Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

Andrew C. Hunt; James Brett Case; Young Jun Park; Longxing Cao; Kejia Wu; Alexandra C. Walls; Zhuoming Liu; John E. Bowen; Hsien Wei Yeh; Shally Saini; Louisa Helms; Yan Ting Zhao; Tien Ying Hsiang; Tyler N. Starr; Inna Goreshnik; Lisa Kozodoy; Lauren Carter; Rashmi Ravichandran; Lydia B. Green; Wadim L. Matochko; Christy A. Thomson; Bastian Vögeli; Antje Krüger; Laura A. VanBlargan; Rita E. Chen; Baoling Ying; Adam L. Bailey; Natasha M. Kafai; Scott E. Boyken; Ajasja Ljubetiè; Natasha Edman; George Ueda; Cameron M. Chow; Max Johnson; Amin Addetia; Mary Jane Navarro; Nuttada Panpradist; Michael Gale; Benjamin S. Freedman; Jesse D. Bloom; Hannele Ruohola-Baker; Sean P.J. Whelan; Lance Stewart; Michael S. Diamond; David Veesler; Michael C. Jewett; David Baker

doi:10.1126/scitranslmed.abn1252

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

Andrew C. Hunt, James Brett Case, Young Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. MatochkoChristy A. Thomson, Bastian Vögeli, Antje Krüger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetiè, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary Jane Navarro, Nuttada Panpradist, Michael Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P.J. Whelan, Lance Stewart, Michael S. Diamond^*, David Veesler^*, Michael C. Jewett^*, David Baker^*

^*Corresponding author for this work

Chemical and Biological Engineering

Research output: Contribution to journal › Article › peer-review

69 Scopus citations

Abstract

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.

Original language	English (US)
Journal	Science translational medicine
Volume	14
Issue number	646
DOIs	https://doi.org/10.1126/scitranslmed.abn1252
State	Published - May 25 2022

Funding

This work was supported by Defense Threat Reduction Agency contracts HDTRA1-15-10052 and HDTRA1-20-10004 (to M.C.J.); the David and Lucile Packard Foundation (to M.C.J.); the Camille Dreyfus Teacher-Scholar Program (to M.C.J.); Department of Defense National Defense Science and Engineering Graduate (NDSEG) Fellowship Program (NDSEG-36373 to A.C.H.); Department of Defense Peer Reviewed Medical Research Program awards W81XWH-21-1-0006 and W81XWH-21-1-0007 (to H.R.-B., D.B., M.G., and B.S.F.); DARPA Synergistic Discovery and Design (SD2) HR0011835403 contract FA8750-17-C-0219 (to I.G., L. Cao, L. Carter, L.K., N.E., R.R., D.V., and D.B.); DOD contracts W81XWH-20-1-0270-2019, AI145296, and AI143265 (to M.G. and T.-Y.H.); the Audacious Project at the Institute for Protein Design (to D.B. and H.-W.Y.); Eric and Wendy Schmidt by recommendation of the Schmidt Futures (to H.-W.Y., W.L.M., L.K, R.R., and I.G.); the Bill & Melinda Gates Foundation (OPP1156262 to D.V. and D.B. and INV-004949 to J.D.B.); the Open Philanthropy Project Improving Protein Design Fund (to D.B. and S.E.B.); a Career Award at the Scientific Interface Grant from the Burroughs Wellcome Fund (to S.E.B.); European Commission MSCA CC-LEGO 792305 (to A.L.); the Wu Tsai Translational Investigator Fund at the Institute for Protein Design (to G.U.); the National Institute of General Medical Sciences (R01GM120553 to D.V.) (NIH1P01GM081619, R01GM097372, and R01GM083867 and the NHLBI Progenitor Cell Biology Consortium U01HL099997 and UO1HL099993 to H.R.-B.); the National Institute of Allergy and Infectious Diseases (DP1AI158186 to D.V.; HHSN272201700059C to D.V., L.S., and D.B.; R37 AI1059371 to S.P.J.W.; and R01 AI145486 to N.P.); the National Institute of Diabetes and Digestive and Kidney Diseases (R01DK117914, R01DK130386, and U01DK127553 to B.S.F. and F31DK130550 to L.H.); the National Center for Advancing Translational Sciences (UG3TR002158 to L.H. and B.S.F.); the United World Antiviral Research Network-UWARN-one of the Centers Researching Emerging Infectious Diseases \"CREIDs\"; U01 AI151698-01 (to D.B., L.S., M.G., and H.-W.Y.); R01 AI157155 (to M.S.D.); a Pew Biomedical Scholars Award (to D.V.); Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (to D.V.); Fast Grants (to D.V. and A.A.); a Helen Hay Whitney Foundation postdoctoral fellowship (to J.B.C.); T90 Training Grant (to Y.T.Z.); an HHMI Fellowship from the Damon Runyon Cancer Research Foundation (to T.N.S.); Howard Hughes Medical Institute (to J.D.B., D.V., and D.B.); the National Institute of Health Cellular and Molecular Biology Training Grant (T32GM007270 to A.A.); the University of Washington Arnold and Mabel Beckman Cryo-EM Center; and National Institute of Health grant S10OD032290 (to D.V.). This project has also been funded, in part, with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN272201700059C (to D.V., L.S., and D.B.). J.D.B., D.V., and D.B. are investigators of the Howard Hughes Medical Institute.

ASJC Scopus subject areas

General Medicine

Access to Document

10.1126/scitranslmed.abn1252

Cite this

Hunt, A. C., Case, J. B., Park, Y. J., Cao, L., Wu, K., Walls, A. C., Liu, Z., Bowen, J. E., Yeh, H. W., Saini, S., Helms, L., Zhao, Y. T., Hsiang, T. Y., Starr, T. N., Goreshnik, I., Kozodoy, L., Carter, L., Ravichandran, R., Green, L. B., ... Baker, D. (2022). Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Science translational medicine, 14(646). https://doi.org/10.1126/scitranslmed.abn1252

@article{509bf47616f4425d901e6d27b687670d,

title = "Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice",

abstract = "New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.",

author = "Hunt, {Andrew C.} and Case, {James Brett} and Park, {Young Jun} and Longxing Cao and Kejia Wu and Walls, {Alexandra C.} and Zhuoming Liu and Bowen, {John E.} and Yeh, {Hsien Wei} and Shally Saini and Louisa Helms and Zhao, {Yan Ting} and Hsiang, {Tien Ying} and Starr, {Tyler N.} and Inna Goreshnik and Lisa Kozodoy and Lauren Carter and Rashmi Ravichandran and Green, {Lydia B.} and Matochko, {Wadim L.} and Thomson, {Christy A.} and Bastian V{\"o}geli and Antje Kr{\"u}ger and VanBlargan, {Laura A.} and Chen, {Rita E.} and Baoling Ying and Bailey, {Adam L.} and Kafai, {Natasha M.} and Boyken, {Scott E.} and Ajasja Ljubeti{\`e} and Natasha Edman and George Ueda and Chow, {Cameron M.} and Max Johnson and Amin Addetia and Navarro, {Mary Jane} and Nuttada Panpradist and Michael Gale and Freedman, {Benjamin S.} and Bloom, {Jesse D.} and Hannele Ruohola-Baker and Whelan, {Sean P.J.} and Lance Stewart and Diamond, {Michael S.} and David Veesler and Jewett, {Michael C.} and David Baker",

note = "Publisher Copyright: Copyright {\textcopyright} 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science.",

year = "2022",

month = may,

day = "25",

doi = "10.1126/scitranslmed.abn1252",

language = "English (US)",

volume = "14",

journal = "Science translational medicine",

issn = "1946-6234",

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Hunt, AC, Case, JB, Park, YJ, Cao, L, Wu, K, Walls, AC, Liu, Z, Bowen, JE, Yeh, HW, Saini, S, Helms, L, Zhao, YT, Hsiang, TY, Starr, TN, Goreshnik, I, Kozodoy, L, Carter, L, Ravichandran, R, Green, LB, Matochko, WL, Thomson, CA, Vögeli, B, Krüger, A, VanBlargan, LA, Chen, RE, Ying, B, Bailey, AL, Kafai, NM, Boyken, SE, Ljubetiè, A, Edman, N, Ueda, G, Chow, CM, Johnson, M, Addetia, A, Navarro, MJ, Panpradist, N, Gale, M, Freedman, BS, Bloom, JD, Ruohola-Baker, H, Whelan, SPJ, Stewart, L, Diamond, MS, Veesler, D, Jewett, MC & Baker, D 2022, 'Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice', Science translational medicine, vol. 14, no. 646. https://doi.org/10.1126/scitranslmed.abn1252

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AU - Hunt, Andrew C.

AU - Case, James Brett

AU - Park, Young Jun

AU - Cao, Longxing

AU - Wu, Kejia

AU - Walls, Alexandra C.

AU - Liu, Zhuoming

AU - Bowen, John E.

AU - Yeh, Hsien Wei

AU - Saini, Shally

AU - Helms, Louisa

AU - Zhao, Yan Ting

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AU - Matochko, Wadim L.

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AU - Boyken, Scott E.

AU - Ljubetiè, Ajasja

AU - Edman, Natasha

AU - Ueda, George

AU - Chow, Cameron M.

AU - Johnson, Max

AU - Addetia, Amin

AU - Navarro, Mary Jane

AU - Panpradist, Nuttada

AU - Gale, Michael

AU - Freedman, Benjamin S.

AU - Bloom, Jesse D.

AU - Ruohola-Baker, Hannele

AU - Whelan, Sean P.J.

AU - Stewart, Lance

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AB - New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.

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Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

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SARS-CoV-2 spike in complex with AHB2-2GS-SB175 (local refinement of the RBD and AHB2)

SARS-CoV-2 spike in complex with AHB2-2GS-SB175

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Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice

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ASJC Scopus subject areas

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SARS-CoV-2 spike in complex with AHB2-2GS-SB175 (local refinement of the RBD and AHB2)

SARS-CoV-2 spike in complex with AHB2-2GS-SB175

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