Methyl substituted β-lactam framework based antibiotics and β-lactamase inhibitors: Proof of concept by computations

Increasing the life-time of the acyl-enzyme complex formed between an inhibitor or drug molecule and the {beta}-lactamase through chemical modifications of existing drug molecules is an important strategy towards developing inhibitors. In this direction, our group proposed a methyl-substituted {beta}-lactam framework for the design of inhibitors for {beta}-lactamases (J. Phys. Chem. B. 2018, 122, 4299). This unconventional design was guided by the transition state structure of the deacylation reaction of the acyl-enzyme complex. Here, we present a proof of principle study of this concept through detailed molecular simulations and free energy calculations. In particular, we improve the antimicrobial activity of the first-generation cephalosporin antibiotic, cephalothin, through C6-methylation. The proposed molecule, (6R,7R)-3-(acetyloxymethyl)-6-methyl-8-oxo-7-[(2-thiophen-2-ylacetyl)amino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylate) slows down the deacylation of the acyl-enzyme complex 109-fold with no apparent effect on its binding to class-C {beta}-lactamase and formation of the acyl-enzyme intermediate. The design strategy presented in this work can be further extended to all {beta}-lactam antibiotics, like monobactams, carbapenems, cephalosporins, and penicillins.