title: Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: observation of extensive dynamics in an enzyme/inhibitor complex.
abstract: The design, synthesis and characterization of a phosphonate inhibitor of N-acetylneuraminate-9-phosphate phosphatase (HDHD4) is described. Compound 3, where the substrate C-9 oxygen was replaced with a nonlabile CH2 group, inhibits HDHD4 with a binding affinity (IC50 11μM) in the range of the native substrate Neu5Ac-9-P (compound 1, Km 47μM). Combined SAR, modeling and NMR studies are consistent with the phosphonate group in inhibitor 3 forming a stable complex with native Mg(2+). In addition to this key interaction, the C-1 carboxylate of the sugar interacts with a cluster of basic residues, K141, R104 and R72. Comparative NMR studies of compounds 3 and 1 with Ca(2+) and Mg(2+) are indicative of a highly dynamic process in the active site for the HDHD4/Mg(2+)/3 complex. Possible explanations for this observation are discussed.
authors.affiliation: Bristol-Myers Squibb Research and Development, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534, USA. soonghoon.kim@bms.com
authors.forename: Soong-Hoon
authors.initials: SH
authors.lastname: Kim
authors.forename: Keith L
authors.initials: KL
authors.lastname: Constantine
authors.forename: Gerald J
authors.initials: GJ
authors.lastname: Duke
authors.forename: Valentina
authors.initials: V
authors.lastname: Goldfarb
authors.forename: John T
authors.initials: JT
authors.lastname: Hunt
authors.forename: Stephen
authors.initials: S
authors.lastname: Johnson
authors.forename: Kevin
authors.initials: K
authors.lastname: Kish
authors.forename: Herbert E
authors.initials: HE
authors.lastname: Klei
authors.forename: Patricia A
authors.initials: PA
authors.lastname: McDonnell
authors.forename: William J
authors.initials: WJ
authors.lastname: Metzler
authors.forename: Luciano
authors.initials: L
authors.lastname: Mueller
authors.forename: Michael A
authors.initials: MA
authors.lastname: Poss
authors.forename: Craig R
authors.initials: CR
authors.lastname: Fairchild
authors.forename: Rajeev S
authors.initials: RS
authors.lastname: Bhide
mesh_terms: D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D062105:Molecular Docking Simulation; D010744:Phosphoric Monoester Hydrolases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D051381:Rats; D012794:Sialic Acids / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism; D013403:Sugar Phosphates / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism
chemical_list: D004791:Enzyme Inhibitors; D012794:Sialic Acids; D013403:Sugar Phosphates; D010744:Phosphoric Monoester Hydrolases; C043518:N-acylneuraminate-9-phosphatase