Computational protocol: A Novel Resveratrol Based Tubulin Inhibitor Induces Mitotic Arrest and Activates Apoptosis in Cancer Cells

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Protocol publication

[…] 3D structure of SS28 was generated in Discovery studio package using in-built dreiding-like force field (Discovery Studio 4.0. Accelrys, USA). 3D crystal structure of α, β-Tubulin bound with colchicine was retrieved from protein databank (PDB ID: 3UT5, www.rcsb.org/pdb). Molecular docking studies were carried out with Autodock4.2 program. Briefly, SS28 was docked in colchicine binding site keeping the grid centres 9.45, 56.62 and 87.95 for X, Y and Z respectively (npts = 50 for X, Y and Z, spacing = 0.375). Rigid docking was carried out using Lamarckian genetic algorithm (GA run was kept 20 with medium search parameter). Best pose was selected according to lower binding energy and presented in the final image using Pymol. […]

Pipeline specifications

Software tools AutoDock, PyMOL
Application Protein interaction analysis
Organisms Mus musculus
Diseases Carcinoma, Non-Small-Cell Lung, Neoplasms, Leukemia, T-Cell, Drug-Related Side Effects and Adverse Reactions
Chemicals Polyphenols