Peptide combinatorial library deconvolution

A special type of combinatorial library is the positional scanning library (43, 49,58). This array contains a set of combinatorial libraries with one or more (two positions = dual positional scan (4, 59))deconvoluted positions. In each of the synthesized libraries the deconvoluted positions are different. After screening one can combine the positions of the spot with the peptides of highest activity of each library to obtain the complete sequence of a peptide with most likely the greatest activity. 

Since it is unlikely for one to be able to synthesize all possible sequences on a single spot, do not start synthesis of a combinatorial library with more than 6 mixture positions. If necessary, start to screen 8mer peptides (6 mixture + 2 deconvoluted positions) and extend the peptide length with each synthesis round by extending the deconvoluted positions and maintaining the number of mixed positions (e.g., 6 mixture + 4 deconvoluted positions). 

Many different methods for the deconvolution of the components of combinatorial libraries exist today. An active mixture of peptides can be separated into components. Conventional reverse-phase HPLC (columns with Cjg) has been used successfully for the separation of peptide mixtures. 

Peptides and Peptidomimetics from Combinatorial Libraries. Mixture-based combinatorial peptide libraries have been extensively explored by Houghten and coworkers and have led to the identification of a variety of peptides with affinity for opioid receptors (see Ref 946 for a review). Early hexapeptide libraries, deconvoluted by binding to p opioid receptors and either iterative deconvolution (947)or positional scanning (948 see Ref 946 for a description of these deconvolution techniques), identified sequences related to the enkephalins. Other nonacetylated peptide libraries have identified more varied peptides, some that resemble opioid peptides and some that do not. Iterative deconvolution of a hexapeptide library resulted in identification of both Tyr-Pro-Phe-Gly-Phe-XNH, (X = one of 20 natural amino acids), reminiscent of the... 

IR spectroscopy is not a very sensitive analytical tool and is, therefore, not well suited to the detection of small amounts of material. If, however, intermediates have intense and well-resolved IR absorptions, the progress of their chemical transformation can be followed by IR spectroscopy [83,88,91-93], Near-infrared spectroscopy, in combination with an acousto-optic tunable filter, can be sufficiently sensitive to enable the on-bead identification of polystyrene-bound di- and tripeptides, even if the peptides have very similar structures (e.g., Leu-Ala-Gly-PS and Val-Ala-Gly-PS) or differ only in their amino acid sequence (e.g., Leu-Val-Gly-PS and Val-Leu-Gly-PS) [94]. Special resins displaying an IR and Raman barcode have been developed, which may facilitate the deconvolution of combinatorial compound libraries prepared by the mix-and-split method [48]. 

In Section II.C we will present novel tricyclic xanthene derived amino acid templates, which allow the construction of libraries of cyclic conformationally constrained peptide loop mimetics using the split-and-mix method without having to use tagging and deconvolution strategies. In Section III we will focus on parallel and combinatorial approaches devoted to the synthesis of small molecule, non-peptidic compound collections, which in addition offer the possibility to incorporate structural features derived from protein epitope mapping into conformationally constrained peptide mimetics. 

Recently, combinatorial technologies and libraries have somewhat replaced NPs as a source of diversity in pharmaceutical research. A comparison of combinatorial technologies with the fermentation of an NP-producing organism show that they both produce a library of compounds. While the former library is structurally determined a priori either by the selected synthetic scheme or by recombinant genetic information in the case of biosynthetic peptide and ON libraries, the latter is the result of the metabolic complexity of the producing strain and has to be deconvoluted in order to... 

Recently, Fmoc-N-protected (3-amino acid synthons have been prepared and used for the synthesis of (3-peptides on solid phase [103]. This methodology facilitates enormously the search for new bioactive compounds, above all through the generation of combinatorial (3-peptide libraries. In this context, (3-amino acids have been used as building blocks for RGD cyclic peptides and for the synthesis of an inhibitor of human cathepsin L, previously identified by screening and deconvolution of pentapeptide amide collections [104,105]. 

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