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Nan JX, Dong J, Cao JQ, Huang GY, Shi XX, Wei XF, Chen Q, Lin HY, Yang GF. Structure-Based Design of 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor as a Potential Herbicide for Cotton Fields. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5783-5795. [PMID: 36977356 DOI: 10.1021/acs.jafc.2c08448] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is one of the most promising herbicide targets for the development of agricultural chemicals owing to its unique mechanism of action in plants. We previously reported on the co-crystal structure of Arabidopsis thaliana (At) HPPD complexed with methylbenquitrione (MBQ), an inhibitor of HPPD that we previously discovered. Based on this crystal structure, and in an attempt to discover even more effective HPPD-inhibiting herbicides, we designed a family of triketone-quinazoline-2,4-dione derivatives featuring a phenylalkyl group through increasing the interaction between the substituent at the R1 position and the amino acid residues at the active site entrance of AtHPPD. Among the derivatives, 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-(1-phenylethyl)quinazoline-2,4(1H,3H)-dione (23) was identified as a promising compound. The co-crystal structure of compound 23 with AtHPPD revealed that hydrophobic interactions with Phe392 and Met335, and effective blocking of the conformational deflection of Gln293, as compared with that of the lead compound MBQ, afforded a molecular basis for structural modification. 3-(1-(3-Fluorophenyl)ethyl)-6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethylquinazoline-2,4(1H,3H)-dione (31) was confirmed to be the best subnanomolar-range AtHPPD inhibitor (IC50 = 39 nM), making it approximately seven times more potent than MBQ. In addition, the greenhouse experiment showed favorable herbicidal potency for compound 23 with a broad spectrum and acceptable crop selectivity against cotton at the dosage of 30-120 g ai/ha. Thus, compound 23 possessed a promising prospect as a novel HPPD-inhibiting herbicide candidate for cotton fields.
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Affiliation(s)
- Jia-Xu Nan
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Jin Dong
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Jun-Qiao Cao
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Yi Huang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Xing-Xing Shi
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Xue-Fang Wei
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Qiong Chen
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Hong-Yan Lin
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, P.R. China
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Berestetskiy A. Modern Approaches for the Development of New Herbicides Based on Natural Compounds. PLANTS (BASEL, SWITZERLAND) 2023; 12:234. [PMID: 36678947 PMCID: PMC9864389 DOI: 10.3390/plants12020234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/24/2022] [Indexed: 05/12/2023]
Abstract
Weeds are a permanent component of anthropogenic ecosystems. They require strict control to avoid the accumulation of their long-lasting seeds in the soil. With high crop infestation, many elements of crop production technologies (fertilization, productive varieties, growth stimulators, etc.) turn out to be practically meaningless due to high yield losses. Intensive use of chemical herbicides (CHs) has led to undesirable consequences: contamination of soil and wastewater, accumulation of their residues in the crop, and the emergence of CH-resistant populations of weeds. In this regard, the development of environmentally friendly CHs with new mechanisms of action is relevant. The natural phytotoxins of plant or microbial origin may be explored directly in herbicidal formulations (biorational CHs) or indirectly as scaffolds for nature-derived CHs. This review considers (1) the main current trends in the development of CHs that may be important for the enhancement of biorational herbicides; (2) the advances in the development and practical application of natural compounds for weed control; (3) the use of phytotoxins as prototypes of synthetic herbicides. Some modern approaches, such as computational methods of virtual screening and design of herbicidal molecules, development of modern formulations, and determination of molecular targets, are stressed as crucial to make the exploration of natural compounds more effective.
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Affiliation(s)
- Alexander Berestetskiy
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia
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Duke SO, Pan Z, Bajsa-Hirschel J. Proving the Mode of Action of Phytotoxic Phytochemicals. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1756. [PMID: 33322386 PMCID: PMC7763512 DOI: 10.3390/plants9121756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Knowledge of the mode of action of an allelochemical can be valuable for several reasons, such as proving and elucidating the role of the compound in nature and evaluating its potential utility as a pesticide. However, discovery of the molecular target site of a natural phytotoxin can be challenging. Because of this, we know little about the molecular targets of relatively few allelochemicals. It is much simpler to describe the secondary effects of these compounds, and, as a result, there is much information about these effects, which usually tell us little about the mode of action. This review describes the many approaches to molecular target site discovery, with an attempt to point out the pitfalls of each approach. Clues from molecular structure, phenotypic effects, physiological effects, omics studies, genetic approaches, and use of artificial intelligence are discussed. All these approaches can be confounded if the phytotoxin has more than one molecular target at similar concentrations or is a prophytotoxin, requiring structural alteration to create an active compound. Unequivocal determination of the molecular target site requires proof of activity on the function of the target protein and proof that a resistant form of the target protein confers resistance to the target organism.
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Affiliation(s)
- Stephen O. Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, MS 38655, USA
| | - Zhiqiang Pan
- Natural Products Utilization Research Unit, Agricultural Research Service, United States Department of Agriculture, Oxford, MS 38655, USA; (Z.P.); (J.B.-H.)
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, Agricultural Research Service, United States Department of Agriculture, Oxford, MS 38655, USA; (Z.P.); (J.B.-H.)
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Clark RD. Putting deep learning in perspective for pest management scientists. PEST MANAGEMENT SCIENCE 2020; 76:2267-2275. [PMID: 32173969 PMCID: PMC7318651 DOI: 10.1002/ps.5820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 03/10/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
'Deep learning' is causing rapid technological changes in many fields of science, and conjectures about its potential for transforming everyone's work and lives is a matter of great debate. Unfortunately, it is all too easy to apply it as a 'black box' tool with little consideration of its potential limitations, especially when the data it is being applied to is less than perfect. In this Perspective, I try to put deep learning into a broader mechanistic and historical context by showing how it relates to older forms of artificial intelligence; by providing a general explanation of how it operates; and by exploring some of the challenges involved in its implementation. Examples wherein it has been applied to pest management problems are provided to illustrate how the technology works and the challenges deep learning faces. At least in the near term, its biggest impact on agrochemical development seems likely to come in automating the tedious work involved in assessing agrochemical efficacy, but getting there will require major investments in building large, well-curated data sets to work from and in providing the expertise required to assess the resulting model predictions in real-world scenarios. Deep learning may also come to complement the machine learning methodologies already available for use in pesticide discovery and development, but it seems unlikely to supplant them. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Gao Y, Li J, Li J, Song Z, Shang S, Rao X. High Add Valued Application of Turpentine in Crop Production through Structural Modification and QSAR Analysis. Molecules 2018; 23:molecules23020356. [PMID: 29419733 PMCID: PMC6017721 DOI: 10.3390/molecules23020356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 12/13/2022] Open
Abstract
Turpentine is a volatile component of resin, which is an abundant forest resource in Southern China. As one of the most important components, the integrated application of β-pinene has been studied. The broad-spectrum evaluation of β-pinene and its analogues has, therefore, been necessary. In an attempt to expand the scope of agro-activity trials, the preparation and the evaluation of the herbicidal activity of a series of β-pinene analogues against three agricultural herbs were carried out. In accordance with the overall herbicidal activity, it is noteworthy that compounds 6k, 6l, and 6m demonstrated extreme activity with IC50 values of 0.065, 0.065, and 0.052 mol active ingredients/hectare against E. crus-galli. The preliminary structure-activity relationship (SAR) was analyzed and the compounds with the appropriate volatility and substituent type that had beneficial herbicidal activity were analyzed. Simultaneously, the quantitative structure-activity relationship (QSAR) model was built and the most important structural features were indicated, which was, to a certain extent, in line with the SAR study. The study aimed to study the application of the forest resource turpentine in agriculture as a potential and alternative approach for comprehensive utilization.
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Affiliation(s)
- Yanqing Gao
- Research & Development Center of Biorational Pesticide, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jingjing Li
- Shaanxi Province Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jian Li
- Shaanxi Province Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhanqian Song
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, Jiangsu, China.
| | - Shibin Shang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, Jiangsu, China.
| | - Xiaoping Rao
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, Jiangsu, China.
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Villaverde JJ, López-Goti C, Alcamí M, Lamsabhi AM, Alonso-Prados JL, Sandín-España P. Quantum chemistry in environmental pesticide risk assessment. PEST MANAGEMENT SCIENCE 2017; 73:2199-2202. [PMID: 28618212 DOI: 10.1002/ps.4641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/08/2017] [Accepted: 06/10/2017] [Indexed: 06/07/2023]
Abstract
The scientific community and regulatory bodies worldwide, currently promote the development of non-experimental tests that produce reliable data for pesticide risk assessment. The use of standard quantum chemistry methods could allow the development of tools to perform a first screening of compounds to be considered for the experimental studies, improving the risk assessment. This fact results in a better distribution of resources and in better planning, allowing a more exhaustive study of the pesticides and their metabolic products. The current paper explores the potential of quantum chemistry in modelling toxicity and environmental behaviour of pesticides and their by-products by using electronic descriptors obtained computationally. Quantum chemistry has potential to estimate the physico-chemical properties of pesticides, including certain chemical reaction mechanisms and their degradation pathways, allowing modelling of the environmental behaviour of both pesticides and their by-products. In this sense, theoretical methods can contribute to performing a more focused risk assessment of pesticides used in the market, and may lead to higher quality and safer agricultural products. © 2017 Society of Chemical Industry.
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Affiliation(s)
| | | | - Manuel Alcamí
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences, Universidad Autónoma de Madrid, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias, Madrid, Spain
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences, Universidad Autónoma de Madrid, Madrid, Spain
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Varejão JO, Barbosa LC, Ramos GÁ, Varejão EV, King-Díaz B, Lotina-Hennsen B. New rubrolide analogues as inhibitors of photosynthesis light reactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 145:11-8. [DOI: 10.1016/j.jphotobiol.2015.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 01/22/2023]
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Movellan J, Rocher F, Chikh Z, Marivingt-Mounir C, Bonnemain JL, Chollet JF. Synthesis and evaluation as biodegradable herbicides of halogenated analogs of L-meta-tyrosine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:4861-70. [PMID: 23224500 DOI: 10.1007/s11356-012-1302-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 11/05/2012] [Indexed: 06/01/2023]
Abstract
L-meta-tyrosine is an herbicidal nonprotein amino acid isolated some years ago from fine fescue grasses and characterized by its almost immediate microbial degradation in soil (half-life <24 h). Nine monohalogenated or dihalogenated analogs of this allelochemical have been obtained through a seven-step stereoselective synthesis from commercial halogenated phenols. Bioassays showed a large range of biological responses, from a growth root inhibition of lettuce seedling similar to that noted with m-tyrosine [2-amino-3-(2-chloro-5-hydroxyphenyl)propanoic acid or compound 8b] to an increase of the primary root growth concomitant with a delay of secondary root initiation [2-amino-3-[2-fluoro-5-hydroxy-3-(trifluoromethyl)phenyl]propanoic acid or compound 8h]. Compound 8b was slightly less degraded than m-tyrosine in the nonsterilized nutritive solution used for lettuce development, while the concentration of compound 8h remained unchanged for at least 2 weeks. These data indicate that it is possible to manipulate both biological properties and degradation of m-tyrosine by halogen addition.
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Affiliation(s)
- Julie Movellan
- Institut de Chimie des Milieux et des Matériaux de Poitiers, Unité Mixte de Recherche CNRS 7285, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022, Poitiers Cedex, France
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Duke S. Our goals is to publish high-quality front matter articles. PEST MANAGEMENT SCIENCE 2013; 69:1-2. [PMID: 23239644 DOI: 10.1002/ps.3466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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