A SARS-CoV-2 entry inhibitor trimerizes to lock the spike protein in a closed conformation
Abstract The SARS-CoV-2 spike protein binds its receptor ACE2 to initiate target-cell infection. To engage ACE2, at least one of the three receptor-binding domains (RBDs) of the spike must adopt the up orientation. Here, we describe S22, a potent, bioavailable, and non-toxic inhibitor of BA.2 and all subsequent Omicron variants. Cryo-EM analyses showed that S22 assembled as a trimer in the central cavity of the spike apex, stabilizing all three RBDs in the down orientation, thereby preventing ACE2 association. Binding studies, especially those using mixed S22-sensitive and -resistant spikes, imply a cooperative assembly of three S22 molecules with three RBDs, resulting in an unusually slow S22 off-rate. Consistent with its slow dissociation and favorable pharmacokinetics, S22 suppressed viral replication and inflammation in the lungs of XBB.1.5-infected female mice. Thus, S22 potently inhibits Omicron entry through a distinct mechanism whereby a small compound assembles cooperatively as a trimer to stabilize spike in an inactive conformation.
Authors
- Gogce C. Crynen (ORCID: https://orcid.org/0000-0001-6066-9900)
- Janarjan Bhandari (ORCID: https://orcid.org/0000-0002-3900-9067)
- Claudia Ruiz Bayona
- Stuart M. Weston (ORCID: https://orcid.org/0000-0001-9840-2953)
- Yuka Otsuka (ORCID: https://orcid.org/0000-0003-3739-5790)
- Matthew B. Frieman (ORCID: https://orcid.org/0000-0003-0107-0775)
- Timothy Spicer (ORCID: https://orcid.org/0000-0002-9080-4226)
- Reuben S. Harris (ORCID: https://orcid.org/0000-0002-9034-9112)
- Michael D. Cameron (ORCID: https://orcid.org/0000-0003-3154-4775)
- Divyasha Saxena (ORCID: https://orcid.org/0009-0000-3952-2066)
- Charles C. Bailey (ORCID: https://orcid.org/0000-0003-0200-3523)
- Louis D. Scampavia (ORCID: https://orcid.org/0000-0002-7734-0105)
- Michael Farzan (ORCID: https://orcid.org/0000-0002-2990-5319)
- Lizhou Zhang (ORCID: https://orcid.org/0000-0002-2637-9712)
- Bo Gao (ORCID: https://orcid.org/0000-0003-4787-594X)
- David Kyle Meyerholz (ORCID: https://orcid.org/0000-0003-1552-3253)
- Fan Bu (ORCID: https://orcid.org/0000-0002-6965-3072)
- Thomas D. Bannister (ORCID: https://orcid.org/0000-0003-0683-8886)
- Hyeryun Choe (ORCID: https://orcid.org/0000-0003-4538-7176)
- Lalit Batra (ORCID: https://orcid.org/0000-0002-4375-9004)
- Claire E. Kitzmiller (ORCID: https://orcid.org/0009-0001-7069-4891)
- Fang Li (ORCID: https://orcid.org/0000-0002-1958-366X)
- Lin Li (ORCID: https://orcid.org/0000-0002-8256-5333)
- Gang Ye (ORCID: https://orcid.org/0000-0001-6034-2174)
- Shuo Zhou (ORCID: https://orcid.org/0000-0001-8684-8341)
- Jyoti Vishwakarma (ORCID: https://orcid.org/0000-0002-6536-2980)
- Huihui Mou (ORCID: https://orcid.org/0000-0001-7358-368X)
- Hao Li
- Jian Zheng
- Yulia Getmanenko
Institutions
- Broad Institute (US)
- Scripps Research Institute (US)
- University of Iowa (US)
- University of Maryland, Baltimore (US)
- Boston Children's Hospital (US)
- University of Minnesota (US)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- University of Louisville (US)
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology (US)
- The University of Texas at San Antonio (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-10-27
- DOI
- https://doi.org/10.1038/s41467-026-78835-9
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases