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Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2

View ORCID ProfileSamantha E Greasley, View ORCID ProfileStephen Noell, View ORCID ProfileOlga Plotnikova, View ORCID ProfileRoseAnn Ferre, View ORCID ProfileWei Liu, View ORCID ProfileBen Bolanos, View ORCID ProfileKimberly Fennell, View ORCID ProfileJennifer Nicki, View ORCID ProfileTim Craig, View ORCID ProfileYuao Zhu, Al E Stewart, View ORCID ProfileClaire M Steppan
doi: https://doi.org/10.1101/2022.01.17.476556
Samantha E Greasley
1Pfizer Worldwide Research, Development & Medical, La Jolla, CA, 92037, USA
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  • ORCID record for Samantha E Greasley
Stephen Noell
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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Olga Plotnikova
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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  • ORCID record for Olga Plotnikova
RoseAnn Ferre
1Pfizer Worldwide Research, Development & Medical, La Jolla, CA, 92037, USA
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Wei Liu
1Pfizer Worldwide Research, Development & Medical, La Jolla, CA, 92037, USA
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  • ORCID record for Wei Liu
Ben Bolanos
1Pfizer Worldwide Research, Development & Medical, La Jolla, CA, 92037, USA
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Kimberly Fennell
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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  • ORCID record for Kimberly Fennell
Jennifer Nicki
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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  • ORCID record for Jennifer Nicki
Tim Craig
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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  • ORCID record for Tim Craig
Yuao Zhu
3Pfizer Worldwide Research, Development & Medical, Pearl River, NY, 10965,USA
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  • ORCID record for Yuao Zhu
Al E Stewart
1Pfizer Worldwide Research, Development & Medical, La Jolla, CA, 92037, USA
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Claire M Steppan
2Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
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  • ORCID record for Claire M Steppan
  • For correspondence: claire.m.steppan@pfizer.com
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Abstract

The COVID-19 pandemic continues to be a public health threat with emerging variants of SARS-CoV-2. Nirmatrelvir (PF-07321332) is a reversible, covalent inhibitor targeting the main protease (Mpro) of SARS-CoV-2 and the active protease inhibitor in PAXLOVID™ (nirmatrelvir tablets and ritonavir tablets). One of the predominant SARS-CoV-2 variants emerging is the B.1.1.529 Omicron harboring a mutation at amino acid position 132 in the Mpro changing a proline to a histidine (P132H). In vitro biochemical enzymatic assay characterization of the enzyme kinetics of the Omicron Mpro (P132H) demonstrate that it is catalytically comparable to wildtype and that nirmatrelvir has similar potency against both wildtype and Omicron (P132H) Mpro with Ki of 0.933nM (wildtype) and 0.635nM (P132H) each, respectively. This observation is reinforced by our structural determination of nirmatrelvir bound to the omicron Mpro at 1.63Å resolution. These in vitro data suggest that PAXLOVID has the potential to maintain plasma concentrations of nirmatrelvir many-fold times higher than the amount required to stop the SARS-CoV-2 variant Omicron from replicating in cells.

Competing Interest Statement

All authors are employees of Pfizer, Inc and may hold or own shares of Pfizer stock.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 19, 2022.
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Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2
Samantha E Greasley, Stephen Noell, Olga Plotnikova, RoseAnn Ferre, Wei Liu, Ben Bolanos, Kimberly Fennell, Jennifer Nicki, Tim Craig, Yuao Zhu, Al E Stewart, Claire M Steppan
bioRxiv 2022.01.17.476556; doi: https://doi.org/10.1101/2022.01.17.476556
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Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2
Samantha E Greasley, Stephen Noell, Olga Plotnikova, RoseAnn Ferre, Wei Liu, Ben Bolanos, Kimberly Fennell, Jennifer Nicki, Tim Craig, Yuao Zhu, Al E Stewart, Claire M Steppan
bioRxiv 2022.01.17.476556; doi: https://doi.org/10.1101/2022.01.17.476556

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