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. 2020 Jun 1:1–13. doi: 10.1080/07391102.2020.1772108

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Figure 3. — (A) Molecular representation of N3 inhibitor within the substrate-binding pocket of SARS-CoV-2 main protease (M^pro) (PDB: 6LU7). (B) Molecular interaction pattern of N3 inhibitor with the conserved residues of M^pro. N3 inhibitor was found to be interacting with Glu166 and Thr190 of M^pro by the formation of hydrogen bonds. Conserved residues participating in other non-bonded interactions are shown in line representation. (C) Molecular interactions of CAPE with SARS-CoV-2 M^pro after docking. Hydrogen bond interactions between CAPE and protease were found to be through Glu166 and Asn142. The other residues participating in other non-bonded interactions are highlighted in orange. The residues conserved in the substrate-binding pocket of various coronaviruses and involved in interaction with all three ligands in this study- N3 inhibitor, CAPE and Wi-N are highlighted in B, C and D using line representation. (D) Molecular interactions of Withanone with SARS-CoV-2 M^pro in the best docking pose. Wi-N was forming one hydrogen bond with Cys145, however many other residues (highlighted in orange) were participating in other non-bonded interactions with the small molecule.