Potent and pan-neutralization of SARS-CoV-2 variants of concern by DARPins

  1. Vikas Chonira
  2. Young Do Kwon
  3. Jason Gorman
  4. James Brett Case
  5. Zhiqiang Ku
  6. Rudo Simeon
  7. Ryan G. Casner
  8. Darcy R. Harris
  9. Adam S. Olia
  10. Tyler Stephens
  11. Lawrence Shapiro
  12. Hannah Boyd
  13. Yaroslav Tsybovsky
  14. Florian Krammer
  15. Michael S. Diamond
  16. Peter D. Kwong
  17. Zhiqiang An
  18. Zhilei Chen

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Abstract

We report the engineering and selection of two synthetic proteins – FSR16m and FSR22 – for possible treatment of SARS-CoV-2 infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon and exhibit broad spectrum neutralization of SARS-Cov-2 strains. The IC 50 values of FSR16m against authentic B.1.351, B.1.617.2 and BA.1.1 variants are 3.4 ng/mL, 2.2 ng/mL and 7.4 ng/mL, respectively, comparable to currently used therapeutic antibodies. Despite the use of the spike protein from a now historical wild-type virus for design, FSR16m and FSR22 both exhibit increased neutralization against newly-emerged variants of concern (39- to 296-fold) in pseudovirus assays. Cryo-EM structures revealed that these DARPins recognize a region of the receptor binding domain (RBD, residues 455-456, 486-489) overlapping a critical portion of the ACE2-binding surface. K18-hACE2 transgenic mice inoculated with a B.1.617.2 variant and receiving intranasally-administered FSR16m were protected as judged by less weight loss and 10-100-fold reductions in viral burden in the upper and lower respiratory tracts. The strong and broad neutralization potency make FSR16m and FSR22 promising candidates for prevention and treatment of infection by current and potential future strains of SARS-CoV-2.

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    SciScore for 10.1101/2022.05.30.493765: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    However, antibodies have several limitations as therapeutics for treating SARS-CoV-2: (a) antibody production requires sophisticated mammalian cell culture and is expensive with limited global manufacturing capacity; (b) IgG antibody requires subcutaneous or intravenous routes of administration that may be inconvenient or impractical for patients and care providers; (c) intravenously and subcutaneously administered antibodies have poor access to mucosal compartments with an estimated 50- to 100-fold lower antibody levels than in blood29-31, necessitating a high therapeutic dose; and (d) many current COVID-19 antibody therapeutics have a narrow neutralization spectrum and require cocktails to maintain efficacy toward newly emerged SARS-CoV-2 variants. The most recent Omicron variant was resistant to bamlanivimab, etesevimab and REGEN-COV (casirivimab and imdevimab)32-35. Through the use of the stringent K18-hACE2 mouse model of SARS-CoV-2 pathogenesis, we showed that intranasal administration of FSR16m on days 1 and 4 post-infection reduced viral burden and weight loss. As several other studies have demonstrated15,36-38, overexpression of hACE2 in these mice results in severe lung inflammation and disease upon infection with SARS-CoV-2. Therefore, the level of protection we observed by intranasal administration of FSR16m is significant. However, the current format of intranasal delivery likely is not directly translatable to humans. To increase the drug exposure, nasally admin...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a protocol registration statement.

    Results from scite Reference Check: We found no unreliable references.

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  2. Version published to 10.1101/2022.05.30.493765v1 on bioRxiv