Understanding the key factors that control the inhibition of type II dehydroquinase by (2R)-2-benzyl-3-dehydroquinic acids.
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.
Peón
Antonio
A
Departamento de Química Orgánica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
Otero
José M
JM
Tizón
Lorena
L
Prazeres
Verónica F V
VF
Llamas-Saiz
Antonio L
AL
Fox
Gavin C
GC
van Raaij
Mark J
MJ
Lamb
Heather
H
Hawkins
Alastair R
AR
Gago
Federico
F
Castedo
Luis
L
González-Bello
Concepción
C
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
C474477:3-dehydroquinic acid; D004791:Enzyme Inhibitors; D011801:Quinic Acid; D006836:Hydro-Lyases; C020000:3-dehydroquinate dehydratase