Binding model for nonpeptide antagonists of alpha(v)beta(3) integrin

A binding model for nonpeptide antagonists of integrin alpha(v)beta(3) has been developed through docking analyses utilizing the MMFFs force field and the recently published crystal structure, 1JV2. Results of this docking study have led to the identification of a novel binding model for selective antagonists of alpha(v)beta(3) over alpha(IIb)beta(3) integrins. Four different chemical classes are shown to bind in a similar fashion providing a measure of confidence in the proposed model. All alpha(v)beta(3) and alpha(IIb)beta(3) antagonists have a basic nitrogen separated some distance from a carboxylic acid to mimic RGD. For the alpha(v)beta(3) antagonists under present consideration, these charged ends are separated by twelve bonds. The basic nitrogen of the active alpha(v)beta(3) ligands are shown to interact with D150 of alpha(v) and the ligands' carboxylic acid interact with R214 of beta(3) while adopting an extended conformation with minimal protein induced internal strain. In addition, an energetically favorable interaction is found with all of the active alpha(v)beta(3) molecules with Y178 of alpha(v) when docked to the crystallographically determined structure. This novel interaction may be characterized as pi-pi stacking for the most active of the alpha(v)beta(3) selective antagonists. The proposed model is consistent with observed activity as well as mutagenicity and photoaffinity cross-linking studies of the alpha(v)beta(3) integrin.