Split-pool synthesis encoding

Fig. 2. The split-pool synthesis of an encoded combinatorial library.

An alternative method for tracking the chemical history is encoding by spatial address. The identity of each entity is defined by its spatial address. A one-dimensional directed split-and-pool procedure, referred to as necklace coding, has been developed for synthesis carried out on SynPhase Crowns and Lanterns.13 Individual supports are strung on a Teflon thread and the position of a particle on the thread (necklace) encoded the previous chemical history (Fig. 1). A similar concept was later reported by Furka and co-workers14,15 Two-and three-dimensional encoding of the directed split-and-pool synthesis platform has been patented by Selectide Corp.16... 

In the laboratory we have several automatic and semiautomatic robotic apparatus including the IRORI Nanokan optical encoding system for split- and pool-synthesis (34) and synthesizers from Advanced ChemTech and the MiniBlock from Mettler, Toledo, OFI. 

Figure 3 Chemically encoded split-and-pool synthesis.

In contrast with the split/pool method, parallel synthesis does not require encoding, produces discrete compounds in measurable quantities, and allows for collection of a full SAR. It is becoming increasingly popular among other combinatorial methods. 

DNA-recorded library is another approach to encode small molecule libraries on DNA templates. Instead of preparing a template pool in which every library compound has already been encoded, in a DNA-recorded library initially all templates share an identical sequence, or even are simply one template. Usually, the chemical reactions on each template are encoded spatially such as the split-pool-split method i.e. the initial template pool is separated into several batches for discrete reactions with various building blocks. Before all the sub-pools are combined, an enzymatic tag is added to the template to record the synthesis. For every step, an additional tag is added. As a matter of fact, DNA-recorded library, similar to Harbury s DNA routing strategy discussed above, does not use DNA to template the reactants into proximity and to increase the effective molarity. 

Baldwin, J. J. and Horlbeck, E. (1997) Encoded libraries may be created using split-pool or direct divide synthesis. US Patent 5,663,046. 

At the end of a split synthesis, because the beads have been pooled and mixed, the exact identity of a molecule on a given bead is unknown. Likewise, the identity and structure of compounds in wells is unknown. Split synthesis is not a spatially addressable method. Fortunately, the exact structure does not need to be known unless a compound shows activity in a screen. If active, the structure of the compound in the well will need to be elucidated through a process called deconvolution. Deconvolution is generally accomplished through one of two methods recursive deconvolution21 or binary encoding.22... 

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. 

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