The Split-Mix Synthesis

Each product formed in a given reaction step of a combinatorial process has to be distributed into samples, then react each sample with one of the monomers of the next reaction step. 

The split-mix method realizes the combinatorial distribution rule by mixing the products after each reaction step, then distributing the mixture into equal portions. 

FIGURE 2.1 The combinatorial tree. Each square in the figure represents a reaction vessel, and their black, gray and white colors symbolize the monomers that are coupled in the vessels. The numbers on the left side indicate the number of the reaction step and the order of branches. The numbers on the right side show three things number of reaction vessels used in the reaction step, the number of executed reaction cycles and the number of products. 

The split-mix method was developed for preparing peptide libraries. The method is based on Merrifield s solid phase procedure, published in 1963 [8], Each coupling cycle of the solid phase synthesis is replaced by the following simple operations  

Dividing the solid support into equal portions  

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The split-mix synthesis technique can allow geometric numbers of compounds to be prepared using an arithmetic number of reaction chambers.5... 

FIGURE 2.2 Scheme of the split-mix synthesis. The triangles represent the solid support. The white, gray and black circles are amino acids or other kinds of monomers. 

The split-mix synthesis has several key features that are crucial in the utility of the method in drug discovery or other kinds of applications. 

The combinatorial principle embodied in the synthesis captured the imagination of many researchers all over the world and had a profound effect on the development of the field. The combinatorial nature of the product of the split-mix synthesis is also reflected in its name, combinatorial library. ... 

In the split-mix synthesis, like in other solid phase procedures, the beads behave very much like tiny reaction vessels, which do not interchange their contents with the other ones. Each of the millions of these reaction vessels preserves its content until the end of the synthesis, when they become containers of a single substance. If peptides are produced, their identity can be determined by automatic sequencing [9], It is sufficient to sacrifice a fraction of the total quantity for this purpose. All this means that the split-mix synthesis is, in fact, a parallel procedure, with unprecedented efficiency, however, leading to individual compounds. This feature of the split and mix synthesis allows screening the products in three different ways ... 

Figure 2 Synthetic scheme of the split-mix synthesis method to generate an OBOC combinatorial library...

Figure 1 The "split-mix synthesis" method to generate a one-bead one-compound combinatorial library (a) and a number of permutations for random peptide libraries (b). P, , and T are building blocks (in this case amino acids).

In this method, peptides or small molecules are prepared by the split-mix synthesis method and cleaved from the resin to form an encoded solution-phase library such that each library compound is tethered to a PNA code via a hydrophilic linker (11). The library then is mixed with the target protein and later exposed to planar oligonucleotide microarrays of predetermined sequences. Alternatively, the encoded soluble library can be hybridized to the oligonucleotide microarrays before incubation with the target protein. 

The major impetus for the development of solid phase synthesis centers around applications in combinatorial chemistry. The notion that new drug leads and catalysts can be discovered in a high tiuoughput fashion has been demonstrated many times over as is evidenced from the number of publications that have arisen (see references at the end of this chapter). A number of )proaches to combinatorial chemistry exist. These include the split-mix method, serial techniques and parallel methods to generate libraries of compounds. The advances in combinatorial chemistry are also accompani by sophisticated methods in deconvolution and identification of compounds from libraries. In a number of cases, innovative hardware and software has been developed tor these purposes. 

The synthesis of libraries of structurally defined compounds can potentially be achieved either by split-mix synthesis or by parallel synthesis of individual compounds. The synthesis requires a reliable methodology of oligosaccharide synthesis, where stereochemistry and regioselectivity have to be achieved unlike other library approaches. Development of synthetic methodologies that can provide access to any oligosaccharide structure is underway. 

While parallel synthesis of arrays of glycopeptides is readily achieved by implementation of the building-block approach (Scheme 14.1, Strategy 2),101 glycopeptide library synthesis in a combinatorial manner via the split-mix method has yet to prove routine. The difficulty lies in the structural analysis of the vast number of compounds generated in picomolar quantities on a single bead. Whereas peptides on... 

We first reported the one-bead one-compound (OBOC) combinatorial library method in 1991.1 In this method, compound beads are prepared by a split-mix synthesis approach1 3 (Fig. 1) that results in the display of many copies of the same compound on one single bead.1,4 Tens of thousands to millions of these compound beads can easily be prepared. The bead library is then mixed with a target molecule, such as a protein, an... 

The expense of screening depends very much on the number of samples tested. Consequently, the density format of titer-plates has increased in recent years from 96-well up to the 9600-well format. The next big step towards miniaturization would be the complete avoidance of any container, which then results in the smallest well possible and a well-less, so-called lawn-format assay develops. This is exactly what is proposed by a number of authors (see review [47]). Screening in a lawn format does not mean avoiding any structure or arrangements. Samples are still prepared on beads, which are produced by split-mix synthesis, but the beads are arrayed directly on the well-less assay. A typical matrix applied for such biological screening is the agarose lawn. Active beads are then picked from the assay matrix and decoded for compound identification. 

Peptides are not the only potential drug candidates. In most cases, other kinds of small organic molecules are preferred, because of their reduced susceptibility to enzymatic degradation. The split-mix method is fully applicable in the synthesis of organic libraries. Both sequential type and cyclic libraries can easily be prepared if the reaction conditions for solid phase are well developed. It has to be emphasized, however, that the advantages of the split-mix method can be fully exploited only in the case of multi-step synthetic procedures. For realization of the one-pot procedures suggested by Ugi [10], for example, the parallel procedures are better-suited. 

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... 

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