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基于从头算分子动力学模拟的α-羟基脲水合作用

Hydration of -Hydroxyurea from Ab Initio Molecular Dynamics Simulations.

作者信息

Balicki Mateusz, Śmiechowski Maciej

机构信息

Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.

出版信息

Molecules. 2024 May 22;29(11):2435. doi: 10.3390/molecules29112435.


DOI:10.3390/molecules29112435
PMID:38893311
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11173572/
Abstract

-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the and conformers spectrally affect, on average, 3.4 and 2.5 of the closest HO molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the conformer of HU is found here to be more stable by 17.4 kJ·mol than the conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in -HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its -alkyl-substituted derivatives, -hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

摘要

羟基脲(HU)是一种重要的化疗药物,在镰状细胞病和β地中海贫血等病症中用作一线治疗药物。尽管羟基脲在血浆或细胞质中作为水合分子的性质对于其与核糖核苷酸还原酶(其分子靶点)的自由基催化位点的结合可能至关重要,但迄今为止,对其研究甚少。这项工作的目的是全面探索羟基脲的水合作用。该课题通过从头算分子动力学(AIMD)模拟进行研究,该模拟采用系统电子密度的第一性原理表示。这使得能够计算红外光谱,该光谱可以在空间上进行分解,以更好地捕捉溶质 - 溶剂相互作用的光谱特征。研究发现该分子水合作用强烈,并且与第一壳层水分子紧密结合。对羟基脲的距离相关光谱的分析表明,在半径分别为3.7 Å和3.5 Å的球体中,顺式和反式构象异构体平均分别对最接近的3.4个和2.5个HO分子产生光谱影响。对应于这些截止半径的距离相关光谱显示,在水的OH伸缩振动带的红移部分吸光度增加,表明溶剂氢键网络的局部增强。径向分辨红外光谱还表明,羟基脲很容易融入水的氢键网络并对该网络具有增强作用。基于AIMD方法的元动力学模拟提供了溶液中羟基脲构象平衡的图景。与先前在气相中对孤立羟基脲分子的研究相反,在这里发现羟基脲的反式构象异构体比顺式构象异构体稳定17.4 kJ·mol,这表明水合作用在决定溶质的构象稳定性方面起着关键作用。羟基脲中OH基团旋转的势能面表明,在水中的羟基脲中不存在分子内氢键,这与气相中的孤立溶质形成鲜明对比。相反,羟基的优选取向垂直于溶质的分子平面。鉴于已知尿素及其N - 烷基取代衍生物的离液序列高的效应,羟基脲是一种独特的尿素衍生物,表现出附近水的促溶有序。该性质对于其与核糖核苷酸还原酶催化位点的结合并伴随水分子的置换可能至关重要。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/6c0d1165ae09/molecules-29-02435-g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/5b70ea2bbee0/molecules-29-02435-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/a2cfc9eb15d3/molecules-29-02435-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/4b0bf591f886/molecules-29-02435-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/5cb6249190d6/molecules-29-02435-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/14849ad2ae61/molecules-29-02435-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/0bd7f77bc4fd/molecules-29-02435-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/207685b4b7d7/molecules-29-02435-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/687fc73bf09c/molecules-29-02435-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/eeb6cd587e9b/molecules-29-02435-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/a33e75954dbc/molecules-29-02435-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/0b3496666697/molecules-29-02435-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/3c61b195793d/molecules-29-02435-g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/6c0d1165ae09/molecules-29-02435-g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/5b70ea2bbee0/molecules-29-02435-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/a2cfc9eb15d3/molecules-29-02435-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/4b0bf591f886/molecules-29-02435-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/5cb6249190d6/molecules-29-02435-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/14849ad2ae61/molecules-29-02435-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/0bd7f77bc4fd/molecules-29-02435-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/207685b4b7d7/molecules-29-02435-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/687fc73bf09c/molecules-29-02435-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/eeb6cd587e9b/molecules-29-02435-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/a33e75954dbc/molecules-29-02435-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/0b3496666697/molecules-29-02435-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/3c61b195793d/molecules-29-02435-g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f3/11173572/6c0d1165ae09/molecules-29-02435-g013.jpg

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