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137. C. Fang, J.-T. Liu, C.-H. Liu, J. Chromatogr. 775 (1), 37 47 (2002). 138. B. Fan, J.T. Stewart, J. Liq. Chromatogr. Related Technol. 25 (6), 937 947 (2002). 139. R. Wang, H. Fan, W. Ma, J. Liq. Chromatogr. Related Technol. 25 (6), 857 864 (2002). 140. B. X. Mayer, U. Hollenstein, M. Brunner, H.-G. Eidler, M. Muller, Electrophoresis 21 (8), 1558 1564 (2000). 141. C. A. Ogawa, C. A. Diagone, F. M. Lancas, J. Liq. Chromatogr. Related Technol. 25 (10 11), 1651 1659 (2002). 142. C. Simo, C. Barbas,A. Cifuentes, J.Agri. Food Chem. 50 (19), 5288 5293 (2002). 143. X. Shang, Y. Zhuobin, Analy. Lett. 35 (6), 985 993 (2002). 144. C.-E. Lin, Y.-C. Chen, C.-C. Chang, D.-Z. Wang, J. Chromatogr. 775 (1 2), 349 357 (1997). 145. C.-E. Lin, W.-C. Lin, W.-C. Chiou, J. Chromatogr. 722 (1 2), 333 343 (1996).
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CHARACTERIZATION OF SPLIT-POOL ENCODED COMBINATORIAL LIBRARIES
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JING JIM ZHANG and WILLIAM L. FITCH
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INTRODUCTION
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The split-pool approach for solid-phase synthesis has been proved an effective way to generate large, diverse chemical libraries. Libraries prepared on beaded resins by the split-pool approach are characterized by the one bead one compound rule. Such libraries, in principle, combine the advantages of split-pool synthesis with those associated with the screening of discrete compounds, since individual beads may be assayed for biological activity. After the synthesis of a split-pool combinatorial library, it is desirable to verify the success of the synthesis before screening the library against biological targets. However, since the beads are randomized in each pooling operation, tracking the reagents and building blocks to which each bead is exposed becomes troublesome, and the identity of the chemical ligand on an active bead may be very hard to determine. Encoding provides a general solution to this problem, whereby a surrogate analyte, or tag, is attached to the beads to allow determination of the reaction history of a certain bead and thus the identity of the nal product attached to it. A variety of encoding strategies have now been proposed; they share the critical property that the code is much easier to analyze than the associated compounds. Encoded combinatorial libraries are a key component of our strategy for accelerating drug discovery,1 3 and the technology required to realize such libraries has evolved continuously in our organization over the last decade. The development of DNA-based encoding4 was a milestone in combinatorial science and led to the invention of polyamide hard tags, 5 9 which have been shown to be compatible with a wide range of synthetic chemistries and of demonstrable utility in drug discovery.10 16
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Analysis and Puri cation Methods in Combinatorial Chemistry, Edited by Bing Yan. ISBN 0-471-26929-8 Copyright 2004 by John Wiley & Sons, Inc.
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characterization of split-pool encoded combinatorial libraries
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Cleavable linker
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Site of ligand
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( i.e.
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Figure 9.1. Encoded synthesis using secondary amine tags on a differentially functionalized polymer support: (A) Functionalized resin; (B) structure of Alloc tagging monomer unit; (C) structure of succinoyl monomer tagging unit; (D) schematic representation of the product of a two-step encoded synthesis.
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Figure 9.1 shows the general structure of a compound prepared on a polymer bead using polyamide tags. It shows the construct for a three-step synthesis where the rst two steps are encoded; the differentiated bead (A), the tagging monomer units (B and C), and the generic nal encoded bead (D). The cleavable linker contains a photo- or acid-cleavable group optimized for screening; the tag will stay with the bead until mineral acid hydrolysis frees it for structure determination. The protecting groups PGL and PGT are normally Fmoc and Boc, respectively. The Alloc protecting
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method for encoding and decoding libraries
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group of (B) masks the branch point and is readily removed for subsequent encoding steps. Building blocks are encoded by mixtures of secondary amines HNR1R2. Decoding entails release of the tags, determination of the tags, and thereby (with reference to a coding table) determining the structure of the ligand that was carried by the bead. A key assumption for the utility of encoded libraries is that the code is predictive of the structure of the attached compound. Decoding must be unambiguous, and the correct compound must have been produced. Obtaining this assurance presents signi cant analytical challenges,17,18 but it is critical to obtain, as poor quality libraries can lead to signi cant wasted time in the screening and re-synthesis of spurious hits. The analytical challenges posed by encoded libraries are largely the result of the small amount of analyte that is available. The beads used in these libraries typically have a few hundred picomoles of synthesis sites. We differentiate the beads such that approximately 90% is ligand and 10% is tag (in more recent libraries we have switched this to 80/20). While larger beads would make analysis easier, it would be more dif cult to prepare libraries of large numbers of compounds, as it is necessary to ensure that many beads bearing each compound will be produced. In addition larger beads often suffer from mechanical instability during synthesis. We will describe the processes by which we determine the quality of encoded libraries and decode biological hits, including the evolution of our code-reading process, and quantitative analysis of libraries.