Bioisosteres in Medicinal Chemistry
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| Format: | Buch |
| Sprache: | English |
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Weinheim
Wiley-VCH
2012
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| Schriftenreihe: | Methods and principles in medicinal chemistry
54 |
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Datensatz im Suchindex
| _version_ | 1819694056109768704 |
|---|---|
| adam_text | IMAGE 1
CONTENTS
LIST O F CONTRIBUTORS X I PREFACE XV
A PERSONAL FOREWORD X V I I
PART O N E PRINCIPLES 1
1 BIOISOSTERISM IN MEDICINAL CHEMISTRY 3
NATHAN BROWN
1.1 INTRODUCTION 3
1.2 ISOSTERISM 3
1.3 BIOISOSTERISM 6
1.4 BIOISOSTERISM IN LEAD OPTIMIZATION 9
1.4.1 C O M M O N REPLACEMENTS IN MEDICINAL CHEMISTRY 9 1.4.2
STRUCTURE-BASED DRUG DESIGN 9
1.4.3 MULTIOBJECTIVE OPTIMIZATION 12 1.5 CONCLUSIONS 13
REFERENCES 14
2 CLASSICAL BIOISOSTERES 15
CATERINA BARILLARI A N D NATHAN BROWN 2.1 INTRODUCTION 15
2.2 HISTORICAL BACKGROUND 15
2.3 CLASSICAL BIOISOSTERES 17
2.3.1 MONOVALENT ATOMS AND GROUPS 17
2.3.2 BIVALENT ATOMS AND GROUPS 17
2.3.3 TRIVALENT ATOMS AND GROUPS 18
2.3.4 TETRAVALENT ATOMS 19
2.3.5 RING EQUIVALENTS 19
2.4 NONCLASSICAL BIOISOSTERES 20
2.4.1 CARBONYL GROUP 20
2.4.2 CARBOXYLIC ACID 21
2.4.3 HYDROXYL GROUP 22
2.4.4 CATECHOL 22
HTTP://D-NB.INFO/1019094524
IMAGE 2
VI C O N T E N T S
2.4.5 HALOGENS 23
2.4.6 AMIDE AND ESTERS 24
2.4.7 THIOUREA 25
2.4.8 PYRIDINE 26
2.4.9 CYCLIC VERSUS NONCYCLIC SYSTEMS 2 7 2.5 SUMMARY 2 7
REFERENCES 27
3 CONSEQUENCES O F BIOISOSTERIC REPLACEMENT 31
DENNIS A. SMITH AND DAVID S. MILLAN 3.1 INTRODUCTION 31
3.2 BIOISOSTERIC GROUPINGS TO IMPROVE PERMEABILITY 32
3.3 BIOISOSTERIC GROUPINGS TO LOWER INTRINSIC CLEARANCE 40 3.4
BIOISOSTERIC GROUPINGS TO IMPROVE TARGET POTENCY 43 3.5 CONCLUSIONS AND
FUTURE PERSPECTIVES 47
REFERENCES 49
PART TWO DATA 53
4 B I O S T E R : A D A T A B A S E O F BIOISOSTERES AND BIOANALOGUES 5
5
ISTVAN UJVARY AND JULIAN HAYWARD
4.1 INTRODUCTION 55
4 . 2 HISTORICAL OVERVIEW AND THE DEVELOPMENT O F BIOSTER 5 6
4.2.1 REPRESENTATION O F CHEMICAL TRANSFORMATIONS FOR REACTION
DATABASES 56
4.2.2 THE CONCEPT O F BIOSTERIC TRANSFORMATION 5 7 4.2.3 OTHER
ANALOGUE AND BIOISOSTERE DATABASES 5 8 4.3 DESCRIPTION O F BIOSTER
DATABASE 59
4.3.1 COVERAGE AND SELECTION CRITERIA 59
4.3.2 SOURCES 59
4.3.3 DESCRIPTION O F THE LAYOUT O F DATABASE RECORDS 60 4.3.3.1 ID CODE
60
4.3.3.2 BIOSTERIC TRANSFORMATION 60 4.3.3.3 CITATION(S) 62
4.3.3.4 ACTIVITY 63
4.3.3.5 FRAGMENTS 63
4.3.3.6 COMPONENT MOLECULES AND FRAGMENTS 64 4.4 EXAMPLES 64
4.4.1 BENZODIOXOLE BIOISOSTERES 65
4.4.2 PHENOL BIOISOSTERES 66
4.4.3 KETOAMIDES 66
4.5 APPLICATIONS 69
4.6 SUMMARY 70
4.7 APPENDIX 70
REFERENCES 71
IMAGE 3
CONTENTS V I I
5 MINING THE CAMBRIDGE STRUCTURAL DATABASE FOR BIOISOSTERES 75
COLIN R. GROOM, TJELVAR S. G. OLSSON, JOHN W. LIEBESCHUETZ, DAVID A.
BARDWELL, IAN J. BRUNO, A N D FRANK H. ALLEN 5.1 INTRODUCTION 75
5.2 THE CAMBRIDGE STRUCTURAL DATABASE 76
5.3 THE CAMBRIDGE STRUCTURAL DATABASE SYSTEM 78
5.3.1 CONQUEST 78
5.3.2 MERCURY 78
5.3.3 WEBCSD 79
5.3.4 KNOWLEDGE-BASED LIBRARIES DERIVED FROM THE CSD 80 5.4 THE
RELEVANCE O F THE CSD TO DRUG DISCOVERY 83
5.5 ASSESSING BIOISOSTERES: CONFORMATIONAL ASPECTS 84 5.6 ASSESSING
BIOISOSTERES: NONBONDED INTERACTIONS 86 5.7 FINDING BIOISOSTERES I N THE
CSD: SCAFFOLD HOPPING AND
FRAGMENT LINKING 91 5.7.1 SCAFFOLD HOPPING 91
5.7.2 FRAGMENT LINKING 92
5.8 A CASE STUDY: BIOISOSTERISM O F LH-TETRAZOLE AND CARBOXYLIC ACID
GROUPS 94 5.8.1 CONFORMATIONAL MIMICRY 94
5.8.2 INTERMOLECULAR INTERACTIONS 94
5.9 CONCLUSIONS 97
REFERENCES 98
6 MINING FOR CONTEXT-SENSITIVE BIOISOSTERIC REPLACEMENTS IN LARGE
CHEMICAL DATABASES 103 GEORGE PAPADATOS, MICHAEL J. BODKIN, VALERIE J.
GILLET, A N D PETER WILLETT 6.1 INTRODUCTION 103
6.2 DEFINITIONS 104
6.3 BACKGROUND 105
6.4 MATERIALS AND METHODS 109
6.4.1 H U M A N MICROSOMAL METABOLIC STABILITY 109 6.4.2 DATA
PREPROCESSING 109
6.4.3 GENERATION O F MATCHED MOLECULAR PAIRS 110 6.4.4 CONTEXT
DESCRIPTORS 111
6.4.4.1 WHOLE MOLECULE DESCRIPTORS 111 6.4.4.2 LOCAL ENVIRONMENT
DESCRIPTORS 112 6.4.5 BINNING O F A P VALUES 112
6.4.6 CHARTS AND STATISTICS 112
6.5 RESULTS AND DISCUSSION 113
6.5.1 GENERAL CONSIDERATIONS 123
6.6 CONCLUSIONS 124
REFERENCES 125
IMAGE 4
VIII C O N T E N T S
PART THREE METHODS 129
7 PHYSICOCHEMICAL PROPERTIES 131
PETER ERTL
7.1 INTRODUCTION 131
7.2 METHODS TO IDENTIFY BIOISOSTERIC ANALOGUES 132
7.3 DESCRIPTORS TO CHARACTERIZE PROPERTIES O F SUBSTITUENTS AND SPACERS
132 7.4 CLASSICAL METHODS FOR NAVIGATION IN THE SUBSTITUENT SPACE 235
7.5 TOOLS TO IDENTIFY BIOISOSTERIC GROUPS BASED ON SIMILARITY I N THEIR
PROPERTIES 136 7.6 CONCLUSIONS 138
REFERENCES 138
8 MOLECULAR TOPOLOGY 141
NATHAN BROWN
8.1 INTRODUCTION 141
8.2 CONTROLLED FUZZINESS 141
8.3 GRAPH THEORY 142
8.4 DATA MINING 144
8.4.1 GRAPH MATCHING 144
8.4.2 FRAGMENTATION METHODS 145
8.5 TOPOLOGICAL PHARMACOPHORES 146
8.6 REDUCED GRAPHS 149
8.7 SUMMARY 151
REFERENCES 152
9 MOLECULAR SHAPE 155
PEDRO J. BALLESTER AND NATHAN BROWN 9.1 METHODS 156
9.1.1 SUPERPOSITION-BASED SHAPE SIMILARITY METHODS 156 9.1.2
SUPERPOSITION-FREE SHAPE SIMILARITY METHODS 158 9.1.3 CHOOSING A SHAPE
SIMILARITY TECHNIQUE FOR A PARTICULAR PROJECT 160
9.2 APPLICATIONS 161
9.3 FUTURE PROSPECTS 164
REFERENCES 165
10 PROTEIN STRUCTURE 167
JAMES E.J. MILLS
10.1 INTRODUCTION 167
10.2 DATABASE O F LIGAND-PROTEIN COMPLEXES 168 10.2.1 EXTRACTION O F
LIGANDS 168
10.2.2 ASSESSMENT O F LIGAND AND PROTEIN CRITERIA 169
IMAGE 5
CONTENTS | I X
10.2.3 CAVITY GENERATION 170
10.2.4 GENERATION AND VALIDATION O F SMILES STRING 170 10.2.5 GENERATION
O F FASTA SEQUENCE FILES 171 10.2.6 IDENTIFICATION O F INTERMOLECULAR
INTERACTIONS 172 10.3 GENERATION O F IDEAS FOR BIOISOSTERES 273
10.3.1 SUBSTRUCTURE SEARCH 173
10.3.2 SEQUENCE SEARCH 175
10.3.3 BINDING POCKET SUPERPOSITION 175 10.3.4 BIOISOSTERE
IDENTIFICATION 176 10.4 CONTEXT-SPECIFIC BIOISOSTERE GENERATION 177 10.5
USING STRUCTURE TO UNDERSTAND C O M M O N BIOISOSTERIC
REPLACEMENTS 178
10.6 CONCLUSIONS 180
REFERENCES 180
PART FOUR APPLICATIONS 183
11 THE DRUG GURU PROJECT 185
KENT D. STEWART, JASON SHANLEY, KARAM B. ALSAYYED A H M E D , A N D J.
PHILLIP BOWEN 11.1 INTRODUCTION 185
11.2 IMPLEMENTATION O F DRUG GURU 187
11.3 BIOISOSTERES 188
11.4 APPLICATION O F DRUG GURU 194
11.5 QUANTITATIVE ASSESSMENT O F DRUG G U R U TRANSFORMATIONS 195 11.6
RELATED WORK 197
11.7 SUMMARY: THE ABBOTT EXPERIENCE WITH THE DRUG G U R U PROJECT 197
REFERENCES 198
12 BIOISOSTERES O F AN NPY-Y5 ANTAGONIST 199
NICHOLAS P. BARTON A N D BENJAMIN R. BELLENIE 12.1 INTRODUCTION 199
12.2 BACKGROUND 199
12.3 POTENTIAL BIOISOSTERE APPROACHES 201 12.4 TEMPLATE MOLECULE
PREPARATION 204
12.5 DATABASE MOLECULE PREPARATION 206
12.6 ALIGNMENT AND SCORING 206
12.7 RESULTS AND MONOMER SELECTION 207
12.8 SYNTHESIS AND SCREENING 208
12.9 DISCUSSION 209
12.10 SAR AND DEVELOPABILITY OPTIMIZATION 211 12.11 SUMMARY AND
CONCLUSION 214
REFERENCES 214
IMAGE 6
PERSPECTIVES FROM MEDICINAL CHEMISTRY 217
NICHOLAS A. MEANWELL, MARCUS CASTREICH, MATTHIAS RAREY, MIKE DEVEREUX,
PAUL L A . POPELIER, CISBERT SCHNEIDER, AND PETER WILLETT INTRODUCTION
217 PRAGMATIC BIOISOSTERE REPLACEMENT IN MEDICINAL CHEMISTRY; A SOFTWARE
MAKER S VIEWPOINT 219 THE ROLE O F Q U A N T U M CHEMISTRY IN
BIOISOSTERE PREDICTION 221
LEARN FROM NATURALLY DRUG-LIKE COMPOUNDS 223 BIOISOSTERISM AT THE
UNIVERSITY O F SHEFFIELD 224 REFERENCES 227
INDEX 231
|
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| dewey-sort | 3615.19 |
| dewey-tens | 610 - Medicine and health |
| discipline | Chemie / Pharmazie Medizin |
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| indexdate | 2024-12-24T02:46:39Z |
| institution | BVB |
| isbn | 9783527330157 9783527654307 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-025177150 |
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| physical | XVIII, 237 S. 15 farb. Ill., 30 schw.-w. Tab. 240 mm x 170 mm |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Wiley-VCH |
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| series | Methods and principles in medicinal chemistry |
| series2 | Methods and principles in medicinal chemistry |
| spellingShingle | Bioisosteres in Medicinal Chemistry Methods and principles in medicinal chemistry Bioisosterie (DE-588)4145607-5 gnd Pharmazeutische Chemie (DE-588)4132158-3 gnd |
| subject_GND | (DE-588)4145607-5 (DE-588)4132158-3 (DE-588)4143413-4 |
| title | Bioisosteres in Medicinal Chemistry |
| title_auth | Bioisosteres in Medicinal Chemistry |
| title_exact_search | Bioisosteres in Medicinal Chemistry |
| title_full | Bioisosteres in Medicinal Chemistry ed. by Nathan Brown ... |
| title_fullStr | Bioisosteres in Medicinal Chemistry ed. by Nathan Brown ... |
| title_full_unstemmed | Bioisosteres in Medicinal Chemistry ed. by Nathan Brown ... |
| title_short | Bioisosteres in Medicinal Chemistry |
| title_sort | bioisosteres in medicinal chemistry |
| topic | Bioisosterie (DE-588)4145607-5 gnd Pharmazeutische Chemie (DE-588)4132158-3 gnd |
| topic_facet | Bioisosterie Pharmazeutische Chemie Aufsatzsammlung |
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