4.4. Molecular Docking

In this work, the Genetic Optimization of Ligand Docking (GOLD v5.2.2) was considered for the molecular docking calculation [39]. The crystal structure of the human SHP2 receptor, bound with known inhibitor SHP099 (PDB ID: 6CMR), was downloaded from the Protein Data Bank (http://www.rcsb.org/) accessed on 20 December 2022. Before performing molecular docking studies, the protein was prepared, all missing atoms were added, and bond orders were corrected using the Clean Protein module, available in DS [40]. The energy minimization of the protein was conducted using a CHARMm27 force field. The binding site of the SHP2 receptor was specified around the bound allosteric inhibitor SHP099. The molecular docking studies using the GOLD Genetic Algorithm (GA) generated a maximum of ten poses for each drug-like molecule subjected to it. Goldscore and Chemscore are the default scoring functions to select potential SHP2 binders. The bound inhibitor SHP099 (REF) was considered the reference criterion for analyzing the docking results. Compounds that displayed better docking scores and optimal binding modes with the mentioned key residues were used for SHP2 inhibition. The results were visualized in DS and compared with the reference inhibitor for further study.