Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran.
Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
Biotechnol J. 2022 Feb;17(2):e2100280. doi: 10.1002/biot.202100280. Epub 2021 Dec 6.
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 B (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.
由于针对霉菌毒素的单克隆抗体生产存在困难，适体探针已被认为是合适的替代品。通过计算技术，可以显著提高 SELEX 程序筛选与小分子结合的高亲和力适体的效率。此前，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模拟成熟策略设计了五个针对黄曲霉毒素 B（AFB1）的新适体，并通过实验测量了它们与目标毒素的亲和力。在这里，我们将整合分子动力学模拟（MDs）研究与分子力学泊松-玻尔兹曼表面积（MM-PBSA）分析相结合，以阐明 6 个 AFB1 结合适体的结合模式、关键相互作用的核酸碱基和能量组成贡献。在第一项工作中被选中的适体 F20 与其他适体相比，具有最佳的自由结合能和复合物稳定性。轨迹分析表明，AFB1 通过沿碱基沟的结合模式识别 F20，并与精确的形状互补。MD 模拟结果表明，动态水中间相互作用也在促进复合物稳定性方面发挥关键作用。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，6 个适体的实验测定亲和力与其溶剂化自由能之间存在高度一致性。通过先前的实验证实的计算结果强调了结合模式、复合物成分的动态水合作用以及总自由相互作用能作为发现高功能适体探针的关键标准。
