Combined 2D and 3D-QSAR, molecular modelling and docking studies of pyrazolodiazepinones as novel phosphodiesterase 2 inhibitors

Abstract

Selective inhibition of phosphodiesterase 2 (PDE2) in cells where it is located elevates cyclic guanosine monophosphate (cGMP) and acts as novel analgesic with antinociceptive activity. Three-dimensional quantitative structure–activity relationship (QSAR) studies for pyrazolodiazepinone inhibitors exhibiting PDE2 inhibition were performed using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and Topomer CoMFA, and two-dimensional QSAR study was performed using a Hologram QSAR (HQSAR) method. QSAR models were generated using training set of 23 compounds and were validated using test set of nine compounds. The optimum partial least squares (PLS) for CoMFA-Focusing, CoMSIA-SDH, Topomer CoMFA and HQSAR models exhibited good ‘leave-one-out’ cross validated correlation coefficient (q²) of 0.790, 0.769, 0.840 and 0.787, coefficient of determination (r²) of 0.999, 0.964, 0.979 and 0.980, and high predictive power (r²_pred) of 0.796, 0.833, 0.820 and 0.803 respectively. Docking studies revealed that those inhibitors able to bind to amino acid Gln859 by cGMP binding orientation called ‘glutamine-switch’, and also bind to the hydrophobic clamp of PDE2 isoform, could possess high selectivity for PDE2. From the results of all the studies, structure–activity relationships and structural requirements for binding to active site of PDE2 were established which provide useful guidance for the design and future synthesis of potent PDE2 inhibitors.

Keywords:

• pyrazolodiazepinone
• PDE2
• 3D-QSAR
• HQSAR
• docking

Acknowledgments

One of the authors (S.G.B.) is grateful to Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, for the award of research fellowship (File no.: 08/281(0025)/2013‒EMR-I). The authors are thankful to Dr S.S. Kadam, Vice Chancellor, Bharati Vidyapeeth University, Pune, and Dr K.R. Mahadik, Principal, Poona College of Pharmacy, Pune, for their encouragement.