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首页> 外文期刊>Applied Biological Chemistry >An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer
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An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer

机译：使用DFT方法和AIM分析的DNA碱基和芳族药物片段之间非共价堆叠相互作用的深入研究：适系，结合能和电荷转移

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摘要

This work is aimed at providing physical insights about the pi-pi stacking interactions of some popular drug fragments (DF) including indole (I), benzothiophene (Bt), benzofuran (Bf) and guanine (G), adenine (A), A-thymine (AT), G-cytosine (GC) base pairs using density functional theory (DFT), the atoms in molecule (AIM) theory, and natural bond orbital (NBO) analysis. Several stable conformers of present molecules and complexes were optimized at the M062X/6-311++G(d,p) level of theory. The result shows that the IG1 (see the notation below) and IA6 have maximum interaction energy in all of the two G-based and A-based conformers; and order of the adsorption strength is IG1 BtG6 BfG1 for G-based complexes and IA6 BtA6 BfG6 for A-based complexes. For the base pair-drug fragment complexes, the order of interaction energy was found according to IAT4 BtAT3 BfAT4 and IGC3 BtGC2 BfGC2, for AT and GC base pairs, respectively. Furthermore, our results show that stacking interaction leads to an increase and decrease in hydrogen bond length that involved in the nucleic base-drug fragment interactions. DFT-calculated interaction energies for all present conformers were found to be in a good agreement with the bond critical points data from AIM analysis. In contrast, no reasonable linear correlation was observed between NBO analysis and stability of the all studied conformers. Finally, in order to verify the DFT and AIM results, docking calculations were performed using AutoDock software. According to the binding energy of drug-DNA from AutoDock calculations, the D2-Bt and D1-Bf are the most and the least stable structures, respectively.
机译：这项工作旨在提供关于一些流行药物片段（DF）的PI-PI堆叠相互作用的身体见解，包括吲哚（I），苯并噻吩（BT），苯并呋喃（BF）和鸟嘌呤（G），腺嘌呤（A），a使用密度官能理论（DFT），分子（AIM）理论的原子和天然键（NBO）分析，碱基（AT），G-胞嘧啶（GC）碱基对。在M062X / 6-311 ++ G（D，P）理论水平上优化了几种稳定的当前分子和复合物的稳定蜂胶。结果表明，IG1（参见下面的符号）和IA6在所有基于G的基于G和基础上具有最大的相互作用能量;和吸附强度的顺序是Ig1＆ BTG6＆GT; BFG1为G基复合物和IA6＆GT; BTA6＆GT; BFG6用于基于型复合物。对于碱基对药物片段复合物，根据IAT4＆GT发现相互作用能量的顺序。 BTAT3＆GT; BFAT4和IGC3＆GT; BTGC2＆GT; BFGC2，用于AT和GC碱基对。此外，我们的结果表明，堆叠相互作用导致官能团基础药物片段相互作用的氢键长度的增加和降低。发现所有当前构造者的DFT计算的相互作用能量与AIM分析的债券关键点数据吻合良好。相反，在NBO分析和所有研究符合特的稳定性之间没有观察到合理的线性相关性。最后，为了验证DFT和AIM结果，使用Autodock软件执行对接计算。根据来自Autodock计算的药物-DNA的结合能量，D2-BT和D1-BF分别是最稳定的结构。

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