3.6. Schrödinger Covalent Docking

To study the effect of covalent docking, ligand JAK3 inhibitors were docked to the model protein 4Z16 using the covalent dock program within Schrödinger software suite. The setup process involved specifying Michael addition or Ketone-Cysteine as the reaction type for the new compounds designed, and the scoring function was set to Extra Precision. Default parameters were used for all other settings.

Reversible (non-covalent) docking involves the prediction of the non-covalent interactions between the ligand and the target protein. These interactions can include hydrogen bonding, van der Waals forces, hydrophobic interactions, and electrostatic interactions. Reversible docking predicts the most favorable binding pose and affinity of the ligand within the target protein without the formation of a covalent bond. Reversible docking is widely used in drug discovery and virtual screening to identify potential lead compounds that can bind to the target protein with high affinity and specificity. One of the advantages of reversible docking is the possibility of ligand dissociation, which allows for the development of drugs with desirable pharmacokinetic properties and reduced toxicity risks.

Before conducting molecular docking, the ligands intended for docking were optimized using Avogadro software 2.0. Subsequently, we obtained the structures of JAK3 and CYP3A4 from the RCSB database (PDB ID:4Z16 and 5VCC). The crystal complex of 4Z16 comprises water molecules and the co-crystallized ligand 4LH bound to the protein 4Z16. To prepare the protein, we eliminated all water molecules and 4LH and added polar hydrogens to the JAK3 protein structure using Discovery Studio software 2021. Similar steps were followed for 5VCC, except that the included ligands were not deleted because they are an important part of the metabolism of CYP3A4. After preparing the ligands and protein, molecular docking was carried out using AD4 and AutoVina to explore the active site of 4Z16 and 5VCC, which is determined by the region encompassing the co-crystallized ligands (4LH and HEM) [53]. The three-dimensional grid was established using the AUTOGRID algorithm, which calculates the binding energy between ligands and their receptor. The default grid size for JAK3 with tofacitinib and CYP3A4 with new compounds was set to x = 60, y = 60, and z = 60, with a spacing of 0.375 Å between grid points. The center of the grid corresponds to the active site of the receptors JAK3-4LH and CYP3A4 HEM, with coordinates (x = −6.68875 Å, y = −14.7757 Å, and z = 1.89597 Å) and (x = −19.3381 Å, y = −30.475 Å, and z = 17.7174 Å), respectively. The docking results obtained from AD4 and Vina were visualized using Discovery Studio software 2021.