In silico identification and characterization of promising drug targets in highly virulent uropathogenic Escherichia coli strain CFT073 by protein-protein interaction network analysis

Urinary tract infections (UTIs) are one of the commonest bacterial infections worldwide. The most common etiological agent is uropathogenic Escherichia coli. The occurrence of high rates of antimicrobial resistance among UPEC has complicated therapeutic management and emphasized the need for new drug targets or newer approaches to tackle the increasing trend of antimicrobial resistance. The use of OMICS technologies provides an attractive alternative to experimental methods to provide momentum in the discovery of drugs and decrease the chances of drug failure in later stages of drug development. The availability of the full genome sequence of many disease-causing organisms and humans in public databases has significantly increased the search for promising drug targets. The present study was performed to identify and characterize promising drug targets against a highly virulent UPEC strain CFT073 by utilizing a novel hierarchical in silico approach. We conducted the study in four phases. In phase 1, three sets of proteins were mined through a chokepoint, virulence, and resistance genes analysis. The proteins selected from phase 1 were further subjected to the nonhomology analysis in phase 2. In phase 3, co-evolution analysis was done to find non-homologous proteins which interact with virulence and resistance genes at high correlation values (≥0.9). We found eight putative drug targets (MurB, MurC, HisC, HyaB, HybO, FliN, FliH, and MotB) that interacted with five virulence (chuU, chuW, iucA, fepA, and hylD) and two resistance genes (arnA and acrB). Most of the identified drug targets are part of distinct metabolic pathways (viz., peptidoglycan biosynthesis, histidine biosynthesis etc). In phase 4, qualitative characterization of the above drug targets including protein location in the bacterial cell, broad-spectrum analysis, interactome analysis, evaluation of druggability by similarity search against drug-target database, and essentiality analysis was performed. PCR-based confirmation of identified drug targets in clinical isolates of UPEC was also carried out. The findings of this study may aid in the discovery of new antibacterial agents for better treatment of E. coli UTIs.