Challenges and Hallmarks of Establishing Alkylacetylphosphonates as Probes of Bacterial 1-Deoxy-d-xylulose 5-Phosphate Synthase

ACS Infect Dis. 2017 Jul 14;3(7):467-478. doi: 10.1021/acsinfecdis.6b00168. Epub 2017 Jun 21.


1-Deoxy-d-xylulose 5-phosphate (DXP) synthase catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate. DXP is at a metabolic branch point in bacteria, feeding into the methylerythritol phosphate pathway to indispensable isoprenoids and acting as a precursor for biosynthesis of essential cofactors in central metabolism, pyridoxal phosphate and ThDP, the latter of which is also required for DXP synthase catalysis. DXP synthase follows a unique random sequential mechanism and possesses an unusually large active site. These features have guided the design of sterically demanding alkylacetylphosphonates (alkylAPs) toward the development of selective DXP synthase inhibitors. alkylAPs studied here display selective, low μM inhibitory activity against DXP synthase. They are weak inhibitors of bacterial growth in standard nutrient rich conditions. However, bacteria are significantly sensitized to most alkylAPs in defined minimal growth medium, with minimal inhibitory concentrations (MICs) ranging from low μM to low mM and influenced by alkyl-chain length. The longest analog (C8) displays the weakest antimicrobial activity and is a substrate for efflux via AcrAB-TolC. The dependence of inhibitor potency on growth environment emphasizes the need for antimicrobial screening conditions that are relevant to the in vivo microbial microenvironment during infection. DXP synthase expression and thiamin supplementation studies offer support for DXP synthase as an intracellular target for some alkylAPs and reveal both the challenges and intriguing aspects of these approaches to study target engagement.

Keywords: 1-deoxy-d-xylulose 5-phosphate synthase; PLP biosynthesis; bacterial metabolic branch point; growth medium effect; isoprenoid biosynthesis; thiamin biosynthesis.

MeSH terms

  • Aldose-Ketose Isomerases / genetics
  • Aldose-Ketose Isomerases / metabolism
  • Anti-Bacterial Agents / chemical synthesis
  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / antagonists & inhibitors*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Catalytic Domain
  • Cloning, Molecular
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / pharmacology*
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Glyceraldehyde 3-Phosphate / metabolism
  • Microbial Sensitivity Tests
  • Organophosphonates / chemical synthesis
  • Organophosphonates / pharmacology*
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Pyridoxal Phosphate / metabolism
  • Pyruvic Acid / metabolism
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Thiamine Pyrophosphate / metabolism
  • Transferases / antagonists & inhibitors*
  • Transferases / genetics
  • Transferases / metabolism


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Enzyme Inhibitors
  • Organophosphonates
  • Recombinant Proteins
  • butylacetylphosphonate
  • Glyceraldehyde 3-Phosphate
  • Pyridoxal Phosphate
  • Pyruvic Acid
  • 1-deoxy-D-xylulose 5-phosphate reductoisomerase
  • Transferases
  • deoxyxylulose-5-phosphate synthase
  • Aldose-Ketose Isomerases
  • Thiamine Pyrophosphate