Inhibition Mechanism of Class D β-Lactamases by Avibactam

Abstract

Escalation of antibiotic resistance due to class D β-lactamases (DBLs) carrying bacteria is a matter of grave concern. This class of enzymes can efficiently hydrolyze the carbapenem group of antibiotics that are the last-reserved therapeutics for infections caused by multidrug-resistant bacteria. The development of efficient inhibitors against DBLs calls for a molecular-level understanding of the hydrolysis mechanism. Here, we investigate the mechanism of inhibition of OXA-48 DBL enzyme by one of the diazobicyclooctane class of inhibitors, namely avibactam, through molecular dynamics simulations and free energy calculations. Hydrolysis as well as inhibition mechanisms are expected to be intricate due to the presence of N-carbamylated lysine (Lys73), multiple acidic and basic active site residues, and active site water molecules. Our extensive mechanistic study characterizes the most probable reaction route and critical reaction intermediates starting from the acylation to the full hydrolysis of the covalent intermediate. This study discerns the residues that act as the general bases at different steps. Free energies and reaction intermediate structures are corroborated with the available experimental kinetics data and crystal structures. We also simulated the deacylation of a β-lactam drug, namely meropenem, which is known to be hydrolyzed efficiently by the enzyme. By comparing the mechanism of meropenem hydrolysis with that of avibactam, our study reveals the important chemical features that are useful for designing inhibitors.

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity

“…It will also provide a broader experimental foundation for investigations of this class of carbapenemases by molecular dynamics, QM/MM, and free-energy calculations. 33,45 Finally, our investigation significantly expands our understanding of the Janus effector role of especially halide anions in modulating enzyme catalysis 46 while at the same time providing valuable experimental information in the fight against antibioticresistant bacteria.…”

Antibiotic Charge Profile Determines the Extent of L3 Dynamics in OmpF: An Expedited Passage for Molecules with a Positive Charge

“…Briefly, the method is similar to the umbrella sampling approach in that it employs a series of harmonic potential biases to efficiently sample configurations along the principal collective variable (CV) of interest. Additionally, within each independent simulation, sampling along several other relevant CVs is enhanced using an adiabatic temperature acceleration scheme. , This method has been utilized previously for the study of the ligand-unbinding process and the energetics of enzymatic reactions. − For the application of the TASS method to antibiotic permeation, we used the same setup procedure as described previously . Briefly, a harmonic potential bias is applied along the z CV, i.e., the projection of the center of mass distance between the antibiotic and the channel along the z -axis that coarsely describes the translocation of the molecule along the pore axis.…”

Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning

“…In the case of class B β-lactamases, the zinc ions in the active site mediate the nucleophilic water attacks and the rapid ligand dissociation, 8–12 while class D β-lactamases use a carboxylated lysine (Lys73-CO 2 ) as the general base for both acylation and deacylation. 13,14…”

“…In the case of class B b-lactamases, the zinc ions in the active site mediate the nucleophilic water attacks and the rapid ligand dissociation, [8][9][10][11][12] while class D b-lactamases use a carboxylated lysine (Lys73-CO 2 ) as the general base for both acylation and deacylation. 13,14 The Klebsiella pneumoniae carbapenemase (KPC) family of ASbLs has been identified as a frequent cause of antibiotic drug resistance. 16 The KPC-2 variant of the KPC sub family has been investigated by pioneering experimental efforts.…”