Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation

Jiansong Fang; Ping Wu; Ranyao Yang; Li Gao; Chao Li; Dongmei Wang; Song Wu; Ai-Lin Liu; Guan-Hua Du

doi:10.1016/j.apsb.2014.10.002

Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation

Acta Pharm Sin B. 2014 Dec;4(6):430-7. doi: 10.1016/j.apsb.2014.10.002. Epub 2014 Nov 22.

Authors

Jiansong Fang¹, Ping Wu¹, Ranyao Yang¹, Li Gao¹, Chao Li¹, Dongmei Wang¹, Song Wu², Ai-Lin Liu³, Guan-Hua Du³

Affiliations

¹ Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
² Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China ; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.
³ Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China ; Beijing Key Laboratory of Drug Target Research and Drug Screening, Beijing 100050, China ; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.

Abstract

In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds.

Keywords: ACh, acetylcholine; AChE, acetylcholinesterase; AChEIs, acetylcholinesterase inhibitors; AD, Alzheimer׳s disease; Acetylcholinesterase (AChE); BuChE, butyrylcholinesterase; BuSCh, S-butyrylthiocholine chloride; CAS, catalytic active site; DTNB, 5,5′-dithiobis-(2-nitrobenzoic acid); G1, 3-(4-methoxyphenyl)-7-(2-(piperidin-1-yl)ethoxy)-4H-chromen-4-one; G2, (S)-3-(4-methoxyphenyl)-7-(2-(2-methylpiperidin-1-yl)ethoxy)-4H-chromen-4-one; GAFF, generalized AMBER force field; Genistein derivatives; Kinetics analysis; MD, molecular dynamics; MM/GBSA; MM/GBSA, molecular mechanics/generalized born surface area; Molecular docking; Molecular dynamics simulation; PAS, peripheral anionic site; PDB, protein data bank; PME, particle mesh Ewald; RMSD, root-mean-square deviation; S-ACh, acetylthiocholine iodide; SASA, solvent accessible surface area; iso-OMPA, tetraisopropyl pyrophosphoramide; ΔEMM, gas-phase interaction energy between receptor and ligand; ΔEele, electrostatic energy contribution; ΔEvdw, van der Waals energy contribution; ΔGGB, polar desolvation energy term; ΔGSA, nonpolar desolvation energy term; ΔGexp, experimental binding free energy; ΔGpred, total binding free energy; ΔS, conformational entropy contribution.