Computational Study of the Mechanism and the Relative Free Energies of Binding of Anticholesteremic Inhibitors to Squalene-Hopene Cyclase

Abstract

The prokaryotic monotopic membrane protein squalene-hopene cyclase (SHC) is homologous to a human enzyme responsible for cholesterol formation. Using molecular dynamics in explicit water, a single monomer of SHC was simulated using the GROMOS 45A3 force field, once in complex with an inhibitor and once in an uncomplexed form. The protein exhibits significant stability on the level of secondary and tertiary structure even outside of its native membrane environment. Analysis of the fluctuations of the complexed and the uncomplexed SHC confirms the previously made suggestions for the ligand entrance channel and reveals some of its novel dynamical features that might be of functional importance. To examine the potential of computationally designing SHC ligands and study their thermodynamics of binding, the relative free energies of binding of a series of structurally similar anticholesteremic inhibitors of SHC were calculated using single-step perturbation (SSP) and thermodynamic integration (TI) techniques. While neither technique succeeds in quantitatively matching the relatively small experimental values, TI qualitatively reproduces the relative order of the experimental affinities, but SSP does not. Detailed comparisons and potential reasons for this are given.