Computational protocol: In vivo evaluation of cetuximab-conjugated poly(γ-glutamic acid)-docetaxel nanomedicines in EGFR-overexpressing gastric cancer xenografts

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Protocol publication

[…] Molecular docking studies of γ-PGA Nps and DOCT drug interaction studies were analyzed by AutoDock Vina software running on the Linux platform by calculating the grid maps, by adapting to the nature of the input systems, cluster and rank of different docked poses of the ligand in a straightforward manner. Binding free energy (BE) between hydrophobic drug DOCT and γ-PGA Nps was computed and visualized using PyMol software. Furthermore, the crystal structure of the CET MAb with PDB code 1YY8 was used for docking studies with the DOCT-γ-PGA Np complex systems to obtain the BE. The resulting CET MAb-conjugated DOCT-γ-PGA Np complex system was further analyzed by PyMol software.AutoDock Tools assigned all of the atoms, and Gasteiger charges were added to prepare γ-PGA and chitosan polymer structure, which was further loaded in the AutoDock 4.0 program and saved in .pdbqt format. AutoDock Vina software performed blind docking by loading the system in the workspace and grid panel; the grid box option was opted, and then grid dimensions and spacing were set to completely occupy the entire γ-PGA Np surface. The γ-PGA Np surface was searched for possible drug binding to obtain its stable complex systems. Furthermore, using the same docking protocol, CET MAb was docked to the entire surface of the DOCT-γ-PGA Np complexes to obtain the antibody affinity toward the Np complex system. […]

Pipeline specifications

Software tools AutoDock Vina, PyMOL, AutoDock
Application Protein interaction analysis
Organisms Homo sapiens, Mus musculus
Diseases Neoplasms, Stomach Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Ethyldimethylaminopropyl Carbodiimide