The Development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates

  1. Gang Ye
  2. Joseph Gallant
  3. Jian Zheng
  4. Christopher Massey
  5. Ke Shi
  6. Wanbo Tai
  7. Abby Odle
  8. Molly Vickers
  9. Jian Shang
  10. Yushun Wan
  11. Lanying Du Dr.
  12. Hideki Aihara
  13. Stanley Perlman
  14. Aaron LeBeau  Is a corresponding author
  15. Fang Li  Is a corresponding author
  1. University of Minnesota, United States
  2. University of Iowa, United States
  3. University of Texas Medical Branch, United States
  4. Lindsley F Kimball Research Institute, United States
  5. Lindsley F Kimball Research Institute, New York Blood Center, United States

Abstract

Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody), Nanosota-1, from a camelid nanobody phage display library. Structural data showed that Nanosota-1 bound to the oft-hidden receptor-binding domain (RBD) of SARS-CoV-2 spike protein, blocking viral receptor ACE2. The lead drug candidate possessing an Fc tag (Nanosota-1C-Fc) bound to SARS-CoV-2 RBD ~3000 times more tightly than ACE2 did and inhibited SARS-CoV-2 pseudovirus ~160 times more efficiently than ACE2 did. Administered at a single dose, Nanosota-1C-Fc demonstrated preventive and therapeutic efficacy against live SARS-CoV-2 infection in both hamster and mouse models. Unlike conventional antibodies, Nanosota-1C-Fc was produced at high yields in bacteria and had exceptional thermostability. Pharmacokinetic analysis of Nanosota-1C-Fc documented an excellent in vivo stability and a high tissue bioavailability. As effective and inexpensive drug candidates, Nanosota-1 may contribute to the battle against COVID-19.

Data availability

Coordinates and structure factors have been deposited to the Protein Data Bank with accession number 7KM5.

Article and author information

Author details

  1. Gang Ye

    Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, United States
    Competing interests
    Gang Ye, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6034-2174
  2. Joseph Gallant

    Pharmacology, University of Minnesota, Minneapolis, United States
    Competing interests
    Joseph Gallant, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4943-1744
  3. Jian Zheng

    Microbiology and Immunology, University of Iowa, Iowa City, United States
    Competing interests
    No competing interests declared.
  4. Christopher Massey

    Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston,, United States
    Competing interests
    No competing interests declared.
  5. Ke Shi

    Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  6. Wanbo Tai

    New York Blood Center, Lindsley F Kimball Research Institute, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9864-8993
  7. Abby Odle

    Microbiology and Immunology, University of Iowa, Iowa City, United States
    Competing interests
    No competing interests declared.
  8. Molly Vickers

    Microbiology and Immunology, University of Iowa, Iowa City, United States
    Competing interests
    No competing interests declared.
  9. Jian Shang

    Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, United States
    Competing interests
    Jian Shang, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
  10. Yushun Wan

    Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, United States
    Competing interests
    Yushun Wan, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
  11. Lanying Du Dr.

    Viral Immunology Laboratory, Lindsley F Kimball Research Institute, New York Blood Center, New York, United States
    Competing interests
    No competing interests declared.
  12. Hideki Aihara

    Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7508-6230
  13. Stanley Perlman

    Microbiology and Immunology, University of Iowa, Iowa City, United States
    Competing interests
    No competing interests declared.
  14. Aaron LeBeau

    Pharmacology, University of Minnesota, Minneapolis, United States
    For correspondence
    alebeau@umn.edu
    Competing interests
    Aaron LeBeau, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
  15. Fang Li

    Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, United States
    For correspondence
    lifang@umn.edu
    Competing interests
    Fang Li, The University of Minnesota has filed a patent on Nanosota-1 drugs with F.L, G.Y., A.M.L., J.P.G., J.S., and Y.W. as inventors..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1958-366X

Funding

National Institutes of Health (R01AI157975)

  • Lanying Du Dr.
  • Stanley Perlman
  • Aaron LeBeau
  • Fang Li

National Institutes of Health (R01AI089728)

  • Fang Li

National Institutes of Health (R35GM118047)

  • Hideki Aihara

University of Minnesota

  • Fang Li

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols of the University of Texas Medical Branch (protocol number 2007072), of the New York Blood Center (protocol number 194.22), of the University of Iowa (protocol number 9051795), and of the University of Minnesota (protocol number 2009-38426A).

Copyright

© 2021, Ye et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,114
    views
  • 425
    downloads
  • 46
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Gang Ye
  2. Joseph Gallant
  3. Jian Zheng
  4. Christopher Massey
  5. Ke Shi
  6. Wanbo Tai
  7. Abby Odle
  8. Molly Vickers
  9. Jian Shang
  10. Yushun Wan
  11. Lanying Du Dr.
  12. Hideki Aihara
  13. Stanley Perlman
  14. Aaron LeBeau
  15. Fang Li
(2021)
The Development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates
eLife 10:e64815.
https://doi.org/10.7554/eLife.64815

Share this article

https://doi.org/10.7554/eLife.64815

Further reading

    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease
    Gillian AM Tarr, Linda Chui ... Tim A McAllister
    Research Article

    Several areas of the world suffer a notably high incidence of Shiga toxin-producing Escherichia coli. To assess the impact of persistent cross-species transmission systems on the epidemiology of E. coli O157:H7 in Alberta, Canada, we sequenced and assembled E. coli O157:H7 isolates originating from collocated cattle and human populations, 2007–2015. We constructed a timed phylogeny using BEAST2 using a structured coalescent model. We then extended the tree with human isolates through 2019 to assess the long-term disease impact of locally persistent lineages. During 2007–2015, we estimated that 88.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 38.0% (95% CI 29.3%, 47.3%) of human isolates. During the later period, six locally persistent lineages continued to be associated with human illness, including 74.7% (95% CI 68.3%, 80.3%) of reported cases in 2018 and 2019. Our study identified multiple locally evolving lineages transmitted between cattle and humans persistently associated with E. coli O157:H7 illnesses for up to 13 y. Locally persistent lineages may be a principal cause of the high incidence of E. coli O157:H7 in locations such as Alberta and provide opportunities for focused control efforts.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Ana Patrícia Graça, Vadim Nikitushkin ... Gerald Lackner
    Research Article

    Mycofactocin is a redox cofactor essential for the alcohol metabolism of mycobacteria. While the biosynthesis of mycofactocin is well established, the gene mftG, which encodes an oxidoreductase of the glucose-methanol-choline superfamily, remained functionally uncharacterized. Here, we show that MftG enzymes are almost exclusively found in genomes containing mycofactocin biosynthetic genes and are present in 75% of organisms harboring these genes. Gene deletion experiments in Mycolicibacterium smegmatis demonstrated a growth defect of the ∆mftG mutant on ethanol as a carbon source, accompanied by an arrest of cell division reminiscent of mild starvation. Investigation of carbon and cofactor metabolism implied a defect in mycofactocin reoxidation. Cell-free enzyme assays and respirometry using isolated cell membranes indicated that MftG acts as a mycofactocin dehydrogenase shuttling electrons toward the respiratory chain. Transcriptomics studies also indicated remodeling of redox metabolism to compensate for a shortage of redox equivalents. In conclusion, this work closes an important knowledge gap concerning the mycofactocin system and adds a new pathway to the intricate web of redox reactions governing the metabolism of mycobacteria.