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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >In Silico Studies toward Understanding the Interactions of DNA Base Pairs with Protonated Linear/Cyclic Diamines
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In Silico Studies toward Understanding the Interactions of DNA Base Pairs with Protonated Linear/Cyclic Diamines

机译：在计算机模拟研究中了解DNA碱基对与质子化线性/环状二胺的相互作用

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摘要

Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc- pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.
机译：质子化的氨基在自然界无处不在，在化学和生物学领域很重要。为了寻找有效的多胺类似物，我们对一些简单的环状且受约束的质子化二胺与DNA碱基对的相互作用进行了DFT计算，并将结果与​​模拟线性生物胺如精胺的线性二胺的相互作用进行了比较。 。相互作用主要受配体与DNA碱基对之间的强氢键控制。 DFT计算表明，与精胺报告的其他可能的相互作用相比，与线性二胺的主要沟槽N7相互作用（GC碱基对）在能量上更受青睐。与线性二胺相比，环状二胺与AT和GC碱基对的N7位点表现出更好的相互作用。对于环系统，为质子化胺氢计算的净原子电荷比对于线性二胺更高，从而导致与DNA碱基对的结合亲和力更好。使用MP2 / aug-cc-pVDZ理论水平预测了环状二胺的稳定构象。这些环状系统中质子化的二胺基团的位置对于与DNA碱基对有效结合至关重要。 DFT计算的结果表明，二季铵（ee）1,2-环己二胺（CHDA）是有前途的候选物，可作为生物多胺的多胺类似物。使用显性水分子进行代表性分子与DNA碱基对相互作用的分子动力学模拟，以检查溶剂分子对此类相互作用的影响。

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