Docking Analysis of Protein Kinases and the effects of stable water molecules in the ligand binding process
Simon Wieschollek, Leon Obendorf
Kinases are a broad and important group of proteins in the human body. These are macromolecules that allow most important processes to happen by catalyzing specific chemical reactions. Regulating many signaling pathways (allowing cells in our body to communicate) as well es protein expression (how many specific proteins are being created in a cell) and modification of these proteins, kinases can play a role in various diseases. Analyzing the binding process of the kinases and their substrate ATP can give insight into possible medical treatments by finding suitable inhibitors for specific kinases. This is done by docking analysis. A computational in silico method that simulates the ligand structure around the binding site of the protein at hand. This process was carried out and compared to a second approach in which stable water molecules (water molecules that remain in a constant position in solution as predicted by molecular dynamics simulations) were added to the docking process. Additionally, it was attempted to calculate the enthalpic and entropic properties of these waters in order to better evaluate the importance they play in the binding process. Results remain ambivalent as to the aiding role of stable water molecules in docking simulations.