Combinatorial peptide library phage display

Figure 16.4 Graph depicting the percentage of lysine residues among peptides that bind to the indicated monoclonal antibodies. The peptides were isolated after affinity selection (biopanning) from a phage-displayed combinatorial peptide library. The peptides are grouped as to whether they are susceptible to formalin fixation, resulting in a loss of immunoreactivity.

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. 

Figure 8. Selection of the phage from the phage-displayed combinatorial peptide library [9]...

S Cabilly. The basic structure of filamentous phage and its use in the display of combinatorial peptide libraries. Mol Biotechnol 12 143-148, 1999. 

R Hyde-DeRuyscher, LA Paige, DJ Christensen, N Hyde-DeRuyscher, A Lim, ZL Fredericks, J Kranz, P Gallant, J Zhang, SM Rocklage, DM Fowlkes, PA Wendler, PT Hamilton. Detection of small-molecule enzyme inhibitors with peptides isolated from phage-displayed combinatorial peptide libraries. Chem Biol 7 17-25, 2000. 

There are two general methods for identifying antibody epitopes (1) evaluate peptides whose composition is based on the sequence of the native protein, or (2) evaluate peptides that are selected from a random combinatorial peptide library. The former is only effective if the epitope is composed of a linear sequence of amino acids in the native protein sequence. If it is, then analysis of overlapping peptides from the native protein is a simple method for identifying antibody epitopes. Each peptide is tested for immunoreactivity to the antibody. Those peptides that are immunoreactive contain the epitope. The other method of epitope identihcation, selection from a random combinatorial library, will identify peptides that represent both linear and conformationally dependent epitopes. The drawback of this method is that biopanning from a random combinatorial peptide library is more time consuming. Phage-displayed peptide libraries have previously been used for epitope identification in this context. ... 

To avoid the possibility that a small peptide from a phage-displayed library will not bind adequately when immobilized on a solid support, Baumbach and Hammond suggested that combinatorial peptide libraries for protein purification be synthesized directly on resins that could be used as chromatographic supports on a large scaled, in this way, any ligand that is identified is already on a platform or format that would facilitate implementation in downstream processing. The one-bead-one-peptide solid phase library format is ideally suited for this purpose, if the library is built on chromatographic resins that can withstand the harsh solvent conditions used for peptide synthesis. 

EMPl, selected by phage display from random peptide libraries, demonstrates that a dimer of a 20-residue peptide can mimic the function of a monomeric 166-residue protein. In contrast to the minimized Z domain, this selected peptide shares neither the sequence nor the structure of the natural hormone. Thus, there can be a number of ways to solve a molecular recognition problem, and combinatorial methods such as phage display allow us to sort through a multitude of structural scaffolds to discover novel solutions. 

Naik, R.R., Brott, L.L., Clarson, S.J. and, Stone, M.O. (2002) Silica-precipitating peptides isolated from a combinatorial phage display peptide library. Journal of Nanoscience and Nanotechnology, 2, 95-100. 

Sompuram SR, Kodela V, Ramanathan H, et al. Synthetic peptides identified from phage-displayed combinatorial libraries as immunodiagnostic assay surrogate quality-control targets. Clin. Chem. 2002 48 410-420. 

K Johnsson, L Ge. Phage display of combinatorial peptide and protein libraries and their applications in biology and chemistry. Curr Top Microbiol Immunol 243 87-105, 1999. 

Since its introduction, this technique has gained more and more importance in the combinatorial field. The main advantage of biological libraries, in comparison to chemical libraries, depends on the possibility of increasing remarkably the number of different molecules that can be screened at the same time. Furthermore, once the phage displaying the active sequence has been selected, it is able to replicate itself by infecting host bacterial cells successive selection and amplification cycles result in an exponential enrichment of the active peptide sequence. 

The third group of alliances focuses on lead optimization. Here, a particular lead is known, such as a small peptide and it is desired to optimize the activity of that lead. In the case of peptides this could be accomplished through phage display and/or peptidomimetic combinatorial chemistry. Companies involved in alliances of this type have proprietary technologies that enable them to generate usually small-molecule libraries built around particular molecular themes, for example, steroid cores. Examples include alliances of Ontogen, Dyax, ArQule, etc. 

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