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采用色散校正密度泛函理论计算和动态分子模拟研究利多卡因对β-环糊精和羟丙基-β-环糊精的构象稳定性。

Dispersion-corrected DFT calculations and dynamic molecular simulations to investigate conformational stability of Lidocaine towards β-CD and HP-β-CD.

作者信息

Kadri Amira, Attoui Yahia Ouassila, Bezzina Belgacem, Khatmi Djamel Eddine, Bouzitouna Amel

机构信息

Laboratory of Applied Organic Chemistry, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar - Annaba University, 12, P.O. Box, 23000, Annaba, Algeria.

Laboratory of Applied Organic Chemistry, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar - Annaba University, 12, P.O. Box, 23000, Annaba, Algeria.

出版信息

J Mol Graph Model. 2025 Jan;134:108910. doi: 10.1016/j.jmgm.2024.108910. Epub 2024 Nov 18.

Abstract

Lidocaine (LDC) is one of the most important local anaesthesia compounds (LAs), designated to treat acute and chronic pain, especially in clinical applications. In the purpose to improve its lower solubility and bioavailability, numerous researches have been conducted to study the exact mode of association between the LDC molecule and cyclodextrins as drug carriers. Although, the reported structural details on LDC/β-CD and LDC/HP-β-CD inclusion complexes remain largely unexplored. The LDC molecule presents different spatial arrangements inside the hydrophobic cavities of the above-mentioned hosts; either the phenyl moiety or the diethylamino part is totally inserted. Hence, in the present work, we attempt to deepen our understanding about conformational preferences on the binding modes of LDC by investigating the quantum mechanical approach results. The PM3 method combined with the pure corrected functional B97D3 revealed the tendency of LDC to enter its diethylamino inside the host, leaving the rest of molecule externally, and consequently form an inclusion complex with HP-β-CD more stable than with the native β-CD by approximately 12 kcal mol. The probability of partial insertion of LDC is further ascertained by MD simulations investigation running for 500 ns. The trajectory analysis of MD process showed that the diethyl amino fragment is accommodated inside the HP-β-CD's cavity for a significant period (82 % of the simulation time), while it is estimated to be 78 % in the case of LDC/β-CD complex. Moreover, the wave function analysis, based on QTAIM, Reduced Density Gradient (RDG) and 2D Fingerprint, illustrated NCIs interactions and sustained the contribution of numerous van der Waals forces and weaker H-bonds interactions in the stability of studied ICs.

摘要

利多卡因(LDC)是最重要的局部麻醉化合物(LAs)之一,用于治疗急性和慢性疼痛,尤其是在临床应用中。为了提高其较低的溶解度和生物利用度,人们进行了大量研究,以探讨LDC分子与作为药物载体的环糊精之间的确切结合方式。尽管如此,关于LDC/β-CD和LDC/HP-β-CD包合物的报道结构细节在很大程度上仍未被探索。LDC分子在上述主体的疏水腔内呈现出不同的空间排列;苯基部分或二乙氨基部分完全插入。因此,在本工作中,我们试图通过研究量子力学方法的结果来加深对LDC结合模式构象偏好的理解。结合纯校正泛函B97D3的PM3方法表明,LDC倾向于将其二乙氨基基团进入主体内部,而分子的其余部分留在外部,因此与HP-β-CD形成的包合物比与天然β-CD形成的包合物更稳定,稳定性约高12千卡/摩尔。通过运行500纳秒的分子动力学(MD)模拟研究进一步确定了LDC部分插入的可能性。MD过程的轨迹分析表明,二乙氨基片段在HP-β-CD腔内存在的时间占比显著(占模拟时间的82%),而在LDC/β-CD复合物的情况下估计为78%。此外,基于量子拓扑原子分子理论(QTAIM)、约化密度梯度(RDG)和二维指纹图谱的波函数分析,阐明了非共价相互作用(NCIs),并支持了众多范德华力和较弱氢键相互作用对所研究包合物稳定性的贡献。

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