Reaction Pathway and Free Energy Profiles for Butyrylcholinesterase-catalyzed Hydrolysis of Acetylthiocholine

Overview

Journal Biochemistry

Specialty Biochemistry

Date 2012 Feb 7

PMID 22304234

Citations 17

Authors

Xi Chen

Lei Fang

Junjun Liu

Chang-Guo Zhan

Affiliations

Soon will be listed here.

Abstract

The catalytic mechanism for butyrylcholineserase (BChE)-catalyzed hydrolysis of acetylthiocholine (ATCh) has been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy (QM/MM-FE) calculations on both acylation and deacylation of BChE. Additional quantum mechanical (QM) calculations have been carried out, along with the QM/MM-FE calculations, to understand the known substrate activation effect on the enzymatic hydrolysis of ATCh. It has been shown that the acylation of BChE with ATCh consists of two reaction steps including the nucleophilic attack on the carbonyl carbon of ATCh and the dissociation of thiocholine ester. The deacylation stage includes nucleophilic attack of a water molecule on the carboxyl carbon of substrate and dissociation between the carboxyl carbon of substrate and hydroxyl oxygen of Ser198 side chain. QM/MM-FE calculation results reveal that the acylation of BChE is rate-determining. It has also been demonstrated that an additional substrate molecule binding to the peripheral anionic site (PAS) of BChE is responsible for the substrate activation effect. In the presence of this additional substrate molecule at PAS, the calculated free energy barrier for the acylation stage (rate-determining step) is decreased by ~1.7 kcal/mol. All of our computational predictions are consistent with available experimental kinetic data. The overall free energy barriers calculated for BChE-catalyzed hydrolysis of ATCh at regular hydrolysis phase and substrate activation phase are ~13.6 and ~11.9 kcal/mol, respectively, which are in reasonable agreement with the corresponding experimentally derived activation free energies of 14.0 kcal/mol (for regular hydrolysis phase) and 13.5 kcal/mol (for substrate activation phase).

Citing Articles

Chemical composition and biological activity of lemongrass volatile oil and n-Hexane extract: GC/MS analysis, in vitro and molecular modelling studies.

Aly S, Uba A, Nilofar N, Majrashi T, El Hassab M, Eldehna W PLoS One. 2025; 20(2):e0319147.

PMID: 39999113 PMC: 11856542. DOI: 10.1371/journal.pone.0319147.

A Comprehensive Review of Cholinesterase Modeling and Simulation.

De Boer D, Nguyen N, Mao J, Moore J, Sorin E Biomolecules. 2021; 11(4).

PMID: 33920972 PMC: 8071298. DOI: 10.3390/biom11040580.

The Preferable Binding Pose of Canonical Butyrylcholinesterase Substrates Is Unproductive for Echothiophate.

Zlobin A, Zalevsky A, Mokrushina Y, Kartseva O, Golovin A, Smirnov I Acta Naturae. 2019; 10(4):121-124.

PMID: 30713771 PMC: 6351040.

Catalytic Reaction Mechanism for Drug Metabolism in Human Carboxylesterase-1: Cocaine Hydrolysis Pathway.

Yao J, Chen X, Zheng F, Zhan C Mol Pharm. 2018; 15(9):3871-3880.

PMID: 30095924 PMC: 7737239. DOI: 10.1021/acs.molpharmaceut.8b00354.

Ensemble Molecular Dynamics of a Protein-Ligand Complex: Residual Inhibitor Entropy Enhances Drug Potency in Butyrylcholinesterase.

Sorin E, Alvarado W, Cao S, Radcliffe A, La P, An Y Bioenergetics. 2017; 6(1).

PMID: 28944107 PMC: 5608097. DOI: 10.4172/2167-7662.1000145.

References

Nemukhin A, Lushchekina S, Bochenkova A, Golubeva A, Varfolomeev S . Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. J Mol Model. 2008; 14(5):409-16. DOI: 10.1007/s00894-008-0287-y. View

Yang W, Pan Y, Zheng F, Cho H, Tai H, Zhan C . Free-energy perturbation simulation on transition states and redesign of butyrylcholinesterase. Biophys J. 2009; 96(5):1931-8. PMC: 2717303. DOI: 10.1016/j.bpj.2008.11.051. View

Zhang Y . Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. J Chem Phys. 2005; 122(2):024114. DOI: 10.1063/1.1834899. View

Shafferman A, Velan B, Ordentlich A, Kronman C, Grosfeld H, Leitner M . Substrate inhibition of acetylcholinesterase: residues affecting signal transduction from the surface to the catalytic center. EMBO J. 1992; 11(10):3561-8. PMC: 556814. DOI: 10.1002/j.1460-2075.1992.tb05439.x. View

Wiley K, Tormos J, Quinn D . A secondary isotope effect study of equine serum butyrylcholinesterase-catalyzed hydrolysis of acetylthiocholine. Chem Biol Interact. 2010; 187(1-3):124-7. PMC: 2912972. DOI: 10.1016/j.cbi.2010.05.007. View

Zhan C . Novel pharmacological approaches to treatment of drug overdose and addiction. Expert Rev Clin Pharmacol. 2010; 2(1):1-4. PMC: 2975360. DOI: 10.1586/17512433.2.1.1. View

Hamza A, Cho H, Tai H, Zhan C . Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants. J Phys Chem B. 2006; 109(10):4776-82. PMC: 2882242. DOI: 10.1021/jp0447136. View

Alvarez-Idaboy J, Galano A, Ruiz M . Rate constant dependence on the size of aldehydes in the NO(3) + aldehydes reaction. An explanation via quantum chemical calculations and CTST. J Am Chem Soc. 2001; 123(34):8387-95. DOI: 10.1021/ja010693z. View

Mesulam M, Guillozet A, Shaw P, Levey A, Duysen E, Lockridge O . Acetylcholinesterase knockouts establish central cholinergic pathways and can use butyrylcholinesterase to hydrolyze acetylcholine. Neuroscience. 2002; 110(4):627-39. DOI: 10.1016/s0306-4522(01)00613-3. View

10.

Liu J, Hamza A, Zhan C . Fundamental reaction mechanism and free energy profile for (-)-cocaine hydrolysis catalyzed by cocaine esterase. J Am Chem Soc. 2009; 131(33):11964-75. PMC: 2738781. DOI: 10.1021/ja903990p. View

11.

Pan Y, Gao D, Yang W, Cho H, Yang G, Tai H . Computational redesign of human butyrylcholinesterase for anticocaine medication. Proc Natl Acad Sci U S A. 2005; 102(46):16656-61. PMC: 1283827. DOI: 10.1073/pnas.0507332102. View

12.

Suarez D, Field M . Molecular dynamics simulations of human butyrylcholinesterase. Proteins. 2005; 59(1):104-17. DOI: 10.1002/prot.20398. View

13.

Suarez D, Diaz N, Fontecilla-Camps J, Field M . A computational study of the deacylation mechanism of human butyrylcholinesterase. Biochemistry. 2006; 45(24):7529-43. DOI: 10.1021/bi052176p. View

14.

Saxena A, Redman A, Jiang X, Lockridge O, Doctor B . Differences in active site gorge dimensions of cholinesterases revealed by binding of inhibitors to human butyrylcholinesterase. Biochemistry. 1997; 36(48):14642-51. DOI: 10.1021/bi971425+. View

15.

Brimijoin S, Gao Y, Anker J, Gliddon L, Lafleur D, Shah R . A cocaine hydrolase engineered from human butyrylcholinesterase selectively blocks cocaine toxicity and reinstatement of drug seeking in rats. Neuropsychopharmacology. 2008; 33(11):2715-25. PMC: 2562914. DOI: 10.1038/sj.npp.1301666. View

16.

Eriksson H, AUGUSTINSSON K . A mechanistic model for butyrylcholinesterase. Biochim Biophys Acta. 1979; 567(1):161-73. DOI: 10.1016/0005-2744(79)90183-9. View

17.

Cisneros G, Wang M, Silinski P, Fitzgerald M, Yang W . The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment. Biochemistry. 2004; 43(22):6885-92. DOI: 10.1021/bi049943p. View

18.

Gao D, Zhan C . Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase. Proteins. 2005; 62(1):99-110. PMC: 2882100. DOI: 10.1002/prot.20713. View

19.

Zhang Y, Kua J, McCammon J . Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc. 2002; 124(35):10572-7. DOI: 10.1021/ja020243m. View

20.

SantAnna C, Viana A, do Nascimento Junior N . A semiempirical study of acetylcholine hydrolysis catalyzed by Drosophila melanogaster acetylcholinesterase. Bioorg Chem. 2006; 34(2):77-89. DOI: 10.1016/j.bioorg.2006.01.002. View