Subtractive Proteomic Approach for The Identification of Potential Drug Targets Using WGS of Indigenous Clinical E.coli Isolate

Abstract

Escherichia coli, a gram negative, rod shaped bacteria belonging to the family; Enterobacteriaceae has become a popular pathogen causing various diseases including diarrhea, pneumonia and urinary tract infections. Increasing mutations has given rise to multidrug resistance due to which conventional therapeutics are becoming less or ineffective thus creating a need to develop new treatment regimens being more efficacious and specific. Identification of potential drug targets using whole genome, a primary step in drug discovery, can provide a better understanding of the pathogen contributing to develop better treatment therapies. In this study, the whole genome of indigenous clinical strain E. coli, was sequenced and exploited to search for the putative drug targets through subtractive proteomic approach. The study comprises of three different stages, stage I revealed that clinical strain collected belonged to UPEC group with 5095 coding sequences and ANI and BLAST assessment revealed its genome had close sequence identity with reference E. coli K12 MG1655/ATCC 47076 as well as with the other reference UPEC strains included in the study. Stage II comprised of the subtractive pipeline used to narrow it down and pinpoint the essential genes involved in different metabolic pathways of pathogen. The filtered ones were subjected to stage III which included their prioritization and qualitative characterization using different Insilico approaches. After adopting thorough filtration process, 9 potential drug targets were identified being cytoplasmic, involved in unique metabolic pathways and owing druggable properties being broad spectrum as well. Binding Pocket analysis revealed the number of binding pockets along with its drug score suggesting the best binding pocket of the target for the suitable interaction with drug. Furthermore, AMRs, virulence factor, broad spectrum analysis, druggability, docking analyses and Virtual screening through DrugBank Library and MTiopen screen paved the way to design promising, specific and effective new drugs. A detail laboratory experimentation is always required to fill the gap between wet and dry laboratory study for authenticating the obtained output, however, it may also contribute in module development as well as circuit designing in systems biology.