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First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase

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Abstract

The worldwide spread of beta-lactamases with hydrolytic activity extended to last resort carbapenems is aggravating the antibiotic resistance problem and endangers the successful antimicrobial treatment of clinically relevant pathogens. As recently highlighted by the World Health Organization, new strategies to contain antimicrobial resistance are urgently needed. Class A carbapenemases include members of the KPC, GES and SFC families. These enzymes have the ability to hydrolyse penicillins, cephalosporins and carbapenems, while also being less susceptible to available beta-lactam inhibitors, such as clavulanic acid. The KPC family is the most prevalent. It is mostly found on plasmids in Klebsiella pneumoniae, meaning that great amounts of attention, in terms of inhibitor design and structural biology, have been dedicated to it, whereas no efforts have yet been dedicated to GES-type enzymes, despite their ability to rapidly and horizontally disseminate. We herein report the first in silico screening against GES-5, which is the most dangerous GES-type beta-lactamase, using a library of 800K commercially available candidates that all share drug-like properties, such as their MW, logP, rotatable bonds and HBA/HBD atoms. The best screening results were filtered to enrich the number of different chemotypes, and then submitted to molecular docking. The 34 most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5. Six hits acted as inhibitors, in the high micromolar range, towards GES-5 and led to the identification of the first, novel chemotypes with inhibitory activity against this clinically relevant carbapenemase.

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Acknowledgements

We kindly acknowledge Molecular Discovery Ltd for providing the FLAP software and for supporting GD. We thank Prof. Sergei Vakulenko (University of Notre Dame du Lac, Indiana, USA) for the generous gift of the blaGES-5 gene, k cloned in pet24a(+), and Dr. Dale J.M. Lawson for critically reading the manuscript.

Funding

The project was funded by a Fondo di Ricerca di Ateneo (Grant No. FAR2014) UNIMORE grant to Donatella Tondi.

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Authors and Affiliations

  1. Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy

    Francesca Spyrakis & Giulia D’Arrigo

  2. Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100, L’Aquila, Italy

    Pierangelo Bellio & Giuseppe Celenza

  3. Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy

    Antonio Quotadamo, Pasquale Linciano & Donatella Tondi

  4. Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy

    Paolo Benedetti

  5. Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123, Perugia, Italy

    Paolo Benedetti

  6. Molecular Discovery Limited, U.501 Centennial Park, Centennial Ave, Elstree, Borehamwood, Hertfordshire, WD6 3FG, UK

    Massimo Baroni

  7. Department of Biology, University of Padua, Viale G. Colombo 3, 35121, Padua, Italy

    Laura Cendron

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  1. Francesca Spyrakis
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Correspondence to Francesca Spyrakis or Donatella Tondi.

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Spyrakis, F., Bellio, P., Quotadamo, A. et al. First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase. J Comput Aided Mol Des 33, 295–305 (2019). https://doi.org/10.1007/s10822-018-0182-2

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