In Silico analysis of Escherichia coli polyphosphate kinase (PPK) as a novel antimicrobial drug target and its high throughput virtual screening against PubChem library

Abstract

Multiple drug resistance (MDR) in bacteria is a global health challenge that needs urgent attention. The 2011 outbreak caused by Escherichia coli O104:H4 in Europe has exposed the inability of present antibiotic arsenal to tackle the problem of antimicrobial infections. It has further posed a tremendous burden on entire pharmaceutical industry to find novel drugs and/or drug targets. Polyphosphate kinase (PPK) in bacteria plays a crucial role in helping latter to adapt to stringent conditions of low nutritional availability thus making it a good target for antibacterials. In spite of this critical role, to best of our knowledge no in-silico work has been carried out to develop PPK as an antibiotic target. In the present study, virtual screening of PPK was carried out against all the 3D compounds with pharmacological action present in PubChem database. Our screening results were further refined by interaction maps to eliminate the false positive data respectively. From our results, compound number 5281927 (PubChem ID) has been found to have significant affinity towards affinity towards PPK active ATP-binding site indicating its therapeutic relevance.

Discovery and antibacterial study of potential PPK1 inhibitors against uropathogenic E. coli

“…᭝ppk1 strain was prepared as our previous study 25 . Liquid cultures of CFT073 and ᭝ppk1 were grown aerobically in LB broth supplemented with different concentrations of compounds 8 and 17 (5,20,40, and 80 lM) and DMSO (vehicle control) at 37 C for 18 h. 5637 cells and SV-HUC-1 cells (1 Â 10 5 cells/well) were seeded respectively into 24-well polystyrene plates and were allowed to adhere overnight. After being washed with PBS, the cells were respectively infected with CFT073 and ᭝ppk1 under each condition for 1.5 h. Cells were washed with PBS and then incubated in experimental medium containing gentamicin (100 lg/mL) for 1 h to kill extracellular bacteria.…”

“…Biofilms of the bacterial cultures can form on 1 Â 1 cm glass piece kept inside the 6-well polystyrene plates. Compounds (5,20,40, and 80 lM) and DMSO (vehicle control) were supplemented to the wells containing the glass slides and the plates were incubated for 24 h to allow for biofilms formation at 37 C. After incubation, the biofilms that were grown on the glass pieces were washed with PBS and stained with 0.01% acridine orange (AO). And then the biofilms were analysed with a confocal laser scanning microscope (LSM 800, Carl Zeiss 200, Germany).…”

“…For example, through in silico and in vitro methods, Inh1 and Inh2 (Figure 1) were predicted to disrupt the function of PPK1 in E. coli and to inhibit biofilm formation 19 . Etoposide (Figure 1) was predicted to bind into the PPK1 through virtual screening 20 . However, no further in-depth study has been reported thus far.…”

Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli

“…The physiological functions of polyP are not fully understood, but it is known to promote survival under different stress conditions by stabilizing unfolded proteins, chelating toxic metals, acting as a phosphate store, increasing translation fidelity, and as a second messenger that regulates the activity of a variety of proteins (12,(14)(15)(16)(17)(18)(19)(20)(21). Importantly, in many bacterial pathogens, deleting the gene encoding PPK (ppk) results in the loss of the ability to cause disease (22)(23)(24)(25)(26)(27)(28), indicating that polyP metabolism may be a potential therapeutic target for use against bacterial infections (29)(30)(31).…”

Genome-wide identification of antimicrobial peptides in the liver fluke, Clonorchis sinensis

“…The extensive use of antibiotics has contributed to the emergence of antimicrobial resistance and the reduced efficacy of the available antimicrobial agents [ 1 ]. Therefore, identification of novel antibiotics is urgently required to overcome the challenges presented by the emergence of multiple drugresistant microorganisms [ 2 ].…”