title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
abstract: As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.
authors.affiliation: Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. dbegley@embios.com
authors.forename: Darren W
authors.initials: DW
authors.lastname: Begley
authors.forename: Robert C
authors.initials: RC
authors.lastname: Hartley
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Davies
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Edwards
authors.forename: Jess T
authors.initials: JT
authors.lastname: Leonard
authors.forename: Jan
authors.initials: J
authors.lastname: Abendroth
authors.forename: Courtney A
authors.initials: CA
authors.lastname: Burris
authors.forename: Janhavi
authors.initials: J
authors.lastname: Bhandari
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Myler
authors.forename: Bart L
authors.initials: BL
authors.lastname: Staker
authors.forename: Lance J
authors.initials: LJ
authors.lastname: Stewart
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D016957:Burkholderia pseudomallei / Q000201:enzymology*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D015195:Drug Design; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D019761:Phosphorus-Oxygen Lyases / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D019761:Phosphorus-Oxygen Lyases