QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases



β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered ‘last resort’ antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to the deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes activation free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency towards carbapenems.


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Supplementary material

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Supporting Information
The Supporting Information contains: a diagram showing the progress coordinates of the QM/MM umbrella sampling MD simulations; an example structure of the active site of class A serine β-lactamases; a structure showing two representative Asn132 conformations from cluster analysis of QM/MM MD simulations; a table of residue interaction energies; a table giving 6α-1R-hydroxyethyl group dihedral values of crystal structures (from the PDB) of acyl-enzymes considered in this study ; and a histogram of dihedral values of SFC-1 Asn132Gly, TEM-1 Asn132Gly and BlaC Gly132Asn from QM/MM umbrella sampling MD simulations.