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Huang J, Xie X, Zheng Z, Ye L, Wang P, Xu L, Wu Y, Yan J, Yang M, Yan Y. De Novo Computational Design of a Lipase with Hydrolysis Activity towards Middle-Chained Fatty Acid Esters. Int J Mol Sci 2023; 24:ijms24108581. [PMID: 37239928 DOI: 10.3390/ijms24108581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Innovations in biocatalysts provide great prospects for intolerant environments or novel reactions. Due to the limited catalytic capacity and the long-term and labor-intensive characteristics of mining enzymes with the desired functions, de novo enzyme design was developed to obtain industrial application candidates in a rapid and convenient way. Here, based on the catalytic mechanisms and the known structures of proteins, we proposed a computational protein design strategy combining de novo enzyme design and laboratory-directed evolution. Starting with the theozyme constructed using a quantum-mechanical approach, the theoretical enzyme-skeleton combinations were assembled and optimized via the Rosetta "inside-out" protocol. A small number of designed sequences were experimentally screened using SDS-PAGE, mass spectrometry and a qualitative activity assay in which the designed enzyme 1a8uD1 exhibited a measurable hydrolysis activity of 24.25 ± 0.57 U/g towards p-nitrophenyl octanoate. To improve the activity of the designed enzyme, molecular dynamics simulations and the RosettaDesign application were utilized to further optimize the substrate binding mode and amino acid sequence, thus keeping the residues of theozyme intact. The redesigned lipase 1a8uD1-M8 displayed enhanced hydrolysis activity towards p-nitrophenyl octanoate-3.34 times higher than that of 1a8uD1. Meanwhile, the natural skeleton protein (PDB entry 1a8u) did not display any hydrolysis activity, confirming that the hydrolysis abilities of the designed 1a8uD1 and the redesigned 1a8uD1-M8 were devised from scratch. More importantly, the designed 1a8uD1-M8 was also able to hydrolyze the natural middle-chained substrate (glycerol trioctanoate), for which the activity was 27.67 ± 0.69 U/g. This study indicates that the strategy employed here has great potential to generate novel enzymes exhibiting the desired reactions.
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Affiliation(s)
- Jinsha Huang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoman Xie
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhen Zheng
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Luona Ye
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengbo Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ying Wu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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2
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Hassanzadeh P. Towards the quantum-enabled technologies for development of drugs or delivery systems. J Control Release 2020; 324:260-279. [DOI: 10.1016/j.jconrel.2020.04.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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3
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Ash T, Debnath T, Sarkar S, Gurey P, Das AK. Exploration of assisting behavior of molecular-MO2 (M = Ti, Zr) reagents towards the detoxication of tabun: A DFT study. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Arodola OA, Soliman MES. Quantum mechanics implementation in drug-design workflows: does it really help? Drug Des Devel Ther 2017; 11:2551-2564. [PMID: 28919707 PMCID: PMC5587087 DOI: 10.2147/dddt.s126344] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The pharmaceutical industry is progressively operating in an era where development costs are constantly under pressure, higher percentages of drugs are demanded, and the drug-discovery process is a trial-and-error run. The profit that flows in with the discovery of new drugs has always been the motivation for the industry to keep up the pace and keep abreast with the endless demand for medicines. The process of finding a molecule that binds to the target protein using in silico tools has made computational chemistry a valuable tool in drug discovery in both academic research and pharmaceutical industry. However, the complexity of many protein-ligand interactions challenges the accuracy and efficiency of the commonly used empirical methods. The usefulness of quantum mechanics (QM) in drug-protein interaction cannot be overemphasized; however, this approach has little significance in some empirical methods. In this review, we discuss recent developments in, and application of, QM to medically relevant biomolecules. We critically discuss the different types of QM-based methods and their proposed application to incorporating them into drug-design and -discovery workflows while trying to answer a critical question: are QM-based methods of real help in drug-design and -discovery research and industry?
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Affiliation(s)
- Olayide A Arodola
- Department of Pharmaceutical Chemistry, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud ES Soliman
- Department of Pharmaceutical Chemistry, University of KwaZulu-Natal, Durban, South Africa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Egypt
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5
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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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6
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Khavrutskii IV, Wallqvist A. β-Aminoalcohols as Potential Reactivators of Aged Sarin-/Soman-Inhibited Acetylcholinesterase. ChemistrySelect 2017. [DOI: 10.1002/slct.201601828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ilja V. Khavrutskii
- Department of Defense Biotechnology High Performance Computing Software Applications Institute; Telemedicine and Advanced Technology Research Center; United States Army Medical Research and Materiel Command; Fort Detrick, Maryland 21702 United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute; Telemedicine and Advanced Technology Research Center; United States Army Medical Research and Materiel Command; Fort Detrick, Maryland 21702 United States
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7
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Sun F, Ding J, Yu H, Gao R, Wang H, Pei C. Identification of new binding sites of human transferrin incubated with organophosphorus agents via Q Exactive LC–MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1022:256-264. [DOI: 10.1016/j.jchromb.2016.04.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/29/2016] [Accepted: 04/15/2016] [Indexed: 01/23/2023]
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8
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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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9
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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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10
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Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat Chem Biol 2014; 10:386-91. [PMID: 24705591 PMCID: PMC4048123 DOI: 10.1038/nchembio.1498] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/10/2014] [Indexed: 01/07/2023]
Abstract
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
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Affiliation(s)
- Sridharan Rajagopalan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Chu Wang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kai Yu
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alexandre P. Kuzin
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA
| | - Scott Lew
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | | | - Megan L. Matthews
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jayaraman Seetharaman
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Min Su
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - John. F. Hunt
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Sirin GS, Zhou Y, Lior-Hoffmann L, Wang S, Zhang Y. Aging mechanism of soman inhibited acetylcholinesterase. J Phys Chem B 2012; 116:12199-207. [PMID: 22984913 PMCID: PMC3475498 DOI: 10.1021/jp307790v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nervous system that hydrolyzes neurotransmitter acetylcholine (ACh) and terminates synaptic signals. The catalytic serine of AChE can be phosphonylated by soman, one of the most potent nerve agents, and subsequently undergo an aging reaction. This phosphonylation and aging process leads to irreversible AChE inhibition, results in accumulation of excess ACh at the synaptic clefts, and causes neuromuscular paralysis. 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 aging mechanism of soman phosphonylated AChE and determined its free energy profile. This aging reaction starts with the scission of the O2-Cα bond, which is followed by methyl migration, and results in a tertiary carbenium intermediate. At the transition state, the scissile O2-Cα bond is already cleaved with an average O-C distance of 3.2 ± 0.3 Å and the migrating methyl group is shared between Cα and Cβ carbons with C-C distances of 1.9 ± 0.1 and 1.8 ± 0.1 Å, respectively. The negatively charged phosphonate group is stabilized by a salt bridge with the imidazole ring of the catalytic histidine. A major product of aging, 2,3-dimethyl-2-butanol can be formed swiftly by the reaction of a water molecule. Our characterized mechanism and simulation results provide new detailed insights into this important biochemical process.
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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
- Department of Chemistry, New York University, New York, New York, 10003
| | - Yanzi Zhou
- Department of Chemistry, New York University, New York, New York, 10003
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Lee Lior-Hoffmann
- Department of Chemistry, New York University, New York, New York, 10003
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, New York, 10003
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York, 10003
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17
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Li Y, Du L, Hu Y, Sun X, Hu J. Theoretical study on the aging and reactivation mechanism of tabun-inhibited acetylcholinesterase by using the quantum mechanical / molecular mechanical method. CAN J CHEM 2012. [DOI: 10.1139/v2012-007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The organophosphorous compound tabun is highly neurotoxic because of its irreversible inhibition on acetylcholinesterase (AChE). It is wildly used as a warfare agent in the military. In this work, the aging and reactivation mechanism of tabun-inhibited AChE were studied by using the quantum mechanical / molecular mechanical (QM/MM) method. Geometry optimization of the stationary points were performed at the B3LYP/6–31G(d) level. Single-point energies were computed at the B3LYP/6–311++G(d,p) level. On the basis of the QM/MM results, a conclusion that the C–O bond scission is caused by water attack on the ethoxy group in the aging mechanism can be drawn. The reactivation process initialed by the antidotes CH2NO– or HLÖ-7 consists of three elemental steps, the nucleophilic attack on the P atom by the antidote, the dephosphorylation process, and the decomposition of the antidote–tabun complex. The highest energy barriers of the aging reaction, CH2NO–-induced reactivation, and HLÖ-7-induced reactivation are 19.9, 20.0, and 14.8 kcal/mol (1 cal = 4.184 J), respectively. The relative lower overall energy barrier of HLÖ-7-induced reactivation compared with that of the aging reaction indicates that HLÖ-7 is able to reactivate tabun-inhibited AChE. In addition, whether a newly designed antidote is able to reactivate tabun-inhibited AChE can be examined by the inequation X < 19.9 kcal/mol,where X means the highest energy barrier of the reactivation reaction of the newly designed antidote.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute, Shandong University, Jinan 250100, P.R. China
| | - Likai Du
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P.R. China
| | - Yueming Hu
- Environment Research Institute, Shandong University, Jinan 250100, P.R. China
| | - Xiaomin Sun
- Environment Research Institute, Shandong University, Jinan 250100, P.R. China
| | - Jingtian Hu
- Environment Research Institute, Shandong University, Jinan 250100, P.R. China
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18
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Peters J, Trovaslet M, Trapp M, Nachon F, Hill F, Royer E, Gabel F, van Eijck L, Masson P, Tehei M. Activity and molecular dynamics relationship within the family of human cholinesterases. Phys Chem Chem Phys 2012; 14:6764-70. [DOI: 10.1039/c2cp23817a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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X-ray crystallographic snapshots of reaction intermediates in the G117H mutant of human butyrylcholinesterase, a nerve agent target engineered into a catalytic bioscavenger. Biochem J 2011; 434:73-82. [PMID: 21091433 DOI: 10.1042/bj20101648] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OPs (organophosphylates) exert their acute toxicity through inhibition of acetylcholinesterase, by phosphylation of the catalytic serine residue. Engineering of human butyrylcholinesterase, by substitution of a histidine residue for the glycine residue at position 117, led to the creation of OP hydrolase activity. However, the lack of structural information and poor understanding of the hydrolytic mechanism of the G117H mutant has hampered further improvements in the catalytic activity. We have solved the crystallographic structure of the G117H mutant with a variety of ligands in its active site. A sulfate anion bound to the active site suggested the positioning for an OP prior to phosphylation. A fluoride anion was found in the active site when NaF was added to the crystallization buffer. In the fluoride complex, the imidazole ring from the His117 residue was substantially shifted, adopting a relaxed conformation probably close to that of the unliganded mutant enzyme. Additional X-ray structures were obtained from the transient covalent adducts formed upon reaction of the G117H mutant with the OPs echothiophate and VX [ethyl ({2-[bis(propan-2-yl)amino]ethyl}sulfanyl](methyl)phosphinate]. The position of the His117 residue shifted in response to the introduction of these adducts, overlaying the phosphylserine residue. These structural data suggest that the dephosphylation mechanism involves either a substantial conformational change of the His117 residue or an adjacent nucleophilic substitution by water.
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Beck JM, Hadad CM. Reaction profiles of the interaction between sarin and acetylcholinesterase and the S203C mutant: model nucleophiles and QM/MM potential energy surfaces. Chem Biol Interact 2010; 187:220-4. [PMID: 20156428 PMCID: PMC2894988 DOI: 10.1016/j.cbi.2010.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/28/2010] [Accepted: 02/08/2010] [Indexed: 11/19/2022]
Abstract
The phosphonylation mechanism of AChE and the S203C mutation by sarin (GB) is evaluated using two reaction schemes: a small model nucleophile (ethoxide, CH(3)CH(2)O(-)) and quantum mechanical/molecular mechanical (QM/MM) simulations. Calculations utilizing small model nucleophiles indicate that the reaction barrier for addition to GB is the rate-limiting step for both ethoxide and ethyl thiolate (CH(3)CH(2)S(-)); moreover, the activation barrier for addition to the phosphorus center of GB by ethyl thiolate is significantly larger (13.2 kcal/mol) than for ethoxide (8.3 kcal/mol). The decomposition transition state for both nucleophiles was determined to be approximately 1 kcal/mol. QM/MM simulations for AChE suggest a similar reaction mechanism for phosphonylation of the catalytic S203; however, the relative energetics are altered significantly compared to the isolated system. QM/MM results indicate that formation of the penta-coordinate intermediate is the rate-limiting step in the enzymatic system, with an activation barrier of 3.6 kcal/mol. Hydrogen-bonding interactions between the fluoride leaving group of GB with Y124 in AChE are observed throughout the reaction profile. The S203C mutation alters the relative energetics of the reaction, increasing the energy barrier for formation of the penta-coordinate intermediate to a value of 4.5 kcal/mol; moreover, the penta-coordinate intermediate (as product) is stabilized by an additional 6 kcal/mol when compared to wild-type AChE.
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Affiliation(s)
- Jeremy M. Beck
- Department of Chemistry, The Ohio State University, 100 West 18Avenue, Columbus, OH 43210, USA
| | - Christopher M. Hadad
- Department of Chemistry, The Ohio State University, 100 West 18Avenue, Columbus, OH 43210, USA
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Nachon F, Carletti E, Worek F, Masson P. Aging mechanism of butyrylcholinesterase inhibited by an N-methyl analogue of tabun: implications of the trigonal-bipyramidal transition state rearrangement for the phosphylation or reactivation of cholinesterases. Chem Biol Interact 2010; 187:44-8. [PMID: 20381476 DOI: 10.1016/j.cbi.2010.03.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/19/2010] [Accepted: 03/31/2010] [Indexed: 11/28/2022]
Abstract
Cholinesterases are the main target of organophosphorus nerve agents (OPs). Their inhibition results in cholinergic syndrome and death. The enzymes are inhibited by phosphylation of the catalytic serine enzyme, but can be reactivated by oximes to some extent. However, phosphylated cholinesterases undergo a side reaction that progressively prevents their reactivatability. This unimolecular reaction, termed "aging", has been investigated for decades. It was shown that most OP-ChE conjugates aged by O-dealkylation of an alkoxy substituent of the phosphorus atom, a mechanism involving the stabilization of a transient carbocation. In this paper we present structural data supporting a substitution-based mechanism for aging of the huBChE conjugate of an N-mono-methyl analogue of tabun. This mechanism involves an adjacent nucleophilic attack followed by Berry pseudorotation. A similar adjacent attack and subsequent rearrangement of the transition state have been recently proposed for tabun phosphylation of AChE. We suggest that a similar mechanism is also possible for oxime reactivation of phosphylated cholinesterases. This opens new perspectives in terms of reactivator design.
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Affiliation(s)
- Florian Nachon
- Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 38702 La Tronche Cedex, France.
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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