Peptide De-formyl Inhibitors Theoretical Research

Peptide Deformylase (PDF), an essential bacterial metalloenzyme, is responsible for the removal of the N-terminal formyl group from methionine residues following protein synthesis. Because PDF is essential in a variety of pathogenic bacteria but is not required for cytoplasmic protein synthesis in eukaryotes, it becomes an attractive target for developing novel antibiotics and PDF inhibitors have appeared to be one of the most promising classes of antibacterial agents discovered to date.As a metallo-enzyme, PDF lends itself to the well precedented mechanism-based rational drug design approach. Using structural and mechanistic information, together with high throughput screening, several types of potent PDF inhibitors have been identified. Most PDF inhibitors identified to date share a common structural feature of a 'chelator + peptidomimetic' scaffold. However, there is still a need for the identification of novel and structurally diverse non-peptidic PDF inhibitors. Thus in this paper, a series of PDF inhibitors have been designed and the interaction modes between them and PDF have been studied using molecular simulation method and quantum mechanics method.The main contents of this thesis are as follows:Firstly, sequence aligning was carried out on all the obtained PDF using VectorNT software and backbone superpose was performed using SPDV program. 1BSK was selected as the acceptor to be used in the molecular docking calculations. The ligands were designed to be compounds with the backbone benzene and furan according to references. Docking was carried out using the Run multiple ligand mode of FlexX method in SYBYL7.0. Compounds with good binding feature with PDF have been obtained according to docking scores and binding mode analysis.Secondly, we select five compounds with good scores and three PDF inhibitors with active data to do molecular dynamics calculations and the using software is Tinker program. The compounds have been divided into three sequences(ligand, backbone and modifying regions, respectively) to calculate the interaction energy of each sequence with its surrounding amino acids. The interaction mode of each sequence has been analyzed in detail.At last, we use density functional theory method B3LYP to study the simplified model of PDF with different ions and the model of PDF catalyzing hydrolysis of polypeptide. The outcomes show that as to the three PDFs with Zn²⁺, Fe²⁺ and Ni²i, Zn²⁺-PDF is the most unstable. The complex of N-hydroxyl-formamide with PDF is more stable than that of water with PDF, thus N-hydroxyl-formamide could act as PDF inhibitor and replace water, thus to inhibit PDF hydration. The hydrolysis of model compound formamide could through two pathways: concerted mechanism and stepwise mechanism, the active energies of these two mechanisms is similar and are 39.58 kcal/mol and 39.56 kcal/mol respectively. In order to consider the effects of PDF on the hydrolysis of formamide, semi-empirical method PM3 was used to study the PDF catalyzing formamide deformylation.The deformylation of polypeptide in vivo is very complex. In order to make the mechanism elusive and to identify novel and structurally diverse PDF inhibitors, much effort should be carried out in future.