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An anti-neurodegeneration activity study was carried out for 80 flavonoid compounds. The structure–activity analysis of the structures was carried out by performing three different anti-neurodegeneration screening tests, showing that in these structures, the presence of a hydroxy substituent group at position C3′ as well as C5′ of ring B and a methoxy substituent group at the C7 position of ring A play a vital role in neuroprotective and antioxidant as well as anti-inflammatory activity. Further, we found structure (<b>5</b>) was the top-performing active structure out of 80 structures. Subsequently, a molecular docking study was carried out for the 3 lead flavonoid compounds (<b>4</b>), (<b>5</b>), and (<b>23</b>) and 21 similar hypothetical proposed structures to estimate the binding strength between the tested compounds and proteins potentially involved in disease causation. Ligand-based pharmacophores were generated to guide future drug design studies.