Dipeptidyl peptidase IV (DPP4) is a promising target for developing novel anti-diabetic and anti-obesity drugs. Pharmacophore based three dimensional quantitative structure activity relationship studies (3D-QSAR) and molecular docking were performed on a series of 56 β-aminoacyl-containing homopiperazine derivatives of DPP4 inhibitors to find out the structural relationship with the activity. The best predictive 3D-QSAR model with pharmacophore based alignment resulted in R2 (training set) value of 0.9407, Q2 (internal test set) value of 0.9053, Pearson-R value of 0.9517 and root mean square error (RMSE) 0.2838. The information rendered by pharmacophore based 3D-QSAR models and docking studies may afford valuable clues to optimize the lead and design of potent, selective inhibitors.
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