Design, Synthesis And Antimicrobial Activities Of Novel Peptide Deformylase Inhibitors

The emergence of multi-drug resistant bacteria has created an urgent demand for new antibacterial agents with novel mechanisms of action and new structures. One of new targets currently receiving widespread interest is peptide deformylase (PDF), the active site of PDF is highly conserved and present in most bacteria, including resistant species of PDF activity which can be characterized by its inhibitor, and the PDF in a number of parasites also play an important role. So PDF is considered a new generation of anti-bacterial, antiparasitic and anticancer properties of the ideal target site. In recent years, PDF has been reported for Mycobacterium tuberculosis research, and has become interesting new antibacterial drug targets.The crystal structure complexes of PDF with inhibitors and the SAR researches have revealed the essential structure demands of a PDF inhibitor:â‘ a moiety capable of chelating the essential metal at the catalytic site;â‘¡a hydrophobic side chain to fill the hydrophobic pocket at the S1'site;â‘¢two amide group;â‘£some hydrophobic groups at the P3'of the inhibitors.The binding modes of a series of PDF inhibitors were explored using molecular docking software (SYBYL7.0 and Autodock 4.0) and new shallow pockets near the known active pocket were found. These pockets could accommodate side chain at the P3'of inhibitors such as aromatic groups, which could enhance the binding affinity. Autodock results were in good agreement with the experimental values, which demonstrated a good linear relationship and indicated that the docking program produces reasonable binding modes.Many PDF inhibitors in literature show poor pharmacokinetics and selectivity due to their apparent peptide characteristics. Our strategy was to substitute the C-terminal amide bond of the lead compound actinonin with some heterocycles that would be hydrolytically stable and meanwhile retained all the important protein binding interactions. Benzimidazole, isoxazole and thiazole were chosen to be incorporated into the newly designed inhibitors. Good binding mode was demonstrated using the docking procedure for most of the newly designed compounds. 2-{[N-(Benzyloxy)formamido]methyl}hexanoic acid, a key intermediate, was synthesized from diethyl malonate, which were treated in turn via substitution, hydrolyzation and decarboxylation to furnish the 2-methylenehexanoic acid. We didn't use the formylation reaction to produce the next step compound in normally, because the yield of that reaction was low and the compounds were difficult to isolate. Firstly, we synthesized the N-(benzyloxy)formamide from acetone, then the N-(benzyloxy)formamide and 2-methylenehexanoic acid were synthesized to afford ethyl 2-{[N-(benzyloxy)formamido]methyl}hexanoate by Michael addition. 2-{[N-(Benzyloxy)formamido]methyl}hexanoic acid was afforded by hydrolyzation of ethyl 2-{[N-(benzyloxy)formamido]methyl}hexanoate.The convergent routes were employed to synthesize the target compounds. The desired benzimidazole, isoxazole and thiazole cycles were constructed via multi-step synthesis firstly.2-{[N-(Benzyloxy)formamido]methyl}hexanoic acid was then coupled to these heterocycles. The target compounds were obtained at the presence of 10%Pd/C as catalyst to remove the benzyl group. Twenty-two new target compounds have been synthesized. All the compounds were characterized by 1H NMR, IR and HRMS, and the results were in agreement with the proposed structures.16 compounds were evaluated by bacterial inhibitory assay. In vitro antibacterial activity assay revealed that most of the benzimidazole and isoxazole containing compounds showed weak antibacterial activity against Gram-negative pathogen (Klebsiella pneumoniae). While four benzimidazole and most isoxazole containing compounds showed moderate inhibitory activities against Gram-positive pathogen (Staphylococcus aureus). Due to being short of time, the in vitro antibacterial activity assay of thiazole containing compounds is under doing. Taken together, these results confirmed the inhibitory mechanism of the target compounds and would directed our design in the future.