Investigating the Interaction of Cyclic RGD Peptidomimetics with alphaVbeta6 Integrin by Biochemical and Molecular Docking Studies.

The interaction of a small library of cyclic RGD (Arg-Gly-Asp) peptidomimetics with alphaVbeta6 integrin has been investigated by means of competitive solid phase binding assays to the isolated receptor and docking calculations in the crystal structure of the alphaVbeta6 binding site. To this aim, a rigid receptor-flexible ligand docking protocol has been set up and then applied to predict the binding mode of the cyclic RGD peptidomimetics to alphaVbeta6 integrin. Although the RGD interaction with alphaVbeta6 recapitulates the RGD binding mode observed in alphaVbeta3, differences between the integrin binding pockets can strongly affect the ligand binding ability. In general, the peptidomimetics exhibited IC50 values for integrin alphaVbeta6 (i.e., the concentration of compound required for 50% inhibition of biotinylated fibronectin binding to isolated alphaVbeta6 integrin) in the nanomolar range (77-345 nM), about 10-100 times higher than those for the related alphaVbeta3 receptor, with a single notable ligand displaying a low nanomolar IC50 value (2.3 nM). Insights from the properties of the binding pocket combined with the analysis of the docking poses provided a rationale for ligand recognition and selectivity.