Fig. 1

Polyphenols form water-mediated H-bonds in static as well as dynamic structures. a A prototypical snapshot from an MD simulation where rosmarinic acid (ROA, carbons denoted as dark-green sticks) binds to the factor X enzyme [16]. We observe several water-mediated H-bond bridges (red lines) within the active binding site that stabilize ROA binding. b The crystal structure (PDB ID: 7B3E) of flavonoid myricetin (MYC, carbons denoted as light-green sticks) covalently bound to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. MYC forms several water-mediated H-bond bridges (red lines) within the binding site. MYC also forms direct H-bonds, which are shown as purple lines