Submission Details
Molecule(s):
O=C(/C=C/c1ccc(O)c2c1[C@H](C(=O)O)[C@H](c1ccc(O)c(O)c1)O2)O[C@@H](Cc1ccc(O)c(O)c1)C(=O)O
COC(=O)[C@H]1c2c(/C=C/C(=O)O[C@@H](Cc3ccc(O)c(O)c3)C(=O)O)ccc(O)c2O[C@H]1c1ccc(O)c(O)c1
Design Rationale:
Compounds ZINC38138562 and ZINC67911817 were designed by virtual screening using a pharmacophoric model based on the antiviral Remdesivir (used with mild success in patients with SARS-CoV-2). The pharmacophoric model was developed taking into acount the docking study of Remdesivir (ligand) and SARS-CoV-2 main protease (5RED) in both dock6.9 and Autodock 4.2.6. The VS study was performed by mean of the ZINC12 database which contains commercially available compounds for structure based virtual screening (about 35 million compounds). Proposed compounds ZINC38138562 and ZINC67911817 were the hits in this structure-based search therefore they were analyzed by means of molecular docking (using dock 6.9 and Autodock 4.2.6) in order to confirm their affinities with 5RED binding pocket in terms of energy and interactions.
Other Notes:
Docking Results (data obtained with Dock6.9 software): Molecule ZINC38138562: Binding E = -35.647915 (KJ/mol), 5 hydrogen bonds. Molecule ZINC67911817: Binding E = -39.054199 (KJ/mol), 2 hydrogen bonds and a Pi-stacking interaction.