Molecular docking

Molecular docking studies were performed using the software AutoDock Vina (28) and visualized using UCSF Chimera 1.15. The NMR structure of human IAPP was assessed from the Protein Data Bank (PDB) under the reference 2L86. This structure was selected since it represents IAPP in its natively amidated form at physiological pH (29). For simplicity of analysis, only the first conformer in the NMR ensemble was used for docking studies. The ligand structures were obtained from the PubChem database (30). All the structures were minimized and prepared for docking using the feature Dock Prep by adding hydrogens and assigning partial charges. The PDBQT files needed for docking were obtained using the python scripts included in the AutoDock MMGLTools software suit. The search space was defined as 31 x 35 x 20 ų, a minimal rectangular parallelepiped enclosing the full polypeptide chain, to allow a “blind” docking simulation. The ligand-receptor affinity was compared through the AutoDock Vina score, which calculates the affinity of protein-ligand binding (31). Each docking solution was further optimized by manual fitting in COOT (32), followed by structure idealization with REFMAC5 (33), and subsequent analysis in PyMol (Version 2.4.1, Schrödinger, LLC). All structural figures were drawn with PyMol.

A refinement of this initial docking procedure was performed using a smaller docking box with 15x18x15 ų and centered in the central cavity of the 2L86 structure. Two other similar trials were performed by increasing the exhaustiveness conformational and space searching parameter to 80 or by using the Vinardo scoring function (34).

Another independent docking trial was performed using MOE v2020.0901 (Molecular Operating Environment V2020.0901, Chemical Computing Group Inc, 2022) using default parameters (triangle matcher placement, best 30 ranked with London dG scoring function and then re-scored with the GBVI/WSA dG function) and the docking site defined by the top ranked position of the epigallocatechin 3-gallate molecule (EGCG; the largest one).