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

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 subsequently arrest the cell cycle in phases G1, S, and G2, which can lead the damaged cell to cell repair or Apoptosis.