Fig. 3.
Predicted binding modes of compounds 30, 26 and 40 to the SARS-CoV-2 PLpro enzyme. In the lefthand figures, oxygen atoms are colored red, nitrogen atoms blue, sulfur atoms yellow, and the carbon atoms of the ligands orange. The same coloring scheme was applied to the interaction diagrams (right), while carbon atoms are colored black on them. These diagrams depict all atoms for the receptor residues forming hydrogen bonds with the ligands. Only receptor residues interacting with the ligands in at least 50% of the analyzed MD snapshots are labeled in the lefthand figures and represented in the interaction diagrams. The compounds are: Isorhamnetin-3-O-(6-O-rhamnosyl-galactoside) (30), 5,7-dihydroxy-4′-methoxyflavanone (26), and (2S,3S,4S,5R,6S)-6-[2-(3,4- Dihydroxyphenyl)-5- hydroxy-4-oxochromen-7- yl]oxy-3,4,5- trihydroxyoxane-2- carboxylic acid (40). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)