Target identification and drug design for human pathogen chlamydophila pneumoniae -in silico analysis

Abstract

Whole genome sequence of the human pathogen Chlamydophila pneumoniae and four other strains of same species were analyzed to identify drug targets. Total number 4388 protein coding genes were studied from four strains; in which 3948 genes were having more than 100 amino acids in their coding sequence were selected; we found 147 genes were identified as non-human homologs and conserved proteins among four strains. These non-human homologs genes and their encoding protein were categorized on the basis of the pathways involved in the basic survival mechanisms of the bacterium. Further, MSA of these genes showed eight different types of proteins as a novel drug target to design a drug. The modeled Holliday junction DNA helicase RuvB protein has more appropriate active sites among all other target proteins. Though all chosen drugs bind to Holliday junction DNA helicase RuvB protein, the binding site on the target protein with the minimum binding energy was selected. By using the active site prediction tools, under the optimized conditions we designed a set of antibiotics. Docking was done with the Autodock 4.0 with the different conformations of each ligand. This is the better drug that binds to the active site of target protein and inhibits their activities, which will effects one
of the most essential pathways involved in DNA replication, recombination, modification and repair. Therefore, this in silico analysis provides rapid and potential approach for
identification of drug target and designing of drug