Molecular operating environment moe version 2019

Molecular docking studies of the following components: cis-abienol, trans-ferruginol, α-cadinol, δ-muurolene and α-pinene were performed to evaluate their binding affinity with the targeted active sites of EGFR, Mcl-1, and caspase-8 proteins. Molecular Operating Environment MOE version 2019.0102 software (Chemical Computing Group, Montreal, Canada) [73 ] was utilized for the docking studies. Protein and ligand structures were prepared as previously described [74 (link)].
The crystal structures of EGFR (PDB: 1M17) [45 (link)], Mcl-1 (PDB: 2NLA) [46 (link)] and caspase-8 (PDB: 1F9E) [47 (link)] were retrieved from the Protein Data Bank (http://www.rcsb.org, accessed on 24 March 2023) [75 ]. The structures of EGFR, MCl-1 and caspase-8 were prepared through the MOE QuickPrep tool.
cis-Abienol, trans-ferruginol, α-cadinol, δ-muurolene, and α-pinene were drawn through the Chemdraw^® (PerkinElmer Informatics, Inc., Buckinghamshire, UK), then transferred to the MOE using smiles canonical. The energy of the components was minimized with root mean square (RMS) gradient 0.1 kcal/mol and finally preparing a database file.

Molecular docking studies of the following components: 7-oxo-dehydroabietic acid, caffeic acid, narcissoside (Isorhamnetin-3-O-rutinoside), isorhamnetin-3-O-glucoside, Syringetin-3-O-glucoside, 15-hydroxy-7-oxo-dehydroabietic acid, 6-O-p-coumaroyl ajugol, luteolin 7-rhamnoside, robustaflavone 7,4′-dimethyl ether, and ferulic acid were performed to evaluate their binding affinity with the targeted active sites of HSP90A, EGFR, and P53 proteins. Molecular Operating Environment MOE version 2019.0102 software (Chemical Computing Group, Montreal, CA) [96 ] was used for the docking studies. The exploited docking placement methodology is triangle matcher. Each ligand was allowed to be flexible, while the protein structure was kept rigid. The scores of the docking energy for the best-fitted poses of the components with the protein active pocket were recorded.

Molecular docking of the major components of A. robusta bark EO (tricyclene, α-pinene, d-camphene, limonene, trans-pinocarveol, borneol, α-phellandren-8-ol and α-terpineol) was performed to provide insight on their binding efficiencies with the active sites of the selected SARS-COVID-19 enzymes. The molecular modelling studies of the components were carried out using Molecular Operating Environment MOE version 2019.0102 software (Chemical Computing Group, Montreal, QC, Canada) [56 ]. The docking placement methodology is triangle matcher, using London dG as the initial scoring function and GBVI/WSAdG as the final scoring function. The receptor was kept rigid, and the ligands were allowed to be flexible during the refinement process. The docking energy scores of the best-fitted poses of the ligands with the active site at the protein sites were recorded.