4.4. Molecular Docking Using AutoDock Vina 4.2

AutoDock tool [75] was used to perform the molecular docking to understand how the mutation at the 835th position interacts with type-I and type-II AML inhibitors. The polar hydrogens, added in the native and mutant FLT3, ahead of docking. We allocated the partial atomic charges to the native and mutant FLT3 proteins using AutoDock Vina 4.2 [76]. The non-polar and polar hydrogen atoms were fused. We applied Gasteiger charges to 10 selected AML inhibitors. The non-polar hydrogens joined and calculated rotatable bonds based on the drug molecule’s nature. The change in free energy (δG) caused by the loss of a torsional degree of freedom upon binding was calculated using TORSDOF. We constructed the peptide backbone bonds in the native and mutant FLT3 proteins. It formed rotatable bonds between selected atoms and all active bonds. The grid maps endorsed inhibitor (ligand) binding and spacing was adjusted to 0.9. We increased the grid size to 31 × 28 × 25 points. For docking, AutoDock Vina employs interaction maps. Before the docking run, Auto Grid calculated these maps. We measured the interaction energy between each ligand atom and the receptor for the entire binding site, which was discretized using a grid, for each ligand atom type. A probe was positioned at each grid point, and it embedded the protein in a 3D grid. At each grid point, the protein’s interaction energy was allocated, and the affinity for each ligand was determined.

Automated docking software AutoDock Vina [76] 4.2 was used to evaluate the binding affinity of 10 AML inhibitors (Crenolanib, FF-10101, Gilteritinib, KW-2449, PLX3397, Ponatinib, Quizartinib, Sorafenib, Sunitinib, and Tandutinib) with native and mutant (D835A, D835E, D835F, D835G, D835H, D835I, D835N, D835V, and D835Y) FLT3 proteins. Using empirical-free energy functions and the Lamarckian genetic algorithm, the docking energy of all inhibitors (ligand molecules) was calculated. Based on different electrostatic, Vander Waal, hydrogen bonding, and desolvation effects, these tools measure the binding-free energy (δG). For each docking run, the docking precision was set to “normal precision” and the ligand-docking mode was set to “flexible.” The AutoDock energy measurements were used to assess the stability of each docked pose. Pymol [74] uses to visualize the interaction residues of native and mutant FLT3 proteins with AML inhibitors.