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Rani P, Rajak BK, Singh DV. Physicochemical parameters for design and development of lead herbicide molecules: Is 'Lipinski's rule of 5' appropriate for herbicide discovery? PEST MANAGEMENT SCIENCE 2023; 79:1931-1943. [PMID: 36656285 DOI: 10.1002/ps.7367] [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: 06/04/2022] [Revised: 12/24/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Herbicide use has been a great add-on in agriculture, aiding weed management in crop fields, thereby escalating crop production. However, the development of resistance in weeds against the existing herbicides is a setback. The development of herbicide resistance has compelled the agrochemical industries to replace existing herbicides with novel agrochemicals. Developing new herbicide molecules through traditional methods is time-consuming and cost-prohibitive. The use of high-throughput virtual screening (HTVS) through physicochemical properties, de novo design and combinatorial design of molecules with cutting-edge computational methods is an alternative to the traditional techniques in lead molecule discovery. The lack of optimal physicochemical criteria for screening herbicide-like molecules has become a hindrance in the process. RESULTS In this study, physicochemical parameters [molecular weight, aromatic atoms, rotatable bonds, hydrogen-bonding capacity, topological polar surface area (TPSA), polarity and solubility] of known herbicide molecules have been studied and evaluated, and optimal criteria have been proposed for target-specific herbicides. Properties including molecular weight and hydrogen (H)-bond acceptor atoms tend to have higher values, but the range of H-bond donor atoms is relatively lower. These are distinguishable characteristics in herbicides when compared with oral drugs. Significant variations in optimal physicochemical parameters between herbicides of different groups (targeting weeds with different modes of action) have been observed. CONCLUSION The proposed parameters for respective target sites could be used as filters for in silico screening, designing and developing of target-specific lead herbicide molecules. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Priyanka Rani
- Molecular Modelling and Computer-Aided Drug Discovery Laboratory, Department of Bioinformatics, Central University of South Bihar, School of Earth Biological and Environmental Sciences, Gaya, India
| | - Bikash Kumar Rajak
- Molecular Modelling and Computer-Aided Drug Discovery Laboratory, Department of Bioinformatics, Central University of South Bihar, School of Earth Biological and Environmental Sciences, Gaya, India
| | - Durg Vijay Singh
- Molecular Modelling and Computer-Aided Drug Discovery Laboratory, Department of Bioinformatics, Central University of South Bihar, School of Earth Biological and Environmental Sciences, Gaya, India
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2
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Sparks TC, Lorsbach BA. Insecticide discovery-"Chance favors the prepared mind". PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105412. [PMID: 37105622 DOI: 10.1016/j.pestbp.2023.105412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
New options for pest insect control, including new insecticides, are needed to ensure a plentiful food supply for an expanding global population. Any new insecticides must meet the increasingly stringent regulatory requirements for mammalian and environmental safety, and also address the need for new chemistries and modes of action to deal with resistance to available insecticides. As underscored by a paraphrase of a quote from Louis Pasteur "Chance favors the prepared mind", the agrochemical industry uses a variety of approaches that attempt to improve on "chance" for the discovery of new insecticides. Although there are a number of approaches to the discovery of new insecticidal active ingredients (AIs), historically most insecticides are based on a pre-existing molecule or product either from a competitor or from an internal company source. As such the first examples of a new insecticide representing a new type or class of AI (First-in-Class: FIC) are important as prototypes for other AIs stimulating further spectrum, efficacy, physicochemical, and environmental safety refinements. FIC insecticides also represent a measure of innovation. Understanding the origins of these FIC compounds and the approaches used in their discovery can provide insights into successful strategies for future new classes of insecticides. This perspective will focus on an analysis of the approaches that have been used for discovery of FIC insecticides highlighting those approaches that have been the most successful and providing a reference point for current and future directions.
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Affiliation(s)
| | - Beth A Lorsbach
- Nufarm, 4020 Aerial Center Parkway Morrisville, NC 27560, USA
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3
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Meanwell NA, Loiseleur O. Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10942-10971. [PMID: 35675050 DOI: 10.1021/acs.jafc.2c00726] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Piperazine and homopiperazine are well-studied heterocycles in drug design that have found gainful application as scaffolds and terminal elements and for enhancing the aqueous solubility of a molecule. The optimization of drug candidates that incorporate these heterocycles in an effort to refine potency, selectivity, and developability properties has stimulated the design and evaluation of a wide range of bioisosteres that can offer advantage. In this review, we summarize the design and application of bioisosteres of piperazine and homopiperazine that have almost exclusively been in the drug design arena. While there are ∼100 approved drugs that incorporate a piperazine ring, only a single marketed agricultural product is built on this heterocycle. As part of the review, we discuss some of the potential reasons underlying the relatively low level of importance of this heterocycle to the design of agrochemicals and highlight the potential opportunities for their use in contemporary research programs.
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543, United States
| | - Olivier Loiseleur
- Syngenta Crop Protection Research, Schaffhauserstrasse, Stein CH-4332, Switzerland
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Yang Z, Xu J, Du L, Yin J, Wang Z, Yi F, Duan L, Li Z, Wang B, Shu K, Tan W. Design, Synthesis, and Action Mechanism of 1,3-Benzodioxole Derivatives as Potent Auxin Receptor Agonists and Root Growth Promoters. FRONTIERS IN PLANT SCIENCE 2022; 13:902902. [PMID: 35755644 PMCID: PMC9226723 DOI: 10.3389/fpls.2022.902902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Deeper and longer roots allow crops to survive and flourish, but our understanding of the plant growth regulators promoting root system establishment is limited. Here, we report that, a novel auxin receptor agonist, named K-10, had a remarkable promotive effect on root growth in both Arabidopsis thaliana and Oryza sativa through the enhancement of root-related signaling responses. Using computer-aided drug discovery approaches, we developed potent lead compound by screening artificial chemicals on the basis of the auxin receptor TIR1 (Transport Inhibitor Response 1), and a series of N-(benzo[d] [1,3] dioxol-5-yl)-2-(one-benzylthio) acetamides, K-1 to K-22, were designed and synthesized. The results of bioassay showed that K-10 exhibited an excellent root growth-promoting activity far exceeding that of NAA (1-naphthylacetic acid). A further morphological investigation of the auxin related mutants (yucQ, tir1) revealed that K-10 had auxin-like physiological functions and was recognized by TIR1, and K-10 significantly enhanced auxin response reporter's (DR5:GUS) transcriptional activity. Consistently, transcriptome analysis showed that K-10 induced a common transcriptional response with auxin and down-regulated the expression of root growth-inhibiting genes. Further molecular docking analysis revealed that K-10 had a stronger binding ability with TIR1 than NAA. These results indicated that this class of derivatives could be a promising scaffold for the discovery and development of novel auxin receptor agonists, and the employment of K-10 may be effective for enhancing root growth and crop production.
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Affiliation(s)
- Zhikun Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou, China
| | - Jiahui Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Lin Du
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiaming Yin
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhao Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Fei Yi
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Liusheng Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhaohu Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Baomin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Weiming Tan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Mei LC, Chen HM, Dong AY, Huang GY, Liu YW, Zhang X, Wang W, Hao GF, Yang GF. Pesticide Informatics Platform (PIP): An International Platform for Pesticide Discovery, Residue, and Risk Evaluation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6617-6623. [PMID: 35617526 DOI: 10.1021/acs.jafc.2c02141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pesticides are widely used agrochemicals for crop protection. The need for novel pesticides becomes urgent as a result of the emergence of resistance and environmental toxicity. Pesticide informatics has been applied in different phase processes of pesticide target identification, active ingredient design, and impact evaluation. However, these valuable resources are scattered over the literature and web, limiting their availability. Here, we summarize and connect research on pesticide informatics resources. A pesticide informatics platform (PIP) was constructed to share these tools. We finally discuss the future direction of pesticide informatics, including pesticide contamination. We expect to share the pesticide informatics approaches and stimulate further research.
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Affiliation(s)
- Long-Can Mei
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Hui-Min Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - An-Yu Dong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550000, People's Republic of China
| | - Guang-Yi Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Ying-Wei Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550000, People's Republic of China
| | - Xiao Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550000, People's Republic of China
| | - Wei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550000, People's Republic of China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550000, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
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6
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Synthesis, insecticidal activities and DFT study of pyrimidin-4-amine derivatives containing the 1,2,4-oxadiazole motif. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2091-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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7
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Krähmer H, Walter H, Jeschke P, Haaf K, Baur P, Evans R. What makes a molecule a pre- or a post-herbicide - how valuable are physicochemical parameters for their design? PEST MANAGEMENT SCIENCE 2021; 77:4863-4873. [PMID: 34176232 PMCID: PMC8519102 DOI: 10.1002/ps.6535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 05/26/2023]
Abstract
Pre-emergence herbicides are taken up by seeds before germination and by roots, hypocotyls, cotyledons, coleoptiles or leaves before emergence, whereas post-emergence herbicides are taken up primarily by foliage and stems. Most modern pre-emergence herbicides are lipophilic, but post-emergence herbicides may be lipophilic or hydrophilic. The metabolic conversion of herbicides to inactive or active metabolites after plant uptake is of major importance for some compound classes. Several herbicides are proherbicides as for example some acetyl-coenzyme A carboxylase (ACCase)-inhibitors. The physicochemical characteristics of proherbicides and herbicides are usually unrelated. A major role can be attributed to the site of action at a cellular level. A great number of herbicides such as photosystem II (PS II)-inhibitors, protoporphyrinogen oxidase (PPO)-inhibitors or carotenoid biosynthesis inhibitors require light for activity. Others, such as cellulose-biosynthesis and mitotic inhibitors seem to be primarily active in belowground organs. Several lipophilic barriers against the uptake of xenobiotics exist in aboveground and belowground plant parts. The relevance of these barriers needs, however, further clarification. Uptake and translocation models are valuable tools for the explanation of the potential movement of compounds. Many factors other than uptake and translocation have, however, to be considered for the design of herbicides. For post-emergence herbicides, ultraviolet (UV) light stability, stability in formulations, and mixability with other agrochemicals have to be kept in mind while, in addition to the aforementioned factors soil interaction plays a major role for pre-emergence herbicides. In our opinion, general physicochemical characteristics of pre- or post-emergence herbicides do, unfortunately not exist yet. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | | | - Peter Jeschke
- Research & Development, Crop Science, Pest Control ChemistryBayer AGMonheim am RheinGermany
| | - Klaus Haaf
- Research & Development, Crop Science, Weed Control ChemistryBayer AGFrankfurt am MainGermany
| | - Peter Baur
- CropPromotion AdviceSchondorf am AmmerseeGermany
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8
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Wang X, Hu N, Kong W, Song B, Li S. Facile and divergent optimization of chromazonarol enabled the identification of simplified drimane meroterpenoids as novel pharmaceutical leads. Eur J Med Chem 2021; 227:113912. [PMID: 34653771 DOI: 10.1016/j.ejmech.2021.113912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/22/2022]
Abstract
The diversity of drimane hydroquinones was significantly expanded by the facile construction of (+)-chromazonarol relevant natural products, isomers, and analogues for the discovery of new pharmaceutical leads. The structure-activity relationship of (+)-chromazonarol relevant (non)-natural products was delineated via the synergistic interaction of the programmable synthesis and bioactivity-guided screening. The first divergent derivatization of (+)-chromazonarol demonstrated that the phenolic hydroxyl group is one inviolable requirement for antifungal effect. Pinpoint modification of (+)-yahazunol manifested the position of hydroxyl group was crucial for both antifungal and antitumor activities. (+)-Albaconol, (+)-neoalbaconol, and two (+)-yahazunol isomers (24 and 25) proved to be the novel pharmaceutical leads. The probable macromolecular targets were estimated to deliver new information about the biological potentials resident in (+)-yahazunol relevant products. This work also featured the first synthesis of (+)-albaconol and (+)-neoalbaconol, the first biological exploration of (+)-dictyvaric acid and improved preparation of (+)-8-epi-puupehedione and a promising pelorol analogue.
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Affiliation(s)
- Xia Wang
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China; Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Weigang 1, Xuanwu District, Nanjing, 210095, China
| | - Nvdan Hu
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Wenlong Kong
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Baoan Song
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Shengkun Li
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China; Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Weigang 1, Xuanwu District, Nanjing, 210095, China.
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9
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Comprehensive machine learning based study of the chemical space of herbicides. Sci Rep 2021; 11:11479. [PMID: 34075109 PMCID: PMC8169684 DOI: 10.1038/s41598-021-90690-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
Widespread use of herbicides results in the global increase in weed resistance. The rotational use of herbicides according to their modes of action (MoAs) and discovery of novel phytotoxic molecules are the two strategies used against the weed resistance. Herein, Random Forest modeling was used to build predictive models and establish comprehensive characterization of structure–activity relationships underlying herbicide classifications according to their MoAs and weed selectivity. By combining the predictive models with herbicide-likeness rules defined by selected molecular features (numbers of H-bond acceptors and donors, logP, topological and relative polar surface area, and net charge), the virtual stepwise screening platform is proposed for characterization of small weight molecules for their phytotoxic properties. The screening cascade was applied on the data set of phytotoxic natural products. The obtained results may be valuable for refinement of herbicide rotational program as well as for discovery of novel herbicides primarily among natural products as a source for molecules of novel structures and novel modes of action and translocation profiles as compared with the synthetic compounds.
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10
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Agatz A, Ashauer R, Sweeney P, Brown CD. A knowledge-based approach to designing control strategies for agricultural pests. AGRICULTURAL SYSTEMS 2020; 183:102865. [PMID: 32747848 PMCID: PMC7294735 DOI: 10.1016/j.agsy.2020.102865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 05/22/2023]
Abstract
Chemical control of insect pests remains vital to agricultural productivity, but limited mechanistic understanding of the interactions between crop, pest and chemical control agent have restricted our capacity to respond to challenges such as the emergence of resistance and demands for tighter environmental regulation. Formulating effective control strategies that integrate chemical and non-chemical management for soil-dwelling pests is particularly problematic owing to the complexity of the soil-root-pest system and the variability that occurs between sites and between seasons. Here, we present a new concept, termed COMPASS, that integrates ecological knowledge on pest development and behaviour together with crop physiology and mechanistic understanding of chemical distribution and toxic action within the rhizosphere. The concept is tested using a two-dimensional systems model (COMPASS-Rootworm) that simulates root damage in maize from the corn rootworm Diabrotica spp. We evaluate COMPASS-Rootworm using 119 field trials that investigated the efficacy of insecticidal products and placement strategies at four sites in the USA over a period of ten years. Simulated root damage is consistent with measurements for 109 field trials. Moreover, we disentangle factors influencing root damage and pest control, including pest pressure, weather, insecticide distribution, and temporality between the emergence of crop roots and pests. The model can inform integrated pest management, optimize pest control strategies to reduce environmental burdens from pesticides, and improve the efficiency of insecticide development.
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Affiliation(s)
- Annika Agatz
- Department of Environment and Geography, University of York, Wentworth Way, Heslington, York, YO10 5NG, United Kingdom
| | - Roman Ashauer
- Department of Environment and Geography, University of York, Wentworth Way, Heslington, York, YO10 5NG, United Kingdom
| | - Paul Sweeney
- Syngenta, Jealott's Hill, Maidenhead Rd., Warfield, Bracknell, RG42 6ES, United Kingdom
| | - Colin D. Brown
- Department of Environment and Geography, University of York, Wentworth Way, Heslington, York, YO10 5NG, United Kingdom
- Corresponding author.
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11
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Fan Z, Shi J, Luo N, Ding M, Bao X. Synthesis, Crystal Structure, and Agricultural Antimicrobial Evaluation of Novel Quinazoline Thioether Derivatives Incorporating the 1,2,4-Triazolo[4,3- a]pyridine Moiety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11598-11606. [PMID: 31560195 DOI: 10.1021/acs.jafc.9b04733] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A total of 22 quinazoline thioether derivatives incorporating a 1,2,4-triazolo[4,3-a]pyridine moiety were designed, synthesized, and evaluated as antimicrobial agents in agriculture. Among these compounds, the chemical structure of compound 6l was further confirmed via single-crystal X-ray diffraction analysis. The bioassay results revealed that some of the compounds possessed noticeable in vitro antibacterial activities against the tested phytopathogenic bacteria. For example, compounds 6b and 6g had EC50 values as low as 10.0 and 24.7 μg/mL against Xanthomonas axonopodis pv. citri (Xac), respectively, which were significantly better than that of the commercial agrobactericide bismerthiazol (56.9 μg/mL). Particularly, compound 6b was also found to be capable of suppressing the pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) approximately 12-fold more potent than control bismerthiazol, in terms of their EC50 values (7.2 versus 89.8 μg/mL). Importantly, the most active compound 6b turned out to be one with the highest hydrophilicity and the lowest molecular weight within the series. In vivo bioassays further showed the application prospect of 6b as a promising plant bactericide for controlling Xoo. Additionally, in vitro antifungal activities of these compounds were also evaluated at the concentration of 50 μg/mL. Overall, the present study demonstrated the potential of 1,2,4-triazolo[4,3-a]pyridine-bearing quinazoline thioether derivatives as efficient agricultural antibacterial agents for crop protection.
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Affiliation(s)
- Zhijiang Fan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals , Guizhou University , Guiyang 550025 , P. R. China
| | - Jun Shi
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals , Guizhou University , Guiyang 550025 , P. R. China
| | - Na Luo
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals , Guizhou University , Guiyang 550025 , P. R. China
| | - Muhan Ding
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals , Guizhou University , Guiyang 550025 , P. R. China
| | - Xiaoping Bao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals , Guizhou University , Guiyang 550025 , P. R. China
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12
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Zeng X, Zhang P, He W, Qin C, Chen S, Tao L, Wang Y, Tan Y, Gao D, Wang B, Chen Z, Chen W, Jiang YY, Chen YZ. NPASS: natural product activity and species source database for natural product research, discovery and tool development. Nucleic Acids Res 2019; 46:D1217-D1222. [PMID: 29106619 PMCID: PMC5753227 DOI: 10.1093/nar/gkx1026] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/18/2017] [Indexed: 01/22/2023] Open
Abstract
There has been renewed interests in the exploration of natural products (NPs) for drug discovery, and continuous investigations of the therapeutic claims and mechanisms of traditional and herbal medicines. In-silico methods have been employed for facilitating these studies. These studies and the optimization of in-silico algorithms for NP applications can be facilitated by the quantitative activity and species source data of the NPs. A number of databases collectively provide the structural and other information of ∼470 000 NPs, including qualitative activity information for many NPs, but only ∼4000 NPs are with the experimental activity values. There is a need for the activity and species source data of more NPs. We therefore developed a new database, NPASS (Natural Product Activity and Species Source) to complement other databases by providing the experimental activity values and species sources of 35 032 NPs from 25 041 species targeting 5863 targets (2946 proteins, 1352 microbial species and 1227 cell-lines). NPASS contains 446 552 quantitative activity records (e.g. IC50, Ki, EC50, GI50 or MIC mainly in units of nM) of 222 092 NP-target pairs and 288 002 NP-species pairs. NPASS, http://bidd2.nus.edu.sg/NPASS/, is freely accessible with its contents searchable by keywords, physicochemical property range, structural similarity, species and target search facilities.
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Affiliation(s)
- Xian Zeng
- Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China.,Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Peng Zhang
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Weidong He
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Chu Qin
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Shangying Chen
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Lin Tao
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore.,Zhejiang Key Laboratory of Gastro-intestinal Pathophysiology, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, School of Medicine, Hangzhou Normal University, Hangzhou 310006, RP China
| | - Yali Wang
- Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Ying Tan
- Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China
| | - Dan Gao
- Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China
| | - Bohua Wang
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, PR China.,College of Life and Environmental Sciences, Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan University of Arts and Science, Changde, Hunan 415000, PR China
| | - Zhe Chen
- Zhejiang Key Laboratory of Gastro-intestinal Pathophysiology, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, School of Medicine, Hangzhou Normal University, Hangzhou 310006, RP China
| | - Weiping Chen
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yu Yang Jiang
- Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China
| | - Yu Zong Chen
- Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China.,Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
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Yan Z, Liu A, Ou Y, Li J, Yi H, Zhang N, Liu M, Huang L, Ren J, Liu W, Hu A. Design, synthesis and fungicidal activity evaluation of novel pyrimidinamine derivatives containing phenyl-thiazole/oxazole moiety. Bioorg Med Chem 2019; 27:3218-3228. [DOI: 10.1016/j.bmc.2019.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/02/2019] [Accepted: 05/18/2019] [Indexed: 01/31/2023]
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Zhang S, Li D, Song Z, Zang C, Zhang L, Song X, Li S. "Carbon Assimilation" Inspired Design and Divergent Synthesis of Drimane Meroterpenoid Mimics as Novel Fungicidal Leads. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9013-9021. [PMID: 28949528 DOI: 10.1021/acs.jafc.7b03126] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With structural diversity and versatile biological properties, drimane meroterpenoids have drawn remarkable attention in drug development. The stagnant progress made in the structure optimization and SAR study of this kind of natural product for agrochemicals was mainly a result of inefficient construction. Compared with the reported challenging coupling reaction ("1 + 1" tactic), "carbon assimilation" was conceived and used for the rapid construction of drimanyl meroterpenoid mimics, in which the newly formed covalent bond was directly from the old one of the drimanyl subunit ("2 + 0" tactic), which features atom economy, step economy, and facile preparation. The accompanying introduction of versatile heterocycles and application of easily available feedstocks are beneficial for novel green agrochemical discovery, in view of economic efficiency and improvement of physicochemical properities. Heterocyclic mimics 3a and 3c are presented as potent fungicidal leads with novel skeletons against Botrytis cinerea, >25-fold and >40-fold more promising than the commercial fungicide carbendazim, respectively. Our design was also rationalized by the 6-step synthesis and antifungal assay of the original model of natural meroterpenoids. This tactic can also be fostered or transferred directly to the design of novel natural product mimics for medicinal chemistry or other related biological exploration.
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Affiliation(s)
- Shasha Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Dangdang Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Zehua Song
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Chuanli Zang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Lu Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Xiushi Song
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
| | - Shengkun Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing 210095, People's Republic of China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University , Guiyang 550025, People's Republic of China
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Mairink SZ, Barbosa LC, Varejão EV, Farias ES, Santos ML, Picanço MC. Larvicidal activity of synthetic tropane alkaloids against Ascia monuste orseis (Lepidoptera: Pieridae). PEST MANAGEMENT SCIENCE 2017; 73:2048-2053. [PMID: 28266104 DOI: 10.1002/ps.4565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Tropane alkaloids are known to play a role in plant defence. By blocking acetylcholine receptors, they exert insecticidal and deterrent effects against herbivore insects. Carbamates are an important class of chemical insecticides that also inhibit acetyl cholinesterase. The objective of this work was to synthesise a series of tropane alkaloids bearing a carbamate group, and to evaluate their effects against the pest Ascia monuste. The effects of the most active compounds were evaluated on the A. monuste predator Solenopsis saevissima and on the pollinator Tetragonisca angustula. RESULTS The synthesis of carbamate-tropane alkaloids was accomplished in 4-5 steps from commercially available ketones. Results from bioassays showed that compounds 6a, 10a and 14a presented higher activities against second-instar larvae of A. monuste, with LD50 values of 1.01, 3.76 and 1.92 µg substance mg-1 insect, and TL50 values of 7.0, 15.0 and 5.0 h respectively. These compounds were also tested for their selectivity in favour of S. saevissima and T. angustula. Compound 6a, which showed the highest activity against A. monuste, also showed lower toxicity against S. saevissima. CONCLUSION Tropane alkaloid derivatives bearing a carbamate group show potential for the development of novel insecticides against A. monuste. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Simone Z Mairink
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Luiz Ca Barbosa
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Department of Chemistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Vv Varejão
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Elizeu S Farias
- Department of Animal Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Márcio Lm Santos
- Department of Animal Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo C Picanço
- Department of Animal Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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First protein drug target’s appraisal of lead-likeness descriptors to unfold the intervening chemical space. J Mol Graph Model 2017; 72:272-282. [DOI: 10.1016/j.jmgm.2016.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
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17
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Li S, Li D, Xiao T, Zhang S, Song Z, Ma H. Design, Synthesis, Fungicidal Activity, and Unexpected Docking Model of the First Chiral Boscalid Analogues Containing Oxazolines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8927-8934. [PMID: 27792876 DOI: 10.1021/acs.jafc.6b03464] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chirality greatly influences the biological and pharmacological properties of a pesticide and will contribute to unnecessary environmental loading and undesired ecological impact. No structure and activity relationship (SAR) of enantiopure succinate dehydrogenase inhibitors (SDHIs) was documented during the structure optimization of boscalids. On the basis of commercial SDHIs, oxazoline natural products, and versatile oxazoline ligands in organic synthesis, the first effort was devoted to explore the chiral SDHIs and the preliminary mechanism thereof. Fine-tuning furnished chiral nicotinamides 4ag as a more promising fungicidal candidate against Rhizoctonia solani, Botrytis cinerea, and Sclerotinia sclerotiorum, with EC50 values of 0.58, 0.42, and 2.10 mg/L, respectively. In vivo bioassay and molecular docking were investigated to explore the potential in practical application and plausible novelty in action mechanism, respectively. The unexpected molecular docking model showed the different chiral effects on the binding site with the amino acid residues. This chiral nicotinamide also featured easy synthesis and cost-efficacy. It will provide a powerful complement to the commercial SDHI fungicides with the introduction of chirality.
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Affiliation(s)
- Shengkun Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
| | - Dangdang Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
| | - Taifeng Xiao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
| | - ShaSha Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
| | - Zehua Song
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
| | - Hongyu Ma
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University , Weigang 1, Xuanwu District, Nanjing, Jiangsu 210095, People's Republic of China
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Foley DJ, Nelson A, Marsden SP. Evaluating New Chemistry to Drive Molecular Discovery: Fit for Purpose? Angew Chem Int Ed Engl 2016; 55:13650-13657. [PMID: 27573303 PMCID: PMC5113762 DOI: 10.1002/anie.201604193] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/01/2016] [Indexed: 12/12/2022]
Abstract
As our understanding of the impact of specific molecular properties on applications in discovery-based disciplines improves, the extent to which published synthetic methods meet (or do not meet) desirable criteria is ever clearer. Herein, we show how the application of simple (and in many cases freely available) computational tools can be used to develop a semiquantitative understanding of the potential of new methods to support molecular discovery. This analysis can, among other things, inform the design of improved substrate scoping studies; direct the prioritization of specific exemplar structures for synthesis; and substantiate claims of potential future applications for new methods.
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Affiliation(s)
- Daniel J Foley
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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Evaluierung neuer Reaktionen zur Steuerung der Wirkstoff-Forschung: ein Eignungstest. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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