Encoded combinatorial library preparation

The structure of the bioactive members of a combinatorial library prepared by split synthesis can be determined by several methods including bioactivity/deconvolution, microanalytical methods and encoding. In a generalized example of the biorecognition/ deconvolution approach, the final sublibraries are not pooled but tested as mixtures. The most active sublibrary then defines the synthon used in the last synthetic step. The synthesis is then repeated to the penultimate step these sublibraries are not mixed, but each is separately reacted with the preferred last-step synthon. These resulting sublibraries are tested the most active then defines the preferred synthon in the penultimate step, and hence the last two synthons present in the most active member of the family are defined. 

Preparation of Encoded Combinatorial Libraries for Drug Discovery... 

In the synthesis of combinatorial libraries, there is a raft of tactical issues that need to be tackled. Will the library be made of mixtures or discrete compounds Prepared by solid-phase or solution-phase Screened in solution or attached to beads What level of purification and characterization is needed Will hits be identified by deconvolution, encoding techniques, or other means These are aU crucial operational aspects of combinatorial chemistry but it is equally important not to concentrate on them to the extent of missing the big picture. At the end of the day, neither a biological assay nor a medicinal chemist care how a compound was made. It is vital, though, that the tactical decisions do not prevent one from making the right compounds. Combinatorial synthesis is a means to an end, not an end in itself. 

Albeit on a miniaturized scale, the DNA-encoded libraries can reach a diversity level far beyond normal HTS libraries. For example, a library by Harbury s DNA routing approach has 100 million compounds Nuevolution announced on their website that their Chemetics library passed the 1 billion compound mark while GSK s DEL-B library has more than 800 million different structures. These numbers are on a par with biopolymer libraries prepared by genetics techniques such as phage-display and mRNA display, while the largest synthetic combinatorial library is around merely 2 million. Therefore, DNA-encoded library is truly an expansion of HTS into a much higher level of molecular diversity. 

Much of the early work in combinatorial chemistry focused on the preparation of large mixtures of compounds. The most widely used technique for mixture synthesis is the split/recombine method which assures that each component of the mixture is present in approximately equimolar concentrations. The structures of the bound ligands are determined either through an iterative, or reclusive, deconvolution strategy or through the use of encoded libraries. 

While considerable efforts have been spent in the past few years in the field of solid supports for combinatorial chemistry [73], most of them were devoted to modified polystyrenic beads with different sizes, loadings or swelling properties [74], or carrying different functionalities or linkers for library synthesis [75], or to solid supports different from resin beads (pins [76], cellulose [77], soluble supports [78], and so on). Few reports dealt with labelled solid supports prepared by chemical reactions (see the previous paragraphs) and significant efforts in the field of material sciences to obtain intrinsically labeled, nonchemically encoded, easily readable, combinatorial solid supports have not been reported. 

Atuegbu A, Maclean D, Nguyen C, Gordon EM, Jacobs JW, Combinatorial modification of natural products preparation of unencoded and encoded libraries of Rauwolfia alkaloids, Bioorg. Med. Chem., 4 1097-1106, 1996. 

A more complex combinatorial strategy based on a natural scaffold was reported by Nicolaou et al. (56) with the synthesis of an epothilone-based SP library L27 (Fig. 4.18). This biased library was prepared asa3x3x5 = 45-member collection, but the final reaction vessels could, theoretically contain 4 different isomeric desoxyepothi-lones (Fig. 4.18), thus leading to a total number of 45 x 4 = 180 components. The library was prepared using a radiofrequency encoding technique (42), and the final... 

OBOC combinatorial bead-libraries can be considered as chemical microarrays that are spatially separable but non-addressable. The identity of the chemical compound on the positive beads can be determined directly with an automatic sequencer if it is an N-terminally unprotected peptide, by mass spectroscopy, or through chemical encoding. i A synthetic scheme for the OBOC library is shown in Figure 2. Using the highly efficient split-mix synthesis method,literally hundreds of thousands to millions of compounds can be prepared within a week. The recent... 

Fig. 5 Immobilization through self-sorting of PNA-encoded libraries. Starting from a bifunctional linker with orthogonal protecting groups, a library is prepared by split and mix combinatorial syntheses where a specific PNA codon is used to encode every building block. The libraries are then cleaved from the solid phase to obtain a mixtiue in solution, which is converted to a SMM by hybridization to an oligonucleotide microarray [51]...

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