An increasing number of peptides with specific binding affinity to various protein and even non-protein targets are being discovered from phage display libraries. The power of this method lies in its ability to efficiently and rapidly identify ligands with a desired target property from a large population of phage clones displaying diverse surface peptides. However, the search for the needle in the haystack does not always end successfully. False positive results may appear. Thus instead of specific binders phage with no actual affinity toward the target are recovered due to their propagation advantages or binding to other components of the screening system, such as the solid phase, capturing reagents, contaminants in the target sample or blocking agents, rather than the target. Biopanning experiments on different targets performed in our laboratory revealed some previously identified and many new target-unrelated peptide sequences, which have already been frequently described and published, but not yet recognized as target-unrelated. Distinguishing true binders from false positives is an important step toward phage display selections of greater integrity. This article thoroughly reviews and discusses already identified and new target-unrelated peptides and suggests strategies to avoid their isolation.

The neutralisation of circulating ghrelin, the only known peripheral orexigenic peptide hormone, is a promising approach for the pharmacological treatment of obesity. To select peptides with an affinity towards ghrelin, 4 selection procedures were carried out with random peptide phage display libraries Ph.D.-7 and Ph.D.-12. Due to the absence of a common consensus motif, a stepwise elimination approach was used. The pool of selected peptides displaying phage clones was thoroughly examined to remove any potential target-unrelated peptides. The affinity of the remaining phage clones for ghrelin was tested with ELISA. An analysis of the binding properties revealed four-phage displayed peptides that bind to ghrelin with moderate affinity, with ADTVPRH and MEMKKTHPVLGA being the most specific. Additional advantage of peptide MEMKKTHPVLGA is an indication of binding to octanoyl group on N-terminal part of ghrelin, involved in receptor interaction. Hence peptide MEMKKTHPVLGA represents the most suitable lead for further investigation.