Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M <sup>Pro</sup> inhibitors with potent in vivo efficacy
The main protease (M<sup>Pro</sup>) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a validated drug target. Starting with a lead-like dihydrouracil chemotype identified in a large-library docking campaign, we improved M<sup>Pro</sup> inhibition >1000-fold by engaging additional M<sup>Pro</sup> subsites and using a latent electrophile to engage Cys<sup>145</sup>. Advanced leads from this series show pan-coronavirus antiviral activity, low clearance in mice, and for <b>AVI-4773</b>, a rapid reduction in viral titers >1,000,000 after just three doses. Both compounds are well distributed in mouse tissues, including brain, where concentrations >1000× the 90% effective concentration are observed 8 hours after oral dosing for <b>AVI-4773</b>. <b>AVI-4516</b> shows minimal inhibition of major cytochrome P450s and human proteases. <b>AVI-4516</b> also exhibits synergy with the RNA-dependent RNA polymerase inhibitor, molnupiravir, in cellular infection models. Related analogs strongly inhibit nirmatrelvir-resistant M<sup>Pro</sup> mutant virus. The properties of this chemotype are differentiated from existing clinical and preclinical M<sup>Pro</sup> inhibitors and will advance therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses.
Authors
- Judd F. Hultquist (ORCID: https://orcid.org/0000-0001-6424-4280)
- Brian K. Shoichet (ORCID: https://orcid.org/0000-0002-6098-7367)
- Maria McCavitt-Malvido (ORCID: https://orcid.org/0009-0006-4731-6047)
- Nevan J. Krogan (ORCID: https://orcid.org/0000-0003-4902-337X)
- Tyler C. Detomasi (ORCID: https://orcid.org/0000-0003-4390-108X)
- Amy Diallo (ORCID: https://orcid.org/0000-0001-9843-2255)
- Zain Alam
- Jezrael L. Revalde (ORCID: https://orcid.org/0000-0002-8794-6784)
- Michelle R. Arkin (ORCID: https://orcid.org/0000-0002-9366-6770)
- Mauricio Montaño (ORCID: https://orcid.org/0000-0002-0353-0037)
- Gilles Degotte (ORCID: https://orcid.org/0000-0001-6318-4626)
- Taha Y. Taha (ORCID: https://orcid.org/0000-0002-7344-7490)
- G.J. Correy (ORCID: https://orcid.org/0000-0001-5155-7325)
- Adam R. Renslo (ORCID: https://orcid.org/0000-0002-1240-2846)
- Kliment A. Verba (ORCID: https://orcid.org/0000-0002-2238-8590)
- Isabella Glenn (ORCID: https://orcid.org/0009-0002-6443-1873)
- R. Jeffrey Neitz (ORCID: https://orcid.org/0000-0002-2247-9345)
- R. Gumpena (ORCID: https://orcid.org/0000-0002-8661-2061)
- Mélanie Ott (ORCID: https://orcid.org/0000-0002-5697-1274)
- Yusuke Matsui (ORCID: https://orcid.org/0000-0002-6016-2867)
- Luca Lizzadro
- James R. Partridge (ORCID: https://orcid.org/0000-0002-5652-4351)
- Alicia Richards (ORCID: https://orcid.org/0000-0002-4869-2945)
- Eric R. Hantz (ORCID: https://orcid.org/0000-0002-2588-7619)
- Charles S. Craik (ORCID: https://orcid.org/0000-0001-7704-9185)
- Danielle L. Swaney (ORCID: https://orcid.org/0000-0001-6119-6084)
- Annemarie F. Charvat (ORCID: https://orcid.org/0009-0002-1164-4816)
- Jiapeng Li (ORCID: https://orcid.org/0000-0003-4321-1150)
- David J. Anderson (ORCID: https://orcid.org/0000-0001-6175-3872)
- Sijie Huang (ORCID: https://orcid.org/0000-0001-5653-0260)
- Rahul K. Suryawanshi (ORCID: https://orcid.org/0000-0001-8374-669X)
- Julia Rosecrans (ORCID: https://orcid.org/0009-0000-3111-5933)
- Francisco J. Zaptero-Belinchón
Institutions
- Northwestern University (US)
- Gladstone Institutes (US)
- University of California, San Francisco (US)
- Quantitative BioSciences (US)
Publication Details
- Journal
- Science Advances
- Published
- 2025-04-23
- DOI
- https://doi.org/10.1126/sciadv.adt7836
- Citations
- 9
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 12.57