A structure-differential binding method for elucidating the interactions between flavonoids and cytochrome-c by ESI-MS and molecular docking.
A structure-differential binding method for elucidating the interactions between flavonoids and cytochrome-c by ESI-MS and molecular docking.
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DOI：
10.1016/j.talanta.2013.05.061
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发表时间：
2013-11
期刊：
影响因子：
6.1
通讯作者：
Xian Wang;Yingzhi Liu;Haidong Wang
中科院分区：
文献类型：
--
作者：
Xian Wang;Yingzhi Liu;Haidong Wang
药物分子和蛋白质之间的非共价相互作用的研究对于理解蛋白质功能的分子机制至关重要，并为新型治疗剂的设计提供了基础。电喷雾电离质谱（ESI-MS）如今已成为分析非共价蛋白质复合物的流行工具，但它通常难以确定相互作用位点和结合机制。在这项工作中，开发了一种新的结构差异结合（SDB）方法，结合ESI-MS和分子对接（MD）技术（SDB-ESIMS-MD），并将其应用于非共价蛋白质-小药物分子复合物中的结合相互作用的研究，以表征结合位点和结合模式。利用这种开发的方法，对类黄酮和类黄酮苷配体以及细胞色素-c (Cyt-c) 的蛋白质复合物进行了详细研究。 ESI-MS用于测定类黄酮-Cyt-c复合物的相对结合亲和力和解离常数，并测量配体结构修饰时蛋白质复合物稳定性的变化，以识别有效结合的官能团。分子对接模拟通过提供每个复合物的蛋白质-配体相互作用概况并显示每个相互作用的结合模式来补充 ESI-MS 实验。这种SDB-ESIMS-MD方法可应用于广泛的蛋白质-药物相互作用，并用于指导药物分子与靶向生物大分子之间结构结合关系的进一步研究。
The study of noncovalent interactions between pharmaceutical molecules and proteins is essential for understanding molecular mechanisms of protein function, and provides foundations forde novotherapeutic agent design. Electrospray ionization mass spectrometry (ESI-MS) has nowadays become a popular tool for analyzing the noncovalent protein complexes, however it usually has difficulty in determining the interaction sites and binding mechanisms. In this work, a new structure-differential binding (SDB) method, combined with ESI-MS and molecular docking (MD) techniques (SDB–ESIMS–MD), was developed and applied to a study of the binding interactions in noncovalent protein–small drug molecule complexes for the characterization of binding sites and binding modes. Using this developed method, protein complexes of flavonoid and flavonoid glycoside ligands and cytochrome-c (Cyt-c) were studied in detail. ESI-MS was used to determine the relative binding affinities and dissociation constants of flavonoid–Cyt-c complexes, and to measure the changes in the stability of the protein complexes with the structural modifications of the ligands for identifying effective binding functional groups. Molecular docking simulations complemented ESI-MS experiments by providing the protein–ligand interaction profile of each complex and displaying the binding mode for each interaction. This SDB–ESIMS–MD method can be applied to a broad range of protein–drug interactions and used to guide further research in the study of structure–binding relationship between drug molecules and targeted biomacromolecules.