The tetrahedral adducts formed during nucleophilic attack by a hydroxyl ion on the carbonyl carbon of a model dipeptide, glycylglycine, were studied by modifiedintermediate-neglect-of-differential-overlap molecular orbital calculations. This dipeptide is taken to represent the D-alanyl-D-alanine terminus of the polypeptides involved in the crosslinking transpeptidation reaction of peptidoglycan in bacterial cell walls. It Twelve years ago it was proposed (1) that the fl-lactam antibiotics derive their antibacterial activity because their structure mimics that of a transition state (TS) species formed when a D-alanyl-D-alanine peptide bond is cleaved at the receptor site of a proteolytic enzyme in bacterial cell walls. This idea has remained viable in the light of most subsequent research (e.g., see refs. 2-7 and references cited therein). The final step in cell wall synthesis, the crosslinking of the peptidoglycan strands via a transpeptidation reaction, is the one that is upset by penicillins and cephalosporins. Depending on the organism and the antibiotic, the inhibition can involve a transpeptidase or a carboxypeptidase, be reversible or irreversible, and lead either directly or indirectly to death of growing bacteria (2,4,(8)(9)(10)(11)(12)(13)(14)(15)(16). In bacteria that have been studied (2), the peptidoglycan crosslinks are polypeptides which in their precursor form have. a D-alanyl-D-alanine terminus. Little is known about the structural details of the TSs through which this dipeptide passes. Tipper and Strominger (1) and later Lee (3) noted that a twisting about the peptide C-N bond from the usual trans planar arrangement produces a structure that is more analogous to that of the fl-lactam antibiotics. Because of their bicyclic ring systems, the antibiotics have a CC-NC dihedral angle (corresponding to the CaC'-NCa dehedral angle in a polypeptide) in the range 132°-157°(17). Calculations (3, 5) on the amount of energy this twisting from 1800 requires have shown such structures to be accessible with the energy derivable from the usual sorts of substrate-receptor interactions.In principle, information about the TS structure could be deduced from the three-dimensional arrangement of the functionalities in the receptor site(s) of the relevant enzymes.The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734
METHODThe approach was to use the computer as a reaction vessel in which to observe the reactants coming together and starting to react. Quantum mechanical computer calculations for "observing" TSs have the advantage of being able to stop the reaction at any point along the reaction path in order to observe at length species which, experimentally, would be very shortlived and not isolable. The "lens" for this "computer microscope" will be the modified-intermediate-neglect-of-differential-overlap (MINDO/3) molecular orbital (MO) method (22). This method has ...