Food & Function
·
2022
·Vol. 13
·期 14
·7529-7539
·
IF 6.317
Hongxia Xiu,Yajie Liu,Huihui Yang,Haibin Ren,Bowen Luo,Zhipeng Wang,Hong Shao,Fengzhong Wang,Jingjian Zhang,Yutang Wang
Umami substances can increase the overall taste of food and bring pleasure to people. However, it is still challenging to identify the umami molecules through virtual screening due to the crystal structure of the umami receptor being undefined. Herein, based on the hypothesis that the molecules with bitter and sweet taste characteristics may be umami molecules, this study proposed an in silico method to identify novel umami-tasting molecules in batch from SWEET-DB and BitterDB databases via the QSAR models, PCA, molecular docking and electronic tongue analysis. In total, 169 potential umami molecules were identified through QSAR modeling, PCA, and molecular docking. Of the 169 molecules, 18 were randomly selected, and all were identified as umami molecules via electronic tongue analysis. Among the 18 chosen molecules, 10 molecules could be traced back to their concentration range in food, and finally, 8 molecules were predicted to be nontoxic. This work provides a simple and efficient strategy to identify novel umami molecules, holding an excellent promise for demonstrating the crystal structure of umami receptors and taste-sensing mechanisms. Furthermore, this study opens the possibility for the practical application of new umami molecules in food.
研究领域:
食品科学
·
计算生物学
·
生物信息学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
CHEMOSPHERE
·
2023
·
IF 8.8
Jia Wang,Xujia Zhang,Lingyun Fan,Limin Su,Yuanhui Zhao
Insecticides are widely used in crop protection against insects and frequently detected in aquatic environment. Photolysis kinetics are directly related with exposure assessment and risk assessment. However, the photolysis mechanism of neonicotinoid insecticides with different structures has not been studied and compared systematically in the literature. In this paper, the photolysis rate constants in water were determined for eleven insecticides under irradiation of simulated sunlight. At the same time, the photolysis mechanism and effect of dissolved organic matter (DOM) on their photolysis were studied. The results showed that photolysis rates of eleven insecticides vary in a large range. The photolysis rates of nitro-substituted neonicotinoids and butenolide insecticide are much faster than that of cyanoimino-substituted neonicotinoids and sulfoximine insecticide. The ROS scavenging activity assays reveal that direct photolysis dominates the degradation of seven insecticides and, on the other hand, self-sensitized photolysis dominates four insecticides. The shading-effect from DOM can reduce the direct photolysis rates, on the other hand, ROSs generated by triplet-state DOM ( 3 DOM*) can also accelerate photolysis of insecticides. According to the photolytic products identified from HPLC-MS, these eleven insecticides have different photolysis pathways. Six insecticides are degraded from the removal of nitro group from their parent compounds and four insecticides are degraded through ·OH reaction or singlet oxygen ( 1 O 2 ) reaction. QSAR (quantitative structure-activity relationship) analysis showed that photolysis rate was directly related to the energy gap between the highest occupied molecular orbital to the lowest unfilled molecular orbital ( E gap = E LUMO − E HOMO ) and dipole moment (δ). These two descriptors reflect the chemical stability and reactivity of insecticides. The pathways developed from identified products and the molecular descriptors of QSAR models can well verify the photolysis mechanisms of eleven insecticides.
研究领域:
环境科学
·
化学
✓ 已验证
DOI
PubMed
高影响因子
FOOD CHEMISTRY
·
2018
·
IF 4.946
Yike Yue,Sheng Geng,Yue Shi,Guizhao Liang,Jinshui Wang,Benguo Liu
Zein has the potential application of establishing the delivery systems for flavonoids . But there are few reports about the effect of the molecular structures of flavonoids on their interaction with zein . In this study, the binding behaviour of 21 flavonoids and zein was investigated by spectrofluorimetry. The corresponding 3D-QSAR model was also established by Topomer CoMFA method, whose steric and electrostatic field analysis could explain the binding performance of the tested flavonoids with zein. The fluorescence analysis suggested that the flavonoids could interact with zein by forming the complex at the molar ratio of 1. The flavonoids with glucosyl groups at ring A exhibited the outstanding binding capacity with zein, and their binding process with zein was driven by hydrophobic force. The synchronous and 3D fluorescence spectra showed that there was no apparent change in the microenvironment surrounding the tyrosine residues of zein during the interaction.
研究领域:
食品科学
·
生物化学
✓ 已验证
DOI
高影响因子
Food & Function
·
2020
·Vol. 11
·期 4
·3043-3052
·
IF 4.171
Wenli Yan,Guimei Lin,Rong Zhang,Zhen Liang,Wenjuan Wu
Two novel effective antioxidative tripeptides GWY and QWY were designed based on 3D-QSAR models. Their activities were confirmed by an improved TEAC assay. The experimental results showed that GWY and QWY possessed good antioxidant activity, equaling 3.32 mM TE and 2.97 mM TE respectively. This indicated that 3D-QSAR models possessed significant predictive capacity for drug design. In addition, molecular docking and molecular dynamics simulation were applied to reveal the potential molecular mechanism of antioxidant peptides. The result showed that GWY and QWY could enhance the stability of Keap1 by interacting with the key residues Arg415, Arg483, Arg380 and Ser555 in the active sites. Interestingly, the key residues were exactly the binding site of Nrf2 in the active pocket of Keap1. Thus, GWY and QWY could compete with Nrf2 for binding to Keap1. This demonstrated that the new tripeptides might have the ability to activate the signaling pathway Keap1–Nrf2–ARE and improve the antioxidant defense system of the body as well.
研究领域:
生物化学
·
药物设计
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2024
·
IF 12.2
Beibei Li,Ruijuan Qu,Ting Wang,Ruixue Guo,Jie Tian,Shuyi Li,Mostafa R. Abukhadra,Rehab Khaled Mahmoud,Zunyao Wang
In this investigation, we conducted a detailed analysis of the oxidation of 16 imidazole ionic liquid variants by Fe(VI) under uniform experimental setups, thereby securing a dataset of second-order reaction rate constants ( k obs ). This methodology ensures superior data consistency and comparability over traditional methods that amalgamate disparate data from varied studies. Utilizing 16 chemical structural parameters obtained via Density Functional Theory (DFT) as descriptors, we developed a Quantitative Structure Activity Relationship (QSAR) model. Through rigorous correlation analysis, Principal Component Analysis (PCA), Multiple Linear Regression (MLR), and Applicability Domain (AD) evaluation, we identified a pronounced negative correlation between the molecular orbital gap energy ( E gap) and k obs . MLR analysis further underscored E gap as a pivotal predictive variable, with its lower values indicating heightened oxidative reactivity towards Fe(VI) in the ionic liquids, leading the QSAR model to achieve a predictive accuracy of 0.95. Furthermore, we integrated an advanced machine learning approach - Random Forest Regression (RFR), which adeptly highlighted the critical factors influencing the oxidation efficiency of imidazole ionic liquids by Fe(VI) through elaborate decision trees , feature importance assessment, Recursive Feature Elimination (RFE), and cross-validation strategies. The RFR model demonstrated a remarkable predictive performance of 0.98. Both QSAR and RFR models pinpointed E gap as a key descriptor significantly affecting oxidation efficiency, with the RFR model presenting lower root mean square errors , establishing it as a more reliable predictive tool. The application of the RFR model in this study significantly improved the model's stability and the intuitive display of key influencing factors, introducing promising advanced analytical tools to the field of environmental chemistry .
研究领域:
环境化学
·
计算化学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Frontiers in Environmental Science
·
2023
·
IF 4.6
Zhang Meilan,Qin Shengnan,Tan Yujia,Shen Zhemin
Introduction: The inorganic coagulant AlCl3 is used in the traditional coagulation method for the decolorization of industrial dye wastewater. We studied its effectiveness in 41 kinds of dye with different structures, including azo, anthraquinone, arylmethane, and indigo dyes.Discussion: The optimal conditions for the removal of dye in the AlCl3 coagulation system were alkaline > neutral > acidic conditions. Under alkaline conditions, the hydrolysis colloid of AlCl3 is positively charged and easily combined with negatively charged anionic dyes by electrostatic adsorption. Therefore, the relationships between the dye removal behavior and molecular parameters under alkaline conditions were analyzed.Methods: Quantitative structure–activity relationship (QSAR) models were built for the color removal rates (Rexp) of 41 dyes and 46 molecular parameters computed by the density functional theory (DFT). Internal validation, external validation, statistical tests, Y-randomization, and applicability domain tests indicated that the optimal models are stable, accurate, reliable, and predictive.Results: The optimal QSAR model showed that surface area (approx.) (SAA) and molecular weight (MW) are two key molecular parameters. Moreover, electrostatic forces and hydrogen bonding are the predominant adsorption forces in this coagulation process.
研究领域:
环境科学
·
化学
✓ 已验证
DOI
高影响因子
MOLECULES
·
2021
·Vol. 26
·期 22
·6948
·
IF 4.412
Mei Huang,Wen-Gui Duan,Gui-Shan Lin,Bao-Yu Li
A series of novel menthol derivatives containing 1,2,4-triazole-thioether moiety were designed, synthesized, characterized structurally, and evaluated biologically to explore more potent natural product-based antifungal agents. The bioassay results revealed that at 50 μg/mL, some of the target compounds exhibited good inhibitory activity against the tested fungi, especially againstPhysalospora piricola. Compounds5b(R =o-CH3Ph),5i(R =o-Cl Ph),5v(R =m,p-OCH3Ph) and5x(R =α-furyl) had inhibition rates of 93.3%, 79.4%, and 79.4%, respectively, againstP. piricola, much better than that of the positive control chlorothalonil. Compounds5v(R =m,p-OCH3Ph) and5g(R =o-Cl Ph) held inhibition rates of 82.4% and 86.5% againstCercospora arachidicolaandGibberella zeae, respectively, much better than that of the commercial fungicide chlorothalonil. Compound5b(R =o-CH3Ph) displayed antifungal activity of 90.5% and 83.8%, respectively, againstColleterichum orbicalareandFusarium oxysporumf. sp.cucumerinum. Compounds5m(R =o-I Ph) had inhibition rates of 88.6%, 80.0%, and 88.0%, respectively, againstF. oxysporumf. sp.cucumerinu,Bipolaris maydisandC. orbiculare. Furthermore, compound5b(R =o-CH3Ph) showed the best and broad-spectrum antifungal activity against all the tested fungi. To design more effective antifungal compounds againstP. piricola, 3D-QSAR analysis was performed using the CoMFA method, and a reasonable 3D-QSAR model (r2= 0.991,q2= 0.514) was established. The simulative binding pattern of the target compounds with cytochrome P450 14α-sterol demethylase (CYP51) was investigated by molecular docking.Keywords:menthol;1,2,4-triazole-thioether;antifungal activity;3D-QSAR;molecular docking
研究领域:
药理学
·
化学信息学
·
真菌学
✓ 已验证
DOI
高影响因子
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2015
·Vol. 23
·期 4
·3609-3620
·
IF 2.828
Su Pingru,Zhu Huicen,Shen Zhemin
Manganese dioxide formed in oxidation process by potassium permanganate exhibits promising adsorptive capacity which can be utilized to remove organic pollutants in wastewater. However, the structure variances of organic molecules lead to wide difference of adsorption efficiency. Therefore, it is of great significance to find a general relationship between removal rate of organic compounds and their quantum parameters. This study focused on building up quantitative structure activity relationship (QSAR) models based on experimental removal rate ( r
exp ) of 25 organic compounds and 17 quantum parameters of each organic compounds computed by Gaussian 09 and Material Studio 6.1. The recommended model is r
pre = −0.502 − 7.742 f (+) x + 0.107 E
HOMO + 0.959 q (H + ) + 1.388 BO
x . Both internal and external validations of the recommended model are satisfied, suggesting optimum stability and predictive ability. The definition of applicability domain and the Y-randomization test indicate all the prediction is reliable and no possibility of chance correlation. The recommended model contains four variables, which are closely related to adsorption mechanism. f (+) x reveals the degree of affinity for nucleophilic attack. E
HOMO represents the difficulty of electron loss. q (H + ) reflect the distribution of partial charge between carbon and hydrogen atom. BO
x shows the stability of a molecule.
研究领域:
环境科学
·
化学
✓ 已验证
DOI
高影响因子
CHEMISTRY & BIODIVERSITY
·
2022
·Vol. 19
·期 4
·e202101025
·
IF 2.745
Rong Li,Bo Cen,Wengui Duan,Guishan Lin
Succinate dehydrogenase (SDH) is an important target enzyme for designing agricultural chemical fungicides. In order to explore novel natural product-based antifungal agents, twenty-one unreported anisaldehyde-derived amide-thiourea compounds were designed and synthesized using the principle of active splicing, and structurally confirmed by 1 H-NMR, 13 C-NMR, ESI-MS, FT-IR, and element analysis. In vitro antifungal activity of the target compounds was evaluated by the agar dilution method. The results showed that some target compounds exhibited better or comparable antifungal activity than that of the commercial fungicide chlorothalonil, in which compounds 5c , 5o , and 5r displayed excellent antifungal activity of 92.6 %, 92.6 % and 99.1 % against P. piricola , respectively, better than that of the positive control. In addition, 3D-QSAR analysis was carried out by the CoMFA method to reveal the relationship between the structures of the target compounds and their inhibitory activities. The simulative binding mode of the target compounds and SDH was also studied by molecular docking. Graphical
研究领域:
农药化学
·
分子生物学
·
药物设计
✓ 已验证
产品关联
DOI
PubMed
高影响因子
ENVIRONMENTAL TECHNOLOGY
·
2025
·
IF 2
Tao Zhao,Minghao Xu,Xuerui Yang,Jean-Marc Chovelon,Lei Zhou
High-valent metal species (HVMS) exhibited exceptional oxidative capabilities and selectivity in advanced oxidation processes (AOPs), making them promising oxidants for environmental remediation. However, their inherent instability has hindered kinetic assessments and limited further applications. This study developed a quantitative structure–activity relationship (QSAR) model for predicting the pseudo-first order rate constants (kobs) of high-valent copper species Cu(III) with typical emerging contaminants (ECs). The optimal model was logkobs = 0.002×PSA – 10.1465 × q(C-)X – 4.5896 × ELUMO – 2.0116. R2adj (0.822), Q2LOO (0.784), and Q2ext (0.951) shown the model’s robust and great predictive ability. Polar surface area (PSA), Hirshfeld charge on carbon atoms (q(C-)X), and the energy of the lowest unoccupied molecular orbital (ELUMO) synergistically controlled the reactivity of Cu(III). A larger PSA was conducive to the diffusion of ECs in aquatic environments. Additionally, Density functional theory (DFT) calculations revealed that a smaller q(C-)X could increase the nucleophilic sites of ECs, thereby enhancing the electrophilic reaction of Cu(III). And a lower ELUMO was beneficial for adjusting the energy gap (EGAP) to enhance the reactivity of ECs. This study filled the gap in the prediction of kobs for Cu(III) and provided a reliable reference for the selective treatment of different ECs by HVMS.
研究领域:
环境科学
·
计算化学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2023
·
IF 9.8
Min Sun,Xian-Zhang Wang,Ren-Ying Xiong,Xiangying Chen,Lin-Feng Zhai,Shaobin Wang
Utilization of sewage sludge for the fabrication of environmental functional materials is highly desirable to achieve pollution mitigation and resource recovery. In the present work, we introduced a novel MgAl-layered double oxide (LDO)@biochar composite adsorbent in-situ fabricated from Al-rich sewage sludge, and its excellent application in nanoplastics adsorption. Initially, fifteen model contaminants with varied conjugate structures, hydrogen bonding and ionic properties were selected for an investigation of adsorption behavior and adsorption selectivity on LDO@biochar. Structural variation of LDO@biochar suggested reconstruction of the layered double hydroxide (LDH) during the adsorption process due to the “memory effect”. Under the synergy of LDH and biochar, the contaminants were adsorbed via multiple adsorbent-adsorbate interactions, including anion exchange, electrostatic interaction, hydrogen bonding and π-π conjugation. Then, a quantitative structure-activity relationship (QSAR) model was constructed by integrating the number of hydrogen bond acceptors, polarity surface area, number of aromatic rings, and Fukui index f(−) x together to reflect the affinity of each contaminant to the adsorbent. Guided by the QSAR model, the negatively charged polystyrene nanoplastics with continuously conjugated aromatic rings were predicted to be effectively adsorbed on LDO@biochar. Experimental tests confirmed a great capacity of LDO@biochar towards the polystyrene nanoplastics, given the equilibrium adsorption capacity as high as 360 mg g −1 at 30–50 °C. This work not only opened up a new avenue for sustainable utilization of sewage sludge towards high-performance environmental functional materials, but also demonstrated the potential of the QSAR analysis as a rapid and accurate approach for guiding the application of an adsorbent to new emerging containments.
研究领域:
环境科学
·
材料科学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
FITOTERAPIA
·
2024
·
IF 2.5
Lin Zhu,Yongle Yu,Youfu Ma,Yenong Shi,Jamal Alzobair Hammad Kowah,Lisheng Wang,Mingqing Yuan,Xu Liu
Sophoridine, which is derived from the Leguminous plant Sophora alopecuroides L., has certain pharmacological activity as a new anticancer drug. Herein, a series of novel N-substituted sophoridine derivatives was designed, synthesized and evaluated with anticancer activity. Through QSAR prediction models, it was discovered that the introduction of a benzene ring as a main pharmacophore and reintroduced into a benzene in para position on the phenyl ring in the novel sophoridine derivatives improved the anticancer activity effectively. In vitro, 28 novel compounds were evaluated for anticancer activity against four human tumor cell lines (A549, CNE-2, HepG-2, and HEC-1-B). In particular, Compound 26 exhibited remarkable inhibitory effects, with an IC 50 value of 15.6 μM against HepG-2 cells, surpassing cis-Dichlorodiamineplatinum (II). Molecular docking studies verified that the derivatives exhibit stronger binding affinity with DNA topoisomerase I compared to sophoridine. In addition, 26 demonstrated significant inhibition of DNA Topoisomerase I and could arrest cells in G 0 /G 1 phase. This study provides valuable insights into the design and synthesis of N-substituted sophoridine derivatives with anticancer activity.
研究领域:
药物化学
·
肿瘤学
·
计算生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）