A surrogate-based approach for post-genomic partner identification

The use of phage display peptide libraries for basic and translational research

Phage display is a molecular technique, whereby genes are displayed in a functional form on the outer surfaces of bacteriophages by fusion to viral coat proteins. The gene product is encoded by a plasmid contained within the virus, which can be recovered and sequenced, linking the genetic information to the function of the protein. Phage display offers a powerful tool for the identification of short peptides or single chain antibodies that can bind and regulate the function of target proteins. One major advantage of phage display lies in its ability to rapidly identify target-specific peptides with pharmacological activity as agonists or antagonists.

Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries

This unit describes the process and analysis of affinity selecting bacteriophage M13 from libraries displaying combinatorial peptides fused to either a minor or major capsid protein. Direct affinity selection uses target protein bound to a microtiter plate followed by purification of selected phage by ELISA. Alternatively, there is a bead-based affinity selection method. These methods allow one to readily isolate peptide ligands that bind to a protein target of interest and use the consensus sequence to search proteomic databases for putative interacting proteins.

Peptides identify multiple hotspots within the ligand binding domain of the TNF receptor 2

BACKGROUND: Hotspots are defined as the minimal functional domains involved in protein:protein interactions and sufficient to induce a biological response. RESULTS: Here we describe the use of complex and high diversity phage display libraries to isolate peptides (called Hotspot Ligands or HSPLs) which sub-divide the ligand binding domain of the tumor necrosis factor receptor 2 (TNFR2; p75) into multiple hotspots. We have shown that these libraries could generate HSPLs which not only subdivide hotspots on protein and non-protein targets but act as agonists or antagonists. Using this approach, we generated peptides which were specific for human TNFR2, could be competed by the natural ligands, TNFalpha and TNFbeta and induced an unexpected biological response in a TNFR2-specific manner. CONCLUSIONS: To our knowledge, this is the first report describing the dissection of the TNFR2 into biologically active hotspots with the concomitant identification of a novel and unexpected biological activity.

Targeting mucosal sites by polymeric immunoglobulin receptor-directed peptides

Polymeric immunoglobulins provide first line humoral defense at mucosal surfaces to which they are specifically transported by the polymeric immunoglobulin receptor (pIgR) on mucosal and glandular epithelial cells. Previous studies from our laboratory suggested that amino acids 402-410 of the Calpha3 domain of dimeric IgA (dIgA) represented a potential binding site for the pIgR. Here by binding human secretory component to overlapping decapeptides of Calpha3, we confirm these residues and also uncover an additional site. Furthermore, we show that the Calpha3 motif appears to be sufficient to direct transport of green fluorescent protein through the pIgR-specific cellular transcytosis system. An alternative approach identified phage peptides, selected from a library by the in vitro Madin Darby Canine Kidney transcytosis assay, for pIgR-mediated transport through epithelial cells. Some transcytosis-selected peptides map to the same 402-410 pIgR-binding Calpha3 site. Further in vivo studies document that at least one of these peptides is transported in a rat model measuring hepatic bile transport. In addition to identifying small peptides that are both bound and transported by the pIgR, this study provides evidence that the pIgR-mediated mucosal secretion system may represent a means of targeting small molecule therapeutics and genes to mucosal epithelial cells.

Target validation and drug discovery using genomic and protein-protein interaction technologies

After the successful completion of the human genome project, mapping of the human proteome has become the next important challenge facing the biotech and pharmaceutical industries. Identification of the 'right' target(s) is now a critical part of the process because of the cost of drug discovery. Compounding this situation is the fact that the pharmaceutical industry faces a further challenge of being able to sustain current and historical growth rates. Hence, the discovery of new drug targets is important for developing new drug leads that can become preclinical drug candidates. Proteomics is the next phase of the effort whereby the human genome can be understood. However, mapping the human proteome presents a daunting challenge. Proteomics involves several essential components with the most significant being the discovery and description of all protein-protein interactions. Once this compendium is available, a secondary and equally important initiative will be to decipher proteins that are differentially expressed in any given disease condition. At this point, the critical focus will be to select the most relevant proteins, understand their partner interactions and then further winnow them to the point where they are relevant pharmaceutical target candidates. This paradigm can be compared to finding the relevant 'needle in the proteome haystack'. This review describes the use of genomic and protein-protein interaction technologies to identify and validate these 'needles' as the first step in the drug discovery process.

Peptides identify the critical hotspots involved in the biological activation of the insulin receptor

We used phage display to generate surrogate peptides that define the hotspots involved in protein-protein interaction between insulin and the insulin receptor. All of the peptides competed for insulin binding and had affinity constants in the high nanomolar to low micromolar range. Based on competition studies, peptides were grouped into non-overlapping Sites 1, 2, or 3. Some Site 1 peptides were able to activate the tyrosine kinase activity of the insulin receptor and act as agonists in the insulin-dependent fat cell assay, suggesting that Site 1 marks the hotspot involved in insulin-induced activation of the insulin receptor. On the other hand, Site 2 and 3 peptides were found to act as antagonists in the phosphorylation and fat cell assays. These data show that a peptide display can be used to define the molecular architecture of a receptor and to identify the critical regions required for biological activity in a site-directed manner.

One from column A and two from column B: the benefits of phage display in molecular-recognition studies

Recent uses of phage-displayed combinatorial peptide and cDNA libraries have proven invaluable in mapping protein-protein interactions, protein-drug interactions, and the generation of 'molecular therapeutics'. This article reviews some of the findings of the past year and points out some of the pros and cons of phage display as compared with those of yeast two-hybrid screening.