Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

Atzori, Alessio; Malviya, Viveka Nand; Malloci, Giuliano; Dreier, Jürg; Pos, Klaas M.; Vargiu, Attilio Vittorio; Ruggerone, Paolo

doi:10.1016/j.bbamem.2018.10.012

Cited by 21 publications

(25 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This study contributes to explain the detailed interactions established by different carbapenem antibiotics with the DP T of AcrB in terms of their intrinsic physico-chemical properties. A retrospective analysis of the previous literature on other antimicrobial compounds [44] revealed the general applicability of our findings [35,55,[59][60][61].…”

Section: Introductionsupporting

confidence: 63%

“…However, MIC values are strongly influenced by the interaction of the drug with many other bacterial components: for instance, the membrane permeability, heavily dependent on intrinsic drug properties, can definitely surpass the specific contribution of active efflux to MDR [53,54]. As an example, while meropenem is a good substrate of the MexAB-OprM efflux pump from P. aeruginosa and imipenem resistance to this organism appears to be predominantly caused by changes in outer membrane pores, the impact of AcrAB-TolC on the activity of IMI and MER in E. coli is still under debate [55]. In this context, direct efflux and affinity measurements [56][57][58], combined with a molecular picture of the interaction between these compounds and AcrB, would be pivotal for the design of more effective antibiotics starting from validated and widely used scaffolds.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli

Atzori

Malloci

Cardamone

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism.

show abstract

Section: Introductionsupporting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli

Atzori

Malloci

Cardamone

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…A blind docking campaign was first performed using Autodock Vina 50 . As done in Atzori et al 51 , a rectangular search space of size 125Å × 125Å × 110Å enclosing the whole portion of the protein potentially exposed to ligands was adopted. The exhaustiveness parameter, related to the extent of the exploration within the search space, was set to 8192 (∼1000 times the default 8) in order to improve the sampling of docking poses within the large box used (∼64 times the default 30Å × 30Å × 30Å).…”

Section: Methodsmentioning

confidence: 99%

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Reading

Ahdash

Fais

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Resistance-nodulation-division (RND) efflux pumps play a key role in inherent and evolved multidrug-resistance (MDR) in bacteria. AcrB is the prototypical member of the RND family and acts to recognise and export a wide range of chemically distinct molecules out of bacteria, conferring resistance to a variety of antibiotics. Although high resolution structures exist for AcrB, its conformational fluctuations and their putative role in function are largely unknown, preventing a complete mechanistic understanding of efflux and inhibition. Here, we determine these structural dynamics in the presence of AcrB substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular modelling, drug binding and bacterial susceptibility studies. We show that the well-studied efflux pump inhibitor phenylalanine-arginine-β-naphthylamide (PAβN) potentiates antibiotic activity by restraining drug-binding pocket dynamics, rather than preventing antibiotic binding. We also reveal that a drug-binding pocket substitution discovered within an MDR clinical isolate, AcrBG288D, modifies the plasticity of the transport pathway, which could explain its altered substrate specificity. Our results provide molecular insight into drug export and inhibition of a major MDR-conferring efflux pump and the important directive role of its dynamics.

show abstract

“…123 Of note, the structure and, in particular, the interactions between MexA and OprM had been correctly predicted earlier by López et al using sequence covariation analysis and microsecond-long MD simulations. 124 This and other successful predictive MD simulations used in the field of efflux pumps [125][126][127][128][129][130][131][132][133] emphasize that the predictive quality has been improving over the years, and will be an additional important asset in deciphering the structure/function relationship of efflux pumps.…”

Section: Structural Properties and Dynamics Of The Acrab(z)-tolc Complexmentioning

confidence: 99%

AcrB: a mean, keen, drug efflux machine

Kobylka

Kuth

Müller

et al. 2019

Annals of the New York Academy of Sciences

Self Cite

108

135

View full text Add to dashboard Cite

Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/ AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.

show abstract

Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

Cited by 21 publications

References 74 publications

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli

Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

AcrB: a mean, keen, drug efflux machine

Contact Info

Product

Resources

About