Computational protocol: Uncovering the molecular and physiological processes of anticancer leads binding human serum albumin: A physical insight into drug efficacy

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[…] Molecular docking were carried out on the ligand-HSA system using Autodock4 [], which possesses a free-energy scoring function based on a linear regression analysis. The AMBER force field and a larger set of diverse protein-ligand complexes with known inhibition constants were used in the simulation. The standard error is around 2.5 kcal/mol, which enough discriminates leads with milli-, micro- and nano-molar inhibition constants. The crystal structure of HSA used for molecular docking was retrieved from Protein Data Bank (PDB ID: 1H9Z). And 3D structures of two leads were built by using the web-tools corina3D. Water molecules were removed from the structure and the missing atoms of side chain were added using Swiss PDB Viewer. Autodock tools were used to prepare protein and ligands. HSA and ligands were protonated and Gasteiger partial charges were assigned. A set of grids of 40×40×40 Å with 0.375 Å spacing was calculated around each docking site using AutoGrid. The non-polar hydrogen atoms were merged for the protein and ligands. The part of myristic acid retained as a “plug” in the original position was prepared by using the Chimera package [], adding the hydrogen atoms and the AM1BCC charges []. The docking results from each of the 500 calculations were clustered and ranked on the basis of root-mean square deviation and the binding free energy, respectively. […]

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