Abstract
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the utility of most monoclonal antibody therapeutics. We previously described a computationally-designed, homotrimeric miniprotein inhibitor, designated TRI2-2, that protects mice against pre-Omicron SARS-CoV-2 variants. Here, we show that TRI2-2 exhibits broadly neutralizing activity of SARS-CoV-2 variants and protects mice against BQ.1.1, XBB.1.5 and BA.2.86 challenge when administered intranasally post-exposure. The resistance of TRI2-2 to viral escape by most variants and the ability to deliver it directly to the upper airways highlight the potential of the multivalent miniprotein inhibitor as an alternative therapeutic modality.
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The sharpened and unsharpened cryoEM reconstructions and atomic models of SARS-CoV-2 BA.2.86 S in complex with TRI2-2 minibinder, SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder, and SARS-CoV-2 BA.2.86 NTD have been deposited in the Electron Microscopy Data Bank and the Protein Data Bank with accession codes EMD-45972 and PDB 9CWR (SARS-CoV-2 BA.2.86 S in complex with TRI2-2 minibinder), EMD-45969 and PDB 9CWP (SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder), and EMD-45971 and PDB 9CWQ (SARS-CoV-2 BA.2.86 NTD). The source data underlying the figures can be found in the Supplementary Data 1 file. Other data will be available from the corresponding author upon request.
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Acknowledgements
This study was supported by the National Institute of Allergy and Infectious Diseases (R01AI160052 to D.B. and D.V., R01 AI157155 and P01 AI168347 to M.S.D., DP1AI158186 and 75N93022C00036 to D.V.), a Pew Biomedical Scholars Award (D.V.), an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (D.V.), and the University of Washington Arnold and Mabel Beckman cryoEM center. D.B. and D.V. are Investigators of the Howard Hughes Medical Institute and D.V. is the Hans Neurath Endowed Chair in Biochemistry at the University of Washington.
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J.L., J.B.C., M.S.D., and D.V. designed the experiments; R.R. recombinantly expressed and purified TRI2-2. L.C. provided reagents for the experiments. J.L. performed binding assays and neutralization assays. J.L. carried out fusion assays with help from M.A.T. J.L. vitrified the specimen and carried out cryoEM data collection. J.L. and Y.J.P. processed the cryoEM data with help from D.A. and D.V. J.L. and D.V. built and refined the atomic models. J.B.C. carried out the mice challenge study with assistance from S.S. J.L., J.B.C., and D.V. analyzed the data and wrote the manuscript with input from all authors; D.B., M.S.D., and D.V. supervised the project.
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J.B.C., Y.J.P., R.R., D.B., M.S.D., and D.V. are co-inventors on a patent application that incorporates discoveries described in this article (application no.: PCT/US2021/034069, title: SARS-CoV-2 inhibitors). M.S.D. is a consultant or advisor for Inbios, Vir Biotechnology, IntegerBio, Akagera Medicines, Moderna, Merck, and GlaxoSmithKline. The Diamond laboratory has received unrelated funding support in sponsored research agreements from Vir Biotechnology, Moderna, Emergent BioSolutions, and IntegerBio. All other authors declare no competing interests.
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Lee, J., Case, J.B., Park, YJ. et al. The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron variants. Commun Biol (2026). https://doi.org/10.1038/s42003-025-09499-2
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DOI: https://doi.org/10.1038/s42003-025-09499-2
