Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands.

Phosphodiesterases are a large class of enzymes mediating a number of physiological processes ranging from immune response to platelet aggregation to cardiac and smooth muscle relaxation. In particular, phosphodiesterase 5 (PDE5) plays an important role in mediating sexual arousal, and it is the central molecular target in treatments of erectile dysfunction. In this study, we look at the mechanism and thermodynamics of the binding of selective inhibitors sildenafil (Viagra) and vardenafil (Levitra) to PDE5 using molecular dynamics simulations. Our simulations of PDE5 with and without sildenafil suggest a binding mechanism in which two loops surrounding the binding pocket of the enzyme (H loop, residues 660-683, and M loop, 787-812) execute sizable conformational changes (∼1 nm), clamping the ligand in the pocket. Also, we note significant changes in the coordination pattern of the divalent ions in the active site of the enzyme, as well as marked changes in the collective motions of the enzyme when the ligand is bound. Using the thermodynamic integration approach we calculate the relative free energies of binding of sildenafil, vardenafil, and demethyl-vardenafil, providing a test of the quality of the force field and the ligand parametrization used. Finally, using the single-step perturbation (SSP) technique, we calculate the relative binding free energies of these three ligands as well. In particular, we focus on critical evaluation of the SSP technique and examine the effects of computational parallelization on the efficiency of the technique. As a technical improvement, we demonstrate that an ensemble of relatively short SSP trajectories (10 × 0.5 ns) markedly outperforms a single trajectory of the same total length (1 × 5 ns) when it comes to sampling efficiency, resulting in significant real-time savings.