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).