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Nie RZ, Luo HM, Chen JY, Sun LH, Wang ZB, Zhang ZP, Bao YR. Molecular insights into the interactions of theaflavin and epicatechin with different lipid bilayer membranes by molecular dynamics simulation. Chem Phys Lipids 2024; 262:105405. [PMID: 38795837 DOI: 10.1016/j.chemphyslip.2024.105405] [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: 03/24/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
At present, consumers increasingly favored the natural food preservatives with fewer side-effects on health. The green tea catechins and black tea theaflavins attracted considerable interest, and their antibacterial effects were extensively reported in the literature. Epicatechin (EC), a green tea catechin without a gallate moiety, showed no bactericidal activity, whereas the theaflavin (TF), also lacking a gallate moiety, exhibited potent bactericidal activity, and the antibacterial effects of green tea catechins and black tea theaflavins were closely correlated with their abilities to disrupt the bacterial cell membrane. In our present study, the mechanisms of membrane interaction modes and behaviors of TF and EC were explored by molecular dynamics simulations. It was demonstrated that TF exhibited markedly stronger affinity for the POPG bilayer compared to EC. Additionally, the hydrophobic interactions of tropolone/catechol rings with the acyl chain part could significantly contribute to the penetration of TF into the POPG bilayer. It was also found that the resorcinol/pyran rings were the key functional groups in TF for forming hydrogen bonds with the POPG bilayer. We believed that the findings from our current study could offer useful insights to better understand the stronger antibacterial effects of TF compared to EC.
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Affiliation(s)
- Rong-Zu Nie
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450001, China; Key Laboratory of Cold Chain Food Processing and Safety Control, Ministry of Education, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Huo-Min Luo
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450001, China; Key Laboratory of Cold Chain Food Processing and Safety Control, Ministry of Education, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Jing-Yu Chen
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Li-Heng Sun
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Zi-Bo Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Zhen-Ping Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Ya-Ru Bao
- Science and Technology Division, Zhengzhou University of Light Industry, Zhengzhou 450001, China.
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2
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Zhang T, Wu J, Wang Y, Zhang H, Zhan X. Alleviating neuronal inflammation induced by Aβ 42 in SH-SY5Y through interaction with polysialic acid-oligomannuronate conjugate. Int J Biol Macromol 2024; 276:133862. [PMID: 39013512 DOI: 10.1016/j.ijbiomac.2024.133862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/08/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
Amyloid beta (Aβ) aggregation is one of the distinctive pathological hallmarks of Alzheimer's disease (AD). Therefore, the development of effective inhibitors against Aβ aggregate formation offers great promise for the treatment of AD. In this study, we designed a novel negatively charged functionalized conjugate aimed at inhibiting Aβ42 aggregation and attenuating neurotoxicity by grafting polysialic acid with mannuronate oligosaccharide, a biocompatible glycan extracted from seaweeds, designated as polysialic acid-mannan conjugate (PSA-MOS). ThT, biological microscopy, TEM and CD confirmed the inhibition of Aβ42 aggregation by PSA-MOS, as well as its ability to inhibit the conformational transition of Aβ42 to β-sheet. CCK-8 assay demonstrated that PSA-MOS was not cytotoxic to SH-SY5Y (p < 0.05) and promoted cell proliferation. In the Aβ42-induced SH-SY5Y injury models, PSA-MOS dose-dependently ameliorated cytotoxicity (p < 0.0001) and significantly reduced the levels of inflammatory factors of IL-1β (p < 0.0001), IL-6 (p < 0.0001) and TNF-α (p < 0.05). MD simulations demonstrated that PSA-MOS effectively impeded the α-helix to β-sheet transition of the Aβ42 monomer via electrostatic interactions with its CTR and NTR regions. These findings demonstrate the therapeutic potential of PSA-MOS as promising glycoconjugate for the treatment of AD.
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Affiliation(s)
- Tiantian Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianrong Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Yuying Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hongtao Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaobei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi 214122, China.
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3
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Gonçalves PB, Cordeiro Y, Rennó Sodero AC. Understanding the mechanisms of green tea EGCG against amyloid β oligomer neurotoxicity through computational studies. RSC Adv 2024; 14:22525-22539. [PMID: 39015669 PMCID: PMC11251396 DOI: 10.1039/d4ra03343d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
Oligomeric species of amyloid β peptide (Aβ) are pivotal in Alzheimer's disease (AD) pathogenesis, making them valuable therapeutic targets. Currently, there is no cure or preventive therapy available for AD, with only a few therapeutics offering temporary alleviation of symptoms. Natural products (NPs) are now considered promising anti-amyloid agents. Green tea catechins have garnered considerable attention due to their ability to remodel the toxic amyloid β peptide oligomers (AβOs) into non-toxic assemblies. Nevertheless, the precise molecular mechanism underlying their effects on AβOs remains unclear. In this study, we employ a combination of binding site prediction, molecular docking, and dynamics simulations to gain mechanistic insights into the binding of the potent anti-amyloid epigallocatechin-3-gallate (EGCG) and the less effective catechin, epicatechin (EC), on the structure of pore-forming Aβ tetramers (PDB ID 6RHY). This recently elucidated structure represents AβO(1-42) with two faces of the hydrophobic β-sheet core and hydrophilic edges. Our simulations revealed three potential druggable binding sites within the AβO: two in hydrophilic edges and one in the β-sheet core. Although both catechins bind via hydrogen bond (H-bond) and aromatic interactions to the three potential binding sites, EGCG interacted with key residues more efficiently than EC. We propose that EGCG may remodel AβOs preventing pore formation by binding to the hydrophilic edge binding sites. Additionally, EGCG interacts with key residues in the oligomer's β-sheet core binding site, crucial for fibrillar aggregation. A better understanding of how anti-amyloid compounds remodelling AβOs could be valuable for the development of new therapeutic strategies targeting Aβ in AD. Further experimental validation using point mutations involving key residues could be useful to define whether the establishment of these interactions is crucial for the EGCG remodelling effect.
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Affiliation(s)
- Priscila Baltazar Gonçalves
- Faculdade de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro RJ 21941-902 Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro RJ 21941-902 Brazil
| | - Ana Carolina Rennó Sodero
- Faculdade de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro RJ 21941-902 Brazil
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Nie RZ, Zhang SS, Yan XK, Feng K, Lao YJ, Bao YR. Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study. Int J Biol Macromol 2023; 253:127002. [PMID: 37729983 DOI: 10.1016/j.ijbiomac.2023.127002] [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: 05/04/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.
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Affiliation(s)
- Rong-Zu Nie
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Shan-Shuo Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao-Ke Yan
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Kun Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yan-Jing Lao
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Ya-Ru Bao
- Science and Technology Division, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
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Zhang Z, Li T, Zhang Y, Shao J, Ye C, Wang H, Zhu B, Zhang Y. Effect of polysaccharides on conformational changes and functional properties of protein-polyphenol binary complexes: A comparative study. Int J Biol Macromol 2023; 253:126890. [PMID: 37716302 DOI: 10.1016/j.ijbiomac.2023.126890] [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: 07/19/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
This study aimed to investigate the effect of different polysaccharides on the binding behavior and functional properties of soybean protein isolate (SPI)-quercetin (Que) complex. The binding behavior was assessed using multi-spectral technique with the Stern-Volmer equation, which confirmed the presence of static fluorescence quenching in Que and SPI. The addition of sodium alginate (SA) resulted in a reduction of the binding affinity between SPI and Que, while dextran (DX) exhibited some promoting effect. A slight blue shift was observed in amide I and amide II bands, indicating the presence of hydrophobic and electrostatic interactions. Circular dichroism spectra revealed the ordered structures transformed into a more disordered state when polysaccharides were added, leading to an increase in random coils (SA: 18.5 %, DX: 15.4 %). Docking and dynamic simulations demonstrated that SA displayed greater stability within the hydrophobic compartments of SPI than DX, increased rigidity and stability of the SPI structure in SPI-Que-SA complexes. Electrostatic forces played a significant role between SPI and SA, while van der Waals forces were the main driving forces in SPI-DX complexes. Overall, the introduction of SA led to a looser and stable structure of SPI-Que complexes, resulting in an improvement of their emulsifying, foaming, and antioxidant properties.
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Affiliation(s)
- Zifan Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Taoran Li
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yubo Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Juanjuan Shao
- Department of Science and Technology, Hebei Agricultural University, Hebei 061100, China
| | - Chengxiang Ye
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongwu Wang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Beibei Zhu
- College of Chinese Medicine Pharmaceutical Engineering, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China..
| | - Yating Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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6
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Mortazavi M, Torkzadeh-Mahani M, Rahimi M, Maleki M, Lotfi S, Riahi-Madvar A. Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study. Int J Biol Macromol 2023; 235:123835. [PMID: 36870640 DOI: 10.1016/j.ijbiomac.2023.123835] [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: 11/17/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran.
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Ali Riahi-Madvar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, Kosar University of Bojnord, Bojnord, Iran
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7
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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8
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Nie RZ, Cai S, Yu B, Fan WY, Li HH, Tang SW, Huo YQ. Molecular insights into the very early steps of Aβ1-42 pentameric protofibril disassembly by PGG: A molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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10
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He M, Nian B, Shi J, Sun X, Du R, Tan CP, Xu YJ, Liu Y. Influence of extraction technology on rapeseed oil functional quality: a study on rapeseed polyphenols. Food Funct 2022; 13:270-279. [PMID: 34888592 DOI: 10.1039/d1fo01507a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction technology can influence the vegetable oil functional quality. Polyphenols in rapeseed oil have been proved to be beneficial for cardiovascular health. In this study, we evaluated the effect of extraction methods on the functional quality of rapeseed oil from the perspective of phenolic compounds. The results showed that hot pressing produces the highest amount of phenolic compounds in rapeseed oil. Its most abundant phenolic compound, sinapine (9.18 μg g-1), showed the highest activity in inhibiting anaerobic choline metabolism with an EC50 value of 1.9 mM, whose downstream products are related to cardiovascular diseases. Molecular docking and molecular dynamics (MD) simulations revealed that sinapine exhibits good binding affinity toward CutC, and CutC-sinapine is a stable complex with fewer conformational fluctuations and similar tightness. Taken together, hot pressing can be considered the best extraction method for rapeseed oil from the perspective of phenolic compounds.
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Affiliation(s)
- Mengxue He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Xian Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Runfeng Du
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Seri Kembangan, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, China.
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11
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Jiang L, Sun Q, Li L, Lu F, Liu F. Molecular Insights into the Inhibitory Effect of GV971 Components Derived from Marine Acidic Oligosaccharides against the Conformational Transition of Aβ42 Monomers. ACS Chem Neurosci 2021; 12:3772-3784. [PMID: 34565139 DOI: 10.1021/acschemneuro.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
GV971 derived from marine acidic oligosaccharides has been used to cure Alzheimer's disease (AD). However, the molecular mechanism of its inhibition of the conformational transition of amyloid β-proteins (Aβ) is still unclear. Herein, molecular dynamics simulations were used to explore the molecular mechanism of the main GV971 components including DiM, TetraM, HexaM, and OctaM to inhibit the conformational conversion of the Aβ42 monomer. It is found that the GV971 components inhibit the conformational transition from α-helix to β-sheet and the hydrophobic collapse of the Aβ42 monomer. In addition, the binding energy analysis implies that both electrostatic and van der Waals interactions are beneficial to the binding of GV971 components to the Aβ42 monomer. Among them, electrostatic interactions occupy the dominant position. Moreover, the GV971 components mainly interact directly with the charged residues D1, R5, K16, and K28 by forming salt bridges and hydrogen bonds, which specifically bind to the N-terminal region of Aβ42.
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Affiliation(s)
- Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Quancheng Sun
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Li Li
- College of Marine and Environmental Science, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
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12
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Nie RZ, Dang MZ, Ge ZZ, Huo YQ, Yu B, Tang SW. Interactions of chlorogenic acid and isochlorogenic acid A with model lipid bilayer membranes: Insights from molecular dynamics simulations. Chem Phys Lipids 2021; 240:105136. [PMID: 34529979 DOI: 10.1016/j.chemphyslip.2021.105136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Because of the negative side-effects of synthetic preservatives, the naturally-occurring polyphenols aroused intense interest of researchers. It has been suggested that chlorogenic acid (CA) and isochlorogenic acid A (iso-CAA) were good candidates to replace the synthetic preservatives. Moreover, the bactericidal activity of iso-CAA was stronger than CA, and the anti-bacterial activities of iso-CAA and CA were highly membrane-dependent. However, the mechanisms were still unclear. Therefore, in the present study, we investigated the mechanisms of the interactions between the two polyphenols and lipid bilayers through molecular dynamics simulations. The results revealed that iso-CAA could be inserted much deeper into POPG lipid bilayer than CA. We also found that hydrophobic interactions and hydrogen bonds both contributed to the insertion of iso-CAA into the POPG lipid bilayer, and the quinic acid moiety was the key structure in iso-CAA to form hydrogen bonds with POPG lipid bilayer. We believed that these findings would provide more useful information to explain the stronger bactericidal activity of iso-CAA than CA at the atomic level.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology·School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Mei-Zhu Dang
- School of Energy and Intelligence Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450002, China
| | - Zhen-Zhen Ge
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Yin-Qiang Huo
- School of Food Science and Technology·School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Bo Yu
- School of Food Science and Technology·School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Shang-Wen Tang
- School of Food Science and Technology·School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China.
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Vignon A, Salvador-Prince L, Lehmann S, Perrier V, Torrent J. Deconstructing Alzheimer's Disease: How to Bridge the Gap between Experimental Models and the Human Pathology? Int J Mol Sci 2021; 22:8769. [PMID: 34445475 PMCID: PMC8395727 DOI: 10.3390/ijms22168769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Discovered more than a century ago, Alzheimer's disease (AD) is not only still present in our societies but has also become the most common dementia, with 50 million people worldwide affected by the disease. This number is expected to double in the next generation, and no cure is currently available to slow down or stop the disease progression. Recently, some advances were made due to the approval of the aducanumab treatment by the American Food and Drug Administration. The etiology of this human-specific disease remains poorly understood, and the mechanisms of its development have not been completely clarified. Several hypotheses concerning the molecular mechanisms of AD have been proposed, but the existing studies focus primarily on the two main markers of the disease: the amyloid β peptides, whose aggregation in the brain generates amyloid plaques, and the abnormally phosphorylated tau proteins, which are responsible for neurofibrillary tangles. These protein aggregates induce neuroinflammation and neurodegeneration, which, in turn, lead to cognitive and behavioral deficits. The challenge is, therefore, to create models that best reproduce this pathology. This review aims at gathering the different existing AD models developed in vitro, in cellulo, and in vivo. Many models have already been set up, but it is necessary to identify the most relevant ones for our investigations. The purpose of the review is to help researchers to identify the most pertinent disease models, from the most often used to the most recently generated and from simple to complex, explaining their specificities and giving concrete examples.
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Affiliation(s)
- Anaïs Vignon
- INM, University of Montpellier, INSERM, 34095 Montpellier, France; (A.V.); (L.S.-P.)
| | - Lucie Salvador-Prince
- INM, University of Montpellier, INSERM, 34095 Montpellier, France; (A.V.); (L.S.-P.)
| | - Sylvain Lehmann
- INM, University of Montpellier, INSERM, CHU Montpellier, 34095 Montpellier, France;
| | - Véronique Perrier
- INM, University of Montpellier, INSERM, CNRS, 34095 Montpellier, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, 34095 Montpellier, France; (A.V.); (L.S.-P.)
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Dietary Phenolic Acids and Their Major Food Sources Are Associated with Cognitive Status in Older Italian Adults. Antioxidants (Basel) 2021; 10:antiox10050700. [PMID: 33946636 PMCID: PMC8145289 DOI: 10.3390/antiox10050700] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Life expectancy is increasing along with the rising prevalence of cognitive disorders. Among the factors that may contribute to their prevalence, modifiable risk factors such as diet may be of primary importance. Unarguably, plant-based diets rich in bioactive compounds, such as polyphenols, showed their potential in decreasing risk of neurodegenerative disorders. Therefore, the aim of the present study is to investigate whether exposure to components of plant-based diets, namely phenolic acids, may affect cognitive status in older Italian adults. METHODS The demographic, lifestyle and dietary habits of a sample of individuals living in southern Italy were analyzed. Dietary intake was assessed through food frequency questionnaires (FFQs). Data on the phenolic acids content in foods were estimated using the Phenol-Explorer database. Cognitive status was evaluated using The Short Portable Mental Status Questionnaire. Multivariate logistic regression analyses were used to assess the associations. RESULTS The mean intake of phenolic acids was 346.6 mg/d. After adjustment for potential confounding factors, individuals in the highest quartile of total phenolic acid intake were less likely to have impaired cognitive status (OR = 0.36 (95% CI: 0.14, 0.92)); similarly, the analysis for subclasses of phenolic acids showed the beneficial effect toward cognitive status of greater intake of hydroxycinnamic acids (OR = 0.35 (95% CI: 0.13, 0.91)). Among individual compounds, only higher intake of caffeic acid was inversely associated with impaired cognitive status (OR = 0.32 (95% CI: 0.11, 0.93)); notably, the association with ferulic acid intake was significant only when adjusting for background characteristics, and not for adherence to the Mediterranean diet. CONCLUSIONS This study revealed that greater intakes of dietary phenolic acids were significantly inversely associated with impaired cognition, emphasizing the possible role of phenolic acids in the prevention of cognitive disorders.
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Yang Y, Guo Y, Zhou Y, Gao Y, Wang X, Wang J, Niu X. Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 Against Escherichia coli. Front Pharmacol 2020; 11:581001. [PMID: 33123013 PMCID: PMC7566295 DOI: 10.3389/fphar.2020.581001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
At present, the resistance of New Delhi metallo-β-lactamase-1 (NDM-1) to carbapenems and cephalosporins, one of the mechanisms of bacterial resistance against β-lactam antibiotics, poses a threat to human health. In this work, based on the virtual ligand screen method, we found that carnosic acid (CA), a natural compound, exhibited a significant inhibitory effect against NDM-1 (IC50 = 27.07 μM). Although carnosic acid did not display direct antibacterial activity, the combination of carnosic acid and meropenem still showed bactericidal activity after the loss of bactericidal effect of meropenem. The experimental results showed that carnosic acid can enhance the antibacterial activity of meropenem against Escherichia coli ZC-YN3. To explore the inhibitory mechanism of carnosic acid against NDM-1, we performed the molecular dynamics simulation and binding energy calculation for the NDM-1-CA complex system. Notably, the 3D structure of the complex obtained from molecular modeling indicates that the binding region of carnosic acid with NDM-1 was not situated in the active region of protein. Due to binding to the allosteric pocket of carnosic acid, the active region conformation of NDM-1 was observed to have been altered. The distance from the active center of the NDM-1-CA complex was larger than that of the free protein, leading to loss of activity. Then, the mutation experiments showed that carnosic acid had lower inhibitory activity against mutated protein than wild-type proteins. Fluorescence experiments verified the results reported above. Thus, our data indicate that carnosic acid is a potential NDM-1 inhibitor and is a promising drug for the treatment of NDM-1 producing pathogens.
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Affiliation(s)
- Yanan Yang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Yan Guo
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yonglin Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jianfeng Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun, China
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