QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

Abstract

Carbapenems, 'last resort' antibiotics for many bacterial infections, can now be broken down by several class A β-lactamases (i.e. carbapenemases). Here, carbapenemase activity is predicted through QM/MM dynamics simulations of acyl-enzyme deacylation, requiring only the 3D structure of the apo-enzyme. This may assist in anticipating resistance and future antibiotic design.

Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition

“…Summarized Δ ‡ Gcalc and relative free energy differences ΔΔ ‡ G (Δ ‡ G KPC-2 -Δ ‡ G TEM-1 ) values for the different enzyme CLA-adducts are reported in Table 1. The calculated deacylation rates for the AEC and ADEC for KPC-2 and TEM-1 are equal for these adducts (ΔΔ ‡ G values are less than the cumulative standard deviation) and are of the same order of magnitude as those reported by Chudyk et al 19 for deacylation of carbapenem AECs by carbapenem-hydrolyzing class A blactamases. 21 This suggests that neither the AEC nor ADEC complex is responsible for irreversible inhibition ( Table 1).…”

“…Furthermore, the computational screening method is able to differentiate enzymes for which CLA is an effective inhibitor (TEM-1) from those for which it is not (KPC-2). Taken together with our previous results on carbapenem deacylation, 19 these data show that QM/MM simulation protocols assessing likelihood of deacylation in class A β-lactamase AECs are applicable to chemically distinct acylated moieties in different enzymes. QM/MM screening of inhibitory activity against class A β-lactamases could thus help design better β-lactamase inhibitors as well as β-lactam antibotics, with the possibility of expanding the procedure to other serine β-lactamases (and other serine hydrolases).…”

“…To understand reactivity and specificity of covalent binders to protein targets, and related drug resistance 18 , combined quantum mechanics/molecular mechanics (QM/MM) methods are a highly promising approach. 15,[19][20][21] Acylation of SBLs by β-lactamase inhibitors is likely to occur with the same mechanism as for β-lactam antibiotics such as benzyl-penicillin (Figs. S1).…”

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

“…Mulholland and coworkers performed QM/MM/MD (with umbrella sampling) simulations to study carbapenem hydrolysis in class A β‐lactamases . The DFTB method and Amber force field were, respectively, used for the QM and classical regions.…”

Structural and Functional Aspects of Class A Carbapenemases

“…5 ). Nonetheless, the carbapenemase activity can be predicted qualitatively with good confidence through QM/MM dynamics simulations of acyl-enzyme deacylation, requiring only the 3D structure of the apo-enzyme [125]. …”