1
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Zheng F, Hou S, Xue L, Yang W, Zhan CG. Human Butyrylcholinesterase Mutants for (-)-Cocaine Hydrolysis: A Correlation Relationship between Catalytic Efficiency and Total Hydrogen Bonding Energy with an Oxyanion Hole. J Phys Chem B 2023; 127:10723-10729. [PMID: 38063500 DOI: 10.1021/acs.jpcb.3c06392] [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: 12/22/2023]
Abstract
A combined computational and experimental study has been carried out to explore and test a quantitative correlation relationship between the relative catalytic efficiency (RCE) of human butyrylcholinesrase (BChE) mutant-catalyzed hydrolysis of substrate (-)-cocaine and the total hydrogen bonding energy (tHBE) of the carbonyl oxygen of the substrate with the oxyanion hole of the enzyme in the modeled transition-state structure (TS1), demonstrating a satisfactory linear correlation relationship between ln(RCE) and tHBE. The satisfactory correlation relationship has led us to computationally predict and experimentally confirm new human BChE mutants that have a further improved catalytic activity against (-)-cocaine, including the most active one (the A199S/F227S/S287G/A328W/Y332G mutant) with a 2790-fold improved catalytic efficiency (kcat/KM = 2.5 × 109 min-1 M-1) compared to the wild-type human BChE. Compared to the reference mutant (the A199S/S287G/A328W/Y332G mutant) tested in the reported clinical development of an enzyme therapy for cocaine dependence treatment, this new mutant (with a newly predicted additional F227S mutation) has an improved catalytic efficiency against (-)-cocaine by ∼2.6-fold. The good agreement between the computational and experimental ln(RCE) values suggests that the obtained correlation relationship is robust for computational prediction. A similar correlation relationship could also be explored in studying BChE or other serine hydrolases/esterases with an oxyanion hole stabilizing the carbonyl oxygen in the rate-determining reaction step of the enzymatic hydrolysis of other substrates.
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Affiliation(s)
- Fang Zheng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Shurong Hou
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Liu Xue
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Wenchao Yang
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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2
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Chen X, Deng X, Zhang Y, Wu Y, Yang K, Li Q, Wang J, Yao W, Tong J, Xie T, Hou S, Yao J. Computational Design and Crystal Structure of a Highly Efficient Benzoylecgonine Hydrolase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiabin Chen
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Xingyu Deng
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Yun Zhang
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Yanan Wu
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Kang Yang
- School of Biological Science and Technology University of Jinan Jinan 250022 China
| | - Qiang Li
- School of Biological Science and Technology University of Jinan Jinan 250022 China
| | - Jiye Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province Zhejiang Police College Hangzhou Zhejiang 310053 China
| | - Weixuan Yao
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province Zhejiang Police College Hangzhou Zhejiang 310053 China
| | - Junsen Tong
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Tian Xie
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Shurong Hou
- College of Pharmacy School of Medicine Hangzhou Normal University Hangzhou Zhejiang 311121 China
| | - Jianzhuang Yao
- School of Biological Science and Technology University of Jinan Jinan 250022 China
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3
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Chen X, Deng X, Zhang Y, Wu Y, Yang K, Li Q, Wang J, Yao W, Tong J, Xie T, Hou S, Yao J. Computational Design and Crystal Structure of a Highly Efficient Benzoylecgonine Hydrolase. Angew Chem Int Ed Engl 2021; 60:21959-21965. [PMID: 34351032 DOI: 10.1002/anie.202108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/26/2021] [Indexed: 11/05/2022]
Abstract
Benzoylecgonine (BZE) is the major toxic metabolite of cocaine and is responsible for the long-term cocaine-induced toxicity owing to its long residence time in humans. BZE is also the main contaminant following cocaine consumption. Here, we identified the bacterial cocaine esterase (CocE) as a BZE-metabolizing enzyme (BZEase), which can degrade BZE into biological inactive metabolites (ecgonine and benzoic acid). CocE was redesigned by a reactant-state-based enzyme design theory. An encouraging mutant denoted as BZEase2, presented a >400-fold improved catalytic efficiency against BZE compared with wild-type (WT) CocE. In vivo, a single dose of BZEase2 (1 mg kg-1 , IV) could eliminate nearly all BZE within only two minutes, suggesting the enzyme has the potential for cocaine overdose treatment and BZE elimination in the environment by accelerating BZE clearance. The crystal structure of a designed BZEase was also determined.
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Affiliation(s)
- Xiabin Chen
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Xingyu Deng
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Yun Zhang
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Yanan Wu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Kang Yang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiye Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Zhejiang Police College, Hangzhou, Zhejiang, 310053, China
| | - Weixuan Yao
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Zhejiang Police College, Hangzhou, Zhejiang, 310053, China
| | - Junsen Tong
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Shurong Hou
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Jianzhuang Yao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
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4
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Chen Q, Yu HL, Cheng X, Xu JH. Structural investigation of the enantioselectivity and thermostability mechanisms of esterase RhEst1. J Mol Graph Model 2018; 85:182-189. [DOI: 10.1016/j.jmgm.2018.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 12/27/2022]
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5
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Zhao X, Lu J, Wu L, Chen X. Efficient construction of 3-substituted-quinazolin-4(3H)-ones and theoretical investigation on the reaction pathways. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2017.1322085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Xinyun Zhao
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, P. R. China
| | - Juanfeng Lu
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, P. R. China
| | - Lamei Wu
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, P. R. China
| | - Xi Chen
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, P. R. China
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6
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Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
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Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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7
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Zhang Y, Huang X, Han K, Zheng F, Zhan CG. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations. Chem Biol Interact 2016; 259:142-147. [PMID: 27163853 DOI: 10.1016/j.cbi.2016.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 04/29/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022]
Abstract
The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental KM values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable.
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Affiliation(s)
- Yuxin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, PR China; Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Xiaoqin Huang
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, PR China
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA.
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8
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Wei D, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA). Org Biomol Chem 2016; 13:6857-65. [PMID: 26018983 DOI: 10.1039/c5ob00737b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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9
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Yao Y, Liu J, Zheng F, Zhan CG. Reaction Pathway for Cocaine Hydrolase-Catalyzed Hydrolysis of (+)-Cocaine. Theor Chem Acc 2016; 135. [PMID: 28250715 DOI: 10.1007/s00214-015-1788-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently designed and discovered cocaine hydrolase (CocH), engineered from human butyrylcholinesterase (BChE), has been proven promising as a novel enzyme therapy for treatment of cocaine overdose and addiction because it is highly efficient in catalyzing hydrolysis of naturally occurring (-)-cocaine. It has been known that the CocH also has a high catalytic efficiency against (+)-cocaine, a synthetic enantiomer of cocaine. Reaction pathway and the corresponding free energy profile for the CocH-catalyzed hydrolysis of (+)-cocaine have been determined, in the present study, by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Acordingt to the QM/MM-FE results, the catalytic hydrolysis process is initiated by the nucleophilic attack on carbonyl carbon of (-)-cocaine benzoyl ester via hydroxyl oxygen of S198 side chain, and the second reaction step (i.e. dissociation of benzoyl ester) is rate-determining. This finding for CocH-catalyzed hydrolysis of (+)-cocaine is remarkably different from that for the (+)-cocaine hydrolysis catalyzed by bacterial cocaine esterase in which the first reaction step of the deacylation is associated with the highest free energy barrier (~17.9 kcal/mol). The overall free energy barrier (~16.0 kcal/mol) calculated for the acylation stage of CocH-catalyzed hydrolysis of (+)-cocaine is in good agreement with the experimental free energy barrier of ~14.5 kcal/mol derivated from the experimental kinetic data.
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Affiliation(s)
- Yuan Yao
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; The Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P.R. China
| | - Junjun Liu
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; Tongji School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, P.R. China
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
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10
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Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding. J Mol Graph Model 2015; 62:319-324. [DOI: 10.1016/j.jmgm.2015.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 11/23/2022]
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11
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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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12
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Lu H, Huang X, AbdulHameed MDM, Zhan CG. Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations. Bioorg Med Chem 2014; 22:2149-56. [PMID: 24631364 PMCID: PMC4012391 DOI: 10.1016/j.bmc.2014.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 02/09/2014] [Accepted: 02/18/2014] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors.
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Affiliation(s)
- Haiting Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States
| | - Mohamed Diwan M AbdulHameed
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States.
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13
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Wei D, Fang L, Tang M, Zhan CG. Fundamental reaction pathway for peptide metabolism by proteasome: insights from first-principles quantum mechanical/molecular mechanical free energy calculations. J Phys Chem B 2013; 117:13418-34. [PMID: 24111489 DOI: 10.1021/jp405337v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteasome is the major component of the crucial non-lysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-O(γ). The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-O(γ), followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-N(z). Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-N(z) to Thr1-O(γ). According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3(b)) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally derived activation free energy of ∼18.3-19.4 kcal/mol, suggesting that the computational results are reasonable.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University , 75 Daxue Road, Zhengzhou, Henan 450052, China
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14
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Qiao Y, Han K, Zhan CG. Fundamental reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of heroin. Biochemistry 2013; 52:6467-79. [PMID: 23992153 DOI: 10.1021/bi400709v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pharmacological function of heroin requires an activation process that transforms heroin into 6-monoacetylmorphine (6-MAM), which is the most active form. The primary enzyme responsible for this activation process in human plasma is butyrylcholinesterase (BChE). The detailed reaction pathway of the activation process via BChE-catalyzed hydrolysis has been explored computationally, for the first time, in this study via molecular dynamics simulation and first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the whole reaction process includes acylation and deacylation stages. The acylation consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the 3-acetyl group of heroin by the hydroxyl oxygen of the Ser198 side chain and the dissociation of 6-MAM. The deacylation also consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate by a water molecule and the dissociation of the acetic acid from Ser198. The calculated free energy profile reveals that the second transition state (TS2) should be rate-determining. The structural analysis reveals that the oxyanion hole of BChE plays an important role in the stabilization of rate-determining TS2. The free energy barrier (15.9 ± 0.2 or 16.1 ± 0.2 kcal/mol) calculated for the rate-determining step is in good agreement with the experimentally derived activation free energy (~16.2 kcal/mol), suggesting that the mechanistic insights obtained from this computational study are reliable. The obtained structural and mechanistic insights could be valuable for use in the future rational design of a novel therapeutic treatment of heroin abuse.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science , Zhongshan Road 457, Dalian 116023, P. R. China
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Li D, Huang X, Lin J, Zhan CG. Catalytic mechanism of cytochrome P450 for N-methylhydroxylation of nicotine: reaction pathways and regioselectivity of the enzymatic nicotine oxidation. Dalton Trans 2013; 42:3812-20. [PMID: 23303461 DOI: 10.1039/c2dt32106h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fundamental reaction mechanism of cytochrome P450 2A6 (CYP2A6)-catalyzed N-methylhydroxylation of (S)-(-)-nicotine and the free energy profile have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical (QM/MM) reaction-coordinate calculations. In the CYP2A6-(S)-(-)-nicotine binding structures that allow for 5'-hydroxylation, the N-methyl group is also sufficiently close to the oxygen of Cpd I for the N-methylhydroxylation reaction to occur. It has been demonstrated that the CYP2A6-catalyzed N-methylhydroxylation reaction is a concerted process involving a hydrogen-transfer transition state on both the quartet and the doublet states. The N-methylhydroxylation reaction proceeds mainly in the doublet state, since the free energy barriers on the doublet state are lower than the corresponding ones on the quartet state. The calculated free energy barriers indicate that (S)-(-)-nicotine oxidation catalyzed by CYP2A6 proceeds with a high regioselective abstraction of the hydrogen at the 5'-position, rather than the hydrogen at the N-methyl group. The predicted regioselectivity of 93% is in agreement with the most recent experimentally reported regioselectivity of 95%. The binding mode of (S)-(-)-nicotine in the active site of CYP2A6 is an important determinant for the stereoselectivity of nicotine (S)-(-)-oxidation, whereas the regioselectivity of (S)-(-)-nicotine oxidation is determined mainly by the free energy barrier difference between the 5'-hydroxylation and N-methylhydroxylation reactions.
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Affiliation(s)
- Dongmei Li
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
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Wei D, Lei B, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile for inhibition of proteasome by Epoxomicin. J Am Chem Soc 2012; 134:10436-50. [PMID: 22697787 DOI: 10.1021/ja3006463] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to provide the first detailed computational study on the possible mechanisms for reaction of proteasome with a representative peptide inhibitor, Epoxomicin (EPX). The calculated results reveal that the most favorable reaction pathway consists of five steps. The first is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is nucleophilic attack on the carbonyl carbon of EPX by the negatively charged Thr1-O(γ) atom, followed by a proton transfer from Thr1-N(z) to the carbonyl oxygen of EPX (third step). Then, Thr1-N(z) attacks on the carbon of the epoxide group of EPX, accompanied by the epoxide ring-opening (S(N)2 nucleophilic substitution) such that a zwitterionic morpholino ring is formed between residue Thr1 and EPX. Finally, the product of morpholino ring is generated via another proton transfer. Noteworthy, Thr1-O(γ) can be activated directly by Thr1-N(z) to form the zwitterionic intermediate (with a free energy barrier of only 9.9 kcal/mol), and water cannot assist the rate-determining step, which is remarkably different from the previous perception that a water molecule should mediate the activation process. The fourth reaction step has the highest free energy barrier (23.6 kcal/mol) which is reasonably close to the activation free energy (∼21-22 kcal/mol) derived from experimental kinetic data. The obtained novel mechanistic insights should be valuable for not only future rational design of more efficient proteasome inhibitors but also understanding the general reaction mechanism of proteasome with a peptide or protein.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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Huang X, Zhao X, Zheng F, Zhan CG. Cocaine esterase-cocaine binding process and the free energy profiles by molecular dynamics and potential of mean force simulations. J Phys Chem B 2012; 116:3361-8. [PMID: 22385120 DOI: 10.1021/jp2111605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profiles for the binding process of (-)-cocaine interacting with wild-type cocaine esterase (CocE) and its mutants (T172R/G173Q and L119A/L169K/G173Q). According to the MD simulations, the general protein-(-)-cocaine binding mode is not affected by the mutations; e.g.. the benzoyl group of (-)-cocaine is always bound in a subsite composed of aromatic residues W151, W166, F261, and F408 and hydrophobic residue L407, while the carbonyl oxygen on the benzoyl group of (-)-cocaine is hydrogen-bonded with the oxyanion-hole residues Y44 and Y118. According to the PMF-calculated free energy profiles for the binding process, the binding free energies for (-)-cocaine with the wild-type, T172R/G173Q, and L119A/L169K/G173Q CocEs are predicted to be -6.4, -6.2, and -5.0 kcal/mol, respectively. The computational predictions are supported by experimental kinetic data, as the calculated binding free energies are in good agreement with the experimentally derived binding free energies, i.e., -7.2, -6.7, and -4.8 kcal/mol for the wild-type, T172R/G173Q, and L119A/L169K/G173Q, respectively. The reasonable agreement between the computational and experimental data suggests that the PMF simulations may be used as a valuable tool in new CocE mutant design that aims to decrease the Michaelis-Menten constant of the enzyme for (-)-cocaine.
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Affiliation(s)
- Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, USA
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