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利用AlphaFold2对马里巴韦诱导的pUL97激酶抑制机制和耐药性突变进行计算机模拟分析及结构预测

In Silico Analysis of Mechanisms of Maribavir-Induced Inhibition and Drug Resistance Mutations in pUL97 Kinase Structural Prediction with AlphaFold2.

作者信息

Piret Jocelyne, Boivin Guy

机构信息

Research Center of the CHU de Quebec-Laval University, Quebec City, QC G1V 4G2, Canada.

Department of Pediatrics, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada.

出版信息

Viruses. 2025 Jul 2;17(7):941. doi: 10.3390/v17070941.

DOI:10.3390/v17070941
PMID:40733558
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12301049/
Abstract

Infections with cytomegalovirus (CMV) can result in increased morbidity and mortality in immunocompromised patients. The pUL97 kinase is a critical enzyme in the regulation of CMV replication. Although it does not phosphorylate deoxynucleosides, this enzyme is involved in the first phosphorylation step of ganciclovir (GCV), a viral DNA polymerase inhibitor. In contrast, maribavir (MBV) is a specific inhibitor of pUL97 kinase activity. In this paper, we analyzed the already-reported amino acid changes, conferring resistance to MBV and cross-resistance to GCV, in the pUL97 protein structure, predicted with AlphaFold2. Docking experiments suggest that MBV is a dual-site inhibitor, targeting ATP binding and substrate phosphorylation. Substitutions that confer resistance to MBV only may directly or indirectly alter the shape of the cavity in the vicinity of the invariant K355 in the putative ATP binding site, without affecting the viral growth. The most frequently encountered T409M substitution may correspond to a gatekeeper mutation. Substitutions that induce cross-resistance to MBV and GCV may directly or indirectly affect the environment of D456 and N461 residues in the catalytic loop, with reduced viral replicative capacity. These results have implications for the clinical use of MBV as well as for the design of novel pUL97 kinase inhibitors.

摘要

巨细胞病毒(CMV)感染可导致免疫功能低下患者的发病率和死亡率增加。pUL97激酶是调节CMV复制的关键酶。虽然它不使脱氧核苷磷酸化,但该酶参与了更昔洛韦(GCV,一种病毒DNA聚合酶抑制剂)的第一步磷酸化反应。相比之下,马立巴韦(MBV)是pUL97激酶活性的特异性抑制剂。在本文中,我们分析了已报道的在通过AlphaFold2预测的pUL97蛋白结构中赋予对MBV耐药性和对GCV交叉耐药性的氨基酸变化。对接实验表明,MBV是一种双位点抑制剂,靶向ATP结合和底物磷酸化。仅赋予对MBV耐药性的替代可能直接或间接改变假定ATP结合位点中不变的K355附近腔的形状,而不影响病毒生长。最常见的T409M替代可能对应于守门人突变。诱导对MBV和GCV交叉耐药性的替代可能直接或间接影响催化环中D456和N461残基的环境,同时降低病毒复制能力。这些结果对MBV的临床应用以及新型pUL97激酶抑制剂的设计具有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/736599e5488d/viruses-17-00941-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/8371760877bc/viruses-17-00941-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/94224ccadca8/viruses-17-00941-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/8263edc9c627/viruses-17-00941-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/319f2fb94b89/viruses-17-00941-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/95059ca0d1c8/viruses-17-00941-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/74a69b13ffc5/viruses-17-00941-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/736599e5488d/viruses-17-00941-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/8371760877bc/viruses-17-00941-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/94224ccadca8/viruses-17-00941-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/8263edc9c627/viruses-17-00941-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/319f2fb94b89/viruses-17-00941-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/95059ca0d1c8/viruses-17-00941-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/74a69b13ffc5/viruses-17-00941-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ff/12301049/736599e5488d/viruses-17-00941-g007.jpg

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本文引用的文献

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Cells. 2024 Aug 13;13(16):1338. doi: 10.3390/cells13161338.
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The prospect of substrate-based kinase inhibitors to improve target selectivity and overcome drug resistance.基于底物的激酶抑制剂改善靶点选择性和克服耐药性的前景。
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Accurate structure prediction of biomolecular interactions with AlphaFold 3.
利用 AlphaFold 3 进行生物分子相互作用的精确结构预测。
Nature. 2024 Jun;630(8016):493-500. doi: 10.1038/s41586-024-07487-w. Epub 2024 May 8.
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Management of Cytomegalovirus Infections in the Era of the Novel Antiviral Players, Letermovir and Maribavir.新型抗病毒药物来特莫韦和马瑞巴韦时代巨细胞病毒感染的管理
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