Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

Abstract

The docking of penicillins to a computer model of the active site of the penicillin-binding protein of Streptomyces R61 produces structures that exhibit a four-centred interaction between the O-H of a serine residue and the (O)C-N of the β-lactam ring. If such a structure is a stationary point on the reaction coordinate for the acylation of the serine OH by the β-lactam carbonyl group, the acylation mechanism would appear to consist of O—C and H—N bond formation, concerted with the cleavage of the C—N bond. The existence of this "N-protonation" mechanism, and the energetics of this mechanism in comparison to the usual "O-protonation" pathway in which proton transfer to oxygen and addition to the carbonyl group precede C—N bond fission, have been examined by ab initio MO calculations on the neutral hydrolysis and methanolysis of N-methylazetidinone, penam, and penam-3α-carboxylate. The geometries of reactants and transition structures have been optimized fully at the 3-21G or 3-21G* levels, the existence of transition structures has been confirmed by vibrational analysis, thermochemical data have been computed, and the one-point energies of all structures have been determined at the MP2/6-31G* level. The N-protonation mechanism is found to exist with all substrates, and to be preferred over the O-protonation mechanism by over 5 kcal/mol. The activation energies are 5 kcal/mol lower in the bicyclic penam than in the monocyclic N-methylazetidinone, and attack from the convex face is preferred over attack from the concave face. The introduction of a 3α-carboxylate group, as in penicillin itself, results in an additional 5 kcal/mol decrease in activation energy. The origins of these trends are discussed. Since the active sites of some penicillin-recognizing enzymes contain at least one water molecule, catalysis of the foregoing reactions by one water molecule has also been examined. The catalysis amounts to over 10 kcal/mol in both the N- and O-protonation mechanisms, and the preference for the N-protonation mechanism is maintained. It is concluded that penicillin complexes to its receptor in such a manner as to allow acylation of the active site serine residue to proceed via the energetically most favourable mechanism.