Structural Basis For Inhibitor Selectivity Of Phosphodiesterase 2

Human cyclic nucleotide phosphodiesterase families (PDEs) play a critical role in regulating cell signal cascades by hydrolyzing the intracellular second messengers cAMP and cGMP. Due to their unique tissue distributions and cellular functions,PDEs are involved in a wide variety of diseases. Due to the structural similarity among PDEs’ catalytic domain, it is essential to investigate the selectivity of drug molecule in developing PDE inhibitors.In recent years, PDE2 had attracted more and more attentions as a valuable therapeutic target for central nervous system (CNS) disorders, including Alzheimer’s disease. However, at present, dut to the lack of available complex crystal structures of PDE2 with selective inhibitors, it is impossible to provide explicit structural models for the rational drug design of PDE2.In this study, we first expressed and purified PDE2 catalytic domain in E.coli cells with a fusion partner. Through large scale crystallization conditon screening and optimization, we obtained apo PDE2 crystal and complex crystal of PDE2 with a selective inhibitor BAY60-7550. We collected crystal diffraction data sets at synchrotron radiation facility beamline and determined the apo and complex crystal structures to 2.0 A and 1.9 A, respectively.By comparing the apo and complex structures, we found that BAY60-7550 molecule binds to a novel inducible pocket of PDE2, which had not been reported previously. Because the residues constituting this pocket are mainly hydrophobic, we designate it as H-pocket (Hydrophobic-pocket). Upon ligand binding, certain residues of the H-pocket underwent significant conformational changes. In addition, we also found that the classical Glutamine-Switch mechanism play an important role in inhibitor binding.We next systematically investigated the binding modes of BAY60-7550 in other PDEs with a full flexibility ligand docking approach. The results demonstrated that the interactions between the inhibitor and the H-Pocket contribute significantly to inhibitor binding affinity, thereby explains the structural origins of the inhibitor selectivity.