title: Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors.
abstract: 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 η1coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2O, 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 Kivalue of ≈500 nm against Pseudomonas aeruginosa IspH.
authors.affiliation: Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: O'Dowd
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Williams
authors.affiliation: Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA.|Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
authors.forename: Hongxin
authors.initials: H
authors.lastname: Wang
authors.affiliation: Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA.
authors.forename: Joo Hwan
authors.initials: JH
authors.lastname: No
authors.affiliation: Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
authors.forename: Guodong
authors.initials: G
authors.lastname: Rao
authors.affiliation: Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA.
authors.forename: Weixue
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA.|Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA.|National Biomedical Computation Resource, University of California at San Diego, La Jolla, CA, 92093, USA.
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.affiliation: Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA.|Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Cramer
authors.affiliation: Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Oldfield
mesh_terms: D019295:Computational Biology; D004578:Electron Spin Resonance Spectroscopy; D004791:Enzyme Inhibitors / Q000378:metabolism*; D045782:Hemiterpenes / Q000378:metabolism*; D006801:Humans; D007501:Iron / Q000378:metabolism*; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D015394:Molecular Structure; D010755:Organophosphates / Q000378:metabolism*; D009943:Organophosphorus Compounds / Q000378:metabolism*; D011487:Protein Conformation; D013455:Sulfur / Q000378:metabolism*
chemical_list: C467061:4-hydroxy-3-methyl-2-butenyl diphosphate; D004791:Enzyme Inhibitors; D045782:Hemiterpenes; D007506:Iron-Sulfur Proteins; D010755:Organophosphates; D009943:Organophosphorus Compounds; C004809:isopentenyl pyrophosphate; D013455:Sulfur; D007501:Iron
keywords: HYSCORE; IspH; NRVS; in silico; isoprenoid