Rabal Obdulia, Pastor Fernando, Villanueva Helena, Soldevilla Mario M, Hervas-Stubbs Sandra, Oyarzabal Julen
Small Molecule Discovery Platform, Center for Applied Medical Research, CIMA, University of Navarra, Pamplona, Spain.
Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, Pamplona, Spain.
Mol Ther Nucleic Acids. 2016 Oct 18;5(10):e376. doi: 10.1038/mtna.2016.84.
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX) technologies with in silico prediction of aptamer binders has attracted a lot of interest in the recent years. We propose a workflow involving 2D structure prediction, 3D RNA modeling using Rosetta and docking to the target protein with 3dRPC for: (i) prediction of the binding mode of our two previously reported potent (Kd < 50 nmol/l) murine TIM3 aptamers, and (ii) the prioritization of TIM3 aptamers that were enriched in the SELEX workflow. The procedure was first validated in five different study cases. As a novelty, cluster analysis of the docked poses was carried out and shown to be useful in reproducing the binding mode or at least in identifying the binding site and the experimental aptamer-protein interactions. For TIM3, our therapeutic target of interest, a plausible binding site and binding mode was identified that might explain the lack of cross-reactivity in murine over human TIM-3. Concerning the prioritization of the aptamers, the inclusion of the cluster analysis as an additional criterion following a rank-by-rank approach is discussed and compared with the performance of the docking scoring function alone for two validation cases and for the prospective assessment of the novel aptamers as TIM3 binders.
近年来，通过指数富集的配体系统进化（SELEX）技术与适体结合剂的计算机模拟预测相结合引起了广泛关注。我们提出了一个工作流程，包括二维结构预测、使用Rosetta进行三维RNA建模以及使用3dRPC与目标蛋白对接，用于：（i）预测我们之前报道的两种强效（Kd < 50 nmol/l）小鼠TIM3适体的结合模式，以及（ii）对在SELEX工作流程中富集的TIM3适体进行优先级排序。该程序首先在五个不同的研究案例中得到验证。新颖的是，对接姿势的聚类分析得以进行，并显示在重现结合模式或至少识别结合位点以及实验性适体 - 蛋白质相互作用方面很有用。对于我们感兴趣的治疗靶点TIM3，确定了一个合理的结合位点和结合模式，这可能解释了小鼠TIM - 3与人TIM - 3之间缺乏交叉反应性的原因。关于适体的优先级排序，讨论了在逐个排序方法之后将聚类分析作为附加标准纳入的情况，并与仅对接评分函数的性能进行比较，用于两个验证案例以及对新型适体作为TIM3结合剂的前瞻性评估。
