Soluble epoxide hydrolase inhibitory components from Rheum undulatum and in silico approach

Abstract

Continuous efforts to identify sEH inhibitors using activity-guided fractionation have revealed 12 known compounds, 2-13, from Rheum undulatum. Compounds 2-13 and 1, which was obtained from the in-house library, were tested for inhibitory activity against sEH. Compounds 1-9, 11, and 12 were shown to have inhibitory activity, with IC 50 values ranging from 2.5 ± 0.5 to 53.2 ± 4.4 mM. They were subjected to enzyme kinetic studies to explore the binding mode between the ligand and receptor. Based on our results, compounds 1, 2, 5-9, and 11 (mixed type) and compounds 3 and 12 (noncompetitive type) had a preferred allosteric site. Compound 4 was identified as a competitive-type interaction in the active site. Molecular docking studies revealed the interacting residues and binding energy between sEH and inhibitors. Additionally, molecular dynamics provided detailed information on the interaction between the ligand and receptor.

Soluble Epoxide Hydrolase Inhibitory Activity of Components Isolated from Apios americana Medik

“…This study showed similar results with previous reports. The right pocket proved to be the position of sEH preferring the interaction with compounds, such as flavonoids, stilbene, and anthraquinone derivatives again [ 8 , 16 ].…”

“…Molecular dynamics revealed that the potential inhibitor ( 2 ) maintained a constant 3.5 Å distance fromVal416 of the receptor during the 10 ns simulation, and with Trp525 at about 2 ns. Resvertol, desoxyrhapontigenin, and rhapontigenin of stilbene are composed of hydrogen bonds with the Val416 residue in the right pocket [ 8 ]. Our findings were analyzed with compound 2 dependently moved according to the mobility of the loop containing Val416.…”

“…The sEH assay was performed as described previously [ 8 ]. Briefly, 130 µL of sEH in 25.0 mM Bis-Tris-HCl buffer (pH 7.0) and 20.0 µL of the compounds (1–0.06 mM concentration) diluted in MeOH, were added in 96-well plate, to which 50.0 µL of 20.0 µM PHOME was added in the mixture.…”

“…Soluble Epoxide Hydrolase (EC 3.3.2.10, sEH), one of the α/β hydrolase enzymes with a C-terminal domain of about 35 kDa, hydrolyzes the epoxide of four major isomers of eicosatrienoic acids (EETs), namely 5,6-EET, 8,9-EET, 11,12-EET, and 14,15-EET, from arachidonic acid [ 6 , 7 ]. The active site of sEH contains a catalytic triad composed of Asp333, Asp495, and His523 [ 8 ]. The Asp333 residue acts as a nucleophile leading to the bridge of the α-hydroxyl acyl-enzyme complex, and the Asp495/His523 residues with a water molecule participate in the conversion of the complex to the corresponding dihydrodiol [ 9 , 10 ].…”

“…To overcome these problems, the scientists researched to find new inhibitors form natural plants. They reported that biflavonoid, selaginellin, stilbene, and anthraquinone derivatives had inhibitory activity on sEH [ 6 , 7 , 8 , 11 ].…”