Binding analysis services

Lead optimization using Pepscan’s peptide-array platform


Schematic visualization of the lead optimization proces. Based on an initial lead (left), full replacement analysis using both natural & non-natural amino acids identifies those amino acids in the lead sequence that are essential to binding, as well as the amino acids that contribute to affinity improvement. Iterative synthesis & screening cycles with affinity-optimized sequences result in an optimized candidate peptide.

Multiple peptide modifications can be evaluated simultaneously using our peptide arrays, where peptides undergo high-throughput synthesis on a solid support (455 wells in polypropylene mini-cards). The format of the lead peptide may be either linear or conformationally constrained, e.g. a CLIPS-constrained peptide. Moreover, our CLIPS technology is often used to improve the binding potential of linear peptides by fixing them in a certain conformation. Binding of the modified peptides to their target of interest (e.g. a protein, (monoclonal) antibody, enzyme, etc.) is determined via read-out in an ELISA-type assay to ultimately identify those peptides that show a sufficient increase in binding.

Non-natural amino acids (both L and D) are also frequently used in our peptide arrays to further extend the horizon for discovering new chemical entities (NCEs) beyond the reach of phage-display-type library optimizations that solely rely on the use of the 20 natural L-amino acids. This not only leads to new NCEs but also opens up novel options for the IP protection of existing peptide drugs.

Our peptide platform has helped identify small peptide binders designed or derived from whole protein sequences, and create constrained (e.g. CLIPS) derivatives of lead sequences with significantly improved binding activity.

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