Design and synthesis of substrate and intermediate analogue inhibitors of S-ribosylhomocysteinase

J Med Chem. 2006 May 18;49(10):3003-11. doi: 10.1021/jm060047g.

Abstract

S-Ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether linkage in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione, the precursor of autoinducer 2. Inhibitors of LuxS should interfere with bacterial interspecies communication and potentially provide a novel class of antibacterial agents. LuxS utilizes a divalent metal ion as a Lewis acid during catalysis. In this work, a series of structural analogues of the substrate SRH and a 2-ketone intermediate were designed and synthesized. Kinetic studies indicate that the compounds act as reversible, competitive inhibitors against LuxS, with the most potent inhibitors having K(I) values in the submicromolar range. These represent the most potent LuxS inhibitors that have been reported to date. Cocrystal structures of LuxS bound with two of the inhibitors largely confirmed the design principles, i.e., the importance of both the homocysteine and ribose moieties in high-affinity binding to the LuxS active site.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amides / chemical synthesis
  • Amides / chemistry
  • Anti-Bacterial Agents / chemical synthesis*
  • Anti-Bacterial Agents / chemistry
  • Bacillus subtilis / enzymology
  • Bacterial Proteins / antagonists & inhibitors*
  • Binding Sites
  • Butyrates / chemical synthesis
  • Butyrates / chemistry
  • Caproates / chemical synthesis
  • Caproates / chemistry
  • Caproates / pharmacology
  • Carbamates / chemical synthesis
  • Carbamates / chemistry
  • Carbon-Sulfur Lyases
  • Crystallography, X-Ray
  • Dioxolanes / chemical synthesis
  • Dioxolanes / chemistry
  • Dioxolanes / pharmacology
  • Drug Design
  • Homocysteine / analogs & derivatives*
  • Homocysteine / chemical synthesis
  • Homocysteine / chemistry
  • Models, Molecular
  • Stereoisomerism
  • Structure-Activity Relationship

Substances

  • Amides
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Butyrates
  • Caproates
  • Carbamates
  • Dioxolanes
  • S-ribosyl-L-homocysteine
  • Homocysteine
  • Carbon-Sulfur Lyases
  • LuxS protein, Bacteria

Associated data

  • PDB/2FQO
  • PDB/2FQT