Computational modeling and surface plasmon resonance analyses in the assessment of peptide ligands interacting with fibrin gamma(312-324) epitope.

Fibrin represents a suitable target for addressing delivery systems loaded by fibrinolytic drugs. Selective ligands capable to recognize fibrin could be used as targeting moieties for such systems. In this study the interactions between the gamma(312-324) epitope of human fibrin and peptidic ligands were analyzed by using experimental and computational methods. Binding free energies were calculated through the molecular mechanics/generalized born surface area approach. Good qualitative agreements between the experimental and calculated data were obtained. The binding affinity seems to be well correlated (R(2)=0.69) with the changes of the nonpolar solvation energy term computed from solvent-accessible surface area calculation. These results indicate that current methods of estimating binding free energies are efficient for achieving information on protein-ligand interactions.

Design of highly specific ligands of fibrin for therapeutic applications.

The work presented here is aimed at designing high-affinity ligands for the fibrin gamma (312-324) epitope. This epitope is specific for fibrin recognition, as it is exposed only on the fibrin surface, while in fibrinogen it is buried in the protein bulk. This property makes it very useful for therapeutic applications. In fact, it may be exploited in driving systems for targeted delivery of thrombolytic drugs toward the specific compartment where they are needed. It will then allow avoidance of serious unwanted side effects produced by a conventional systemic administration. The approach chosen for designing putative ligands is based on the known three-dimensional (3D) structure of the epitope. A wide virtual library made up of oligo-peptides and analogues designed by a combinatorial approach, on the basis of chemical complementarity criteria, has been screened by means of a docking/scoring approach (DOCK program). The peculiarity of the problem under study required a considerable effort in finding a method enabling the experimental validation of the design work results. In fact the selected biological target is absolutely new, so that neither a endogenous, nor a synthetic high-affinity ligand is known up to now. It does not allow for the validation of computational results by means of classical binding tests based on the use of known labeled high-affinity ligands. Preliminary binding essayes were so carried out by means of the Plasmon Surface Resonance (PSR) technique. The experimental results suggested that most of the molecules predicted to be good ligands by means of the selected computational tools, could carry the wanted affinity toward the selected target.