DNA可编程蛋白质降解:通过DNA杂交和链置换对蛋白酶靶向嵌合体活性进行动态控制

DNA-Programmable Protein Degradation: Dynamic Control of Proteolysis-Targeting Chimera Activity via DNA Hybridization and Strand Displacement.

作者信息

Kashyap Disha, Haider Shozeb, Milne Thomas A, Booth Michael J

机构信息

Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.

MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, U.K.

出版信息

JACS Au. 2025 Jul 31;5(8):3799-3807. doi: 10.1021/jacsau.5c00422. eCollection 2025 Aug 25.

Abstract

Targeted protein degradation is a powerful therapeutic approach: expanding the druggable proteome, providing enhanced selectivity, and having the ability to overcome conventional resistance mechanisms. A major class of such molecules is proteolysis-targeting chimeras (PROTACs). PROTACs are catalytic heterobifunctional small molecules that simultaneously bind a protein of interest (POI) and an E3 ligase. And thus, PROTACs induce a proximity-dependent ubiquitination of the POI and its subsequent degradation by the ubiquitin-proteasome system. While PROTACs have successfully transitioned from academia to industry, increasing awareness of off-target effects and related toxicities highlights the urgent need for precise control mechanisms over activity. Achieving this level of control, however, remains challenging, with traditional chemistries. DNA nanotechnology, with its unparalleled programmability and structural versatility, presents a powerful tool for achieving such control. Here, we report the design and characterization of oligonucleotide-linked PROTACs (OligoPROTACs). These constructs comprise PROTAC warheads covalently linked to separate complementary DNA strands, brought together in space via DNA hybridization. OligoPROTACs are able to degrade the POI in a distance-dependent manner. Furthermore, we demonstrate the first instance of a dynamic off-switch mechanism for PROTAC activity, enabled by toehold-mediated strand displacement using a third DNA strand. This work highlights the potential of DNA nanotechnology combined with the clinical emergence of nucleic acid therapeutics to enhance the safety and functionality of PROTAC systems, paving the way for more refined and translatable therapeutic strategies.

摘要

靶向蛋白质降解是一种强大的治疗方法

它可扩展可成药蛋白质组,提供更高的选择性,并能够克服传统的耐药机制。这类分子的一个主要类别是蛋白酶靶向嵌合体(PROTACs)。PROTACs是催化性异双功能小分子,可同时结合目标蛋白(POI)和E3连接酶。因此,PROTACs可诱导POI发生邻近依赖性泛素化,并随后被泛素-蛋白酶体系统降解。虽然PROTACs已成功从学术界过渡到工业界,但对脱靶效应和相关毒性的认识不断提高,凸显了对其活性进行精确控制机制的迫切需求。然而,用传统化学方法实现这种控制水平仍然具有挑战性。DNA纳米技术具有无与伦比的可编程性和结构多功能性,是实现这种控制的有力工具。在此,我们报告了寡核苷酸连接的PROTACs(OligoPROTACs)的设计与表征。这些构建体包含与单独的互补DNA链共价连接的PROTAC弹头,通过DNA杂交在空间上聚集在一起。OligoPROTACs能够以距离依赖性方式降解POI。此外,我们展示了通过使用第三条DNA链进行的链置换介导的PROTAC活性动态关闭开关机制的首个实例。这项工作突出了DNA纳米技术与核酸治疗临床应用相结合的潜力,以提高PROTAC系统的安全性和功能性,为更精细且可转化的治疗策略铺平道路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce74/12381747/12726bd1f368/au5c00422_0001.jpg

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