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Peptide Libraries

The use of peptide libraries as a research tool in chemistry and biology laboratories has increased significantly in recent years. In the peptide-based drug discovery process, the conventional one protein-one experiment strategy is too time-consuming and costly. What is required is high throughput screening that screens a large number of compounds quickly and efficiently in a parallel manner. Peptide libraries is a good choice. To determine the sequences of a peptide library, the selection process has the following considerations:

As the length of the peptide grows, the number of peptides to synthesize decreases.
As the offset number grows (i.e. the number of residues that the peptide sequence shifts from the original protein sequence), the number of peptides to synthesize decreases.
As the peptide sequence grows longer, the potential to achieve multiple hits (i.e. the peptide sequences that contain all of the essential residues in the epitope) increases.

The length of the protein sequence will determine the number of peptides in the library. Choosing a longer sequence and a shorter offset number would be ideal, but the monetary cost could become too great. Shorter peptide lengths, in contrast, will lead to more peptide sequences to synthesize and are more economical. Because it may be difficult to predetermine the ideal minimum number of peptides needed, the common practice is to use 8 to 20 residues (preferably in the 12 to 16 range) with the offset number being approximately 1/3 of the peptide length.

Peptide Library Types and Startegies

Alanine Scanning Library

Each amino acid is substituted individually and systematically for alanine. Alanine scanning allows the easy identification of the specific amino acids that are responsible for the conformation, activity, and function of a protein.
Positional Scanning Library

A selected position or positions in a peptide sequence are each systematically replaced with different amino acids. The resulting change in activity reveals the preferred amino acid residues at these positions.
Overlapping Library

Individual peptides can be divided in to several fragments that overlap. The resulting overlapping peptide libraries can then be used for processes including continuous and linear epitope mapping.
Truncation peptide libraries

Peptides can be cleaved systematically into small fragments. The library of truncated peptides could then be used to predict the minimum length amino acid that could be used to achieve optimal epitope activity.
Random Peptide Library

Selected positions are substituted with all 20 natural amino acids simultaneously, which might increase peptide activity.
Scrambled Library

These libraries are designed using variations of the original sequence of a peptide. The resulting peptides are used generally as negative controls to show that a specific sequence is critical to the protein function or activity. It is also a random screening tool used to find new leads.

The last step for peptide-based drug development is sequence stabilization.Structural stabilization of the peptide needs to be done to preserve their potency over time. Three different strategies can be employed to achieve this goal:

The most common method is to substitute selected amino acids with non-standard amino acids, like either homolog of natural amino acids (ex. ornithine, homolysine, norleucine, and norvaline) or the chiral analogs (D-forms) or the naturally-occurring amino acids (L-forms).
Another method is to incorporate intramolecular bridges to form cyclic structures.
The stabilization can be achieved through the chemical modification of the N- and C-termini (usually by acetylation and amidation, respectively).