Skip to content
naulon
Get started

No retraction, correction or concern found when last checked on Oct 30, 2026.

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

Longxing Cao, Inna Goreshnik, Brian Coventry and 12 more

Science · 2020 · CC BY

doi:10.1126/science.abd9909

Abstract

Miniproteins against SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is decorated with spikes, and viral entry into cells is initiated when these spikes bind to the host angiotensin-converting enzyme 2 (ACE2) receptor. Many monoclonal antibody therapies in development target the spike proteins. Cao et al. designed small, stable proteins that bind tightly to the spike and block it from binding to ACE2. The best designs bind with very high affinity and prevent SARS-CoV-2 infection of mammalian Vero E6 cells. Cryo–electron microscopy shows that the structures of the two most potent inhibitors are nearly identical to the computational models. Unlike antibodies, the miniproteins do not require expression in mammalian cells, and their small size and high stability may allow formulation for direct delivery to the nasal or respiratory system. Science , this issue p. 426

References 39

  1. 1.

    Y. J. Hou, K. Okuda, C. E. Edwards, D. R. Martinez, T. Asakura, K. H. Dinnon 3rd, T. Kato, R. E. Lee, B. L. Yount, T. M. Mascenik, G. Chen, K. N. Olivier, A. Ghio, L. V. Tse, S. R. Leist, L. E. Gralinski, A. Schäfer, H. Dang, R. Gilmore, S. Nakano, L. Sun, M. L. Fulcher, A. Livraghi-Butrico, N. I. Nicely, M. Cameron, C. Cameron, D. J. Kelvin, A. de Silva, D. M. Margolis, A. Markmann, L. Bartelt, R. Zumwalt, F. J. Martinez, S. P. Salvatore, A. Borczuk, P. R. Tata, V. Sontake, A. Kimple, I. Jaspers, W. K. O’Neal, S. H. Randell, R. C. Boucher, R. S. Baric, SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract. Cell 182, 429–446.e14 (2020 ).

    Not in our library10.1016/j.cell.2020.05.042

  2. 2.

    R. Shi, C. Shan, X. Duan, Z. Chen, P. Liu, J. Song, T. Song, X. Bi, C. Han, L. Wu, G. Gao, X. Hu, Y. Zhang, Z. Tong, W. Huang, W. J. Liu, G. Wu, B. Zhang, L. Wang, J. Qi, H. Feng, F. S. Wang, Q. Wang, G. F. Gao, Z. Yuan, J. Yan, A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 584, 120–124 (2020 ).

    Not in our library10.1038/s41586-020-2381-y

  3. 3.

    D. Pinto, Y.-J. Park, M. Beltramello, A. C. Walls, M. A. Tortorici, S. Bianchi, S. Jaconi, K. Culap, F. Zatta, A. De Marco, A. Peter, B. Guarino, R. Spreafico, E. Cameroni, J. B. Case, R. E. Chen, C. Havenar-Daughton, G. Snell, A. Telenti, H. W. Virgin, A. Lanzavecchia, M. S. Diamond, K. Fink, D. Veesler, D. Corti, Structural and functional analysis of a potent sarbecovirus neutralizing antibody. bioRxiv 023903 [Preprint] 10 April 2020;.

    Not in our library10.1101/2020.04.07.023903

  4. 4.

    J. Lan, J. Ge, J. Yu, S. Shan, H. Zhou, S. Fan, Q. Zhang, X. Shi, Q. Wang, L. Zhang, X. Wang, Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215–220 (2020 ).

    Not in our library10.1038/s41586-020-2180-5

  5. 5.

    M. Yuan, N. C. Wu, X. Zhu, C. D. Lee, R. T. Y. So, H. Lv, C. K. P. Mok, I. A. Wilson, A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science 368, 630–633 (2020 ).

    Not in our library10.1126/science.abb7269

  6. 6.
    A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2 · 2020
    No notice
  7. 7.

    K. L. Winarski, J. Tang, L. Klenow, J. Lee, E. M. Coyle, J. Manischewitz, H. L. Turner, K. Takeda, A. B. Ward, H. Golding, S. Khurana, Antibody-dependent enhancement of influenza disease promoted by increase in hemagglutinin stem flexibility and virus fusion kinetics. Proc. Natl. Acad. Sci. U.S.A. 116, 15194–15199 (2019 ).

    Not in our library10.1073/pnas.1821317116

  8. 8.

    A. Taylor, S.-S. Foo, R. Bruzzone, L. V. Dinh, N. J. C. King, S. Mahalingam, Fc receptors in antibody-dependent enhancement of viral infections. Immunol. Rev. 268, 340–364 (2015 ).

    Not in our library10.1111/imr.12367

  9. 9.

    B. S. Graham, Rapid COVID-19 vaccine development. Science 368, 945–946 (2020 ).

    Not in our library10.1126/science.abb8923

  10. 10.

    A. C. Walls, Y.-J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, D. Veesler, Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein. bioRxiv 956581 [Preprint] 20 February 2020..

    Not in our library10.1101/2020.02.19.956581

  11. 11.

    A. Chevalier, D. A. Silva, G. J. Rocklin, D. R. Hicks, R. Vergara, P. Murapa, S. M. Bernard, L. Zhang, K. H. Lam, G. Yao, C. D. Bahl, S. I. Miyashita, I. Goreshnik, J. T. Fuller, M. T. Koday, C. M. Jenkins, T. Colvin, L. Carter, A. Bohn, C. M. Bryan, D. A. Fernández-Velasco, L. Stewart, M. Dong, X. Huang, R. Jin, I. A. Wilson, D. H. Fuller, D. Baker, Massively parallel de novo protein design for targeted therapeutics. Nature 550, 74–79 (2017 ).

    Not in our library10.1038/nature23912

  12. 12.

    J. Dou, A. A. Vorobieva, W. Sheffler, L. A. Doyle, H. Park, M. J. Bick, B. Mao, G. W. Foight, M. Y. Lee, L. A. Gagnon, L. Carter, B. Sankaran, S. Ovchinnikov, E. Marcos, P. S. Huang, J. C. Vaughan, B. L. Stoddard, D. Baker, De novo design of a fluorescence-activating β-barrel. Nature 561, 485–491 (2018 ).

    Not in our library10.1038/s41586-018-0509-0

  13. 13.

    W. B. Alsoussi, J. S. Turner, J. B. Case, H. Zhao, A. J. Schmitz, J. Q. Zhou, R. E. Chen, T. Lei, A. A. Rizk, K. M. McIntire, E. S. Winkler, J. M. Fox, N. M. Kafai, L. B. Thackray, A. O. Hassan, F. Amanat, F. Krammer, C. T. Watson, S. H. Kleinstein, D. H. Fremont, M. S. Diamond, A. H. Ellebedy, A potently neutralizing antibody protects mice against SARS-CoV-2 infection. J. Immunol. 205, 915–922 (2020 ).

    Not in our library10.4049/jimmunol.2000583

  14. 14.

    D. A. Silva, S. Yu, U. Y. Ulge, J. B. Spangler, K. M. Jude, C. Labão-Almeida, L. R. Ali, A. Quijano-Rubio, M. Ruterbusch, I. Leung, T. Biary, S. J. Crowley, E. Marcos, C. D. Walkey, B. D. Weitzner, F. Pardo-Avila, J. Castellanos, L. Carter, L. Stewart, S. R. Riddell, M. Pepper, G. J. L. Bernardes, M. Dougan, K. C. Garcia, D. Baker, De novo design of potent and selective mimics of IL-2 and IL-15. Nature 565, 186–191 (2019 ).

    Not in our library10.1038/s41586-018-0830-7

  15. 15.

    J. Shang, G. Ye, K. Shi, Y. Wan, C. Luo, H. Aihara, Q. Geng, A. Auerbach, F. Li, Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020 ).

    Not in our library10.1038/s41586-020-2179-y

  16. 16.

    Q. Wang, Y. Zhang, L. Wu, S. Niu, C. Song, Z. Zhang, G. Lu, C. Qiao, Y. Hu, K. Y. Yuen, Q. Wang, H. Zhou, J. Yan, J. Qi, Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell 181, 894–904.e9 (2020 ).

    Not in our library10.1016/j.cell.2020.03.045

  17. 17.
    Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 · 2020
    No notice
  18. 18.
    RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design · 2011
    No notice
  19. 19.

    N. Koga, R. Tatsumi-Koga, G. Liu, R. Xiao, T. B. Acton, G. T. Montelione, D. Baker, Principles for designing ideal protein structures. Nature 491, 222–227 (2012 ).

    Not in our library10.1038/nature11600

  20. 20.

    D. M. Hoover, J. Lubkowski, DNAWorks: An automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 30, e43 (2002 ).

    Not in our library10.1093/nar/30.10.e43

  21. 21.
    Structure-based design of prefusion-stabilized SARS-CoV-2 spikes · 2020
    No notice
  22. 22.

    C. Suloway, J. Pulokas, D. Fellmann, A. Cheng, F. Guerra, J. Quispe, S. Stagg, C. S. Potter, B. Carragher, Automated molecular microscopy: The new Leginon system. J. Struct. Biol. 151, 41–60 (2005 ).

    Not in our library10.1016/j.jsb.2005.03.010

  23. 23.

    D. Tegunov, P. Cramer, Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019 ).

    Not in our library10.1038/s41592-019-0580-y

  24. 24.

    A. Punjani, J. L. Rubinstein, D. J. Fleet, M. A. Brubaker, cryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017 ).

    Not in our library10.1038/nmeth.4169

  25. 25.
    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 · 2016
    No notice
  26. 26.
    New tools for automated high-resolution cryo-EM structure determination in RELION-3 · 2018
    No notice
  27. 27.

    A. Punjani, H. Zhang, D. J. Fleet, Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction. bioRxiv 877092 [Preprint] 16 December 2019..

    Not in our library10.1101/2019.12.15.877092

  28. 28.
    A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis · 2019
    No notice
  29. 29.
    High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy · 2013
    No notice
  30. 30.

    E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004 ).

    Not in our library10.1002/jcc.20084

  31. 31.
    Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data · 2020
    No notice
  32. 32.

    B. Frenz, S. Rämisch, A. J. Borst, A. C. Walls, J. Adolf-Bryfogle, W. R. Schief, D. Veesler, F. DiMaio, Automatically fixing errors in glycoprotein structures with Rosetta. Structure 27, 134–139.e3 (2019 ).

    Not in our library10.1016/j.str.2018.09.006

  33. 33.

    F. DiMaio, Y. Song, X. Li, M. J. Brunner, C. Xu, V. Conticello, E. Egelman, T. Marlovits, Y. Cheng, D. Baker, Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat. Methods 12, 361–365 (2015 ).

    Not in our library10.1038/nmeth.3286

  34. 34.
    Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta · 2016
    No notice
  35. 35.

    C. J. Williams, J. J. Headd, N. W. Moriarty, M. G. Prisant, L. L. Videau, L. N. Deis, V. Verma, D. A. Keedy, B. J. Hintze, V. B. Chen, S. Jain, S. M. Lewis, W. B. Arendall 3rd, J. Snoeyink, P. D. Adams, S. C. Lovell, J. S. Richardson, D. C. Richardson, MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018 ).

    Not in our library10.1002/pro.3330

  36. 36.
    Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix · 2019
    No notice
  37. 37.

    J. Agirre, J. Iglesias-Fernández, C. Rovira, G. J. Davies, K. S. Wilson, K. D. Cowtan, Privateer: Software for the conformational validation of carbohydrate structures. Nat. Struct. Mol. Biol. 22, 833–834 (2015 ).

    Not in our library10.1038/nsmb.3115

  38. 38.

    B. A. Barad, N. Echols, R. Y.-R. Wang, Y. Cheng, F. DiMaio, P. D. Adams, J. S. Fraser, EMRinger: Side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015 ).

    Not in our library10.1038/nmeth.3541

  39. 39.

    T. D. Goddard, C. C. Huang, E. C. Meng, E. F. Pettersen, G. S. Couch, J. H. Morris, T. E. Ferrin, UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018 ).

    Not in our library10.1002/pro.3235

Cited by papers we hold 10

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.