title: Identification of B. anthracis N(5)-carboxyaminoimidazole ribonucleotide mutase (PurE) active site binding compounds via fragment library screening.
abstract: The de novo purine biosynthesis pathway is an attractive target for antibacterial drug design, and PurE from this pathway has been identified to be crucial for Bacillus anthracis survival in serum. In this study we adopted a fragment-based hit discovery approach, using three screening methods-saturation transfer difference nucleus magnetic resonance (STD-NMR), water-ligand observed via gradient spectroscopy (WaterLOGSY) NMR, and surface plasmon resonance (SPR), against B. anthracis PurE (BaPurE) to identify active site binding fragments by initially testing 352 compounds in a Zenobia fragment library. Competition STD NMR with the BaPurE product effectively eliminated non-active site binding hits from the primary hits, selecting active site binders only. Binding affinities (dissociation constant, KD) of these compounds varied between 234 and 301μM. Based on test results from the Zenobia compounds, we subsequently developed and applied a streamlined fragment screening strategy to screen a much larger library consisting of 3000 computationally pre-selected fragments. Thirteen final fragment hits were confirmed to exhibit binding affinities varying from 14μM to 700μM, which were categorized into five different basic scaffolds. All thirteen fragment hits have ligand efficiencies higher than 0.30. We demonstrated that at least two fragments from two different scaffolds exhibit inhibitory activity against the BaPurE enzyme.
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Lei
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Jones
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA.
authors.forename: Tian
authors.initials: T
authors.lastname: Zhu
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA.
authors.forename: Kavankumar
authors.initials: K
authors.lastname: Patel
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, USA.
authors.forename: Nina M
authors.initials: NM
authors.lastname: Wolf
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, USA.
authors.forename: Leslie W-M
authors.initials: LW
authors.lastname: Fung
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA. Electronic address: danielhl@uic.edu.
authors.forename: Hyun
authors.initials: H
authors.lastname: Lee
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland Ave., IL 60607, USA. Electronic address: mjohnson@uic.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Johnson
mesh_terms: D001408:Bacillus anthracis / Q000201:enzymology*; D020134:Catalytic Domain / Q000187:drug effects; D004305:Dose-Response Relationship, Drug; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D057166:High-Throughput Screening Assays; D019751:Intramolecular Transferases / Q000037:antagonists & inhibitors* / Q000302:isolation & purification / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D015394:Molecular Structure; D054852:Small Molecule Libraries / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D020349:Surface Plasmon Resonance
chemical_list: D004791:Enzyme Inhibitors; D054852:Small Molecule Libraries; D019751:Intramolecular Transferases; C498062:N(5)-carboxyaminoimidazole ribonucletide mutase
keywords: Bacillus anthracis; Fragment library screening; NMR; PurE; SPR