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Römer CI, Ashauer R, Escher BI, Hollender J, Burkhard R, Höfer K, Muehlebach M, Buchholz A. Comparison of absorption and excretion of test compounds in sucking versus chewing pests. PLoS One 2025; 20:e0321302. [PMID: 40294073 PMCID: PMC12036848 DOI: 10.1371/journal.pone.0321302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 03/04/2025] [Indexed: 04/30/2025] Open
Abstract
A critical understanding of how pests interact with active ingredients is essential for the development of new insect control solutions to maintain crop quality and quantity by reducing insect damage. Absorption of insecticides into insect bodies of targeted pest species is the first critical step that confounds the efficacy of insecticides. This study investigated how different feeding behaviour of two pests, Myzus persicae and Spodoptera littoralis, affects the absorption, metabolism, and excretion (AME) of seven insecticidally inactive test compounds. A feeding contact assay for the chewing pest (Lepidopteran larvae) and an oral ingestion assay for the sucking pest (aphids) was used to investigate the AME of test compounds with agrochemical-like structural motifs. The standardized assays comprised of an exposure period with treated diet and a subsequent depuration period with untreated diet. The results showed that S. littoralis larvae differed from M. persicae in their compound quantities absorbed into the insect body and in their excretion products at the end of the exposure or depuration periods. We suggest that this is caused by their different ingestion types and rates resulting in different absorption and excretion quantities. Further, we found differences in the metabolism (timing and biotransformation pathways) of compounds between both species. Notably, certain compounds remained detectable in both pests after the depuration period, suggesting compound and species-specific metabolism and excretion. Our results highlight the complex interplay between feeding biology of insects, in particular the critical role of excretion products, and the exposure to different compounds that lead to species-specific AME.
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Affiliation(s)
- Clara I. Römer
- Syngenta Crop Protection AG, Research Biology and Chemistry, Stein, Switzerland
| | - Roman Ashauer
- Syngenta Crop Protection AG, Basel, Switzerland,
- Department of Environment, University of York, Wentworth Way, Heslington, York, United Kingdom
| | - Beate I. Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Eberhard Karls University Tübingen, Environmental Toxicology, Tübingen, Germany
| | - Juliane Hollender
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollution Dynamics, ETH Zürich, Zürich, Switzerland,
| | - René Burkhard
- Syngenta Crop Protection AG, Münchwilen, Switzerland
| | - Kristin Höfer
- Syngenta Crop Protection AG, Research Biology and Chemistry, Stein, Switzerland
| | - Michel Muehlebach
- Syngenta Crop Protection AG, Research Biology and Chemistry, Stein, Switzerland
| | - Anke Buchholz
- Syngenta Crop Protection AG, Research Biology and Chemistry, Stein, Switzerland
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Guo W, Song X, Gao Y, Yang S, Tang J, Zhao C, Wang H, Ren J, Zeng L, Xu H. Exploring Insecticidal Molecules with Random Forest: Toward High Insecticidal Activity and Low Bee Toxicity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:5573-5584. [PMID: 39978807 DOI: 10.1021/acs.jafc.4c08587] [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: 02/22/2025]
Abstract
Insecticidal molecules with high activity are crucial for global pesticide reduction and food security. However, their usage is limited by their concomitant high toxicity to bees. Balancing insecticidal activity and bee toxicity remains a critical challenge in the exploitation of new insecticidal molecules. In this study, we propose a novel strategy for exploiting molecules that are both highly effective against pests and minimally harmful to bees. A series of molecules were synthesized and tested to train a machine learning (ML) model for predicting insecticidal activity against pests. Meanwhile, another ML model was trained by using publicly available data to predict bee toxicity. The models demonstrated good performance, with mean AUC values of 0.88 ± 0.05 for insecticidal activity and 0.91 ± 0.01 for bee toxicity. By integrating these two models, we successfully predicted and experimentally validated a molecule that exhibited a high insecticidal activity and low bee toxicity. This dual-ML-model approach offers a promising pathway for the development of insecticidal molecules that are both effective and environmentally safe, thereby contributing to sustainable agricultures.
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Affiliation(s)
- Wei Guo
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Xiangmin Song
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yongchao Gao
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Shuai Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jiahong Tang
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Chen Zhao
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Haojing Wang
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jiajun Ren
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 100875 Beijing, People's Republic of China
| | - Lingda Zeng
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hanhong Xu
- State Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
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3
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Yang R, Ma Z, Wei Z, Wang F, Yang G. Improved Ensemble Model for Insecticide Recognition by Incorporating Insect Toxicity Data. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:24219-24227. [PMID: 39439124 DOI: 10.1021/acs.jafc.4c04252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Pesticide molecules, such as insecticides, play a critical role in modern agricultural production. Traditional pesticide development methods are often inefficient and expensive, while data-driven artificial intelligence (AI) techniques have emerged as a useful tool to facilitate drug discovery. However, currently available commercial pesticide data is limited, which makes the trained models unsatisfactory in terms of performance and generalization. From a domain knowledge perspective, insect toxicity data were incorporated to improve the insecticide recognition of AI models. Compared to the models trained with the original data set, the new models performed better in the external validation, and their generalization was more desirable. In addition, by integrating different types of individual models, we obtained an ensemble model with better performance. Based on this, an online platform was developed to provide researchers with free access to insecticide screening (https://dpai.ccnu.edu.cn/InsectiVS/). Finally, two potential insecticide molecules with insecticidal activity against Plutella xylostella were successfully identified in a real-world scenario. In conclusion, this idea connects the fields of AI and agricultural chemistry and is expected to have wide application in pesticide research.
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Affiliation(s)
- Ruoqi Yang
- National Pesticide Engineering Research Center, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P.R. China
- 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
| | - Zhepeng Ma
- 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
| | - Zhiheng 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
| | - Fan Wang
- 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
| | - Guangfu Yang
- National Pesticide Engineering Research Center, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P.R. China
- 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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Melo TS, Andrade BS. Advancing rational pesticide development against Drosophila suzukii: bioinformatics tools and applications-a systematic review. J Mol Model 2024; 30:319. [PMID: 39222282 DOI: 10.1007/s00894-024-06113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
CONTEXT Drosophila suzukii (Matsumura, 1931) is a widespread agricultural pest responsible for significant damage to various soft-skinned fruit hosts. The revolutionary potential of bioinformatics in agriculture emerges from its ability to provide extensive information on pests, fungi, chemical resistance, implications of non-target species, and other critical aspects. This wealth of information allows researchers to engage in projects and applied research in diverse agricultural domains that face these challenges. In this context, bioinformatics tools play a fundamental role. The negative impact of pests on crops, resulting in substantial economic losses, has highlighted the importance of in silico methods. METHODS To achieve this, we conducted a systematic search in scientific databases using as keywords "Drosophila suzukii," "biopesticides," "simulations computational," and "in-silico." After applying the filters of relevance and publication date, we organized the articles and prioritized those that directly addressed that matched the keywords and the use of bioinformatics tools. Additionally, we included studies focusing on in silico assays of biopesticides, such as molecular docking. Our review aimed to present a collection of recent literature on biopesticides against Drosophila suzukii, emphasizing bioinformatics methods. Through this work, we strive to contribute to the literature of new perspectives on the development and efficiency of biopesticides, along with to advance research that may improve pest control strategies. RESULTS In the results of the systematic review, we found 2734 articles related to the selected keywords. Six of these articles directly address Drosophila suzukii and the use of bioinformatics tools in the search for alternatives in pest control. In the selected studies, we observed that two articles tend to focus on phylogenetic approaches, searching for gene sequences, amino acids, and constructing phylogenetic trees. The other three articles used molecular modeling and docking of receptors such as GABA and TRP with plant-derived and synthetic compounds to study intermolecular interactions. However, we identified gaps in these studies that could lead to further research in the biorational development of biopesticides using bioinformatics tools.
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Affiliation(s)
- Tarcisio Silva Melo
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil.
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
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Zhou X, Liu S, Wang T, Li Z. Seawater quality criteria derivation and ecological risk assessment for dichlorvos in China. MARINE POLLUTION BULLETIN 2024; 206:116669. [PMID: 38991609 DOI: 10.1016/j.marpolbul.2024.116669] [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: 03/14/2024] [Revised: 05/14/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Dichlorvos (DDVP) is a widely used organophosphorus pesticide (OPP) that has been frequently detected in the marine environment of China. Water quality criteria (WQC) is however not available for this emergent pollutant in the marine environment, which hinders its ecological risk assessment. This study, therefore, screened toxicity values of DDVP and conducted toxicity tests on six marine species to supplement toxicity data. The WQC for DDVP was derived with the species sensitivity distribution (SSD) methodology, based on which the ecological risk of DDVP in the seawater of China was assessed. The results showed that the recommended short-term (SWQC) and long-term water quality criteria (LWQC) for DDVP were 1.47 and 0.0521 μg/L, respectively. Most marine waters of China showed low or negligible risk (HQ < 1, ORP < 2 %), whereas some estuarine waters warrant further concern due to higher risk. This study provides the scientific basis for seawater quality standard formulation and ecological risk management for DDVP.
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Affiliation(s)
- Xingzheng Zhou
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Shuai Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Teng Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Zhengyan Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
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Li T, Zhou Y, Fu X, Yang L, Liu H, Zhou X, Liu L, Wu Z, Yang S. Identification of novel 4-substituted 7H-pyrrolo[2,3-d]pyrimidine derivatives as new FtsZ inhibitors: Bioactivity evaluation and computational simulation. Bioorg Chem 2024; 150:107534. [PMID: 38896935 DOI: 10.1016/j.bioorg.2024.107534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Bacterial infections and the consequent outburst of bactericide-resistance issues are fatal menace to both global health and agricultural produce. Hence, it is crucial to explore candidate bactericides with new mechanisms of action. The filamenting temperature-sensitive mutant Z (FtsZ) protein has been recognized as a new promising and effective target for new bactericide discovery. Hence, using a scaffold-hopping strategy, we designed new 7H-pyrrolo[2,3-d]pyrimidine derivatives, evaluated their antibacterial activities, and investigated their structure-activity relationships. Among them, compound B6 exhibited the optimal in vitro bioactivity (EC50 = 4.65 µg/mL) against Xanthomonas oryzae pv. oryzae (Xoo), which was superior to the references (bismerthiazol [BT], EC50 = 48.67 µg/mL; thiodiazole copper [TC], EC50 = 98.57 µg/mL]. Furthermore, the potency of compound B6 in targeting FtsZ was validated by GTPase activity assay, FtsZ self-assembly observation, fluorescence titration, Fourier-transform infrared spectroscopy (FT-IR) assay, molecular dynamics simulations, and morphological observation. The GTPase activity assay showed that the final IC50 value of compound B6 against XooFtsZ was 235.0 μM. Interestingly, the GTPase activity results indicated that the B6-XooFtsZ complex has an excellent binding constant (KA = 103.24 M-1). Overall, the antibacterial behavior suggests that B6 can interact with XooFtsZ and inhibit its GTPase activity, leading to bacterial cell elongation and even death. In addition, compound B6 showed acceptable anti-Xoo activity in vivo and low toxicity, and also demonstrated a favorable pharmacokinetic profile predicted by ADMET analysis. Our findings provide new chemotypes for the development of FtsZ inhibitors as well as insights into their underlying mechanisms of action.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Ya Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xichun Fu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Linli Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Hongwu Liu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
| | - Liwei Liu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhibing Wu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
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Kim K, Chen P, Li C, Li B. Novel Inhibitor of Glutamate-Cysteine Ligase Catalytic Subunit against Tribolium castaneum: High-Throughout Virtual Screening, Molecular Docking and Dynamics Simulation, and Bioassay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17813-17823. [PMID: 39080857 DOI: 10.1021/acs.jafc.4c02089] [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: 08/15/2024]
Abstract
The enzyme glutamate-cysteine ligase catalytic subunit (Gclc) is a rate-limiting enzyme in the biosynthesis of glutathione that is involved in antioxidant defense, detoxification of xenobiotics, and/or its metabolites and regulates the cell cycle and immune function. Therefore, Gclc presents an appealing target for the development of novel insecticides. In this study, we conducted high-throughput virtual screening from the ZINC20 database and identified three compounds with high binding affinity to the Tribolium castaneum Gclc (TcGclc). Ultimately, we selected ZINC000032992384 due to its superior stability and lowest binding energy, as determined through molecular dynamics simulations. Bioassay results revealed that the IC50 value of ZINC000032992384 was 19.70 μM lower than that of BSO (49.67 μM). Furthermore, the larval mortality in the ZINC000032992384 treated group was 63.8%, significantly higher than that of the controls (29.1% in the dichlorvos group and 6.4% in the acetone group). This study provides novel insights for the development of a Gclc-targeted inhibitor as a potent insecticide based on the interaction between receptors and ligands.
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Affiliation(s)
- KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
- Department of Life-Science, University of Science, Pyongyang 999093, Democratic People's Republic of Korea
| | - Peng Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Dong L, Wang W, Zhou L, Yang W, Xu Z, Cheng J, Shao X, Xu X, Li Z. Design, Synthesis, and Bioactivity of Trifluoroethylthio-Substituted Phenylpyrazole Derivatives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11949-11957. [PMID: 38757770 DOI: 10.1021/acs.jafc.4c00340] [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: 05/18/2024]
Abstract
As the first marketed phenylpyrazole insecticide, fipronil exhibited remarkable broad-spectrum insecticidal activity. However, it poses a significant threat to aquatic organisms and bees due to its high toxicity. Herein, 35 phenylpyrazole derivatives containing a trifluoroethylthio group on the 4 position of the pyrazole ring were designed and synthesized. The predicted physicochemical properties of all of the compounds were within a reasonable range. The biological assay results revealed that compound 7 showed 69.7% lethality against Aedes albopictus (A. albopictus) at the concentration of 0.125 mg/L. Compounds 7, 7g, 8d, and 10j showed superior insecticidal activity for the control of Plutella xylostella (P. xylostella). Notably, compound 7 showed similar insecticidal activity against Aphis craccivora (A. craccivora) compared with fipronil. Potential surface calculation and molecular docking suggested that different lipophilicity and binding models to the Musca domestica (M. domestica) gamma-aminobutyric acid receptors may be responsible for the decreased activity of the tested derivatives. Toxicity tests indicated that compound 8d (LC50 = 14.28 mg/L) induced obviously 14-fold lower toxicity than fipronil (LC50 = 1.05 mg/L) on embryonic-juvenile zebrafish development.
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Affiliation(s)
- Lefeng Dong
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weiguo Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liqi Zhou
- Shanghai GreenTech Laboratory Co. Ltd, 650 Shunqing Road, Shanghai 100093, China
| | - Wulin Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiping Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoyong Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
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9
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de Souza Rodrigues R, de Souza AQL, Feitoza MDO, Alves TCL, Barbosa AN, da Silva Santiago SRS, de Souza ADL. Biotechnological potential of actinomycetes in the 21st century: a brief review. Antonie Van Leeuwenhoek 2024; 117:82. [PMID: 38789815 DOI: 10.1007/s10482-024-01964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/07/2024] [Indexed: 05/26/2024]
Abstract
This brief review aims to draw attention to the biotechnological potential of actinomycetes. Their main uses as sources of antibiotics and in agriculture would be enough not to neglect them; however, as we will see, their biotechnological application is much broader. Far from intending to exhaust this issue, we present a short survey of the research involving actinomycetes and their applications published in the last 23 years. We highlight a perspective for the discovery of new active ingredients or new applications for the known metabolites of these microorganisms that, for approximately 80 years, since the discovery of streptomycin, have been the main source of antibiotics. Based on the collected data, we organize the text to show how the cosmopolitanism of actinomycetes and the evolutionary biotic and abiotic ecological relationships of actinomycetes translate into the expression of metabolites in the environment and the richness of biosynthetic gene clusters, many of which remain silenced in traditional laboratory cultures. We also present the main strategies used in the twenty-first century to promote the expression of these silenced genes and obtain new secondary metabolites from known or new strains. Many of these metabolites have biological activities relevant to medicine, agriculture, and biotechnology industries, including candidates for new drugs or drug models against infectious and non-infectious diseases. Below, we present significant examples of the antimicrobial spectrum of actinomycetes, which is the most commonly investigated and best known, as well as their non-antimicrobial spectrum, which is becoming better known and increasingly explored.
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Affiliation(s)
- Rafael de Souza Rodrigues
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil.
| | - Antonia Queiroz Lima de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | | | | | - Anderson Nogueira Barbosa
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Sarah Raquel Silveira da Silva Santiago
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Afonso Duarte Leão de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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10
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Chowdhury R, Bhuia MS, Al Hasan MS, Ansari SA, Ansari IA, Gurgel APAD, Coutinho HDM, Islam MT. Anticonvulsant effect of (±) citronellal possibly through the GABAergic and voltage-gated sodium channel receptor interaction pathways: In vivo and in silico studies. Neurochem Int 2024; 175:105704. [PMID: 38395152 DOI: 10.1016/j.neuint.2024.105704] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
This study aimed to investigate the anticonvulsant effects of citronellal (CIT) and possible underlying mechanisms through an isoniazid (INH)-induced seizure (convulsion) via in vivo and in silico studies. For this, convulsions were induced by the oral administration of INH (300 mg/kg) to the mice. The animals were treated orally with different doses of CIT (50, 100, and 200 mg/kg). Vehicle served as a negative control (NC), while diazepam (DZP) (2 mg/kg) and carbamazepine (CAR) (80 mg/kg) were provided (p.o.) as positive controls (PC). A combination therapy of CIT (middle dose) with DZP and CAR was also given to two separate groups of animals to estimate the synergistic or antagonistic effects. Molecular docking and visualization of ligand-receptor interactions are also estimated through different computational tools. The results of the in vivo study showed that CIT dose-dependently significantly (p < 0.05) exhibited a higher onset of seizures while reducing the frequency and duration of seizures in mice compared to the NC group. Besides these, in combination therapy, CIT significantly antagonized the activity of CAR and DZP, leading to a reduction in the onset of seizures and an increase in their frequency and duration compared to treatment with CAR and DZP alone. Additionally, molecular docking revealed that the CIT exhibited a moderate binding affinity (-5.8 kcal/mol) towards the GABAA receptor and a relative binding affinity (-5.3 kcal/mol) towards the voltage-gated sodium channel receptor by forming several bonds. In conclusion, CIT showed moderate anticonvulsant activity in INH-induced convulsion animals, possibly by enhancing GABAA receptor activity and inhibiting the voltage-gated sodium channel receptor.
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Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Md Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioluster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Md Sakib Al Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioluster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Irfan Aamer Ansari
- Department of Drug Science and Technology, University of Turin, Turin, 10124, Italy
| | | | - Henrique Douglas Melo Coutinho
- Department of Biological Chemistry, Laboratory of Microbiology and Molecular Biology, Regional University of Cariri, Crato CE, 63105-000, Brazil CE, 63105-000, Brazil.
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
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11
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Elebiju OF, Oduselu GO, Ogunnupebi TA, Ajani OO, Adebiyi E. In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance. Pharmaceuticals (Basel) 2024; 17:543. [PMID: 38794114 PMCID: PMC11124240 DOI: 10.3390/ph17050543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 05/26/2024] Open
Abstract
The inhibition of O-acetyl sulphydrylase synthase isoforms has been reported to represent a promising approach for the development of antibiotic adjuvants. This occurs via the organism developing an unpaired oxidative stress response, causing a reduction in antibiotic resistance in vegetative and swarm cell populations. This consequently increases the effectiveness of conventional antibiotics at lower doses. This study aimed to predict potential inhibitors of Salmonella typhimurium ortho acetyl sulphydrylase synthase (StOASS), which has lower binding energy than the cocrystalized ligand pyridoxal 5 phosphate (PLP), using a computer-aided drug design approach including pharmacophore modeling, virtual screening, and in silico ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) evaluation. The screening and molecular docking of 4254 compounds obtained from the PubChem database were carried out using AutoDock vina, while a post-screening analysis was carried out using Discovery Studio. The best three hits were compounds with the PubChem IDs 118614633, 135715279, and 155773276, possessing binding affinities of -9.1, -8.9, and -8.8 kcal/mol, respectively. The in silico ADMET prediction showed that the pharmacokinetic properties of the best hits were relatively good. The optimization of the best three hits via scaffold hopping gave rise to 187 compounds, and they were docked against StOASS; this revealed that lead compound 1 had the lowest binding energy (-9.3 kcal/mol) and performed better than its parent compound 155773276. Lead compound 1, with the best binding affinity, has a hydroxyl group in its structure and a change in the core heterocycle of its parent compound to benzimidazole, and pyrimidine introduces a synergistic effect and consequently increases the binding energy. The stability of the best hit and optimized compound at the StOASS active site was determined using RMSD, RMSF, radius of gyration, and SASA plots generated from a molecular dynamics simulation. The MD simulation results were also used to monitor how the introduction of new functional groups of optimized compounds contributes to the stability of ligands at the target active site. The improved binding affinity of these compounds compared to PLP and their toxicity profile, which is predicted to be mild, highlights them as good inhibitors of StOASS, and hence, possible antimicrobial adjuvants.
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Affiliation(s)
- Oluwadunni F. Elebiju
- Department of Chemistry, College of Science and Technology, Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota 112233, Ogun State, Nigeria; (O.F.E.); (G.O.O.); (T.A.O.); (O.O.A.)
- Department of Chemistry, College of Science and Technology, Covenant University, Ota 112233, Ogun State, Nigeria
| | - Gbolahan O. Oduselu
- Department of Chemistry, College of Science and Technology, Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota 112233, Ogun State, Nigeria; (O.F.E.); (G.O.O.); (T.A.O.); (O.O.A.)
| | - Temitope A. Ogunnupebi
- Department of Chemistry, College of Science and Technology, Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota 112233, Ogun State, Nigeria; (O.F.E.); (G.O.O.); (T.A.O.); (O.O.A.)
- Department of Chemistry, College of Science and Technology, Covenant University, Ota 112233, Ogun State, Nigeria
| | - Olayinka O. Ajani
- Department of Chemistry, College of Science and Technology, Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota 112233, Ogun State, Nigeria; (O.F.E.); (G.O.O.); (T.A.O.); (O.O.A.)
- Department of Chemistry, College of Science and Technology, Covenant University, Ota 112233, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Department of Chemistry, College of Science and Technology, Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota 112233, Ogun State, Nigeria; (O.F.E.); (G.O.O.); (T.A.O.); (O.O.A.)
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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12
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Ma H, Wang K, Wang B, Wang Z, Liu Y, Wang Q. Design, Synthesis, and Biological Activities of Novel Coumarin Derivatives as Pesticide Candidates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4658-4668. [PMID: 38388372 DOI: 10.1021/acs.jafc.3c08161] [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: 02/24/2024]
Abstract
Food security is an important issue in the 21st century; preventing and controlling crop diseases and pests are the key to solve this problem. The creation of new pesticides based on natural products is an important and effective method. Herein, coumarins were selected as parent structures, and a series of their derivatives were designed, synthesized, and evaluated for their antiviral activities, fungicidal activities, and insecticidal activities. We found that coumarin derivatives exhibited good to excellent antiviral activities against tobacco mosaic virus (TMV). The antiviral activities of I-1, I-2a, I-4b, II-2c, II-2g, II-3, and II-3b are better than that of ribavirin at 500 μg/mL. Molecular docking research showed that these compounds had a strong interaction with TMV CP. These compounds also showed broad-spectrum fungicidal activities against 14 plant pathogenic fungi. The EC50 values of I-1, I-2a, I-3c, and II-2d are in the range of 1.56-8.65 μg/mL against Rhizoctonia cerealis, Physalospora piricola, Sclerotinia sclerotiorum, and Pyricularia grisea. Most of the compounds also displayed good insecticidal activities against Mythimna separata. Pesticide-likeness analysis showed that these compounds are following pesticide-likeness and have the potential to be developed as pesticide candidates. The present work lays a foundation for the discovery of novel pesticide lead compounds based on coumarin derivatives.
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Affiliation(s)
- Henan Ma
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, China
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Kaihua Wang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Beibei Wang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Ziwen Wang
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, China
| | - Yuxiu Liu
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Qingmin Wang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, College of Chemistry, Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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13
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Djoumbou-Feunang Y, Wilmot J, Kinney J, Chanda P, Yu P, Sader A, Sharifi M, Smith S, Ou J, Hu J, Shipp E, Tomandl D, Kumpatla SP. Cheminformatics and artificial intelligence for accelerating agrochemical discovery. Front Chem 2023; 11:1292027. [PMID: 38093816 PMCID: PMC10716421 DOI: 10.3389/fchem.2023.1292027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/09/2023] [Indexed: 10/17/2024] Open
Abstract
The global cost-benefit analysis of pesticide use during the last 30 years has been characterized by a significant increase during the period from 1990 to 2007 followed by a decline. This observation can be attributed to several factors including, but not limited to, pest resistance, lack of novelty with respect to modes of action or classes of chemistry, and regulatory action. Due to current and projected increases of the global population, it is evident that the demand for food, and consequently, the usage of pesticides to improve yields will increase. Addressing these challenges and needs while promoting new crop protection agents through an increasingly stringent regulatory landscape requires the development and integration of infrastructures for innovative, cost- and time-effective discovery and development of novel and sustainable molecules. Significant advances in artificial intelligence (AI) and cheminformatics over the last two decades have improved the decision-making power of research scientists in the discovery of bioactive molecules. AI- and cheminformatics-driven molecule discovery offers the opportunity of moving experiments from the greenhouse to a virtual environment where thousands to billions of molecules can be investigated at a rapid pace, providing unbiased hypothesis for lead generation, optimization, and effective suggestions for compound synthesis and testing. To date, this is illustrated to a far lesser extent in the publicly available agrochemical research literature compared to drug discovery. In this review, we provide an overview of the crop protection discovery pipeline and how traditional, cheminformatics, and AI technologies can help to address the needs and challenges of agrochemical discovery towards rapidly developing novel and more sustainable products.
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Affiliation(s)
| | - Jeremy Wilmot
- Corteva Agriscience, Crop Protection Discovery and Development, Indianapolis, IN, United States
| | - John Kinney
- Corteva Agriscience, Farming Solutions and Digital, Indianapolis, IN, United States
| | - Pritam Chanda
- Corteva Agriscience, Farming Solutions and Digital, Indianapolis, IN, United States
| | - Pulan Yu
- Corteva Agriscience, Crop Protection Discovery and Development, Indianapolis, IN, United States
| | - Avery Sader
- Corteva Agriscience, Crop Protection Discovery and Development, Indianapolis, IN, United States
| | - Max Sharifi
- Corteva Agriscience, Regulatory and Stewardship, Indianapolis, IN, United States
| | - Scott Smith
- Corteva Agriscience, Farming Solutions and Digital, Indianapolis, IN, United States
| | - Junjun Ou
- Corteva Agriscience, Crop Protection Discovery and Development, Indianapolis, IN, United States
| | - Jie Hu
- Corteva Agriscience, Farming Solutions and Digital, Indianapolis, IN, United States
| | - Elizabeth Shipp
- Corteva Agriscience UK Limited, Regulation Innovation Center, Abingdon, United Kingdom
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14
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Li K, Li M, Zhong H, Tang L, Lv Y, Fan Z. Design and Synthesis of Pyrimidine Amine Containing Isothiazole Coumarins for Fungal Control. ACS OMEGA 2023; 8:37471-37481. [PMID: 37841179 PMCID: PMC10568580 DOI: 10.1021/acsomega.3c05734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
Developing new fungicides is always crucial to protecting crops. A series of 4-(3,4-dichloroisothiazol-5-yl)-7-(2-((5-(5-pyrimidin-4-yl)amino)ethoxy)-8-methyl) coumarin derivatives were designed and synthesized by Williamson ether condensation and substitution reactions. Structure determinations were clarified by 1H NMR, 13C NMR, and HRMS, and compound 4h crystallized by the fusion method for further structural confirmation. The in vitro bioassay results showed that the target compounds displayed good fungicidal activity against Alternaria solani, Botrytis cinerea, Cercospora arachidicola, Fusarium graminearum, Physalospora piricola, Rhizoctonia solani, and Sclerotinia sclerotiorum. Among them, compounds 4b and 4d showed higher inhibitory activity against R. solani, with EC50 values of 11.3 and 13.7 μg/mL, respectively, and they were more active than the positive control diflumetorim with an EC50 value of 19.8 μg/mL. Molecular docking suggested that compound 4b and diflumetorim may have similar interactions with complex I NADH oxidoreductase. Density functional theory calculation and pesticide-likeness analysis studies gave a rational explanation of their fungicidal activity. These results indicated that compounds 4b and 4d deserved further optimization according to the principle of pesticide-likeness.
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Affiliation(s)
- Kun Li
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers
Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Mengyuan Li
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers
Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Haolin Zhong
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers
Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Liangfu Tang
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers
Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - You Lv
- College
of Agricultural and Biological Engineering, Heze University, Heze 274015, P. R. China
| | - Zhijin Fan
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers
Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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15
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Synthesis and Antifungal Activity of New butenolide Containing Methoxyacrylate Scaffold. Molecules 2022; 27:molecules27196541. [PMID: 36235077 PMCID: PMC9573425 DOI: 10.3390/molecules27196541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
In order to improve the antifungal activity of new butenolides containing oxime ether moiety, a series of new butenolide compounds containing methoxyacrylate scaffold were designed and synthesized, based on the previous reports. Their structures were characterized by 1H NMR, 13C NMR, HR-MS spectra, and X-ray diffraction analysis. The in vitro antifungal activities were evaluated by the mycelium growth rate method. The results showed that the inhibitory activities of these new compounds against Sclerotinia sclerotiorum were significantly improved, in comparison with that of the lead compound 3-8; the EC50 values of V-6 and VI-7 against S. sclerotiorum were 1.51 and 1.81 mg/L, nearly seven times that of 3-8 (EC50 10.62 mg/L). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observation indicated that compound VI-3 had a significant impact on the structure and function of the hyphal cell of S. sclerotiorum mycelium and the positive control trifloxystrobin. Molecular simulation docking results indicated that the introduction of methoxyacrylate scaffold is beneficial to improving the antifungal activity of these compounds against S. sclerotiorum, which can be used as the lead for further structure optimization.
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16
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Wang Y, Xiong Y, Garcia EAL, Wang Y, Butch CJ. Drug Chemical Space as a Guide for New Herbicide Development: A Cheminformatic Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9625-9636. [PMID: 35915870 DOI: 10.1021/acs.jafc.2c01425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Herbicides are critical resources for meeting agricultural demand. While similar in structure and function to pharmaceuticals, the development of new herbicidal mechanisms of action and new scaffolds against known mechanisms of action has been much slower than in pharmaceutical sciences. We hypothesized that this may be due in part to a relative undersampling of possible herbicidal chemistries and set out to test whether this difference in sampling existed and whether increasing the diversity of possible herbicidal chemistries would be likely to result in more efficacious herbicides. To conduct this work, we first identified databases of commercially available herbicides and clinically approved pharmaceuticals. Using these databases, we created a two-dimensional embedding of the chemical, which provides a qualitative visualization of the degree to which each chemotype is distributed within the combined chemical space and shows a moderate degree of overlap between the two sets. Next, we trained several machine learning models to classify herbicides versus drugs based on physicochemical characteristics. The most accurate of these models has an accuracy of 93% with the key differentiating characteristics being the number of polar hydrogens, number of amide bonds, LogP, and polar surface area. We then used several types of scaffold decomposition to quantitatively evaluate the chemical diversity of each molecular family and showed herbicides to have considerably fewer unique structural fragments. Finally, we used molecular docking as an in silico evaluation of further structural diversification in herbicide development. To this end, we identified herbicides with well-characterized binding sites and modified those scaffolds based on similar structural subunits from the drug dataset not present in any commercial herbicide while using the machine-learned model to ensure that required herbicide properties were maintained. Redocking the original and modified scaffolds of several herbicides showed that even this simple design strategy is capable of yielding new molecules with higher predicted affinity for the target enzymes. Overall, we show that herbicides are distinct from drugs based on physicochemical properties but less diverse in their chemistry in a way not governed by these properties. We also demonstrate in silico that increasing the diversity of herbicide scaffolds has the potential to increase potency, potentially reducing the amount needed in agricultural practice.
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Affiliation(s)
- Yisheng Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Youjin Xiong
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | | | - Yiqing Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Christopher J Butch
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Blue Marble Space Institute for Science, Seattle, Washington 98104, United States
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17
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Martins FA, Daré JK, Freitas MP. Computer-Assisted Proposition of Promising Aryloxyacetic Acid Derivatives as HPPD Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8986-8993. [PMID: 35848390 DOI: 10.1021/acs.jafc.2c02954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A series of aryloxyacetic acid derivatives have demonstrated promising herbicidal performance by inhibition of the hydroxyphenylpyruvate deoxygenase (HPPD) enzyme. We hereby applied quantitative structure-activity relationship (QSAR) and docking strategies to model and chemically understand the bioactivities of these compounds and subsequently propose unprecedented analogues aiming at improving the herbicidal and environmental properties. Bulky halogens at the 2-, 3-, 4-, and 6-positions of an aromatic ring, CF3 in 4-position, and the 2-NO2 group in a phenyl ring appear to favor the HPPD inhibition. At the same time, Me and OMe substituents contribute to decreasing the pKi values. Accordingly, a few compounds were proposed and the candidate with 2,4,6-triBr substituents demonstrated an estimated pKi similar to those of the best library compounds. This finding was corroborated by the docking scores of the ligand-enzyme interactions. In addition, the high calculated lipophilicity of some proposed agrochemicals suggests that they should have low soil mobility and, therefore, are not prone to easily leach out and reach groundwater, despite causing other ecological issues.
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Affiliation(s)
- Francisco Antonio Martins
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, 37200-900 Lavras, MG, Brazil
| | - Joyce K Daré
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, 37200-900 Lavras, MG, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, 37200-900 Lavras, MG, Brazil
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18
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Yang D, Qi X, Kalinina TA, Glukhareva TV, Tang L, Li Z, Fan Z. Synthesis of novel N-(2-phenyl-3-pyridyl) thiadiazole/isothiazole carboxamide analogs as potent plant elicitors. PEST MANAGEMENT SCIENCE 2022; 78:1138-1145. [PMID: 34799969 DOI: 10.1002/ps.6728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/01/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant elicitors are a class of plant protection agents that can stimulate plant immunity against phytopathogen without a potential resistance problem. In searching for novel plant elicitor candidates, a series of novel N-(2-phenyl-3-pyridyl) thiadiazole/isothiazole carboxamide analogs were designed and synthesized. RESULTS In vitro bioassay showed that all new compounds exhibited weak direct fungicidal activity. However, compounds 3b, 3g, 3n and 3o showed broad spectrum of in vivo activity against four plant fungi tested. In particularly, 3g showed 80% activity against Rhizoctonia solani in a glasshouse at a concentration of 1 μg mL-1 . For induction activity of tobacco against tobacco mosaic virus (TMV), compounds 3c and 3v showed 67% and 68% inhibitory activity, respectively, which were superior to the positive controls ribavirin and ningnanmycin. Compound 3g showed moderate induction activity (41%). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis found that, 3g could up-regulate expression of genes that are related to reactive oxygen species (ROS), pathogenesis-related protein (PRP) and salicylic acid (SA) signalling. CONCLUSION These results indicated that 3g as an elicitor candidate might act on the SA signalling pathway. According to our findings, N-(2-phenyl-3-pyridyl) thiadiazole/isothiazole carboxamide analogs might be promising lead scaffolds as a novel plant elicitor for further investigation.
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Affiliation(s)
- Dongyan Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, P. R. China
- School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, P. R. China
| | - Xin Qi
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, P. R. China
| | - Tatiana A Kalinina
- Department of Technology for Organic Synthesis, Institute of Chemical Technology, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Tatiana V Glukhareva
- Department of Technology for Organic Synthesis, Institute of Chemical Technology, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, P. R. China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, P. R. China
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