Solid-Phase Organic Synthesis E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 781

Veröffentlichungsjahr: 2012

Beschreibung

Presents both the fundamental concepts and the most recent applications in solid-phase organic synthesis

With its emphasis on basic concepts, Solid-Phase Organic Synthesis guides readers through all the steps needed to design and perform successful solid-phase organic syntheses. The authors focus on the fundamentals of heterogeneous supports in the synthesis of organic molecules, explaining the use of a solid material to facilitate organic synthesis. This comprehensive text not only presents the fundamentals, but also reviews the most recent research findings and applications, offering readers everything needed to conduct their own state-of-the-art science experiments.

Featuring chapters written by leading researchers in the field, Solid-Phase Organic Synthesis is divided into two parts:

• Part One, Concepts and Strategies, discusses the linker groups used to attach the synthesis substrate to the solid support, colorimetric tests to identify the presence of functional groups, combinatorial synthesis, and diversity-oriented synthesis. Readers will discover how solid-phase synthesis is currently used to facilitate the discovery of new molecular functionality. The final chapter discusses how using a support can change or increase reaction selectivity.

• Part Two, Applications, presents examples of the solid-phase synthesis of various classes of organic molecules. Chapters explore general asymmetric synthesis on a support, strategies for heterocyclic synthesis, and synthesis of radioactive organic molecules, dyes, dendrimers, and oligosaccharides.

Each chapter ends with a set of conclusions that underscore the key concepts and methods. References in each chapter enable readers to investigate any topic in greater depth.

With its presentation of basic concepts as well as recent findings and applications, Solid-Phase Organic Synthesis is the ideal starting point for students and researchers in organic, medicinal, and combinatorial chemistry who want to take full advantage of current solid-phase synthesis techniques.

Leseprobe

Contents

Cover

Title Page

Copyright

Preface

Acknowledgments

Contributors

Part I: Concepts and Strategies

Chapter 1: Linker Strategies In Modern Solid-Phase Organic Synthesis

1.1 Introduction

1.2 Classical Linker Strategies

1.3 Multifunctional Linker Strategies

1.4 Conclusions

References

Chapter 2: Colorimetric Test For Solid-Phase Organic Synthesis

2.1 Introduction

2.2 Functional Group Tests

2.3 Conclusions

References

Chapter 3: Practical Aspects of Combinatorial Solid-Phase Synthesis

3.1 Introduction

3.2 Strategies in Combinatorial Solid-Phase Synthesis

3.3 Equipment and Instrumentation

3.4 Characterization and Purification

3.5 Conclusions

Acknowledgments

References

Chapter 4: Diversity-Oriented Synthesis

4.1 Introduction

4.2 Small Molecules and Biology

4.3 Diversity-Oriented Synthesis, Target-Oriented Synthesis, and Combinatorial Chemistry

4.4 Molecular Diversity

4.5 Diversity-Oriented Synthesis on Solid Phase

4.6 Diversity-Oriented Synthesis Around Privileged Scaffolds

4.7 Diversity Linker Units in Solid-Phase Organic Synthesis

4.8 Conclusions

References

Chapter 5: Diversity-Oriented Synthesis of Privileged Heterocycles Using Divergent Strategy

5.1 Introduction

5.2 Divergent Synthesis of Natural Product-Like Polyheterocycles Using a Cyclic Iminium as a Single Key Intermediate

5.3 Conclusions

References

Chapter 6: Chemo- and Regioselectivity Enhancement in Solid-Supported Reactions

6.1 Introduction

6.2 Transition Metal-Mediated Solid-Supported Reactions

6.3 Non-Transition Metal-Mediated Solid-Supported Reactions

6.4 Traceless Cleavage

6.5 Conclusions

References

Part II: Applications

Chapter 7: Asymmetric Synthesis on Solid Support

7.1 Introduction

7.2 Asymmetric Chemical Transformations of Solid-Supported Substrates

7.3 Asymmetric Transformations Using Resin-Bound Chiral Catalysts and Auxiliaries

7.4 Conclusions

References

Chapter 8: Recent Advances in Microwave-Assisted Solid-Phase Synthesis of Heterocycles

8.1 Introduction

8.2 Fused 1,3-Oxazin-6-ones

8.3 Thiazolo[4,5-d]pyrimidine-5,7-diones

8.4 Pyrazoles

8.5 Hsp70 Modulators

8.6 Benzimidazo[2,1-b]quinazolin-12(5H)-ones

8.7 Imidazoles

8.8 1,4-Naphthoquinones

8.9 Phthalocyanines

8.10 1,2,3,4-Tetrahydroquinolines

8.11 1,2,3-Triazoles

8.12 2,8-Diaminopurines

8.13 Imidazolidin-4-ones

8.14 Indoles

8.15 1,2,3,4-Tetrahydroquinolines Using a SmI2-Cleavable Linker

8.16 Hydantoins

8.17 Imatinib

8.18 Isoindolines

8.19 2-(Benzylthio)imidazo[1,2a]-pyrimidin-5-ones

8.20 2-Aminobenzothiazoles

8.21 Pyrimidines, Pyrazoles, and Isoxazoles

8.22 Quinolin-2(1H)-ones and Coumarins

8.23 Benzofurans

8.24 i-Condensed Purines

8.25 2(1H)-Pyrazinones

8.26 Conclusions

References

Chapter 9: Solid-Phase Synthesis of Heterocycles From Peptides and Amino Acids

9.1 Introduction

9.2 Synthesis of Various Heterocycles

References

Chapter 10: Generation of Drug-Like Five-Membered Heterocyclic Libraries Using Carbon Disulfide and Merrifield Resin

10.1 Introduction

10.2 Solid-Phase Synthesis of Related Thiazole Compounds

10.3 Solid-Phase Synthesis of Benzoxazoles

10.4 Solid-Phase Synthesis of Related Pyrazole Compounds and 1,3,4-Triazoles via a Dithiocarbazate Linker

10.5 Solid-Phase Synthesis of 1,3,4-Oxadiazoles and 1,3,4-Thiadiazoles via Selective Cyclization

10.6 Solid-Phase Synthesis of 1,2,4-Thiadiazoles

10.7 Summary

References

Chapter 11: Recent Advances in Solid-Phase 1,3-Dipolar Cycloaddition Reactions

11.1 Introduction

11.2 Solid-Phase Synthesis of Pyrrolidines, Pyrrolines, and Pyrroles

11.3 Synthesis of Pyrazolines and Pyrazoles

11.4 Solid-Phase Synthesis of Imidazoles, 1,2,4-Triazoles, and 1,2,3-Triazoles

11.5 Solid-Phase Synthesis of Isoxazolidines, Isoxazolines, and Isoxazoles

11.6 Conclusions

References

Chapter 12: Sulfones in Solid-Phase Heterocycle Synthesis

12.1 Introduction

12.2 Linkers

12.3 Conclusions

References

Chapter 13: Solid-Phase Organic Radiosynthesis

13.1 Introduction

13.2 Solid-Phase Organic Radiosynthesis with Fluorine-18

13.3 Solid-Phase Organic Radiosynthesis with Carbon-11

13.4 Solid-Phase Organic Radiosynthesis with Other Radioisotopes

13.5 Conclusions

References

Chapter 14: Solid-Phase Synthesis of Dyes and Their Application As Sensors and Bioimaging Probes

14.1 Introduction

14.2 On-Bead Sensors

14.3 Solid-Phase Approaches in Fluorescent Labeling

14.4 Solid-Phase Derivatization of Fluorescent Scaffolds

14.5 Diversity-Oriented Fluorescent Libraries

14.6 Conclusions

14.7 Acknowledgments

References

Chapter 15: Dendritic Molecules on Solid Support: Solid-Phase Synthesis and Applications

15.1 Introduction

15.2 Synthesis

15.3 Applications of Dendronized Supports

15.4 Conclusions

References

Chapter 16: Oligosaccharide Synthesis on Solid, Soluble Polymer, and Tag Supports

16.1 Introduction

16.2 Solid-Phase Methods for Synthesis of Oligosaccharides

16.3 Polymer-Supported and Tag-Assisted Oligosaccharide Synthesis in Solution

16.4 Conclusions

16.5 Acknowledgments

References

Index

Color Plates

Copyright © 2012 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

Solid-phase organic synthesis: concepts, strategies, and applications / edited by Patrick H.Toy,Yulin Lam. – 1st ed.

p. cm.

Includes bibliographical references and index.

ISBN 978-0-470-59914-3 (hardback)

1. Solid-phase synthesis. I. Toy, Patrick H. II. Lam, Yulin.

QD262S584 2012

547′.2–dc23

2011019936

Preface

Merrifield first introduced the concept of solid-phase peptide synthesis nearly half a century ago, and since then the use of heterogeneous materials to facilitate synthesis has evolved and become widespread in many contexts. For example, the automated solid-phase synthesis of oligomeric biomolecules, such as polypeptides and polynucleotides, has become the standard methodology for the production of such compounds.

The aim of this book is to highlight the state of the art regarding the use of a solid material to support and thereby facilitate organic synthesis. The book is divided into two parts: Part I introduces some general concepts and strategies, while Part II presents specific examples of the solid-phase synthesis of various classes of organic molecules. Since the field regarding solid-phase synthesis of polypeptides and polynucleotides is very mature and well understood, these topics are not included in this book. However, since the solid-phase synthesis of oligosaccharides is not yet routine and straightforward, a chapter on this subject is presented.

Part I includes chapters focusing on the linker groups used to attach the synthesis substrate to the solid support, colorimetric tests that identify the presence of functional groups, combinatorial synthesis (especially interesting due to its historical perspective), and diversity-oriented synthesis. These contributions showcase solid-phase synthesis that is currently used to facilitate the discovery of new molecular functionality. Finally, a chapter highlighting how using a support can change or increase reaction selectivity closes this part. Part II includes chapters on general asymmetric synthesis on a support, various strategies for heterocycle synthesis (including one focusing on the use of microwave heating), synthesis of radioactive organic molecules, dyes, dendrimers, and, last but not least, oligosaccharides.

It is hoped that this book will serve as an introduction and a starting point for those new to this field and interested in using concepts and techniques of solid-phase synthesis. As already mentioned, the application of this technology in the synthesis of small, nonoligomeric organic molecules is relatively underdeveloped compared to other applications, and thus new minds and different perspectives can help to advance this field.

Patrick H. Toy Yulin Lam

Acknowledgments

We would like to thank all the contributors to this book. Their time is very valuable, and thus their generosity in working on this book is priceless. We also wish to thank Tracy Yuen-Sze But, Julia Hermeke, and Jinni Lu for their editorial assistance.

Contributors

Prasad Appukkuttan, Laboratory for Organic & Microwave-Assisted Chemistry, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium

Baburaj Baskar, Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

Young-Tae Chang, Department of Chemistry, National University of Singapore, Singapore

Wenteng Chen, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, P. R. China

Alexander Deiters, Department of Chemistry, North Carolina State University, Raleigh, NC, USA

Koichi Fukase, Department of Chemistry, Osaka University, Osaka, Japan

Warren R. J. D. Galloway, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Marc Giulianotti, Torrey Pines Institute for Molecular Studies, San Diego, CA, USA

Young-Dae Gong, Department of Chemistry, Dongguk University, Seoul, South Korea

Kerem Goren, School of Chemistry, Tel Aviv University, Tel Aviv, Israel

Hyung-Ho Ha, Department of Chemistry, National University of Singapore, Singapore

Kirsi Harju, Division of Pharmaceutical Chemistry, University of Helsinki, Helsinki, Finland

Jan Hlavá, Department of Organic Chemistry, Palacky University, Olomouc, Czech Republic

Raphaël Hoareau, Department of Radiology, University of Michigan, Ann Arbor, MI, USA

Richard A. Houghten, Torrey Pines Institute for Molecular Studies, San Diego, CA, USA

Brett M. Ibbeson, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Albert Isidro-Llobet, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Jonghoon Kim, Department of Chemistry, Seoul National University, Seoul, South Korea

Viktor Krchák, Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA

Kamal Kumar, Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

Yulin Lam, Department of Chemistry, National University of Singapore, Singapore

Sung Chan Lee, Department of Chemistry, National University of Singapore, Singapore

Taeho Lee, Center for High Throughput Synthesis Platform Technology, Korea Research Institute of Chemical Technology, Daejeon, South Korea

Zhi Li, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, P. R. China

Vaibhav P. Mehta, Laboratory for Organic & Microwave-Assisted Chemistry, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium

Kieron M. G. O'Connell, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Cornelius J. O'Connor, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Seung Bum Park, Department of Chemistry, Seoul National University, Seoul, South Korea

Moshe Portnoy, School of Chemistry, Tel Aviv University, Tel Aviv, Israel

Peter J. H. Scott, Department of Radiology, University of Michigan, Ann Arbor, MI, USA

Chai Hoon Soh, Department of Chemistry, National University of Singapore, Singapore

Miroslav Soural, Department of Organic Chemistry, Palacky University, Olomouc, Czech Republic

David R. Spring, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Katsunori Tanaka, Department of Chemistry, Osaka University, Osaka, Japan

Yan Teng, Department of Chemistry, University of Hong Kong, Hong Kong, P. R. China

Patrick H. Toy, Department of Chemistry, University of Hong Kong, Hong Kong, P. R. China

Erik Van der Eycken, Laboratory for Organic & Microwave-Assisted Chemistry, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium

Marc Vendrell, Department of Chemistry, National University of Singapore, Singapore

Jari Yli-Kauhaluoma, Division of Pharmaceutical Chemistry, University of Helsinki, Helsinki, Finland

Douglas D. Young, Department of Chemistry, North Carolina State University, Raleigh, NC, USA

Yongping Yu, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, P. R. China

Part I: Concepts and Strategies

Chapter 1

Linker Strategies in Modern Solid-Phase Organic Synthesis

Peter J. H. Scott

1.1 Introduction

The vast array of linker units available to the modern solid-phase organic chemist is impressive and allows a lot of exciting chemistry to be carried out using solid-phase techniques.1–11 Linker units are molecules that possess a functional group that is used to attach substrates to a solid support and can release them at a later date upon treatment with the appropriate “cleavage cocktail.” With this in mind, linker units have long been regarded as solid-supported protecting groups. Moreover, linker units are frequently lengthy molecules, which improve reactivity by holding substrates away from the polymer matrix to create a pseudo-solution-phase environment. Typically, linker units are conveniently categorized by the functionality left at the “cleavage site” in the target molecule (Scheme 1.1). Initially, following the late Prof. Merrifield's original investigations into preparing peptides on solid supports, solid-phase organic synthesis (SPOS) focused on strategies for preparing peptides and oligonucleotides. This focus was, in part, due to the relative simplicity of peptide chemistry that meant it could easily be adapted for use with solid-phase techniques. Moreover, the ease of automating peptide chemistry allowed straightforward preparation of multiple target peptides in parallel and signaled the beginning of combinatorial chemistry. Many of the classical linker units developed during this period (1960s–1990s) still represent some of the most widely used linker units in use today and an overview of these linker strategies is presented in Section 1.2. When employing a classical linker unit, a common (typically polar) functionality, that was the site of attachment of the molecule to the solid support, remains following cleavage of the target molecule.

Scheme 1.1 Classification of modern linker units.

In the 1990s, the use of solid-phase organic synthesis experienced an explosion in popularity. This was driven by the advent of combinatorial chemistry, as well as strategies such as split-and-mix, which exploited techniques for automating thousands of reactions in a parallel fashion. A combination of the ability to (i) run many solid-phase reactions in parallel using fritted tubes and commercial shakers, (ii) drive reactions to completion using excess reagents, and (iii) easily purify reactions by simple washing and filtration made SPOS particularly attractive to the combinatorial chemists.

Out of the combinatorial chemistry boom came the framework for modern solid-phase organic synthesis. While a lot of the early work with SPOS focused on reliable and relatively straightforward peptide coupling reactions, the ambitious library syntheses of the 1990s required access to a much more extensive array of solid-phase reactions. That decade saw initial strides made in adapting many well-known solution-phase reactions for use in the solid-phase arena, development that continues to the present day,12–27 and a move beyond peptide and nucleotide chemistry toward preparation of small molecule libraries on solid phase.

In time, the vast libraries of combinatorial chemistry have given way to the smaller designed libraries of diversity-oriented synthesis (DOS). Rather than preparing multimillion compound libraries in the hope of finding new lead scaffolds, DOS concentrates on preparing smaller “focused” libraries for lead development.28 Moreover, with the advent of chemical genetics, the interest in generating diverse compound libraries to explore chemical space has become a significant synthetic objective in its own right. These fields of research, in combination with related computational methods, are receiving much attention in the continuing quest to discover new biologically active compounds in chemical space. Reflecting these new challenges, the science of linker design in the last two decades has predominantly focused on the design and synthesis of new multifunctional linker units. Unlike the classical linker units described above that use a common cleavage cocktail for all members of a library, multifunctional linker units maximize diversity by using the cleavage step to incorporate additional structural variation into compound libraries. This final class of linker unit is discussed in Section 1.3.

1.2 Classical Linker Strategies

1.2.1 Acid and Base Cleavable Linker Units

In 1963, Merrifield reported the first example of a synthesis carried out using substrates immobilized on an insoluble polymer support.29 In this work, the polymer Merrifield used was a chloromethylated copolymer of styrene and divinylbenzene, a polymer support that now bears his name. This polymer was functionalized with a benzyloxy group and then Merrifield was able to construct the L-Leu-L-Ala-Gly-Val tetrapeptide 1 by exploiting the Cbz protecting group strategy (Scheme 1.2). Cleavage from the ester linker unit was achieved using sodium hydroxide or a methanolic solution of sodium methoxide to generate the salt of the carboxylic acid 2 or methyl ester 3, respectively. This work in itself represents a simple and straightforward example of multifunctional cleavage that will be discussed further later.

Scheme 1.2 Merrifield's original solid-phase synthesis of a tetrapeptide.

Reflecting this genesis in solid-phase peptide and oligonucleotide synthesis, many early linker units typically possessed a polar functional group (e.g., OH, CO2H, NH2, SH) that was used to attach substrates to a solid support. These linker units can be classified according to whether acidic or basic conditions are required for cleavage of target molecules, and many of them are still employed routinely in twenty-first century solid-phase organic synthesis. The main advantage is that cleavage of substrates from acid and base labile linker units can be readily achieved using mild conditions. Moreover, target molecules can frequently be isolated in sufficient purity by simple evaporation of volatile cleavage reagents.

Two of the most used acid labile linker units, illustrated in Table 1.1, are the hydroxymethylphenyl linker unit reported by Wang (Table 1.1, Entry 1)30 and the aminomethylphenyl linker (Table 1.1, Entries 2 and 3), stabilized by an additional anisole unit, developed by Rink.31 The para-oxygen atom in the Wang linker has a stabilizing effect on the cation generated upon treatment with acid, allowing cleavage to be achieved using 50% trifluoroacetic acid (TFA) in dichloromethane(DCM). As a comparison, greater stabilization of the intermediate carbocation occurs in the presence of the ortho- and para-methoxy groups of the Rink linker. This enhanced stability allows cleavage to be realized under comparatively milder conditions (e.g., 0.1–50% TFA/DCM). For example, trichloroacetylurea was cleaved from the Rink linker using 5% TFA in DCM (Table 1.1, Entry 2).32 The use of methoxy groups to afford greater stability to the intermediate carbocation has also been exploited in development of the hyperlabile SASRIN (or HMPB) linker (Table 1.1, Entry 4).33–36 Similar to the Rink linker, cleavage of substrates from the SASRIN linker can be achieved using mild conditions such as 0.1–1% TFA.36

Table 1.1 Common Acid Cleavable Linker Units.

Other acid labile linker units from which substrates can be cleaved by treatment with TFA include the trityl linker units. Typically, the chlorotrityl linker unit is employed (Table 1.1, Entries 5 and 6) because it is more stable than the parent trityl linker unit, although cleavage can still be achieved using 1% TFA or acetic acid.38,55 One advantage of using trityl linker units over, for example, the benzyl linker units discussed above is that the steric bulkiness of the trityl group makes the linkage more stable against nucleophilic bases. On the other hand, however, this steric bulkiness can cause problems if the substrate to be attached is itself a large molecule. In such situations, steric interference can reduce loading efficiency and should be taken into account before employing the trityl linker unit.

All these TFA labile linker units are well suited to SPOS using the Fmoc protective group strategy. Thus, Fmoc protecting group manipulations can be achieved using piperidine without risk of cleaving the acid labile substrate. However, if a SPOS design plans to use the Boc peptide strategy (i.e., TFA deprotection of Boc groups throughout the synthesis), then a linker unit from which substrates are cleavable with TFA is clearly not suitable. Apart from the TFA labile linkers previously discussed, a number of other acid labile linker units have been reported, allowing the ability to tailor the choice of linker unit to a given synthetic application. If it is necessary to employ the Boc protective group strategy throughout SPOS, one might select the phenylacetamide (PAM) linker (Table 1.1, Entry 7). Substrates are attached to the PAM linker through an ester linkage that is reasonably stable toward TFA. After completion of SPOS, the target molecule can then be cleaved using a stronger acid such as HF or HBr.40

Note that many of the linker units described above are available in multiple forms, allowing a range of substrates to be attached and cleaved. A discussion of all these related linker units is outside the scope of this chapter, but Kurosu has written a comprehensive review.56 By way of example, multiple versions of the Rink (Table 1.1, Entries 2 and 3) and trityl linker units (Table 1.1, Entries 5 and 6)39 are commercially available and can be selected according to the desired substrate. However, beyond these general linker units, there are also examples of substrate-specific linker units. For example, the benzhydrylamine (BHA, Table 1.1, Entry 8)57 and Sieber (Table 1.1, Entry 9)42–44 linkers find widespread use as acid labile carboxamide linker units, while the DHP (Table 1.1, Entry 10)45–48 and silyl linker units (e.g., Table 1.1, Entry 11) can be used to attach alcohols to polymer supports.58

A number of linker units designed specifically for immobilization of amines have also been developed. One noticeable example exploits the versatility of the 9-phenylfluorenyl-9-yl group (PHFI). The PHFI group has previously been used as a protecting group for amines and was adapted into a linker unit by Bleicher (Table 1.1, Entry 12).51 Cleavage from this linker unit can be achieved by treating with 50% TFA in DCM with addition of Et3SiH as a scavenger. Other linker units for amines have been developed based on supported aldehydes or diazonium salts. For example, amino substrates can be loaded onto aldehyde linker units (e.g., the AMEBA linker unit, Table 1.1, Entry 13) via reductive amination and subsequently cleaved upon treatment with TFA in the presence of Et3SiH.52,59–62 In the case of supported diazonium salts, amino substrates are loaded and form a triazene bond with the polymer support (Table 1.1, Entry 14).53,63 The triazene linkage is stable against a range of reaction conditions but can be conveniently cleaved to release functionalized amines upon treatment with 10–50% TFA.

Finally, linker units based on common protecting groups for carbonyl groups have also been adapted for use as linker units. Acetals represent one of the most commonly employed carbonyl protecting groups. Thus, if carbonyl-containing substrates are reacted with resin-bound diols, they can be immobilized through an acetal linkage (Table 1.1, Entry 15).54 Upon completion of SPOS, acid cleavage reforms the carbonyl group and liberates the target molecule. Note that the converse approach is also true and diols can be loaded onto resin-bound carbonyls.64

In the event that acid labile linker units are unacceptable for a given SPOS series because, for example, acid-sensitive substrates are being employed, alternatives are available, including mild enzyme cleavable linkers65 or an equally extensive array of base labile linker units.66 Merrifield employed such a base labile ester-based linker unit in his original peptide synthesis, as shown in Scheme 1.2. Thus, treating with sodium hydroxide or sodium methoxide cleaved the peptide as the carboxylic acid 2 or methyl ester 3, respectively. Since its inception by Merrifield, saponification of substrates attached to support via ester linkages as a cleavage strategy has continued to find application in SPOS (Table 1.2). For example, saponification can be used to cleave carboxylic acids and esters (Table 1.2, Entries 1 and 2),67,68 or alcohols, including nucleosides (Table 1.2, Entry 3)69, by tailoring the linker and cleavage conditions accordingly.

Table 1.2 Common Base Cleavable Linker Units.

Aminolysis, in which the nucleophile promoting cleavage is an amine, has also been widely used as a SPOS cleavage strategy. Aminolysis can be used to prepare, for example, amides using ester linkers (Table 1.2, Entry 4)70 and sulfonamides using sulfonate ester linkers (Table 1.2, Entry 5)70 and can be enhanced by Lewis acid catalysis (Table 1.2, Entry 6)71. Reflecting the importance of ureas in biologically active molecules, urea library synthesis has also been investigated using SPOS. One example of note is the preparation of tetrasubstituted ureas reported by Janda and coworkers (Table 1.2, Entry 7), in which aminolytic cleavage was used to introduce the third and fourth points of diversity.72 Brown also developed amino cleavage for allyl phenyl ethers (Table 1.2, Entry 8).73 This was a palladium-mediated process that Brown used to prepare a range of allylic amines. Other amines are also viable cleavage reagents for substrates attached through ester (and ester-like) linkages. For example, hydrazones (Table 1.2, Entry 9)74 and hydroxylamines (Table 1.2, Entry 10)75 have both been employed in nucleophilic cleavage cocktails.

Apart from the common heteroatom-derived nucleophiles described, cleavage with other nucleophiles is also possible. For example, reductive cleavage with hydride sources is possible. For ester-linked substrates, Kurth et al. reported an example in which substituted propane-1,3-diols were prepared (Table 1.2, Entry 11).76 In related work, Chandrasekhar et al. prepared tertiary alcohols by treating an ester-linked substrate with excess Grignard reagent (Table 1.2, Entry 12).77 If, however, it is desirable to prepare the carbonyl derivative (and not reduce all the way to the corresponding alcohol), then Weinreb-type linker units can be used (Table 1.2, Entries 13 and 14).78 Treatment of substrates attached via such linkers with LAH will provide the corresponding aldehyde (Table 1.2, Entry 13), while cleavage with a Grignard reagent will give the ketone products (Table 1.2, Entry 14).

1.2.2 Cyclorelease Linker Units

As described previously, cleavage of substrates from acid and base labile linker units can be readily achieved using mild conditions. However, a significant drawback of such linker units, which has limited their application in more general organic synthesis, is that a common polar functional group is introduced into every target molecule in a compound library during cleavage. While the polar functional group might be an integral feature of the library, frequently it is not, and the presence of such functionality can greatly affect the desired (biological) activity and must be removed. The removal of such functionality can be far from straightforward, and so research aimed at developing linker units, which avoid this issue, has been extensive.

The first solution proposed to address this problem involved the use of cyclorelease linker units (Scheme 1.1).79–81 When using such linker units to prepare cyclic species, the cyclization and cleavage steps are combined (cyclative cleavage), offering a number of benefits. First, there is no residual polar functionality left behind in the SPOS cleavage product and, second, only the final linear precursor is capable of undergoing cyclorelease. This will provide cleaved products of higher purity than other SPOS protocols because failed intermediates or other synthetic by-products generated (despite the use of excess reagents) are unable to cyclize and remain attached to the polymer support following cleavage. For example, Pavia and coworkers showed that treatment of immobilized amino acid 4 with acid did not result in cleavage of the substrate.82 However, reaction with isocyanate provided urea 5 that on treatment with 6 M HCl cyclized to form the hydantoin 6 (Scheme 1.3). Unreacted amino acid remained bound to the polymer support providing hydantoin products in high purity.

Scheme 1.3 Pavia's cyclorelease linker unit.

Pavia's linker unit exploits amide or urea bond formation with concomitant displacement of the solid support, which is by far the most common approach for achieving cyclative cleavage. The first example of such an approach was Marshall's preparation of cyclic dipeptides, as shown in Table 1.3, Entry 1.83 Besides this, such classical cyclization CࢤN bond forming reactions have been used to prepare ambitious synthetic targets using SPOS, including hydantoins (Table 1.3, Entry 2),84 ureas (Table 1.3, Entry 3),85 phthalimides (Table 1.3, Entry 4),86 pyrimidinones (Table 1.3, Entry 5),87 quinazolinones (Table 1.3, Entry 6),88 and spirodiketopiperazines (Table 1.3, Entry 7).89 Similarly, CࢤO bond formation is a viable cyclative cleavage strategy. Lactone formation is the most common method, such as the synthesis of phthalides reported by Tois and Koskinen (Table 1.3, Entry 8).90 In certain cases, linker units are amenable to CࢤN or CࢤO bond forming cyclorelease, and different products can be prepared, from a common supported intermediate, by varying the cleavage conditions. This is attractive from a multifunctional cleavage viewpoint. For example, microwaving a common resin-bound intermediate in the presence and absence of an amine provided pyrrolidinones and butyrolactones, respectively (Table 1.3, Entries 9 and 10).91

Table 1.3 Common Cyclorelease Linker Units.

Beyond the formation of CࢤN bonds and CࢤO bonds to achieve cyclorelease, there are also examples of CࢤC bond formation with concurrent cleavage. For example, Jeon prepared polymer-supported sulfonamides (Table 1.3, Entry 11).92 Treatment with sodium hydride, exploiting the acidic proton α to the sulfone, allowed cyclization with the ester linkage and release of the cyclic sulfonamide. Alternatively, other cyclic CࢤC bond forming reactions have also been adapted for cyclorelease cleavage. For example, the intramolecular Claisen-like Lacey–Dieckmann reaction has been used to achieve concomitant formation and cleavage of tetramic acids (Table 1.3, Entry 12).93

Rhodium-mediated olefin metathesis is Nobel Prize-winning chemistry that has become increasingly powerful, and popular, since the discovery of the Grubbs I catalysts in the early 1990s. Cross-metathesis (CM) can be used to generate internal alkenes and has been exploited as a multifunctional cleavage strategy (Section 1.7). Likewise, the cyclic ring-closing metathesis (RCM) variant has very quickly become one of the preferred CࢤC bond forming reactions for routine preparation of cyclic species. Various cyclic species of differing sizes, ranging from five-membered rings to, for example, 30-membered macrocyclic species, have been generated using RCM. Such chemistry is clearly suitable for adaptation to cyclorelease SPOS and, indeed, numerous examples have been reported that have been recently reviewed.95 For example, Table 1.3, Entry 13, illustrates van Maarseveen's preparation of seven-membered lactams, employing RCM for final cyclative cleavage.

The major advantage of using cyclorelease linker units is that the polar functional group used to attach a substrate to the polymer support remains attached to the support, rather than the target compound, upon cleavage. While this is ideal for the substrates described above, this substrate scope is limited. Noticeably, many target molecules are not cyclic or the ring size is unsuitable for cyclative cleavage. In such situations, alternative linker strategies to avoid the unwanted linking functionality are required and this initially led to development of traceless linker units and, subsequently, multifunctional linker units.

1.2.3 Traceless Linker Units

Traceless linker units are typically defined as those that leave a hydrogen residue behind upon cleavage (note that many traceless linkers can also behave as multifunctional linker units, by modifying cleavage conditions, and rather than a focus here will be discussed throughout this chapter). Traceless linkers were pioneered by Ellman and Plunkett in 1995 with the introduction of a silicon-based linker unit.96 Ellman exploited ipso substitution at silicon to leave a hydrogen residue at the cleavage site of the target molecule. Proof of concept was demonstrated in the synthesis of benzodiazepines (Table 1.4, Entry 1), and this work ultimately was the catalyst for development of many traceless linker units that have been reviewed.8,10,97 Traceless cleavage using ipso substitution at silicon has led to the development of many silicon-based traceless linker units, which will be discussed further in Section 1.10. However, germanium linker units are amenable to similar chemistry. Germanium linker units were initially reported by Ellman and Plunkett (Table 1.4, Entry 2),98 but they have been extensively developed and refined by Spivey's group (Table 1.4, Entry 3).99–102

Table 1.4 Common Traceless Linker Units.

An alternative traceless cleavage strategy worthy of mention is immobilization of arenes through transition metal carbonyl linker units, such as chromium (Table 1.4, Entries 4 and 5), cobalt (Table 1.4, Entry 6), and manganese (Table 1.4, Entry 7) based linker units.103 While these linker units do not leave a hydrogen residue upon cleavage, because substrates are immobilized through the arene ring, no trace of the support remains upon cleavage, and so, for the purposes of classification, they can be considered traceless linker units in their own right. These linker units are attractive because arene rings are present in many potential substrates for SPOS. Gibson and coworkers reported the first example (Table 1.4, Entry 4) in which supported substrates were attached as [(arene)(CO)2(PPh3)Cr(0)] complexes and then traceless cleavage could be realized simply by heating in pyridine.104,105 Alternatively, cleavage could be achieved by treating with iodine or UV light (Table 1.4, Entry 5).106 Other than arenes, alkynes and unsaturated carbonyl compounds are also amenable to this SPOS strategy. For example, alkyne-containing aldehydes were prepared using a cobalt linker and cleaved using UV light (Table 1.4, Entry 6),107,108 while α,β-unsaturated ketones were immobilized on a manganese linker (Table 1.4, Entry 7) and cleaved by treatment with N-methylmorpholine N-oxide (NMO).109

1.2.4 Photolabile Linker Units

Photolabile linker units developed from the corresponding photolabile protecting groups are attractive linker units available to the solid-phase organic chemist because cleavage is achieved using only light.110 Such mild cleavage conditions essentially eliminate unwanted side reactions that might otherwise occur when using, for example, strong acid or base cleavage cocktails. Early work concentrated on linker units based on the o-nitrobenzyloxy group, and many variants of this linker unit have since been reported. Cleavage of substrates from the o-nitrobenzyloxy linker can be achieved by irradiating at 350–365 nm (Table 1.5, Entry 1).111 Related linkers based on the o-nitrobenzylamino (Table 1.5, Entry 2),112–114o-nitrobenzyl (Table 1.5, Entry 3),115,116 and nitroveratryl (Table 1.5, Entry 4)117 groups have also been reported. This allows variation in substrates that can be attached to the linker units, but cleavage is still simply a matter of irradiating with 350–366 nm light.

Table 1.5 Common Photolabile Linker Units.

Photolabile linker units based on the phenacyl group have also been developed. The linker is essentially a functionalized resin since it is easily prepared by Friedel–Crafts acylation of typical polystyrene resin. Like the nitrobenzyl linkers, cleavage from the phenacyl linker units can be achieved by irradiating at 350 nm (Table 1.5, Entry 5).118 A related linker unit is the para-methoxyphenacyl linker and, in this case, the para-methoxy group improves the efficiency of the photolysis and, thus, cleavage times are reduced.119

Other photolabile leaving groups including the benzoin group (Table 1.5, Entry 6),120,121 pivaloyl group (Table 1.5, Entry 7),122 nitroindolines (Table 1.5, Entry 8),123 and thiohydroxamic (Table 1.5, Entry 9)124 functionality have all been adapted as linker units for photolabile cleavage in SPOS with high degrees of success.

1.2.5 Safety-Catch Linker Units

As outlined above, a drawback of using acid or base labile linker units is that unwanted cleavage can occur when reagents employed in the synthetic sequence resemble the cleavage conditions. One elegant solution to this problem is the safety-catch linker unit.125,126 In such linkers, the latent bond requires activation before cleavage can occur. Many of the linker units discussed elsewhere in this chapter could be considered safety-catch linker units. For example, photolytic activation described in Section 1.2.4 and cyclorelease discussed in Section 1.2.2 are essentially safety-catch strategies. This section, however, will concentrate on synthetic activation. The first example of such an approach was a sulfonamide linker reported by Kenner et al. in 1971.127 The sulfonamide 7 is stable to both acidic and basic conditions, making it synthetically valuable. However, alkylation of the nitrogen with, for example, diazomethane or iodoacetonitrile, gave 8, from which substrates (e.g., carboxylic acids 9) could be cleaved under nucleophilic conditions (Scheme 1.4).

Scheme 1.4 Kenner's safety-catch linker unit.

Low loading efficiencies limited the use of Kenner's original linker, but an improved version was later reported by Ellman.128 Kiessling and coworkers also reported an alternative palladium-catalyzed allylation strategy for activation of the linker unit for cleavage.129 A number of other safety-catch linker units exploit the varying reactivity of sulfur in its different states. For example, a number of thioether-based linkers behave as safety-catch linkers and can be activated for cleavage by oxidation to the corresponding sulfoxides (Table 1.6, Entry 1)130 or sulfones (Table 1.6, Entries 2 and 3).131,132

Chapter 2

Colorimetric TestS For Solid-Phase Organic Synthesis

Yan Teng and Patrick H. Toy

2.1 Introduction

While the use of a solid support in organic synthesis imparts advantages with regard to performing and working up reactions, monitoring of the reactions becomes more complicated than when performing a reaction using traditional solution-phase methodology. For example, thin layer chromatography cannot be used to monitor a solid-phase reaction unless a cleavage reaction is performed to remove some of the synthesis substrate/product mixture from the support. Therefore, a popular methodology for “on-bead” reaction monitoring of the appearance or disappearance of a functional group from a solid-support attached synthesis substrate is to use a colorimetric test.1,2 In such tests, the solid support is treated with reagents that react with the functional group to be monitored, imparting a visible color to the material when a reaction occurs. Such tests are generally reliable, fast, and easy to perform. Perhaps their main drawback is that they are generally destructive and sometimes require the consumption of a significant amount of the synthesis product. This can be critical if the synthesis is performed on a small scale and only a few support beads are used per synthetic target.

In this chapter, the reported colorimetric tests for solid-phase organic synthesis are presented and the examples are organized based on the functional group they were originally reported to detect. Clearly, since the reactivities of many functional groups such as alcohols and thiols are similar, some of the tests presented are useful in multiple different applications.

2.2 Functional Group Tests

2.2.1 Amine Groups

It is perhaps not surprising, given the history of solid-phase synthesis, that the most widely tested functional groups attached to a solid support are amines.

2.2.1.1 Ninhydrin (Kaiser) Test3

Basic Reagent:

Other Reagents: Phenol and potassium cyanide.

Comments: Commercially available. Detects primary amines to a limit of 5 μmol/g. Provides an intense blue color or in some cases a brown/reddish brown color. First used to detect incomplete coupling reactions in peptide synthesis.

2.2.1.2 TNBSA Test4,5

Basic Reagent:

Other Reagent: N,N-Diisopropylethylamine (used sometimes).5

Comments: Commercially available. Detects primary and secondary amines to a limit of 3 mmol/g. Provides an orange or red color.

2.2.1.3 Bromophenol Blue Test6–8

Basic Reagent:

Comments: Commercially available. A noninvasive qualitative and quantitative test. Provides a deep blue color.

2.2.1.4 Chloranil Test9–11

Basic Reagent:

Other Reagents: Acetaldehyde (for primary and secondary amines)9,10 and acetone (for secondary amines).9

Comments: Commercially available. Detects primary9 and secondary10 aliphatic amines as well as primary aromatic amines11 to a limit of 5 μmol/g for aromatic amines. Provides a green/blue color9,10 or a red color.11

2.2.1.5 DABITC Test12

Basic Reagent:

Comments: Commercially available. Detects primary and secondary amines. Provides a yellow or orange color.

2.2.1.6 MGI Test12

Basic Reagent:

Comments: Commercially available. Detects primary and secondary amines. Provides a green or deep blue color.

2.2.1.7 Isatin Test12

Basic Reagent:

Other Reagent: Boc-phenylalanine.

Comments: Commercially available. Used specifically for the analysis of proline. Provides a blue color.

2.2.1.8 DESC Test13

Basic Reagent:

Other Reagent: N,N-Diisopropylethylamine (for secondary amines).

Comments: Not commercially available. Detects primary and secondary amines to a limit of 9 μmol/g for primary amines. Can also be used to detect thiols. Provides a red to dark orange color.

2.2.1.9 NPIT Test14

Basic Reagent:

Other Reagent: Trifluoroacetic acid.

Comments: Not commercially available. Detects less reactive primary and secondary amines. Provides a red color.

2.2.1.10 NF31 Test 15–18

Basic Reagent:

Other Reagent: 4-Dimethylaminopyridine (for detecting alcohols, phenols, and thiols—NF31/DMAP test).17

Comments: Commercially available. Detects sterically hindered primary amines, secondary amines,15 and aromatic amines.16 In the presence of DMAP, alcohols, phenols, and primary thiols can also be detected.17 Detection limit of 3.4 μmol/g for aniline groups16 and 3–5 μmol/g for NF31/DMAP test.17 Provides a red color. May give positive results for free hydroxyl groups even without DMAP.18

2.2.1.11 Nondestructive NF31 Test 19

Basic Reagent:

Other Reagents: 1,8-Diazabicyclo[5.4.0]undec-7-ene and 4-dimethylaminopyridine.

Comments: Not commercially available. Detects primary and secondary amines as well as thiols. Tested resin can be regenerated and used for ensuing reaction. Provides a red color.

2.2.1.12 Naphthol Test20

Basic Reagent:

Other Reagent: NaNO2.

Comments: Commercially available. Detects aromatic amines. Provides a red color.

2.2.1.13 2-Amino-3-chloro-1,4-naphthoquinone Test 21

Basic Reagent:

Other Reagents: 2,6-Di-tert-butylpyridine and trifluoroacetic acid.

Comments: Commercially available. Detects primary and secondary alkyl amines, and aromatic amines to a limit of 10 μmol/g. Quantitative analysis based on the chromogens cleaved from the resin. Provides a red color.

2.2.2 Alcohols

There are some significant applications regarding the detection of hydroxyl groups on solid support. Unsurprisingly, some of the above-mentioned reagents, such as NF31, can been used to detect hydroxyl groups in addition to amine groups.

2.2.2.1 PNBP Test 22–24

Basic Reagent:

Other Reagents: 4-Toluenesulfonyl chloride, piperidine (for detecting alcohols),22 and triethylamine (for chlorine groups).24

Comments: Commercially available. Detects primary, secondary, and tertiary alcohols as well as phenols22 (negative result was obtained for some tertiary alcohols25) to a limit of 16 μmol/g.22 Provides a violet to pink color for alcohol and chlorine detection22,24 and a red color for chloroacetyl detection.23

2.2.2.2 TCT–AliR and TCT–Fluorescein Test 2627

Basic Reagents:

Other Reagents: N-Methylmorpholine, dimethoxytrityl chloride, and trichloroacetic acid (for quantification).

Comments: Commercially available. Detects primary, secondary, and tertiary alcohols as well as phenols. Other nucleophilic groups, such as primary and secondary amines, and thiols can also be detected. Quantification analysis of primary and secondary alcohol groups can be performed with the TCT–AliR test. Provides a red color in the TCT–AliR test and a yellow-green color in the TCT–fluorescein test.

2.2.2.3 Diphenyldichlorosilane–Methyl Red Test25

Basic Reagents:

Other Reagents: Triethylamine and formic acid (for further confirmation).

Comments: Commercially available. Reportedly reliable result for tertiary alcohols and other alcohols and phenols to a detection limit of 0.07 mmol/g. Provides an orange to red color, and a purple color with formic acid rinsing.

2.2.2.4 9-Anthronylnitrile Test28

Basic Reagent:

Other Reagent: Quinuclidine.

Comments: Commercially available. Provides direct quantification based on the consumption of 9-anthronylnitrile using UV–visible spectroscopic measurements to a detection limit of 0.05 mmol/g and fluorescent bead under 350–360 nm UV illumination. Also works for unhindered primary amines.

2.2.2.5 NMA Test29

Basic Reagent:

Comments: Commercially available. Detects primary and secondary alcohols to a detection limit of 3 μmol/g. Also works for primary amines. Fluorescent beads using a 365 nm UV lamp.

2.2.2.6 Protecting Group NPB Test 30

Basic Reagent:

Other Reagents: N,N′-Dicyclohexylcarbodiimide, 4-dimethylaminopyridine, and hydrazine acetate.

Comments: Not commercially available. After cleavage, nitrophthalhydrazide results in an orange-colored solution.

2.2.2.7 Methyl Red/DIC Test 31

Basic Reagent:

Other Reagents: 1,3-Diisopropylcarbodiimide (DIC) and 4-dimethylaminopyridine.

Comments: Commercially available. Methyl red reacts directly with hydroxyl groups without intermediates to a detection limit of 0.042 mmol/g. Provides an orange-red color.

2.2.2.8 Other Methods

The NF31/DMAP test described above also detects alcohols and phenols.17

2.2.3 Thiol Groups

2.2.3.1 Ellman's Test 32–34

Basic Reagent:

Comments: Commercially available. Provides quantitative analysis and a yellow color.

2.2.3.2 Other Methods

The DESC,13 NF31/DMAP,17 nondestructive NF31,19 TCT–AliR, and TCT–fluorescein26,27 tests described above also detect thiol groups.

2.2.4 Halogen Groups

2.2.4.1 Fluorescein Test 2

Basic Reagent:

Other Reagent: Triethylamine.

Comments: Commercially available. Provides a fluorescent green color. May not be suitable for hindered or secondary halogens due to possible elimination reactions.

2.2.4.2 Other Methods

The PNBP test described above can also be used to detect chloroacetyl23 and chloromethyl24 groups.

2.2.5 Carboxylic Acid Groups

2.2.5.1 Malachite Green Test 35

Basic Reagent:

Other Reagent: Triethylamine.

Comments: Commercially available. Provides indirect quantitative analysis and a green color.

2.2.5.2 PDAM Test 28

Basic Reagent:

Comments: Commercially available. Provides direct quantification based on the consumption of PDAM using UV–visible spectroscopic measurements and fluorescent beads under 350–360 nm UV illumination.

2.2.6 Aldehyde and Ketone Groups

2.2.6.1 Fluorescent Dansylhydrazine Test 36

Basic Reagent:

Comments: Commercially available. Provides direct quantification of aldehyde and ketone groups based on the consumption of dansylhydrazine using fluorescence spectroscopy and fluorescent bead under 350–360 nm UV illumination.

2.2.6.2 p-Anisaldehyde Test 37

Basic Reagent:

Other Reagents: Sulfuric acid and acetic acid.

Comments: Commercially available. Detects aromatic and aliphatic aldehyde groups. Provides an orange to red color.

2.2.6.3 Purpald Test 38

Basic Reagent:

Other Reagent: Sodium hydroxide.

Comments: Commercially available. Test is specific for aldehyde groups to a detection limit of 20 μmol/g. Provides a dark brown to purple color.

2.3 Conclusions

After the introduction of Kaiser's ninhydrin test for the on-bead detection of primary amines, many other such colorimetric tests have been reported in the literature, not only for amines but also for other functional groups. Many of these tests are simple and quick to perform and use readily available reagents. Furthermore, some even allow quantitative determination of functional group loading levels. Given the current high level of interest in the development of fluorescent dyes, it is easy to imagine that such tools will be widely useful in monitoring solid-phase organic synthesis reactions.

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23. S. Manabe, Y. Ito, J. Am. Chem. Soc.2002, 124, 12638–12639.

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Chapter 3

Practical Aspects of Combinatorial Solid-Phase Synthesis

Jan Hlavá, Miroslav Soural, and Viktor Krchák

3.1 Introduction

In the middle of the nineteenth century, gold was discovered at Coloma in California by the American pioneer James Wilson Marshall. The discovery started the famous “Forty-Niners” gold rush in the West that brought great expectations and excitement, as well as disappointment. At the end of the last millennium, the West was in a fever again, but this time the vision of wealth was to be attained using a new technology that promised to enormously accelerate the drug discovery process. The technique, known as combinatorial chemistry, once again caused great excitement and substantial disappointment. Since the early times of combinatorial chemistry (“combi-chem”) in Tucson1 and San Diego2 (both papers were published side by side in Nature in 1991), drug discovery companies have been driven to find the modern equivalent of a “Mother Lode.”3 In this case, the treasure is represented by a compound collection from which biologically active and unique compounds would be mined and subsequently developed into drugs. Thus, chemical combinatorial methods became a field of great interest during the last decade of the twentieth century. The numerous attributes, advances, and large amount of interest in combinatorial chemistry are demonstrated by the number of new journals dedicated to the subject, the number of new combinatorial chemistry companies, and the amount of money invested in combinatorial chemistry and related technologies. There are several excellent books and review articles covering combinatorial technologies, and the interested reader is referred to Refs 11 and 12 for a summary of synthetic procedures and also to recent general reviews of the subject.13–18

3.1.1 What Is Combinatorial Chemistry

Combinatorial chemistry is a technique for producing a collection of compounds (a library) from a given number of starting materials in a combinatorial fashion.19 Several definitions of combinatorial chemistry have been offered, such as “combinatorial chemistry is a new subfield of chemistry with the goal of synthesizing very large numbers of chemical entities by condensing a small number of reagents together in all possible combinations” by Czarnik21 or “combinatorial synthesis is the intentional construction of a collection of molecules based on logical design and involving the selective combination of building blocks by means of simultaneous chemical reactions. The collection of molecules resulting from a combinatorial synthesis is a combinatorial library” by Curran and Wipf.22

The starting materials used to prepare or “build” the required products are generally referred to as building blocks. While the number of building blocks increases in an arithmetic progression, the number of compounds prepared increases in a geometric progression. This is achieved by combining each of the building blocks from the first combinatorial step with all the building blocks used in the subsequent combinatorial steps. The technique is best illustrated with an example. Suppose a series of benzimidazoles are to be synthesized according to the chemistry illustrated in Scheme 3.1 using 10 primary amines, 10 o-fluoronitrobenzenes, and 10 carboxylic acids.23 Each amine is immobilized via a reductive amination procedure on a support functionalized with an aldehyde moiety. When each resin is combined (reacted) with the 10 o-fluoronitrobenzenes, 100 (10 × 10 = 100) o-nitroanilines are formed. After reduction of the nitro group, each of the o-phenylenediamine intermediates is derivatized with each of the 10 acids, producing 1000 (10 × 10 × 10 = 1000) benzimidazole precursors, which upon cleavage and cyclization afford 1000 benzimidazoles. In summary, using 30 building blocks (10 + 10 + 10), 1000 compounds (10 × 10 × 10) are prepared.

Scheme 3.1 Combinatorial synthesis of benzimidazoles: using 30 (10 + 10 + 10) building blocks to prepare 1000 (10 × 10 × 10) products in a combinatorial fashion. Reagents: (i) amine/NaBH(AcO)3 in DMF/AcOH; (ii) o-fluoronitrobenzene, DMSO, rt, overnight; (iii) SnCl2·2H2O in NMP, rt, overnight; (iv) acid chloride/DIEA in DCM, rt, overnight; (v) AcOH, 80°C, overnight.

Each chemical transformation that uses a series of building blocks is referred to as a combinatorial step; the above example represents a synthesis with three combinatorial steps. A compound array prepared using only one set of building blocks is considered to be a parallel synthesis rather than a combinatorial synthesis.

Combinatorial syntheses can be performed in two ways: (i) split-and-pool (also referred to as the split-and-mix or the split-and-recombine method)1,2,24 and its variant directed sorting4,25–31 and (ii) parallel synthesis.5,6,32,33 A hybrid approach is the split-and-split technique.34,35

Although combinatorial chemistry may be applied to a variety of areas of chemistry, to date, the majority of practical applications have been dedicated to drug discovery projects. Combinatorial chemistry is undoubtedly an efficient method for the preparation of compounds in a variety of library sizes. This approach, however, also makes combinatorial chemistry an efficient method for the production of useless or “inactive” compounds. For this reason, the technique has sometimes been referred to as an “irrational design” process, in contrast to the accepted “rational” drug design process traditionally practiced by medicinal chemists.

3.1.2 What Is Not Combinatorial Chemistry

Although solid-phase synthesis is frequently linked to combinatorial chemistry, this is not a requirement. Other synthetic methodologies, such as solution-phase synthesis36–38 and soluble polymer-supported synthesis,39–42 have also been used to effect the combinatorial synthesis process. However, solid-phase synthesis allows the most efficient combinatorial synthesis. The advantages and problems with solid-supported synthesis are described in later chapters. Thus, combinatorial chemistry is not solid-phase chemistry, albeit combinatorial chemistry can be advantageously performed on the solid phase.

Combinatorial chemistry encompasses a wide range of techniques and synthetic goals, and library sizes may range from millions of compounds to a few tens of compounds. Combinatorial chemistry also involves the synthesis of small collections of compounds that may be prepared in a completely manual manner or by the use of simple tools. The equipment and human resources required to meet the goals of a particular combinatorial project vary considerably, and hence the equipment required to successfully pursue combinatorial chemistry ranges from cheap, simple, manually operated apparatus to multimillion dollar automated robots. Although nobody today would prepare chemical libraries without efficient tools, their presence in combinatorial synthesis is not required. Thus, combinatorial chemistry is not the synthesis of chemical libraries using a million dollar robot or any other instrumentation, albeit combinatorial chemistry can be performed using such a robot or instrumentation.

Solid-phase combinatorial synthesis can be performed using the split-and-pool technique based on the combination of variously substituted compounds together for the same reaction in an appropriate reaction step, as well as by parallel synthesis, in which all compounds are segregated during all the reaction steps (see next chapters). Although parallel synthesis is an efficient way to prepare arrays of structurally unrelated compounds, it is not necessarily a combinatorial approach conventionally based on substituent modifications of one structural motif. Thus, combinatorial chemistry is not parallel synthesis, albeit combinatorial chemistry can be performed in parallel fashion.

The obvious requirement for a synthesis to be regarded as combinatorial is that it is undertaken in a combinatorial manner, independent of the synthetic approach, size of a library, and degree of automation.

3.1.3 History of Combinatorial Chemistry: Breakthrough Discoveries That Shaped the Future of the Combinatorial Chemistry Field

Although no single invention triggered scientific and research activities in combinatorial chemistry, there were several milestone discoveries that helped reveal the concepts of combinatorial technologies and prepare the general chemical community for the “combinatorial way of thinking.”

3.1.3.1 Solid-Phase Synthesis

The first, and possibly the most crucial, was solid-phase peptide synthesis by Bruce Merrifield43 published in 1963. The solid-phase synthesis of peptides by Bruce Merrifield is undoubtedly considered to be a landmark in chemistry as a whole and had a critical impact on combinatorial chemistry. Although the concept of solid-phase peptide synthesis is, similar to many other ingenious ideas, very simple and straightforward, Bruce Merrifield was the first to recognize its potential and develop a workable method.

The repetitive and tedious nature of solution-phase peptide synthesis prompted Merrifield to develop the solid-phase peptide synthesis. Contemporary solid-phase synthesis follows the original Merrifield concept (Scheme 3.2), but differs only in the types of amine protecting groups, carboxyl group activating agents, and the variety of linkers that are now available. In a typical Merrifield solid-phase peptide synthesis procedure, an N-protected (t-butyloxycarbonyl group (Boc)) amino acid is attached to an insoluble polymer support, chloromethyl-copoly(styrene-1% divinylbenzene) resin, via an ester bond. The protecting group of the resulting resin-bound ester is cleaved, most often by TFA diluted with DCM, the TFA salt of the liberated amino group is neutralized, and the amino groups thus produced are acylated with the next amino acid. The most common method of activation of the carboxyl group of the amino acid uses a carbodiimide, often in the presence of HOBt. This two-step cycle is repeated until the target peptide is assembled. At the end of the synthesis, the side-chain protecting groups are removed and the peptide is cleaved from the resin; in this example, liquid HF is used.

Scheme 3.2 Merrifield solid-phase synthesis of peptides.

Solid-phase synthesis in general has several inherent characteristics. As it is not possible to purify the growing substrate during solid-phase synthesis, the reaction has to be driven as close to completion as possible. Therefore, a large excess of reagents is often used. Suppose each reaction proceeded with 95% conversion, a very acceptable yield for solution-phase synthesis. However, for a 10-step synthesis, the purity of the final product would be 63% (0.959 × 100). Therefore, an efficient synthesis must be developed before library synthesis.

The three most attractive aspects of solid-phase organic synthesis include the following: (i) a very simple separation of synthetic intermediates bound to the solid support from soluble components of a reaction mixture by simple filtration and washing of the resin. A consequence of this is the ability to use a high boiling reaction solvent, such as DMF, DMSO, NMP, and so on, without the need to evaporate the solvent. (ii) A high concentration of reactants in solution that facilitates reaction completion. (iii) A simple repetitive process (adding reagents, mixing, washing) allows integration and automation of solid-phase synthesis.

Other aspects of solid-phase synthesis that need to be considered are as follows: (i) solid-phase synthesis starts with attachment of the first building block and ends with release of the target compound from the insoluble support, thus adding two chemical transformations to the total number of synthetic steps. (ii) In solution-phase synthesis, the isolation of products may often be difficult or time-consuming. In some cases, chemical transformations may take only minutes, and thus three or more consecutive reactions on solid phase may be more time efficient when compared to one chemical reaction in solution, followed by a tedious isolation procedure to provide the intermediate for the next reaction step. (iii) The kinetics of solid-phase reactions tend to be slower than those of the equivalent solution-phase reaction. This is generally because the kinetics of a reaction on the solid phase are controlled by diffusion/accessibility of the reagents into the bead. (iv) Although the ability of a large excess of reagents to drive reactions to completion is an advantage, this requires the use of greater quantities of reactants that may be expensive or difficult to obtain. This may play a critical role in designing, or choosing between, solid- versus solution-phase synthetic routes.