Chen Long, Zhang Bibi, Wu Zengrui, Liu Guixia, Li Weihua, Tang Yun
Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
Comput Struct Biotechnol J. 2023 Jan 11;21:1005-1013. doi: 10.1016/j.csbj.2023.01.002. eCollection 2023.
With advances in force fields and algorithms, robust tools have been developed for molecular simulation of three-dimensional structures of nucleic acids and investigation of aptamer-target interactions. The traditional aptamer discovery technique, Systematic Evolution of Ligands by EXponential enrichment (SELEX), continues to suffer from high investment and low return, while in vitro screening by simulated SELEX remains a challenging task, where more accurate structural modeling and enhanced sampling limit the large-scale application of the method. Here, we proposed a modified aptamer enhanced library design strategy to facilitate the screening of target-binding aptamers. In this strategy, a comprehensive analysis of the original complexes and the target secondary structure were used to construct an enhanced initial library for screening. Our enhanced sequence library design strategy based on the target secondary structure explored a certain sequence space while ensuring the accuracy of the structural conformation and the calculation method. In an enhanced library of only a few dozen sequences, four sequences showed a similar or better binding free energy than the original aptamer, with consistently high binding stability over three rounds of multi-timescale simulations, ranging from - 30.27 to - 32.25 kcal/mol. Consequently, the enhanced library strategy based on the target secondary structure is shown to have very significant potential as a new aptamer design and optimization strategy.
随着力场和算法的进步，已经开发出了强大的工具用于核酸三维结构的分子模拟以及适体-靶标相互作用的研究。传统的适体发现技术——指数富集配体系统进化技术（SELEX），仍然面临着高投入、低回报的问题，而通过模拟SELEX进行体外筛选仍然是一项具有挑战性的任务，其中更精确的结构建模和增强的采样限制了该方法的大规模应用。在此，我们提出了一种改进的适体增强文库设计策略，以促进对靶标结合适体的筛选。在该策略中，对原始复合物和靶标二级结构进行综合分析，以构建用于筛选的增强初始文库。我们基于靶标二级结构的增强序列文库设计策略在确保结构构象准确性和计算方法的同时，探索了一定的序列空间。在仅包含几十条序列的增强文库中，有四条序列显示出与原始适体相似或更好的结合自由能，在三轮多时间尺度模拟中具有始终如一的高结合稳定性，范围从-30.27至-32.25千卡/摩尔。因此，基于靶标二级结构的增强文库策略作为一种新的适体设计和优化策略显示出非常巨大的潜力。
