The binding modes of urokinase-type plasminogen activator(uPA)with five inhibitors(1-(7-Sulfonamidoisoquinolinyl)guanidine derivatives)were predicted based on molecular dynamic simulations.MM/PBSA free energy calculations and MM/GBSA free energy decomposition analyses were performed on the studied complexes.The calculated binding free energies are in reasonable agreement with the experimental values.The decomposition analyses of the free energy elucidate the different energy contributions of some structurally important residues of the protein-ligand interactions in each complex.The results indicate that the inhibitors mainly interact with the S1 pocket of uPA,wherein the hydrogen-bonds and the interactions between guanidines and the corresponding residues play an important role.Moreover,hydrogen bond analyses show the water-mediated hydrogen-bond network near the S1 pocket between uPA and the ligand probably leads to excellent selectivity of these inhibitors on uPA.