Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance

Ioannis Galdadas, Silvia Lovera, Guillermo Pérez-Hernández, Melissa D. Barnes, Jess Healy, Hamidreza Afsharikho, Neil Woodford, Robert A. Bonomo, Francesco L. Gervasio, Shozeb Haider*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    18 Citations (Scopus)

    Abstract

    The rise of multi-drug resistance in bacterial pathogens is one of the grand challenges facing medical science. A major concern is the speed of development of β-lactamase-mediated resistance in Gram-negative species, thus putting at risk the efficacy of the most recently approved antibiotics and inhibitors, including carbapenems and avibactam, respectively. New strategies to overcome resistance are urgently required, which will ultimately be facilitated by a deeper understanding of the mechanisms that regulate the function of β-lactamases such as the Klebsiella Pneumoniae carbapenemases (KPCs). Using enhanced sampling computational methods together with site-directed mutagenesis, we report the identification of two “hydrophobic networks” in the KPC-2 enzyme, the integrity of which has been found to be essential for protein stability and corresponding resistance. Present throughout the structure, these networks are responsible for the structural integrity and allosteric signaling. Disruption of the networks leads to a loss of the KPC-2 mediated resistance phenotype, resulting in restored susceptibility to different classes of β-lactam antibiotics including carbapenems and cephalosporins. The ”hydrophobic networks” were found to be highly conserved among class-A β-lactamases, which implies their suitability for exploitation as a potential target for therapeutic intervention.

    Original languageEnglish
    Article number12916
    JournalScientific Reports
    Volume8
    Issue number1
    DOIs
    Publication statusPublished - 1 Dec 2018

    Bibliographical note

    Funding Information:
    Competing Interests: NW: No personal interests to declare. However, PHE’s AMRHAI Reference Unit has received financial support for conference attendance, lectures, research projects or contracted evaluations from numerous sources, including: Achaogen Inc, Allecra Antiinfectives GmbH, Amplex, AstraZeneca UK Ltd, Becton Dickinson Diagnostics, The BSAC, Cepheid, Check-Points B.V., Cubist Pharmaceuticals, Department of Health, Enigma Diagnostics, European Centre for Disease Prevention and Control, Food Standards Agency, GlaxoSmithKline Services Ltd, Helperby Therapeutics, Henry Stewart Talks, IHMA Ltd, Innovate UK, Kalidex Pharmaceuticals, Melinta Therapeutics, Merck Sharpe & Dohme Corp, Meiji Seika Pharma Co., Ltd, Mobidiag, Momentum Biosciences Ltd, Neem Biotech, NIHR, Nordic Pharma Ltd, Norgine Pharmaceuticals, Rempex Pharmaceuticals Ltd, Roche, Rokitan Ltd, Smith &amp Nephew UK Ltd, Shionogi &amp Co. Ltd, Trius Therapeutics, VenatoRx Pharmaceuticals, Wockhardt Ltd., and the World Health Organization. IG is funded by Astra Zeneca-EPSRC case studentship award to FLG and SH. RB has research grants from Allecra, Entasis Therapeutics, Merck & Co. (Kenilworth, NJ), Roche, and Wockhardt. SL is a postdoc at UCB BioPharma SPRL.

    Funding Information:
    S.H. and F.L.G. would like to thank Astra Zeneca-EPSRC case studentship award to I.G. F.L.G. acknowledges EPSRC for financial support [grant no. EP/P022138/1, EP/P011306/1, EP/M013898/1]. We thank PRACE and HecBioSim for computer time.

    Publisher Copyright:
    © 2018, The Author(s).

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