The Molecular Dynamics Effects of Rutin on CDKS 2, 4 and 6: In Silico Modelling and Molecular Dynamics

Eurasian Journal of Medicine and Oncology Pub Date : 2022-01-01 DOI:10.14744/ejmo.2022.39682

J. S. Chaleshtori

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Abstract

Objectives: This simulated study has mechanistically evaluated the molecular dynamics effects of rutin on CDKs 2, 4, and 6 in cell cycling. Methods: Protein Data Bank (http://www.rcsb.org) was used to obtain the PDB file of CDK 2, 4, and 6. After simulation of CDKs in Gromacs software, AutoDock 4.2 was used to run 200 stages of molecular docking of CDKs in the presence of the rutin. CDK 2, 4, and 6 were simulated in the presence of rutin after docking. Results: Rutin had the highest tendency to bind the CDK-2 and CDK-6 via binding 16 and 18 residues in the binding site with hydrogen and hydrophobic bonds (respectively). Also, they had the highest amount of binding energy released. Rutin decreased total energy in CDKs and reduced the radius of gyration in CDK-2 and CDK-6 after docking. The secondary coil structure increased in CDK-2 and decreased in CDK-4 and 6. Conclusion: Conformational changes in CDK2 and 6 via rutin can inhibit the activity of these proteins and subsequent-ly arrest the cell cycle in phases G1, S, and G2, which can lead the damaged cell to cell repair or Apoptosis. Abstract Article:

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芦丁对CDKS 2、4和6的分子动力学影响:硅模拟和分子动力学

目的:模拟研究芦丁对细胞周期中cdk2、4和6的分子动力学影响。方法:利用蛋白质数据库(http://www.rcsb.org)获取cdk2、4、6的PDB文件。在Gromacs软件中模拟CDKs后，使用AutoDock 4.2在芦丁存在的情况下运行200个阶段的CDKs分子对接。对接后，在芦丁存在的情况下模拟cdk2、4和6。结果:芦丁对CDK-2和CDK-6的结合倾向最高，分别通过氢键和疏水键结合结合位点的16个和18个残基。而且，它们释放的结合能最多。芦丁降低了cdk的总能量，减小了对接后CDK-2和CDK-6的旋转半径。次级线圈结构在CDK-2中增加，在CDK-4和6中减少。结论:通过芦丁改变CDK2和6的构象可以抑制这些蛋白的活性，从而使细胞周期停滞在G1、S和G2期，从而导致受损细胞修复或凋亡。摘要文章:

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Eurasian Journal of Medicine and Oncology

CiteScore

5.60

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