1
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Hu D, Lu ZY, Liao X, Jia XW, Song WH, Hu YY, He YC. Engineering an Epoxide Hydrolase for Chemoenzymatic Asymmetric Synthesis of Chiral Triazole Fungicide ( S)- and ( R)-Flutriafol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21741-21751. [PMID: 39297229 DOI: 10.1021/acs.jafc.4c07318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Flutriafol, a globally utilized triazole fungicide in agriculture, is typically applied as a racemic mixture, but its enantiomers differ in bioactivity and environmental impact. The synthesis of flutriafol enantiomers is critically dependent on chiral precursors: 2,2-bisaryl-substituted oxirane [(2-fluorophenyl)-2-(4-fluorophenyl)oxirane, 1a] and 1,2-diol [1-(2-fluorophenyl)-1-(4-fluorophenyl)ethane-1,2-diol, 1b]. Here, we engineered a Rhodotorula paludigensis epoxide hydrolase (RpEH), obtaining mutant Escherichia coli/RpehH336W/L360F with a 6.4-fold enhanced enantiomeric ratio (E) from 5.5 to 35.4. This enabled a gram-scale resolution of rac-1a by E. coli/RpehH336W/L360F, producing (S)-1a (98.2% ees) and (R)-1b (75.0% eep) with 44.3 and 55.7% analytical yields, respectively. As follows, chiral (S)-flutriafol (98.2% ee) and (R)-flutriafol (75.0% ee) were easily synthesized by a one-step chemocatalytic process from (S)-1a and a two-step chemocatalytic process from (R)-1b, respectively. This chemoenzymatic approach offers a superior alternative for the asymmetric synthesis of flutriafol enantiomers. Furthermore, molecular dynamics simulations revealed insight into the enantioselectivity improvement of RpEH toward bulky 2,2-bisaryl-substituted oxirane 1a.
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Affiliation(s)
- Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Zhi-Yi Lu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Xiang Liao
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Xue-Wei Jia
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Wen-Hao Song
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Yu-Ye Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Yu-Cai He
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
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2
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Tang Y, Liu X, Qi P, Cai Y, Wang H, Qin Y, Gu W, Wang C, Sun Y, Zhu C. Single-Atom Ce-Doped Metal Hydrides with High Phosphatase-like Activity Amplify Oxidative Stress-Induced Tumor Apoptosis. ACS NANO 2024; 18:25685-25694. [PMID: 39223090 DOI: 10.1021/acsnano.4c07851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Phosphates within tumors function as key biomolecules, playing a significant role in sustaining the viability of tumors. To disturb the homeostasis of cancer cells, regulating phosphate within the organism proves to be an effective strategy. Herein, we report single-atom Ce-doped Pt hydrides (Ce/Pt-H) with high phosphatase-like activity for phosphate hydrolysis. The resultant Ce/Pt-H exhibits a 26.90- and 6.25-fold increase in phosphatase-like activity in comparison to Ce/Pt and Pt-H, respectively. Mechanism investigations elucidate that the Ce Lewis acid site facilitates the coordination with phosphate groups, while the surface hydrides enhance the electron density of Pt for promoting catalytic ability in H2O cleavage and subsequent nucleophilic attack of hydroxyl groups. Finally, by leveraging its phosphatase-like activity, Ce/Pt-H can effectively regulate intracellular phosphates to disrupt redox homeostasis and amplify oxidative stress within cancer cells, ultimately leading to tumor apoptosis. This work provides fresh insights into noble-metal-based phosphatase mimics for inducing tumor apoptosis.
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Affiliation(s)
- Yinjun Tang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Xupeng Liu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Pengcheng Qi
- Institute of Nano-Science and Technology, College of Physical Science and Technology, Central China Normal University, Wuhan 430079, P. R. China
| | - Yujia Cai
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hengjia Wang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ying Qin
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Wenling Gu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Canglong Wang
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, P. R. China
| | - Yao Sun
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Chengzhou Zhu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
- College of Material Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou 311121, P. R. China
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3
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Sun B, Cui X, Zhang J, Tang Y, Sun H. Highly sensitive hydrolytic nanozyme-based sensors for colorimetric detection of aluminum ions. Anal Bioanal Chem 2024:10.1007/s00216-024-05462-y. [PMID: 39085422 DOI: 10.1007/s00216-024-05462-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
Hydrolytic nanozyme-based visual colorimetry has emerged as a promising strategy for the detection of aluminum ions. However, most studies focus on simulating the structure of natural enzymes while neglecting to regulate the rate of hydrolysis-related steps, leading to low enzyme-like activity for hydrolytic nanozymes. Herein, we constructed a ruthenium dioxide (RuO2) in situ embedded cerium oxide (CeO2) nanozyme (RuO2/CeO2) with a Lewis acid-base pair (Ce-O-Ru-OH), which can simulate the catalytic behavior of phosphatase (PPase) and can be quantitatively quenched by Al3+ to achieve accurate and sensitive Al3+ colorimetric sensing detection. The incorporation of Ru into CeO2 nanorods accelerates the dissociation of H2O, followed by subsequent combination of hydroxide species to Lewis acidic Ce-O sites. This synergistic effect facilitates substrate activation and significantly enhances the hydrolysis activity of the nanozyme. The results show that the RuO2/CeO2 nanozyme exhibits a limit of detection as low as 0.5 ng/mL. We also demonstrate their efficacy in detecting Al3+ in various practical food samples. This study offers novel insights into the advancement of highly sensitive hydrolytic nanozyme engineering for sensing applications.
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Affiliation(s)
- Baohong Sun
- Jiangsu Key Laboratory of New Power Batteries, National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
- Anhui Engineering Technology Research Center of Biochemical Pharmaceutical, School of Pharmacy, Bengbu Medical University, Bengbu, 233030, P. R. China.
| | - Xin Cui
- Jiangsu Key Laboratory of New Power Batteries, National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Jiachen Zhang
- Jiangsu Key Laboratory of New Power Batteries, National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Yawen Tang
- Jiangsu Key Laboratory of New Power Batteries, National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Hanjun Sun
- Jiangsu Key Laboratory of New Power Batteries, National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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4
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Xu W, Cai X, Wu Y, Wen Y, Su R, Zhang Y, Huang Y, Zheng Q, Hu L, Cui X, Zheng L, Zhang S, Gu W, Song W, Guo S, Zhu C. Biomimetic single Al-OH site with high acetylcholinesterase-like activity and self-defense ability for neuroprotection. Nat Commun 2023; 14:6064. [PMID: 37770453 PMCID: PMC10539540 DOI: 10.1038/s41467-023-41765-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Neurotoxicity of organophosphate compounds (OPs) can catastrophically cause nervous system injury by inhibiting acetylcholinesterase (AChE) expression. Although artificial systems have been developed for indirect neuroprotection, they are limited to dissociating P-O bonds for eliminating OPs. However, these systems have failed to overcome the deactivation of AChE. Herein, we report our finding that Al3+ is engineered onto the nodes of metal-organic framework to synthesize MOF-808-Al with enhanced Lewis acidity. The resultant MOF-808-Al efficiently mimics the catalytic behavior of AChE and has a self-defense ability to break the activity inhibition by OPs. Mechanism investigations elucidate that Al3+ Lewis acid sites with a strong polarization effect unite the highly electronegative -OH groups to form the enzyme-like catalytic center, resulting in superior substrate activation and nucleophilic attack ability with a 2.7-fold activity improvement. The multifunctional MOF-808-Al, which has satisfactory biosafety, is efficient in reducing neurotoxic effects and preventing neuronal tissue damage.
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Affiliation(s)
- Weiqing Xu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Xiaoli Cai
- Department of Nutrition, Hygiene and Toxicology, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, P.R. China
| | - Yu Wu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Yating Wen
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Rina Su
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Yu Zhang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Yuteng Huang
- Department of Nutrition, Hygiene and Toxicology, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, P.R. China
| | - Qihui Zheng
- Department of Nutrition, Hygiene and Toxicology, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, P.R. China
| | - Liuyong Hu
- School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, P.R. China
| | - Xiaowen Cui
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics Department, Chinese Academy of Sciences Institution, Beijing, 100049, P.R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics Department, Chinese Academy of Sciences Institution, Beijing, 100049, P.R. China
| | - Shipeng Zhang
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P.R. China
| | - Wenling Gu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
| | - Weiyu Song
- State Key Laboratory of Heavy Oil Processing, College of New Energy and Materials, China University of Petroleum, Beijing, 102249, P.R. China
| | - Shaojun Guo
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P.R. China.
| | - Chengzhou Zhu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China.
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5
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Bzówka M, Mitusińska K, Raczyńska A, Skalski T, Samol A, Bagrowska W, Magdziarz T, Góra A. Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases? PLoS Comput Biol 2022; 18:e1010119. [PMID: 35580137 PMCID: PMC9140254 DOI: 10.1371/journal.pcbi.1010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 05/27/2022] [Accepted: 04/19/2022] [Indexed: 12/27/2022] Open
Abstract
The evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins—one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels’ evolution analysis based on entropy values calculated for tunnels’ residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a ‘perforation’ mechanism for new tunnels design via the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzyme’s performance and can be applied widely for enzymes with buried active sites. So far very little is known about proteins tunnels evolution. The goal of this study is to evaluate the evolution of tunnels in the family of soluble epoxide hydrolases—representatives of numerous α/β-hydrolase fold enzymes. As a result two types of tunnels evolution analysis were proposed (a general and a detailed approach), as well as a ‘perforation’ mechanism which can mimic native evolution in proteins and can be used as an additional strategy for enzymes redesign.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Skalski
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Aleksandra Samol
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Weronika Bagrowska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Magdziarz
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
- * E-mail:
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6
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Jiang Y, Qu G, Sheng X, Tong F, Sun Z. Unraveling the mechanism of enantio-controlling switches of an alcohol dehydrogenase toward sterically small ketone. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00031h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient synthesis of chiral compounds under mild conditions is highly desirable in the chemical and pharmaceutical communities, but it often faces difficulties. Although various enzymes have been harnessed as biocatalysts...
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7
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Hu D, Hu BC, Wen Z, Zhang D, Liu YY, Zang J, Wu MC. Nearly perfect kinetic resolution of racemic o-nitrostyrene oxide by AuEH2, a microsomal epoxide hydrolase from Aspergillus usamii, with high enantio- and regio-selectivity. Int J Biol Macromol 2020; 169:1-7. [PMID: 33316339 DOI: 10.1016/j.ijbiomac.2020.12.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022]
Abstract
Only a few known epoxide hydrolases (EHs) displayed activity towards o-nitrostyrene oxide (4a), presumably owing to the large steric hindrance caused by o-nitro substituent. Therefore, excavating EHs with high activity and enantio- and/or regio-selectivity towards racemic (rac-) 4a is essential but challenging. Here, AuEH2 from Aspergillus usamii was expressed in E. coli BL21(DE3). E. coli/Aueh2, an E. coli transformant expressing AuEH2, possessed EH activities of 16.2-184 U/g wet cell towards rac-styrene oxide (1a) and its derivatives (2a-13a), and the largest enantiomeric ratio of 96 towards rac-4a. The regioselectivity coefficients, βR and βS, of AuEH2 were determined to be 99.2% and 98.9%, suggesting that it regiopreferentially attacks the Cβ in the oxirane rings of (R)- and (S)-4a. Then, the nearly perfect kinetic resolution of 20 mM rac-4a in pure water was carried out using 20 mg/mL wet cells of E. coli/Aueh2 at 25 °C for 50 min, retaining (S)-4a with over 99% ees and 48.9% yields, while producing (R)-o-nitrophenyl-1,2-ethanediol (4b) with 95.3% eep and 49.8% yieldp. To elucidate the molecular mechanism of AuEH2 with high enantiopreference for (R)-4a, its crystal structure was solved by X-ray diffraction and the molecular docking of AuEH2 with (R)- or (S)-4a was simulated.
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Affiliation(s)
- Die Hu
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, PR China
| | - Bo-Chun Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Zheng Wen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Dong Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - You-Yi Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, PR China
| | - Jia Zang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi 214002, PR China.
| | - Min-Chen Wu
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, PR China.
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8
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Das Mahapatra A, Choubey R, Datta B. Small Molecule Soluble Epoxide Hydrolase Inhibitors in Multitarget and Combination Therapies for Inflammation and Cancer. Molecules 2020; 25:molecules25235488. [PMID: 33255197 PMCID: PMC7727688 DOI: 10.3390/molecules25235488] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
The enzyme soluble epoxide hydrolase (sEH) plays a central role in metabolism of bioactive lipid signaling molecules. The substrate-specific hydrolase activity of sEH converts epoxyeicosatrienoic acids (EETs) to less bioactive dihydroxyeicosatrienoic acids. EETs exhibit anti-inflammatory, analgesic, antihypertensive, cardio-protective and organ-protective properties. Accordingly, sEH inhibition is a promising therapeutic strategy for addressing a variety of diseases. In this review, we describe small molecule architectures that have been commonly deployed as sEH inhibitors with respect to angiogenesis, inflammation and cancer. We juxtapose commonly used synthetic scaffolds and natural products within the paradigm of a multitarget approach for addressing inflammation and inflammation induced carcinogenesis. Structural insights from the inhibitor complexes and novel strategies for development of sEH-based multitarget inhibitors are also presented. While sEH inhibition is likely to suppress inflammation-induced carcinogenesis, it can also lead to enhanced angiogenesis via increased EET concentrations. In this regard, sEH inhibitors in combination chemotherapy are described. Urea and amide-based architectures feature prominently across multitarget inhibition and combination chemotherapy applications of sEH inhibitors.
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Affiliation(s)
- Amarjyoti Das Mahapatra
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
| | - Rinku Choubey
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
| | - Bhaskar Datta
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India
- Correspondence: ; Tel.: +079-2395-2073; Fax: +079-2397-2622
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9
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Hu B, Hu D, Zhang D, Wen Z, Zang J, Wu M. Manipulating the regioselectivity of a Solanum lycopersicum epoxide hydrolase for the enantioconvergent synthesis of enantiopure alkane- and alkene-1,2-diols. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00990c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This work engineered a superior double-site mutant SlEH1W106T/F189L used for the enantioconvergent biosynthesis of (R)-1b–6b with high eep values.
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Affiliation(s)
- Bochun Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Die Hu
- Wuxi School of Medicine
- Jiangnan University
- Wuxi 214122
- China
| | - Dong Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Zheng Wen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Jia Zang
- The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University
- Wuxi 214002
- China
| | - Minchen Wu
- Wuxi School of Medicine
- Jiangnan University
- Wuxi 214122
- China
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10
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Li C, Zhao J, Hu D, Hu BC, Wang R, Zang J, Wu MC. Multiple site-directed mutagenesis of a Phaseolus vulgaris epoxide hydrolase to improve its catalytic performance towards p-chlorostyrene oxide based on the computer-aided re-design. Int J Biol Macromol 2019; 121:326-332. [DOI: 10.1016/j.ijbiomac.2018.10.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/25/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
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11
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Li FL, Kong XD, Chen Q, Zheng YC, Xu Q, Chen FF, Fan LQ, Lin GQ, Zhou J, Yu HL, Xu JH. Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02622] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Fu-Long Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Xu-Dong Kong
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei-Fei Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Li-Qiang Fan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Guo-Qiang Lin
- Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiahai Zhou
- Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
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12
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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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13
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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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14
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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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15
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Qu G, Lonsdale R, Yao P, Li G, Liu B, Reetz MT, Sun Z. Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis. Chembiochem 2018; 19:239-246. [PMID: 29314451 DOI: 10.1002/cbic.201700562] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Peiyuan Yao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
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16
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Bendigiri C, Harini K, Yenkar S, Zinjarde S, Sowdhamini R, RaviKumar A. Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether. RSC Adv 2018; 8:12918-12926. [PMID: 35541265 PMCID: PMC9079618 DOI: 10.1039/c8ra00628h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/26/2018] [Indexed: 11/22/2022] Open
Abstract
Glycidyl ethers and their vicinal diols are important building blocks in the organic synthesis of anti-cancer and anti-obesity drugs. Ylehd, an epoxide hydrolase from tropical marine yeast Yarrowia lipolytica, was explored for its enantioselective properties by kinetic, thermodynamic and in silico studies. Kinetic resolution of racemic phenyl glycidyl ether (PGE) yielded (S)-epoxide while for benzyl glycidyl ether (BGE) (R)-epoxide was obtained, with vicinal diols of the opposite configuration. Amongst the enantiomers of PGE and BGE, the (S)-selective conversion of benzyl glycidyl ether to its corresponding diol, (S)-3-benzyloxy-1,2-propanediol while retaining (R)-BGE was most favourable with 95% ee in 20 min. Enantioselective conversion of specific enantiomer of BGE to its corresponding diols was attributed to the favourable kinetic and thermodynamic parameters as well as to the number and proximity of water molecules near the base H325 in the active site pocket. The easily available and highly active Ylehd could be a potential biocatalyst for large scale preparation of pharmaceutically relevant chiral (R)-benzyl glycidyl ether and (S)-3-benzyloxy-1,2-propanediol. Ylehd, an enantioselective epoxide hydrolase with potential application in resolution of racemic benzyl glycidyl ether.![]()
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Affiliation(s)
- Chandrika Bendigiri
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - K. Harini
- National Centre for Biological Sciences
- Bengaluru
- India
| | - Sajal Yenkar
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - R. Sowdhamini
- National Centre for Biological Sciences
- Bengaluru
- India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
- Department of Biotechnology
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17
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18
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Bakhtin S, Shved E, Bespal'ko Y. Nucleophile-electrophile interactions in the reaction of oxiranes with carboxylic acids in the presence of tertiary amines. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3717] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Elena Shved
- Faculty of Chemistry; Vasyl' Stus Donetsk National University; Vinnytsia Ukraine
| | - Yuliia Bespal'ko
- Faculty of Chemistry; Vasyl' Stus Donetsk National University; Vinnytsia Ukraine
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19
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Hvorecny KL, Bahl CD, Kitamura S, Lee KSS, Hammock BD, Morisseau C, Madden DR. Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase. Structure 2017; 25:697-707.e4. [PMID: 28392259 DOI: 10.1016/j.str.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/20/2017] [Accepted: 03/09/2017] [Indexed: 02/07/2023]
Abstract
Pseudomonas aeruginosa secretes an epoxide hydrolase with catalytic activity that triggers degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) and perturbs other host defense networks. Targets of this CFTR inhibitory factor (Cif) are largely unknown, but include an epoxy-fatty acid. In this class of signaling molecules, chirality can be an important determinant of physiological output and potency. Here we explore the active-site chemistry of this two-step α/β-hydrolase and its implications for an emerging class of virulence enzymes. In combination with hydrolysis data, crystal structures of 15 trapped hydroxyalkyl-enzyme intermediates reveal the stereochemical basis of Cif's substrate specificity, as well as its regioisomeric and enantiomeric preferences. The structures also reveal distinct sets of conformational changes that enable the active site to expand dramatically in two directions, accommodating a surprising array of potential physiological epoxide targets. These new substrates may contribute to Cif's diverse effects in vivo, and thus to the success of P. aeruginosa and other pathogens during infection.
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Affiliation(s)
- Kelli L Hvorecny
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Christopher D Bahl
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Seiya Kitamura
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California at Davis, Davis, CA 95616, USA
| | - Kin Sing Stephen Lee
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California at Davis, Davis, CA 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California at Davis, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California at Davis, Davis, CA 95616, USA
| | - Dean R Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA.
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20
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Cossio-Pérez R, Palma J, Pierdominici-Sottile G. Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. J Chem Inf Model 2017; 57:826-834. [PMID: 28301154 DOI: 10.1021/acs.jcim.6b00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
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Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
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21
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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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22
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Karami L, Saboury AA, Rezaee E, Tabatabai SA. Investigation of the binding mode of 1, 3, 4-oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:445-459. [PMID: 27928588 DOI: 10.1007/s00249-016-1188-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/03/2016] [Accepted: 11/17/2016] [Indexed: 01/24/2023]
Abstract
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH. The results obtained from the binding free energy (ΔG binding) calculation and normal mode analysis indicate that the major favorable contributors are the van der Waals and electrostatic terms, whereas the polar solvation term opposes binding. In addition, a good agreement between the calculated ΔG binding and the experimental IC50 was obtained [correlation coefficient, r 2 = 0.89 (with) and 0.87 (without) entropy]. Besides, comparison of the enthalpy changes (ΔG MM-GBSA) with entropy changes (-TΔS) indicates that binding process of all inhibitors to sEH is enthalpy-driven. Based on the ΔG binding on per residue decomposition, Asp335 and Tyr383 residues from the active site and Trp336, Leu499 and His524 residues from hydrophobic pockets contribute the most to ΔG binding. Moreover, hydrogen bond analysis reveals that Tyr383, Tyr466 and Asp335 residues have an important role in the binding to inhibitors by forming hydrogen bonds with high occupancies. Our obtained results are useful for the understanding of the sEH-inhibitor interactions and may have great importance in the design of future sEH inhibitors.
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Affiliation(s)
- Leila Karami
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Elham Rezaee
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Abbas Tabatabai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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23
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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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24
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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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25
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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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26
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Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective enzymes by computational design and in silico screening. Angew Chem Int Ed Engl 2015; 54:3726-30. [PMID: 25651000 DOI: 10.1002/anie.201411415] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 01/08/2023]
Abstract
Computational enzyme design holds great promise for providing new biocatalysts for synthetic chemistry. A strategy to design small mutant libraries of complementary enantioselective epoxide hydrolase variants for the production of highly enantioenriched (S,S)-diols and (R,R)-diols is developed. Key features of this strategy (CASCO, catalytic selectivity by computational design) are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high-throughput molecular dynamics simulations. Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.
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Affiliation(s)
- Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
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27
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Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective Enzymes by Computational Design and In Silico Screening. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411415] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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28
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Xue F, Liu ZQ, Wan NW, Zhu HQ, Zheng YG. Engineering the epoxide hydrolase from Agromyces mediolanus for enhanced enantioselectivity and activity in the kinetic resolution of racemic epichlorohydrin. RSC Adv 2015. [DOI: 10.1039/c5ra02492g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The biocatalytic production of enantiopure epichlorohydrin (ECH) has been steadily attracting more attention.
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Affiliation(s)
- Feng Xue
- Institute of Bioengineering
- Zhejiang University of Technology
- Hangzhou
- P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education
| | - Zhi-Qiang Liu
- Institute of Bioengineering
- Zhejiang University of Technology
- Hangzhou
- P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education
| | - Nan-Wei Wan
- Institute of Bioengineering
- Zhejiang University of Technology
- Hangzhou
- P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education
| | - Hang-Qin Zhu
- Institute of Bioengineering
- Zhejiang University of Technology
- Hangzhou
- P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education
| | - Yu-Guo Zheng
- Institute of Bioengineering
- Zhejiang University of Technology
- Hangzhou
- P. R. China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education
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29
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Xue F, Liu ZQ, Zou SP, Wan NW, Zhu WY, Zhu Q, Zheng YG. A novel enantioselective epoxide hydrolase from Agromyces mediolanus ZJB120203: Cloning, characterization and application. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Horsman GP, Lechner A, Ohnishi Y, Moore BS, Shen B. Predictive model for epoxide hydrolase-generated stereochemistry in the biosynthesis of nine-membered enediyne antitumor antibiotics. Biochemistry 2013; 52:5217-24. [PMID: 23844627 DOI: 10.1021/bi400572a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nine-membered enediyne antitumor antibiotics C-1027, neocarzinostatin (NCS), and kedarcidin (KED) possess enediyne cores to which activity-modulating peripheral moieties are attached via (R)- or (S)-vicinal diols. We have previously shown that this stereochemical difference arises from hydrolysis of epoxide precursors by epoxide hydrolases (EHs) with different regioselectivities. The inverting EHs, such as SgcF, hydrolyze an (S)-epoxide substrate to yield an (R)-diol in C-1027 biosynthesis, whereas the retaining EHs, such as NcsF2 and KedF, hydrolyze an (S)-epoxide substrate to yield an (S)-diol in NCS and KED biosynthesis. We now report the characterization of a series of EH mutants and provide a predictive model for EH regioselectivity in the biosynthesis of the nine-membered enediyne antitumor antibiotics. A W236Y mutation in SgcF increased the retaining activity toward (S)-styrene oxide by 3-fold, and a W236Y/Q237M double mutation in SgcF, mimicking NcsF2 and KedF, resulted in a 20-fold increase in the retaining activity. To test the predictive utility of these mutations, two putative enediyne biosynthesis-associated EHs were identified by genome mining and confirmed as inverting enzymes, SpoF from Salinospora tropica CNB-440 and SgrF (SGR_625) from Streptomyces griseus IFO 13350. Finally, phylogenetic analysis of EHs revealed a familial classification according to inverting versus retaining activity. Taken together, these results provide a predictive model for vicinal diol stereochemistry in enediyne biosynthesis and set the stage for further elucidating the origins of EH regioselectivity.
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Affiliation(s)
- Geoffrey P Horsman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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31
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Kotik M, Zhao W, Iacazio G, Archelas A. Directed evolution of metagenome-derived epoxide hydrolase for improved enantioselectivity and enantioconvergence. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Barrozo A, Borstnar R, Marloie G, Kamerlin SCL. Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci 2012. [PMID: 23202907 PMCID: PMC3497281 DOI: 10.3390/ijms131012428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
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Affiliation(s)
- Alexandre Barrozo
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Rok Borstnar
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gaël Marloie
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +46-18-471-4423; Fax: +46-18-530-396
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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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34
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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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35
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Kotik M, Archelas A, Faměrová V, Oubrechtová P, Křen V. Laboratory evolution of an epoxide hydrolase – Towards an enantioconvergent biocatalyst. J Biotechnol 2011; 156:1-10. [DOI: 10.1016/j.jbiotec.2011.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/25/2011] [Accepted: 08/03/2011] [Indexed: 11/29/2022]
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36
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Zhao J, Chu YY, Li AT, Ju X, Kong XD, Pan J, Tang Y, Xu JH. An Unusual (R)-Selective Epoxide Hydrolase with High Activity for Facile Preparation of Enantiopure Glycidyl Ethers. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Zheng H, Reetz MT. Manipulating the Stereoselectivity of Limonene Epoxide Hydrolase by Directed Evolution Based on Iterative Saturation Mutagenesis. J Am Chem Soc 2010; 132:15744-51. [DOI: 10.1021/ja1067542] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huabao Zheng
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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38
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Reetz MT. Gerichtete Evolution stereoselektiver Enzyme: Eine ergiebige Katalysator‐Quelle für asymmetrische Reaktionen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000826] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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39
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Reetz MT. Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Ed Engl 2010; 50:138-74. [DOI: 10.1002/anie.201000826] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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40
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Zheng H, Kahakeaw D, Acevedo JP, Reetz M. Directed Evolution of Enantioconvergency: The Case of an Epoxide Hydrolase-Catalyzed Reaction of a Racemic Epoxide. ChemCatChem 2010. [DOI: 10.1002/cctc.201000122] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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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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42
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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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43
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Hajjar E, Dejaegere A, Reuter N. Challenges in pKa Predictions for Proteins: The case of Asp213 in Human Proteinase 3. J Phys Chem A 2009; 113:11783-92. [DOI: 10.1021/jp902930u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric Hajjar
- Department of Physics, University of Cagliari (CA), Italy, Biocomputing Group, IGBMC, Université de Strasbourg, Illkirch, France, and Computational Biology Unit, BCCS, Department of Molecular Biology, University of Bergen, Norway
| | - Annick Dejaegere
- Department of Physics, University of Cagliari (CA), Italy, Biocomputing Group, IGBMC, Université de Strasbourg, Illkirch, France, and Computational Biology Unit, BCCS, Department of Molecular Biology, University of Bergen, Norway
| | - Nathalie Reuter
- Department of Physics, University of Cagliari (CA), Italy, Biocomputing Group, IGBMC, Université de Strasbourg, Illkirch, France, and Computational Biology Unit, BCCS, Department of Molecular Biology, University of Bergen, Norway
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44
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Topal KG, Atilgan C, Demir AS, Aviyente V. Understanding the mode of action of ThDP in benzoylformate decarboxylase. Biopolymers 2009; 93:32-46. [PMID: 19688812 DOI: 10.1002/bip.21291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26, and H281 are catalytically active amino acids. H281 functions as a base to accept H(donor) in the first nucleophilic attack and as an acid in the second, to donate the proton back to O(acceptor). S26 assists H281 in deprotonation of the donor aldehyde and protonation of the acceptor aldehyde. In both the first and second nucleophilic attacks, H70 interacts with O(aldehyde) and aligns it toward the nucleophilic center. H70 has been found to have an electrostatic effect on the approaching aldehyde whose absence would block the initiation of the reaction. The reactivity difference between benzaldehyde (BA) and acetaldehyde (AA) is mainly explained by the steric interactions of the acceptor aldehyde with the surrounding amino acids in the active center of the enzyme.
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45
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Reetz MT, Bocola M, Wang LW, Sanchis J, Cronin A, Arand M, Zou J, Archelas A, Bottalla AL, Naworyta A, Mowbray SL. Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage. J Am Chem Soc 2009; 131:7334-43. [PMID: 19469578 DOI: 10.1021/ja809673d] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Directed evolution of enzymes as enantioselective catalysts in organic chemistry is an alternative to traditional asymmetric catalysis using chiral transition-metal complexes or organocatalysts, the different approaches often being complementary. Moreover, directed evolution studies allow us to learn more about how enzymes perform mechanistically. The present study concerns a previously evolved highly enantioselective mutant of the epoxide hydrolase from Aspergillus niger in the hydrolytic kinetic resolution of racemic glycidyl phenyl ether. Kinetic data, molecular dynamics calculations, molecular modeling, inhibition experiments, and X-ray structural work for the wild-type (WT) enzyme and the best mutant reveal the basis of the large increase in enantioselectivity (E = 4.6 versus E = 115). The overall structures of the WT and the mutant are essentially identical, but dramatic differences are observed in the active site as revealed by the X-ray structures. All of the experimental and computational results support a model in which productive positioning of the preferred (S)-glycidyl phenyl ether, but not the (R)-enantiomer, forms the basis of enhanced enantioselectivity. Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mulheim/Ruhr, Germany.
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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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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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48
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Bruice TC. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 2007; 106:3119-39. [PMID: 16895321 DOI: 10.1021/cr050283j] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas C Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA.
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49
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De Vivo M, Ensing B, Dal Peraro M, Gomez GA, Christianson DW, Klein ML. Proton shuttles and phosphatase activity in soluble epoxide hydrolase. J Am Chem Soc 2007; 129:387-94. [PMID: 17212419 PMCID: PMC2533064 DOI: 10.1021/ja066150c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, a novel metal Mg2+-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, the sEH N-terminal fold belongs to the haloacid dehalogenase (HAD) superfamily, which comprises a vast majority of phosphotransferases. Herein, we present the results of a computational study of the sEH phosphatase activity, which includes classical molecular dynamics (MD) simulations and mixed quantum mechanical/molecular mechanics (QM/MM) calculations. On the basis of experimental results, a two-step mechanism has been proposed and herein investigated: (1) phosphoenzyme intermediate formation and (2) phosphoenzyme intermediate hydrolysis. Building on our earlier work, we now provide a detailed description of the reaction mechanism for the whole catalytic cycle along with its free energy profile. The present computations suggest metaphosphate-like transition states for these phosphoryl transfers. They also reveal that the enzyme promotes water deprotonation and facilitates shuttling of protons via a metal-ligand connecting water bridge (WB). These WB-mediated proton shuttles are crucial for the activation of the solvent nucleophile and for the stabilization of the leaving group. Moreover, due to the conservation of structural features in the N-terminal catalytic site of sEH and other members of the HAD superfamily, we suggest a generalization of our findings to these other metal-dependent phosphatases.
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Affiliation(s)
- Marco De Vivo
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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50
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Celik L, Lund JDD, Schiøtt B. Conformational dynamics of the estrogen receptor alpha: molecular dynamics simulations of the influence of binding site structure on protein dynamics. Biochemistry 2007; 46:1743-58. [PMID: 17249692 DOI: 10.1021/bi061656t] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present 158 ns of unrestrained all-atom molecular dynamics (MD) simulations of the human estrogen receptor alpha ligand binding domain (ERalpha LBD) sampling the conformational changes upon binding of estradiol. The pivotal role of His524 in maintaining the protein structure in the biologically active agonist conformation is elucidated. With His524 modeled as the epsilon-tautomer, a conserved hydrogen bond to the ligand is found in the active complex. Helices 3 and 11 are held together by a hydrogen-bonding network from His524 to Glu339 via Glu419 and Lys531, arresting the ligand in the binding pocket and creating the "mouse trap" binding site for helix 12 (H12). The simulations reveal how His524 serves as a communication point between the two. When estradiol is bound, His524 is positioned correctly for the hydrogen bond network to be established. H12 is then positioned for interaction with the co-activator protein, leading to the biologically active complex. The conformational dynamics of ERalpha LBD is further investigated from simulations of antagonist and apo conformations of the protein. These simulations suggest a likely sequence of events for the transition from the inactive apo structure to the transcriptionally active conformation of ERalpha LBD. Stable conformations are identified where H12 is placed neither in the "mouse trap" nor in the co-activator binding groove, as is the case for antagonist structures of ERalpha LBD. Finally, the influence of such conformations on the biological function of ERalpha is discussed in relationship to the interaction with selective estrogen receptor modulators and endocrine-disrupting compounds.
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Affiliation(s)
- Leyla Celik
- Interdisciplinary Nanoscience Centre (iNANO) and Centre for Insoluble Protein Structures (inSPIN), Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
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