Structural and functional studies of the inhibition of peptide deformylase – A potential antibiotic target

The increase in antimicrobial resistance among pathogens has prompted a new interest in the development of novel antibiotics. A promising target for such new antibiotics is the metalloenzyme peptide deformylase (PDF), which catalyses the removal of the N-terminal formyl group of nascent polypeptide chains. This process, being essential for bacterial protein synthesis and survival, while not being a part of the eukaryotic cytoplasmic protein synthesis, gives PDF its appeal as a target for new antibacterial drugs. A potential PDF-targeting drug should, however, exhibit specificity towards the bacterial PDFs as a human homolog, which may participate in mitochondrial protein synthesis, has been identified. In this thesis we sought to investigate the structure and function of three PDF homologs; Staphylococcus aureus PDF (type II), Neisseria gonorrhoeae PDF (type IB), and the human mitochondrial PDF (type IA), as representatives of the three PDF types in order to establish them as model test systems for the development of new antibiotic drugs targeting PDF. Expression and purification protocols for obtaining catalytically active samples of all three PDFs have been established. Further, enzymatic activity assays have been developed and used in determination of the enzymatic activity and actinonin-induced inhibition of the three PDFs. In order to gain further insight into the structural basis of PDF activity, the structure of S. aureus PDF has been determined using protein crystallography, while initial crystallization conditions for N. gonorrhoeae PDF have been established. The project has paved the way to investigate the interaction of the selected bacterial PDFs and human mitochondrial PDF with new synthesized anti-PDF compounds.