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David A Scheinberg – 1st expert on this subject based on the ideXlab platform
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.Journal of Molecular Biology, 2009Co-Authors: Sindy Escobar-alvarez, Yueming Li, Yehuda Goldgur, Guangli Yang, Ouathek Ouerfelli, David A ScheinbergAbstract:
Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. The first structural model of a mammalian PDF (1.7 A), HsPDF, shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs. The HsPDF C-terminus topology and the presence of a helical loop (H2 and H3), however, shape a characteristic active site entrance. The structure of HsPDF bound to the peptidomimetic inhibitor Actinonin (1.7 A) identified the substrate-binding site. A defined S1′ pocket, but no S2′ or S3′ substrate-binding pockets, exists. A conservation of PDF-Actinonin interaction across PDFs was observed. Despite the lack of true S2′ and S3′ binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2’and P3′ positions of a formylated peptide substrate to turnover.
human mitochondrial peptide deformylase a new anticancer target of Actinonin based antibioticsJournal of Clinical Investigation, 2004Co-Authors: Michael J Soskis, Christopher Borella, Jeffrey R Gardner, Paula Hayes, Benzon M Dy, Mark L Heaney, Mark R Philips, William G Bornmann, Francis M Sirotnak, David A ScheinbergAbstract:
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.
a new human peptide deformylase inhibitable by ActinoninBiochemical and Biophysical Research Communications, 2003Co-Authors: Christophe Antczak, David A Scheinberg, William G Bornmann, Francis M Sirotnak, Yueming LiAbstract:
Abstract Peptide deformylases (PDFs) have been investigated as potential specific targets for antibiotics, but the possible existence of a functional human PDF (HsPDF) presents a potential hurdle to the design of specific drugs. We have expression cloned a HsPDF that has deformylase activity, although it is a slower and catalytically less active enzyme than bacterial or plant PDFs. A cobalt-substituted form of HsPDF (but not nickel or zinc) is active, and the enzyme appears to be active at a pH between 6.0 and 7.2, a temperature range of 25–50 °C, and in a low KCl ionic strength buffer. Actinonin inhibits HsPDF activity with an IC50 of 43 nM and kills Daudi and HL60 human cancer cell lines with an LC50 of 5.3 and 8.8 μM, respectively. The inhibition of HsPDF may provide an explanation for the mechanism by which Actinonin is cytotoxic against various human tumor cell lines.
Joaquim Trias – 2nd expert on this subject based on the ideXlab platform
Resistance of Streptococcus pneumoniae to Deformylase Inhibitors Is Due to Mutations in defBAntimicrobial Agents and Chemotherapy, 2001Co-Authors: Peter S Margolis, C J Hackbarth, Wen Wang, Zhengyu Yuan, Richard G. White, Sara L. Lopez, Mita Maniar, Joaquim TriasAbstract:
Resistance to peptide deformylase inhibitors in Escherichia coli or Staphylococcus aureus is due to inactivation of transformylase activity. Knockout experiments in Streptococcus pneumoniae R6x indicate that the transformylase (fmt) and deformylase (defB) genes are essential and that a def paralog (defA) is not. Actinonin-resistant mutants of S. pneumoniae ATCC 49619 harbor mutations in defB but not in fmt. Reintroduction of the mutated defB gene into wild-type S. pneumoniae R6x recreates the resistance phenotype. The altered enzyme displays decreased sensitivity to Actinonin.
Peptide Deformylase in Staphylococcus aureus: Resistance to Inhibition Is Mediated by Mutations in the Formyltransferase GeneAntimicrobial Agents and Chemotherapy, 2000Co-Authors: Peter S Margolis, Dawn Chen, C J Hackbarth, Wen Wang, Dennis C. Young, Zhengyu Yuan, Richard G. White, Joaquim TriasAbstract:
Peptide deformylase, a bacterial enzyme, represents a novel target for antibiotic discovery. Two deformylase homologs, defA and defB , were identified in Staphylococcus aureus . The defA homolog, located upstream of the transformylase gene, was identified by genomic analysis and was cloned from chromosomal DNA by PCR. A distinct homolog, defB , was cloned from an S. aureus genomic library by complementation of the arabinose-dependent phenotype of a P BAD -def Escherichia coli strain grown under arabinose-limiting conditions. Overexpression in E. coli of defB , but not defA , correlated to increased deformylase activity and decreased susceptibility to Actinonin, a deformylase-specific inhibitor. The defB gene could not be disrupted in wild-type S. aureus , suggesting that this gene, which encodes a functional deformylase, is essential. In contrast, the defA gene could be inactivated; the function of this gene is unknown. Actinonin-resistant mutants grew slowly in vitro and did not show cross-resistance to other classes of antibiotics. When compared to the parent, an Actinonin-resistant strain produced an attenuated infection in a murine abscess model, indicating that this strain also has a growth disadvantage in vivo. Sequence analysis of the Actinonin-resistant mutants revealed that each harbors a loss-of-function mutation in the fmt gene. Susceptibility to Actinonin was restored when the wild-type fmt gene was introduced into these mutant strains. An S. aureus Δ fmt strain was also resistant to Actinonin, suggesting that a functional deformylase activity is not required in a strain that lacks formyltransferase activity. Accordingly, the defB gene could be disrupted in an fmt mutant.
Actinonin a naturally occurring antibacterial agent is a potent deformylase inhibitorBiochemistry, 2000Co-Authors: Dawn Chen, Dinesh V Patel, C J Hackbarth, Wen Wang, Geoffrey B Dreyer, Dennis Young, Peter S Margolis, Charlotte Wu, Zijie Ni, Joaquim TriasAbstract:
Peptide deformylase (PDF) is essential in prokaryotes and absent in mammalian cells, thus making it an attractive target for the discovery of novel antibiotics. We have identified Actinonin, a naturally occurring antibacterial agent, as a potent PDF inhibitor. The dissociation constant for this compound was 0.3 × 10-9 M against Ni−PDF from Escherichia coli; the PDF from Staphylococcus aureus gave a similar value. Microbiological evaluation revealed that Actinonin is a bacteriostatic agent with activity against Gram-positive and fastidious Gram-negative microorganisms. The PDF gene, def, was placed under control of PBAD in E. coli tolC, permitting regulation of PDF expression levels in the cell by varying the external arabinose concentration. The susceptibility of this strain to Actinonin increases with decreased levels of PDF expression, indicating that Actinonin inhibits bacterial growth by targeting this enzyme. Actinonin provides an excellent starting point from which to derive a more potent PDF inhibi…
Vincent Mikol – 3rd expert on this subject based on the ideXlab platform
the crystal structures of four peptide deformylases bound to the antibiotic Actinonin reveal two distinct types a platform for the structure based design of antibacterial agentsJournal of Molecular Biology, 2002Co-Authors: J P Guilloteau, Magali Mathieu, Carmela Giglione, Veronique Blanc, A Dupuy, Miline Chevrier, Alain Famechon, Thierry Meinnel, Vincent MikolAbstract:
Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic Actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of Actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.