Koshmanova Anastasia A, Artyushenko Polina V, Shchugoreva Irina A, Fedotovskaya Victoriya D, Luzan Natalia A, Kolovskaya Olga S, Zamay Galina S, Lukyanenko Kirill A, Veprintsev Dmitriy V, Khilazheva Elena D, Zamay Tatiana N, Ivanova Daria A, Kastyuk Maria R, Lapin Ivan N, Svetlichnyi Valery A, Tomilin Felix N, Shved Nikita A, Gulaia Valeriia S, Kumeiko Vadim V, Berezovski Maxim V, Kichkailo Anna S
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", 660036 Krasnoyarsk, Russia.
Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia.
Cancers (Basel). 2024 Dec 8;16(23):4111. doi: 10.3390/cancers16234111.
Oncological diseases are a major focus in medicine, with millions diagnosed each year, leading researchers to seek new diagnostic and treatment methods. One promising avenue is the development of targeted therapies and rapid diagnostic tests using recognition molecules. The pharmaceutical industry is increasingly exploring nucleic acid-based therapeutics. However, producing long oligonucleotides, especially aptamers, poses significant production challenges. This study aims to demonstrate the efficacy of using molecular modeling, supported by experimental procedures, for altering aptamer nucleotide sequences while maintaining their binding capabilities. The focus is on reducing production costs and enhancing binding dynamics by removing nonfunctional regions and minimizing nonspecific binding. A molecular modeling approach was employed to elucidate the structure of a DNA aptamer, Gli-55, facilitating the truncation of nonessential regions in the Gli-55 aptamer, which selectively binds to glioblastoma (GBM). This process aimed to produce a truncated aptamer, Gli-35, capable of forming similar structural elements to the original sequence with reduced nonspecific binding. The efficiency of the truncation was proved by flow cytometry, fluorescence polarization (FP), and confocal microscopy. The molecular design indicated that the new truncated Gli-35 aptamer retained the structural integrity of Gli-55. In vitro studies showed that Gli-35 had a binding affinity comparable to the initial long aptamer while the selectivity increased. Gli-35 internalized inside the cell faster than Gli-55 and crossed the blood-brain barrier (BBB), as demonstrated in an in vitro model. The success of this truncation approach suggests its potential applicability in scenarios where molecular target information is limited. The study highlights a strategic and resource-efficient methodology for aptamer development. By employing molecular modeling and truncation, researchers can reduce production costs and avoid trial and error in sequence selection. This approach is promising for enhancing the efficiency of therapeutic agent development, particularly in cases lacking detailed molecular target insights.
肿瘤疾病是医学的主要关注焦点，每年有数百万例确诊病例，这促使研究人员寻求新的诊断和治疗方法。一个有前景的途径是利用识别分子开发靶向疗法和快速诊断测试。制药行业越来越多地探索基于核酸的疗法。然而，生产长链寡核苷酸，尤其是适体，面临着重大的生产挑战。本研究旨在证明在实验程序的支持下，使用分子建模来改变适体核苷酸序列同时保持其结合能力的有效性。重点是通过去除无功能区域和最小化非特异性结合来降低生产成本并增强结合动力学。采用分子建模方法来阐明DNA适体Gli-55的结构，从而便于截断Gli-55适体中与胶质母细胞瘤（GBM）选择性结合的非必需区域。这一过程旨在产生一种截短的适体Gli-35，它能够形成与原始序列相似的结构元件，同时减少非特异性结合。通过流式细胞术、荧光偏振（FP）和共聚焦显微镜证实了截断的效率。分子设计表明，新的截短的Gli-35适体保留了Gli-55的结构完整性。体外研究表明，Gli-35具有与初始长适体相当的结合亲和力，同时选择性增加。如体外模型所示，Gli-35比Gli-55更快地内化到细胞内并穿过血脑屏障（BBB）。这种截断方法的成功表明其在分子靶点信息有限的情况下具有潜在的适用性。该研究突出了一种用于适体开发的策略性和资源高效的方法。通过采用分子建模和截断，研究人员可以降低生产成本并避免在序列选择中进行反复试验。这种方法对于提高治疗剂开发的效率很有前景，特别是在缺乏详细分子靶点见解的情况下。
