The long-term objectives of this project are to understand the molecular mechanism of peptide deformylase, a small zinc-containing enzyme (169 amino acids in Escherichia coli), and design deformylase inhibitors and deformylase activated prodrugs as potential antibacterial agents. Ribosomal protein synthesis universally initiates with a methionine residue. In prokaryotes and the organelles of eukaryotes, the methionyl moiety attached to initiator tRNA is N-formylated prior to its incorporation. Following translational initiation, the N-formyl group is removed from the vast majority of bacterial proteins, a process catalyzed by the peptide deformylase. It has been demonstrated that proper deformylation of nascent polypeptides is essential for bacterial survival, as deletion of the deformylase gene (def) is lethal in E. coli. However, this deformylation process is apparently dispensable in eukaryotes. Therefore, deformylase appears to be an ideal target for developing broad-spectrum antibiotics, since formylation is a conserved feature in all eubacteria.
Specific aims i nclude: 1) Determination of the substrate specificity of deformylase using synthetic substrate analogues and combinatorial library screening; 2) Determination of catalytic mechanism using isotope exchange and chemical trapping experiments; 3) Determination of its 3-D structure by X-ray crystallography; 4) Determination of the function of its Zn2+ ion and identification of active-site residues by spectroscopic methods and site-directed mutagenesis; and 5) Design and synthesis of deformylase inhibitors and prodrugs that could be activated by deformylase action in vivo.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Biochemistry Study Section (BIO)
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Ohio State University
Schools of Medicine
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Shen, Gang; Zhu, Jinge; Simpson, Anthony M et al. (2008) Design and synthesis of macrocyclic peptidyl hydroxamates as peptide deformylase inhibitors. Bioorg Med Chem Lett 18:3060-3
Nguyen, Kiet T; Pei, Dehua (2008) High-throughput screening of peptide deformylase inhibitors. Methods Mol Med 142:117-30
Nguyen, Kiet T; Wu, Jen-Chieh; Boylan, Julie A et al. (2007) Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase. Arch Biochem Biophys 468:217-25
Joo, Sang Hoon; Xiao, Qing; Ling, Yun et al. (2006) High-throughput sequence determination of cyclic peptide library members by partial Edman degradation/mass spectrometry. J Am Chem Soc 128:13000-9
Rajan, Rakhi; Zhu, Jinge; Hu, Xubo et al. (2005) Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate. Biochemistry 44:3745-53
Nguyen, Kiet T; Pei, Dehua (2005) Purification and characterization of enzymes involved in the degradation of chemotactic N-formyl peptides. Biochemistry 44:8514-22
Jain, Rinku; Hao, Bing; Liu, Ren-Peng et al. (2005) Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal. J Am Chem Soc 127:4558-9
Pei, Dehua; Zhu, Jinge (2004) Mechanism of action of S-ribosylhomocysteinase (LuxS). Curr Opin Chem Biol 8:492-7
Nguyen, Kiet T; Hu, Xubo; Pei, Dehua (2004) Slow-binding inhibition of peptide deformylase by cyclic peptidomimetics as revealed by a new spectrophotometric assay. Bioorg Chem 32:178-91
Robien, Mark A; Nguyen, Kiet T; Kumar, Abhinav et al. (2004) An improved crystal form of Plasmodium falciparum peptide deformylase. Protein Sci 13:1155-63

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