Selective binding and cleavage of peptides : a combinatorial approach

This work presents a novel class of two-armed receptors that bind to peptides with high
sequence selectivity. These receptors are composed of a diketopiperazine derived from
hydroxyproline as a template and two peptidic arms. The excellent binding properties
have been rationalised by the analysis of the influence of the template structure on the
binding properties. Exchange of the diketopiperazine against other templates resulted in
an entire loss of intermolecular binding ability. Analysis of the diketopiperazine
conformation by X-ray crystal structure analysis and by 1H-NMR-spectroscopy revealed,
that diketopiperazine receptors with pseudo-axial standing substituents are excellent
templates for two armed receptors. These studies demonstrated that the template has the
largest impact on the binding properties. The second largest effect comes from the first
amino acid that is coupled to the template. The receptors are currently applied for the
development of sensors[69] and liquid crystallin materials70] and might be used for the
development of diagnostics.
The second part shows by the use of a combinatorial fluorophore-quencher library, that
peptides containing two acidic amino acids are preferably cleaved under Fenton
conditions. Such peptides were shown to coordinate to iron more strongly than other
peptides. Due to the iron coordination, upon the addition of ascorbic acid and H2O2,
radicals are generated in the vicinity of the peptide. These peptides are therefore cleaved
more than peptides that are not able to coordinate to iron.
The presented results are designed to serve as a starting point for the development of
selective proteolytic receptors. By coupling a proteolytically active metal complex (e.g.
Fe-EDTA)[71] to, for example a diketopiperazine receptor, peptides will not only be
bound, but, in a second step cleaved selectively (as shown in figure 5.)