Design, Synthesis And Antibacterial Activity Of Novel Potent Peptide Deformvlase Inhibitors

The increased prevalence of multidrug-resistant (MDR) bacteria in clinical isolates has made the search for new antibacterial agents with novel modes of action even more important. One of the new targets currently receiving widespread attention from both academic and industrial research groups is peptide deformylase (PDF). PDF is an iron-containing metalloenzyme involved in the post-translational modification of nascent polypeptides in bacterial cells. The catalytic mechanism of PDF enzymes containing zinc, iron, cobalt, and nickel dications were studied by Nino Russo in 2006. Protein synthesis is initiated in bacterial cells by ribosomal binding to a formyl methionine-charged transfer RNA, but most mature proteins do not retain the N-formyl group or the terminal methionine residue. Therefore, removal of the N-formyl moiety catalyzed by PDF is a crucial step in bacterial protein biosynthesis and growth. On the other hand, mammalian cytosolic protein synthesis does not produce N-formylated polypeptides and does not require PDF. The difference between bacterial and mammalian protein synthesis makes PDF an attractive and unique target for treating resistant bacteria.The first PDF inhibitor, actinonin, was isolated from an actinomycete by Gordon in 1962. Actinonin exhibits moderate antibacterial activity against several Gram-positive and Gram-negative bacteria, but it does not exhibit good in vivo antibacterial activity, which could be attributed to either poor absorption or quick clearance. LBM415 and BB83698 were the first two PDF inhibitors to undergo human clinical trials, and they exhibited much better in vitro and in vivo efficacies when compared to the original lead compound actinonin. GSK1322322 completed a phase II trial for acute bacterial skin and structure infections in April 2012. This compound possesses potent activity against not only methicillin-resistant Staphylococcus aureus (MRSA), but also against the respiratory pathogens Haemophilus influenzae and Streptococcus pneumoniae. However, no PDF inhibitors are currently marketed.In this dissertation, novel PDF inhibitors bearing (2S,3aR,7aS)-octahydro-lH-indole-2-carboxylic acid, (2S,4S)-4-fluoropyrrolidine-2-carboxylic acid, and (2S, 4S)-4-methylpyrrolidine-2-carboxylic acid were designed and synthesized. Chapter 2 is about the design and synthesis of novel PDF inhibitors containing (2S,3aR,7aS)-octahydro-lH-indole-2-carboxylic acid. By introducing (2S,3aR,7aS)-octahydro- 1H-indole-2-carboxylic acid to the P2’ position and various heterocyclic aromatic amines to the P3’position, six PDF inhibitor candidates were designed and synthesized. In the in-vitro antibacterial activity test, compounds bearing octahydroindole at the P2’ position exhibited only moderate antibacterial activity, which may be attributed to the large steric hindrance of the octahydroindole.To reduce the large steric hindrance of octahydroindole, (2S,4S)-4-fluoropyrrolidine-2-carboxylic acid was selected as the P2’ group of the new PDF inhibitors in chapter 3. The in-vitro antibacterial activity test showed that the 3-fluoropyrrolidine formyl hydroxyamino derivatives exhibited moderate to good antibacterial activity.To further improve antibacterial activity, (2S,4S)-4-methylpyrrolidine-2-carboxylic acid was selected as the P2’ group of the new PDF inhibitor in chapter 4. Good to excellent antibacterial activities were observed when 3-methylpyrrolidine was introduced into the P2’position. Notably, compound 4b containing an n-butyl group at the P1’ position and 2-amino-5-fluoropyridine-N-oxide at the P3’position exhibited better in vitro antibacterial activity than the positive control LBM415. Finally,2-amino-5-fluoropyridine-N-oxide derivative 4b and 5-methylthiazol-2-amino derivative 2g were selected as representative candidates to evaluate in-vivo efficacy based on their robust activities in broader antibacterial profiling. Compound 4b had better protective effects than positive control linezolid. The high PPB rate of compound 2g (99% PPB rate) may be responsible for the lower efficacy in vivo despite its good in vitro activity and pharmacokinetic properties.Chapter 5 is about the synthesis and modification of GSK1322322. We achieved the total synthesis of GSK1322322 in 15 steps, with an overall yield of 3.6%. The structure modification of GSK1322322 was carefully designed. A novel synthesis route for the fragments was successfully designed and synthesized. Further studies on the coupling of fragments to prepare GSK1322322 derivatives are currently in progress.