Tsvetkov Vladimir B, Varizhuk Irina V, Kurochkin Nikolay N, Surzhikov Sergei A, Smirnov Igor P, Stomakhin Andrey A, Kolganova Natalia A, Timofeev Edward N
Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia.
Institute of Biodesign and Complex System Modeling, Sechenov First Moscow State Medical University, 119146 Moscow, Russia.
Int J Mol Sci. 2022 Mar 30;23(7):3820. doi: 10.3390/ijms23073820.
Oligonucleotide-peptide conjugates (OPCs) are a promising class of biologically active compounds with proven potential for improving nucleic acid therapeutics. OPCs are commonly recognized as an efficient instrument to enhance the cellular delivery of therapeutic nucleic acids. In addition to this application field, OPCs have an as yet unexplored potential for the post-SELEX optimization of DNA aptamers. In this paper, we report the preparation of designer thrombin aptamer OPCs with peptide side chains anchored to a particular thymidine residue of the aptamer. The current conjugation strategy utilizes unmodified short peptides and support-bound protected oligonucleotides with activated carboxyl functionality at the T3 thymine nucleobase. The respective modification of the oligonucleotide strand was implemented using N3-derivatized thymidine phosphoramidite. Aptamer OPCs retained the G-quadruplex architecture of the parent DNA structure and showed minor to moderate stabilization. In a series of five OPCs, conjugates bearing T3-Ser-Phe-Asn (SFN) or T3-Tyr-Trp-Asn (YWN) side chains exhibited considerably improved anticoagulant characteristics. Molecular dynamics studies of the aptamer OPC complexes with thrombin revealed the roles of the amino acid nature and sequence in the peptide subunit in modulating the anticoagulant activity.
寡核苷酸 - 肽缀合物（OPCs）是一类很有前景的生物活性化合物，已被证明具有改善核酸治疗的潜力。OPCs通常被认为是增强治疗性核酸细胞递送的有效工具。除了这一应用领域外，OPCs在DNA适体的SELEX后优化方面还有尚未被探索的潜力。在本文中，我们报告了设计的凝血酶适体OPCs的制备，其肽侧链锚定在适体的特定胸腺嘧啶残基上。当前的缀合策略利用未修饰的短肽和在T3胸腺嘧啶碱基处具有活化羧基功能的固相支持的保护寡核苷酸。寡核苷酸链的相应修饰使用N3 - 衍生的胸腺嘧啶亚磷酰胺进行。适体OPCs保留了亲本DNA结构的G - 四链体结构，并显示出轻微至中度的稳定作用。在一系列五个OPCs中，带有T3 - Ser - Phe - Asn（SFN）或T3 - Tyr - Trp - Asn（YWN）侧链的缀合物表现出显著改善的抗凝特性。对适体OPC与凝血酶复合物的分子动力学研究揭示了肽亚基中氨基酸性质和序列在调节抗凝活性中的作用。
