Discovering a New Antibiotic Agent Using Nuclear Magnetic Resonance Spectroscopy

Protein peptide deformylase (PDF) is an important enzyme involved in bacterial protein maturation. Researchers from Ruhr University Bochum shows how PDF could be used to develop more effective treatments against bacterial infections, according to Journal of Medicinal Chemistry (1).

PDFs are unique for its deformylation, which is a feature normally used to design novel antibiotics (2). It is an important enzyme in both gram-positive and gram-negative bacteria (3). Peptide deformylase removes formyl groups from N-terminal peptides, producing free N-terminal peptides as part of protein maturation (3). Blocking this enzyme halts bacterial growth (3).

A microscopic image of a bacteriophage virus attacking a bacterial cell, with long tendrils wrapping around the host | Image Credit: © EC Tech - stock.adobe.com

As a result, the search for potent PDFIs has been a long-standing objective in medicinal chemistry, driven by the urgent need for new antibiotics (1). The research led by lead author Raphael Stoll has identified a promising new structural scaffold for these inhibitors, potentially enhancing their selectivity and efficacy (1). The team’s focus on PDF inhibitors (PDFIs) could improve treatments against bacterial infections to address the growing concern of improved antibiotic resistance.

The research team adopted an approach that incorporated a full NMR backbone assignment of Escherichia coli PDF (ecPDF 1-147) when complexed with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, which was referred to as compound 2 (1). This assignment has provided critical insights into the emergent additional protein backbone resonances, which are pivotal for understanding the interaction between the inhibitor and the enzyme (1).

One of the most notable achievements of this research is the determination of the complex crystal structures of E. coli PDF and compound 2 (1). The crystal structure revealed an alternative ligand conformation within the protein, offering a potential new pathway for enhancing the selectivity of PDFIs (1). What this alternative orientation points to is a specific region of the S1′ pocket that varies between bacterial and human PDFs, suggesting a target for further refinement to minimize off-target effects in human cells (1).

Furthermore, the study utilized NMR TITAN line shape analysis to investigate the binding mechanism of compound 2 (1). An induced fit mechanism was discovered, where the binding of the inhibitor induces conformational changes in the PDF enzyme, optimizing the interaction and enhancing the inhibitor’s effectiveness (1). This insight is crucial for designing more potent and selective PDFIs.

Stoll and the team’s work is a significant advancement in the quest for new antibiotics. By identifying and characterizing a novel PDFI scaffold and elucidating its binding mechanisms, the study lays the groundwork for the development of next-generation antibiotics. These findings not only advance the understanding of PDFIs, but they also highlight the potential of NMR and crystallography in drug discovery (1).

The implications of this research extend beyond just a new class of antibiotics. The methodology and findings could inspire similar approaches in other areas of drug development, where enzyme inhibitors play a critical role (1). The identification of a new PDFI scaffold with promising selectivity and the detailed understanding of its binding mode represent a significant leap forward, offering hope for new antibiotic therapies.

References

(1) Kirschner, H.; Heister, N.; Zouatom; et al. Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. J. Med. Chem. 2024, 67 (8), 6384–6396. DOI: 10.1021/acs.jmedchem.3c02382

(2) Nguyen, K. T.; Hu, X.; Colton, C. Characterization of a Human Peptide Deformylase: Implications for Antibacterial Drug Design. Biochem. 2003, 42 (33), 9952–9958. DOI: 10.1021/bi0346446

(3) Wang, W.; White, R.; Yuan, Z. Proteomic Study of Peptide Deformylase Inhibition in Streptococcus pneumoniae and Staphylococcus aureus. Antimicrob. Agents Chemother. 2006, 50 (5), 1656–1663. DOI: 10.1128/AAC.50.5.1656-1663.2006