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使用 AlphaFold 模型能多准确地预测药物结合模式?

How accurately can one predict drug binding modes using AlphaFold models?

机构信息

Biophysics Program, Stanford University, Stanford, United States.

Department of Computer Science, Stanford University, Stanford, United States.

出版信息

Elife. 2023 Dec 22;12:RP89386. doi: 10.7554/eLife.89386.


DOI:10.7554/eLife.89386
PMID:38131311
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10746139/
Abstract

Computational prediction of protein structure has been pursued intensely for decades, motivated largely by the goal of using structural models for drug discovery. Recently developed machine-learning methods such as AlphaFold 2 (AF2) have dramatically improved protein structure prediction, with reported accuracy approaching that of experimentally determined structures. To what extent do these advances translate to an ability to predict more accurately how drugs and drug candidates bind to their target proteins? Here, we carefully examine the utility of AF2 protein structure models for predicting binding poses of drug-like molecules at the largest class of drug targets, the G-protein-coupled receptors. We find that AF2 models capture binding pocket structures much more accurately than traditional homology models, with errors nearly as small as differences between structures of the same protein determined experimentally with different ligands bound. Strikingly, however, the accuracy of ligand-binding poses predicted by computational docking to AF2 models is not significantly higher than when docking to traditional homology models and is much lower than when docking to structures determined experimentally without these ligands bound. These results have important implications for all those who might use predicted protein structures for drug discovery.

摘要

几十年来,人们一直强烈追求蛋白质结构的计算预测,主要目标是使用结构模型进行药物发现。最近开发的机器学习方法,如 AlphaFold 2(AF2),极大地提高了蛋白质结构预测的准确性,报告的准确性接近实验确定结构的准确性。这些进展在多大程度上能够更准确地预测药物和候选药物与它们的靶蛋白结合的方式?在这里,我们仔细研究了 AF2 蛋白质结构模型在预测药物样分子与最大类药物靶点,即 G 蛋白偶联受体结合构象方面的效用。我们发现,AF2 模型比传统的同源建模更准确地捕获结合口袋结构,误差几乎与用不同配体结合实验确定的同一蛋白质结构之间的差异一样小。然而,令人惊讶的是,通过计算对接预测配体结合构象的准确性与对接传统同源模型时没有显著提高,并且比对接没有这些配体结合的实验确定结构时要低得多。这些结果对所有可能使用预测蛋白质结构进行药物发现的人都有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/5c67e102150b/elife-89386-fig5-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/8017f2ab4266/elife-89386-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/d2a4a30e2433/elife-89386-fig1-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/12fcd5575006/elife-89386-fig1-figsupp2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/e50d3a66dc95/elife-89386-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/fa2ec7c1151c/elife-89386-fig2-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/0ad471b512f0/elife-89386-fig2-figsupp2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/f4a27ef2bde1/elife-89386-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/7bca6fc3c09e/elife-89386-fig3-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/68eff9602290/elife-89386-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/2b3d8a155e19/elife-89386-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/5c67e102150b/elife-89386-fig5-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/8017f2ab4266/elife-89386-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/d2a4a30e2433/elife-89386-fig1-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/12fcd5575006/elife-89386-fig1-figsupp2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/e50d3a66dc95/elife-89386-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/fa2ec7c1151c/elife-89386-fig2-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/0ad471b512f0/elife-89386-fig2-figsupp2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/f4a27ef2bde1/elife-89386-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/7bca6fc3c09e/elife-89386-fig3-figsupp1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/68eff9602290/elife-89386-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/2b3d8a155e19/elife-89386-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2fe0/10746139/5c67e102150b/elife-89386-fig5-figsupp1.jpg

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[1]
How accurately can one predict drug binding modes using AlphaFold models?

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[6]
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[8]
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[9]
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[10]
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本文引用的文献

[1]
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures.

J Chem Inf Model. 2023-3-27

[2]
How good are AlphaFold models for docking-based virtual screening?

iScience. 2022-12-30

[3]
Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.

Comput Struct Biotechnol J. 2022-12-1

[4]
UniProt: the Universal Protein Knowledgebase in 2023.

Nucleic Acids Res. 2023-1-6

[5]
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery.

Mol Syst Biol. 2022-9

[6]
Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors.

Brief Bioinform. 2022-9-20

[7]
AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors.

Acta Pharmacol Sin. 2023-1

[8]
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.

Front Mol Biosci. 2022-6-13

[9]
Multi-state modeling of G-protein coupled receptors at experimental accuracy.

Proteins. 2022-11

[10]
Structural biology is solved - now what?

Nat Methods. 2022-1

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