title: IspE inhibitors identified by a combination of in silico and in vitro high-throughput screening.
abstract: CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens.
authors.affiliation: Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Naomi
authors.initials: N
authors.lastname: Tidten-Luksch
authors.forename: Raffaella
authors.initials: R
authors.lastname: Grimaldi
authors.forename: Leah S
authors.initials: LS
authors.lastname: Torrie
authors.forename: Julie A
authors.initials: JA
authors.lastname: Frearson
authors.forename: William N
authors.initials: WN
authors.lastname: Hunter
authors.forename: Ruth
authors.initials: R
authors.lastname: Brenk
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D045782:Hemiterpenes / Q000737:chemistry; D057166:High-Throughput Screening Assays; D006801:Humans; D008024:Ligands; D009943:Organophosphorus Compounds / Q000737:chemistry; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000037:antagonists & inhibitors* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D029968:Escherichia coli Proteins; D045782:Hemiterpenes; D008024:Ligands; D009943:Organophosphorus Compounds; C004809:isopentenyl pyrophosphate; D017853:Phosphotransferases (Alcohol Group Acceptor); C404502:IspE protein, E coli; D051357:Cyclin-Dependent Kinase 2