A Computational Study on the Blocking Ability of Selected Commercially Available Anticancer Drugs and Their Hypothetic Derivatives on the CCR5

Assay and Drug Development Technologies
Rahim Ghadari, Yousef Mohammadzadeh

Abstract

Computational studies were done on the complexes between some commercially available anticancer drugs and their hypothetic derivatives and the CCR5 protein. At first step, the docking studies were done to obtain the best ligand that can inhibit the CCR5 protein. Based on the binding energy results obtained from the docking studies, 16 complexes were selected. Molecular dynamic studies were carried out on these structures and then molecular mechanics-generalized Born surface area calculations were done to find the binding energies of the ligands to the CCR5 protein. Based on the investigation of the binding modes of the ligands to the CCR5 protein, the TYR and ALA have more tendency to bind to the ligand moieties. By decomposing of the binding energies, it was found that the van der Waals interactions have the most important role in the binding of ligands to the protein in comparison with the electrostatic and hydrogen bonding interactions. The results of the interaction potential surface map analysis showed that the nitrogen and oxygen atoms have a relatively similar role in the binding of ligands to the CCR5 protein structure.

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Apr 29, 2009·Journal of Computational Chemistry·Garrett M MorrisArthur J Olson
Aug 21, 2012·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Koichi TsutaharaNorio Nonomura
Jan 18, 2013·Archives of Pharmacal Research·Changdev G GadheSeung Joo Cho
Nov 9, 2014·Inflammation·Jing YuanWei Liu
Dec 18, 2014·ACS Medicinal Chemistry Letters·Wieslaw M KazmierskiManon Villeneuve
Sep 11, 2012·Journal of Chemical Theory and Computation·Bill R MillerAdrian E Roitberg
Sep 14, 2016·Molecular and Cellular Endocrinology·Bartosz SłomińskiAgnieszka Brandt
Oct 26, 2016·Bioorganic & Medicinal Chemistry·Christopher K ArnattYan Zhang
Nov 12, 2016·The Journal of Biological Chemistry·Stefanie KarlshøjMette Marie Rosenkilde
Feb 1, 2017·Scandinavian Journal of Gastroenterology·Xiaoyan YeYingqiang Zhong

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Methods Mentioned

BETA
X-ray

Software Mentioned

Visual Molecular Dynamics
AutoDockTools
AmberTools
AutoDock Vina
Gaussian
py
MMPBSA

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