Antibiotic Binding to Monozinc CphA β-Lactamase from Aeromonas hydropila:  Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies

Abstract

The active-site dynamics of apo CphA beta-lactamase from Aeromonas hydropila and its complex with a beta-lactam antibiotic molecule (biapenem) are simulated using a quantum mechanical/molecular mechanical (QM/MM) method and density functional theory (DFT). The quantum region in the QM/MM simulations, which includes the Zn(II) ion and its ligands, the antibiotic molecule, the catalytic water, and an active-site histidine residue, was treated using the self-consistent charge density functional tight binding (SCC-DFTB) model. Biapenem is docked at the active site unambiguously, based on a recent X-ray structure of an enzyme-intermediate complex. The substrate is found to form the fourth ligand of the zinc ion with its 3-carboxylate oxygen and to hydrogen bond with several active-site residues. The stability of the metal-ligand bonds and the hydrogen-bond network is confirmed by 500 ps molecular dynamics simulations of both the apo enzyme and the substrate-enzyme complex. The structure and dynamics of the substrate-enzyme complex provide valuable insights into the mode of catalysis in such enzymes that is central to the bacterial resistance to beta-lactam antibiotics.

Catalytic Mechanism of Class B2 Metallo-β-lactamase

“…We report here a detailed theoretical investigation on the catalytic mechanism of the CphA enzyme in hydrolyzing a carbapenems antibiotic (biapenem). It dovetails our recent work on the Michaelis complex of the same system using a quantum mechanical/molecular mechanical (QM/MM) 2 method and density functional theory (DFT) (18). We focus on the initial nucleophilic substitution step of the catalytic hydrolysis reaction and examine the putative nucleophilic role of the nonmetal-binding water in the proposed mechanism using the same theoretical methods.…”

“…This selection of the reaction coordinate does not specifically assign the general base, which can be either His-118 or Asp-120, as suggested by our previous simulations of the binding dynamics (18). In addition, this choice may also shed light on the nature of the reaction path.…”

“…The advantages are particularly conspicuous for metalloenzymes, because the metal-ligand bonds are notoriously difficult to model with force fields. Following our earlier work (18), a QM/MM method is used to study the catalytic mechanism of the CphA enzyme.…”

“…The model construction has been discussed in detail in our recent publication on the binding dynamics of CphA complexed with biapenem (18). Here, only a short description is given.…”

X-ray Absorption Spectroscopy of the Zinc-Binding Sites in the Class B2 Metallo-β-lactamase ImiS from Aeromonas veronii bv. sobria

“…The B2 enzymes are less well-characterized, with comparably fewer physicochemical studies available (73)(74)(75)(76)(77)(78)(79)(80)(81). Recently, the first crystal structure of a B2 enzyme was reported (82).…”