Computational protocol: Niclosamide inhibition of STAT3 synergizes with erlotinib in human colon cancer

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Protocol publication

[…] As one of the most widely used computational approaches for structure-based drug design, molecular docking study was used to predict the binding pose of compound in STAT3 SH2-binding site by using the software AutoDock (version 4.2.6). The crystallographic coordinate for human STAT3 SH2 (Protein Data Bank [PDB] ID: 1BG1) was obtained from the PDB. Prior to docking, protein structures were prepared by removing water molecules and other ligands using PyMol software. A grid box size of 60×60×60 dimensions with a spacing of 0.375 Å between the grid points was implemented and covered almost the entire SH2-binding site. The grid parameter files were created setting up the map files directly. The Lamarckian genetic algorithm was applied to deal with the interactions of protein and inhibitors. The number of individuals in population was set to 300, and trials of 100 dockings and maximum number of energy evaluations were set as default along with other settings. AutoDockTools version 1.5.6 and PyMol were used to analyze the docking results. […]

Pipeline specifications

Software tools AutoDock, PyMOL
Applications Drug design, Protein interaction analysis
Organisms Homo sapiens
Diseases Cestode Infections, Colonic Neoplasms
Chemicals Niclosamide