Molecular dynamics and quantum mechanical calculations on the mononuclear zinc-β-lactamase from Bacillus cereus: Protonation state of the active site and imipenem binding

Zinc-β-lactamases exhibit important differences in their mode of action that hamper the development of effective inhibitors. This fact has prompted a considerable theoretical interest in these metalloenzymes in order to increase our knowledge at the molecular level. Herein, we present results from molecular dynamics (MD) simulations of the mononuclear BcII enzyme and its Michaelis complex with imipenem. Four protonation patterns of the active site were modeled in aqueous solution and their relative stability was estimated by means of linear-scaling semiempirical quantum mechanical (QM) energy calculations. Two binding modes of the imipenem substrate were examined: (a) the substrate interacts only with protein residues; (b) the β-lactam carbonyl group becomes a fifth ligand around the Zn ion. For the free enzyme, the energetically most stable configurations present a Zn-OH moiety, a neutral Asp120 and a neutral His263 residue. In contrast, for the complex formed between the BcII enzyme and imipenem, the energetic analyses predict that the configuration with a Zn-OH fragment and a doubly protonated His263 residue becomes stabilized. Moreover, the MD simulations and energy calculations reveal that binding of the β-lactam carbonyl group to the Zn ion results in a proper enzyme/imipenem orientation for catalysis.