Discovery of potent polyphosphate kinase 1 (PPK1) inhibitors using structure‐based exploration of PPK1Pharmacophoric space coupled with docking analyses

Abstract

Inorganic polyphosphate (polyP) is present in all living forms of life. Studied mainly in prokaryotes, polyP and its associated enzymes are vital in diverse metabolic activities, in some structural functions, and most importantly in stress responses. Bacterial species, including many pathogens, encode a homolog of a major polyP synthesis enzyme, Poly Phosphate Kinase (PPK) with 2 different genes coding for PPK1 and PPK2. Genetic deletion of the ppk1 gene leads to reduced polyP levels and the consequent loss of virulence and stress adaptation responses. This far, no PPK1 homolog has been identified in higher-order eukaryotes, and, therefore, PPK1 represents a novel target for chemotherapy. The aim of the current study is to investigate PPK1 from Escherichia coli with comprehensive understanding of the enzyme's structure and binding sites, which were used to design pharmacophores and screen a library of compounds for potential discovery of selective PPK1 inhibitors. Verification of the resultant inhibitors activities was conducted using a combination of mutagenic and chemical biological approaches. The metabolic phenotypic maps of the wild type E. coli (WT) and ppk1 knockout mutant were generated and compared with the metabolic map of the chemically inhibited WT. In addition, biofilm formation ability was measured in WT, ppk1 knockout mutant, and the chemically inhibited WT. The results demonstrated that chemical inhibition of PPK1, with the designed inhibitors, was equivalent to gene deletion in altering specific metabolic pathways, changing the metabolic fingerprint, and suppressing the ability of E. coli to form a biofilm.

The Polyphosphate Kinase of Escherichia coli Is Required for Full Production of the Genotoxin Colibactin

“…Several studies have focused on finding inhibitors of PPK (25,(41)(42)(43). One of the iden- SEMs (n = 4 independent experimental replicates).…”

A Stringent Analysis of Polyphosphate Dynamics in Escherichia coli

“…This remarkable work shows that there is significant potential for PPK inhibitors in the clinic. Indeed, additional inhibitors are currently being sought by a number of groups (77)(78)(79). The importance of understanding polyP metabolism extends beyond clinical applications.…”

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

“…Over the past decade, only a few compounds were reported to interact with PPK1 of E. coli. 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 .…”