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Caspase-3 has become an attractive target in the treatment of many diseases such as Alzheimer, Parkinson’s, myocardial infarction and cancer. In the present study, molecular three-dimensional quantitative structure activity relationship (3D-QSAR) and docking studies were performed on a series of caspase-3 activators. Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and step-wise k-nearest neighboring molecular field analysis [(SW) kNN MFA] were performed to gain insight into the key structural factors affecting the activity. The results of 3D-QSAR are reliable and significant having high predictive (q2) ability showing good correlation between predicted and observed activity. The lower value of standard error of estimation shows that most of the observed values cluster fairly close to the regression line. Molecular docking was performed with the GOLD docking program used to explore the binding mode between the ligands and the receptor.