GRID / tetrahedral intermediate computational approach to the study of selectivity of penicillin G acylase in amide bond synthesis

Molecular modelling was used to investigate the catalytic site of penicillin G acylase (PGA) by building up a simple enzyme–ligand model able to describe and predict the enzyme selectivity. The investigation was based on a double computational approach: first, the GRID computational procedure was applied to gain a qualitative description of the chemical features of the PGA active site; second, a classical “transition state approach” was used to simulate the tetrahedral intermediates and to evaluate their energies. GRID calculations employed different probes which gave a complete description of the chemical interactions occurring upon binding of different ligands, thus indicating those structures having good affinity with the active site of the enzyme. Tetrahedral intermediates were constructed on the basis of GRID results and provided both geometrical features and energies of enzyme–substrate interaction. Such energies were compared to experimental kinetic data obtained in the enzymatic acylation of l-phenylglycine methyl ester using various methyl phenylacetate derivatives. The good agreement of computational results with experimental evidence demonstrates the validity of the model as a rapid and flexible tool to describe and predict the enzyme selectivity.