-588)7688784-4 gnd |
| topic_facet | Screening Chemische Genetik |
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