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. 2024 Sep 18;15(41):16928-16937.
doi: 10.1039/d4sc04937c. Online ahead of print.

Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol

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Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol

Helen G Smith et al. Chem Sci. .

Abstract

The breakthrough cephalosporin cefiderocol, approved for clinical use in 2019, has activity against many Gram-negative bacteria. The catechol group of cefiderocol enables it to efficiently enter bacterial cells via the iron/siderophore transport system thereby reducing resistance due to porin channel mutations and efflux pump upregulation. Limited information is reported regarding the binding of cefiderocol to its key proposed target, the transpeptidase penicillin binding protein 3 (PBP3). We report studies on the reaction of cefiderocol and the related cephalosporins ceftazidime and cefepime with Pseudomonas aeruginosa PBP3, including inhibition measurements, protein observed mass spectrometry, and X-ray crystallography. The three cephalosporins form analogous 3-exomethylene products with P. aeruginosa PBP3 following elimination of the C3' side chain. pIC50 and k inact/K i measurements with isolated PBP3 imply ceftazidime and cefiderocol react less efficiently than cefepime and, in particular, meropenem with P. aeruginosa PBP3. Crystal structures inform on conserved and different interactions involved in binding of the three cephalosporins and meropenem to P. aeruginosa PBP3. The results will aid development of cephalosporins with improved PBP3 inhibition properties.

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Conflict of interest statement

The authors have no conflicts to declare.

Figures

Fig. 1
Fig. 1. Reaction of P. aeruginosa PBP3 with cephalosporins in competition with meropenem (1 : 1 ratio) informs on the efficiency of reaction. Electrospray-ionisation quadrupole time-of-flight (ESI-Q-TOF) mass spectra imply that cefepime (C) reacts more efficiently with PBP3 than cefiderocol (D), which reacts more efficiently than ceftazidime (D). The spectra shown are representative of three technical repeats.
Fig. 2
Fig. 2. Reaction of cephalosporins with the nucleophilic serine of P. aeruginosa PBP3 proceeds with elimination of the C3 side chain. Evidence for elimination is provided by X-ray crystallography and protein-observed mass spectrometry of P. aeruginosa PBP3 following reaction with; (A) cefiderocol, (mFo-DFc polder OMIT map contoured at 5.82σ), (B) ceftazidime, (mFo-DFc polder OMIT map contoured at 5.00σ), (C) cefepime, (mFo-DFc polder OMIT map contoured at 3.30σ) and (D) meropenem, (mFo-DFc polder OMIT map contoured at 4.68σ). In each case the deconvoluted mass spectra following reaction of the cephalosporins with P. aeruginosa PBP3 support elimination of the C3 side chain from the cephalosporin.
Fig. 3
Fig. 3. Crystallographic studies indicate that cephalosporins react with the active site serine of P. aeruginosa PBP3 resulting in elimination of the C3 group. (A) Superimposition of P. aeruginosa PBP3 active site following reaction with cefiderocol (green, PDB:9FZ7) and meropenem (blue, PDB:9FZE). Interaction map displaying polar interactions formed between (B) cefiderocol (PDB:9FZ7), (C) meropenem (PDB:9FZE) and residues within the P. aeruginosa PBP3 active site. Compounds are coloured grey, interacting residues are green. Distances are in Å.
Scheme 1
Scheme 1. Outline mechanism for reaction of P. aeruginosa PBP3 with pyrrolidinium cephalosporins resulting in elimination of the C3 group. Reaction may either be concerted (blue arrows) or proceed via an anionic intermediate (red arrows). Elimination of the C3 side chain from cefiderocol produces an identical PBP3-bound complex to that generated on ceftazidime binding (Fig. 2).

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References

    1. Yao J. Wang J. Chen M. Cai Y. Front. Med. 2021;8:741940. doi: 10.3389/fmed.2021.741940. - DOI - PMC - PubMed
    1. Sato T. Yamawaki K. Clin. Infect. Dis. 2019;69:S538–S543. doi: 10.1093/cid/ciz826. - DOI - PMC - PubMed
    1. Ito A. Sato T. Ota M. Takemura M. Nishikawa T. Toba S. Kohira N. Miyagawa S. Ishibashi N. Matsumoto S. Nakamura R. Tsuji M. Yamano Y. Antimicrob. Agents Chemother. 2018;62:e01454. doi: 10.1128/AAC.01454-17. - DOI - PMC - PubMed
    1. Zhanel G. G. Golden A. R. Zelenitsky S. Wiebe K. Lawrence C. K. Adam H. J. Idowu T. Domalaon R. Schweizer F. Zhanel M. A. Lagacé-Wiens P. R. S. Walkty A. J. Noreddin A. Lynch III J. P. Karlowsky J. A. Drugs. 2019;79:271–289. doi: 10.1007/s40265-019-1055-2. - DOI - PubMed
    1. Tacconelli E., Magrini N., Carmeli Y., Harbarth S., Kahlmeter G., Kluytmans J., Mendelson M., Pulcini C., Singh N. and Theuretzbacher U., World Health Organisation Global Priority List of Antibiotic Resistant Bacteria to Guide Research, Discovery and Development of New Antibiotics, Geneva, 2017

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