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. 2024 Sep 3;68(10):e00562-24. doi: 10.1128/aac.00562-24

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Copyright © 2024 Poli et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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Fig 3 — Manual overlap of the benzoxepine scaffold on Mpro inhibitor structures. (A) Manual overlay of the benzoxazepine scaffold (light blue) to PF-00835231 using PDB 6xhl showing SARS-CoV-2 in complex with PF-00835231, aligning the carbonyl H-bond showing the potential to fill the P2 Leu pocket. (B) Manual overlay of the benzoxazepine scaffold (light blue) to PF-07321332 using PDB 7si9 showing SARS-CoV-2 in complex with PF-07321332, aligning the carbonyl H-bond showing the potential to fill the P2 Leu pocket. (C) The 2-D structure of PF-00835231 is highlighted to show regions of overlap. (D) The 2-D structure of PF-07321332, nirmatrelvir, is highlighted to show regions of overlap. (E) 2-D structure of compound 1, the prototype Mpro inhibitor, is highlighted to show the benzoxazepine motif. Modeled structures were obtained using Mol Soft, LLC.