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Zhao LX, Hu W, Jiang ZB, Wang JY, Wang K, Gao S, Fu Y, Ye F. Design, Synthesis, and Bioactivity of Novel 2-(Arylformyl)cyclohexane-1,3-dione Derivatives as HPPD Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17678-17688. [PMID: 37946464 DOI: 10.1021/acs.jafc.3c04651] [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: 11/12/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase inhibitors (Echinochloa crus-galli 1.13.11.27, HPPD) have gained significant popularity as one of the best-selling herbicides worldwide. To identify highly effective HPPD inhibitors, a rational design approach utilizing bioisosterism was employed to create a series of 2-(arylformyl)cyclohexane-1,3-dione derivatives. A total of 29 novel compounds were synthesized and characterized through various techniques, including IR, 1H NMR, 13C NMR, and HRMS. Evaluation of their inhibitory activity against Arabidopsis thaliana HPPD (AtHPPD) revealed that certain derivatives exhibited superior potency compared to mesotrione (IC50 = 0.204 μM). Initial herbicidal activity tests demonstrated that compounds 27 and 28 were comparable to mesotrione in terms of weed control and crop safety, with compound 28 exhibiting enhanced safety in canola crops. Molecular docking analyses indicated that the quinoline rings of compounds 27 and 28 formed more stable π-π interactions with the amino acid residues Phe-360 and Phe-403 in the active cavity of AtHPPD, surpassing the benzene ring of mesotrione. Molecular dynamics simulations and molecular structure comparisons confirmed the robust binding capabilities of compounds 27 and 28 to AtHPPD. This study provides a valuable reference for the development of novel triketone herbicide structures, serving as a blueprint for future advancements in this field.
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Affiliation(s)
- Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Wei Hu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Zi-Bin Jiang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Jia-Yu Wang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Kui Wang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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Leng XY, Gao S, Ma YF, Zhao LX, Wang M, Ye F, Fu Y. Discovery of novel HPPD inhibitors: Virtual screening, molecular design, structure modification and biological evaluation. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105390. [PMID: 37105629 DOI: 10.1016/j.pestbp.2023.105390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD, a Fe(II)/α-ketoglutarate dependent oxygenases), is a popular herbicide target. In this work, two pharmacophore models based on common molecular characteristics (HipHop) and receptor-ligand complex (CBP) were generated for virtual screening for HPPD inhibitors. About 1,000,000 molecules containing diketone structure from PubChem were filtered by Lipinski's rules to build a 3D database. Then the database was screened through combining HipHop model, CBP model, ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction and molecular docking. Subsequently, based on the specific binding mode and affinity of HPPD inhibitors, 4 molecules with high -CDOCKER energy, good aqueous solubility and human safety predicative properties values were screened. From the screening results and combined with previous work, three novel HPPD inhibitors were designed and synthesized through fragment splicing and bioisosterism strategies. Compound IV-a exhibited similar inhibition of Arabidopsis thaliana HPPD (AtHPPD) and herbicidal activity as mesotrione. Crop selectivity showed that compound IV-a had better crop safety than mesotrione. Comparing the molecular properties, ADMET and molecular docking studies indicated that compounds IV-a exhibited better properties than mesotrione, which could be further modified as novel HPPD inhibitor herbicides.
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Affiliation(s)
- Xin-Yu Leng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yi-Fan Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Meng Wang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China.
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China.
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Lin HY, Dong J, Dong J, Yang WC, Yang GF. Insights into 4-hydroxyphenylpyruvate dioxygenase-inhibitor interactions from comparative structural biology. Trends Biochem Sci 2023; 48:568-584. [PMID: 36959016 DOI: 10.1016/j.tibs.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) plays a key role in tyrosine metabolism and has been identified as a promising target for herbicide and drug discovery. The structures of HPPD complexed with different types of inhibitors have been determined previously. We summarize the structures of HPPD complexed with structurally diverse molecules, including inhibitors, natural products, substrates, and catalytic intermediates; from these structures, the detailed inhibitory mechanisms of different inhibitors were analyzed and compared, and the key structural factors determining the slow-binding behavior of inhibitors were identified. Further, we propose four subpockets that accommodate different inhibitor substructures. We believe that these analyses will facilitate in-depth understanding of the enzymatic reaction mechanism and enable the design of new inhibitors with higher potency and selectivity.
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Affiliation(s)
- Hong-Yan Lin
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Jin Dong
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Jiangqing Dong
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Wen-Chao Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
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4
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Wu P, Gu Y, Liao L, Wu Y, Jin J, Wang Z, Zhou J, Shaik S, Wang B. Coordination Switch Drives Selective C−S Bond Formation by the Non‐Heme Sulfoxide Synthases**. Angew Chem Int Ed Engl 2022; 61:e202214235. [DOI: 10.1002/anie.202214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering School of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yang Gu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Langxing Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yanfei Wu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Jiaoyu Jin
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhanfeng Wang
- Center for Advanced Materials Research Beijing Normal University Zhuhai 519087 China
| | - Jiahai Zhou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
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Li L, Lai S, Lin H, Zhao X, Li X, Chen X, Liu J, Yang G, Zhan C. QM/MM study on the O2 activation reaction of 4-hydroxylphenyl pyruvate dioxygenase reveals a common mechanism for α-ketoglutarate dependent dioxygenase. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Lorquin F, Piccerelle P, Orneto C, Robin M, Lorquin J. New insights and advances on pyomelanin production: from microbial synthesis to applications. J Ind Microbiol Biotechnol 2022; 49:6575554. [PMID: 35482661 PMCID: PMC9338888 DOI: 10.1093/jimb/kuac013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/14/2022]
Abstract
Pyomelanin is a brown-black phenolic polymer and results from the oxidation of homogentisic acid (HGA) in the L-tyrosine pathway. As part of the research for natural and active ingredients issued from realistic bioprocesses, this work re-evaluates the HGA pigment and makes an updated inventory of its syntheses, microbial pathways, and properties, with tracks and recent advances for its large-scale production. The mechanism of the HGA polymerization is also well documented. In alkaptonuria, pyomelanin formation leads to connective tissue damages and arthritis, most probably due to the ROS issued from HGA oxidation. While UV radiation on human melanin may generate degradation products, pyomelanin is not photodegradable, is hyperthermostable, and has other properties better than the L-Dopa melanin. This review aims to raise awareness about the potential of this pigment for various applications, not only for skin coloring and protection but also for other cells, materials, and as a promising (semi)conductor for bioelectronics and energy.
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Affiliation(s)
- Faustine Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France.,Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Philippe Piccerelle
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Caroline Orneto
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Maxime Robin
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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Lin HY, Chen X, Dong J, Yang JF, Xiao H, Ye Y, Li LH, Zhan CG, Yang WC, Yang GF. Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study. J Am Chem Soc 2021; 143:15674-15687. [PMID: 34542283 DOI: 10.1021/jacs.1c06227] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing demands for efficient and versatile chemical reactions have prompted innovations in enzyme engineering. A major challenge in engineering α-ketoglutarate-dependent oxygenases is to develop a rational strategy which can be widely used for directly evolving the desired mutant to generate new products. Herein, we report a strategy for rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations. This strategy enriched our understanding of the HPPD catalytic reaction pathway and led to the discovery of a series of HPPD mutants producing hydroxyphenylacetate (HPA) as the alternative product other than the native product homogentisate. The predicted HPPD-Fe(IV)═O-HPA intermediate was further confirmed by the crystal structure of Arabidopsis thaliana HPPD/S267W complexed with HPA. These findings not only provide a good understanding of the structure-function relationship of HPPD but also demonstrate a generally applicable platform for the development of biocatalysts.
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Affiliation(s)
- Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Xi Chen
- College of Chemistry and Material Science, South-Central University for Nationalities, Wuhan 430074, P.R. China
| | - Jin Dong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Han Xiao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Ying Ye
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Lin-Hui Li
- College of Chemistry and Material Science, South-Central University for Nationalities, Wuhan 430074, P.R. China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
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8
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Functional role of residues involved in substrate binding of human 4-hydroxyphenylpyruvate dioxygenase. Biochem J 2021; 478:2201-2215. [PMID: 34047349 DOI: 10.1042/bcj20210005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022]
Abstract
4-Hydroxylphenylpyruvate dioxygenase (HPPD) catalyzes the conversion of 4-hydroxylphenylpyruvate (HPP) to homogentisate, the important step for tyrosine catabolism. Comparison of the structure of human HPPD with the substrate-bound structure of A. thaliana HPPD revealed notably different orientations of the C-terminal helix. This helix performed as a closed conformation in human enzyme. Simulation revealed a different substrate-binding mode in which the carboxyl group of HPP interacted by a H-bond network formed by Gln334, Glu349 (the metal-binding ligand), and Asn363 (in the C-terminal helix). The 4-hydroxyl group of HPP interacted with Gln251 and Gln265. The relative activity and substrate-binding affinity were preserved for the Q334A mutant, implying the alternative role of Asn363 for HPP binding and catalysis. The reduction in kcat/Km of the Asn363 mutants confirmed the critical role in catalysis. Compared to the N363A mutant, the dramatic reduction in the Kd and thermal stability of the N363D mutant implies the side-chain effect in the hinge region rotation of the C-terminal helix. The activity and binding affinity were not recovered by double mutation; however, the 4-hydroxyphenylacetate intermediate formation by the uncoupled reaction of Q334N/N363Q and Q334A/N363D mutants indicated the importance of the H-bond network in the electrophilic reaction. These results highlight the functional role of the H-bond network in a closed conformation of the C-terminal helix to stabilize the bound substrate. The extremely low activity and reduction in Q251E's Kd suggest that interaction coupled with the H-bond network is crucial to locate the substrate for nucleophilic reaction.
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9
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Wang X, Lin H, Liu J, Zhao X, Chen X, Yang W, Yang G, Zhan CG. The structure of 4-hydroxylphenylpyruvate dioxygenase complexed with 4-hydroxylphenylpyruvic acid reveals an unexpected inhibition mechanism. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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10
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Tsukamoto M, Kikugawa H, Nagayama S, Suganuma T, Okita T, Miyamoto H. Discovery and structure optimization of a novel corn herbicide, tolpyralate. JOURNAL OF PESTICIDE SCIENCE 2021; 46:152-159. [PMID: 34135677 PMCID: PMC8175215 DOI: 10.1584/jpestics.d20-031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Tolpyralate, a new selective postemergence herbicide developed for the weed control in corn, possesses a unique chemical structure with a 1-alkoxyethyl methyl carbonate group on the N-ethyl pyrazole moiety. This compound shows high herbicidal activity against many weed species, including glyphosate-resistant Amaranthus tuberculatus. Tolpyralate targets 4-hydroxyphenylpyruvate dioxygenase (4-HPPD), which is involved in the tyrosine degradation pathway. Inhibition of the enzyme destroys the chlorophyll, thereby killing the susceptible weeds. Details of tolpyralate discovery, structure optimization, and biological activities are described.
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Affiliation(s)
- Masamitsu Tsukamoto
- Bioscience Business Headquarters, Ishihara Sangyo Kaisha, Ltd., 1–3–15 Edobori, Nishi-ku, Osaka 550–0002, Japan
| | - Hiroshi Kikugawa
- Bioscience Business Headquarters, Ishihara Sangyo Kaisha, Ltd., 1–3–15 Edobori, Nishi-ku, Osaka 550–0002, Japan
| | | | | | - Tatsuya Okita
- Central Research Institute, Ishihara Sangyo Kaisha, Ltd
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Latifi R, Minnick JL, Quesne MG, de Visser SP, Tahsini L. Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways. Dalton Trans 2020; 49:4266-4276. [PMID: 32141456 DOI: 10.1039/d0dt00007h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Matthew G Quesne
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon, OX110FA, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester M1 7DN, UK.
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
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He B, Wu FX, Yu LK, Wu L, Chen Q, Hao GF, Yang WC, Lin HY, Yang GF. Discovery of Novel Pyrazole-Quinazoline-2,4-dione Hybrids as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5059-5067. [PMID: 32286826 DOI: 10.1021/acs.jafc.0c00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) has been identified as one of the most significant targets in herbicide discovery for resistant weed control. In a continuing effort to discover potent novel HPPD inhibitors, we adopted a ring-expansion strategy to design a series of novel pyrazole-quinazoline-2,4-dione hybrids based on the previously discovered pyrazole-isoindoline-1,3-dione scaffold. One compound, 3-(2-chlorophenyl)-6-(5-hydroxy-1,3-dimethyl-1H-pyrazole-4-carbonyl)-1,5-dimethylquinazoline-2,4(1H,3H)-dione (9bj), displayed excellent potency against AtHPPD, with an IC50 value of 84 nM, which is approximately 16-fold more potent than pyrasulfotole (IC50 = 1359 nM) and 2.7-fold more potent than mesotrione (IC50 = 226 nM). Furthermore, the co-crystal structure of the AtHPPD-9bj complex (PDB ID 6LGT) was determined at a resolution of 1.75 Å. Similar to the existing HPPD inhibitors, compound 9bj formed a bidentate chelating interaction with the metal ion and a π-π stacking interaction with Phe381 and Phe424. In contrast, o-chlorophenyl at the N3 position of quinazoline-2,4-dione with a double conformation was surrounded by hydrophobic residues (Met335, Leu368, Leu427, Phe424, Phe392, and Phe381). Remarkably, the greenhouse assay indicated that most compounds displayed excellent herbicidal activity (complete inhibition) against at least one of the tested weeds at the application rate of 150 g of active ingredient (ai)/ha. Most promisingly, compounds 9aj and 9bi not only exhibited prominent weed control effects with a broad spectrum but also showed very good crop safety to cotton, peanuts, and corn at the dose of 150 g of ai/ha.
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Affiliation(s)
- Bo He
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Liang-Kun Yu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Lei Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
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13
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Feng AN, Huang CW, Lin CH, Chang YL, Ni MY, Lee HJ. Role of the N-terminus in human 4-hydroxyphenylpyruvate dioxygenase activity. J Biochem 2020; 167:315-322. [PMID: 31722428 DOI: 10.1093/jb/mvz092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/22/2019] [Indexed: 11/14/2022] Open
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a key enzyme in tyrosine catabolism, catalysing the oxidation of 4-hydroxyphenylpyruvate to homogentisate. Genetic deficiency of this enzyme causes type III tyrosinaemia. The enzyme comprises two barrel-shaped domains formed by the N- and C-termini, with the active site located in the C-terminus. This study investigated the role of the N-terminus, located at the domain interface, in HPPD activity. We observed that the kcat/Km decreased ∼8-fold compared with wild type upon removal of the 12 N-terminal residues (ΔR13). Interestingly, the wild-type level of activity was retained in a mutant missing the 17 N-terminal residues, with a kcat/Km 11-fold higher than that of the ΔR13 mutant; however, the structural stability of this mutant was lower than that of wild type. A 2-fold decrease in catalytic efficiency was observed for the K10A and E12A mutants, indicating synergism between these residues in the enzyme catalytic function. A molecular dynamics simulation showed large RMS fluctuations in ΔR13 suggesting that conformational flexibility at the domain interface leads to lower activity in this mutant. These results demonstrate that the N-terminus maintains the stability of the domain interface to allow for catalysis at the active site of HPPD.
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Affiliation(s)
- An-Ning Feng
- Department of Cardiology, Cheng Hsin General Hospital, No. 45, Cheng Hsin St. Pai-Tou, Taipei 11220, Taiwan
| | - Chih-Wei Huang
- Department of Pharmacy Practice, Tri-Service General Hospital, No. 325, Sec. 2, Chenggong Rd., Neihu, Taipei 11490, Taiwan.,School of Pharmacy, National Defense Medical Center, No. 161, Sec. 6, Minchuan East Rd., Neihu, Taipei 11490, Taiwan
| | - Chi-Huei Lin
- Department of Biochemistry, National Defense Medical Center, No. 161, Sec. 6, Minchuan East Rd., Neihu, Taipei 11490, Taiwan
| | - Yung-Lung Chang
- Department of Biochemistry, National Defense Medical Center, No. 161, Sec. 6, Minchuan East Rd., Neihu, Taipei 11490, Taiwan
| | - Meng-Yuan Ni
- Department of Biochemistry, National Defense Medical Center, No. 161, Sec. 6, Minchuan East Rd., Neihu, Taipei 11490, Taiwan
| | - Hwei-Jen Lee
- Department of Biochemistry, National Defense Medical Center, No. 161, Sec. 6, Minchuan East Rd., Neihu, Taipei 11490, Taiwan
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14
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Wang MM, Huang H, Shu L, Liu JM, Zhang JQ, Yan YL, Zhang DY. Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors. Beilstein J Org Chem 2020; 16:233-247. [PMID: 32180842 PMCID: PMC7059547 DOI: 10.3762/bjoc.16.25] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
A series of aryloxyacetic acid derivatives were designed and synthesized as 4-hydoxyphenylpyruvate dioxygenase (HPPD) inhibitors. Preliminary bioassay results reveal that these derivatives are promising Arabidopsis thaliana HPPD (AtHPPD) inhibitors, in particular compounds I12 (Ki = 0.011 µM) and I23 (Ki = 0.012 µM), which exhibit similar activities to that of mesotrione, a commercial HPPD herbicide (Ki = 0.013 µM). Furthermore, the newly synthesized compounds show significant greenhouse herbicidal activities against tested weeds at dosages of 150 g ai/ha. In particular, II4 exhibited high herbicidal activity for pre-emergence treatment that was slightly better than that of mesotrione. In addition, compound II4 was safe for weed control in maize fields at a rate of 150 g ai/ha, and was identified as the most potent candidate for a novel HPPD inhibitor herbicide. The compounds described herein may provide useful guidance for the design of new HPPD inhibiting herbicides and their modification.
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Affiliation(s)
- Man-Man Wang
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Hao Huang
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Lei Shu
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jian-Min Liu
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jian-Qiu Zhang
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yi-Le Yan
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Da-Yong Zhang
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
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15
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Singh W, Quinn D, Moody TS, Huang M. Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes. J Phys Chem B 2019; 123:7801-7811. [PMID: 31469562 DOI: 10.1021/acs.jpcb.9b06064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.
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Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom.,Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Thomas S Moody
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate , Athlone , Co. Roscommon , Ireland
| | - Meilan Huang
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom
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16
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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17
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Quesne MG, Silveri F, de Leeuw NH, Catlow CRA. Advances in Sustainable Catalysis: A Computational Perspective. Front Chem 2019; 7:182. [PMID: 31032245 PMCID: PMC6473102 DOI: 10.3389/fchem.2019.00182] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
The enormous challenge of moving our societies to a more sustainable future offers several exciting opportunities for computational chemists. The first principles approach to "catalysis by design" will enable new and much greener chemical routes to produce vital fuels and fine chemicals. This prospective outlines a wide variety of case studies to underscore how the use of theoretical techniques, from QM/MM to unrestricted DFT and periodic boundary conditions, can be applied to biocatalysis and to both homogeneous and heterogenous catalysts of all sizes and morphologies to provide invaluable insights into the reaction mechanisms they catalyze.
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Affiliation(s)
- Matthew G Quesne
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Fabrizio Silveri
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Nora H de Leeuw
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
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18
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Lu J, Lai W. Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations. ChemistryOpen 2019; 8:228-235. [PMID: 30828510 PMCID: PMC6382310 DOI: 10.1002/open.201800259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/30/2019] [Indexed: 12/03/2022] Open
Abstract
NOV1, a stilbene cleavage oxygenase, catalyzes the cleavage of the central double bond of stilbenes to two phenolic aldehydes, using a 4-His Fe(II) center and dioxygen. Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the reaction mechanism of the central double bond cleavage of phytoalexin resveratrol by NOV1. Our results showed that the oxygen molecule prefers to bind to the iron center in a side-on fashion, as suggested from the experiment. The quintet Fe-O2 complex with the side-on superoxo antiferromagnetic coupled to the resveratrol radical is identified as the reactive oxygen species. The QM/MM results support the dioxygenase mechanism involving a dioxetane intermediate with a rate-limiting barrier of 10.0 kcal mol-1. The alternative pathway through an epoxide intermediate is ruled out due to a larger rate-limiting barrier (26.8 kcal mol-1). These findings provide important insight into the catalytic mechanism of carotenoid cleavage oxygenases and also the dioxygen activation of non-heme enzymes.
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Affiliation(s)
- Jiarui Lu
- Department of ChemistryRenmin University of ChinaNo. 59 Zhongguancun Street, Haidian DistrictBeijing100872P. R. China
| | - Wenzhen Lai
- Department of ChemistryRenmin University of ChinaNo. 59 Zhongguancun Street, Haidian DistrictBeijing100872P. R. China
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19
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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20
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Li HB, Li L, Li JX, Han TF, He JL, Zhu YQ. Novel HPPD inhibitors: triketone 2H-benzo[b][1,4]oxazin-3(4H)-one analogs. PEST MANAGEMENT SCIENCE 2018; 74:579-589. [PMID: 28941309 DOI: 10.1002/ps.4739] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Herbicides that inhibit 4-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) are very important for grass weed control. In order to discover novel HPPD herbicides, a series of triketone 2H-benzo[b] oxazin-3(4H)-one analogs was designed and synthesized. RESULTS In comparison with the commercial triketone HPPD herbicide mesotrione (IC50 = 0.252 μM), some of these new triketone analogs displayed excellent HPPD inhibitory potency in vitro, for example B39 (IC50 = 0.172 μM) and B41 (IC50 = 0.156 μM). In addition, some of these compounds exhibited pre- and post-emergence herbicidal activity similar to mesotrione when applied at 375 g/ha. CONCLUSION Many of the title compounds described in this paper could be important lead structures for the further development of novel HPPD herbicides. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Hua-Bin Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
- National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, Tianjin, China
| | - Lei Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Jun-Xian Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Ting-Feng Han
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Jing-Li He
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - You-Quan Zhu
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
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21
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Fu Y, Sun YN, Yi KH, Li MQ, Cao HF, Li JZ, Ye F. Combination of Virtual Screening Protocol by in Silico toward the Discovery of Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Front Chem 2018; 6:14. [PMID: 29468151 PMCID: PMC5807903 DOI: 10.3389/fchem.2018.00014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) is a potent new bleaching herbicide target. Therefore, in silico structure-based virtual screening was performed in order to speed up the identification of promising HPPD inhibitors. In this study, an integrated virtual screening protocol by combining 3D-pharmacophore model, molecular docking and molecular dynamics (MD) simulation was established to find novel HPPD inhibitors from four commercial databases. 3D-pharmacophore Hypo1 model was applied to efficiently narrow potential hits. The hit compounds were subsequently submitted to molecular docking studies, showing four compounds as potent inhibitor with the mechanism of the Fe(II) coordination and interaction with Phe360, Phe403, and Phe398. MD result demonstrated that nonpolar term of compound 3881 made great contributions to binding affinities. It showed an IC50 being 2.49 μM against AtHPPD in vitro. The results provided useful information for developing novel HPPD inhibitors, leading to further understanding of the interaction mechanism of HPPD inhibitors.
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Affiliation(s)
- Ying Fu
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Yi-Na Sun
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Ke-Han Yi
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Ming-Qiang Li
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Hai-Feng Cao
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fei Ye
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, China
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22
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Ndikuryayo F, Moosavi B, Yang WC, Yang GF. 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors: From Chemical Biology to Agrochemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8523-8537. [PMID: 28903556 DOI: 10.1021/acs.jafc.7b03851] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The development of new herbicides is receiving considerable attention to control weed biotypes resistant to current herbicides. Consequently, new enzymes are always desired as targets for herbicide discovery. 4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is an enzyme engaged in photosynthetic activity and catalyzes the transformation of 4-hydroxyphenylpyruvic acid (HPPA) into homogentisic acid (HGA). HPPD inhibitors constitute a promising area of discovery and development of innovative herbicides with some advantages, including excellent crop selectivity, low application rates, and broad-spectrum weed control. HPPD inhibitors have been investigated for agrochemical interests, and some of them have already been commercialized as herbicides. In this review, we mainly focus on the chemical biology of HPPD, discovery of new potential inhibitors, and strategies for engineering transgenic crops resistant to current HPPD-inhibiting herbicides. The conclusion raises some relevant gaps for future research directions.
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Affiliation(s)
- Ferdinand Ndikuryayo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, P. R. China
| | - Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, P. R. China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 30071, P. R. China
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23
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Fu Y, Sun YN, Yi KH, Li MQ, Cao HF, Li JZ, Ye F. 3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors. Molecules 2017; 22:molecules22060959. [PMID: 28598377 PMCID: PMC6152767 DOI: 10.3390/molecules22060959] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 06/05/2017] [Indexed: 11/16/2022] Open
Abstract
p-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only the useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical herbicides. A combined in silico structure-based pharmacophore and molecular docking-based virtual screening were performed to identify novel potential HPPD inhibitors. The complex-based pharmacophore model (CBP) with 0.721 of ROC used for screening compounds showed remarkable ability to retrieve known active ligands from among decoy molecules. The ChemDiv database was screened using CBP-Hypo2 as a 3D query, and the best-fit hits subjected to molecular docking with two methods of LibDock and CDOCKER in Accelrys Discovery Studio 2.5 (DS 2.5) to discern interactions with key residues at the active site of HPPD. Four compounds with top rankings in the HipHop model and well-known binding model were finally chosen as lead compounds with potential inhibitory effects on the active site of target. The results provided powerful insight into the development of novel HPPD inhibitors herbicides using computational techniques.
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Affiliation(s)
- Ying Fu
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yi-Na Sun
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Ke-Han Yi
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Ming-Qiang Li
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Hai-Feng Cao
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, 199 West Donggang Rd., Lanzhou 730000, China.
| | - Fei Ye
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin 150030, China.
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24
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Qiao QA, Li Q, Liu C, Sun X, Cai H, Sun L, Wang H. A Theoretical Study on the Mechanism of Decarboxylations for Hydroxymandelate Synthase. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qing-An Qiao
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Qiuxian Li
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Changchun Liu
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Xiao Sun
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Honglan Cai
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Lixiang Sun
- School of Chemistry and Materials Science; Ludong University; Yantai 264025 China
| | - Huayang Wang
- School of Physics and Optoelectronic Engineering; Ludong University; Yantai 264025 China
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25
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Álvarez-Barcia S, Kästner J. Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem B 2017; 121:5347-5354. [PMID: 28490178 DOI: 10.1021/acs.jpcb.7b03477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.
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Affiliation(s)
- Sonia Álvarez-Barcia
- Institute for Theoretical Chemistry, University of Stuttgart , Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart , Pfaffenwaldring 55, 70569 Stuttgart, Germany
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26
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Wei WJ, Siegbahn PEM, Liao RZ. Theoretical Study of the Mechanism of the Nonheme Iron Enzyme EgtB. Inorg Chem 2017; 56:3589-3599. [PMID: 28277674 DOI: 10.1021/acs.inorgchem.6b03177] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sulfoxidation or the S-C bond formation takes place first. The calculations suggest that the S-O bond formation occurs first between the thiolate and the ferric superoxide, followed by homolytic O-O bond cleavage, very similar to the case of cysteine dioxygenase. Subsequently, proton transfer from a second-shell residue Tyr377 to the newly generated iron-oxo moiety takes place, which is followed by proton transfer from the TMH imidazole to Tyr377, facilitated by two crystallographically observed water molecules. Next, the S-C bond is formed between γGC and TMH, followed by proton transfer from the imidazole CH moiety to Tyr377, which was calculated to be the rate-limiting step for the whole reaction, with a barrier of 17.9 kcal/mol in the quintet state. The calculated barrier for the rate-limiting step agrees quite well with experimental kinetic data. Finally, this proton is transferred back to the imidazole nitrogen to form the product. The alternative thiyl radical attack mechanism has a very high barrier, being 25.8 kcal/mol, ruling out this possibility.
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Affiliation(s)
- Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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27
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Santucci A, Bernardini G, Braconi D, Petricci E, Manetti F. 4-Hydroxyphenylpyruvate Dioxygenase and Its Inhibition in Plants and Animals: Small Molecules as Herbicides and Agents for the Treatment of Human Inherited Diseases. J Med Chem 2017; 60:4101-4125. [PMID: 28128559 DOI: 10.1021/acs.jmedchem.6b01395] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review mainly focuses on the physiological function of 4-hydroxyphenylpyruvate dioxygenase (HPPD), as well as on the development and application of HPPD inhibitors of several structural classes. Among them, one illustrative example is represented by compounds belonging to the class of triketone compounds. They were discovered by serendipitous observations on weed growth and were developed as bleaching herbicides. Informed reasoning on nitisinone (NTBC, 14), a triketone that failed to reach the final steps of the herbicidal design and development process, allowed it to become a curative agent for type I tyrosinemia (T1T) and to enter clinical trials for alkaptonuria. These results boosted the research of new compounds able to interfere with HPPD activity to be used for the treatment of the tyrosine metabolism-related diseases.
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Affiliation(s)
- Annalisa Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Elena Petricci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , via A. Moro 2, I-53100 Siena, Italy
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , via A. Moro 2, I-53100 Siena, Italy
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28
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Dong G, Ryde U. O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162. Inorg Chem 2016; 55:11727-11735. [DOI: 10.1021/acs.inorgchem.6b01732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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29
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Peck SC, van der Donk WA. Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes. J Biol Inorg Chem 2016; 22:381-394. [PMID: 27783267 DOI: 10.1007/s00775-016-1399-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
This review discusses the current mechanistic understanding of a group of mononuclear non-heme iron-dependent enzymes that catalyze four-electron oxidation of their organic substrates without the use of any cofactors or cosubstrates. One set of enzymes acts on α-ketoacid-containing substrates, coupling decarboxylation to oxygen activation. This group includes 4-hydroxyphenylpyruvate dioxygenase, 4-hydroxymandelate synthase, and CloR involved in clorobiocin biosynthesis. A second set of enzymes acts on substrates containing a thiol group that coordinates to the iron. This group is comprised of isopenicillin N synthase, thiol dioxygenases, and enzymes involved in the biosynthesis of ergothioneine and ovothiol. The final group of enzymes includes HEPD and MPnS that both carry out the oxidative cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate but generate different products. Commonalities amongst many of these enzymes are discussed and include the initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species.
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Affiliation(s)
- Spencer C Peck
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
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30
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Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
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31
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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32
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Catalytic strategies of the non-heme iron dependent oxygenases and their roles in plant biology. Curr Opin Chem Biol 2016; 31:126-35. [PMID: 27015291 PMCID: PMC4879150 DOI: 10.1016/j.cbpa.2016.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 12/18/2022]
Abstract
Current evidence for iron-oxo reactive intermediates is reviewed. In crystallo intermediates detected in a native extradiol dioxygenase reaction. Carotenoid cleavage dioxygenases catalyse strigolactone biosynthesis. Identification of plant cysteine oxidases involved in the plant hypoxic response. Applications of enzyme manipulation to plant biology and agriculture are discussed.
Non-heme iron-dependent oxygenases catalyse the incorporation of O2 into a wide range of biological molecules and use diverse strategies to activate their substrates. Recent kinetic studies, including in crystallo, have provided experimental support for some of the intermediates used by different subclasses of this enzyme family. Plant non-heme iron-dependent oxygenases have diverse and important biological roles, including in growth signalling, stress responses and secondary metabolism. Recently identified roles include in strigolactone biosynthesis, O-demethylation in morphine biosynthesis and regulating the stability of hypoxia-responsive transcription factors. We discuss current structural and mechanistic understanding of plant non-heme iron oxygenases, and how their chemical/genetic manipulation could have agricultural benefit, for example, for improved yield, stress tolerance or herbicide development.
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33
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Wójcik A, Radoń M, Borowski T. Mechanism of O2 Activation by α-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study. J Phys Chem A 2016; 120:1261-74. [PMID: 26859709 DOI: 10.1021/acs.jpca.5b12311] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Four mechanisms previously proposed for dioxygen activation catalyzed by α-keto acid dependent oxygenases (α-KAO) were studied with dispersion-corrected DFT methods employing B3LYP and TPSSh functionals in combination with triple-ζ basis set (cc-pVTZ). The aim of this study was to revisit mechanisms suggested in the past decade and resolve remaining issues related to dioxygen activation. Mechanism A, which runs on the quintet potential energy surface (PES) and includes formation of an Fe(III)-superoxide radical anion complex, subsequent oxidative decarboxylation, and O-O bond cleavage, was found to be most likely. However, mechanism B taking place on the septet PES involves a rate limiting barrier comparable to the one found for mechanism A, and thus it cannot be excluded, though two other mechanisms (C and D) were ruled out. Mechanism C is a minor variation of mechanism A, whereas mechanism D proceeds through formation of a triplet Fe(IV)-alkyl peroxo bridged intermediate. The study covered also full optimization of relevant minimum energy crossing points (MECPs). The relative energy of critical intermediates was also studied with the CCSD(T) method in order to benchmark TPSSh and B3LYP functionals with respect to their credibility in predicting relative energies of septet and triplet spin states of the ternary enzyme-Fe-α-keto glutarate (α-KG)-O2 complex.
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Affiliation(s)
- Anna Wójcik
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , ul. Gronostajowa 7, 30-387 Cracow, Poland
| | - Mariusz Radoń
- Department of Chemistry, Jagiellonian University , ul. Ingardena 3, 30-060 Cracow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8, 30-239 Cracow, Poland
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34
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Lei K, Hua XW, Tao YY, Liu Y, Liu N, Ma Y, Li YH, Xu XH, Kong CH. Discovery of (2-benzoylethen-1-ol)-containing 1,2-benzothiazine derivatives as novel 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibiting-based herbicide lead compounds. Bioorg Med Chem 2016; 24:92-103. [DOI: 10.1016/j.bmc.2015.11.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
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35
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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36
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Shah DD, Moran GR. 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase: 2-Oxo Acid-Dependent Oxygenases of Importance to Agriculture and Medicine. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite a separate evolutionary lineage, 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are appropriately grouped with the 2-oxo acid-dependent oxygenase (2OADO) family of enzymes. HPPD and HMS accomplish highly similar overall chemistry to that observed in the majority of 2OADOs but require only two substrates rather than three. 2OADOs typically use the 2-oxo acid of 2-oxoglutarate (2OG) as a source of electrons to reduce and activate dioxygen in order to oxidize a third specific substrate. HPPD and HMS use instead the pyruvate substituent of 4-hydroxyphenylpyruvate to activate dioxygen and then proceed to also hydroxylate this substrate, each yielding a distinctly different aromatic product. HPPD catalyses the second and committed step of tyrosine catabolism, a pathway common to nearly all aerobes. Plants require the HPPD reaction to biosynthesize plastoquinones and therefore HPPD inhibitors can have potent herbicidal activity. The ubiquity of the HPPD reaction, however, has meant that HPPD-specific molecules developed as herbicides have other uses in different forms of life. In humans herbicidal HPPD inhibitors can be used therapeutically to alleviate specific inborn defects and also to retard the progress of certain bacterial and fungal infections. This review is intended as a concise overview of the contextual and catalytic chemistries of HPPD and HMS.
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Affiliation(s)
- Dhara D. Shah
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
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37
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Sheet D, Bhattacharya S, Paine TK. Dioxygen activation and two consecutive oxidative decarboxylations of phenylpyruvate by nonheme iron(II) complexes: functional models of hydroxymandelate synthase (HMS) and CloR. Chem Commun (Camb) 2015; 51:7681-4. [PMID: 25850011 DOI: 10.1039/c5cc01652e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two mononuclear iron(ii)-phenylpyruvate complexes of monoanionic facial N3 ligands are reported to react with dioxygen to undergo two consecutive oxidative decarboxylation steps via an iron-mandelate complex mimicking the function of HMS and CloR.
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Affiliation(s)
- Debobrata Sheet
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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38
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Wang DW, Lin HY, Cao RJ, Yang SG, Chen Q, Hao GF, Yang WC, Yang GF. Synthesis and herbicidal evaluation of triketone-containing quinazoline-2,4-diones. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11786-11796. [PMID: 25405813 DOI: 10.1021/jf5048089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Exploring novel 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) inhibitors is one of the most promising research directions in herbicide discovery. To discover new triketone herbicides with broad-spectrum weed control as well as excellent crop selectivity, a series of (total 52) novel triketone-containing quinazoline-2,4-dione derivatives were synthesized and further bioevaluated. The greenhouse testing indicated that many of the newly synthesized compounds showed better or excellent herbicidal activity against broadleaf and monocotyledonous weeds at the dosages of 37.5-150 g of active ingredient (ai)/ha. The structure and activity relationship in this study indicated that the triketone-containing quinazoline-2,4-dione motif has possessed great impact on herbicide activity and may be used for further optimization. Among the new compounds, III-b and VI-a-VI-d displayed a broader spectrum of weed control than mesotrione. In addition, the compound III-b also demonstrated comparatively superior crop selectivity to mesotrione, thus possessing great potential for weed control in the field.
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Affiliation(s)
- Da-Wei Wang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan, Hubei 430079, People's Republic of China
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39
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Senn HM. Insights into enzymatic halogenation from computational studies. Front Chem 2014; 2:98. [PMID: 25426489 PMCID: PMC4227530 DOI: 10.3389/fchem.2014.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.
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Affiliation(s)
- Hans M. Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, UK
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40
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Wójcik A, Broclawik E, Siegbahn PEM, Lundberg M, Moran G, Borowski T. Role of Substrate Positioning in the Catalytic Reaction of 4-Hydroxyphenylpyruvate Dioxygenase—A QM/MM Study. J Am Chem Soc 2014; 136:14472-85. [DOI: 10.1021/ja506378u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Wójcik
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
- Department
of Computational Biophysics and Bioinformatics, Faculty of Biochemistry,
Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Cracow, Poland
| | - Ewa Broclawik
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
| | - Per E. M. Siegbahn
- Department
of Organic Chemistry, Stockholm University, S-106 91, Stockholm, Sweden
| | - Marcus Lundberg
- Ångstrom
Laboratory, Department of Chemistry, Uppsala University, Box 518, SE-751 20 Uppsala, Sweden
| | - Graham Moran
- Department
of Chemistry and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Tomasz Borowski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
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41
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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42
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de Visser SP, Quesne MG, Martin B, Comba P, Ryde U. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. Chem Commun (Camb) 2014; 50:262-82. [DOI: 10.1039/c3cc47148a] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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43
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Borowski T, Broclawik E. Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/978-3-642-28554-7_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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44
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4-Hydroxyphenylpyruvate dioxygenase and hydroxymandelate synthase: exemplars of the α-keto acid dependent oxygenases. Arch Biochem Biophys 2013; 544:58-68. [PMID: 24211436 DOI: 10.1016/j.abb.2013.10.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are outliers within the α-keto acid dependent oxygenase (αKAO) family. HPPD and HMS catalyze the chemistry of the majority of enzymes within the αKAO family but are clearly mechanistically convergent, having a grossly different structural topology. Some of the unique characteristics of HPPD and HMS have elucidated select parts of the catalytic cycle that are obscured in other family members. Moreover, the inhibitory chemistry of HPPD is a phenomenon with ever-expanding relevance across all kingdoms of life. This review is a synopsis of the literature pertaining to HPPD and HMS. It is not intended as an exhaustive compilation of all observations made for these enzymes but rather a condensed narrative that connects those studies that have advanced the understanding of the chemistry of both enzymes.
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45
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Shah DD, Conrad JA, Moran GR. Intermediate Partitioning Kinetic Isotope Effects for the NIH Shift of 4-Hydroxyphenylpyruvate Dioxygenase and the Hydroxylation Reaction of Hydroxymandelate Synthase Reveal Mechanistic Complexity. Biochemistry 2013; 52:6097-107. [DOI: 10.1021/bi400534q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dhara D. Shah
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
| | - John A. Conrad
- Department
of Chemistry, University of Nebraska—Omaha,
6001 Dodge Street, Omaha, Nebraska 68182-0109, United States
| | - Graham R. Moran
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
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46
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Di Giuro CML, Konstantinovics C, Rinner U, Nowikow C, Leitner E, Straganz GD. Chiral hydroxylation at the mononuclear nonheme Fe(II) center of 4-(S) hydroxymandelate synthase--a structure-activity relationship analysis. PLoS One 2013; 8:e68932. [PMID: 23935907 PMCID: PMC3720870 DOI: 10.1371/journal.pone.0068932] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 06/04/2013] [Indexed: 11/18/2022] Open
Abstract
(S)-Hydroxymandelate synthase (Hms) is a nonheme Fe(II) dependent dioxygenase that catalyzes the oxidation of 4-hydroxyphenylpyruvate to (S)-4-hydroxymandelate by molecular oxygen. In this work, the substrate promiscuity of Hms is characterized in order to assess its potential for the biosynthesis of chiral α-hydroxy acids. Enzyme kinetic analyses, the characterization of product spectra, quantitative structure activity relationship (QSAR) analyses and in silico docking studies are used to characterize the impact of substrate properties on particular steps of catalysis. Hms is found to accept a range of α-oxo acids, whereby the presence of an aromatic substituent is crucial for efficient substrate turnover. A hydrophobic substrate binding pocket is identified as the likely determinant of substrate specificity. Upon introduction of a steric barrier, which is suspected to obstruct the accommodation of the aromatic ring in the hydrophobic pocket during the final hydroxylation step, the racemization of product is obtained. A steady state kinetic analysis reveals that the turnover number of Hms strongly correlates with substrate hydrophobicity. The analysis of product spectra demonstrates high regioselectivity of oxygenation and a strong coupling efficiency of C-C bond cleavage and subsequent hydroxylation for the tested substrates. Based on these findings the structural basis of enantioselectivity and enzymatic activity is discussed.
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Affiliation(s)
- Cristiana M. L. Di Giuro
- Institute for Biotechnology and Biochemical Engineering, Graz University of Technology, Graz, Austria
| | - Cornelia Konstantinovics
- Institute for Biotechnology and Biochemical Engineering, Graz University of Technology, Graz, Austria
| | - Uwe Rinner
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Christina Nowikow
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Graz, Austria
| | - Grit D. Straganz
- Institute for Biotechnology and Biochemical Engineering, Graz University of Technology, Graz, Austria
- * E-mail:
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47
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Lundberg M, Borowski T. Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.03.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Abstract
From a generated PES, one can determine the relative energies of species involved, the sequence in which they occur, and the activation barrier(s) associated with individual steps or the overall mechanism. Furthermore, they can provide more insights than a simple indication of a path of sequential mechanistic structures and their energetic relationships. The investigation into the activation of O2 by alpha-ketoglutarate-dependent dioxygenase (AlkB) clearly shows the opportunity for spin inversion, where one can see that the lowest energy product may be formed via several possible routes. In the investigation of uroporphyrinogen decarboxylase III (UROD), the use of QM/MM methods allowed for the inclusion of the anisotropic protein environment providing greater insight into the rate-limiting barrier. Lastly, the mechanism of 6-phospho-α-glucosidase (GlvA) was discussed using different active site models. In particular, a continuum model PES was compared to the gas-phase PES.
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49
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Miłaczewska A, Broclawik E, Borowski T. On the Catalytic Mechanism of (S)-2-Hydroxypropylphosphonic Acid Epoxidase (HppE): A Hybrid DFT Study. Chemistry 2012; 19:771-81. [DOI: 10.1002/chem.201202825] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/10/2022]
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50
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Wójcik A, Broclawik E, Siegbahn PEM, Borowski T. Mechanism of benzylic hydroxylation by 4-hydroxymandelate synthase. A computational study. Biochemistry 2012; 51:9570-80. [PMID: 23126679 DOI: 10.1021/bi3010957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to an Fe(IV)═O-hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe(IV)═O to perform hydroxylation of the benzylic carbon, whereas in HPPD, the reactive oxoferryl intermediate attacks the aromatic ring of HPA. This study focuses on this part of the HMS catalytic cycle that starts from the oxoferryl intermediate and aims to identify interactions within the active site that are responsible for enzyme specificity. To this end, a HMS-Fe(IV)═O-HPA complex was modeled with molecular dynamics simulations. On the basis of the molecular dynamics-equilibrated structure, an active site model suitable for quantum chemical investigations was constructed and used for density functional theory (B3LYP) calculations of the mechanism of the native reaction of HMS, i.e., benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of this study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role in directing the reaction of Fe(IV)═O into either the HMS or the HPPD channel.
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Affiliation(s)
- Anna Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
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