A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry

Julian Valero; Laia Civit; Daniel M. Dupont; Denis Selnihhin; Line S. Reinert; Manja Idorn; Brett A. Israels; Aleksandra M. Bednarz; Claus Bus; Benedikt Asbach; David Peterhoff; Finn S. Pedersen; Victoria Birkedal; Ralf Wagner; Søren R. Paludan; Jørgen Kjems

doi:10.1073/pnas.2112942118

A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry

Julian Valero^*, Laia Civit, Daniel M. Dupont, Denis Selnihhin, Line S. Reinert, Manja Idorn, Brett A. Israels, Aleksandra M. Bednarz, Claus Bus, Benedikt Asbach, David Peterhoff, Finn S. Pedersen, Victoria Birkedal, Ralf Wagner, Søren R. Paludan, Jørgen Kjems^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2⁰-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer–spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.

Original language	English
Article number	e2112942118
Journal	Proceedings of the National Academy of Sciences
Volume	118
Issue	50
Number of pages	10
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.2112942118
Publication status	Published - Dec 2021

Keywords

Aptamer multimerization
Aptamer selection
SARS-CoV-2 targeting
Spike protein
Viral neutralization

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8685691/pdf/pnas.202112942.pdfLicence: CC BY

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Valero, J., Civit, L., Dupont, D. M., Selnihhin, D., Reinert, L. S., Idorn, M., Israels, B. A., Bednarz, A. M., Bus, C., Asbach, B., Peterhoff, D., Pedersen, F. S., Birkedal, V., Wagner, R., Paludan, S. R., & Kjems, J. (2021). A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proceedings of the National Academy of Sciences, 118(50), Article e2112942118. https://doi.org/10.1073/pnas.2112942118

@article{e7a8838efa644ba98ca68a2889775870,

title = "A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry",

abstract = "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 20-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer–spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.",

keywords = "Aptamer multimerization, Aptamer selection, SARS-CoV-2 targeting, Spike protein, Viral neutralization",

author = "Julian Valero and Laia Civit and Dupont, {Daniel M.} and Denis Selnihhin and Reinert, {Line S.} and Manja Idorn and Israels, {Brett A.} and Bednarz, {Aleksandra M.} and Claus Bus and Benedikt Asbach and David Peterhoff and Pedersen, {Finn S.} and Victoria Birkedal and Ralf Wagner and Paludan, {S{\o}ren R.} and J{\o}rgen Kjems",

year = "2021",

month = dec,

doi = "10.1073/pnas.2112942118",

language = "English",

volume = "118",

journal = "Proceedings of the National Academy of Sciences",

issn = "0027-8424",

publisher = "The National Academy of Sciences of the United States of America",

number = "50",

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Valero, J , Civit, L, Dupont, DM, Selnihhin, D, Reinert, LS , Idorn, M, Israels, BA, Bednarz, AM, Bus, C, Asbach, B, Peterhoff, D, Pedersen, FS, Birkedal, V, Wagner, R, Paludan, SR & Kjems, J 2021, 'A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry', Proceedings of the National Academy of Sciences, vol. 118, no. 50, e2112942118. https://doi.org/10.1073/pnas.2112942118

A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. / Valero, Julian ; Civit, Laia; Dupont, Daniel M. et al.
In: Proceedings of the National Academy of Sciences, Vol. 118, No. 50, e2112942118, 12.2021.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry

AU - Valero, Julian

AU - Civit, Laia

AU - Dupont, Daniel M.

AU - Selnihhin, Denis

AU - Reinert, Line S.

AU - Idorn, Manja

AU - Israels, Brett A.

AU - Bednarz, Aleksandra M.

AU - Bus, Claus

AU - Asbach, Benedikt

AU - Peterhoff, David

AU - Pedersen, Finn S.

AU - Birkedal, Victoria

AU - Wagner, Ralf

AU - Paludan, Søren R.

AU - Kjems, Jørgen

PY - 2021/12

Y1 - 2021/12

N2 - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 20-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer–spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.

AB - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 20-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer–spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.

KW - Aptamer multimerization

KW - Aptamer selection

KW - SARS-CoV-2 targeting

KW - Spike protein

KW - Viral neutralization

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U2 - 10.1073/pnas.2112942118

DO - 10.1073/pnas.2112942118

M3 - Journal article

C2 - 34876524

AN - SCOPUS:85121034006

SN - 0027-8424

VL - 118

JO - Proceedings of the National Academy of Sciences

JF - Proceedings of the National Academy of Sciences

IS - 50

M1 - e2112942118

ER -

A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry

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Keywords

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