Molecular Insights on the Release of Avibactam from the Acyl-Enzyme Complex

The primary pharmacology of ceftazidime/avibactam: in vitro translational biology

Previous reviews of ceftazidime/avibactam have focused on in vitro molecular enzymology and microbiology or the clinically associated properties of the combination. Here we take a different approach. We initiate a series of linked reviews that analyse research on the combination that built the primary pharmacology data required to support the clinical and business risk decisions to perform randomized controlled Phase 3 clinical trials, and the additional microbiological research that was added to the above, and the safety and chemical manufacturing and controls data, that constituted successful regulatory licensing applications for ceftazidime/avibactam in multiple countries, including the USA and the EU. The aim of the series is to provide both a source of reference for clinicians and microbiologists to be able to use ceftazidime/avibactam to its best advantage for patients, but also a case study of bringing a novel β-lactamase inhibitor (in combination with an established β-lactam) through the microbiological aspects of clinical development and regulatory applications, updated finally with a review of resistance occurring in patients under treatment. This first article reviews the biochemistry, structural biology and basic microbiology of the combination, showing that avibactam inhibits the great majority of serine-dependent β-lactamases in Enterobacterales and Pseudomonas aeruginosa to restore the in vitro antibacterial activity of ceftazidime. Translation to efficacy against infections in vivo is reviewed in the second co-published article, Nichols et al. (J Antimicrob Chemother 2022; dkac172).

Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam

Backbone chemical shift assignments for the Toho-1 β-lactamase (263 amino acids, 28.9 kDa) are reported based on triple resonance solution-state NMR experiments performed on a uniformly 2H,13C,15N-labeled sample. These assignments allow for subsequent site-specific characterization at the chemical, structural, and dynamical levels. At the chemical level, titration with the non-β-lactam β-lactamase inhibitor avibactam is found to give chemical shift perturbations indicative of tight covalent binding that allow for mapping of the inhibitor binding site. At the structural level, protein secondary structure is predicted based on the backbone chemical shifts and protein residue sequence using TALOS-N and found to agree well with structural characterization from X-ray crystallography. At the dynamical level, model-free analysis of 15N relaxation data at a single field of 16.4 T reveals well-ordered structures for the ligand-free and avibactam-bound enzymes with generalized order parameters of ~ 0.85. Complementary relaxation dispersion experiments indicate that there is an escalation in motions on the millisecond timescale in the vicinity of the active site upon substrate binding. The combination of high rigidity on short timescales and active site flexibility on longer timescales is consistent with hypotheses for achieving both high catalytic efficiency and broad substrate specificity: the induced active site dynamics allows variously sized substrates to be accommodated and increases the probability that the optimal conformation for catalysis will be sampled.

A theoretical approach for the acylation/deacylation mechanisms of avibactam in the reversible inhibition of KPC-2

Klebsiella pneumoniae carbapenemase (KPC-2) is the most commonly encountered class A β-lactamase variant worldwide, which confer high-level resistance to most available antibiotics. In this article we address the issue by a combined approach involving molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The study contributes to improve the understanding, at molecular level, of the acylation and deacylation stages of avibactam involved in the inhibition of KPC-2. The results show that both mechanisms, acylation and deacylation, the reaction occur via the formation of a tetrahedral intermediate. The formation of this intermediate corresponds to the rate limiting stage. The activation barriers are 19.5 kcal/mol and 23.0 kcal/mol for the acylation and deacylation stages, respectively. The associated rate constants calculated, using the Eyring equation, are 1.2 × 10⁻¹ and 3.9 × 10⁻⁴ (s⁻¹). These values allow estimating a value of 3.3 × 10⁻³ for the inhibition constant, in good agreement with the experimental value.

Nosocomial Pneumonia in the Era of Multidrug-Resistance: Updates in Diagnosis and Management

Nosocomial pneumonia (NP), including hospital-acquired pneumonia in non-intubated patients and ventilator-associated pneumonia, is one of the most frequent hospital-acquired infections, especially in the intensive care unit. NP has a significant impact on morbidity, mortality and health care costs, especially when the implicated pathogens are multidrug-resistant ones. This narrative review aims to critically review what is new in the field of NP, specifically, diagnosis and antibiotic treatment. Regarding novel imaging modalities, the current role of lung ultrasound and low radiation computed tomography are discussed, while regarding etiological diagnosis, recent developments in rapid microbiological confirmation, such as syndromic rapid multiplex Polymerase Chain Reaction panels are presented and compared with conventional cultures. Additionally, the volatile compounds/electronic nose, a promising diagnostic tool for the future is briefly presented. With respect to NP management, antibiotics approved for the indication of NP during the last decade are discussed, namely, ceftobiprole medocaril, telavancin, ceftolozane/tazobactam, ceftazidime/avibactam, and meropenem/vaborbactam.

Theoretical Evidence for the Nonoccurrence of Tetrahedral Intermediates in the Deacylation Pathway of the Oxacillinase-24/Avibactam Complex

Oxacillinases (OXAs) β-lactamases are of special interest because of their capacity to hydrolyze antibacterial drugs such as cephalosporins and carbapenems, which are frequently used as the last option for the treatment of multidrug-resistant bacteria. Although the comprehension of the involved mechanisms at the atomic level is crucial for the rational design of new inhibitors and antibiotics, currently there is no study on the acylation/deacylation mechanisms of the OXA-24/avibactam complex from first principles; therefore, mechanistic details such as activation barriers, characterization of intermediates, and transition states are still uncertain. In this article, we address the deacylation of the OXA-24/avibactam complex by molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics computations. The study supplies mechanistic details not available so far, namely, topology of the potential energy surfaces, characterization of transition states and intermediates, and calculation of the respective activation barriers. The results show that the deacylation occurs via a mechanism of two stages; the first one involves the formation of a dianionic intermediate with a computed activation barrier of 24 kcal/mol. The second stage corresponds to the cleavage of the O_S81-C bond promoted by the protonation of the O_S81 atom by the carboxylated Lys84 and the concomitant formation of the C₇-N₆ bond, allowing the liberation of avibactam and recovery of the enzyme. The calculated activation barrier for the second stage is 13 kcal/mol. The structure of the intermediate, formed in the first stage, does not fulfill the characteristics of a tetrahedral intermediate. These results suggest that the recyclization of avibactam from the OXA-24/avibactam complex may occur without the emergence of tetrahedral intermediates, unlike that observed in the class A CTX-M-15.

Structural Insights into the Inhibition of the Extended-Spectrum β-Lactamase PER-2 by Avibactam

The diazabicyclooctane (DBO) avibactam (AVI) reversibly inactivates most serine-β-lactamases. Previous investigations showed that inhibition constants of AVI toward class A PER-2 are reminiscent of values observed for class C and D β-lactamases (i.e., k ₂/K of ≈10³ M^-1 s^-1) but lower than other class A β-lactamases (i.e., k ₂/K = 10⁴ to 10⁵ M^-1 s^-1). Herein, biochemical and structural studies were conducted with PER-2 and AVI to explore these differences. Furthermore, biochemical studies on Arg220 and Thr237 variants with AVI were conducted to gain deeper insight into the mechanism of PER-2 inactivation. The main biochemical and structural observations revealed the following: (i) both amino-acid substitutions in Arg220 and the rich hydrophobic content in the active site hinder the binding of catalytic waters and acylation, impairing AVI inhibition; (ii) movement of Ser130 upon binding of AVI favors the formation of a hydrogen bond with the sulfate group of AVI; and (iii) the Thr237Ala substitution alters the AVI inhibition constants. The acylation constant (k ₂/K) of PER-2 by AVI is primarily influenced by stabilizing hydrogen bonds involving AVI and important residues such as Thr237 and Arg220. (Variants in Arg220 demonstrate a dramatic reduction in k ₂/K) We also observed that displacement of Ser130 side chain impairs AVI acylation, an observation not made in other extended-spectrum β-lactamases (ESBLs). Comparatively, relebactam combined with a β-lactam is more potent against Escherichia coli producing PER-2 variants than β-lactam-AVI combinations. Our findings provide a rationale for evaluating the utility of the currently available DBO inhibitors against unique ESBLs like PER-2 and anticipate the effectiveness of these inhibitors toward variants that may eventually be selected upon AVI usage.