Protein preparation tool

Molecular docking was performed using the Schrodinger software (Schrödinger, Inc., New York, NY, USA). The 3D structure of p53 were retrieved from the protein data bank (PDB ID: 1TSR). In LM-p53 covalent docking, the protein p53 was prepared by Protein Preparation Tool in Schrodinger including optimized hydrogen bond network at pH 7.0 with PROKA tool. The ligand LM was prepared by Avogadro Tool to obtain the structural optimization.

Molecular docking was performed using the Schrodinger software (Schrödinger, Inc., New York, NY, USA). The 3D structure of Trx1 and TrxR were retrieved from the protein data bank (PDB ID: 4PUF_C) and (PDB ID: 2zzb). In LH-TrxR1 covalent docking, the protein TrxR was prepared by Protein Preparation Tool in Schrodinger including optimized hydrogen bond network at pH 7.0 with PROKA tool, restrained minimization in OPLS3 force field with converge heavy atoms to 0.3 Å. The energy optimization of ligand LH was prepared by Ligand Preparation Tool with OPLS3 force field to produce low energy conformation. Covalent docking was performed around the reactive residue Cys497 and Cys498 within 25 Å. In LH-Trx1 covalent docking, the preparation of the protein Trx1 and LH was performed as described above except the restrained minimization was in OPLS-2005 force field before covalent docking was performed around the reactive residue Cys32 and Cys35 within 30 Å.

The homology structure of human active MOR and the crystal structures of active DOR (PDB code: 6PT3), active KOR (PDB code: 6B73), inactive MOR (4DKL), inactive DOR (4N6H) and inactive KOR (4DJH) were imported into the Schrödinger software package. The protein structures were prepared with the Protein Preparation Tool in the Schrödinger package, and Asn, Gln and His residues were automatically checked for protonated states. Hydrogen atoms were added into the three structures at the physiology pH environment by the PROPKA tool in Maestro with an optimized hydrogen bond network.

The four selected carbohydrate‐digesting proteins for this study with their co‐crystallized ligands were the human pancreatic α‐amylase in complex with montbretin A (Pdb ID:4w93), human lysosomal acid‐α‐glucosidase, GAA, in complex with acarbose (Pdb ID:5nn8), the N‐terminal sucrase‐isomaltase with kotalanol (Pdb ID:3lpp), and the C‐terminal subunit of human maltase‐glucoamylase in complex with acarbose (Pdb ID:3top) whose crystallographic data were obtained from the Protein Data Bank (PDB) website (https://www.rcsb.org/).
The Schrödinger platform was employed to prepare the chosen proteins via Protein Preparation tool in order to add hydrogen and correct problems like incomplete loops or side chains, flipped residues or unclear protonation states. Forcefield of OPLS2005 was applied for energy minimization after optimization of the preprocessed protein; moreover, ionization states were selected as 7.4 pH and water molecules were kept based on their important role in interactions (AbdelRazek et al., 2023 (link); Torky et al., 2021 (link)).