1
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Fındık BK, Cilesiz U, Bali SK, Atilgan C, Aviyente V, Dedeoglu B. Investigation of iron release from the N- and C-lobes of human serum transferrin by quantum chemical calculations. Org Biomol Chem 2022; 20:8766-8774. [DOI: 10.1039/d2ob01518h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cluster models of iron binding sites of the N- and C-lobes highlights the inequivalence of each lobe in iron release.
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Affiliation(s)
- Basak Koca Fındık
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Umut Cilesiz
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Semiha Kevser Bali
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı-Tuzla, Istanbul, 34956, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Burcu Dedeoglu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey
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2
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Bzówka M, Mitusińska K, Hopko K, Góra A. Computational insights into the known inhibitors of human soluble epoxide hydrolase. Drug Discov Today 2021; 26:1914-1921. [PMID: 34082135 DOI: 10.1016/j.drudis.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023]
Abstract
Human soluble epoxide hydrolase (hsEH) is involved in the hydrolysis of epoxyeicosatrienoic acids (EETs), which have potent anti-inflammatory properties. Given that EET conversion generates nonbioactive molecules, inhibition of this enzyme would be beneficial. Past decades of work on hsEH inhibitors resulted in numerous potential compounds, of which a hundred hsEH-ligand complexes were crystallized and deposited in the Protein Data Bank (PDB). We analyzed all deposited hsEH-ligand complexes to gain insight into the binding of inhibitors and to provide feedback on the future drug design processes. We also reviewed computationally driven strategies that were used to propose novel hsEH inhibitors.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland; Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, ul. Krzywoustego 4, Faculty of Chemistry, Silesian University of Technology, Gliwice 44-100, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Katarzyna Hopko
- Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland.
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4
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Stojanovski G, Dobrijevic D, Hailes HC, Ward JM. Identification and catalytic properties of new epoxide hydrolases from the genomic data of soil bacteria. Enzyme Microb Technol 2020; 139:109592. [PMID: 32732040 PMCID: PMC7429986 DOI: 10.1016/j.enzmictec.2020.109592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/07/2020] [Accepted: 05/07/2020] [Indexed: 11/25/2022]
Abstract
Epoxide hydrolases (EHs) catalyse the conversion of epoxides into vicinal diols. These enzymes have extensive value in biocatalysis as they can generate enantiopure epoxides and diols which are important and versatile synthetic intermediates for the fine chemical and pharmaceutical industries. Despite these benefits, they have seen limited use in the bioindustry and novel EHs continue to be reported in the literature. We identified twenty-nine putative EHs within the genomes of soil bacteria. Eight of these EHs were explored in terms of their activity. Two limonene epoxide hydrolases (LEHs) and one ⍺/β EH were active on a model compound styrene oxide and its ring-substituted derivatives, with low to good percentage conversions of 18-86%. Further exploration of the substrate scope with enantiopure (R)-styrene oxide and (S)-styrene oxide, showed different epoxide ring opening regioselectivities. Two enzymes, expressed from plasmids pQR1984 and pQR1990 de-symmetrised the meso-epoxide cyclohexene oxide, forming the (R,R)-diol with high enantioselectivity. Two LEHs, from plasmids pQR1980 and pQR1982 catalysed the hydrolysis of (+) and (-) limonene oxide, with diastereomeric preference for the (1S,2S,4R)- and (1R,2R,4S)-diol products, respectively. The enzyme from plasmid pQR1982 had a good substrate scope for a LEH, being active towards styrene oxide, its analogues, cyclohexene oxide and 1,2-epoxyhexane in addition to (±)-limonene oxide. The enzymes from plasmids pQR1982 and pQR1984 had good substrate scopes and their enzymatic properties were characterised with respect to styrene oxide. They had comparable temperature optima and pQR1984 had 70% activity in the presence of 40% of the green solvent MeOH, a useful property for bio-industrial applications. Overall, this study has provided novel EHs with potential value in industrial biocatalysis.
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Affiliation(s)
- Gorjan Stojanovski
- Department of Biochemical Engineering, University College London, Bernard Katz, London WC1E 6BT, UK.
| | - Dragana Dobrijevic
- Department of Biochemical Engineering, University College London, Bernard Katz, London WC1E 6BT, UK.
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - John M Ward
- Department of Biochemical Engineering, University College London, Bernard Katz, London WC1E 6BT, UK.
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5
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Sheng X, Kazemi M, Planas F, Himo F. Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
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6
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Mitusińska K, Raczyńska A, Bzówka M, Bagrowska W, Góra A. Applications of water molecules for analysis of macromolecule properties. Comput Struct Biotechnol J 2020; 18:355-365. [PMID: 32123557 PMCID: PMC7036622 DOI: 10.1016/j.csbj.2020.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/26/2020] [Accepted: 02/01/2020] [Indexed: 01/12/2023] Open
Abstract
Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly via a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties. Here, we present a list of several software programs that use the information provided by water molecules to: i) analyse protein structures and provide the optimal positions of water molecules for protein hydration, ii) identify high-occupancy water sites in order to analyse ligand binding modes, and iii) detect and describe tunnels and cavities. The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on the functionality, transportation network and location of functionally relevant residues. Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.
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Affiliation(s)
| | | | | | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
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7
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Abis G, Charles RL, Kopec J, Yue WW, Atkinson RA, Bui TTT, Lynham S, Popova S, Sun YB, Fraternali F, Eaton P, Conte MR. 15-deoxy-Δ 12,14-Prostaglandin J 2 inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanism. Commun Biol 2019; 2:188. [PMID: 31123712 PMCID: PMC6525171 DOI: 10.1038/s42003-019-0426-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 01/01/2023] Open
Abstract
Human soluble epoxide hydrolase (hsEH) is an enzyme responsible for the inactivation of bioactive epoxy fatty acids, and its inhibition is emerging as a promising therapeutical strategy to target hypertension, cardiovascular disease, pain and insulin sensitivity. Here, we uncover the molecular bases of hsEH inhibition mediated by the endogenous 15-deoxy-Δ12,14-Prostaglandin J2 (15d-PGJ2). Our data reveal a dual inhibitory mechanism, whereby hsEH can be inhibited by reversible docking of 15d-PGJ2 in the catalytic pocket, as well as by covalent locking of the same compound onto cysteine residues C423 and C522, remote to the active site. Biophysical characterisations allied with in silico investigations indicate that the covalent modification of the reactive cysteines may be part of a hitherto undiscovered allosteric regulatory mechanism of the enzyme. This study provides insights into the molecular modes of inhibition of hsEH epoxy-hydrolytic activity and paves the way for the development of new allosteric inhibitors.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Rebecca L. Charles
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Jolanta Kopec
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - R. Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Tam T. T. Bui
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, The James Black Centre, King’s College London, London, SE5 9NU UK
| | - Simona Popova
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Philip Eaton
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
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8
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Abis G, Charles RL, Eaton P, Conte MR. Expression, purification, and characterisation of human soluble Epoxide Hydrolase (hsEH) and of its functional C-terminal domain. Protein Expr Purif 2018; 153:105-113. [PMID: 30218745 PMCID: PMC6189638 DOI: 10.1016/j.pep.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/30/2018] [Accepted: 09/05/2018] [Indexed: 12/30/2022]
Abstract
The human soluble Epoxide Hydrolase (hsEH) is an enzyme involved in the hydrolysis of endogenous anti-inflammatory and cardio-protective signalling mediators known as epoxyeicosatrienoic acids (EETs). EETs’ conversion into the corresponding diols by hsEH generates non-bioactive molecules, thereby the enzyme inhibition would be expected to enhance the EETs bioavailability, and their beneficial properties. Numerous inhibitors have been developed to target the enzyme, some of which are showing promising antihypertensive and anti-inflammatory properties in vivo. Thus far, the preparation of the recombinant enzyme for enzymatic and structural in vitro studies has been performed mainly using a baculovirus expression system. More recently, it was reported that the enzyme could be exogenously expressed and isolated from E. coli, although limited amounts of active protein were obtained. We herein describe two novel methods to yield pure recombinant enzyme. The first describes the expression and purification of the full-length enzyme from eukaryotic cells HEK293-F, whilst the second concerns the C-terminal domain of hsEH obtained from the cost-effective and rapid E. coli prokaryotic system. The two methods successfully generated satisfactory amounts of functional enzyme, with virtually identical enzymatic activity. Overall, the protocols described in this paper can be employed for the recombinant expression and purification of active hsEH, to be used in future biomedical investigations and for high-throughput screening of inhibitors for potential use in the treatment of cardiovascular disease. hsEH is a key regulator of cardiovascular homeostasis. A HEK293-F mammalian expression system for hsEH full-length (FL) was developed. An E. coli expression system for the hsEH C-terminal Domain (CTD) was established. Both proteins exhibited the same enzymatic specific activity in vitro. The CTD preparation provides benefits of easy operation, and high yield and purity.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Excellence, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, United Kingdom.
| | - Rebecca L Charles
- Cardiovascular Division and British Heart Foundation Centre of Excellence, The Rayne Institute, King´s College London, St Thomas' Hospital, London, SE1 7EH, United Kingdom
| | - Philip Eaton
- Cardiovascular Division and British Heart Foundation Centre of Excellence, The Rayne Institute, King´s College London, St Thomas' Hospital, London, SE1 7EH, United Kingdom
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Excellence, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, United Kingdom.
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9
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Serrano-Hervás E, Casadevall G, Garcia-Borràs M, Feixas F, Osuna S. Epoxide Hydrolase Conformational Heterogeneity for the Resolution of Bulky Pharmacologically Relevant Epoxide Substrates. Chemistry 2018; 24:12254-12258. [DOI: 10.1002/chem.201801068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Eila Serrano-Hervás
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Guillem Casadevall
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry; University of California, Los Angeles (UCLA); 607 Charles E. Young Drive Los Angeles CA 90095 USA
| | - Ferran Feixas
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Sílvia Osuna
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
- ICREA; Pg. Lluís Companys 23 08010 Barcelona Spain
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10
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Serrano-Hervás E, Garcia-Borràs M, Osuna S. Exploring the origins of selectivity in soluble epoxide hydrolase from Bacillus megaterium. Org Biomol Chem 2018; 15:8827-8835. [PMID: 29026902 PMCID: PMC5708342 DOI: 10.1039/c7ob01847a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Epoxide hydrolase (EH) enzymes catalyze the hydration of racemic epoxides to yield their corresponding vicinal diols. In this work, the Bacillus megaterium epoxide hydrolase (BmEH)-mediated hydrolysis of racemic styrene oxide (rac-SO) and its para-nitro styrene oxide (rac-p-NSO) derivative are computationally investigated using density functional theory (DFT).
Epoxide hydrolase (EH) enzymes catalyze the hydration of racemic epoxides to yield their corresponding vicinal diols. These enzymes present different enantio- and regioselectivity depending upon either the substrate structure or the substitution pattern of the epoxide ring. In this study, we computationally investigate the Bacillus megaterium epoxide hydrolase (BmEH)-mediated hydrolysis of racemic styrene oxide (rac-SO) and its para-nitro styrene oxide (rac-p-NSO) derivative using density functional theory (DFT) and an active site cluster model consisting of 195 and 197 atoms, respectively. Full reaction mechanisms for epoxide ring opening were evaluated considering the attack at both oxirane carbons and considering two possible orientations of the substrate at the BmEH active site. Our results indicate that for both SO and p-NSO substrates the BmEH enantio- and regioselectivity is opposite to the inherent (R)-BmEH selectivity, the attack at the benzylic position (C1) of the (S)-enantiomer being the most favoured chemical outcome.
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Affiliation(s)
- Eila Serrano-Hervás
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain.
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11
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Zaugg J, Gumulya Y, Bodén M, Mark AE, Malde AK. Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J Chem Inf Model 2018; 58:630-640. [DOI: 10.1021/acs.jcim.7b00353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Julian Zaugg
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, 4072 Brisbane, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, 4072 Brisbane, Australia
| | - Alpeshkumar K. Malde
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
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12
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13
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Saenz-Méndez P, Katz A, Pérez-Kempner ML, Ventura ON, Vázquez M. Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and molecular docking calculations. Proteins 2017; 85:720-730. [DOI: 10.1002/prot.25251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/07/2016] [Accepted: 12/18/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Patricia Saenz-Méndez
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
- Department of Chemistry and Molecular Biology; University of Gothenburg; Göteborg 405 30 Sweden
| | - Aline Katz
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
| | - María Lucía Pérez-Kempner
- Pharmaceutical Science Department; Facultad de Química; UdelaR, General Flores 2124 Montevideo 11800 Uruguay
| | - Oscar N. Ventura
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
| | - Marta Vázquez
- Pharmaceutical Science Department; Facultad de Química; UdelaR, General Flores 2124 Montevideo 11800 Uruguay
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14
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Lind MES, Himo F. Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01562] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maria E. S. Lind
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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15
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Structure, substitution and hydrolysis of Bis(trifluorobenzoylacetonato-O,O′)dichloro titanium(IV): An experimental and computational study. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.08.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Lee KSS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys 2016; 613:1-11. [PMID: 27983948 DOI: 10.1016/j.abb.2016.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an important therapeutic target of many diseases, such as chronic obstructive pulmonary disease (COPD) and diabetic neuropathic pain. It acts by hydrolyzing and thus regulating specific bioactive long chain polyunsaturated fatty acid epoxides (lcPUFA), like epoxyeicosatrienoic acids (EETs). To better predict which epoxides could be hydrolyzed by sEH, one needs to dissect the important factors and structural requirements that govern the binding of the substrates to sEH. This knowledge allows further exploration of the physiological role played by sEH. Unfortunately, a crystal structure of sEH with a substrate bound has not yet been reported. In this report, new photoaffinity mimics of a sEH inhibitor and EET regioisomers were prepared and used in combination with peptide sequencing and computational modeling, to identify the binding orientation of different regioisomers and enantiomers of EETs into the catalytic cavity of sEH. Results indicate that the stereochemistry of the epoxide plays a crucial role in dictating the binding orientation of the substrate.
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Affiliation(s)
- Kin Sing Stephen Lee
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Connie J Ng
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Weitao Jia
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Armann Andaya
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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17
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de Oliveira GS, Adriani PP, Borges FG, Lopes AR, Campana PT, Chambergo FS. Epoxide hydrolase of Trichoderma reesei: Biochemical properties and conformational characterization. Int J Biol Macromol 2016; 89:569-74. [DOI: 10.1016/j.ijbiomac.2016.05.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
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18
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Bauer P, Carlsson ÅJ, Amrein BA, Dobritzsch D, Widersten M, Kamerlin SCL. Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. Org Biomol Chem 2016; 14:5639-51. [PMID: 27049844 PMCID: PMC5315018 DOI: 10.1039/c6ob00060f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/31/2016] [Indexed: 01/11/2023]
Abstract
Potato epoxide hydrolase 1 (StEH1) is a biocatalytically important enzyme that exhibits rich enantio- and regioselectivity in the hydrolysis of chiral epoxide substrates. In particular, StEH1 has been demonstrated to enantioconvergently hydrolyze racemic mixes of styrene oxide (SO) to yield (R)-1-phenylethanediol. This work combines computational, crystallographic and biochemical analyses to understand both the origins of the enantioconvergent behavior of the wild-type enzyme, as well as shifts in activities and substrate binding preferences in an engineered StEH1 variant, R-C1B1, which contains four active site substitutions (W106L, L109Y, V141K and I155V). Our calculations are able to reproduce both the enantio- and regioselectivities of StEH1, and demonstrate a clear link between different substrate binding modes and the corresponding selectivity, with the preferred binding modes being shifted between the wild-type enzyme and the R-C1B1 variant. Additionally, we demonstrate that the observed changes in selectivity and the corresponding enantioconvergent behavior are due to a combination of steric and electrostatic effects that modulate both the accessibility of the different carbon atoms to the nucleophilic side chain of D105, as well as the interactions between the substrate and protein amino acid side chains and active site water molecules. Being able to computationally predict such subtle effects for different substrate enantiomers, as well as to understand their origin and how they are affected by mutations, is an important advance towards the computational design of improved biocatalysts for enantioselective synthesis.
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Affiliation(s)
- P. Bauer
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - Å. Janfalk Carlsson
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - B. A. Amrein
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - D. Dobritzsch
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - M. Widersten
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - S. C. L. Kamerlin
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
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19
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Epoxide hydrolase-catalyzed enantioselective conversion of trans -stilbene oxide: Insights into the reaction mechanism from steady-state and pre-steady-state enzyme kinetics. Arch Biochem Biophys 2016; 591:66-75. [DOI: 10.1016/j.abb.2015.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022]
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20
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Hopmann KH, Himo F. Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase. J Chem Theory Comput 2015; 4:1129-37. [PMID: 26636366 DOI: 10.1021/ct8000443] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dehalogenation reaction of haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 was investigated theoretically using hybrid density functional theory methods. HheC catalyzes the enantioselective conversion of halohydrins into their corresponding epoxides. The reaction is proposed to be mediated by a catalytic Ser132-Tyr145-Arg149 triad, and a distinct halide binding site is suggested to facilitate halide displacement by stabilizing the free ion. We investigated the HheC-mediated dehalogenation of (R)-2-chloro-1-phenylethanol using three quantum chemical models of various sizes. The calculated barriers and reaction energies give support to the suggested reaction mechanism. The dehalogenation occurs in a single concerted step, in which Tyr145 abstracts a proton from the halohydrin substrate and the substrate oxyanion displaces the chloride ion, forming the epoxide. Characterization of the involved stationary points is provided. Furthermore, by using three different models of the halide binding site, we are able to assess the adopted modeling methodology.
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Affiliation(s)
- Kathrin H Hopmann
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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21
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Amrein BA, Bauer P, Duarte F, Janfalk Carlsson Å, Naworyta A, Mowbray SL, Widersten M, Kamerlin SCL. Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. ACS Catal 2015; 5:5702-5713. [PMID: 26527505 PMCID: PMC4613740 DOI: 10.1021/acscatal.5b01639] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/15/2015] [Indexed: 11/30/2022]
Abstract
Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broad range of substrates. The enzyme can be engineered to increase the yield of optically pure products as a result of changes in both enantio- and regioselectivity. It is thus highly attractive in biocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals. The present work aims to establish the principles underlying the activity and selectivity of the enzyme through a combined computational, structural, and kinetic study using the substrate trans-stilbene oxide as a model system. Extensive empirical valence bond simulations have been performed on the wild-type enzyme together with several experimentally characterized mutants. We are able to computationally reproduce the differences between the activities of different stereoisomers of the substrate and the effects of mutations of several active-site residues. In addition, our results indicate the involvement of a previously neglected residue, H104, which is electrostatically linked to the general base H300. We find that this residue, which is highly conserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonated form in order to provide charge balance in an otherwise negatively charged active site. Our data show that unless the active-site charge balance is correctly treated in simulations, it is not possible to generate a physically meaningful model for the enzyme that can accurately reproduce activity and selectivity trends. We also expand our understanding of other catalytic residues, demonstrating in particular the role of a noncanonical residue, E35, as a "backup base" in the absence of H300. Our results provide a detailed view of the main factors driving catalysis and regioselectivity in this enzyme and identify targets for subsequent enzyme design efforts.
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Affiliation(s)
- Beat A. Amrein
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Paul Bauer
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Åsa Janfalk Carlsson
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 Uppsala, Sweden
| | - Agata Naworyta
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Sherry L. Mowbray
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Mikael Widersten
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
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22
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Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases? Molecules 2015; 20:17789-806. [PMID: 26404218 PMCID: PMC6331936 DOI: 10.3390/molecules201017789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 12/23/2022] Open
Abstract
Candida Antarctica lipase B (CALB) is a well-known enzyme, especially because of its promiscuous activity. Due to its properties, CALB was widely used as a benchmark for designing new catalysts for important organic reactions. The active site of CALB is very similar to that of soluble epoxide hydrolase (sEH) formed by a nucleophile-histidine-acid catalytic triad and an oxyanion hole typical for molecular structures derived from processes of α/β hydrolases. In this work we are exploring these similarities and proposing a Ser105Asp variant of CALB as a new catalyst for epoxide hydrolysis. In particular, the hydrolysis of the trans-diphenylpropene oxide (t-DPPO) is studied by means of quantum cluster models mimicking the active site of both enzymes. Our results, based on semi-empirical and DFT calculations, suggest that mutant Ser105Asp CALB is a good protein scaffold to be used for the bio-synthesis of chiral compounds.
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23
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Hopmann KH. Iron/Brønsted Acid Catalyzed Asymmetric Hydrogenation: Mechanism and Selectivity-Determining Interactions. Chemistry 2015; 21:10020-30. [DOI: 10.1002/chem.201500602] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 12/29/2022]
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Xu J, Morisseau C, Yang J, Mamatha DM, Hammock BD. Epoxide hydrolase activities and epoxy fatty acids in the mosquito Culex quinquefasciatus. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 59:41-9. [PMID: 25686802 PMCID: PMC4387068 DOI: 10.1016/j.ibmb.2015.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/05/2015] [Accepted: 02/05/2015] [Indexed: 05/27/2023]
Abstract
Culex mosquitoes have emerged as important model organisms for mosquito biology, and are disease vectors for multiple mosquito-borne pathogens, including West Nile virus. We characterized epoxide hydrolase activities in the mosquito Culex quinquefasciatus, which suggested multiple forms of epoxide hydrolases were present. We found EH activities on epoxy eicosatrienoic acids (EETs). EETs and other eicosanoids are well-established lipid signaling molecules in vertebrates. We showed EETs can be synthesized in vitro from arachidonic acids by mosquito lysate, and EETs were also detected in vivo both in larvae and adult mosquitoes by LC-MS/MS. The EH activities on EETs can be induced by blood feeding, and the highest activity was observed in the midgut of female mosquitoes. The enzyme activities on EETs can be inhibited by urea-based inhibitors designed for mammalian soluble epoxide hydrolases (sEH). The sEH inhibitors have been shown to play diverse biological roles in mammalian systems, and they can be useful tools to study the function of EETs in mosquitoes. Besides juvenile hormone metabolism and detoxification, insect epoxide hydrolases may also play a role in regulating lipid signaling molecules, such as EETs and other epoxy fatty acids, synthesized in vivo or obtained from blood feeding by female mosquitoes.
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Affiliation(s)
- Jiawen Xu
- Department of Entomology and UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Dadala M Mamatha
- Department of Entomology and UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA
| | - Bruce D Hammock
- Department of Entomology and UC Davis Comprehensive Cancer Center, University of California, Davis, CA 95616, USA.
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25
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Hopmann KH. Full Reaction Mechanism of Nitrile Hydratase: A Cyclic Intermediate and an Unexpected Disulfide Switch. Inorg Chem 2014; 53:2760-2. [DOI: 10.1021/ic500091k] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kathrin H. Hopmann
- Centre for Theoretical and
Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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26
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Taxak N, Kalra S, Bharatam PV. Mechanism-Based Inactivation of Cytochromes by Furan Epoxide: Unraveling the Molecular Mechanism. Inorg Chem 2013; 52:13496-508. [DOI: 10.1021/ic401907k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nikhil Taxak
- Department
of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar
(Mohali), 160 062 Punjab, India
| | - Sourav Kalra
- Department
of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar
(Mohali), 160 062 Punjab, India
| | - Prasad V. Bharatam
- Department
of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar
(Mohali), 160 062 Punjab, India
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27
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Liao RZ, Thiel W. Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein FosA from QM/MM Calculations. J Phys Chem B 2013; 117:1326-36. [DOI: 10.1021/jp4002719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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28
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Carlsson ÅJ, Bauer P, Ma H, Widersten M. Obtaining optical purity for product diols in enzyme-catalyzed epoxide hydrolysis: contributions from changes in both enantio- and regioselectivity. Biochemistry 2012; 51:7627-37. [PMID: 22931287 DOI: 10.1021/bi3007725] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzyme variants of the plant epoxide hydrolase StEH1 displaying improved stereoselectivities in the catalyzed hydrolysis of (2,3-epoxypropyl)benzene were generated by directed evolution. The evolution was driven by iterative saturation mutagenesis in combination with enzyme activity screenings where product chirality was the decisive selection criterion. Analysis of the underlying causes of the increased diol product ratios revealed two major contributing factors: increased enantioselectivity for the corresponding epoxide enantiomer(s) and, in some cases, a concomitant change in regioselectivity in the catalyzed epoxide ring-opening half-reaction. Thus, variant enzymes that catalyzed the hydrolysis of racemic (2,3-epoxypropyl)benzene into the R-diol product in an enantioconvergent manner were isolated.
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Affiliation(s)
- Åsa Janfalk Carlsson
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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29
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Lonsdale R, Hoyle S, Grey DT, Ridder L, Mulholland AJ. Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. Biochemistry 2012; 51:1774-86. [PMID: 22280021 PMCID: PMC3290109 DOI: 10.1021/bi201722j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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30
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Active site analysis of cis-epoxysuccinate hydrolase from Nocardia tartaricans using homology modeling and site-directed mutagenesis. Appl Microbiol Biotechnol 2011; 93:2377-86. [DOI: 10.1007/s00253-011-3548-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/03/2011] [Accepted: 08/13/2011] [Indexed: 10/17/2022]
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31
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Cui FC, Pan XL, Liu W, Liu JY. Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: A density functional study. J Comput Chem 2011; 32:3068-74. [DOI: 10.1002/jcc.21890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 05/17/2011] [Accepted: 06/22/2011] [Indexed: 11/07/2022]
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32
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Kim J, Yoo E, Chang S, Lee YS. Electronic and chelation effects on the unusual C2-methylation of N-(para-substituted)phenylaziridines with lithium organocuprates. J Comput Chem 2011; 32:1859-68. [PMID: 21455961 DOI: 10.1002/jcc.21768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 01/10/2011] [Accepted: 01/14/2011] [Indexed: 11/09/2022]
Abstract
Density functional theory calculations with the B3LYP functional were performed for the title ring-opening reaction to understand the intrinsic activating and directing effects of the N-substituents, as well as the electron donating effect of the para-substituted (Y = Cl, H, Me) phenyl group at the more hindered benzylic C2 atom. The N-tosyl group (i.e., N-Tos) or the N-(2-pyridyl)sulfonyl group (i.e., N-Py) was introduced to activate the ring nitrogen atom (N1) and the para-substituted (Y = Cl, H, Me) phenyl group for the activation of the C2 atom. Conformational searches and geometry optimizations were performed for the N-(para-substituted)phenylaziridines (1∼6). Calculations indicate that the aziridine 6 (i.e., Py/Me) has the most elongated C2-N1 bond intrinsically due to the electronic activating effects, implying the aziridine 6 to be the most potent candidate for the more-hindered C2 opening. Transition states (TSs) were investigated for the prospective ring-opening paths (I∼IV), considering the types of intermolecular push-pull interactions between the N-activated phenylaziridines and the cuprate. The N-Py group provides an unique C2-favored TS along the path IV, which the N-Tos group cannot afford, due to the less charge transfer from the nucleophilic CH 3δ- of the cuprate into the electrophilic C2 atom. Furthermore, the e-donating effect of the para-substituents (Y = Cl, H, Me) enhances the C2 opening for the path IV. This study enables us to understand the unusual ring-opening phenomena in terms of electronic and directing effects and hence may serve as a tool to design substrates for highly regioselective ring openings.
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Affiliation(s)
- Jongtaek Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
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33
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Liao RZ, Yu JG, Himo F. Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation. J Chem Theory Comput 2011; 7:1494-501. [PMID: 26610140 DOI: 10.1021/ct200031t] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.
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Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden.,College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jian-Guo Yu
- College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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34
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Siegbahn PE, Himo F. The quantum chemical cluster approach for modeling enzyme reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.13] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Li X, Zheng QC, Zhang JL, Zhang HX. Theoretical study on the mechanism of rearrangement reaction catalyzed by N5-carboxyaminoimidazole ribonucleotide mutase. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Lo HY, Man CC, Fleck RW, Farrow NA, Ingraham RH, Kukulka A, Proudfoot JR, Betageri R, Kirrane T, Patel U, Sharma R, Hoermann MA, Kabcenell A, Lombaert SD. Substituted pyrazoles as novel sEH antagonist: investigation of key binding interactions within the catalytic domain. Bioorg Med Chem Lett 2010; 20:6379-83. [PMID: 20934334 DOI: 10.1016/j.bmcl.2010.09.095] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 10/19/2022]
Abstract
A novel series of pyrazole sEH inhibitors is reported. Lead optimization efforts to replace the aniline core are also described. In particular, 2-pyridine, 3-pyridine and pyridazine analogs are potent sEH inhibitors with favorable CYP3A4 inhibitory and microsomal stability profiles.
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Affiliation(s)
- Ho Yin Lo
- Boehringer Ingelheim Pharmaceuticals Inc., Biomolecular Screening, 900 Ridgebury Rd., PO Box 368, Ridgefield, CT 06877, USA.
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37
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Georgieva P, Himo F. Quantum chemical modeling of enzymatic reactions: the case of histone lysine methyltransferase. J Comput Chem 2010; 31:1707-14. [PMID: 20082388 DOI: 10.1002/jcc.21458] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.
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Affiliation(s)
- Polina Georgieva
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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38
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Cui FC, Pan XL, Liu JY. Catalytic Mechanism of Hydroxynitrile Lyase from Hevea brasiliensis: A Theoretical Investigation. J Phys Chem B 2010; 114:9622-8. [DOI: 10.1021/jp100373e] [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]
Affiliation(s)
- Feng-Chao Cui
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Xiao-Liang Pan
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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Lindberg D, de la Fuente Revenga M, Widersten M. Temperature and pH dependence of enzyme-catalyzed hydrolysis of trans-methylstyrene oxide. A unifying kinetic model for observed hysteresis, cooperativity, and regioselectivity. Biochemistry 2010; 49:2297-304. [PMID: 20146441 DOI: 10.1021/bi902157b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The underlying enzyme kinetics behind the regioselective promiscuity shown by epoxide hydrolases toward certain epoxides has been studied. The effects of temperature and pH on regioselectivity were investigated by analyzing the stereochemistry of hydrolysis products of (1R,2R)-trans-2-methylstyrene oxide between 14-46 degrees C and pH 6.0-9.0, either catalyzed by the potato epoxide hydrolase StEH1 or in the absence of enzyme. In the enzyme-catalyzed reaction, a switch of preferred epoxide carbon that is subjected to nucleophilic attack is observed at pH values above 8. The enzyme also displays cooperativity in substrate saturation plots when assayed at temperatures < or = 30 degrees C and at intermediate pH. The cooperativity is lost at higher assay temperatures. Cooperativity can originate from a kinetic mechanism involving hysteresis and will be dependent on the relationship between k(cat) and the rate of interconversion between two different Michaelis complexes. In the case of the studied reactions, the proposed different Michaelis complexes are enzyme-substrate complexes in which the epoxide substrate is bound in different binding modes, allowing for separate pathways toward product formation. The assumption of separated, but interacting, reaction pathways is supported by that formation of the two product enantiomers also displays distinct pH dependencies of k(cat)/K(M). The thermodynamic parameters describing the differences in activation enthalpy and entropy suggest that (1) regioselectivity is primarily dictated by differences in activation entropy with positive values of both DeltaDeltaH(++) and DeltaDeltaS(++) and (2) the hysteretic behavior is linked to an interconversion between Michaelis complexes with rates increasing with temperature. From the collected data, we propose that hysteresis, regioselectivity, and, when applicable, hysteretic cooperativity are closely linked properties, explained by the kinetic mechanism earlier introduced by our group.
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Affiliation(s)
- Diana Lindberg
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
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40
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Widersten M, Gurell A, Lindberg D. Structure–function relationships of epoxide hydrolases and their potential use in biocatalysis. Biochim Biophys Acta Gen Subj 2010; 1800:316-26. [DOI: 10.1016/j.bbagen.2009.11.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/09/2009] [Accepted: 11/23/2009] [Indexed: 10/20/2022]
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41
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Domínguez de María P, van Gemert RW, Straathof AJJ, Hanefeld U. Biosynthesis of ethers: unusual or common natural events? Nat Prod Rep 2010; 27:370-92. [PMID: 20179877 DOI: 10.1039/b809416k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ether bonds are found in a wide variety of natural products--mainly secondary metabolites--including lipids, oxiranes, terpenoids, flavonoids, polyketides, and carbohydrate derivatives, to name some representative examples. To furnish such a biodiversity of structures, a large number of different enzymes are involved in several different biosynthetic pathways. Depending on the compound and on the (micro) environment in which the reaction is performed, ethers are produced by very different (enzymatic) reactions, thus providing an impressive display of how Nature has combined evolution and thermodynamics to be able to produce a vast number of compounds. In addition, many of these compounds possess different biological activities of pharmacological interest. Moreover, some of these ethers (i.e., epoxides) have high chemical reactivity, and can be useful starting materials for further synthetic processes. This review aims to provide an overview of the different strategies that are found in Nature for the formation of these "bioethers". Both fundamental and practical insights of the biosynthetic processes will be discussed.
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42
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Idupulapati NB, Mainardi DS. Quantum Chemical Modeling of Methanol Oxidation Mechanisms by Methanol Dehydrogenase Enzyme: Effect of Substitution of Calcium by Barium in the Active Site. J Phys Chem A 2010; 114:1887-96. [DOI: 10.1021/jp9083025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nagesh B. Idupulapati
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
| | - Daniela S. Mainardi
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
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43
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Sevastik R, Whitman CP, Himo F. Reaction mechanism of cis-3-chloroacrylic acid dehalogenase: a theoretical study. Biochemistry 2009; 48:9641-9. [PMID: 19725565 DOI: 10.1021/bi900879a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reaction mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) is studied using the B3LYP density functional theory method. This enzyme catalyzes the hydrolytic dehalogenation of cis-3-chloroacrylic acid to yield malonate semialdehyde and HCl. The uncatalyzed reaction is first considered, and excellent agreement is found between the calculated barrier and the measured rate constant. The enzymatic reaction is then studied with an active site model consisting of 159 atoms. The results suggest an alternative mechanism for cis-CaaD catalysis and different roles for some active site residues in this mechanism.
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Affiliation(s)
- Robin Sevastik
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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44
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Lindberg D, Gogoll A, Widersten M. Substrate-dependent hysteretic behavior in StEH1-catalyzed hydrolysis of styrene oxide derivatives. FEBS J 2008; 275:6309-20. [DOI: 10.1111/j.1742-4658.2008.06754.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Georgieva P, Himo F. Density functional theory study of the reaction mechanism of the DNA repairing enzyme alkylguanine alkyltransferase. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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46
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Alstrup Lie M, Schiøtt B. A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models. J Comput Chem 2008; 29:1037-47. [PMID: 18058864 DOI: 10.1002/jcc.20860] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thiamin diphosphate (ThDP) is the biologically active form of vitamin B1 and an essential cofactor for a number of enzymes. The effect of solvent polarity on the tautomeric equilibria of ThDP using three model systems of the 4'-aminopyrimidine ring is studied by density functional theory calculations (B3LYP/6-311+G(d,p)//B3LYP/6-31G(d)) in the gas phase and selected solvents (cyclohexane, ether, dichloroethane, and water). Solvation effects are investigated using three different schemes: implicit solvation by a continuum model, explicit solvation by inclusion of three water molecules mimicking the first solvation shell of the enzymatic environment, and by a mixed implicit/explicit solvation model. The 4'-aminopyrimidine tautomer is more stable than the 1',4'-iminopyrimidine tautomer in all solvation schemes employed; however, the trend for the stabilities of the 1',4'-iminopyrimidine tautomer in the solvents depends on the specific ThDP-model. Formation of the catalytic important ylide for ThDP-dependent enzymes by deprotonation of ThDP(C2) is also investigated by localization of transition states for two possible pathways. Only the less stable tautomer, 1',4'-iminopyrimidine ThDP, is able to form the catalytic active ylide. Generation of the ylide through a direct intramolecular proton transfer from ThDP(C2) to the ThDP(N4') nitrogen lone pair is favored by 6 kcal/mol in the gas phase, as compared to a water-mediated ylide generation. However, inclusion of a dielectric medium reduces this difference dramatically. Furthermore, inclusion of two water molecules to model the apoenzymatic environment lowers the activation energies of both direct and water-mediated ylide generation.
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Affiliation(s)
- Mette Alstrup Lie
- Center for Catalysis, Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
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47
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Hopmann KH, Himo F. Cyanolysis and Azidolysis of Epoxides by Haloalcohol Dehalogenase: Theoretical Study of the Reaction Mechanism and Origins of Regioselectivity. Biochemistry 2008; 47:4973-82. [DOI: 10.1021/bi800001r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kathrin H. Hopmann
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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48
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Chen SL, Fang WH, Himo F. Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0430-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Kóňa J. Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease. Org Biomol Chem 2008; 6:359-65. [DOI: 10.1039/b715828a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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50
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Weijers CAGM, Könst PM, Franssen MCR, Sudhölter EJR. Stereochemical preference of yeast epoxide hydrolase for the O-axial C3 epimers of 1-oxaspiro[2.5]octanes. Org Biomol Chem 2007; 5:3106-14. [PMID: 17878969 DOI: 10.1039/b709742e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1-oxaspiro[2.5]octane moiety is a common motif in many biologically active spiroepoxide compounds. Stereochemistry plays an important role in the action of these spiroepoxides, since the O-axial C3 epimers are predominantly responsible for biological activity. In view of this, the reactivity of the yeast epoxide hydrolase (YEH) from Rhodotorula glutinis towards both O-axial and O-equatorial C3 epimers of various 1-oxaspiro[2.5]octanes was investigated. O-axial C3 Epimers were hydrolyzed faster than the O-equatorial C3 epimers. The stereochemical preference was greatly dependent on the type of substitution on the cyclohexane ring. The preference of YEH for O-axial C3 epimers, found throughout this study, illustrates the effectiveness of YEH in enzymatic detoxification of spiroepoxides.
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Affiliation(s)
- Carel A G M Weijers
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703HB, Wageningen, The Netherlands
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