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人工智能与生物分子预测软件时代的神经精神药理学

Neuropsychopharmacology in the era of artificial intelligence and biomolecule prediction software.

作者信息

García-Reyes Rubén A, Massó Quiñones Laura N, Ruy Hajin, Castro Daniel C

机构信息

Biophotonics Research Center, Mallinckrodt Institute of Radiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA.

Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA.

出版信息

NPP Digit Psychiatry Neurosci. 2025;3(1):16. doi: 10.1038/s44277-025-00038-9. Epub 2025 Jun 30.

DOI:10.1038/s44277-025-00038-9
PMID:40606791
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12208904/
Abstract

The development and adoption of artificial intelligence (AI) provides moonshot opportunities to redefine how we generate treatments for neuropsychiatric disease. Despite the rapid advancement of AI across biomedical spheres, its implementation in drug discovery, proteomics, and neurobiology has been met with new and unexpected limitations. Historically, neuropharmacology research has used observational and invasive experimental approaches to identify novel therapeutics. Unfortunately, this classic approach suffers from laborious chemical synthesis and in vivo testing which ultimately leads to translational bottlenecks. With the implementation of AI, we are now able to expedite this early testing by modeling how a drug or protein complex may interact with a receptor of interest. By applying powerful, precision-based protein structure prediction tools, we can better tailor therapeutics and minimize undesired outcomes. Though promising, important caveats like predicting chirality of molecules, conformational changes upon binding, and determining downstream signaling elements remain critical roadblocks that functionally limit the efficacy of prediction software. This Perspective article will briefly discuss how AI-powered protein prediction software will impact drug development to transform neuropsychopharmacology research and therapeutics, while also providing insights into the limitations of these digital tools.

摘要

人工智能(AI)的发展与应用为重新定义我们如何研发神经精神疾病的治疗方法带来了巨大机遇。尽管AI在生物医学领域取得了快速进展,但其在药物发现、蛋白质组学和神经生物学中的应用却遇到了新的、意想不到的限制。从历史上看,神经药理学研究一直采用观察性和侵入性实验方法来确定新的治疗方法。不幸的是,这种传统方法存在化学合成繁琐和体内测试的问题,最终导致转化瓶颈。随着AI的应用,我们现在能够通过模拟药物或蛋白质复合物与感兴趣的受体之间的相互作用来加速早期测试。通过应用强大的、基于精度的蛋白质结构预测工具,我们可以更好地定制治疗方法并将不良结果降至最低。尽管前景广阔,但诸如预测分子的手性、结合时的构象变化以及确定下游信号元件等重要警告仍然是功能上限制预测软件功效的关键障碍。这篇观点文章将简要讨论人工智能驱动的蛋白质预测软件将如何影响药物开发,以改变神经精神药理学研究和治疗方法,同时也深入探讨这些数字工具的局限性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/61aa/12208904/903a18e6d740/44277_2025_38_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/61aa/12208904/7d3b9b82c58b/44277_2025_38_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/61aa/12208904/903a18e6d740/44277_2025_38_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/61aa/12208904/7d3b9b82c58b/44277_2025_38_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/61aa/12208904/903a18e6d740/44277_2025_38_Fig2_HTML.jpg

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本文引用的文献

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AlphaFold prediction of structural ensembles of disordered proteins.无序蛋白质结构集合的AlphaFold预测。
Nat Commun. 2025 Feb 14;16(1):1632. doi: 10.1038/s41467-025-56572-9.
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AlphaFold 3 is great - but it still needs human help to get chemistry right.阿尔法折叠3很强大——但要想让化学原理正确无误,它仍需要人工协助。
Nature. 2025 Jan;637(8046):548. doi: 10.1038/d41586-025-00111-5.
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AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors.AlphaFold3与实验结构:配体结合型G蛋白偶联受体准确性评估
Acta Pharmacol Sin. 2025 Apr;46(4):1111-1122. doi: 10.1038/s41401-024-01429-y. Epub 2024 Dec 6.
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Deciphering proteins in Alzheimer's disease: A new Mendelian randomization method integrated with AlphaFold3 for 3D structure prediction.解析阿尔茨海默病中的蛋白质:一种与AlphaFold3集成用于三维结构预测的新孟德尔随机化方法。
Cell Genom. 2024 Dec 11;4(12):100700. doi: 10.1016/j.xgen.2024.100700. Epub 2024 Dec 4.
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AlphaFold 3 - Aided Design of DNA Motifs To Assemble into Triangles.AlphaFold 3 辅助设计 DNA 基序以组装成三角形。
J Am Chem Soc. 2024 Sep 18;146(37):25422-25425. doi: 10.1021/jacs.4c08387. Epub 2024 Sep 5.
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Evaluation of AlphaFold 3's Protein-Protein Complexes for Predicting Binding Free Energy Changes upon Mutation.评估 AlphaFold 3 的蛋白质-蛋白质复合物在预测突变时结合自由能变化的能力。
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