Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification With an Acrylamide Warhead

Molecules. 2019 Dec 30;25(1):147. doi: 10.3390/molecules25010147.

Abstract

Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.

Keywords: FBDD; HSQC; STD; acrylamide warhead; covalent inhibition; docking; glutaredoxin; trNOE.

Publication types

  • Comparative Study

MeSH terms

  • Acrylamide / chemistry*
  • Anti-Bacterial Agents / chemical synthesis*
  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry
  • Glutaredoxins / antagonists & inhibitors*
  • Glutaredoxins / chemistry
  • Humans
  • Kinetics
  • Lead / chemistry*
  • Models, Molecular
  • Molecular Docking Simulation
  • Molecular Structure
  • Nuclear Magnetic Resonance, Biomolecular
  • Pseudomonas aeruginosa / drug effects
  • Pseudomonas aeruginosa / enzymology*
  • Small Molecule Libraries / chemical synthesis*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology
  • Species Specificity
  • Structure-Activity Relationship

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Glutaredoxins
  • Small Molecule Libraries
  • Acrylamide
  • Lead