We have studied in this molecular docking investigation the different activities of all phytocompounds revealed in C. europaea polyphenolic extract, including healing activity (casein kinase-1 and glycogen synthase kinase-3β), analgesic activity (cyclooxygenase-2), antileukemic activity (Tyrosine kinase), and apoptotic effect (TRADD).
The SDF format of phenolic compounds identified in the polyphenolic extract of C. europaea and molecules used as a positive control was retrieved from the PubChem database. Then, they were prepared for molecular docking using the OPLS3 force field and the LigPrep tool in the Maestro 11.5 release of the Schrödinger Software. In all, 32 stereoisomers were generated for each ligand, taking into account ionization states at pH 7.0 and 2.0.
The crystal structures of CK1, GSK3, cyclooxygenase-2, tyrosine kinase, and TRADD were obtained from the Protein Data Bank in PDB format using the designated PDB IDs: 6GZD, 1Q5K, 6COX, 1IEP, and 1F3V, respectively. The Schrödinger-Maestro v11.5 software was used to prepare and construct the structures. Selenomethionines were converted into methionines, heavy atoms were given hydrogens, and all waters were removed. Charges and bond ordering were also allocated. The maximum heavy atom RMSD (root-mean-square-deviation) was set to 0.30 during minimization using the force field OPLS3.
The process of generating the receptor grid starts by selecting any atom of the ligand, and the grid is spaced at 20 × 20 × 20 intervals. The non-cis/trans-amide bond was penalized during SP flexible ligand docking in Glide of Schrödinger (Maestro v 11.5). The partial charge cutoff and van der Waals scaling factor were set at 0.15 and 0.80, respectively. The final score, known as the glide score, was determined based on the most energy-efficient positions. The ligand’s best-docked position with the lowest glide score value was recorded for each ligand [54 (link)].
The SDF format of phenolic compounds identified in the polyphenolic extract of C. europaea and molecules used as a positive control was retrieved from the PubChem database. Then, they were prepared for molecular docking using the OPLS3 force field and the LigPrep tool in the Maestro 11.5 release of the Schrödinger Software. In all, 32 stereoisomers were generated for each ligand, taking into account ionization states at pH 7.0 and 2.0.
The crystal structures of CK1, GSK3, cyclooxygenase-2, tyrosine kinase, and TRADD were obtained from the Protein Data Bank in PDB format using the designated PDB IDs: 6GZD, 1Q5K, 6COX, 1IEP, and 1F3V, respectively. The Schrödinger-Maestro v11.5 software was used to prepare and construct the structures. Selenomethionines were converted into methionines, heavy atoms were given hydrogens, and all waters were removed. Charges and bond ordering were also allocated. The maximum heavy atom RMSD (root-mean-square-deviation) was set to 0.30 during minimization using the force field OPLS3.
The process of generating the receptor grid starts by selecting any atom of the ligand, and the grid is spaced at 20 × 20 × 20 intervals. The non-cis/trans-amide bond was penalized during SP flexible ligand docking in Glide of Schrödinger (Maestro v 11.5). The partial charge cutoff and van der Waals scaling factor were set at 0.15 and 0.80, respectively. The final score, known as the glide score, was determined based on the most energy-efficient positions. The ligand’s best-docked position with the lowest glide score value was recorded for each ligand [54 (link)].
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