Mmff94x force field

The crystal structure
of the carbohydrate recognition domain of the H1 subunit of the ASGPR
was obtained from the RCSB protein data bank (https://www.rcsb.org/) with a code
of 1DV8. The
isomeric SMILES corresponding to the chemical structure of the studied
ligand (carbohydrate); glycyrrhetinic acid was obtained using PubChem.
The corresponding 3D chemical structures were generated using the
builder function of MOE version 2014.0901 (Chemical Computing Group
Inc., Montreal, Canada). Further, energy minimization was performed
using MMFF94x forcefield of the same software.^{34 (link)−36} The docking
analysis was employed using MOE version 2014.0901 (Chemical Computing
Group Inc., Montreal, Canada). The pdb file of the protein nanoparticle
matrix was imported to MOE where the identification of the binding
sites was performed using the MOE’s “Site finder”
tool^{37 (link)} to be ready for docking using the
“triangle matcher” as a placement method. This software
creates dummy atoms around the docking target atoms. These dummy atoms
are considered the docking positions. The software-integrated London
score was utilized for calculating the binding energy scoring value.^{38 (link)−41 (link)}