Moe software 2020

Figures showing protein structures were prepared using PyMOL 2.5.2 (Schrodinger, LLC). Sequences were aligned using Clustal W. The 2D interaction of the docking pose of CDK9/127 was analyzed by MOE ligand analysis using Molecular Operating Environment (MOE) software 2020.0901 (Chemical Computing Group).

The crystal structures of sGC receptor in the activated state (PDB ID: 7D9R) and in the inactivated state (PDB ID: 7D9T) were downloaded from pdb (www.rcsb.org). The compounds prevailed in S. samarangense extract were downloaded as SDF files from PubChem (https://pubchem.ncbi.nlm.nih.gov/). The chemical structures of the compounds were corrected by adding the hydrogen atoms, then energy was minimized, and their partial charges were assigned according to the physiological pH. The compounds’ structures were then compiled into one database that was used for docking. Molecular operating environment (MOE) software, 2020.0901 (Chemical Computing Group Inc.; Montreal, QC, Canada, H3A 2R7, 2022) was used to run the docking rounds. The docking protocol was validated by docking the co-crystallized compounds riociguat (a stimulator of sGC) and the haem-independent sGC activator; cinaciguat into the activated and the inactivated receptor’s states, respectively, applying the same docking protocol. The docked ligands showed optimum superimposition on the co-crystallized ligands in the binding site with Rmsd values less than 1.5.