2. Academic Validation
  3. Covalent inhibitors of bacterial peptidoglycan biosynthesis enzyme MurA with chloroacetamide warhead

Covalent inhibitors of bacterial peptidoglycan biosynthesis enzyme MurA with chloroacetamide warhead

  • Eur J Med Chem. 2022 Dec 5;243:114752. doi: 10.1016/j.ejmech.2022.114752.
Katarina Grabrijan 1,  Martina Hrast 2,  Matic Proj 3,  Ana Dolšak 4,  Irena Zdovc 5,  Tímea Imre 6,  László Petri 7,  Péter Ábrányi-Balogh 8,  György M Keserű 9,  Stanislav Gobec 10
Affiliations

Affiliations

  • 1 Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: katarina.grabrijan@ffa.uni-lj.si.
  • 2 Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: martina.hrast@ffa.uni-lj.si.
  • 3 Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: matic.proj@ffa.uni-lj.si.
  • 4 Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: ana.dolsak@ffa.uni-lj.si.
  • 5 Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia. Electronic address: irena.zdovc@vf.uni-lj.si.
  • 6 Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary. Electronic address: imre.timea@ttk.hu.
  • 7 Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary. Electronic address: petri.laszlo@ttk.hu.
  • 8 Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology, Szt. Gellért tér 4., H-1117, Budapest, Hungary. Electronic address: abranyi-balogh.peter@ttk.hu.
  • 9 Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology, Szt. Gellért tér 4., H-1117, Budapest, Hungary. Electronic address: keseru.gyorgy@ttk.hu.
  • 10 Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: stanislav.gobec@ffa.uni-lj.si.
PMID: 36126388 DOI: 10.1016/j.ejmech.2022.114752
Abstract

MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) catalyzes the first committed step in the cytoplasmic part of peptidoglycan biosynthesis and is a validated target Enzyme for Antibacterial drug discovery; the inhibitor fosfomycin has been used clinically for decades. Like fosfomycin, most MurA inhibitors are small heterocyclic compounds that inhibit the Enzyme by forming a covalent bond with the active site cysteine. The reactive chloroacetamide group was selected from a series of suitable electrophilic thiol-reactive warheads. The predominantly one-step synthesis led to the construction of the final library of 47 fragment-sized chloroacetamide compounds. Several new E. coli MurA inhibitors were identified, with the most potent compound having an IC50 value in the low micromolar range. The electrophilic reactivity of all chloroacetamide fragments in our library was evaluated by a high-throughput spectrophotometric assay using the reduced Ellman reagent as a surrogate for the cysteine thiol. LC-MS/MS experiments confirmed the covalent binding of the most potent inhibitor to Cys115 of the digested MurA Enzyme. The covalent binding was further investigated by a biochemical time-dependent assay and a dilution assay, which confirmed the irreversible and time-dependent mode of action. The efficacy of chloroacetamide derivatives against MurA does not correlate with their thiol reactivity, making the active fragments valuable starting points for fragment-based development of new Antibacterial agents targeting MurA.

Keywords

Antibacterial agents; Thiol reactivity; UDP-N-Acetylglucosamine enolpyruvyl transferase.

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