Because of problems with transport and stability, proteins, which are big molecules, are typically unsuccessful as medicines. A protein is a big molecule that can perform a variety of biological tasks, each of which is determined by the localized interactions of a particular sequence of amino acids with another protein or a ligand that is not a protein. The traditional one protein-one experiment technique is too time- and money-consuming for the peptide-based drug development process. High throughput screening is necessary, which screens a lot of chemicals fast and effectively in parallel.
Drug development is divided into a number of separate stages. The initial stage in the process is to "map" the active sequences (i.e., epitope) of a protein. This is done by a procedure called epitope mapping, which also identifies the peptide's minimal sequence that constitutes the protein's active domain. By using overlapping peptide sequences from the original protein, epitope mapping creates a library of peptides. The selection procedure takes into account the following factors in order to determine a peptide library's sequences:
The quantity of peptides required for synthesis reduces as peptide length increases.
The number of peptides required for synthesis reduces as the offset number (i.e., the number of residues that the peptide sequence shifts from the original protein sequence) increases.
The likelihood of obtaining many hits (i.e., peptide sequences containing each of the necessary epitope residues) rises as the length of the peptide sequence does as well.
The amount of peptides in the library will depend on how long the protein sequence is. It would be nice to choose a longer sequence and a smaller offset number, but the cost might be too high. In contrast, shorter peptides are more cost-effective to synthesize and will result in more peptide sequences. The standard approach is to employ 8 to 20 residues (ideally in the 12 to 16 range), with the offset number being around 1/3 of the peptide length, although it may be difficult to predict the appropriate minimum number of peptides required.
Peptide sequence optimization, the following step in drug research, uses four useful methodologies to ascertain the structural and functional correlations of the targeted epitope.
Alanine Scanning Library: Alanine is methodically substituted for each amino acid position in the epitope in the alanine scanning library since it is the smallest amino acid that maintains chirality. A considerable decrease in activity would occur if alanine were to replace an essential amino acid. The degree of activity reduction could potentially be used to gauge the relative significance of that particular amino acid.
Truncation library: This technique involves systematically trimming flanking residues to obtain the peptide's ideal minimum length.
Random Library: A broad approach, says Random Library. Selected residues in the peptide sequence (also known as the wobble sequence) are concurrently substituted with a mixture of all 20 amino acids or a predetermined combination of amino acids. After then, the combinations of these random libraries are examined.
Positional Scanning Library: Different amino acids are each gradually substituted for a chosen location or places in a peptide sequence. The preferred amino acid residues at these sites are revealed by the ensuing shift in activity.
Sequence stabilization is the last stage in the creation of peptide-based drugs. To maintain the peptides' effectiveness over time, structural stability is necessary. To do this, one can use one of three strategies:
The most often used technique involves replacing specific amino acids with non-standard amino acids, such as homologs of natural amino acids (for example, ornithine, homolysine, norleucine, and norvaline), chiral analogs (D-forms), or naturally-occurring amino acids (L-forms).
Intramolecular bridges can also be used to create cyclic structures.
The N- and C-termini can be chemically altered to achieve stability (often through acetylation and amidation, respectively).
To market PEPscreen(R) Custom Peptide Libraries, Sigma-Aldrich and CPC entered into a distribution agreement in 2009. PEPscreen® is a powerful tool for peptide-based drug discovery, and Sigma's patented peptide synthesis platform makes it possible to quickly and effectively synthesize milligram amounts of peptides in parallel at high throughput. With the use of this experience, CPC is now able to provide direct client assistance for custom peptide libraries.
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