Transition state structures of a dipeptide related to the mode of action of beta-lactam antibiotics.

Abstract

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 ...

Crystal Structures of Complexes between the R61 DD-peptidase and Peptidoglycan-mimetic β-Lactams: A Non-covalent Complex with a “Perfect Penicillin”

“…21 Structureactivity studies 22,23 and the evidence from conformationally restricted penicillin analogues 24 suggested that the more broadly biologically active form has the "open" or "S-puckered" conformation. In particular, evidence from studies with the conformationally restricted penicillins suggested that this form was the more reactive with the R61 DD-peptidase.…”

“…26 Boyd provided evidence for this idea from computational studies of the relevant structures. 21 Figure 4(c) shows the overlap between the E2 complex and an energy-minimized model of the tetrahedral intermediate for acylation of the R61 DD-peptidase by 1. Interestingly, the similarity between the peptide and b-lactam is more striking in Figure 4(c) than that observed in the crystallographic structures as shown in Figure 4(a), particularly around the reaction center.…”

The Road to Avibactam: The First Clinically Useful Non-β-Lactam Working Somewhat Like a β-Lactam

“…In this regard, the Tipper-Strominger hypothesis [67], in other words, that β-lactam antibacterials mimic the conformation of the D-Ala-D-Ala component of the PBP bacterial cell wall substrate, may be relevant [68], in that in order to get to the stage where reaction to the acylenzyme complex can occur the β-lactam antibacterial must efficiently compete with the natural substrate for binding [69]. Following from biophysical evidence that some nucleophilic serine enzymes may bind their substrates in a high-energy conformation which strains the amide bond [70][71][72], a refinement of the Tipper-Strominger hypothesis suggests that (some) β-lactam antibacterials may mimic a strained conformation of the D-Ala-D-Ala entity (Figure 2) [73][74][75]. Thus, (at least some) β-lactam antibacterials may be highly optimized to bind both noncovalently and covalently; following noncovalent binding, they undergo covalent reaction to form an initial acyl-enzyme complex which at least, in some cases, can undergo either covalent fragmentation [52,53,76] or conformational rearrangement [23,52,[55][56][57]59,62,77] to form (a) more stable complexes.…”

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium

“…β-Lactam recognition by these enzymes exploits the structural similarity of the β-lactams to the d -Ala- d -Ala substrate motif of these enzymes as first discerned by Tipper and Strominger. Their hypothesis persists as a durable theme in β-lactam structural biochemistry. − Chart shows this structural mimicry and compares the structure of an intact and clinically used cephalosporin β-lactam and the β-lactam-opened structure of an inactivated transpeptidase. Scheme gives a rudimentary kinetic scheme, which contrasts the peptidoglycan substrate and the β-lactam as inactivator.…”