3D-QSAR Combination with Molecular Dynamics Simulations to Effectively Design the Active Ryanodine Receptor Agonists against Spodoptera frugiperda DOI
Zhenwu Yu, Yuting Huang, Jiagao Cheng

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2023, Volume and Issue: 71(44), P. 16504 - 16520

Published: Oct. 30, 2023

Computer-aided molecular modeling was applied to design a series of Spodoptera frugiperda RyR agonists. Comparative field analysis (CoMFA) and comparative similarity indices (CoMSIA) were used generate 3D-QSAR models. MD simulations in the complex with S. native, mutant RyR, mammalian RyR1 under physiological conditions validate detailed binding mechanism. Binding free energy calculation by mechanics generalized surface area (MM-GBSA) explained role key amino acid residues ligand–receptor binding. Therefore, 14 new compounds effectively designed synthesized, bioassay indicated that A-2 A-3 showed comparable activity chloranthraniliprole LC50 values 0.27, 0.18, 0.20 mg L–1, respectively, against frugiperda. Most target also displayed good Mythinma separata at 0.1 L–1. Molecular docking MM-GBSA calculations demonstrated had better capacity native RyRs.

Language: Английский

Synthesis of novel 6-aminocoumarin derivatives as potential –biocompatible antimicrobial and anticancer agents DOI
Yasser Fakri Mustafa

Journal of Molecular Structure, Journal Year: 2024, Volume and Issue: 1320, P. 139658 - 139658

Published: Aug. 15, 2024

Language: Английский

Citations

9
Natural compounds of plant origin in the control of fungi and mycotoxins in foods DOI Creative Commons
Xiaoxi Qi, Bingcan Chen, Jiajia Rao

et al.

Current Opinion in Food Science, Journal Year: 2023, Volume and Issue: 52, P. 101054 - 101054

Published: May 25, 2023

Language: Английский

Citations

12
Computation-Directed Molecular Design, Synthesis, and Fungicidal Activity of Succinate Dehydrogenase Inhibitors DOI
Kun Li,

Shuang Hong,

Zhenwu Yu

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2023, Volume and Issue: 71(49), P. 19372 - 19384

Published: Dec. 4, 2023

Succinate dehydrogenase inhibitors (SDHIs) are a class of fungicides targeting the pathogenic fungi mitochondrial SDH. Here, molecular docking, three-dimensional quantitative structure–activity relationship (3D-QSAR), and dynamics (MD) simulations were used to guide SDHI innovation. Molecular docking was performed explore binding modes SDH its inhibitors. 3D-QSAR models carried out on 33 compounds with activity against Rhizoctonia cerealis (R. cerealis); their relationships analyzed using comparative field analysis similarity indices analysis. MD assess stability complexes under physiological conditions, results consistent docking. Binding free energy calculated through mechanics generalized born surface area method, decomposed. The bioassay indicate that van der Waals lipophilic interactions contribute most in process. Afterward, we designed synthesized 12 guidance above-mentioned analyses, found F9 active R. EC50 value 9.43 μg/mL, F4, F5, Botrytis cinerea an values 5.80, 3.17, 1.63 respectively. They all showed good between positive controls pydiflumetofen thifluzamide. Our study provides new considerations for effective SDHIs discovery.

Language: Английский

Citations

10
Metabolomic profiles and differential metabolites of volatile components in Citrus aurantium Changshan-huyou pericarp during different growth and development stages DOI Creative Commons

Qi Cui,

Lijie Jiang, Lele Wen

et al.

Food Chemistry X, Journal Year: 2024, Volume and Issue: 23, P. 101631 - 101631

Published: July 16, 2024

Citrus fruits possess a distinctive aroma and flavor, with

Language: Английский

Citations

3
Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations DOI Creative Commons
Zinan Wang, Fei Pan, Min Zhang

et al.

Heliyon, Journal Year: 2024, Volume and Issue: 10(9), P. e30389 - e30389

Published: April 26, 2024

The structure-activity analysis (SAR) and machine learning were used to investigate potential anti-

Language: Английский

Citations

1
Peroxyl Radical Trapping Antioxidant Activity of Essential Oils and Their Phenolic Components DOI
Wenkai Pan, Albert Velasco Abadia, Yafang Guo

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2024, Volume and Issue: 72(43), P. 23832 - 23843

Published: Oct. 21, 2024

Essential oils (EOs) are gaining importance as sustainable food antioxidants, but kinetic data on peroxyl radical trapping missing. Thirteen EOs from 11 botanical species were studied in the inhibited autoxidation of cumene by oxygen-uptake kinetics. Juniperus oxycedrus, Syzygium aromaticum, Thymus vulgaris, Thymbra capitata, Betula alba, Pimenta racemosa, and Satureja montana, containing 23–86% phenolic components gas chromatography/mass spectrometry (GC–MS) analysis, afforded inhibition rate constants kinh order 104 M–1 s–1 at 30 °C similar to reference butylhydroxytoluene (2,6-di-tert-butyl-4-methylphenol) (BHT). They matched or outperformed BHT protection olive oil. The Daucus carota Cedrus atlantica with <1% phenols those Apium graveolens Tagetes minuta no phenolics had chain-breaking activity. Key carvacrol, thymol, eugenol, dihydroeugenol, umbelliferone, conyferyl alcohol, o-cresol, m-cresol, p-cresol, 4-allylphenol, 2,3-xylenol, 2,4-xylenol, phenol range 103–104 and, along them, could potentially replace products.

Language: Английский

Citations

1
Unveiling Drug Discovery Insights Through Molecular Electrostatic Potential Analysis DOI

Mambatta Haritha,

Cherumuttathu H. Suresh

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2024, Volume and Issue: 14(6)

Published: Nov. 1, 2024

ABSTRACT Molecular electrostatic potential (MESP) analysis has emerged as a pivotal tool in drug discovery, providing insights into molecular reactivity and noncovalent interactions essential for function. While widely used MESP‐on‐isodensity surface offers interpretations of electron‐rich or deficient regions molecule, the MESP topology parameters such spatial minimum ( V min ) at nuclei n provide quantitative understanding. The investigation correlation between various properties lipophilicity, pK (acidity/basicity), conformations, tautomeric forms is crucial understanding impact on biological activity drugs facilitating design. Moreover, serves fundamental elucidating pharmacological behavior compounds optimizing their therapeutic efficacy. A study utilizing to assess hydrogen bond propensity presents novel strategy investigating drug‐receptor with increased precision. qualitative features drugs, including applications cancer, tuberculosis, tumors, inflammation, infectious diseases malaria, bacterial infections, fungal viral conducted this review.

Language: Английский

Citations

1
Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning DOI
Gen Lu, Fei Pan, Xiaotong Li

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: 42(13), P. 6645 - 6659

Published: July 24, 2023

Flavonoids, especially their inhibitory effect on DPP-IV activity, have been widely recognized for antidiabetic effects. However, the variety of natural flavonoid derivatives is very rich, and even subtle structural differences can lead to several orders magnitude in activities against DPP-IV, which makes it challenging find novel potent anti-DPP-IV experimentally. Therefore, there an urgent need develop efficient screening pipeline that targets active products. Here, we propose a fusion strategy based QSAR model, simplify this process, was applied discovery with activity. First, high-quality model (Rtest2 = 0.816, MAEtest 0.14, MSEtest 0.026) composed seven key molecular property parameters, were constructed genetic algorithm (GA) passed leave-one-out cross-validation evaluation. A total 1,668 obtained from product enriched by NPCD fingerprint similarity (> 0.8). Further, further predicted screened using QED score combined 33 (IC50pre < 6.5 μM) found. Subsequently, three (5,7,3',5'-tetrahydroxyflavone, 3,7-dihydroxy-5,3',4'-trimethoxyflavone, 5,7,2',5'-tetrahydroxyflavone) highly effective activity ADMET analysis. Finally, potential these verified 100 ns MD simulation MM/PB(GB)SA.Communicated Ramaswamy H. Sarma.

Language: Английский

Citations

3
3D-QSAR Combination with Molecular Dynamics Simulations to Effectively Design the Active Ryanodine Receptor Agonists against Spodoptera frugiperda DOI
Zhenwu Yu, Yuting Huang, Jiagao Cheng

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2023, Volume and Issue: 71(44), P. 16504 - 16520

Published: Oct. 30, 2023

Computer-aided molecular modeling was applied to design a series of Spodoptera frugiperda RyR agonists. Comparative field analysis (CoMFA) and comparative similarity indices (CoMSIA) were used generate 3D-QSAR models. MD simulations in the complex with S. native, mutant RyR, mammalian RyR1 under physiological conditions validate detailed binding mechanism. Binding free energy calculation by mechanics generalized surface area (MM-GBSA) explained role key amino acid residues ligand–receptor binding. Therefore, 14 new compounds effectively designed synthesized, bioassay indicated that A-2 A-3 showed comparable activity chloranthraniliprole LC50 values 0.27, 0.18, 0.20 mg L–1, respectively, against frugiperda. Most target also displayed good Mythinma separata at 0.1 L–1. Molecular docking MM-GBSA calculations demonstrated had better capacity native RyRs.

Language: Английский

Citations

3