Computational protocol: Design, synthesis, docking study and cytotoxic activity evaluation of some novel letrozole analogs

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Protocol publication

[…] Marvin was used for chemical drawing, displaying and characterizing chemical structures, calculator plugins were used for structure property prediction and calculation, (version: Marvin 6.0.3, 2013, ChemAxon scientific package, [...] Docking studies for selected compounds were performed using Autodock Vina (ver. 1.1.1) []. The crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione (code ID: 3EQM, resolution [Å]: 2.90) was retrieved from protein data bank [-]. Crystal structure was cleaned from Co-crystallized ligand and water molecules and the protein was converted to pdbqt format using Autodock Tools (1.5.4) []. 2Dstructures of ligands converted to 3D in pdbqt format by Openbabel (ver. 2.3.1) []. The docking parameters were set on vina docking parameter as follow: center_x = 85.027; center_y = 54.737; center_z = 46.428; size_x =50; size_y =50; size_z =50;. The other parameters were left as default for the program. Finally, the conformation for the best free energy of binding was selected for analyzing the interactions between the macromolecule and selected inhibitors. 3D models of ligand-receptor interactions are generated by using the Autodock Tools (1.5.4) []. […]

Pipeline specifications

Software tools Marvin, Calculator Plugins, AutoDock Vina, Open Babel, AutoDock
Applications Drug design, Protein interaction analysis
Organisms Homo sapiens
Diseases Breast Neoplasms, Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Etoposide