Second-generation libraries

A variation of the pharmacophore library was seen in an approach used to determine CD4+ T cell epitopes.31 In a 14-mer peptide, the researchers keep residues in positions 1, 4, and 6 constant since they functioned as anchor positions for binding receptor, and proceeded to vary the other residues in the peptide. This allowed the use of a shorter synthetic route compared to one that would be needed if all positions were to be varied. Limiting the size of the library allowed the authors to obtain better assays. By doing a partial release of the peptides, the authors were able to find the final peptide that represented the epitope of the T cell receptor. In another example, the epitope to inhibit stimulation of the thyrotropin receptor also was found via combinatorial libraries.32 Since the synthesis of a totally random hexapeptide library was deemed impractical, the authors opted to hold one position constant while the other five residues were randomized. This method was repeated for each residue in the peptide. The residues that were determined to be the most active were used as a basis for a second-generation library. The only limitation of the library was not the quantity of product synthesized, but to properly pinpoint the peptides in an assay. 

An extended family of poly-guanidinium lipids was obtained by exploiting a combinatorial chemistiy approach (Figure 15.21). In application of the concept of libraries from libraries , a second generation library of mono-functionalized (polyguanidinium)-amines was synthesized and introduced into cationic lipids (Byk et al., 1998b). 

Byk, G., Soto, J., Mattler, C., Frederic, M. and Scherman, D. (1998b) Novel non-viral vectors for gene delivery Synthesis of a second generation library of mono-functionalized poly-(guanidinium)amines. Biotech. Bioeng., 61, 81-87. 

The testing of a 7.5 x 106 membered octapeptide library with fixed N-terminal 7i-(CH3)-histidine (Pmh) and C-terminal alanine resulted in identification of catalysts with higher activity than DMAP for the acetylation of sec-phenylethanol [17]. The identified catalyst Boc-Pmh-L-Asn(Trt)-D-Val-L-His(Trt)-D-Phe-D-Val-D-Val-L-Ala-resin 10 then served as a parent compound for a second-generation library. This screening yielded catalysts with yet greater activity and specificity. Interestingly, all... 

The diversity clustering analysis that was used to choose the final components of the directed library proved useful to design a second generation library quickly. We re-examined the clusters of the top scoring components, and generated a small library of 39 compounds from other components in those clusters. These are components that combiBUILD predicted would bind well, and which were similar to compounds that had already been shown experimentally to bind well. Almost all (92%) had IC50 better than lpM, and 18% were nanomolar inhibitors, the best with a Ki of 9nM. 

Figure 7-20. Second generation library of diimines as chiral activators (A A )...

A second-generation library of 486 PBAEs was generated to examine the structure-function relationships with greater resolution. High-throughput screening of luciferase DNA transfection in COS-7 cells followed by biophysical... 

To become a technology platform to truly evolve, the selection of active small molecules is another important aspect for further development. First, it should be able to construct a second-generation library directly from a selected library population without multiple steps of manipulations as in Vipergen s rolling translation second, it should be able to introduce mutations and recombination to the chemical genes for library diversification and finally, it would ideally be a dynamic system so that non-binders are removed and the selection is iterated automatically. 

Assemble a second-generation library by creating a second collection of terpyridine monomers with modifications of the initial lead, and repeat from step 1. 

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