研究动态
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抑制自噬以对抗癌症的评估:(钒配合物)-蛋白相互作用、参数化和新力场的验证。

Evaluation of autophagy inhibition to combat cancer: (vanadium complex)-protein interactions, parameterization, and validation of a new force field.

发表日期:2023 Mar 30
作者: Taináh M R Santos, Camila A Tavares, Ander F Pereira, Elaine F F da Cunha, Teodorico C Ramalho
来源: Protein & Cell

摘要:

自噬作用因其与化疗过程相比显著优势而引起了科学界的关注。其中之一的优势是直接作用于癌细胞,避免了可能的副作用,而化疗则会影响身体内的健康细胞,导致患者生活质量大大降低。因此,人们知道钒配合物(VC)[VO(oda)(phen)]已被证明对胰腺癌细胞的自噬过程具有抑制作用。基于此,分子动力学(MD)模拟可被视为研究金属配合物与其生物靶点相互作用的良好策略。但是,此类模拟强烈依赖于合适的力场(FF)选择。因此,本文提出了开发AMBER FF参数用于VC的建议,其起始点为通过B3LYP/def2-TZVP水平的DFT计算加上钒原子的ECP获得的最小能量结构。在真空中进行了一次MD模拟以验证开发的FF。从结构分析中,得到了满意的VC键长和角度值,其中与实验数据和量子参考之间存在良好的一致性。RMSD分析显示平均值仅为0.3%。最后,我们进行了VC与PI3K之间的对接和MD(120ns)模拟,该过程采用明显的溶剂。总的来说,我们的发现鼓励对具有显著生物应用的金属配合物进行新的参数化,并有助于阐明自噬复杂过程。©2023年。作者,独家许可Springer-Verlag GmbH Germany出版,为Springer Nature的一部分。
Autophagy has drawn attention from the scientific community, mainly because of its significant advantages over chemotherapeutic processes. One of these advantages is its direct action on cancer cells, avoiding possible side effects, unlike chemotherapy, which reaches tumor cells and affects healthy cells in the body, leading to a great loss in the quality of life of patients. In this way, it is known that vanadium complex (VC) [VO(oda)(phen)] has proven inhibition effect on autophagy process in pancreatic cancer cells. Keeping that in mind, molecular dynamics (MD) simulations can be considered excellent strategies to investigate the interaction of metal complexes and their biological targets. However, simulations of this type are strongly dependent on the appropriate choice of force field (FF). Therefore, this work proposes the development of AMBER FF parameters for VC, having a minimum energy structure as a starting point, obtained through DFT calculations with B3LYP/def2-TZVP level of theory plus ECP for the vanadium atom. An MD simulation in vacuum was performed to validate the developed FF. From the structural analyses, satisfying values of VC bond lengths and angles were obtained, where a good agreement with the experimental data and the quantum reference was found. The RMSD analysis showed an average of only 0.3%. Finally, we performed docking and MD (120 ns) simulations with explicit solvent between VC and PI3K. Overall, our findings encourage new parameterizations of metal complexes with significant biological applications, as well as allow to contribute to the elucidation of the complex process of autophagy.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.