2.3 Molecular modelling and docking studies
The experimental structure of the open hERG channel (PDB ID: 5va2) was selected as a receptor for molecular docking studies. The structure was prepared for docking with Protein Preparation Wizard on default settings including modelling of missing loops using Prime. The centroid of residues Y652 from every subunit was defined as the centre of the docking binding site. HCQ and AZM structures were obtained from PubChem and prepared for docking using LigPrep. The recently proposed Induced Fit Docking (IFD) protocol was used (Negami, Araki, Okuno & Terada, 2019). Protein Preparation Wizard, LigPrep, Prime, and IFD were executed as parts of the Maestro software suite 2018-4 (Schrödinger, LLC, NY).