Atomistic and molecular level portrayal of DNA – 1,8-napthalimide interaction

IF 1.9 4区化学 Q4 CHEMISTRY, PHYSICAL Molecular Simulation Pub Date : 2023-09-07 DOI:10.1080/08927022.2023.2249122

R. Radhika, R. Shankar

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Abstract

ABSTRACT The present work reports the physicochemical interaction between DNA and 1,8-napthalimide drugs to enlighten the field of drug discovery. Molecular dynamic studies of 1,8-napthalimide interacted DNA revealed distortions and destabilisation of the DNA. Among the drugs (Amonafide Azonafide and NNM-25), NNM-25 is found to have a strong interaction with DNA in gas and water phases by using the ONIOM method by investigating deformation and interaction energies. The reason for the higher interaction energy is attributed to the higher deformation of DNA during the interaction with NNM-25. Furthermore, the complex is investigated by the quantum chemical method to find the detailed observation of the direct Interaction of the 1,8-napthalimides with the DNA base pairs. NBO analysis is done to understand the charge transfer mechanism of 1,8-napthalimides’ interacted DNA and also it is observed that highly stabilised complexes are found to have the highest interaction energies. The density functional theory is used to calculate the chemical reactivity and site selectivity of the molecular system to explore the results that may call for further experimental studies.

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DNA - 1,8-萘酰亚胺相互作用的原子和分子水平表征

摘要本文报道了DNA与1,8-萘酰亚胺类药物之间的物理化学相互作用，以期对药物发现领域有所启发。分子动力学研究1,8-萘酰亚胺相互作用的DNA揭示了DNA的扭曲和不稳定。在这些药物(Amonafide Azonafide和NNM-25)中，通过对变形和相互作用能的研究，利用ONIOM方法发现NNM-25在气相和水相与DNA有很强的相互作用。相互作用能较高的原因是DNA在与NNM-25相互作用过程中变形较大。此外，利用量子化学方法对配合物进行了研究，详细观察了1,8-萘酰亚胺与DNA碱基对的直接相互作用。通过NBO分析了解1,8-萘酰亚胺与DNA相互作用的电荷转移机制，并观察到高度稳定的配合物具有最高的相互作用能。利用密度泛函理论计算了分子体系的化学反应性和位点选择性，以探索可能需要进一步实验研究的结果。

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来源期刊

Molecular Simulation 化学-物理：原子、分子和化学物理

CiteScore

3.80

自引率

9.50%

发文量

128

审稿时长

3.1 months

期刊介绍： Molecular Simulation covers all aspects of research related to, or of importance to, molecular modelling and simulation. Molecular Simulation brings together the most significant papers concerned with applications of simulation methods, and original contributions to the development of simulation methodology from biology, biochemistry, chemistry, engineering, materials science, medicine and physics. The aim is to provide a forum in which cross fertilization between application areas, methodologies, disciplines, as well as academic and industrial researchers can take place and new developments can be encouraged. Molecular Simulation is of interest to all researchers using or developing simulation methods based on statistical mechanics/quantum mechanics. This includes molecular dynamics (MD, AIMD), Monte Carlo, ab initio methods related to simulation, multiscale and coarse graining methods.