Docking of cyclohexanol-derivatives into the active site of liver alcohol dehydrogenase. Using computer graphics and energy minimization

Abstract

Model building and energy minimization procedures have been used to determine a productive substrate binding mode in liver alcohol dehydrogenase for secondary alcohols. These docking results have been compared to some of the extensive amounts of kinetic data available for this enzyme. The indirect diamond lattice approach first suggested by Prelog (Prelog, V. (1964) Pure Appl. Chem. 9, 119-130) to describe the active site of an enzyme has been used to build a direct diamond lattice from the crystallographic model of the enzyme. This lattice was oriented and positioned into the active site using the productive binding mode of cyclohexanol derivatives obtained from model building. We then classified the positions as allowed, forbidden, or boundary depending on their distances to protein atoms. We found very good agreement between the classification of our direct diamond lattice points and those of the indirect lattice obtained by others from kinetic studies. Finally we have extended the lattice as an aid to predict the stereospecificity of the enzyme for molecules which cover other regions of the active site.