Figure 3.
Mpro dimer visualized in surface representation (a), with monomers in gray and light purple (PDB: 6Y2E), and a detail of the active site pocket (b), as circled in (a). The active site dyad, modeled Z604 (purple), cocrystallized (R)-X77 (cyan), and M040 (red) are shown in stick representation. Molecular structures of reference molecules (R)-X77, M040, and Z604 (c) and their derivatives (d–i). Secondary amines 30a–d (d), their corresponding tertiary amines 31a–d (e), derivatives based on 30b or 30d involving amide bonds 32–34 (f–h), and four-armed derivatives with amide bonds (35a–b), which are hybrids of Z604 and (R)-X77 (i). The subpockets are indicated for the cocrystallized compounds and for Z604 from our modeling data.