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The elevated urokinase-type plasminogen activator (uPA) expression is associated with cancer progression, metastasis and shortened survival in patients. Therefore, uPA has been considered as a promising molecular target for development of anticancer agents. In the present study, 3D-QSAR analyses were carried on a series of isocoumarin-based inhibitors of uPA using linear and non-linear regression analysis methods. Among the several generated 3D-QSARs, the best models selected on the basis of their statistical significance and predictive potential were used for comparative analyses. The significance of steric, electrostatic and hydrophobic properties on uPA inhibitory activity of the molecules under study is discussed based on the best derived 3D-QSAR models.