Catalyst/HypoGen pharmacophore modeling approach and three-dimensional quantitative structure-activityrelationship (3D-QSAR)/comparative molecular similarity indices analysis (CoMSIA) methods have beensuccessfully applied to explain the cytotoxic activity of a set of 51 natural and synthesized naphthoquinonederivatives tested in human promyelocytic leukemia HL-60 cell line. The computational models havefacilitated the identification of structural elements of the ligands that are key for antitumoral properties. Thefour most salient features of the highly active
-cycled-pyran-1,2-naphthoquinones [0.1
M < IC
50 < 0.6
M] are the hydrogen-bond interactions of the carbonyl groups at C-1 (HBA1) and C-2 (HBA2), the hydrogen-bond interaction of the oxygen atom of the pyran ring (HBA3), and the interaction of methyl groups (HYD)at the pyran ring with a hydrophobic area at the receptor. The moderately active 1,4-naphthoquinonederivatives accurately fulfill only three of these features. The results of our study provide a valuable tool indesigning new and more potent cytotoxic analogues.