由于霉菌毒素特异性单克隆抗体生产的困难,适体探针已被认为是合适的替代品。SELEX程序在筛选高亲和力适体以结合作为小分子的霉菌毒素中的低效率可以通过计算技术得到显著改善。以前,我们基于已知的适体序列(专利:PCT/CA2010/001292,Apt1),通过基于遗传算法的计算机成熟策略,设计了五种新的黄曲霉毒素B1(AFB1)适体,并通过实验测量了它们对靶毒素的亲和力。这里,集成分子动力学模拟(MD)研究与分子力学泊松-玻尔兹曼表面积(MM-PBSA)分析,以阐明结合模式,六个AFB1结合适体中关键的相互作用核酸碱基和能量成分的贡献。在第一项工作中选择的适体F20,与其他适体相比,显示出最佳的自由结合能和复合物稳定性。轨迹分析表明,AFB1通过凹槽结合模式以及精确的形状互补性识别F20。MD模拟结果表明,动态水中间相互作用在促进复杂稳定性方面也起着关键作用。根据MM-PBSA计算,范德华接触被确定为所有复合物中的主要能量成分。有趣的是,在实验获得的六个适体的结合亲和力与它们的自由能溶剂化之间观察到高一致性。计算结果,通过以前的实验证实,突出显示了绑定模式,复杂组分的动态水合和总自由相互作用能是发现高功能适体探针的关键标准。
Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.