Synthesis and docking studies of some novel heterocyclic moieties acting as superior inhibitors

Abstract

We created new xanthene derivatives in this study for the traditional approach and the derivatives validity is supported by mass spectral, NMR and infrared imaging methods. In the current situation, the virus has been affecting a large number of people worldwide for the last two years. Docking studies were conducted to explore the potential binding mechanism of the target compounds and xanthene derivatives were used in the prediction of molecular docking for novel compounds. The lowest binding energies, which were verified by protein binding to the compounds, were -5.43, -5.57, -6.25, -5.99 and -5.47 kcal/mol, appropriate binding confirmation for the docking validates the hydrogen bonding interactions. Compound 3 molecular researches revealed that the three main interactions involving this ligands attachment to the SARS-CoV-2 acceptor are the presence of hydrogen bonds, hydrophobic contacts and moderate polar interactions. The docked compound 3 two-dimensional interaction diagram showed that hydrophobic residues like CYSA:42 and HISA:101 surround the ligand. This observation led to the conclusion that the binding process involves both de-solvation effects and hydrophobic contacts. Moreover, the target ligand 3 surface is surrounded by hydrophilic residues such as THRA:41, GLYA:40, PROA:10, ASPA:39, SERA:8 and LEUA:37. Compound 3 (para-methoxy substituted) among the synthesised compounds 1-6 exhibited a good docking score of -6.25 and binding energy of -4.60 kcal/mol. Compound 3 appears to have superior ligand-protein interactions while the remaining moieties show only moderate activity in docking tests.