Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases

Martina Hrast,Kaja Rožman,Iza Ogris,Veronika Škedelj,Delphine Patin,Matej Sova,Hélène Barreteau,Stanislav Gobec,Simona Golič Grdadolnik,Anamarija Zega

doi:10.1080/14756366.2019.1608981

Abstract

The Mur ligases form a series of consecutive enzymes that participate in the intracellular steps of bacterial peptidoglycan biosynthesis. They therefore represent interesting targets for antibacterial drug discovery. MurC, D, E and F are all ATP-dependent ligases. Accordingly, with the aim being to find multiple inhibitors of these enzymes, we screened a collection of ATP-competitive kinase inhibitors, on Escherichia coli MurC, D and F, and identified five promising scaffolds that inhibited at least two of these ligases. Compounds 1, 2, 4 and 5 are multiple inhibitors of the whole MurC to MurF cascade that act in the micromolar range (IC50, 32–368 µM). NMR-assisted binding studies and steady-state kinetics studies performed on aza-stilbene derivative 1 showed, surprisingly, that it acts as a competitive inhibitor of MurD activity towards D-glutamic acid, and additionally, that its binding to the D-glutamic acid binding site is independent of the enzyme closure promoted by ATP.

Highlights

The increasing emergence of bacterial strains resistant to currently available antibiotics has created medical needs for antibacterial therapy that remain unmet today
There has been increasing interest in exploiting Mur ligases, the enzymes involved in the intracellular steps of the biosynthesis of peptidoglycan, an essential cell-wall polymer unique to prokaryotic cells (Figure 1)[5,6,7]
Mur ligases catalyse the formation of a peptide or amide bond between a uridine diphosphate N-acetylglucosamine (UDP)-substrate and a condensing amino acid

Summary

Introduction

The increasing emergence of bacterial strains resistant to currently available antibiotics has created medical needs for antibacterial therapy that remain unmet today. Despite large efforts in this area over recent decades, the introduction of mechanistically novel antibacterial agents into clinical practice has been a rarely achieved goal of antibacterial research[1,2,3,4] In this context, there has been increasing interest in exploiting Mur ligases, the enzymes involved in the intracellular steps of the biosynthesis of peptidoglycan, an essential cell-wall polymer unique to prokaryotic cells (Figure 1)[5,6,7]. Mur ligases catalyse the formation of a peptide or amide bond between a uridine diphosphate N-acetylglucosamine (UDP)-substrate and a condensing amino acid They operate through similar chemical mechanisms, and as shown for MurC and MurF, by an ordered kinetic mechanism[8,9]. The resulting tetrahedral high-energy intermediate collapses, with elimination of inorganic phosphate and concomitant formation of a peptide or amide bond

Methods

Results

Conclusion