Uropathogenic Escherichia coli Antibiotic Resistance and in silico Virtual Screening Using Pharmit Technique

Abstract

Increasing the rate of antibiotic-resistant pathogens causing serious infections and death has become a global health threat. However, the synthesis of antibiotics and new drugs is expensive and undertaken through multi phases and clinical trials. Therefore, repurposing old drugs to treat antibiotic-resistant bacteria is a good alternative way. Escherichia coli (E.coli) is a common pathogen of urinary tract infection, and its capability to form bifilms further contributes to its virulence and antibiotic resistance, posing a big crisis to global public health. Uropathogenic E.coli were isolated then tested by Vitek2 and disk diffusion method to know which antibiotics are resistant to E.coli. Then, real-time PCR, conventional PCR, and genes sequences tools were used to identify the strain of isolates E.coli. To do repurposing antibacterial drugs or to find a new compound, we performed a virtual screening on Pharrmit provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape, and energy minimization to predict a compound that has biological activity against the uropathogenic E. coli. A total of 14678 small molecules from the Drug Bank database were subjected to screening via Pharmit. Nine potential hits were obtained (100009383 - 1531009). Molecular docking can be used to evaluate the affinity of the new compounds to predict the binding affinity to FimH receptor.