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Peptide Library

Powerful peptides are leading to many discoveries. Developing new techniques for screening and synthesizing peptides can result in efficient and cost-effective methods which make drugs more effective, diseases easier to cure, and lives to last longer.

Several covalent bonds, called peptide bonds, join amino acids together to form proteins. A peptide forms between the amino acid group of one amino acid and the carboxyl group of another. Further, a peptide library is a tool for protein-related study. Further, a hexapeptide is a peptide that contains six amino acid residues.

What does "mer" mean in the context of a peptide library?

The term "mer" signifies the quantity of residues in a peptide. For instance, a peptide comprising 21 amino acid residues may be labeled as either a decapeptide or a 21-mer peptide. It's important to note that "mer" doesn't convey information about the molecular weight (Mr or MW) of the peptide. This "mer" nomenclature is also applied to other polymers, indicating the count of residues in the polymer.

Peptide Libraries: A Practical Solution

A peptide library contains a great number of peptides that have a systematic combination of amino acids. Usually, a peptide library is synthesized on solid phase, mostly on resin, which can be a flat surface or beads.

The peptide library provides a powerful tool for:
• Drug development and design
• Protein-protein interactions
• Other biochemical and pharmaceutical applications

By producing large numbers of peptides, for which each differs from the other by one single amino acid, it is possible to ascertain which amino acid substitutions make binding to a receptor the strongest, and which make that binding process weaker. The challenge is how to conveniently and cost-effectively create thousands, or even millions of peptides so that they can be utilized in binding studies. One solution is to synthesize the peptides, or to combine them.

At each point in a sequence, a mix of desired amino acids can be generated. Thus, it is possible to develop a library of 20 different polypeptides along with just one amino acid residue randomly, with all the rest being the same. There is a limit, however, in that scientists cannot go past 70 acids in length.

However, since there are 20 natural amino acids, the synthesis of a linear peptide (n amino acids in length) can be produced in 20n different combinations. That equals 64,000,000 hexapeptides that can be created. So peptide libraries are very capable tools for biological and pharmaceutical research. Here huge numbers of peptides are screened so as to isolate and identify critical bioactive peptides that are used for new ways to cure diseases and cancers.

These tools help to:
• Guide scientists through steps that isolate the minimum length of active peptide sequences
- This helps scientists to replicate, or copy peptide sequences for purposes such as research
• Identify critical amino acid residues
- This helps explain of what the peptides are made
• Design analogs for sequence optimization
- This assists in knowing what is the most important within a sequence, thus avoiding the use of lengthy peptide chains.

One-bead, One-compound (OBOC) Libraries

Synthetizing methods for developing one-bead, one-compound (OBOC) peptide libraries have shown to be superior to that of standard assay formats and pooling strategies. The OBOC format is responsive to off-bead assays. In an off-bead assay, the peptide is released from the resin bead, but it maintains its proximity to the bead. Allocation of the library and a test cell line within a soft agar matrix followed by a partial peptide release will result in high concentrations of peptide in the agar surrounding each bead. Peptides that display the desired activity are identified by zones of reduced cell growth, or by other indicators such as color changes. These beads are then isolated and analyzed.

This method identifies peptide ligands as well as cytoxic peptides that may prove useful in developing anti-cancer agents. The unique screening technique as described above uses peptide chemistry along with the OBOC library format.

Other unique screening methods in peptide chemistry include:
• Direct visualization of cancer cells binding to peptides on beads
• Fluorescence-activated cell sorter (FACS)

OBOC libraries are very powerful tools that are utilized for the discovery of cysteine-rich peptides for protein tagging as well as cysteine-rich pharmaceuticals, and more. The OBOC technique is used to reproduce libraries, which has been found to be very successful. This enables scientists to enlist simple screening methods by applying only one sequence on each bead. Pooled sequencing techniques could soon be a thing of the past.

Libraries in and of themselves can prove even more uniform than other methods in demonstrating full-length ligands during screening since molecular weight degeneracy can be eliminated right during the sequencing process versus during the synthesis, thus making the entirety of the technique much more simplified and less costly.

Combinatorial Peptide Libraries and Ligands: More Effective Techniques

A ligand can be referred to as an «electron donor» that is attracted to the electron acceptor at the center of a complex, for which the ligand [ion or molecule] binds to a central metal atom and forms a complex. Ligands, which can be negatively charged or neutral, provide both of the electrons for the bond that forms between itself and the central metal atom or ion.

New methods that help reveal affinity ligands for glycosylated hemoglobin (HbA1c) are influential in the control of diabetes. This relatively new approach to using ligands is excellent for large-scale synthesis. Using ligands as opposed to antibodies is beneficial because:
• Antibodies are much more expensive to produce
• Antibodies are unstable
• Ligands are equally efficient as are antibodies because ligands bind to the analyte the same way antibodies do.

Combinatorial Synthetic Peptide Libraries & Antimicrobial Peptides (AMP)

Houghten, et.al, as reported in «Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery» bypassed the limitations of more popular methods used for synthesis and screening of large numbers of peptides. Typical challenges to existing techniques are an inability to produce and screen the requisite number (in the millions) of peptides, as well as general inabilities to create unmodified peptides in high enough numbers that have the ability to interact in solution. In short, Houghten and his colleagues were able to develop new antimicrobial peptides.

Antimicrobial peptides (AMPs) are unique and multi-functioning peptides. AMPs are peptides that contain <100 amino acid residues. AMPs have a net charge equaling +2 to +9. They are comprised of positively charged amino acids (e.g.: lysine and arginine) as well as a fair amount of hydrophobic residues. Structural and physiochemical properties of AMPs are directly related to their precision to target cells.

AMPs serve as multidimensional effector molecules. Antimicrobial peptides contain unusual and valuable amino acids for which each unique property delivers a different mode of action. Some of their amazing roles include:
• Signaling molecules
• Immune modulators
• Mitogens (triggering cell division)
• Anti-tumor agents
• Contraceptive agents

AMPs have been researched as drug delivery routes for permeating (otherwise impermeable) cells for delivering life-saving pharmaceuticals directly to the cell interior.

A Bright Future for Peptides

Combinatorial peptide libraries are coupled with computer modeling techniques for the utmost in bioactive peptide applications for human disease and cancer therapies, along with drug efficacies. The future for continuing AMP research, and even clinical trials, looks bright, with special research emphasis on AMPs' structural and biological properties, as well as their prophylactic and therapeutic applications. Peptides are quickly having a profound effect on the future of scientific discovery, chemistry, biochemistry, pharmaceuticals, and modern medicine.

References
1. Houghten RA, Pinilla C, Blondelle SE, Appel JR, Dooley CT, Cuervo JH. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 354, 84-86 (07 November 1991). [PubMed].
2. Liu, R. and Lam, K. S. Peptide Combinatorial Libraries. Wiley Encyclopedia of Chemical Biology. 2008, 1-13. [Article].
3. B. Chen et al. The synthesis and screening of a combinatorial peptide library for affinity ligands for glycosylated haemoglobin. Biosensors & Bioelectronics 13 (1998) 779-785. [PubMed].
4. Wah Y. Wong, Hasmukh B. Sheth, Arne Holm, Robert S. Hodges, Randall T. Irvin. Representative Combinatorial Peptide Libraries: An Approach to Reduce both Synthesis and Screening Efforts. A Companion to Methods in Enzymology 6, 404-410 (1994). [Article].