Synthesis and Antibacterial Activity of Peptide Deformylase Inhibitors

Abstract

Peptide deformylase catalyzes the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria. Its essential character in bacterial cells makes it an attractive target for antibacterial drug design. In this work, we have rationally designed and synthesized a series of peptide thiols that act as potent, reversible inhibitors of purified recombinant peptide deformylase from Escherichia coli and Bacillus subtilis. The most potent inhibitor has a K(I) value of 11 nM toward the B. subtilis enzyme. These inhibitors showed antibacterial activity against both Gram-positive and Gram-negative bacteria, with minimal inhibitory concentrations (MIC) as low as 5 microM ( approximately 2 microg/mL). The PDF inhibitors induce bacterial cell lysis and are bactericidal toward all four bacterial strains that have been tested, B. subtilis, Staphylococcus epidermidis, Enterococcus faecalis, and E. coli. Resistance evaluation of one of the inhibitors (1b) against B. subtilis showed that no resistant clone could be found from >1 x 10(9) cells. Quantitative analysis using a set of inhibitors designed to possess varying potencies against the deformylase enzyme revealed a linear correlation between the MIC values and the K(I) values. These results suggest that peptide deformylase is the likely molecular target responsible for the antibacterial activity of these inhibitors and is therefore a viable target for antibacterial drug design.

N-Alkyl Urea Hydroxamic Acids as a New Class of Peptide Deformylase Inhibitors with Antibacterial Activity

“…The urea hydroxamates appear to be bacteriostatic against S. aureus, as was observed previously for other PDF inhibitors against both S. aureus and E. coli (4,13,34). Huntington et al (25) reported the lysis of Bacillus subtilis by a peptide thiol PDF inhibitor, although the compound appeared to be bacteriostatic when tested with log-phase organisms. In contrast to the situation with S. aureus, VRC4232 and VRC4307 both had a killing effect on S. pneumoniae and H. influenzae, two pathogens that cause upper respiratory tract infections.…”

Peptide Deformylase as an Antibacterial Drug Target: Target Validation and Resistance Development

“…Although bacteriostatic action has also been described for actinonin (11), this may not be a general characteristic of PDF inhibitors, as a series of peptide thiols described recently (15) show bactericidal activity. However, this was only convincingly demonstrated in Bacillus subtilis, which may be particularly susceptible to this class of compounds.…”

Peptide Deformylase Inhibitors as Antibacterial Agents: Identification of VRC3375, a Proline-3-Alkylsuccinyl Hydroxamate Derivative, by Using an Integrated Combinatorial and Medicinal Chemistry Approach

“…Although Huntington et al reported that a series of peptide thiols were potent PDF inhibitors with whole-cell activity (12), the majority of PDF inhibitors reported to have significant antibacterial activity contain either a hydroxamate or reverse hydroxamate as the metal chelator (31). In fact, in a recent study for which compounds of the same P 1 Ј-P 3 Ј peptidomimetic but with different metal binding groups were prepared, only hydroxamate-and N-formyl hydroxylamine-containing compounds showed antibacterial activity (12a, 30).…”