Combinatorial Chemistry From Theory to Application,9783527306930

Combinatorial Chemistry From Theory to Application

by ; ; ; ;
Edition: 2nd
ISBN13: 9783527306930
ISBN10: 3527306935
Format: Hardcover
Pub. Date: 2006-05-12
Publisher(s): Wiley-VCH
List Price: $348.25

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Summary

The new edition of this practice-oriented handbook features thoroughly updated contents, including recent developments in parallel synthesis. A new chapter on screening complements the overview of combinatorial strategy and synthetic methods. "Experimental details and complete reaction data [...] are a constant theme running through this work" (Angewandte Chemie) "Recommended to newcomers in the field of combinatorial chemical synthesis because of its broad scope" (Journal of the American Chemical Society)

Author Biography

Willi Bannwarth is full Professor for Organic Chemistry at the Albert-Ludwigs University Freiburg (Germany). Having studied Chemistry in M��er and Konstanz, he worked as a postdoctoral fellow with Sir A. Battersby in Cambridge (UK). In 1979, he joined Roche in Basel (Switzerland) where he was head of nucleotide and peptide chemistry and later was named head of combinatorial chemistry, a technique which he had introduced at Roche. In 1996 he moved to Byk Gulden Pharmaceuticals (now Altanapharma) in Konstanz to build a cominatorial chemistry facility there. In 1999 he was appointed professor for Organic chemistry at the University of Freiburg where he focuses on combinatorial and bioorganic chemistry.

Table of Contents

Preface XV
General introduction XVII
List of Authors XXI
1 Purification Principles in High-Speed Solution-Phase Synthesis
1(32)
Steffen Weinbrenner and C. Christoph Tzschucke
1.1 Introduction
1(1)
1.2 Liquid-Liquid Extraction
2(8)
1.2.1 Aqueous Work-Up
2(4)
1.2.2 Phase-Separation Techniques
6(1)
1.2.3 Fluorous Biphasic Systems
6(3)
1.2.4 Ionic Liquids
9(1)
1.3 Solid-Phase Extraction
10(9)
1.3.1 Silica Gel and Alumina
10(1)
1.3.2 Fluorous Silica Gel
11(3)
1.3.3 Ion Exchange
14(5)
1.4 Covalent Scavengers
19(2)
1.4.1 Solution Scavengers
19(2)
1.5 Polymer-Assisted Solution-Phase Chemistry (PA SP)
21(5)
1.5.1 Scavenger Resins
21(3)
1.5.2 Resin Capture
24(2)
1.6 Complex Purification Strategies
26(3)
1.7 Conclusion and Outlook
29(1)
References
29(4)
2 Linkers for Solid-Phase Organic Synthesis (SPOS) and Combinatorial Approaches on Solid Supports
33(78)
Willi Bannwarth
2.1 General
33(1)
2.2 Linkers for Functional Groups
34(27)
2.2.1 Linkers for Carboxyl Functions
34(2)
2.2.2 Linkers for Amino Functions
36(1)
2.2.2.1 Linkers Based on Benzyloxycarbonyl (Z)
36(1)
2.2.2.2 Linker Based on tert-Butyloxycarbonyl (Boc)
40(1)
2.2.2.3 A Urethane Linker Cleavable by Fluoride Ions
41(1)
2.2.2.4 Benzyl-Linked Approaches for Secondary Amines
42(1)
2.2.2.5 Linkers Based on Acetyldimedone
44(1)
2.2.2.6 Trityl Linker
46(4)
2.2.3 Linkers for the Attachment of Alcohols or Phenols
50(1)
2.2.3.1 Linker Based on the Tetrahydropyranyl (THP) Group
50(1)
2.2.3.2 Silyl Linker for the Attachment of Alcohols
53(1)
2.2.3.3 Miscellaneous Linkers for Alcohols
56(1)
2.2.3.4 Serine-Based Linker for Phenols
57(1)
2.2.3.5 Carboxy-Functionalized Resins for the Attachment of Phenols
58(1)
2.2.4 Acetal Linker for the Preparation of Aldehydes
58(3)
2.3 Traceless Linker Systems
61(28)
2.3.1 Application of Hofmann Elimination in Linker Design
61(3)
2.3.2 Traceless Linkers Based on Silyl Functionalization
64(4)
2.3.3 Traceless Linkers Based on C–C Coupling Strategies
68(3)
2.3.4 Traceless Linkers Based on π-Complexation
71(1)
2.3.5 Traceless Linkers Based on Olefin Metathesis
71(7)
2.3.6 Traceless Synthesis Using Polymer-Bound Triphenylphosphine
78(2)
2.3.7 Decarboxylation-Based Traceless Linking
80(1)
2.3.8 Traceless Linker Based on Aryl Hydrazides
81(2)
2.3.9 Triazene-Based Traceless Linker
83(2)
2.3.10 Traceless Linker Based on Sulfones
85(1)
2.3.11 Traceless Concept Based on Cycloaddition-Cycloreversion
85(4)
2.4 Photolabile Linker Units
89(4)
2.4.1 Introduction
89(1)
2.4.2 Linkers Based on o-Nitrobenzyl
89(2)
2.4.3 Photocleavable Linker Based on Pivaloyl Glycol
91(2)
2.5 Safety-Catch Linkers
93(8)
2.6 Dual Linkers and Analytical Constructs
101(4)
2.7 Summary and Outlook
105(1)
References
105(6)
3 Cyclative Cleavage: A Versatile Concept in Solid-Phase Organic Chemistry
111(32)
Josef Pernerstorfer
3.1 Principles
111(1)
3.2 Carbon-Heteroatom Bond Formation
112(21)
3.2.1 Hydantoins
112(3)
3.2.2 Pyrazolones
115(1)
3.2.3 2-Aminoimidazolones
116(2)
3.2.4 Urazoles and Thiourazoles
118(1)
3.2.5 Oxazolidinones
119(1)
3.2.6 Diketopiperazine Derivatives
120(3)
3.2.7 4,5-Dihydro-3(2H)-pyridazinones
123(1)
3.2.8 Dihydropyridines
124(1)
3.2.9 5,6-Dihydropyrimidine-2,4-diones
125(1)
3.2.10 2,4-(1H,3H)-Quinazolinediones
126(1)
3.2.11 Quinazolin-4(3H)-ones
126(2)
3.2.12 4-Hydroxyquinolin-2(114)-ones
128(1)
3.2.13 3,4-Dihydroquinoxalin-2-ones
128(1)
3.2.14 1,4-Benzodiazepine-2,5-diones
129(1)
3.2.15 Oxacephams
129(1)
3.2.16 Lactones
130(3)
3.2.17 Tetrahydrofurans
133(1)
3.3 Formation of C–C Bonds
133(4)
3.3.1 Tetramic Acids
133(1)
3.3.2 Wittig-Type Reactions
134(2)
3.3.3 Stille Reactions
136(1)
3.3.4 S-Ylides
137(1)
3.3.5 Ring-Closing Metathesis
137(1)
3.4 Miscellaneous
137(3)
3.4.1 Furans
138(1)
3.4.2 Phenols
138(2)
3.5 Summary
140(1)
References
140(3)
4 C–C Bond-Forming Reactions
143(218)
Wolfgang K.-D. Brill and Gianluca Papeo
4.1 General
143(1)
4.2 Transition Metal-Mediated Vinylations, Arylations, and Alkylations
143(46)
4.2.1 The Suzuki Coupling
144(15)
4.2.2 The Heck Reaction
159(5)
4.2.3 The Sonogashira Coupling
164(8)
4.2.4 The Stille Coupling
172(2)
4.2.5 Remarks on Pd-mediated Couplings on a Polymeric Support
174(1)
4.2.6 Experimental Approach
175(1)
4.2.6.1 Materials and Methods
175(14)
4.3 Miscellaneous Aryl-Aryl Couplings
189(4)
4.3.1 Ullmann/Wurz Coupling on a Polymeric Support
189(1)
4.3.2 Intermolecular Alkyl-Alkyl Coupling
190(2)
4.3.3 Negishi Couplings
192(1)
4.4 Alkene Metathesis Reactions
193(7)
4.4.1 Ring-Closing Metathesis (RCM) Reactions
195(4)
4.4.2 Cross-Metathesis (CM) Reactions
199(1)
4.5 Cycloaddition Reactions on a Polymeric Support
200(63)
4.5.1 Cl Fragments (Additions of Carbenes to Alkenes)
201(6)
4.5.2 Electron-Deficient C2 Fragments (Cycloadditions Involving Azomethines, Nitrones, Nitrile Oxides, and Dienes)
207(9)
4.5.3 Electron-Rich C2 Fragments ([2 + 1], [2 + 2], [2 + 3], [2 + 4]- Cycloadditions, Additions with Nitrile Imines, Nitrile Oxides, and Chalcones)
216(8)
4.5.4 C–X Fragment on Solid Support
224(5)
4.5.5 C–C–X Fragments on the Polymeric Support
229(4)
4.5.6 C–X–C Fragment
233(2)
4.5.7 C–X–Y-Fragment (Nitrile Oxide on Solid Phase)
235(2)
4.5.8 C–C–C–C Fragments on Solid Phase
237(15)
4.5.9 C–C–C–X Fragments on Solid Support
252(2)
4.5.10 C–C–X–C Fragment on Solid Support (Grieco Three-Component Condensation)
254(1)
4.5.11 C–X–X–C Fragment on Solid Support
255(2)
4.5.12 C–C–X–X Fragment on Solid Support ([4 + 1]-Cycloaddition)
257(1)
4.5.13 Cycloadditions Involving Larger Support-Bound Fragments: Intramolecular Hetero Diels-Alder
257(3)
4.5.14 Pauson-Khand and Nicolas Reaction
260(3)
4.5.15 C-Nitroalkene Additions
263(1)
4.6 Multicomponent Reactions (MCRs)
263(15)
4.6.1 Ugi Four-Component Reaction
264(1)
4.6.1.1 Ugi Reaction with Solid-Supported Isonitriles
264(1)
4.6.1.2 Ugi reaction with Solid-Supported Amines
267(1)
4.6.1.3 Ugi Reaction with Solid-Supported Carboxylic Acid
269(1)
4.6.1.4 Derivatization of Boronic Acids
270(1)
4.6.2 Other MCRs Using Isonitriles
271(1)
4.6.2.1 Petasis (Borono-Mannich) Condensation
271(1)
4.6.2.2 Imidazo[1,2-α]pyridines
272(1)
4.6.2.3 Biginelli Dihydropyrimidines Synthesis
273(1)
4.6.2.4 Thiophene Synthesis
275(1)
4.6.2.5 Tetrahydropyridones
276(1)
4.6.2.6 Cyclization
278(1)
4.6.2.7 Cleavage
278(1)
4.7 Electrophiles Bound to the Polymeric Support
278(36)
4.7.1 Reactions with Organyls of Zn, Mg, Li
278(1)
4.7.1.1 Reactions Involving Grignard Reagents, Organolithium, and Organozinc Reagents
279(1)
4.7.1.2 Reactions with Water-Sensitive Reagents such as Grignard Reagents, Lithium Alkyls, or Zinc Organyls [375] on Solid Phases
279(3)
4.7.2 Indium-Mediated Allylation of Support-Bound Aldehydes
282(2)
4.7.3 Sn/Pd-Mediated C-Allylation of Solid-Phase-Bound Aldehydes
284(2)
4.7.4 Metal-free Alkylations by Acyl Halides on Polymeric Supports
286(1)
4.7.5 Nucleophilic Aromatic Substitution with C-Nucleophiles
286(3)
4.7.6 Pyridine-N-Oxides
289(1)
4.7.7 Trapping Phosphorus Ylides with a Ketone Bound to the Solid Phase
289(1)
4.7.8 Michael Acceptor on Solid Phase (Route to 3,4,6-Trisubstituted Pyrid2-ones)
290(1)
4.7.9 Solid phase N-Acyliminium Ions, Imines and Glyoxylate Chemistry
291(3)
4.7.10 Solid-Supported Imines and Glyoxylate
294(5)
4.7.11 Solid-Phase Pictet-Spengler Reactions
299(8)
4.7.12 Solid-Phase Baylis-Hillman Reaction
307(3)
4.7.13 Solid-Phase Fischer Indole Synthesis
310(1)
4.7.14 Solid-Phase Madelung Indole Synthesis
311(1)
4.7.15 Boron Enolates with Support-Bound Aldehydes
312(2)
4.7.16 Summary of Solid-Supported Electrophiles
314(1)
4.8 Generation of Carbanions on Solid Supports
314(26)
4.8.1 Transition Metal-Mediated Carbanion Equivalent Formations
320(1)
4.8.2 Lewis Acid-Mediated Electrophilic Substitutions
321(6)
4.8.3 Generation of Stabilized Carbanions Under Basic Conditions
327(7)
4.8.4 Experimental Approach
334(6)
4.8.5 Stereoselective Alkylations on a Chiral Solid Phase
340(1)
4.9 Solid-Phase Radical Reactions
340(7)
4.10 Outlook
347(1)
References
347(14)
5 Combinatorial Synthesis of Heterocycles
361(96)
Eduard R. Felder and Andreas L. Marzinzik
5.1 Introduction
361(2)
5.2 Benzodiazepines
363(6)
5.3 Hydantoins and Thiohydantoins
369(6)
5.4 β-Lactams (Azetidin-2-ones)
375(1)
5.5 β-Sultams
376(3)
5.6 Imidazoles
379(5)
5.7 Pyrazoles and Isoxazoles
384(3)
5.8 Thiazolidinones
387(3)
5.9 Triazoles
390(6)
5.10 Oxadiazoles
396(5)
5.10.1 1,2,4-Oxadiazoles
397(2)
5.10.2 1,3,4-Oxadiazoles
399(2)
5.11 Piperazinones
401(5)
5.12 Piperazinediones (Diketopiperazines)
406(7)
5.12.1 Diketopiperazines via Backbone Amide Linker (BAL) [117]
406(3)
5.12.2 Piperazinediones by Acid Cyclative Cleavage; Method A, including Reductive Alkylation
409(1)
5.12.3 Piperazinediones by Acid Cyclative Cleavage; Method B, including SN2 Displacement
410(3)
5.13 Diketomorpholines
413(1)
5.14 Triazines
413(4)
5.15 Pyrimidines
417(4)
5.16 Indoles
421(7)
5.17 Quinazolines
428(11)
5.18 Benzopiperazinones and Tetrahydroquinoxalines
439(4)
5.19 Tetrahydro-β-carbolines
443(6)
5.20 Outlook
449(1)
References
449(8)
6 Polymer-Supported Reagents: Preparation and Use in Parallel Organic Synthesis
457(56)
Berthold Hinzen and Michael G. Hahn
6.1 Introduction
457(2)
6.2 Preparation and Use of PSRs
459(38)
6.2.1 Covalent Linkage Between the Active Species and Support
459(1)
6.2.1.1 PSRs Prepared by Solid-Phase Chemistry
459(1)
6.2.1.2 PSRs Prepared by Polymerization
483(7)
6.2.2 Immobilization Using Ionic Interactions
490(1)
6.2.2.1 Oxidants
490(1)
6.2.2.2 Reducing Agents
492(1)
6.2.2.3 Alkoxides Bound to a Polymer Support
494(1)
6.2.2.4 Horner-Emmons Reagents on Supports
494(1)
6.2.2.5 Halogenating Agents
495(2)
6.3 Support-Bound Sequestering and Scavenging Agents
497(1)
6.4 Combination of PSRs
497(12)
6.5 Summary and Conclusion
509(1)
References
509(4)
7 Encoding Strategies for Combinatorial Libraries
513(6)
Berthold Hinzen
7.1 Introduction
513(1)
7.2 Positional Encoding
514(1)
7.3 Graphical/Barcode Encoding
514(1)
7.4 Chemical Encoding
514(1)
7.5 Mass Spectrometric Encoding
515(1)
7.6 Radiofrequency Encoding
516(1)
7.7 Conclusion
516(1)
References
516(3)
8 Automation and Devices for Combinatorial Chemistry and Parallel Organic Synthesis
519(40)
Christian Zechel
8.1 Introduction
519(1)
8.2 Synthesis
520(30)
8.2.1 General Remarks
520(2)
8.2.2 Manual Systems
522(18)
8.2.3 Semi-Automated Systems
540(1)
8.2.4 Automated Systems
540(6)
8.2.5 Special Applications
546(1)
8.2.5.1 Process Development
546(1)
8.2.5.2 Equipment for Parallel Reactive Gas Chemistry
549(1)
8.3 Liquid-Liquid Extraction
550(1)
8.4 Equipment for High-Throughput Evaporation
551(4)
8.5 Automated Solid and Resin Dispensing
555(1)
8.6 Suppliers
556(3)
9 Computer-Assisted Library Design
559(56)
Andreas Dominik
9.1 Introduction
559(7)
9.1.1 Optimizing Combinatorial Libraries
559(1)
9.1.2 A Computer-Assisted Design Strategy
560(2)
9.1.3 What is Diversity?
562(1)
9.1.3.1 First Examples
562(1)
9.1.3.2 Diversity of Drug Molecules
562(1)
9.1.3.3 Diversity and Similarity
564(2)
9.2 How Do We Compute Diversity?
566(2)
9.2.1 An Overview
566(1)
9.2.2 Descriptors
567(1)
9.2.3 Classification and Mapping
567(1)
9.2.4 Interpretation of Results: Summary
568(1)
9.3 Descriptors
568(19)
9.3.1 Simple Filters
571(1)
9.3.2 Physico-chemical Constants
571(1)
9.3.2.1 Estimation of logP Values
571(1)
9.3.2.2 Estimation of pKA Values
572(1)
9.3.3 Drug-Likeness
572(1)
9.3.3.1 The Rule of 5
572(1)
9.3.3.2 Artificial Neural Networks
573(1)
9.3.3.3 Further Improvements of Drug-Likeness Prediction
573(1)
9.3.3.4 ADME and Toxicity Profiling
574(1)
9.3.4 Molecular Fingerprints
575(1)
9.3.5 Substructure Descriptors
575(1)
9.3.6 Single Atom Properties
576(1)
9.3.6.1 Atom Charges
577(1)
9.3.6.2 Atomic Lipophilicity Parameters
577(1)
9.3.7 Topological Indices
577(1)
9.3.7.1 Atom Indices
577(1)
9.3.7.2 Molecule Indices
578(1)
9.3.8 Topological Autocorrelation and Cross-correlation Coefficients
578(2)
9.3.9 Scaffold-based Similarity
580(1)
9.3.10 Descriptors from a Pharmacophore Model
580(1)
9.3.11 Stereochemistry
581(1)
9.3.12 Descriptors from the Three-Dimensional Structure
582(1)
9.3.13 Polar Surface Area (PSA)
583(1)
9.3.14 Distance Matrix
583(1)
9.3.15 Autocorrelation Coefficients
583(1)
9.3.15.1 Based on Atom Coordinates
585(1)
9.3.15.2 Based on Surface Properties
585(1)
9.3.15.3 Based on Potential Fields
586(1)
9.3.16 Radial Basis Function (RBF)
586(1)
9.3.17 Virtual Screening
586(1)
9.4 Clustering and Mapping Algorithms
587(6)
9.4.1 Distance Metric
587(1)
9.4.1.1 Tanimoto Coefficient
587(1)
9.4.1.2 Euclidean Distance
589(1)
9.4.1.3 Nonlinear Distance Scaling
589(1)
9.4.1.4 Mahalanobis Distance
589(1)
9.4.2 Dissimilarity-Based Selection
589(1)
9.4.3 Mapping-Based Selection
590(1)
9.4.3.1 Nonlinear Mapping
590(1)
9.4.3.2 Self-Organizing Maps
591(1)
9.4.3.3 Minimal Spanning Tree
592(1)
9.4.4 Cluster-Based Selection
592(1)
9.4.4.1 Hierarchical Clustering Analysis
592(1)
9.4.5 Partition-Based Selection
593(1)
9.5 Strategies for Compound Selection
593(6)
9.5.1 Optimization Based on Diversity of Building Blocks
594(1)
9.5.1.1 Advantages of Educt-Based Optimization
594(1)
9.5.2 Optimization Based on Diversity of Product Libraries
595(1)
9.5.2.1 Advantages of Product-Based Optimization
595(2)
9.5.3 Library Selection
597(1)
9.5.4 Evolutionary Design Circle
598(1)
9.6 Comparison of Descriptors and Selection Methods
599(4)
9.6.1 Topological Descriptors
599(3)
9.6.2 Descriptors Based on Three-Dimensional Structure
602(1)
9.6.3 Clustering Methods
602(1)
9.6.4 Summary
603(1)
9.7 Example Library of Thrombin Inhibitors
603(7)
9.7.1 Virtual Library Design
605(1)
9.7.2 Final Library Design
606(1)
9.7.2.1 Maximum Diversity Library
607(1)
9.7.2.2 Targeted Library
607(1)
9.7.2.3 Descriptor Sets
607(1)
9.7.3 Comparison of the Libraries
607(2)
9.7.4 Summary
609(1)
References
610(5)
10 Assays for High-Throughput Screening in Drug Discovery 615(44)
Christian M. Apfel and Thilo Enderle
10.1 Screening in Drug Discovery
615(6)
10.1.1 The Role of HTS
615(2)
10.1.2 Overview of Screening Assays
617(1)
10.1.3 Requirements for Successful HTS
617(2)
10.1.4 Target Classes
619(1)
10.1.4.1 Overview
619(1)
10.1.4.2 G-Protein-Coupled Receptors (GPCR)
619(2)
10.2 Assay Methods Based on Different Readouts
621(25)
10.2.1 Radioactivity
621(1)
10.2.1.1 General
621(1)
10.2.1.2 Scintillation Proximity Assay (SPA)
622(1)
10.2.1.3 FlashPlate™/Scintistrip™/Cytostar-T™
624(1)
10.2.1.4 Instrumentation for Radioisotope Assays
625(1)
10.2.2 Colorimetry
626(2)
10.2.3 Fluorescence
628(1)
10.2.3.1 General
628(1)
10.2.3.2 Fluorescence Intensity (FI)
631(1)
10.2.3.3 Fluorescence Polarization (FP)
632(1)
10.2.3.4 Fluorescence Resonance Energy Transfer (FRET)
635(1)
10.2.3.5 Time-Resolved Fluorescence (TRF)
637(1)
10.2.3.6 Fluorescence Lifetime (FLT)
641(1)
10.2.3.7 Fluorescence Correlation Spectroscopy (FCS)
641(1)
10.2.3.8 Fluorescent Intensity Distribution Analysis (FIDA)
641(1)
10.2.4 Chemiluminescence and Bioluminescence
642(1)
10.2.4.1 General
642(1)
10.2.4.2 Aequorin Ca²+ Assay
643(1)
10.2.4.3 AlphaScreen™
644(1)
10.2.4.4 BRET™
645(1)
10.3 Special Assay Applications with Optical Readout
646(3)
10.3.1 Fluorimetric Imaging Plate Reader (FLIPR)
646(1)
10.3.2 Reporter Assays
646(2)
10.3.3 Assays Based on Enzyme Fragment Complementation (EFC)
648(1)
10.3.3.1 General
648(1)
10.3.3.2 Low Affinity Complementation System
648(1)
10.3.3.3 High Affinity Complementation System
648(1)
Abbreviations
649(1)
Trademarks and Suppliers
650(1)
References
651(8)
Appendix: Cheminformatics and Web Resources for Combinatorial Chemistry 659(4)
Berthold Hinzen and Johannes Köbberling
A.1 Websites
659(1)
A.2 (Online) Journals
660(1)
A.3 Companies and Academic Groups Involved in Combinatorial Chemistry
660(1)
A.4 Reaction Databases
661(1)
A.5 Summary
661(2)
Index 663

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