Targeting HER2 with DNA Aptamers for Efficient Anticancer Drug Delivery: A Combined Experimental and Computational Study.

IF 4 2区 化学 Q1 BIOCHEMICAL RESEARCH METHODS
Bioconjugate Chemistry Pub Date : 2025-06-18 Epub Date: 2025-05-22 DOI:10.1021/acs.bioconjchem.5c00022
Konstantin E Katsuba, Lidia M Zabegina, Daniil S Plevako, Andrey A Gurtovenko, Anastasia V Malek
{"title":"Targeting HER2 with DNA Aptamers for Efficient Anticancer Drug Delivery: A Combined Experimental and Computational Study.","authors":"Konstantin E Katsuba, Lidia M Zabegina, Daniil S Plevako, Andrey A Gurtovenko, Anastasia V Malek","doi":"10.1021/acs.bioconjchem.5c00022","DOIUrl":null,"url":null,"abstract":"<p><p>Targeted delivery of cytostatic drugs is a powerful approach to achieving tumor tissue selectivity, reducing systemic toxicity, and ultimately improving the efficacy of anticancer chemotherapy. Targeting can be achieved using a wide range of molecular ligands, with DNA aptamers being a promising representative. In this work, we employed flow cytometry, a AuNP-aptasensor, and atomic-scale computer modeling to assess the affinity of several DNA aptamers (Anti-HER2, HB5, Apt-6, HeA2_1, and HeA2_3) for human epidermal growth factor receptor 2 (HER2), which is known to be one of the factors that promote the growth of breast cancer cells. Flow cytometry showed that short aptamers (HeA2_1 and HeA2_3) had a higher affinity for HER2 on MDAMB453 cancer cells than longer aptamers (HB5, Apt-6). HER2-negative MDA-MB-231 cells served as the negative control. The HeA2_3 aptamer has a high average affinity (HeA2_3:23.6, HeA2_1:13.1, Apt-6:3.6; HB5:3.5; Anti-HER2:3.2) and a nearly Gaussian distribution across the cells, while HeA2_1 forms a fraction of cells with a relatively high fluorescence signal intensity (HeA2_1:11.6; HeA2_3:5.9; Apt-6:3.4; HB5:3.1; Anti-HER2:2.1). Most of the findings for cancer cells also hold for the HER2-positive small extracellular vesicles studied using the AuNP-aptasensor. Computer simulations confirmed that short aptamers are characterized by stronger binding to the extracellular domain of HER2. A detailed analysis of the free energy allowed us to show for the first time that tight binding to HER2 correlates with well-separated hot and cold spots on the protein surface. For the aptamers that meet these criteria (HeA2_1, HeA2_3, and Anti-HER2), favorable interactions with HER2 are driven by the local attraction of nucleotides to arginine and lysine residues of HER2 and possibly stabilized by intermolecular hydrogen bonds. For longer aptamers (Apt-6 and HB5), hot and cold spots on the HER2 surface overlap and the aptamers show much weaker binding. Overall, our findings show that binding of DNA aptamers to HER2 cannot be characterized merely by the dissociation equilibrium constant. A more sophisticated approach that combines experimental and computational methods allowed us to unlock the molecular mechanisms behind the aptamer-HER2 bindings. The results of our study also suggest that computer modeling has become a reliable and accurate tool for aptamer prescreening prior to laboratory experiments.</p>","PeriodicalId":29,"journal":{"name":"Bioconjugate Chemistry","volume":" ","pages":"1180-1196"},"PeriodicalIF":4.0000,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioconjugate Chemistry","FirstCategoryId":"1","ListUrlMain":"https://doi.org/10.1021/acs.bioconjchem.5c00022","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/5/22 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

Abstract

Targeted delivery of cytostatic drugs is a powerful approach to achieving tumor tissue selectivity, reducing systemic toxicity, and ultimately improving the efficacy of anticancer chemotherapy. Targeting can be achieved using a wide range of molecular ligands, with DNA aptamers being a promising representative. In this work, we employed flow cytometry, a AuNP-aptasensor, and atomic-scale computer modeling to assess the affinity of several DNA aptamers (Anti-HER2, HB5, Apt-6, HeA2_1, and HeA2_3) for human epidermal growth factor receptor 2 (HER2), which is known to be one of the factors that promote the growth of breast cancer cells. Flow cytometry showed that short aptamers (HeA2_1 and HeA2_3) had a higher affinity for HER2 on MDAMB453 cancer cells than longer aptamers (HB5, Apt-6). HER2-negative MDA-MB-231 cells served as the negative control. The HeA2_3 aptamer has a high average affinity (HeA2_3:23.6, HeA2_1:13.1, Apt-6:3.6; HB5:3.5; Anti-HER2:3.2) and a nearly Gaussian distribution across the cells, while HeA2_1 forms a fraction of cells with a relatively high fluorescence signal intensity (HeA2_1:11.6; HeA2_3:5.9; Apt-6:3.4; HB5:3.1; Anti-HER2:2.1). Most of the findings for cancer cells also hold for the HER2-positive small extracellular vesicles studied using the AuNP-aptasensor. Computer simulations confirmed that short aptamers are characterized by stronger binding to the extracellular domain of HER2. A detailed analysis of the free energy allowed us to show for the first time that tight binding to HER2 correlates with well-separated hot and cold spots on the protein surface. For the aptamers that meet these criteria (HeA2_1, HeA2_3, and Anti-HER2), favorable interactions with HER2 are driven by the local attraction of nucleotides to arginine and lysine residues of HER2 and possibly stabilized by intermolecular hydrogen bonds. For longer aptamers (Apt-6 and HB5), hot and cold spots on the HER2 surface overlap and the aptamers show much weaker binding. Overall, our findings show that binding of DNA aptamers to HER2 cannot be characterized merely by the dissociation equilibrium constant. A more sophisticated approach that combines experimental and computational methods allowed us to unlock the molecular mechanisms behind the aptamer-HER2 bindings. The results of our study also suggest that computer modeling has become a reliable and accurate tool for aptamer prescreening prior to laboratory experiments.

利用DNA适体靶向HER2高效抗癌药物递送:实验与计算相结合的研究。
细胞抑制药物的靶向递送是实现肿瘤组织选择性,降低全身毒性,最终提高抗癌化疗疗效的有力途径。靶向可以使用广泛的分子配体来实现,DNA适体是一个有前途的代表。在这项工作中,我们采用流式细胞术、aunp适配体传感器和原子尺度的计算机模型来评估几种DNA适配体(Anti-HER2、HB5、Apt-6、HeA2_1和HeA2_3)对人表皮生长因子受体2 (HER2)的亲和力,HER2是已知的促进乳腺癌细胞生长的因素之一。流式细胞术显示,短适配体(HeA2_1和HeA2_3)对MDAMB453癌细胞的HER2亲和力高于长适配体(HB5, Apt-6)。以her2阴性的MDA-MB-231细胞为阴性对照。HeA2_3适体具有较高的平均亲和力(HeA2_3:23.6, HeA2_3: 13.1, apt - 6:6 .6;HB5:3.5;Anti-HER2:3.2),在细胞间呈近似高斯分布,而HeA2_1在细胞中形成了相对较高的荧光信号强度(HeA2_1:11.6;HeA2_3:5.9;Apt-6:3.4;HB5:3.1;Anti-HER2:2.1)。大多数关于癌细胞的发现也适用于使用aunp -适配体传感器研究的her2阳性的小细胞外囊泡。计算机模拟证实,短适配体的特点是与HER2的细胞外结构域结合更强。对自由能的详细分析使我们首次表明,与HER2的紧密结合与蛋白质表面上分离良好的热点和冷点有关。对于符合这些标准的适体(HeA2_1, HeA2_3和Anti-HER2),与HER2的良好相互作用是由核苷酸对HER2的精氨酸和赖氨酸残基的局部吸引驱动的,并可能由分子间氢键稳定。对于较长的适体(Apt-6和HB5), HER2表面的热点和冷点重叠,适体的结合弱得多。总之,我们的发现表明DNA适体与HER2的结合不能仅仅通过解离平衡常数来表征。一种结合实验和计算方法的更复杂的方法使我们能够解开适配体- her2结合背后的分子机制。我们的研究结果还表明,计算机建模已成为实验室实验之前适体预筛选的可靠和准确的工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Bioconjugate Chemistry
Bioconjugate Chemistry 生物-化学综合
CiteScore
9.00
自引率
2.10%
发文量
236
审稿时长
1.4 months
期刊介绍: Bioconjugate Chemistry invites original contributions on all research at the interface between man-made and biological materials. The mission of the journal is to communicate to advances in fields including therapeutic delivery, imaging, bionanotechnology, and synthetic biology. Bioconjugate Chemistry is intended to provide a forum for presentation of research relevant to all aspects of bioconjugates, including the preparation, properties and applications of biomolecular conjugates.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信