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Luo D, Bai Z, Bai H, Liu N, Han J, Ma C, Wu D, Bai L, Li Z. A first-in-class dimethyl 2-acetamido terephthalate inhibitor targeting Conyza canadensis SHMT1 with a novel herbicidal mode-of-action. J Adv Res 2024; 62:59-70. [PMID: 37820886 PMCID: PMC11331707 DOI: 10.1016/j.jare.2023.10.003] [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: 08/12/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
INTRODUCTION Herbicide application is a highly efficiency method of weed control that boots agricultural output and assures food security. The development of novel herbicides focuses on improved bioactivity and new modes of action. The amino acid biosynthesis was validated as a promising novel mode of action for herbicidal compounds. However, the amino acid biosynthesis enzyme remains largely unexplored for herbicidal targets. OBJECTIVES Serine hydroxymethyl transferase (SHMT) is an essentialenzyme in the photorespiratory cycle. The study aims to explore Conyza canadensis SHMT1 (CcSHMT1) as a promising target for herbicide discovery. METHODS Structure determination of CcSHMT1 was resolved by X-ray crystallography. Virtual screening docking experiments were performed with Glide version 5.5. Novel derivatives of dimethyl 2-acetamido terephthalate were further designed, synthesized, and bioassay. The druggability of the inhibitor was evidenced by ultrastructural changes in mitochondria, in vivo and vitro enzyme activity assays, and genetics analysis. RESULTS CcSHMT1 has a typical PLP-dependent enzyme 3D structure. The dimethyl 2-acetamido terephthalate-containing compounds had herbicidal activity. Dimethyl 2-(2-(4-(2-(4-bromo-2-chlorophenoxy) acetyl)piperazin-1-yl)acetamido) terephthalate (Compound 9ay, EC50 = 193.8 g a.i./ ha) exhibited the highest herbicidal activity on tested weed among the synthesized compounds. Compound 9ay had no obvious adverse effect on the growth of maize and honeybees. Compound 9ay was verified to target CcSHMT1 as an herbicide candidate. CONCLUSION A first-in-class CcSHMT1 inhibitor that could be developed as a potent herbicide with a new mode of action and provide an avenue for discovering novel inhibitors of pyridoxal-5-phosphate-dependent enzymes.
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Affiliation(s)
- Dingfeng Luo
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Zhendong Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haodong Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Na Liu
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Jincai Han
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Changsheng Ma
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Di Wu
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lianyang Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China.
| | - Zuren Li
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China.
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Milićević J, Petrović S, Tošić S, Vrecl M, Arsić B. Recent Computer-Aided Studies on Herbicides: A Short Review. Chem Biodivers 2024:e202400531. [PMID: 38948948 DOI: 10.1002/cbdv.202400531] [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: 03/05/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
Current industrial herbicides have a negative impact on the environment and have widespread resistance, so computational studies on their properties, elimination, and overcoming resistance can be helpful. On the other hand, developing new herbicides, especially bioherbicides, is slow and costly. Therefore, computational studies that guide the design and search for new herbicides that exist in various plant sources, can alleviate the pain associated with the many obstacles. This review summarizes for the first time the most recent studies on both aspects of herbicides over 10 years.
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Affiliation(s)
- Jelena Milićević
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, Mike Petrovića Alasa 12-14, 11351, Vinča, Belgrade, Republic of Serbia
| | - Stefan Petrović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106, Niš, Republic of Serbia
| | - Snežana Tošić
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106, Niš, Republic of Serbia
| | - Milka Vrecl
- Institute for Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, 1000, Ljubljana, Slovenia
| | - Biljana Arsić
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106, Niš, Republic of Serbia
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Nakayama Y, Morishita S, Doi H, Hirano T, Kaneko H. Molecular Design of Novel Herbicide and Insecticide Seed Compounds with Machine Learning. ACS OMEGA 2024; 9:18488-18494. [PMID: 38680296 PMCID: PMC11044161 DOI: 10.1021/acsomega.4c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/27/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024]
Abstract
Pesticides are widely used to improve crop productivity by eliminating weeds and pests. Conventional pesticide development involves synthesizing compounds, testing their activities, and studying their effects on the ecosystem. However, as pesticide discovery has an extremely low success rate, many compounds must be synthesized and tested. To overcome the high human, financial, and time costs of this process, machine learning is attracting increasing attention. In this study, we used machine learning for the molecular design of novel seed compounds for herbicides and insecticides. Classification models were constructed by using compounds that had been tested as herbicides and insecticides, and an inverse analysis of the constructed models was conducted. In the molecular design of herbicides, we proposed 186 new samples as herbicides using ensemble learning and a method for expressing explanatory variables that consider the relationships among eight weed species. For the molecular design of insecticides, we used undersampling and ensemble learning for the analysis of unbalanced data. Based on approximately 340,000 compounds, 12 potential insecticides were proposed, of which 2 exhibited actual activity when tested. These results demonstrate the potential of the developed machine-learning method for rapidly identifying novel herbicides and insecticides.
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Affiliation(s)
- Yuki Nakayama
- Department
of Applied Chemistry, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Saki Morishita
- Hokko
Chemical Industry Co., Ltd., 2165, Toda, Atsugi-shi, Kanagawa 243-0023, Japan
| | - Hayato Doi
- Hokko
Chemical Industry Co., Ltd., 2165, Toda, Atsugi-shi, Kanagawa 243-0023, Japan
| | - Tatsuya Hirano
- Hokko
Chemical Industry Co., Ltd., 2165, Toda, Atsugi-shi, Kanagawa 243-0023, Japan
| | - Hiromasa Kaneko
- Department
of Applied Chemistry, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Niu Z, Rehman T, Young J, Johnson WG, Yokoo T, Young B, Jin J. Hyperspectral Analysis for Discriminating Herbicide Site of Action: A Novel Approach for Accelerating Herbicide Research. SENSORS (BASEL, SWITZERLAND) 2023; 23:9300. [PMID: 38067672 PMCID: PMC10708448 DOI: 10.3390/s23239300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
In agricultural weed management, herbicides are indispensable, yet innovation in their modes of action (MOA)-the general mechanisms affecting plant processes-has slowed. A finer classification within MOA is the site of action (SOA), the specific biochemical pathway in plants targeted by herbicides. The primary objectives of this study were to evaluate the efficacy of hyperspectral imaging in the early detection of herbicide stress and to assess its potential in accelerating the herbicide development process by identifying unique herbicide sites of action (SOA). Employing a novel SOA classification method, eight herbicides with unique SOAs were examined via an automated, high-throughput imaging system equipped with a conveyor-based plant transportation at Purdue University. This is one of the earliest trials to test hyperspectral imaging on a large number of herbicides, and the study aimed to explore the earliest herbicide stress detection/classification date and accelerate the speed of herbicide development. The final models, trained on a dataset with nine treatments with 320 samples in two rounds, achieved an overall accuracy of 81.5% 1 day after treatment. With the high-precision models and rapid screening of numerous compounds in only 7 days, the study results suggest that hyperspectral technology combined with machine learning can contribute to the discovery of new herbicide MOA and help address the challenges associated with herbicide resistance. Although no public research to date has used hyperspectral technology to classify herbicide SOA, the successful evaluation of herbicide damage to crops provides hope to accelerate the progress of herbicide development.
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Affiliation(s)
- Zhongzhong Niu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; (Z.N.); (T.Y.)
| | - Tanzeel Rehman
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA;
| | - Julie Young
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (J.Y.); (W.G.J.); (B.Y.)
| | - William G. Johnson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (J.Y.); (W.G.J.); (B.Y.)
| | - Takayuki Yokoo
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; (Z.N.); (T.Y.)
- Health and Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., Takarazuka 665-8555, Hyogo, Japan
| | - Bryan Young
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (J.Y.); (W.G.J.); (B.Y.)
| | - Jian Jin
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; (Z.N.); (T.Y.)
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Berestetskiy A. Modern Approaches for the Development of New Herbicides Based on Natural Compounds. PLANTS (BASEL, SWITZERLAND) 2023; 12:234. [PMID: 36678947 PMCID: PMC9864389 DOI: 10.3390/plants12020234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/24/2022] [Indexed: 05/12/2023]
Abstract
Weeds are a permanent component of anthropogenic ecosystems. They require strict control to avoid the accumulation of their long-lasting seeds in the soil. With high crop infestation, many elements of crop production technologies (fertilization, productive varieties, growth stimulators, etc.) turn out to be practically meaningless due to high yield losses. Intensive use of chemical herbicides (CHs) has led to undesirable consequences: contamination of soil and wastewater, accumulation of their residues in the crop, and the emergence of CH-resistant populations of weeds. In this regard, the development of environmentally friendly CHs with new mechanisms of action is relevant. The natural phytotoxins of plant or microbial origin may be explored directly in herbicidal formulations (biorational CHs) or indirectly as scaffolds for nature-derived CHs. This review considers (1) the main current trends in the development of CHs that may be important for the enhancement of biorational herbicides; (2) the advances in the development and practical application of natural compounds for weed control; (3) the use of phytotoxins as prototypes of synthetic herbicides. Some modern approaches, such as computational methods of virtual screening and design of herbicidal molecules, development of modern formulations, and determination of molecular targets, are stressed as crucial to make the exploration of natural compounds more effective.
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Affiliation(s)
- Alexander Berestetskiy
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia
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Discovery of novel HPPD inhibitors based on a combination strategy of pharmacophore, consensus docking and molecular dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hulme PE. Hierarchical cluster analysis of herbicide modes of action reveals distinct classes of multiple resistance in weeds. PEST MANAGEMENT SCIENCE 2022; 78:1265-1271. [PMID: 34854224 PMCID: PMC9299916 DOI: 10.1002/ps.6744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The number of weed species resistant to multiple herbicide modes of action (MoAs) has increased over the last 30 years and may in the future render existing herbicide MoAs obsolete for many cropping systems. Yet few predictive tools exist to manage this risk. Using a worldwide dataset of weed species resistant to multiple herbicide MoAs, hierarchical clustering was used to classify MoAs into similar groups in relation to the suite of resistant weed species they have in common. Network analyses then were used to explore the relative importance of species prevalence and similarity in cluster patterns. RESULTS Hierarchical clustering identified three similarly sized clusters of herbicide MoAs that were linked by the co-occurrence of resistant weeds: Herbicide Resistance Action Committee (HRAC) groups 2, 4, 5 and 9; HRAC groups 12, 14 and 15; and HRAC groups 1, 3 and 22. Cluster membership was consistent with similarities in the physiological or biochemical target of the herbicide MoAs. Network analyses revealed that the number of weed species resistant to two different MoAs was related to the number of weeds known to be resistant to each individual herbicide MoA. CONCLUSIONS Hierarchical cluster analysis provided new insights into the risk of weeds becoming resistant to more than one herbicide MoA. By clustering herbicide MoAs into three distinct groups, the potential exists for farmers to manage resistance by rotating herbicides between rather than within clusters, as far as crop, weed and environmental conditions allow.
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Affiliation(s)
- Philip E Hulme
- Bio‐Protection Research CentreLincoln UniversityChristchurchNew Zealand
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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Teixeira MG, Alvarenga ES, Lopes DT, Oliveira DF. Herbicidal activity of isobenzofuranones and in silico identification of their enzyme target. PEST MANAGEMENT SCIENCE 2019; 75:3331-3339. [PMID: 31026360 DOI: 10.1002/ps.5456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/23/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Given the weed resistance to various herbicides with different mechanisms of action, the search for new compounds that are more effective and exhibit low levels of impact to other species in nature has been imperative in the field of the agriculture. For this purpose, 16 phthalides, and furan-2(5H)-one were synthetized and evaluated for their effectiveness as herbicides in seeds of Sorghum bicolor (sorghum), Cucumis sativus (cucumber), and Allium cepa (onion). Furthermore, a preliminary in silico study was carried out to identify the enzyme target of the most active compounds. RESULTS In the assays with S. bicolor, the mixture rac-(3aR,4R,5S,6S,7S,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one + rac-(3aR,4R,5R,6R,7S,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (15a + 15b) showed comparable inhibitory activity to (S)-metolachlor, which was used as control herbicide at concentrations ranging from 50 μm to 1000 μm. The developments of the seeds evaluated were altered by all 17 compounds, either stimulating or inhibiting. The best results were presented by compounds 15a, and 15b, either in their pure form or as a mixture. CONCLUSION The results presented by 15a, and 15b were superior to the activity of the commercial herbicide (S)-metolachlor in the assays with C. sativus, and A. cepa. The in silico study provides strong evidence that the most active compounds bind to strigolactones esterases D14 through the same binding site of (5R)-5-hydroxy-3-methylfuran-2(5H)-one (H3M), which is one of the strigolactones (SLs) cleavage products. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Milena G Teixeira
- Departament of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elson S Alvarenga
- Departament of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Dayane T Lopes
- Departament of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
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Identification of novel inhibitors of p-hydroxyphenylpyruvate dioxygenase using receptor-based virtual screening. J Taiwan Inst Chem Eng 2019. [DOI: 10.1016/j.jtice.2019.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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