Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity

J Med Chem. 2020 Dec 10;63(23):14805-14820. doi: 10.1021/acs.jmedchem.0c01215. Epub 2020 Nov 19.

Abstract

UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of Lipid A, an essential component of the cell envelope of Gram-negative bacteria. The most advanced, disclosed LpxC inhibitors showing antibacterial activity coordinate zinc through a hydroxamate moiety with concerns about binding to other metalloenzymes. Here, we describe the discovery, optimization, and efficacy of two series of compounds derived from fragments with differing modes of zinc chelation. A series was evolved from a fragment where a glycine moiety complexes zinc, which achieved low nanomolar potency in an enzyme functional assay but poor antibacterial activity on cell cultures. A second series was based on a fragment that chelated zinc through an imidazole moiety. Structure-guided design led to a 2-(1S-hydroxyethyl)-imidazole derivative exhibiting low nanomolar inhibition of LpxC and a minimum inhibitory concentration (MIC) of 4 μg/mL against Pseudomonas aeruginosa, which is little affected by the presence of albumin.

MeSH terms

  • Amidohydrolases / antagonists & inhibitors*
  • Anilides / pharmacology
  • Anti-Bacterial Agents / chemical synthesis
  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / antagonists & inhibitors*
  • Chelating Agents / chemical synthesis
  • Chelating Agents / pharmacology*
  • Drug Discovery
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / pharmacology*
  • Escherichia coli / drug effects
  • Escherichia coli / enzymology
  • Imidazoles / pharmacology
  • Microbial Sensitivity Tests
  • Molecular Structure
  • Piperidines / pharmacology
  • Pseudomonas aeruginosa / drug effects
  • Pseudomonas aeruginosa / enzymology
  • Structure-Activity Relationship
  • Zinc / chemistry

Substances

  • Anilides
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Chelating Agents
  • Enzyme Inhibitors
  • Imidazoles
  • Piperidines
  • Amidohydrolases
  • UDP-3-O-acyl-N-acetylglucosamine deacetylase
  • Zinc