Zabolotny Institute of Microbiology and Virology of NASU, 154 Acad. Zabolotny Str., Kyiv, 03143, Ukraine.
Sci Rep. 2023 Apr 3;13(1):5395. doi: 10.1038/s41598-023-32595-4.
Cancer as an acquired genetic disease is based on changes both in the genome itself and in transcription processes. Accordingly, it is at the DNA level that it makes sense to search for and design agents capable of effective and selective anticancer action. In this study, we used an iterative approach based on a molecular dynamics simulation to design a highly selective DNA-intercalating agent called HASDI. To confirm its selective affinity to DNA, we conducted two simulation experiments: HASDI in a complex with a DNA fragment of the EBNA1 gene (it targets 16 nucleotide pairs of this gene) and HASDI in a complex with a random DNA fragment of the KCNH2 gene. The molecular dynamics simulation was carried out in the GROMACS 2019 package. The binding energy was calculated by gmx_MMPBSA 1.5.2. The further analysis was performed using the built-in utilities of GROMACS, gmx_MMPBSA and also XMGRACE and Pymol 1.8. As a result, we determined that the EBNA1-50nt/HASDI complex was stable throughout the whole simulation trajectory. HASDI, due to the presence of a linker modified depending on a specific pair of nitrogenous bases, formed an average of 32 hydrogen bonds with a sequence of 16 nucleotide pairs. Phenazine rings were stably intercalated every 2 base pairs. The root-mean-square deviation of HASDI in such a complex fluctuated around the value of 6.5 Å and had no tendency to increase. The calculated value of the binding free energy was - 235.3 ± 7.77 kcal/mol. The KCNH2-50nt/HASDI complex, as an example of the intercalation of the designed structure into a random part of the human genome, maintained the stability of its position at a level comparable to the EBNA1-50nt/HASDI complex. The phenazine rings were constantly intercalated in their original positions, and the root-mean-square deviation fluctuated around one value, although it had a tendency to chaotic changes. At the same time, this complex was characterized by 17-19 hydrogen bonds, on average, and the binding free energy was - 193.47 ± 14.09 kcal/mol. Moreover, the DNA duplex had local single-nucleotide melting in the region of the 4th linker. According to a significant decrease in the number of hydrogen bonds, a decrease in energy gain, as well as a decrease in the stability of the DNA duplex characteristic of the KCNH2-50nt/HASDI complex compared to the target EBNA1-50nt/HASDI complex, the molecule we designed can be considered a potentially selective DNA polyintercalating agent capable of relatively accurate recognition of 16 base pairs.
癌症作为一种获得性遗传疾病，其基础是基因组本身和转录过程的变化。因此，在 DNA 水平上寻找和设计能够有效和选择性地抗癌的药物是有意义的。在这项研究中，我们使用基于分子动力学模拟的迭代方法来设计一种高度选择性的 DNA 插入剂，称为 HASDI。为了确认其对 DNA 的选择性亲和力，我们进行了两个模拟实验：HASDI 与 EBNA1 基因的 DNA 片段（靶向该基因的 16 个核苷酸对）的复合物，以及 HASDI 与 KCNH2 基因的随机 DNA 片段的复合物。分子动力学模拟在 GROMACS 2019 包中进行。结合能通过 gmx_MMPBSA 1.5.2 计算。进一步的分析使用 GROMACS 的内置实用程序 gmx_MMPBSA 和 XMGRACE 和 Pymol 1.8 进行。结果表明，整个模拟轨迹中 EBNA1-50nt/HASDI 复合物是稳定的。由于存在根据特定的碱基对修饰的连接子，HASDI 与 16 个核苷酸对的序列形成了平均 32 个氢键。苯并嗪环每 2 个碱基稳定地插入。在这样的复合物中，HASDI 的均方根偏差波动在 6.5Å 左右，没有增加的趋势。结合自由能的计算值为-235.3±7.77 kcal/mol。作为设计结构插入人类基因组随机部分的插入实例，KCNH2-50nt/HASDI 复合物保持其位置的稳定性与 EBNA1-50nt/HASDI 复合物相当。苯并嗪环不断地在其原始位置插入，均方根偏差在一个值附近波动，尽管它有向混沌变化的趋势。同时，该复合物的平均氢键数为 17-19 个，结合自由能为-193.47±14.09 kcal/mol。此外，DNA 双链在第 4 个连接子区域发生局部单核苷酸熔解。与靶标 EBNA1-50nt/HASDI 复合物相比，HASDI 设计的分子与 KCNH2-50nt/HASDI 复合物相比，氢键数量显著减少，能量增益减少，以及 DNA 双链的稳定性降低，表明该分子可以被认为是一种潜在的选择性 DNA 多插入剂，能够相对准确地识别 16 个碱基对。
