Graphical abstract

KPC-2 (Klebsiella pneumoniaecarbapenemase-2) is a globally disseminated serine-β-lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate β-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent β-lactams, evade activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently catalyze deacylation of carbapenem-derived acyl-enzymes. We present high-resolution (1.25-1.4 Å) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin) and carbapenems (imipenem, meropenem and ertapenem), obtained utilizing an isosteric deacylation-deficient mutant (E166Q). Mobility of the Ω-loop (residues 165—170) negatively correlates with antibiotic turnover rates (k) cat), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different β-lactams. Carbapenem-derived acyl-enzyme structures reveal predominance of the Δ1-(2R) imine tautomer, except for the imipenem acyl-enzyme, which is present in dual occupancy in both Δ1-(2R) and (2S) configurations. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations of deacylation of the KPC-2:meropenem acyl-enzyme, using an adaptive string method (ASM), show that the Δ1-(2R) isomer has a 7 kcal/mol higher barrier for the (rate-determining) formation of the tetrahedral deacylation intermediate than the Δ2 tautomer. The simulations identify tautomer-specific differences in hydrogen bonding networks involving the carbapenem C-3 carboxylate and the deacylating water, that, together with stabilization by protonated N-4 of accumulating negative charge during oxyanion formation, accelerate deacylation of the Δ2-enamine acyl-enzyme compared to the Δ1-imine. Taken together, our data show how the flexible Ω-loop helps confer broad spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Δ2-enamine acyl-enzyme tautomer. Differentiation of the barriers associated with deacylation of these subtly different β-lactam isomers further identifies ASM as a sensitive method for calculation of reaction energetics that can accurately model turnover and, potentially, predict the impact of substrate modifications or point mutations upon activity.

Dronedarone is a non-iodinated analogue of the Class III antiarrhythmic agent amiodarone. It exerts potent inhibition of "hERG" potassium channels that underpin the cardiac rapid delayed rectifier potassium current, IKr. This study aimed to extend understanding of interactions between dronedarone and the hERG channel. Whole-cell patch-clamp recordings were made at 37C of hERG channel current (IhERG) from HEK-293 cells expressing wild-type (WT) hERG or alanine mutants of residues in the channel's pore-helix/selectivity filter region (T623, S624, V625) or S6 helices (S649, Y652, F656, V659). Molecular docking simulations were performed using a cryo-EM structure of hERG and a MthK-based homology model. The half-maximal inhibitory (IC50) value for WT IhERG inhibition by dronedarone was 42.6 ± 3.9 nM (n= at least 5 cells for each of 6 concentrations). 600 nM dronedarone exerted reduced WT IhERG block when the direction of K + flux was reversed, consistent with interactions between the drug and permeant ion. In contrast with recently reported data for amiodarone, the S624A mutation did not attenuate IhERG blockade, whilst T623A and V625A channels exhibited modestly attenuated block. The S649A mutation was without significant effect and the Y652A and F656A mutations exhibited modest reductions in block. The V659A mutation produced the most marked effect on dronedarone action. Docking simulations were generally consistent with modest interactions with canonical binding residues and suggested an indirect rather than direct effect of the V659A mutation on the drug's action. These findings leave open the possibility that as yet unexplored residue(s) could act as key determinants of high affinity hERG channel block by dronedarone.