Molecular design: concepts and applications
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Weinheim
WILEY-VCH
2008
|
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XV, 262 S. Ill., graph. Darst. 240 mm x 170 mm |
| ISBN: | 9783527314324 3527314326 |
Staff View
MARC
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| 650 | 4 | |a Drug Design | |
| 650 | 4 | |a Models, Molecular | |
| 650 | 4 | |a Molecular Structure | |
| 650 | 4 | |a Molecular structure |x Computer simulation | |
| 650 | 4 | |a Molecular structure |x Computer simulation |v Problems, exercises, etc | |
| 650 | 4 | |a Molecules |x Computer simulation | |
| 650 | 4 | |a Molecules |x Computer simulation |v Problems, exercises, etc | |
| 650 | 4 | |a Molecules |x Models |x Computer simulation | |
| 650 | 4 | |a Molecules |x Models |x Computer simulation |v Problems, exercises, etc | |
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Record in the Search Index
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|---|---|
| adam_text |
XIII
Contents
Foreword V
Preface IX
1
Molecular Objects and Design Objectives
1
1.1
What is a Molecule?
1
1.2
Simplistic Molecular Representations
2
1.3
The Molecular Surface
3
1.4
Molecular Shape
7
1.5
The Topological Molecular Graph
8
1.6
Molecular Properties and Graph Invariants
11
1.7
The Drug-likeness Concept
14
1.8
Scaffolds, Linkers, and Side-chains
16
1.9
Substructure Similarity and "Privileged Motifs"
19
1.10
Molecules as Strings
23
1.11
Constructing Molecules from Strings
25
1.12
From Elements to Atom Types
27
1.13
Entering the Third Dimension: Automatic
Conformer
Generation
29
1.14
The "Bioactive" Conformation
32
Literature
33
2
Receptor-Ligand Interaction
35
2.1
The Thermodynamics of Protein-Iigand Interaction
35
2.2
The
Entropie
Contribution
38
2.3
From Theory to Experiment:
K¡
and
ÍC50
45
2.4
QSAR: Estimating Quantitative Structure-Activity Relationships
47
2.4.1
Free-Wilson Analysis
49
2.4.2
The Hansch Model
52
2.4.3
3D-QSAR
52
2.5
Types of Receptor-Ligand Interaction
54
2.6
The "Biophore" Concept
58
2.7
Potential Pharmacophoric Points
62
2.8
The Correlation Vector Approach to Pharmacophore Modeling
66
XIV
Contents
2.9
"Hard Sphere" and "Fuzzy" Pharmacophore Models
68
2.10
Lessons from Automated Ligand Docking and Scoring: What Works and
What Does Not
74
2.11
Fits Like a Glove: Alternative Ligand Binding Modes and Induced Fit
Effects
77
Literature
84
3
Creating the Design
87
3.1
Why We Need Computer-assisted Molecular Design
87
3.2
The Number of Drug Targets is Limited
89
3.3
Ligand Binding Sites
100
3.4
Ligand-based Design of Compound Libraries
208
3.5
Similar Compounds Do Not Necessarily Interact with Their Target in
Similar Ways 111
3.6
The Same Ligand Can Adopt Multiple Binding Modes
113
3.7
GPCRs Represent a Challenging Target Family
114
3.8
Natural Products Are a Source of Inspiration
116
3.9
Transition State Analogs Are Potent Enzyme Inhibitors
119
3.10
New Targets Sometimes Require a New Ligand Design Concept
123
3.11
De novo
Design Concepts
124
3.12
Primary and Secondary Constraints in
de novo
Design
125
Literature
145
4
Virtual Screening Triage
249
4.1
The Drag Discovery Pipeline
250
4.2
High-throughput Screening
(HTS):
Why Is It Successful?
252
4.3
From Hit to Lead
253
4.4
Rationalizing the Design Process
254
4.5
From High to Low Diversity
256
4.6
Quantifying Diversity is Difficult
260
4.7
From Negative Design to Positive Design
262
4.8
Watch Out for Frequent Hitters!
265
4.9
Shape-matching: A Coarse-grained Filtering Step
167
4.10
The Ultimate Goal: Scaffold-hopping
270
4.11
Assessing Chemotype Diversity in Focused Libraries
272
4.12
It Works! Examples of Successful Scaffold-hops Found by Virtual
Screening
272
4.13
Case Studies
278
4.13.1
Design of Kvl.5 Ion Channel Modulators
278
4.13.2
Virtual Screening of a Natural-product-derived Combinatorial Library
for Novel 5-Iipoxygenase Inhibitors
183
4.13.3
Scaffold
de novo
Design for Cannabinoid-l (CB-l) Receptor
Ligands
186
Literature
189
Contents XV
5
Secondary Design Constraints and Machine Learning
193
5.1
Physicochemistry and Pharmacokinetics
193
5.2
The "Rule of
5" 297
5.3
Pharmacokinetics
197
5.4
Absorption
199
5.5
Distribution
202
5.6
Metabolism
203
5.7
Elimination
206
5.8
Toxicity
207
5.9
Prodrugs and Bioisosteres
210
5.10
Machine Learning Methods Support Lead Finding and
Optimization
212
5.11
An Important Step: Data Scaling
232
5.12
Application of Machine Learning to Compound Library Design
233
5.13
A "Pharmacophore Road Map"
238
5.14
Case Studies
242
5.14.1
Predicting Cross-activities of Allosteric Modulators of Metabotropic
Glutamate
Receptors (mGluR)
242
5.14.2
Dopamine D3 Antagonists and ACE Inhibitors
243
5.14.3
An Artificial Ant System for Combinatorial Optimization
248
Literature
254
Subject Index
257 |
| adam_txt |
XIII
Contents
Foreword V
Preface IX
1
Molecular Objects and Design Objectives
1
1.1
What is a Molecule?
1
1.2
Simplistic Molecular Representations
2
1.3
The Molecular Surface
3
1.4
Molecular Shape
7
1.5
The Topological Molecular Graph
8
1.6
Molecular Properties and Graph Invariants
11
1.7
The Drug-likeness Concept
14
1.8
Scaffolds, Linkers, and Side-chains
16
1.9
Substructure Similarity and "Privileged Motifs"
19
1.10
Molecules as Strings
23
1.11
Constructing Molecules from Strings
25
1.12
From Elements to Atom Types
27
1.13
Entering the Third Dimension: Automatic
Conformer
Generation
29
1.14
The "Bioactive" Conformation
32
Literature
33
2
Receptor-Ligand Interaction
35
2.1
The Thermodynamics of Protein-Iigand Interaction
35
2.2
The
Entropie
Contribution
38
2.3
From Theory to Experiment:
K¡
and
ÍC50
45
2.4
QSAR: Estimating Quantitative Structure-Activity Relationships
47
2.4.1
Free-Wilson Analysis
49
2.4.2
The Hansch Model
52
2.4.3
3D-QSAR
52
2.5
Types of Receptor-Ligand Interaction
54
2.6
The "Biophore" Concept
58
2.7
Potential Pharmacophoric Points
62
2.8
The Correlation Vector Approach to Pharmacophore Modeling
66
XIV
Contents
2.9
"Hard Sphere" and "Fuzzy" Pharmacophore Models
68
2.10
Lessons from Automated Ligand Docking and Scoring: What Works and
What Does Not
74
2.11
Fits Like a Glove: Alternative Ligand Binding Modes and Induced Fit
Effects
77
Literature
84
3
Creating the Design
87
3.1
Why We Need Computer-assisted Molecular Design
87
3.2
The Number of Drug Targets is Limited
89
3.3
Ligand Binding Sites
100
3.4
Ligand-based Design of Compound Libraries
208
3.5
Similar Compounds Do Not Necessarily Interact with Their Target in
Similar Ways 111
3.6
The Same Ligand Can Adopt Multiple Binding Modes
113
3.7
GPCRs Represent a Challenging Target Family
114
3.8
Natural Products Are a Source of Inspiration
116
3.9
Transition State Analogs Are Potent Enzyme Inhibitors
119
3.10
New Targets Sometimes Require a New Ligand Design Concept
123
3.11
De novo
Design Concepts
124
3.12
Primary and Secondary Constraints in
de novo
Design
125
Literature
145
4
Virtual Screening Triage
249
4.1
The Drag Discovery Pipeline
250
4.2
High-throughput Screening
(HTS):
Why Is It Successful?
252
4.3
From Hit to Lead
253
4.4
Rationalizing the Design Process
254
4.5
From High to Low Diversity
256
4.6
Quantifying Diversity is Difficult
260
4.7
From Negative Design to Positive Design
262
4.8
Watch Out for Frequent Hitters!
265
4.9
Shape-matching: A Coarse-grained Filtering Step
167
4.10
The Ultimate Goal: Scaffold-hopping
270
4.11
Assessing Chemotype Diversity in Focused Libraries
272
4.12
It Works! Examples of Successful Scaffold-hops Found by Virtual
Screening
272
4.13
Case Studies
278
4.13.1
Design of Kvl.5 Ion Channel Modulators
278
4.13.2
Virtual Screening of a Natural-product-derived Combinatorial Library
for Novel 5-Iipoxygenase Inhibitors
183
4.13.3
Scaffold
de novo
Design for Cannabinoid-l (CB-l) Receptor
Ligands
186
Literature
189
Contents XV
5
Secondary Design Constraints and Machine Learning
193
5.1
Physicochemistry and Pharmacokinetics
193
5.2
The "Rule of
5" 297
5.3
Pharmacokinetics
197
5.4
Absorption
199
5.5
Distribution
202
5.6
Metabolism
203
5.7
Elimination
206
5.8
Toxicity
207
5.9
Prodrugs and Bioisosteres
210
5.10
Machine Learning Methods Support Lead Finding and
Optimization
212
5.11
An Important Step: Data Scaling
232
5.12
Application of Machine Learning to Compound Library Design
233
5.13
A "Pharmacophore Road Map"
238
5.14
Case Studies
242
5.14.1
Predicting Cross-activities of Allosteric Modulators of Metabotropic
Glutamate
Receptors (mGluR)
242
5.14.2
Dopamine D3 Antagonists and ACE Inhibitors
243
5.14.3
An Artificial Ant System for Combinatorial Optimization
248
Literature
254
Subject Index
257 |
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| id | DE-604.BV023069491 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:32:24Z |
| indexdate | 2024-07-20T09:29:35Z |
| institution | BVB |
| isbn | 9783527314324 3527314326 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016272653 |
| oclc_num | 191889929 |
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| physical | XV, 262 S. Ill., graph. Darst. 240 mm x 170 mm |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | WILEY-VCH |
| record_format | marc |
| spelling | Schneider, Gisbert 1965- Verfasser (DE-588)1089568355 aut Molecular design concepts and applications Gisbert Schneider ; Karl-Heinz Baringhaus Weinheim WILEY-VCH 2008 XV, 262 S. Ill., graph. Darst. 240 mm x 170 mm txt rdacontent n rdamedia nc rdacarrier Computer Simulation Drug Design Models, Molecular Molecular Structure Molecular structure Computer simulation Molecular structure Computer simulation Problems, exercises, etc Molecules Computer simulation Molecules Computer simulation Problems, exercises, etc Molecules Models Computer simulation Molecules Models Computer simulation Problems, exercises, etc Arzneimitteldesign (DE-588)4278218-1 gnd rswk-swf Arzneimitteldesign (DE-588)4278218-1 s DE-604 Baringhaus, Karl-Heinz Verfasser aut text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2973458&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=016272653&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Schneider, Gisbert 1965- Baringhaus, Karl-Heinz Molecular design concepts and applications Computer Simulation Drug Design Models, Molecular Molecular Structure Molecular structure Computer simulation Molecular structure Computer simulation Problems, exercises, etc Molecules Computer simulation Molecules Computer simulation Problems, exercises, etc Molecules Models Computer simulation Molecules Models Computer simulation Problems, exercises, etc Arzneimitteldesign (DE-588)4278218-1 gnd |
| subject_GND | (DE-588)4278218-1 |
| title | Molecular design concepts and applications |
| title_auth | Molecular design concepts and applications |
| title_exact_search | Molecular design concepts and applications |
| title_exact_search_txtP | Molecular design concepts and applications |
| title_full | Molecular design concepts and applications Gisbert Schneider ; Karl-Heinz Baringhaus |
| title_fullStr | Molecular design concepts and applications Gisbert Schneider ; Karl-Heinz Baringhaus |
| title_full_unstemmed | Molecular design concepts and applications Gisbert Schneider ; Karl-Heinz Baringhaus |
| title_short | Molecular design |
| title_sort | molecular design concepts and applications |
| title_sub | concepts and applications |
| topic | Computer Simulation Drug Design Models, Molecular Molecular Structure Molecular structure Computer simulation Molecular structure Computer simulation Problems, exercises, etc Molecules Computer simulation Molecules Computer simulation Problems, exercises, etc Molecules Models Computer simulation Molecules Models Computer simulation Problems, exercises, etc Arzneimitteldesign (DE-588)4278218-1 gnd |
| topic_facet | Computer Simulation Drug Design Models, Molecular Molecular Structure Molecular structure Computer simulation Molecular structure Computer simulation Problems, exercises, etc Molecules Computer simulation Molecules Computer simulation Problems, exercises, etc Molecules Models Computer simulation Molecules Models Computer simulation Problems, exercises, etc Arzneimitteldesign |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=2973458&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=016272653&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT schneidergisbert moleculardesignconceptsandapplications AT baringhauskarlheinz moleculardesignconceptsandapplications |