Diverse peptide libraries

Cyclic Peptide Libraries with Sequential and Chemical Diversity... 

In addition to sequential and chemical diversity, cyclic peptide libraries offer the possibility of conformational diversity where all components of the library differ from each other in their conformation, despite the identical connectivity. In this context two complementary approaches have been proposed, i.e. spatial screening based on head-to-tail cyclic peptides and cycloscan where the rest of the modes of cyclization are exploited. 

While in normal combinatorial peptide libraries (either chemical or phage display) each component has a unique sequence that is different from all others, in the cycloscan libraries all components have the same sequence, but differ in their conformation. This conformational diversity is generated in a dendrimeric hierarchy as shown exemplarily in Scheme 27 for the parent linear heptapeptide A-B-C-D-E-F-G. The diversity of the 1st order sublibrary (this nomenclature was adopted from Furka[468l) is based on the mode of cyclization. Excluding the head-to-tail cyclization there are seven different modes of cyclization that can be used for cycloscan three natural modes of cyclization and four modes of N-backbone cyclization. In addition there are five theoretical modes of C-backbone cyclization (see Scheme 1) which are not included in Scheme 27. 

Pavia, M. R. Whitesides, G. M. Hangauer, D. G. Hediger, M. E. A Method for Preparing and Selecting Pharmaceutically Useful Non-Peptide Compounds from a Structurally Diverse Universal Library WO 95/04277, 1995. 

We have selected many unnatural a-amino acids to study their sequencing profiles. Table III summarizes the RT of 74 PTH derivatives of both natural and unnatural amino acids. Through Table III it is easy to select 4(M-5 amino acids with ART greater than 0.10 min as building blocks to construct peptide libraries. This greatly increases the diversity of the peptide libraries that can be generated. 

Glycosylation of peptides is an efficient method to stabilize peptide by inhibition of enzymatic degradation, to conformationally modify peptide and usually to increase peptide solubility. Peptides glycosylation also creates additional diversity in peptide libraries since the high functionalities and variability of sugar moieties. 

A typical random peptide library displays polypeptides usually from 6 to 15 amino acids long. The length of the peptides is chosen based on the type of ligand one wants to select, the number of randomized positions, and the size of the library. For example, ligands for affinity purification should be short in order to diminish the cost of peptide synthesis. A longer peptide would probably work better as a live vaccine. A larger number of randomized positions would increase sequence diversity and the size of the complete library. 

Christian et al. [69] evaluated the genetic diversity of their dodeca-peptide library by a modified colony hybridization protocol. This protocol allows the discrimination of perfect matches by hybridizing 17 degenerated oligonucleotide probes to the library clones and washing by incrementing the temperature until the perfect matches alone are able to hybridize. The observed number of positive clones for each oligonucleotide probe is correlated with the theorized number. 

Interest in making non-native isomers arises because peptide analogues are widely regarded as valuable drug leads and in recent years there has been much effort directed towards the development of peptide libraries. It has been of particular interest to develop methods to increase the surface variability of peptides because the diversity of peptide libraries is, to some extent, limited by the use of the 20 natural amino acids. The study described above shows that the use of alternative disulfide bond connectivities provides another way of altering molecular conformations without modifying the sequence. 

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