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Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation

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Abstract

Owing to the emergence of antibiotic resistance, the polymyxin colistin has been recently revived to treat acute, multidrug-resistant Gram-negative bacterial infections. Positively charged colistin binds to negatively charged lipids and damages the outer membrane of Gram-negative bacteria. However, the MCR-1 protein, encoded by the mobile colistin resistance (mcr) gene, is involved in bacterial colistin resistance by catalysing phosphoethanolamine (PEA) transfer onto lipid A, neutralising its negative charge, and thereby reducing its interaction with colistin. Our preliminary results showed that treatment with a reference pyrazolone compound significantly reduced colistin minimal inhibitory concentrations in Escherichia coli expressing mcr-1 mediated colistin resistance (Hanpaibool et al. in ACS Omega, 2023). A docking-MD combination was used in an ensemble-based docking approach to identify further pyrazolone compounds as candidate MCR-1 inhibitors. Docking simulations revealed that 13/28 of the pyrazolone compounds tested are predicted to have lower binding free energies than the reference compound. Four of these were chosen for in vitro testing, with the results demonstrating that all the compounds tested could lower colistin MICs in an E. coli strain carrying the mcr-1 gene. Docking of pyrazolones into the MCR-1 active site reveals residues that are implicated in ligand–protein interactions, particularly E246, T285, H395, H466, and H478, which are located in the MCR-1 active site and which participate in interactions with MCR-1 in ≥ 8/10 of the lowest energy complexes. This study establishes pyrazolone-induced colistin susceptibility in E. coli carrying the mcr-1 gene, providing a method for the development of novel treatments against colistin-resistant bacteria.

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Acknowledgements

C.H. thanks the Science Achievement Scholarship of Thailand for the Ph.D. scholarship, the 90th Anniversary of Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund, GCUGR1125623025D), and Ponlawoot Raksat for designing primer knowledge; Nguyet Luong, Zongfan Yang, and Kittika Kiratikunakorn for kindly supporting us. J.S. and A.J.M. thank the U.K. Engineering and Physical Sciences (EPSRC EP/M027546/1 (BristolBridge) and EP/M022609/1) and Medical (MRC MR/P007295/1) Research Councils. This work was in part carried out using the computational facilities of the Advanced Computing Research Centre, University of Bristol—http://www.bris.ac.uk/acrc/.

Funding

This study was funded by the 90th Anniversary of Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund, GCUGR1125623025D). Additional support from the U.K. Engineering and Physical Sciences (EPSRC EP/M027546/1 (BristolBridge) and EP/M022609/1) and Medical (MRC MR/P007295/1) Research Councils is acknowledged.

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Authors and Affiliations

  1. Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand

    Chonnikan Hanpaibool & Thanyada Rungrotmongkol

  2. Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand

    Puey Ounjai

  3. Center of Excellence On Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, 10400, Thailand

    Puey Ounjai

  4. Center of Excellence for Innovation in Chemistry (PERCH-CIC), Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand

    Sirilata Yotphan

  5. Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK

    Adrian J. Mulholland

  6. School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK

    James Spencer

  7. Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand

    Natharin Ngamwongsatit

  8. Laboratory of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand

    Natharin Ngamwongsatit

  9. Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand

    Thanyada Rungrotmongkol

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  1. Chonnikan Hanpaibool
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Contributions

The authors responsible for the conceptualization of the research study are PO, NN, and TR; SY synthesized the compounds; CH wrote the manuscript, carried out experiments and simulations and performed formal analysis, prepared data curation and visualization; AJM provided computational discussion; JS, NN, and TR wrote the revision and editing manuscript; JS and NN were both involved in the microbiology technique; NN and TR provided resources and supervision.

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Correspondence to Natharin Ngamwongsatit or Thanyada Rungrotmongkol.

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Hanpaibool, C., Ounjai, P., Yotphan, S. et al. Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation. J Comput Aided Mol Des 37, 479–489 (2023). https://doi.org/10.1007/s10822-023-00519-z

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