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.

Inhibition of Shikimate Kinase and Type II Dehydroquinase for Antibiotic Discovery: Structure-Based Design and Simulation Studies

“…8A and C) [49]. These crystal structures reveal that these compounds inhibit DHQ2 because their aromatic functional groups block the catalytic arrangement of the tyrosine and the arginine, i.e., it avoids the cation-π interaction between the guanidinium group of Arg17/Arg19 and the phenol group of the tyrosine side chain.…”

“…8C and D) [49,50]. In all cases, the essential Arg17 is expelled from the active site and faces away from the essential Tyr22.…”

“…In fact, this approach allowed the resolution of the M. tuberculosis loop containing residues 20-25 for the first time (Fig. 8A, PDB entry 2XB8, [49]). It is important to highlight that the 2R-substituted derivatives 28 still contain the axial hydrogen that could be removed by the essential tyrosine, the residue that triggers the dehydration reaction.…”

“…Thus, all of the inhibitors cause a dramatic reduction of the loop flexibility, albeit by a different mechanism ( Fig. 8C and D) [49,50]. For instance, the perfluorobenzyl derivative 27d causes the complete closure of the active site through the formation of a strong π -π stacking interaction with the aromatic ring of Tyr24 and a favorable electrostatic interaction with the guanidinium group of Arg19.…”

“…In particular, the aromatic moiety of 28b interacts with the catalytic tyrosine by π-stacking and, more importantly, expels the arginine sidechain from the active site. Moreover, MD simulations suggest that the benzyl groups of ligands 28 inactivate the enzyme by causing a significant conformational change of the substrate-covering loop and a dramatic reduction of its flexibility, which is essential for the function of the enzyme [49]. In fact, this approach allowed the resolution of the M. tuberculosis loop containing residues 20-25 for the first time (Fig.…”