Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics

Abstract

Peptide deformylase activity was thought to be limited to ribosomal protein synthesis in prokaryotes, where new peptides are initiated with an N-formylated methionine. We describe here a new human peptide deformylase (Homo sapiens PDF, or HsPDF) that is localized to the mitochondria. HsPDF is capable of removing formyl groups from N-terminal methionines of newly synthesized mitochondrial proteins, an activity previously not thought to be necessary in mammalian cells. We show that actinonin, a peptidomimetic antibiotic that inhibits HsPDF, also inhibits the proliferation of 16 human cancer cell lines. We designed and synthesized 33 chemical analogs of actinonin; all of the molecules with potent activity against HsPDF also inhibited tumor cell growth, and vice versa, confirming target specificity. Small interfering RNA inhibition of HsPDF protein expression was also antiproliferative. Actinonin treatment of cells led to a tumor-specific mitochondrial membrane depolarization and ATP depletion in a time-and dose-dependent manner; removal of actinonin led to a recovery of the membrane potential consistent with indirect effects on the electron transport chain. In animal models, oral or parenteral actinonin was well tolerated and inhibited human prostate cancer and lung cancer growth. We conclude that HsPDF is a new human mitochondrial enzyme that may provide a novel selective target for anticancer therapy by use of actinonin-based antibiotics.

CHR-2797: An Antiproliferative Aminopeptidase Inhibitor that Leads to Amino Acid Deprivation in Human Leukemic Cells

“…In contrast, related compounds which are poorly lipophilic are only weakly active in cell proliferation assays despite good activity against the same class of aminopeptidases, e.g., CHR-79888. The evidence that the target for these effects lay within the cell focused attention on aminopeptidases, histone deacetylases, MetAP-2, or peptide deformylase as intracellular metalloenzyme targets (2,10,(24)(25)(26). CHR-2797 has been shown to be inactive against a number of these targets (histone deacetylase, MetAP-2) and/or to affect the proliferation of a different spectrum of tumor cell lines than inhibitors of some of these targets (histone deacetylase, peptide deformylase; refs.…”

“…CHR-2797 has been shown to be inactive against a number of these targets (histone deacetylase, MetAP-2) and/or to affect the proliferation of a different spectrum of tumor cell lines than inhibitors of some of these targets (histone deacetylase, peptide deformylase; refs. 25,26). That the target is most likely to be one or more members of the aminopeptidase class of metalloenzyme is indicated by the findings that (a) all active antiproliferative agents related to CHR-2797 were aminopeptidase inhibitors and (b) tumor cells that were sensitive to CHR-2797 were also sensitive to high concentrations of bestatin, a well-established, structurally distinct, aminopeptidase inhibitor (9).…”

Inhibition of Human Peptide Deformylase Disrupts Mitochondrial Function

“…In order to rule out that the observed effect of actinonin on mitochondrial DNA-encoded COX subunits was due to a possible unknown indirect effect following inhibition of APN, we treated cells with the APN inhibitor bestatin, which does not inhibit PDF (25). Bestatin did not have an effect on the COX or the complex II 70-kDa subunit levels.…”

“…Despite the slow kinetic properties of HsPDF in an in vitro deformylation assay (24,29,35), we have shown that small interfering RNA (siRNA) interference of HsPDF decreases human cancer cell proliferation. Similarly, pharmacologic inhibition with the PDF antibiotic inhibitor actinonin and its analogs results in mitochondrial membrane depolarization and promotes cell death or proliferation arrest in a wide variety of cancer cell lines (18,25). However, the cellular function of HsPDF remains elusive, and others have proposed that it has none (29).…”

Interplay Between N-Terminal Methionine Excision and FtsH Protease Is Essential for Normal Chloroplast Development and Function in Arabidopsis

“…Two PDFs have been identified in plants: mitochondrion-targeted PDF1A and PDF1B, which are targeted to both mitochondria and plastids (Giglione et al, 2000;Dirk et al, 2001). Only PDF1A has been found in humans and other animals (Giglione et al, 2000;Nguyen et al, 2003;Serero et al, 2003;Lee et al, 2004), and a PDF3 was identified in trypanosomatids (Bouzaidi-Tiali et al, 2007). Note that the many proteins encoded by the nuclear genome, which are further imported in the plastids, are not processed by the chloroplastic NME (cNME) but rather by a dedicated transit stromal peptidase.…”