Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors

Chembiochem. 2017 May 18;18(10):914-920. doi: 10.1002/cbic.201700052. Epub 2017 Apr 7.


Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.

Keywords: HYSCORE; IspH; NRVS; in silico; isoprenoid.

Publication types

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

MeSH terms

  • Computational Biology
  • Electron Spin Resonance Spectroscopy
  • Enzyme Inhibitors / metabolism*
  • Hemiterpenes / metabolism*
  • Humans
  • Iron / metabolism*
  • Iron-Sulfur Proteins / chemistry*
  • Iron-Sulfur Proteins / metabolism*
  • Models, Molecular
  • Molecular Structure
  • Organophosphates / metabolism*
  • Organophosphorus Compounds / metabolism*
  • Protein Conformation
  • Sulfur / metabolism*


  • 4-hydroxy-3-methyl-2-butenyl diphosphate
  • Enzyme Inhibitors
  • Hemiterpenes
  • Iron-Sulfur Proteins
  • Organophosphates
  • Organophosphorus Compounds
  • isopentenyl pyrophosphate
  • Sulfur
  • Iron