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Mu X, Yuan S, Zhang D, Lai R, Liao C, Li G. Selective modulation of alkali metal ions on acetylcholinesterase. Phys Chem Chem Phys 2023; 25:30308-30318. [PMID: 37934509 DOI: 10.1039/d3cp02887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Acetylcholinesterase (AChE) is an important hydrolase in cholinergic synapses and a candidate target in the treatment of Alzheimer's disease. The lithium treatment widely used in neurological disorders can alter the AChE activity, yet the underlying mechanism of how the ion species regulate the enzymatic activity remains unclear. In this work, we performed combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations and well-tempered metadynamics to understand the modulation of human AChE (hAChE) activity using three alkali metal ions (Li+, Na+, and K+) in different concentrations. Our simulations show that the binding affinity and catalytic activity are affected by different ion species through allosteric ion coordination geometries on the hAChE complex and distant electrostatic screening effect. A Li+ cluster involving D330, E393, and D397 residues and three Li+ ions was found to be highly conserved and can be critical to the enzyme activity. Binding energy calculations indicate that the electrostatic screening from allosterically bound cations can affect the key residues at the catalytic site and active-site gorge, including E199. Furthermore, an increase in ion concentration can lead to lower reactivity, especially for Li+ ions, which exhibit more cation-hAChE contacts than Na+ and K+. The selective ion binding and their preferred modulation on hAChE are highly related to ion species. This work provides a molecular perspective on selective modulation by different ion species of the enzyme catalytic processes.
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Affiliation(s)
- Xia Mu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Shengwei Yuan
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China
| | - Dinglin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Chenyi Liao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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2
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Semenov VE, Zueva IV, Lushchekina SV, Suleimanov EG, Gubaidullina LM, Shulaeva MM, Lenina OA, Petrov KA. Novel Uracil-Based Inhibitors of Acetylcholinesterase with Potency for Treating Memory Impairment in an Animal Model of Alzheimer's Disease. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227855. [PMID: 36431954 PMCID: PMC9694926 DOI: 10.3390/molecules27227855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Novel derivatives based on 6-methyluracil and condensed uracil, 2,4-quinazoline-2,4-dione, were synthesized with terminal meta- and para-benzoate moieties in polymethylene chains at the N atoms of the pyrimidine ring. In the synthesized compounds, the polymethylene chains were varied from having tris- to hexamethylene chains and quaternary ammonium groups; varying substituents (ester, salt, acid) at benzene ring were introduced into the chains and benzoate moieties. In vivo biological experiments demonstrated the potency of these compounds in decreasing the number of β-amyloid plaques and their suitability for the treatment of memory impairment in a transgenic model of Alzheimer's disease.
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Affiliation(s)
- Vyacheslav E. Semenov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
- Correspondence: (V.E.S.); (K.A.P.); Tel.: +7-843-279-47-09 (V.E.S.); +7-843-273-93-64 (K.A.P.)
| | - Irina V. Zueva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
| | | | - Eduard G. Suleimanov
- Alexander Butlerov Institute of Chemistry, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlyovskaya str. 18, Kazan 420008, Russia
| | - Liliya M. Gubaidullina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
| | - Marina M. Shulaeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
| | - Oksana A. Lenina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
| | - Konstantin A. Petrov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, Kazan 420088, Russia
- Alexander Butlerov Institute of Chemistry, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlyovskaya str. 18, Kazan 420008, Russia
- Correspondence: (V.E.S.); (K.A.P.); Tel.: +7-843-279-47-09 (V.E.S.); +7-843-273-93-64 (K.A.P.)
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3
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Gerbelli BB, Filho PLO, Cortez B, Sodré PT, Coutinho-Neto MD, Hamley IW, Seitsonen J, Alves WA. Interaction between glyphosate pesticide and amphiphilic peptides for colorimetric analysis. NANOSCALE ADVANCES 2022; 4:3592-3599. [PMID: 36134354 PMCID: PMC9400510 DOI: 10.1039/d2na00345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
The large-scale use of glyphosate pesticides in food production has attracted attention due to environmental damage and toxicity risks. Several regulatory authorities have established safe limits or concentrations of these pesticides in water and various food products consumed daily. The irreversible inhibition of acetylcholinesterase (AChE) activity is one of the strategies used for pesticide detection. Herein, we found that lipopeptide sequences can act as biomimetic microenvironments of AChE, showing higher catalytic activities than natural enzymes in an aqueous solution, based on IC50 values. These biomolecules contain in the hydrophilic part the amino acids l-proline (P), l-arginine (R), l-tryptophan (W), and l-glycine (G), covalently linked to a hydrophobic part formed by one or two long aliphatic chains. The obtained materials are referred to as compounds 1 and 2, respectively. According to fluorescence assays, 2 is more hydrophobic than 1. The circular dichroism (CD) data present a significant difference in the molar ellipticity values, likely related to distinct conformations assumed by the proline residue in the lipopeptide supramolecular structure in solution. The morphological aspect was further characterized using small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM), which showed that compounds 1 and 2 self-assembly into cylindrical and planar core-shell structures, respectively. The mimetic AchE behaviour of lipopeptides was confirmed by Ellman's hydrolysis reaction, where the proline residue in the peptides act as a nucleophilic scavenger of organophosphate pesticides. Moreover, the isothermal titration calorimetry (ITC) experiments revealed that host-guest interactions in both systems were dominated by enthalpically-driven thermodynamics. UV-vis kinetic experiments were performed to assess the inhibition of the lipopeptide catalytic activity and the IC50 values were obtained, and we found that the detection limit correlated with the increase in hydrophobicity of the lipopeptides, implying the micellization process is more favorable.
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Affiliation(s)
- Barbara B Gerbelli
- University of Reading, Department of Chemistry Reading UK
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas São Paulo SP Brazil
| | - Pedro L O Filho
- University of Copenhagen, Niels Bohr Institute Copenhagen Denmark
- Universidade de São Paulo, Instituto de Física São Paulo SP Brazil
| | - Bruna Cortez
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas São Paulo SP Brazil
| | - Pedro T Sodré
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas São Paulo SP Brazil
| | | | - Ian W Hamley
- University of Reading, Department of Chemistry Reading UK
| | - Jani Seitsonen
- Nanomicroscopy Center, Aalto University Puumiehenkuja 2 FIN-02150 Espoo Finland
| | - Wendel A Alves
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas São Paulo SP Brazil
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Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion. Nat Commun 2022; 13:1449. [PMID: 35304453 PMCID: PMC8933493 DOI: 10.1038/s41467-022-28938-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Glucuronoyl esterases (GEs) are α/β serine hydrolases and a relatively new addition in the toolbox to reduce the recalcitrance of lignocellulose, the biggest obstacle in cost-effective utilization of this important renewable resource. While biochemical and structural characterization of GEs have progressed greatly recently, there have yet been no mechanistic studies shedding light onto the rate-limiting steps relevant for biomass conversion. The bacterial GE OtCE15A possesses a classical yet distinctive catalytic machinery, with easily identifiable catalytic Ser/His completed by two acidic residues (Glu and Asp) rather than one as in the classical triad, and an Arg side chain participating in the oxyanion hole. By QM/MM calculations, we identified deacylation as the decisive step in catalysis, and quantified the role of Asp, Glu and Arg, showing the latter to be particularly important. The results agree well with experimental and structural data. We further calculated the free-energy barrier of post-catalysis dissociation from a complex natural substrate, suggesting that in industrial settings non-catalytic processes may constitute the rate-limiting step, and pointing to future directions for enzyme engineering in biomass utilization. Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
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Makhaeva GF, Elkina NA, Shchegolkov EV, Boltneva NP, Lushchekina SV, Serebryakova OG, Rudakova EV, Kovaleva NV, Radchenko EV, Palyulin VA, Burgart YV, Saloutin VI, Bachurin SO, Richardson RJ. Synthesis, molecular docking, and biological evaluation of 3-oxo-2-tolylhydrazinylidene-4,4,4-trifluorobutanoates bearing higher and natural alcohol moieties as new selective carboxylesterase inhibitors. Bioorg Chem 2019; 91:103097. [DOI: 10.1016/j.bioorg.2019.103097] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
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6
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Silva SG, da Costa RA, de Oliveira MS, da Cruz JN, Figueiredo PLB, Brasil DDSB, Nascimento LD, Chaves Neto AMDJ, de Carvalho Junior RN, Andrade EHDA. Chemical profile of Lippia thymoides, evaluation of the acetylcholinesterase inhibitory activity of its essential oil, and molecular docking and molecular dynamics simulations. PLoS One 2019; 14:e0213393. [PMID: 30849129 PMCID: PMC6407782 DOI: 10.1371/journal.pone.0213393] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
The essential oils of the fresh and dry flowers, leaves, branches, and roots of Lippia thymoides were obtained by hydrodistillation and analyzed using gas chromatography (GC) and GC-mass spectrometry (MS). The acetylcholinesterase inhibitory activity of the essential oil of fresh leaves was investigated on silica gel plates. The interactions of the key compounds with acetylcholinesterase were simulated by molecular docking and molecular dynamics studies. In total, 75 compounds were identified, and oxygenated monoterpenes were the dominant components of all the plant parts, ranging from 19.48% to 84.99%. In the roots, the main compounds were saturated and unsaturated fatty acids, having contents varying from 39.5% to 32.17%, respectively. In the evaluation of the anticholinesterase activity, the essential oils (detection limit (DL) = 0.1 ng/spot) were found to be about ten times less active than that of physostigmine (DL = 0.01ng/spot), whereas thymol and thymol acetate presented DL values each of 0.01 ng/spot, equivalent to that of the positive control. Based on the docking and molecular dynamics studies, thymol and thymol acetate interact with the catalytic residues Ser203 and His447 of the active site of acetylcholinesterase. The binding free energies (ΔGbind) for these ligands were -18.49 and -26.88 kcal/mol, demonstrating that the ligands are able to interact with the protein and inhibit their catalytic activity.
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Affiliation(s)
- Sebastião Gomes Silva
- Program of Post-Graduation in Chemistry, Federal University of Pará, Belém, PA, Brazil
| | | | - Mozaniel Santana de Oliveira
- LABEX/FEA (Faculty of Food Engineering), Program of Post-Graduation in Food Science and Technology, Federal University of Para, Belém, PA, Brazil
| | - Jorddy Neves da Cruz
- Laboratory of Preparation and Computation of Nanomaterials, Federal University of Pará, Belém, PA, Brazil
| | - Pablo Luis B. Figueiredo
- Program of Post-Graduation in Chemistry, Federal University of Pará, Belém, PA, Brazil
- Department of Natural Sciences, State University of Pará, Belém, PA, Brazil
| | | | - Lidiane Diniz Nascimento
- Program of Post-Graduation in Engineering of Natural Resources of Amazon, Federal University of Pará, Belém, PA, Brazil
- Adolpho Ducke Laboratory, Botany Coordinating, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Antônio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials, Federal University of Pará, Belém, PA, Brazil
- Program of Post-Graduation in Engineering of Natural Resources of Amazon, Federal University of Pará, Belém, PA, Brazil
| | - Raul Nunes de Carvalho Junior
- LABEX/FEA (Faculty of Food Engineering), Program of Post-Graduation in Food Science and Technology, Federal University of Para, Belém, PA, Brazil
- Program of Post-Graduation in Engineering of Natural Resources of Amazon, Federal University of Pará, Belém, PA, Brazil
- * E-mail:
| | - Eloisa Helena de Aguiar Andrade
- Program of Post-Graduation in Chemistry, Federal University of Pará, Belém, PA, Brazil
- Adolpho Ducke Laboratory, Botany Coordinating, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
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7
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Kots ED, Khrenova MG, Nemukhin AV, Varfolomeev SD. Aspartoacylase: a central nervous system enzyme. Structure, catalytic activity and regulation mechanisms. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Lushchekina S, Masson P. Catalytic bioscavengers against organophosphorus agents: mechanistic issues of self-reactivating cholinesterases. Toxicology 2018; 409:91-102. [DOI: 10.1016/j.tox.2018.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/21/2022]
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9
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Varfolomeev SD, Kots ED, Khrenova MG, Lushchekina SV, Nemukhin AV. Supercomputer technologies for structural-kinetic study of mechanisms of enzyme catalysis: A quantum-chemical description of aspartoacylase catalysis. DOKLADY PHYSICAL CHEMISTRY 2017. [DOI: 10.1134/s0012501617060045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Driant T, Nachon F, Ollivier C, Renard PY, Derat E. On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach. Chembiochem 2017; 18:666-675. [PMID: 28106328 DOI: 10.1002/cbic.201600646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Acetylcholinesterase (AChE), an enzyme of the serine hydrolase superfamily, is a mediator of signal transmission at cholinergic synapses by catalyzing acetylcholine cleavage into acetate and choline. This enzyme is vulnerable to covalent inhibition by organophosphate compounds (like VX). Covalent inhibition of AChE does not revert spontaneously. Known reactivator compounds have limited action in restoring catalytic activity. QM/MM simulations of VX-inhibited AChE reactivation by pralidoxime (2-PAM), a classical reactivator, were performed. These afforded a broad view of the effect of protonation states of active-site residues, and provide evidence for the role of Glu202, which needs to be protonated for reactivation to occur. In situ deprotonation of 2-PAM for both protonation states of Glu202 showed that His447 is able to deprotonate 2-PAM with the assistance of Glu202. Because the active site of serine hydrolases is highly conserved, this work provides new insights on the interplay between the catalytic triad residues and this glutamate, newly identified as protonatable.
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Affiliation(s)
- Thomas Driant
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91223, Brétigny-sur-Orge Cédex, France
| | - Cyril Ollivier
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Pierre-Yves Renard
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université Rouen-Normandie, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Etienne Derat
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
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11
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Molecular polymorphism of human enzymes as the basis of individual sensitivity to drugs. Supercomputer-assisted modeling as a tool for analysis of structural changes and enzymatic activity of proteins. Russ Chem Bull 2017. [DOI: 10.1007/s11172-016-1487-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Masson P, Lushchekina SV. Emergence of catalytic bioscavengers against organophosphorus agents. Chem Biol Interact 2016; 259:319-326. [DOI: 10.1016/j.cbi.2016.02.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 12/16/2015] [Accepted: 02/10/2016] [Indexed: 02/05/2023]
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13
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Fletcher TL, Popelier PLA. Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning. J Chem Theory Comput 2016; 12:2742-51. [DOI: 10.1021/acs.jctc.6b00457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timothy L. Fletcher
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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14
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Nemukhin AV, Kulakova AM, Lushchekina SV, Ermilov AY, Varfolomeev SD. Modeling chemical transformations at the active sites of cholinesterases by quantum-based simulations. ACTA ACUST UNITED AC 2016. [DOI: 10.3103/s0027131415060061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Kulakova A, Lushchekina S, Grigorenko B, Nemukhin A. Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Human butyrylcholinesterase (BChE) is a bioscavenger that protects the enzyme which is critical for the central nerve system, acetylcholinesterase, from poisoning by organophosphorus agents. Elucidating the details of the hydrolysis reaction mechanism is important to understand how the phosphorylated BChE can be reactivated. Application of the QM(DFTB)/MM(AMBER) method to construct the minimum energy pathways for the hydrolysis reaction of the diethylphosphorylated BChE allowed us to suggest a mechanism of reactivation of the wild-type and the G117H mutated enzyme. Unlike previous approaches assuming that either His438 or His117 serves as a general base in the catalysis, in our proposal the Glu197 residue is responsible for activation of the nucleophilic water molecule (Wat) leading to the chemical transformations that restore the catalytic Ser198 residue in BChE. In agreement with the experimental data, it is shown that the G117H mutation facilitates the reactivation of the inhibited enzyme.
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Affiliation(s)
- Anna Kulakova
- Chemistry Department, M. V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Sofya Lushchekina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russia
| | - Bella Grigorenko
- Chemistry Department, M. V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russia
| | - Alexander Nemukhin
- Chemistry Department, M. V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russia
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16
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Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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17
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Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC, Nandan SR, Pissurlenkar RR. Quantifying ligand–receptor interactions for gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. J Biomol Struct Dyn 2014; 33:1107-25. [DOI: 10.1080/07391102.2014.931824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Sirin GS, Zhang Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J Phys Chem A 2014; 118:9132-9. [PMID: 24786171 PMCID: PMC4183371 DOI: 10.1021/jp502712d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Acetylcholinesterase (AChE) is a
crucial enzyme in the cholinergic
nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic
signals by reducing the effective concentration of ACh in the synaptic
clefts. Organophosphate compounds irreversibly inhibit AChEs, leading
to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella
sampling, a state-of-the-art approach to simulate enzyme reactions,
we have characterized the covalent inhibition mechanism between AChE
and the nerve toxin soman and determined its free energy profile for
the first time. Our results indicate that phosphonylation of the catalytic
serine by soman employs an addition–elimination mechanism,
which is highly associative and stepwise: in the initial addition
step, which is also rate-limiting, His440 acts as a general base to
facilitate the nucleophilic attack of Ser200 on the soman’s
phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate;
in the subsequent elimination step, Try121 of the catalytic gorge
stabilizes the leaving fluorine atom prior to its dissociation from
the active site. Together with our previous characterization of the
aging mechanism of soman inhibited AChE, our simulations have revealed
detailed molecular mechanistic insights into the damaging function
of the nerve agent soman.
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Affiliation(s)
- Gulseher Sarah Sirin
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine , New York, New York 10016, United States
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19
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Silva NNS, Silva JRA, Alves CN, Andrade EHA, da Silva JKR, Maia JGS. Acetylcholinesterase Inhibitory Activity and Molecular Docking Study of 1-Nitro-2-Phenylethane, the Main Constituent ofAniba canelillaEssential Oil. Chem Biol Drug Des 2014; 84:192-8. [DOI: 10.1111/cbdd.12304] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 12/11/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Nayla N. S. Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas; Universidade Federal do Pará; Belém PA 66075-970 Brazil
| | - José R. A. Silva
- Programa de Pós-Graduação em Química; Universidade Federal do Pará; Belém PA 66075-970 Brazil
| | - Claudio N. Alves
- Programa de Pós-Graduação em Química; Universidade Federal do Pará; Belém PA 66075-970 Brazil
| | - Eloisa H. A. Andrade
- Programa de Pós-Graduação em Química; Universidade Federal do Pará; Belém PA 66075-970 Brazil
| | - Joyce K. R. da Silva
- Programa de Pós-Graduação em Biotecnologia; Universidade Federal do Pará; Belém PA 66075-970 Brazil
| | - José G. S. Maia
- Programa de Pós-Graduação em Ciências Farmacêuticas; Universidade Federal do Pará; Belém PA 66075-970 Brazil
- Programa de Pós-Graduação em Química; Universidade Federal do Pará; Belém PA 66075-970 Brazil
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20
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Lushchekina SV, Nemukhin AV, Varfolomeev SD, Masson P. Molecular modeling evidence for His438 flip in the mechanism of butyrylcholinesterase hysteretic behavior. J Mol Neurosci 2013; 52:434-45. [PMID: 24310732 DOI: 10.1007/s12031-013-0178-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/07/2013] [Indexed: 11/24/2022]
Abstract
Cholinesterases display a hysteretic behavior with certain substrates and irreversible inhibitors. For years, this behavior has remained puzzling. However, several lines of evidence indicated that it is caused by perturbation of the catalytic triad and its water environment. In the present study, using molecular dynamics simulations of Ala328Cys BuChE mutant and wild-type BuChE in the absence and presence of a co-solvent (sucrose, glycerol), we provide evidence that hysteresis originates in a flip of the catalytic triad histidine (His438). This event is controlled by water molecules that interact with active site residues. The physiological significance of this phenomenon is still an issue.
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Affiliation(s)
- Sofya V Lushchekina
- Computer Modeling of Biomolecular Systems Lab, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina St., 119334, Moscow, Russia,
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21
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Bennion BJ, Lau EY, Fattebert JL, Huang P, Schwegler E, Corning W, Lightstone FC. MODELING THE BINDING OF CWAs TO AChE AND BuChE. ACTA ACUST UNITED AC 2013. [DOI: 10.31482/mmsl.2013.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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23
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On quantum mechanical – molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase. Chem Biol Interact 2013; 203:51-6. [DOI: 10.1016/j.cbi.2012.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/29/2012] [Accepted: 08/31/2012] [Indexed: 11/20/2022]
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24
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Rozengart EV, Basova NE, Moralev SN, Lushchekina SV, Masson P, Varfolomeev SD. Research on cholinesterases in the Soviet Union and Russia: A historical perspective. Chem Biol Interact 2013; 203:3-9. [DOI: 10.1016/j.cbi.2013.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Polyakov IV, Grigorenko BL, Moskovsky AA, Pentkovski VM, Nemukhin AV. Towards quantum-based modeling of enzymatic reaction pathways: Application to the acetylholinesterase catalysis. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC. First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans? J Biomol Struct Dyn 2012; 30:546-58. [DOI: 10.1080/07391102.2012.687521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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27
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Quantum mechanical/molecular mechanical analysis of mechanisms of enzyme action. Human acetylcholinesterase. Russ Chem Bull 2012. [DOI: 10.1007/s11172-011-0338-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Chen X, Fang L, Liu J, Zhan CG. Reaction pathway and free energy profiles for butyrylcholinesterase-catalyzed hydrolysis of acetylthiocholine. Biochemistry 2012; 51:1297-305. [PMID: 22304234 DOI: 10.1021/bi201786s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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).
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Affiliation(s)
- Xi Chen
- Key Laboratory of Pesticide & Chemical Biology of the Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
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29
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Chen X, Fang L, Liu J, Zhan CG. Reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of acetylcholine. J Phys Chem B 2010; 115:1315-22. [PMID: 21175195 DOI: 10.1021/jp110709a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A catalytic mechanism for the butyrylcholinesterase (BChE)-catalyzed hydrolysis of acetylcholine (ACh) has been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy calculations on both acylation and deacylation of BChE. It has been shown that the acylation with ACh includes two reaction steps, including nucleophilic attack on the carbonyl carbon of ACh and dissociation of choline ester. The deacylation stage includes nucleophilic attack of a water molecule on the carboxyl carbon of the substrate and dissociation between the carboxyl carbon of the substrate and the hydroxyl oxygen of the Ser198 side chain. Notably, despite the fact that acetylcholinesterase (AChE) and BChE are very similar enzymes, the acylation of BChE with ACh is rate-determining, which is remarkably different from the AChE-catalyzed hydrolysis of ACh, in which the deacylation is rate-determining. The computational prediction is consistent with available experimental kinetic data. The overall free energy barrier calculated for BChE-catalyzed hydrolysis of ACh is 13.8 kcal/mol, which is in good agreement with the experimentally derived activation free energy of 13.3 kcal/mol.
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Affiliation(s)
- Xi Chen
- Key Laboratory of Pesticide & Chemical Biology of the Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P R China
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30
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Zhou Y, Wang S, Zhang Y. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J Phys Chem B 2010; 114:8817-25. [PMID: 20550161 DOI: 10.1021/jp104258d] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
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31
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Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies. Chem Biol Interact 2010; 187:59-63. [DOI: 10.1016/j.cbi.2010.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/26/2010] [Accepted: 04/06/2010] [Indexed: 11/22/2022]
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32
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Del Carlo M, Compagnone D. Recent strategies for the biological sensing of pesticides: from the design to the application in real samples. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s12566-010-0012-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Modeling of the mechanism of hydrolysis of succinylcholine in the active site of native and modified (Asp70Gly) human butyrylcholinesterase. Russ Chem Bull 2010. [DOI: 10.1007/s11172-010-0044-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Kwasnieski O, Verdier L, Malacria M, Derat E. Fixation of the two Tabun isomers in acetylcholinesterase: a QM/MM study. J Phys Chem B 2009; 113:10001-7. [PMID: 19569635 DOI: 10.1021/jp903843s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dysfunction of acetylcholinesterase (AChE) due to inhibition by organophosphorus (OP) compounds is a major threat since AChE is a key enzyme in neurotransmission. To more rigorously design reactivation agents, it is of prime importance to understand the mechanism of inhibition of AChE by OP compounds. Tabun is one of the more potent nerve agents. It is produced as a mixture of two enantiomers, one of them (the levorotatory isomer) being 6.3 times more potent. Could it be that the inhibition mechanism is different for the two enantiomers? To address this critical issue, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) methodology. Calculations were performed using BP86 functional and TZVP basis set. Single points were also done with B3LYP and PBE0 functionals. We studied the four possible attacks of tabun on the oxygen of Ser203 using two crystallographic structures (PDB codes 2C0P and 3DL7): (S) tabun with the cyano group syn to the oxygen of Ser203 and (R) tabun with the cyano group anti, corresponding to the experimental X-ray structure; (S) tabun with the cyano group anti to the oxygen of Ser203 and (R) tabun with the cyano group syn, leading to a different isomer than was experimentally seen. We found that the most active enantiomer is (S) tabun with the cyano group syn to the oxygen of Ser203. Thus it seems that the cyano group does not leave anti to the oxygen of Ser203 due to repulsive polar interactions between cyanide and aromatic residues in the active site.
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Affiliation(s)
- Ophélie Kwasnieski
- Institut de chimie moléculaire, UMR CNRS 7201, UPMC University Paris 06, C. 229, 4 place Jussieu, 75005 Paris, France
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35
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Delfino RT, Figueroa-Villar JD. Nucleophilic Reactivation of Sarin-Inhibited Acetylcholinesterase: A Molecular Modeling Study. J Phys Chem B 2009; 113:8402-11. [DOI: 10.1021/jp810686k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Reinaldo T. Delfino
- Seção de Engenharia Química, Instituto Militar de Engenharia, Praça Gen Tibúrcio, 80, Praia Vermelha, 22290-070, Rio de Janeiro - RJ, Brazil
| | - José D. Figueroa-Villar
- Seção de Engenharia Química, Instituto Militar de Engenharia, Praça Gen Tibúrcio, 80, Praia Vermelha, 22290-070, Rio de Janeiro - RJ, Brazil
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36
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Lushchekina SV, Nemukhin AV, Morozov DI, Varfolomeev SD. Quantum chemical justification of the specificity of enzyme catalysis: Correlations between the rate of enzyme catalysis by acetylcholinesterase and substrate structure. DOKLADY PHYSICAL CHEMISTRY 2009. [DOI: 10.1134/s0012501609050054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Molecular polymorphism of human enzymes: New biotechnological and instrumental platforms for diagnostics and individual medicine. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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