Computational and biological investigation of the soybean lecithin–gallic acid complex for ameliorating alcoholic liver disease in mice with iron overload

Wu, Xiangqun; Wang, Yan; Jia, Ran; Fang, Fang; Liu, Ya; Cui, Weiwei

doi:10.1039/c9fo01022j

Cited by 17 publications

(11 citation statements)

References 58 publications

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“…Furthermore, GaMD was successfully applied on simulations of protein enzymes for structure‐based drug design of anti‐malarial drugs, 81 design of inhibitors targeting Staphylococcus aureus enzyme MnaA, 84 investigations of soybean lecithin–gallic acid complex formation to aid in alcoholic liver disease (ALD), 86 usefulness of antioxidative agent for treating vascular endothelial deficits, 85 and understanding of drug resistance mechanism of rifampin 91 . Simulations using GaMD and replica‐exchange solute tempering (REST2) 142 were performed to understand the mechanism of the transactivation of estrogen receptor 78 …”

Section: Applicationsmentioning

confidence: 99%

“…In this review, we will present the principles and the most recent applications of GaMD. Robust GaMD has been established for advanced simulation studies of a wide range of biomolecular systems, especially the protein-nucleic acid interactions [63][64][65] such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene-editing system, 66,67 protein-protein/peptide interactions, [68][69][70][71][72] protein-ligand binding, 55,56,[73][74][75][76] protein folding, 77 protein enzymes, 52,58,[78][79][80][81][82][83][84][85][86][87][88][89][90][91][92] membrane proteins (including GPCRs, 68,69,73,76,[93][94][95] ion channels, 53,96 and γ-secretase 97 ) and carbohydrates, [98][99][100]…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Gaussian accelerated molecular dynamics: Principles and applications

Wang

Arantes

Bhattarai

et al. 2021

WIREs Comput Mol Sci

201

204

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Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., “Gaussian approximation”). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica‐exchange GaMD (rex‐GaMD) and replica‐exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new “selective GaMD” algorithms including the Ligand GaMD (LiGaMD) and Peptide GaMD (Pep‐GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small‐molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein–protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Molecular and Statistical Mechanics > Free Energy Methods

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Section: Applicationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Gaussian accelerated molecular dynamics: Principles and applications

Wang

Arantes

Bhattarai

et al. 2021

WIREs Comput Mol Sci

201

204

View full text Add to dashboard Cite

show abstract

“…The GA–HSPC complex nanoformulation increased the antioxidant capacity against CCL 4 -induced hepatotoxicity [ 37 ]. The soybean lecithin–GA complex exerted hepatoprotective effects on alcohol-induced hepatic damage [ 38 ]. GA could be utilized for the synthesis of gold nanoparticles in drug delivery for breast cancer treatment [ 39 ].…”

Section: Gallic Acid As a Natural Antioxidantmentioning

confidence: 99%

Gallic Acid and Diabetes Mellitus: Its Association with Oxidative Stress

Tang

Zhang

et al. 2021

Molecules

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Diabetes mellitus (DM) is a severe chronic metabolic disease with increased mortality and morbidity. The pathological progression of DM is intimately connected with the formation and activation of oxidative stress (OS). Especially, the involvement of OS with hyperglycemia, insulin resistance, and inflammation has shown a vital role in the pathophysiological development of DM and related complications. Interestingly, accumulating studies have focused on the exploration of natural antioxidants for their improvement on DM. Of specific interest is gallic acid (GA), which is rich in many edible and herbal plants and has progressively demonstrated robust antioxidative and anti-inflammatory effects on metabolic disorders. To provide a better understanding of its potential therapeutic impacts and enhancement of human health care, the available research evidence supporting the effective antidiabetic properties of GA and relevant derivatives are needed to be summarized and discussed, with emphasis on its regulation on OS and inflammation against DM. This review aims to highlight the latest viewpoints and current research information on the role of OS in diabetes and to provide scientific support for GA as a potential antihypoglycemic agent for DM and its complications.

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“…Numerous recent studies have focused their attention on the possibility of pharmacologically modulating HEPC expression [65], with the intent to reduce anemia in chronic diseases. Among these molecules, some natural compounds could be used as nutraceuticals [73][74][75][76][77][78].…”

Section: Figurementioning

confidence: 99%

Iron Absorption in Celiac Disease and Nutraceutical Effect of 7-Hydroxymatairesinol. Mini-Review

et al. 2020

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Anemia is the main extra-gastrointestinal symptom in inflammatory bowel diseases (IBDs). Interleukin-6 (IL-6) and other cytokines are secreted and act in the microenvironment of the small intestine mucous membrane of IBD patients. Iron is essential for multiple cell functions and its homeostasis is regulated by the hepcidin–ferroportin axis. Hepcidin (HEPC) is mainly produced by the liver in response to iron needs but is also an acute phase protein. During inflammation, hepcidin is upregulated by IL-6 and is responsible for iron compartmentalization within cells, in turn causing anemia of inflammation. Tissues other than liver can produce hepcidin in response to inflammatory stimuli, in order to decrease iron efflux at a local level, then acting in an autocrine–paracrine manner. In IBDs and, in particular, in celiac disease (CeD), IL-6 might trigger the expression, upregulation and secretion of hepcidin in the small intestine, reducing iron efflux and exacerbating defective iron absorption. 7-Hydroxymatairesinol (7-HMR) belongs to the family of lignans, polyphenolic compounds produced by plants, and has nutraceutical antioxidant, anti-inflammatory and estrogenic properties. In this mini-review we revise the role of inflammation in IBDs and in particular in CeD, focusing our attention on the close link among inflammation, anemia and iron metabolism. We also briefly describe the anti-inflammatory and estrogenic activity of 7-HMR contained in foods that are often consumed by CeD patients. Finally, considering that HEPC expression is regulated by iron needs, inflammation and estrogens, we explored the hypothesis that 7-HMR consumption could ameliorate anemia in CeD using Caco-2 cells as bowel model. Further studies are needed to verify the regulation pathway through which 7-HMR may interfere with the local production of HEPC in bowel.

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Computational and biological investigation of the soybean lecithin–gallic acid complex for ameliorating alcoholic liver disease in mice with iron overload

Abstract: The soybean lecithin–gallic acid complex ameliorates hepatic damage and iron-overload induced by alcohol and exerts hepatoprotective effects.

Cited by 17 publications

References 58 publications

Gaussian accelerated molecular dynamics: Principles and applications

Gaussian accelerated molecular dynamics: Principles and applications

Gallic Acid and Diabetes Mellitus: Its Association with Oxidative Stress

Iron Absorption in Celiac Disease and Nutraceutical Effect of 7-Hydroxymatairesinol. Mini-Review

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