Computational protocol: Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions

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Protocol publication

[…] While it is suggested that the binding affinity of a small molecule can be regulated by a phosphorylation site within 12 Å of the site of binding [], there is still a lack of information regarding the occurrences and influence of PTMs near drug-target binding. Therefore, we proposed a method in this study to identify PTM sites involved in drug binding. Figure illustrates the workflow for extracting sites of drug-target binding in protein 3D structure. The entire process can be divided into two steps: 1) the processing of experimentally verified binding sites, and 2) molecular docking of drug binding. In step 1, we collected the structural information of small molecules that have associated keywords such as “drug,” “inhibitor,” “agonist” or “antagonist” and have drug annotations in the DrugBank []. A total of 34,555 PDB structures and 4803 small drug molecules which have DrugBank annotations were obtained. Then, the PoseView [] method was employed to check the binding sites of each drug in the target proteins. PoseView provides a two-dimensional (2D) diagram showing how the drug ligand and the amino acid residues of the target protein may be arranged at the site of interaction. The nature of the interaction is presented in three ways. Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid lines show hydrophobic interactions and green dashed lines represent π-π and π-cation interactions.In step 2, a docking program, iGEMDOCK 2.0 [], was utilized for the computational extraction of drug binding sites. We followed the four sequential steps in iGEMDOCK to perform the drug-target interaction analysis: target and database preparations, molecular docking and post-docking analyses. First, coordinates of the target protein atoms acquired from PDB, the ligand binding area, the atom’s formal charge and the atom types were specified. This procedure allowed iGEMDOCK to read the atom coordinates of a ligand from the prepared ligand database. After the ligand database and the target proteins were determined, docking was analyzed for each ligand using the flexible docking function provided by iGEMDOCK. The final step constituted the re-ranking and sorting of all docked ligand conformations based on an empirical scoring function and an evolutionary approach. The output of the program consisted of details regarding the docking result of each binding site, as well as the atomic characteristics of the target residues that interact with a specific drug ligand by hydrogen bonding (H), electrostatic (E) and van der Waal contact (V). A total of 1991 approved drugs from the DrugBank with 1632 target proteins were investigated by this proposed method. After mapping the experimentally verified PTM sites to the PDB structures, the PTM sites located in a drug binding site were determined to have strong associations with drug-binding, while those in the side chains that were within 12 Å of a drug-binding site were considered to be have relatively weak association with drug binding. […]

Pipeline specifications

Software tools ProteinsPlus, iGEMDOCK
Databases DrugBank
Application Protein interaction analysis
Diseases Protein Deficiency