Diversity-Oriented Synthesis Basics and Applications in Organic Synthesis, Drug Discovery, and Chemical Biology

Discover an enhanced synthetic approach to developing and screening chemical compound libraries

Diversity-oriented synthesis is a new paradigm for developing large collections of structurally diverse small molecules as probes to investigate biological pathways. This book presents the most effective methods in diversity-oriented synthesis for creating small molecule collections. It offers tested and proven strategies for developing diversity-oriented synthetic libraries and screening methods for identifying ligands. Lastly, it explores some promising new applications based on diversity-oriented synthesis that have the potential to dramatically advance studies in drug discovery and chemical biology.

Diversity-Oriented Synthesis begins with an introductory chapter that explores the basics, including a discussion of the relationship between diversity-oriented synthesis and classic combinatorial chemistry. Divided into four parts, the book:

• Offers key chemical methods for the generation of small molecules using diversity-oriented principles, including peptidomimetics and macrocycles
• Expands on the concept of diversity-oriented synthesis by describing chemical libraries
• Provides modern approaches to screening diversity-oriented synthetic libraries, including high-throughput and high-content screening, small molecule microarrays, and smart screening assays
• Presents the applications of diversity-oriented synthetic libraries and small molecules in drug discovery and chemical biology, reporting the results of key studies and forecasting the role of diversity-oriented synthesis in future biomedical research

This book has been written and edited by leading international experts in organic synthesis and its applications. Their contributions are based on a thorough review of the current literature as well as their own firsthand experience developing synthetic methods and applications.

Clearly written and extensively referenced, Diversity-Oriented Synthesis introduces novices to this highly promising field of research and serves as a springboard for experts to advance their own research studies and develop new applications.

ANDREA TRABOCCHI, PhD, is Assistant Professor of Organic Chemistry at the University of Florence. Dr. Trabocchi leads research in diversity-oriented synthesis, peptidomimetic chem-istry, chemical genetics, and conformational analysis.

Foreword

Stuart L. Schreiber

Preface

List of Contributors

Abbreviations

1 The Basics of Diversity-Oriented Synthesis
Kieron M. G. O’Connell, Warren R. J. D. Galloway and David R. Spring

1.1 Introduction

1.2 What is Diversity-Oriented Synthesis?

1.3 Small Molecules and Biology

1.4 Comparing DOS, TOS and Combinatorial Chemistry (Focused Library Synthesis)

1.5 Molecular Diversity

1.6 Molecular Diversity and Chemical Space

1.7 Synthetic Strategies for Creating Molecular Diversity

1.8 Reagent-Based Approaches to Diversity Generation

1.9 A Substrate-Based Approach to Skeletal Diversity Generation

1.10 Other Build/Couple/Pair Examples

1.11 Concluding Remarks

1.12 References

Part I Chemical Methodology in Diversity-Oriented Synthesis

2 Strategies Applications of Multicomponent Reactions (MCRs) to Diversity-Oriented Synthesis
John M. Knapp, Mark J. Kurth, Jared T. Shaw and Ashkaan Younai

2.1 Introduction

2.2 MCR Products for HTS

2.3 MCRs as Starting Points for DOS

2.4 Conclusion

2.5 References

3 Cycloaddition Reactions in Diversity-Oriented Synthesis
Giovanni Muncipinto

3.1 Introduction

3.2 [4+2] Cycloaddition Reactions

3.3 Diels-Alder Reaction

3.4 Inverse Electron Demand Diels-Alder Reaction

3.5 1,3-dipolar Cycloaddition Reactions

3.6 Miscellaneous Cycloadditions

3.7 Conclusion

3.8 References

4 Phosphine Organocatalysis as the Platform for Diversity-Oriented Synthesis
Ohyun Kwon and Zhiming Wang

4.1 Introduction

4.2 DOS using Phosphine Organocatalysis

4.2.1 Phosphine Organocatalysis of Allenes with Imines

4.3 Skeletal Diversity Based on a Phosphine Catalysis/Combinatorial Scaffolding Strategy

4.4 A DOS Library Based on Phosphine Organocatalysis: Biological Screening, Analogue Synthesis, and Structure–Activity Relationship Analysis

4.5 Conclusions

4.6 References

5 Domino Reactions in Library Synthesis
Matthew G. LaPorte, John R. Goodell, Sammi Tsegay and Peter Wipf

5.1 Introduction

5.2 Pericyclic Domino Reactions

5.3 Anionic Domino Reactions

5.4 Transition Metal Mediated Domino Reactions

5.5 Radical Domino Reactions

5.6 Conclusions

5.7 References

6 Diversity-Oriented Synthesis of Amino Acid-Derived Scaffolds and Peptidomimetics: A Perspective
Andrea Trabocchi

6.1 Introduction

6.2 Definition and Classification of Peptidomimetics

6.3 Early Combinatorial Approaches to Peptidomimetic Scaffolds

6.4 Amino Acid-Derived Scaffolds

6.5 Macrocyclic Peptidomimetic Scaffolds

6.6 Conclusion

6.7 References

7 Solid-phase Synthesis Enabling Chemical Diversity
Viktor Krchňák and Nadĕ?da Cankařová

7.1 Introduction

7.2 Skeletal Diversity

7.3 Substrate-Based Strategy (Folding Process)

7.4 Stereochemical Diversity

7.5 Appendages Diversity

7.6 Build/Couple/Pair Strategy

7.7 Scaffold Hopping

7.8 Conclusion

7.9 References

8 Macrocycles as Templates for Diversity Generation in Drug Discovery
Eric Marsault

8.1 Introduction

8.2 Challenges Associated with Macrocycles

8.3 Macrocyclic Peptides

8.4 Peptidomimetic Macrocycles

8.5 Diversity-Oriented Strategies Based on Nonpeptidic Natural Products

8.6 Conclusion

8.7 References

Part II Chemical Libraries and Diversity-Oriented Synthesis

9 Diversity-Oriented Synthesis of Natural Product-Based Libraries
Mark Dow, Francesco Marchetti and Adam Nelson

9.1 Introduction

9.2 Libraries Inspired by Natural Product Scaffolds

9.3 Folding Pathways in the Synthesis of Natural Product-Like Libraries

9.4 Branching Pathways in the Synthesis of Natural Product-Like Libraries

9.5 Oligomer-Based Approaches to Natural Product-Like Libraries

9.6 Summary 9.7 References

10 Chemoinformatic Characterization of the Chemical Space and Molecular Diversity of Compound Libraries
José Luis Medina-Franco

10.1 Introduction

10.2 Concept of Chemical Space

10.3 General Aspects of Chemoinformatic Methods to Analyze the Chemical Space

10.4 Chemoinformatic-Based Analysis of Libraries Using Different Representations

10.5 Recent Trends in Computational Approaches to Characterize Compound Libraries

10.6 Concluding Remarks

10.7 References

11 DNA-Encoded Chemical Libraries
Luca Mannocci

11.1 Introduction

11.2 DNA-Encoded Chemical Libraries (DECL)

11.3 Selection and Decoding

11.4 Drug Discovery by DNA-Encoded Chemical Libraries

11.5 DNA-Encoded Chemical Libraries: Prospects and Outlook

11.6 Conclusion

11.7 References

PART III Screening Methods and Lead Identification

12 Experimental Approaches for Rapid Profiling and Characterization of Specific Biological Effects of Diversity-Oriented Synthesis Compounds
Eduard A. Sergienko and Susanne Heynen-Genel

12.1 Introduction

12.2 Basic Principles of HTS

12.3 Common Assay Methods and Techniques

12.4 Future Perspectives

12.5 References

13 Small-Molecule Microarrays
Hongyan Sun

13.1 Introduction

13.2 Chemical Library Design and Synthesis

13.3 Fabrication of SMMs

13.4 Applications of SMM

13.5 Summary and Outlook

13.6 References

14 Yeast as a Model in High-Throughput Screening of Small Molecule Libraries
Duccio Cavalieri, Carlotta De Filippo and Irene Stefanini

14.1 Introduction

14.2 Chemical Genetics and S. cerevisiae

14.3 Chemical Genomics and S. cerevisiae

14.4 Conclusions: the Route of Drug Discovery with the Budding Yeast

14.5 References

15 Virtual Screening Methods
Jürgen Bajorath

15.1 Introduction

15.2 Basic Virtual Screening Concepts

15.3 Molecular Similarity in Virtual Screening

15.4 Spectrum of Virtual Screening Approaches

15.5 Docking

15.6 Similarity Searching

15.7 Compound Classification

15.8 Machine Learning

15.9 Conclusions

15.10 References

16 Structure-Activity Relationship Data Analysis: Activity Landscapes and Activity Cliffs
Jürgen Bajorath

16.1 Introduction

16.2 Numerical SAR Analysis Functions

16.3 Principles and Intrinsic Limitations of Activity Landscape Design

16.4 Activity Landscape Representations

16.5 Defining and Identifying Activity Cliffs

16.6 Activity Cliff Survey

16.7 Activity Cliffs and SAR Information

16.8 Concluding Remarks

16.9 References

PART IV Applications in Chemical Biology and Drug Discovery

17 Diversity-Oriented Synthesis and Drug Development: Facilitating the Discovery of Novel Probes and Therapeutics
Jeremy R. Duvall, Eamon Comer and Sivaraman Dandapani

17.1 Introduction

17.2 Case Study 1 - Inhibition of Cytokine-Induced -Cell Apoptosis

17.3 Case Study 2 - Identification of Anti-Malarials

17.4 Case Study 3 - Targeting Protein-Protein and Protein-DNA Interactions

17.5 Conclusion

17.6 References

18 DOS-Derived Small-Molecule Probes in Chemical Biology
Nicholas Hill, Lingyan Du and Qiu Wang

18.1 Introduction

18.2 DOS-Derived Small-Molecule Probes

18.3 Developing Small-Molecule Probes of Complex Biological Pathways

18.4 Expanding the Collection of Important Biological Probes

18.5 Developing Probes for Therapeutically Desirable Phenotypes

18.6 Natural Product-Inspired Small-Molecule Probes Developed from DOS and Biology-Oriented Synthesis

18.7 Summary and Outlook

18.8 References

Index

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