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Finding a new treatment for cancer is one of the most interested fields for pharmaceutical research worldwide. Enzyme histone deacetylase 2 (HDAC2), being a member of HDAC class I appear to be an important druggable target.This study focused on rational design of novel HDAC2 inhibitorsusing molecular descriptors derived from ISIDA fragmentor methodology. Quantitative structure-activity relationship was explored to develop mathematical models able to predict HDAC2 inhibitory bioactivity of acid hydroxamic derivatives. Multiple linear regression (MLR) algorithm implemented in STATISTICA 8.0 was used for model development. Consequently 3 QSAR models were obtained showing acceptable performance r2> 0.70 for further use. Based on these models 10 important fragments attributing to better inhibitory potency were identified. Finally several novel hydroxamic derivatives were designed and screened for HDAC2 inhibitory activity.