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Mechanism of time-dependent inhibition of polypeptide deformylase by actinonin

Glenn S Van Aller1, Ravi Nandigama, Chantal M Petit

  • 1Enzymology and Mechanistic Pharmacology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.

Biochemistry
|January 5, 2005
PubMed

Insights

Polypeptide deformylase (PDF) is inhibited by actinonin through a slow, two-step binding mechanism, leading to a 2000-fold increase in potency. This study enhances understanding of PDF inhibitors for novel antibiotic development.

Area of Science:

  • Biochemistry
  • Microbiology
  • Pharmacology

Background:

  • Polypeptide deformylase (PDF) is a crucial bacterial enzyme.
  • PDF removes N-formyl groups from nascent polypeptides.
  • Inhibiting PDF can lead to antibacterial effects.

Purpose of the Study:

  • To characterize the inhibition of bacterial PDF by actinonin.
  • To elucidate the binding mechanism of actinonin to PDF.
  • To compare actinonin's inhibition with other PDF inhibitors.

Main Methods:

  • Steady-state and transient kinetic methods.
  • Progress curve analysis.
  • Stopped-flow fluorescence measurements.
  • Rapid dilution studies.

Main Results:

  • Actinonin exhibits slow, two-step binding to PDF, forming a tight complex (EI*) with a very slow dissociation rate (>0.77 days).
  • Potency of actinonin increases over 2000-fold upon complex tightening (K(i) = 530 nM to K(i)* ≤ 0.23 nM).
  • BB-3497 also acts as a time-dependent PDF inhibitor with a slow off-rate, similar to actinonin.

Conclusions:

  • The two-step inhibition model for actinonin and BB-3497 is consistent with previous findings.
  • Understanding this inhibition mechanism is key for developing new antibiotics targeting bacterial PDF.
  • Actinonin's slow-binding mechanism offers a promising avenue for novel antibacterial drug design.

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