Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity

J Med Chem. 2024 Oct 10;67(19):17363-17391. doi: 10.1021/acs.jmedchem.4c01262. Epub 2024 Sep 20.

Abstract

In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.

MeSH terms

  • Amidohydrolases* / antagonists & inhibitors
  • Amidohydrolases* / metabolism
  • Animals
  • Anti-Bacterial Agents* / chemical synthesis
  • Anti-Bacterial Agents* / chemistry
  • Anti-Bacterial Agents* / pharmacology
  • Enzyme Inhibitors* / chemical synthesis
  • Enzyme Inhibitors* / chemistry
  • Enzyme Inhibitors* / pharmacology
  • Humans
  • Hydroxamic Acids / chemical synthesis
  • Hydroxamic Acids / chemistry
  • Hydroxamic Acids / metabolism
  • Hydroxamic Acids / pharmacology
  • Microbial Sensitivity Tests
  • Molecular Docking Simulation*
  • Molecular Dynamics Simulation
  • Structure-Activity Relationship

Substances

  • Amidohydrolases
  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Hydroxamic Acids
  • LpxC deacetylase, Pseudomonas
  • UDP-3-O-acyl-N-acetylglucosamine deacetylase