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There are two nearly identical copies of RBD- On the basis of our crystal structure, we fur- correspond to the inactive spike (Fig. 4B).
Nb20 complexes in one asymmetric unit, with ther modeled the structure of the best neu- Our analysis indicates a potential mecha-
a root mean square deviation of 0.277 Å over tralizer Nb21 with the RBD (materials and nism by which Nbs 20 and 21 (epitope I) lock
287 Ca atoms. In the structure, all three CDRs methods). Only four residues vary between RBDs in their down conformation with ultra-
of Nb20 interact with the RBD by binding to Nbs 20 and 21 (fig. S9A), all of which are on high affinity. Combined with the steric interfer-
its large extended external loop with two short CDRs. Two substitutions are at the RBD bind- ence with hACE2 binding in the RBD open
b strands (Fig. 3A) (31). Glu484 of the RBD forms ing interface. Ser52 and Met55 in the CDR2 of conformation (Fig. 4A), these mechanisms
hydrogen bonding and ionic interactions with Nb20 are replaced by two asparagine residues may explain the exceptional neutralization
the side chains of Arg31 (CDR1) and Tyr104 (Asn52 and Asn55) in Nb21. In our super- potencies of epitope I Nbs.
(CDR3) of Nb20, whereas Gln493 of the RBD imposed structure, Asn52 forms a new H bond Other epitope binders do not fit into this
forms hydrogen bonds with the main-chain with Asn450 of the RBD (fig. S9B). Although inactive conformation without steric clashes
carbonyl of Ala29 (CDR1) and the side chain Asn55 does not engage in additional inter- and appear to use different neutralization
of Arg97 (CDR3) of Nb20. These interactions actions with the RBD, it creates a salt bridge strategies (Fig. 4C). For example, epitope II
constitute a major polar interaction network with the side chain of Arg31, which stabilizes (Nb93) colocalizes with the hACE2 binding
at the RBD and Nb20 interface. Arg31 of Nb20 the polar interaction network among Arg31 site and can bind the spike in the one RBD
also engages in a cation p interaction with the and Tyr104 of Nb21 and Gln484 of the RBD (fig. “up” conformation (Fig. 4D; PDB ID 6VSB)
side chain of Phe490 of the RBD (Fig. 3B). In S9B). All of those likely contribute to a slower (3). This epitope may neutralize the virus by
addition, Met55 from the CDR2 of Nb20 packs off-rate of Nb21 (Fig. 1F and fig. S4A) and blocking the hACE2 binding site. Epitope III
against residues Leu452, Phe490, and Leu492 of stronger neutralization potency. Structural and IV Nbs can bind only when two or three
the RBD to form hydrophobic interactions at comparison of RBD-Nb20 or RBD-Nb21 and RBDs are in their up conformations (PDB ID
the interface. Another small patch of hydro- RBD-hACE2 [Protein Data Bank (PDB) ID 6XCN) (24), in which the epitopes are exposed.
S10). They remained highly potent for pseu- constructs (40) to improve pharmacokinetics. 27. M. P. Rout, A. Sali, Cell 177, 1384–1403 (2019).
dovirus neutralization after lyophilization and These high-quality Nbs can also be applied as 28. C. Yu, L. Huang, Anal. Chem. 90, 144–165 (2018).
29. A. Leitner, M. Faini, F. Stengel, R. Aebersold, Trends Biochem.
aerosolization (materials and methods and rapid and economic point-of-care diagnostics. Sci. 41, 20–32 (2016).
fig. S11, B to G), indicating the marked stability We envision that the Nb technology described 30. B. T. Chait, M. Cadene, P. D. Olinares, M. P. Rout, Y. Shi, J. Am.
and potential flexibility of administration. here will contribute to curbing the current Soc. Mass Spectrom. 27, 952–965 (2016).
31. Q. Wang et al., Cell 181, 894–904.e9 (2020).
Most of the RBD mutations observed in the pandemic and possibly a future event. 32. T. Li et al., bioRxiv 2020.06.09.143438 [Preprint].
Global Initiative on Sharing Avian Influenza 24 September 2020.
RE FERENCES AND NOTES 33. J. D. Walter et al., bioRxiv 2020.04.16.045419 [Preprint].
Data (GISAID) (35) are very low in frequency
1. N. Zhu et al., N. Engl. J. Med. 382, 727–733 (2020). 16 May 2020.
(<0.0025), which may increase under Nb se- 2. P. Zhou et al., Nature 579, 270–273 (2020). 34. J. Huo et al., Nat. Struct. Mol. Biol. 27, 846–854 (2020).
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5. Y. Cai et al., Science 369, 1586–1592 (2020). 37. Y. Bar-On et al., Nat. Med. 24, 1701–1707 (2018).
taneously bind a variety of epitopes with po- 38. M. Marovich, J. R. Mascola, M. S. Cohen, JAMA 324, 131–132
6. X. Fan, D. Cao, L. Kong, X. Zhang, Nat. Commun. 11, 3618
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will likely efficiently block virus mutational 7. Y. Cao et al., Cell 182, 73–84.e16 (2020). 39. I. Jovčevska, S. Muyldermans, BioDrugs 34, 11–26 (2020).
40. Z. Shen et al., bioRxiv 2020.08.19.257725 [Preprint].
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20 August 2020.
9. J. Hansen et al., Science 369, 1010–1014 (2020).
In our study, in vivo antibody affinity mat- 10. L. Liu et al., Nature 584, 450–456 (2020).
uration followed by advanced proteomics (25) 11. P. J. M. Brouwer et al., Science 369, 643–650 (2020). AC KNOWLED GME NTS
12. D. Wrapp et al., Cell 181, 1436–1441 (2020). We thank the staff at the GM/CA of APS in the Argonne
enabled the rapid discovery of a diverse re-
13. A. Z. Wec et al., Science 369, 731–736 (2020). National Laboratory (USA) for their assistance with x-ray
pertoire of high-affinity RBD Nbs, including 14. T. Zohar, G. Alter, Nat. Rev. Immunol. 20, 392–394 (2020). diffraction data collection. We thank the UPMC Genome Center for
an ultrapotent neutralizer with subpicomolar 15. N. Eroshenko et al., Nat. Biotechnol. 38, 789–791 Illumina MiSeq, Z. Wei (Southern University of Science and
affinity, which is unusual for natural, single- (2020). Technology) for the help with crystal structure determination, and
16. S. Muyldermans, Annu. Rev. Biochem. 82, 775–797 Y. Liu for critical reading of the manuscript. Funding: This work
domain antibody fragments. We demon- (2013). was supported by the University of Pittsburgh School of Medicine
strated the simplicity and versatility of Nb 17. P. Vanlandschoot et al., Antiviral Res. 92, 389–407 (Y.S.), a Clinical and Translational Science Institute (CTSI) pilot
bioengineering and the desirable physico- (2011). fund (Y.S.), NIH grant R35GM137905 (Y.S.), the University of
18. L. Detalle et al., Antimicrob. Agents Chemother. 60, 6–13 Pittsburgh and the Center for Vaccine Research (W.P.D.), NIH
chemical properties of the monomeric Nbs (2015). grant R35GM128641 (C.Z.), ISF 1466/18 (D.S.-D.), and Israeli
and their multivalent forms. To our knowl- 19. R. Konwarh, Front. Immunol. 11, 1531 (2020). Ministry of Science and Technology (D.S.-D.). Author
edge, the multivalent constructs represent 20. T. F. Custódio et al., bioRxiv 2020.06.23.165415 [Preprint]. contributions: Y.S. and D.S.-D. conceived the study. Y.X.
23 June 2020. performed most of the experiments. S.N. performed the PRNT
the most potent SARS-CoV-2 neutralizers to SARS-CoV-2 neutralization assay. Z.X. produced the multivalent
21. C. Liu et al., bioRxiv 2020.03.02.972927 [Preprint].
date. Flexible and efficient administration, 5 March 2020. Nbs and performed thermostability measurements. C.Z.
such as inhalation, may further improve their 22. J. Gai et al., bioRxiv 2020.08.09.242867 [Preprint]. determined the x-ray structure, with the help of H.L. Y.X., Y.S.,
14 August 2020. D.S.-D., C.Z., Z.S., S.N., and W.P.D. analyzed the data. Y.S. supervised
antiviral efficacy while minimizing the dose, the study and drafted the manuscript. All authors edited the
23. C. J. Bracken et al., bioRxiv 2020.08.08.242511 [Preprint].
cost, and potential toxicity for clinical applica- 10 August 2020. manuscript. Competing interests: Y.X. and Y.S. are co-inventors
tions. The high sequence similarity between 24. C. O. Barnes et al., Cell 182, 828–842.e16 (2020). on a provisional patent filed by the University of Pittsburgh
25. Y. Xiang et al., bioRxiv 2020.08.21.261917 [Preprint]. covering the Nbs described in this manuscript. Data and
Nbs and human IgGs may restrain the immu-
23 August 2020. materials availability: The coordinates and structure factors for
nogenicity (39). It is possible to fuse the anti- 26. W. B. Klimstra et al., J. Gen. Virol. 10.1099/jgv.0.001481 the SARS-CoV-2 RBD with Nb20 have been deposited in the
viral Nbs with highly stable albumin-Nb (2020). Protein Data Bank under PDB ID 7JVB. The proteomics data
of chemical cross-link and mass spectrometric analysis have been apply to figures/photos/artwork or other content included in the Tables S1 to S4
deposited into the MassIVE data repository with accession code article that is credited to a third party; obtain authorization from References (41–60)
MSV000086198. Plasmids are being deposited at Addgene and are the rights holder before using such material. MDAR Reproducibility Checklist
available from Y.S. in the interim. This work is licensed under a
Creative Commons Attribution 4.0 International (CC BY 4.0) View/request a protocol for this paper from Bio-protocol.
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