Rational and Combinatorial Design of Peptide Affinity Ligands for Diagnostic Assays

Peptides are promising affinity ligands for detection of proteins in biological samples. We describe a synergistic approach to peptide design based on a combination of biological display and chemical syntheses methods. S-protein and s-peptide were used as a model protein-peptide system in this study. S-peptide is a natural ligand that binds to s-protein with a very high affinity (~30 nM). Based on the crystal structure of s-protein and the amino acid sequence of s-peptide, we designed candidate peptide libraries to be screened for binding to s-protein. Peptide libraries were synthesized using a high throughput peptide synthesizer and screened for binding to s-protein using peptide microarrays. We discovered a range of peptides with varying binding affinities to s-protein. The peptides discovered in this study were used to design single-step, high sensitivity, diagnostic assays for detecting s-protein as a model biomarker in human serum. This study elucidates a systematic approach for the design and discovery of peptide affinity ligands for the detection of protein biomarkers of interest.