title: Understanding the key factors that control the inhibition of type II dehydroquinase by (2R)-2-benzyl-3-dehydroquinic acids.
abstract: The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p-methoxybenzyl derivative 4 a, have been solved at 2.40 Å and 2.75 Å, respectively. This has allowed the resolution of the M. tuberculosis DHQ2 loop containing residues 20-25 for the first time. These structures show the key interactions of the aromatic ring in the active site of both enzymes and additionally reveal an important change in the conformation and flexibility of the loop that closes over substrate binding. The loop conformation and the binding mode of compounds 4 b-d has been also studied by molecular dynamics simulations, which suggest that the benzyl group of inhibitors 4 prevent appropriate orientation of the catalytic tyrosine of the loop for proton abstraction and disrupts its basicity.
authors.affiliation: Departamento de Química Orgánica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Peón
authors.forename: José M
authors.initials: JM
authors.lastname: Otero
authors.forename: Lorena
authors.initials: L
authors.lastname: Tizón
authors.forename: Verónica F V
authors.initials: VF
authors.lastname: Prazeres
authors.forename: Antonio L
authors.initials: AL
authors.lastname: Llamas-Saiz
authors.forename: Gavin C
authors.initials: GC
authors.lastname: Fox
authors.forename: Mark J
authors.initials: MJ
authors.lastname: van Raaij
authors.forename: Heather
authors.initials: H
authors.lastname: Lamb
authors.forename: Alastair R
authors.initials: AR
authors.lastname: Hawkins
authors.forename: Federico
authors.initials: F
authors.lastname: Gago
authors.forename: Luis
authors.initials: L
authors.lastname: Castedo
authors.forename: Concepción
authors.initials: C
authors.lastname: González-Bello
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry*; D016480:Helicobacter pylori / Q000201:enzymology; D006836:Hydro-Lyases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D017434:Protein Structure, Tertiary; D011801:Quinic Acid / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C474477:3-dehydroquinic acid; D004791:Enzyme Inhibitors; D011801:Quinic Acid; D006836:Hydro-Lyases; C020000:3-dehydroquinate dehydratase