4.6. Docking Study

The Protein Data Bank (PDB) (https://www.rcsb.org/, accessed on 17 December 2021) was used to obtain the crystal structures of topoisomerase I enzymes (PDB IDs: 1T8I, 1K4T, and 1RR8), topoisomerase II enzymes (PDB IDs: 3QX3 and 1ZXM), aurora B kinases (PDB ID: 4C2V), and CDK4 kinases (PDB ID: 2W96) [48]. Avogadro software (Version 1.2.0) was used to optimize the 3D structures of the ligands (farnesol, farnesyl acetone, and eicosane), and these were retrieved from the PubChem database (http://pubchem.ncbi.nlm.nih.gov/, accessed on 17 December 2021) [48]. On 17–18 December 2021, the web-based program CB-DOCK (http://clab.labshare.cn/cb-dock/php/, accessed on 17 December 2021) was used to execute blind docking. The input files were reviewed by CB-Dock after submission, and OpenBabel and MGLTools translated them into pdbqt format. The protein cavities were then predicted using CB-Dock, which also determined the locations and dimensions of the top N (n = 5 by default) cavities. The docking of all the centers, sizes, and pdbqt files was performed using AutoDock Vina. The findings were presented following the computation of N rounds [36]. Using the Discovery Studio program (Version 21.1.0.20298), interaction and visualization profiles were created for the best-docked complexes [36].