Download MendeleyToward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase.
Kirschner, H., Heister, N., Zouatom, M., Zhou, T., Hofmann, E., Scherkenbeck, J., Stoll, R.(2024) J Med Chem 67: 6384-6396
- PubMed: 38574272 Search on PubMed
- DOI: https://doi.org/10.1021/acs.jmedchem.3c02382
- Primary Citation Related Structures:
8RHR - PubMed Abstract:
Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1 H -indol-3-yl)- N -hydroxyacetamide ( 2 ), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2 . Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1' pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism.
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany.
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