Insights into the activity of cefiderocol against PER-2 producing Enterobacterales

Abstract

The PER-2 β-lactamase is a unique class A enzyme conferring broad spectrum cephalosporin resistance. In this study, we explored the stability of cefiderocol (FDC) against PER-2 β-lactamase to gain insights into structure activity relationships (SAR) of this synthetic siderophore-conjugated antibiotic. Herein, we show that the MICs of FDC for PER-2 producing isolates and transformants ranged between 0.125 and 64 µg/mL; diazabicyclooctanes (DBOs) reduced the MIC values. In PER-2 mutants, MIC values decreased up to 10-12 dilutions in agreement with previous observations especially in the case of Arg220 substitutions. Catalytic efficiency for PER-2 was 0.072 µM^-1 s^-1, comparable with PER-1 (0.046 µM^-1 s^-1) and NDM-1 (0.067 µM^-1 s^-1). In silico models revealed that FDC within the active site of PER-2 demonstrates unique interactions as a result of the inverted Ω loop fold and extension of the β3-β4 connecting loop.

Keywords: Arg220; ESBL; diazabicyclooctanes; docking; enzyme kinetics; siderophore-conjugated.

Fig 1

Upper panel: chemical structure of FDC. Middle panel: most energetically favorable conformations of FDC docked in the active site of PER-2: conformation 1: −9.1 kcal/mol; conformation 2: −8.5 kcal/mol. Lower panel: surface view showing the active site cavity of PER-2, colored according to hydrophobicity scale (red = hydrophobic; white = polar) and the two energetically favored FDC conformations.

Fig 2

In silico models of FDC docked into the active sites of PER-2 reveal the details of the non-covalent (Michaelis) complex of both possible conformations of FDC (cyan sticks), showing the main hydrogen bond interactions (dashed yellow lines). PER-2 residues are shown as orange sticks.

Fig 3

In silico models of FDC docked into the active sites of PER-2 demonstrating differential hydrogen bonds (dashed yellow lines) found in the acyl-enzyme complex of PER-2 with “conformation 1” or “conformation 2” (magenta sticks) of FDC. PER-2 residues are shown as orange sticks.

Fig 4

In silico models of FDC docked into the active sites of PER-2 and CTX-M-96. Left: comparison between the interaction of FDC and the main amino acids in the active site of PER-2 (orange sticks) and CTX-M-96 (gray sticks); only hydrogen bonds occurring with CTX-M-96 are shown (yellow dashed lines). Right: surface view of the active site residues of PER-2 (upper panel) and CTX-M-96 (lower panel), colored according to hydrophobicity scale (red = hydrophobic; white = polar).