Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens

Nat Microbiol. 2020 Jan;5(1):67-75. doi: 10.1038/s41564-019-0604-5. Epub 2019 Nov 18.


Gram-negative bacterial infections are a significant public health concern, and the lack of new drug classes for these pathogens is linked to the inability of most drug leads to accumulate inside Gram-negative bacteria1-7. Here, we report the development of a web application-eNTRyway-that predicts compound accumulation (in Escherichia coli) from its structure. In conjunction with structure-activity relationships and X-ray data, eNTRyway was utilized to re-design Debio-1452-a Gram-positive-only antibiotic8-into versions that accumulate in E. coli and possess antibacterial activity against high-priority Gram-negative pathogens. The lead compound Debio-1452-NH3 operates as an antibiotic via the same mechanism as Debio-1452, namely potent inhibition of the enoyl-acyl carrier protein reductase FabI, as validated by in vitro enzyme assays and the generation of bacterial isolates with spontaneous target mutations. Debio-1452-NH3 is well tolerated in vivo, reduces bacterial burden in mice and rescues mice from lethal infections with clinical isolates of Acinetobacter baumannii, Klebsiella pneumoniae and E. coli. This work provides tools for the facile discovery and development of high-accumulating compounds in E. coli, and a general blueprint for the conversion of Gram-positive-only compounds into broad-spectrum antibiotics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacokinetics
  • Anti-Bacterial Agents / pharmacology*
  • Benzofurans / chemistry
  • Benzofurans / pharmacokinetics
  • Benzofurans / pharmacology
  • Cell Line
  • Cell Survival / drug effects
  • Drug Discovery / methods*
  • Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) / antagonists & inhibitors*
  • Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) / genetics
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacokinetics
  • Enzyme Inhibitors / pharmacology*
  • Escherichia coli / drug effects
  • Escherichia coli / metabolism
  • Gram-Negative Bacteria / drug effects*
  • Gram-Negative Bacteria / metabolism
  • Gram-Negative Bacterial Infections / drug therapy
  • Humans
  • Mice
  • Microbial Sensitivity Tests
  • Pyrones / chemistry
  • Pyrones / pharmacokinetics
  • Pyrones / pharmacology
  • Software
  • Structure-Activity Relationship


  • API 1252
  • Anti-Bacterial Agents
  • Benzofurans
  • Enzyme Inhibitors
  • Pyrones
  • Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)