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作为潜在肿瘤坏死因子调节剂的酸类:结合分子对接、动力学模拟、ADMET分析和基因表达分析的综合研究

, , and Acids as Potential TNF Modulators: An Integrated Study Combining Molecular Docking, Dynamics Simulations, ADMET Profiling, and Gene Expression Analysis.

作者信息

Manakbayeva Adolat, Bogoyavlenskiy Andrey, Kerimov Timur, Yershov Igor, Alexyuk Pavel, Alexyuk Madina, Berezin Vladimir, Dushenkov Vyacheslav

机构信息

Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan.

Department of Natural Sciences, Hostos Community College CUNY, Bronx, NY 10451, USA.

出版信息

Molecules. 2025 Jul 29;30(15):3175. doi: 10.3390/molecules30153175.


DOI:10.3390/molecules30153175
PMID:40807350
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12348193/
Abstract

Organic acids, as natural metabolites, play crucial roles in human metabolism and health. Tumor Necrosis Factor (TNF), a pivotal mediator in immune regulation and inflammation, is a key therapeutic target. We evaluated ten organic acids as TNF modulators using in silico molecular docking, followed by detailed ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiling and molecular dynamics (MD) simulations for three lead candidates: , , and acids. Their effects on TNF gene expression were then assessed using a mouse leukocyte model. The in silico results indicated that had the highest TNF binding affinity (-5.6 to -4.6 kcal/mol), while acid formed the most stable protein-ligand complex during MD simulations, and acid established hydrogen bond interactions. ADMET analysis suggested potential pharmacokinetic limitations, including low permeability. Contrasting its high predicted binding affinity, gene expression analysis revealed that stimulated TNF synthesis, whereas and acids acted as inhibitors. This research explores organic acids as potential TNF modulators, highlighting their complex interactions and providing a foundation for developing these compounds as anti-inflammatory agents targeting TNF-mediated diseases.

摘要

有机酸作为天然代谢产物,在人体新陈代谢和健康中发挥着关键作用。肿瘤坏死因子(TNF)是免疫调节和炎症中的关键介质,是一个重要的治疗靶点。我们使用计算机辅助分子对接评估了十种有机酸作为TNF调节剂,随后对三种先导候选物:[具体酸名1]、[具体酸名2]和[具体酸名3]酸进行了详细的ADMET(吸收、分布、代谢、排泄和毒性)分析以及分子动力学(MD)模拟。然后使用小鼠白细胞模型评估它们对TNF基因表达的影响。计算机模拟结果表明,[具体酸名1]具有最高的TNF结合亲和力(-5.6至-4.6千卡/摩尔),而[具体酸名2]酸在MD模拟过程中形成了最稳定的蛋白质-配体复合物,并且[具体酸名3]酸建立了氢键相互作用。ADMET分析表明存在潜在的药代动力学限制,包括低渗透性。与其高预测结合亲和力形成对比的是,基因表达分析显示[具体酸名1]刺激TNF合成,而[具体酸名2]和[具体酸名3]酸则起抑制剂作用。本研究探索了有机酸作为潜在的TNF调节剂,突出了它们的复杂相互作用,并为将这些化合物开发为针对TNF介导疾病的抗炎药物提供了基础。

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本文引用的文献

[1]
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Nucleic Acids Res. 2025-1-6

[2]
ADME/PK Insights of Crocetin: A Molecule Having an Unusual Chemical Structure with Druglike Features.

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Pflugers Arch. 2024-4

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Unrecognized Role of Organic Acid in Natural Attenuation of Pollutants by Mackinawite (FeS): The Significance of Carbon-Center Free Radicals.

Environ Sci Technol. 2023-12-12

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[8]
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Front Pharmacol. 2022-11-16

[9]
The involvement of organic acids in soil fertility, plant health and environment sustainability.

Arch Microbiol. 2022-11-20

[10]
Prospects of organic acids as safe alternative to antibiotics in broiler chickens diet.

Environ Sci Pollut Res Int. 2022-5

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