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Nuñez M, Wang Y, Russinova E, Estévez-Braun A, Amesty A, Olea AF, Mellado M, Díaz K, Espinoza Catalán L. Synthesis, Biological Activity, and Molecular-Docking Studies of New Brassinosteroid Analogs. Int J Mol Sci 2024; 25:10158. [PMID: 39337642 PMCID: PMC11432311 DOI: 10.3390/ijms251810158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/29/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Much work has been dedicated to the quest to determine the structure-activity relationship in synthetic brassinosteroid (BR) analogs. Recently, it has been reported that analogs with phenyl or benzoate groups in the alkyl chain present activities comparable to those shown by natural BRs, depending on the nature of the substituent in the aromatic ring. However, as it is well known that the activity depends on the structure of the whole molecule, in this work, we have synthesized a series of compounds with the same substituted benzoate in the alkyl chain and a hydroxyl group at C3. The main goal was to compare the activities with analogs with -OH at C2 and C3. Additionally, a molecular-docking study and molecular dynamics simulations were performed to establish a correlation between the experimental and theoretical results. The synthesis of eight new BR analogs was described. All the analogs were fully characterized by spectroscopical methods. The bioactivity of these analogs was assessed using the rice lamina inclination test (RLIT) and the inhibition of the root and hypocotyl elongation of Arabidopsis thaliana. The results of the RLIT indicate that at the lowest tested concentration (1 × 10-8 M), in the BR analogs in which the aromatic ring was substituted at the para position with methoxy, the I and CN substituents were more active than brassinolide (50-72%) and 2-3 times more active than those analogs in which the substituent group was F, Cl or Br atoms. However, at the highest concentrations, brassinolide was the most active compound, and the structure-activity relationship changed. On the other hand, the results of the A. thaliana root sensitivity assay show that brassinolide and the analogs with I and CN as substituents on the benzoyl group were the most active compounds. These results are in line with those obtained via the RLIT. A comparison of these results with those obtained for similar analogs that had a hydroxyl group at C2 indicates the importance of considering the whole structure. The molecular-docking results indicate that all the analogs adopted a brassinolide-like orientation, while the stabilizing effect of the benzoate group on the interactions with the receptor complex provided energy binding values ranging between -10.17 and -13.17 kcal mol-1, where the analog with a nitrile group was the compound that achieved better contact with the amino acids present in the active site.
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Affiliation(s)
- María Nuñez
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
| | - Yaowei Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; (Y.W.); (E.R.)
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; (Y.W.); (E.R.)
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Estévez-Braun
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain; (A.E.-B.); (A.A.)
| | - Angel Amesty
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain; (A.E.-B.); (A.A.)
| | - Andrés F. Olea
- Grupo QBAB, Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, Santiago 8900000, Chile;
| | - Marco Mellado
- Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile;
| | - Katy Díaz
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
| | - Luis Espinoza Catalán
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile;
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Richmond V, Falcone BN, Maier MS, Arroyo Máñez P. Putting the Puzzle Together To Get the Whole Picture: Molecular Basis of the Affinity of Two Steroid Derivatives to Acetylcholinesterase. ACS OMEGA 2023; 8:25610-25622. [PMID: 37483177 PMCID: PMC10357547 DOI: 10.1021/acsomega.3c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that has no cure because its etiology is still unknown, and its main treatment is the administration of acetylcholinesterase (AChE) inhibitors. The study of the mechanism of action of this family of compounds is critical for the design of new more potent and specific inhibitors. In this work, we study the molecular basis of an uncompetitive inhibitor (compound 1, 2β, 3α-dihydroxy-5α-cholestan-6-one disulfate), which we have proved to be a peripheral anionic site (PAS)-binding AChE inhibitor. The pipeline designed in this work is key to the development of other PAS inhibitors that not only inhibit the esterase action of the enzyme but could also modulate the non-cholinergic functions of AChE linked to the process of amylogenesis. Our studies showed that 1 inhibits the enzyme not simply by blocking the main gate but by an allosteric mechanism. A detailed and careful analysis of the ligand binding position and the protein dynamics, particularly regarding their secondary gates and active site, was necessary to conclude this. The same analysis was executed with an inactive analogue (compound 2, 2β, 3α-dihydroxy-5α-cholestan-6-one). Our first computational results showed no differences in affinity to AChE between both steroids, making further analysis necessary. This work highlights the variables to be considered and develops a refined methodology, for the successful design of new potent dual-action drugs for AD, particularly PAS inhibitors, an attractive strategy to combat AD.
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Affiliation(s)
- Victoria Richmond
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Bruno N. Falcone
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Marta S. Maier
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Pau Arroyo Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
- Departamento
de Química Orgánica, Universitat
de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
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Synthesis of New Steroidal Carbamates with Plant-Growth-Promoting Activity: Theoretical and Experimental Evidence. Int J Mol Sci 2021; 22:ijms22052330. [PMID: 33652675 PMCID: PMC7956523 DOI: 10.3390/ijms22052330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022] Open
Abstract
A priority of modern agriculture is to use novel and environmentally friendly plant-growth promoter compounds to increase crop yields and avoid the indiscriminate use of synthetic fertilizers. Brassinosteroids are directly involved in the growth and development of plants and are considered attractive candidates to solve this problem. Obtaining these metabolites from their natural sources is expensive and cumbersome since they occur in extremely low concentrations in plants. For this reason, much effort has been dedicated in the last decades to synthesize brassinosteroids analogs. In this manuscript, we present the synthesis and characterization of seven steroidal carbamates starting from stigmasterol, β-sitosterol, diosgenin and several oxygenated derivatives of it. The synthesis route for functionalization of diosgenin included epoxidation and epoxy opening reactions, reduction of carbonyl groups, selective oxidation of hydroxyl groups, among others. All the obtained compounds were characterized by 1H and 13C NMR, HRMS, and their melting points are also reported. Rice lamina inclination test performed at different concentrations established that all reported steroidal carbamates show plant-growth-promoting activity. A molecular docking study evaluated the affinity of the synthesized compounds towards the BRI1-BAK1 receptor from Arabidopsis thaliana and three of the docked compounds displayed a binding energy lower than brassinolide.
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Demissie ZA, Huang F, Song H, Todd AT, Vrinten P, Loewen MC. Barley "uzu" and Wheat "uzu-like" Brassinosteroid Receptor BRI1 Kinase Domain Variations Modify Phosphorylation Activity In Vitro. Biochemistry 2020; 59:2986-2997. [PMID: 32786402 DOI: 10.1021/acs.biochem.0c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brassinosteroid insensitive1 (BRI1), a leucine-rich repeat receptor kinase, is responsible for the perception of the brassinosteroid (BR) phytohormone in plants. While recent evidence has implicated a naturally occurring Hordeum vulgare V. (barley) HvBRI1 kinase domain (KD) variant (H857R; "uzu" variation) in increased fungal disease resistance, the impact of the variation on receptor function and thus the mechanism by which disease resistance might be imparted remain enigmatic. Here, the functional implications of the uzu variation as well as the effects of newly identified naturally occurring Triticum aestivum L. (wheat) TaBRI1-KD variants are investigated. Recombinantly produced KDs of wild-type (WT) and uzu HvBRI1 were assessed for phosphorylation activity in vitro, yielding WT KM and VMAX values similar to those of other reports, but the uzu variation delayed saturation and reduced turnover levels. In silico modeling of the H857R variation showed it to be surface-exposed and distal from the catalytic site. Further evaluation of three naturally occurring wheat TaBRI1 variants, A907T, A970V, and G1019R (barley numbering) identified in the A, B, and D subgenomic genes, respectively, highlighted a significant loss of activity for A907T. A907T is located on the same surface as the H857R variation and a negative regulatory phosphorylation site (T982) in Arabidopsis thaliana BRI1. A fourth variation, T1031A (barley numbering), unique to both subgenomic A proteins and localized to the BKI1 binding site, also decreased activity. The outcomes are discussed with respect to the predicted structural contexts of the variations and their implications with respect to mechanisms of action.
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Affiliation(s)
- Zerihun A Demissie
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Fang Huang
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Halim Song
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Andrea T Todd
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Patricia Vrinten
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Michele C Loewen
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
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Díaz K, Espinoza L, Carvajal R, Conde-González M, Niebla V, Olea AF, Coll Y. Biological Activities and Molecular Docking of Brassinosteroids 24-Norcholane Type Analogs. Int J Mol Sci 2020; 21:E1832. [PMID: 32155857 PMCID: PMC7084776 DOI: 10.3390/ijms21051832] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/13/2020] [Accepted: 03/04/2020] [Indexed: 01/11/2023] Open
Abstract
The quest and design of new brassinosteroids analogs is a matter of current interest. Herein, the effect of short alkyl side chains and the configuration at C22 on the growth-promoting activity of a series of new brassinosteroid 24-norcholan-type analogs have been evaluated by the rice leaf inclination test using brassinolide as positive control. The highest activities were found for triol 3 with a C22(S) configuration and monobenzoylated derivatives. A docking study of these compounds into the active site of the Brassinosteroid Insensitive 1(BRI1)-ligand-BRI1-Associated Receptor Kinase 1 (BAK1) complex was performed using AutoDock Vina, and protein-ligand contacts were analyzed using LigPlot+. The results suggest that the hydrophobic interactions of ligands with the receptor BRI1LRR and hydrogen bonding with BAK1 in the complex are important for ligand recognition. For monobenzoylated derivatives, the absence of the hydrophobic end in the alkyl chain seems to be compensated by the benzoyl group. Thus, it would be interesting to determine if this result depends on the nature of the substituent group. Finally, mixtures of S/R triols 3/4 exhibit activities that are comparable or even better than those found for brassinolide. Thus, these compounds are potential candidates for application in agriculture to improve the growth and yield of plants against various types of biotic and abiotic stress.
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Affiliation(s)
- Katy Díaz
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile; (K.D.); (L.E.); (R.C.)
| | - Luis Espinoza
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile; (K.D.); (L.E.); (R.C.)
| | - Rodrigo Carvajal
- Departamento de Química, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2340000, Chile; (K.D.); (L.E.); (R.C.)
| | - Marcos Conde-González
- Center for Natural Products Research, Faculty of Chemistry, University of Havana. Zapata y G, La Habana 10400, Cuba; (M.C.-G.); (V.N.)
| | - Vladimir Niebla
- Center for Natural Products Research, Faculty of Chemistry, University of Havana. Zapata y G, La Habana 10400, Cuba; (M.C.-G.); (V.N.)
| | - Andrés F. Olea
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, Santiago 8900000, Chile
| | - Yamilet Coll
- Center for Natural Products Research, Faculty of Chemistry, University of Havana. Zapata y G, La Habana 10400, Cuba; (M.C.-G.); (V.N.)
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Aldukhi F, Deb A, Zhao C, Moffett AS, Shukla D. Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1. J Phys Chem B 2020; 124:355-365. [PMID: 31873025 DOI: 10.1021/acs.jpcb.9b09377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Brassinosteroids (BRs) are essential phytohormones, which bind to the plant receptor, BRI1, to regulate various physiological processes. The molecular mechanism of the perception of BRs by the ectodomain of BRI1 remains not fully understood. It also remains elusive why a substantial difference in biological activity exists between the BRs. In this work, we study the binding mechanisms of the two most bioactive BRs, brassinolide (BLD) and castasterone (CAT), using molecular dynamics simulations. We report free-energy landscapes of the binding processes of both ligands, as well as detailed ligand binding pathways. Our results suggest that CAT has a lower binding affinity compared to BLD due to its inability to form hydrogen-bonding interactions with a tyrosine residue in the island domain of BRI1. We uncover a conserved nonproductive binding state for both BLD and CAT, which is more stable for CAT and may further contribute to the bioactivity difference. Finally, we validate past observations about the conformational restructuring and ordering of the island domain upon BLD binding. Overall, this study provides new insights into the fundamental mechanism of the perception of the two most bioactive BRs, which may create new avenues for genetic and agrochemical control of their signaling cascade.
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Affiliation(s)
| | - Aniket Deb
- Department of Food Technology and Biochemical Engineering , Jadavpur University , Kolkata , West Bengal 700032 , India
| | | | | | - Diwakar Shukla
- National Center for Supercomputing Applications , Urbana , Illinois 61801 , United States
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7
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Abstract
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
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8
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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9
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Biological Activity of Brassinosteroids - Direct Comparison of Known and New Analogs in planta. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201600305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Lei B, Heng N, Dang X, Liu J, Yao X, Zhang C. Structure based in silico identification of potentially non-steroidal brassinosteroids mimics. MOLECULAR BIOSYSTEMS 2017; 13:1364-1369. [DOI: 10.1039/c7mb00214a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of non-steroidal BRs-like molecules via structure-based pharmacophore virtual screening, molecular docking and bioassay.
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Affiliation(s)
- Beilei Lei
- Center of Bioinformatics
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Ningjuan Heng
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Xiaoxue Dang
- Center of Bioinformatics
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education
- Northwest A&F University
- Yangling
- China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Cunli Zhang
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
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Ding Y, Zhu Z, Zhao J, Nie Y, Zhang Y, Sheng J, Meng D, Mao H, Tang X. Effects of Postharvest Brassinolide Treatment on the Metabolism of White Button Mushroom (Agaricus bisporus) in Relation to Development of Browning During Storage. FOOD BIOPROCESS TECH 2016. [DOI: 10.1007/s11947-016-1722-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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