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 af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › 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.

Originalsprog	Engelsk
Artikelnummer	e2112942118
Tidsskrift	Proceedings of the National Academy of Sciences
Vol/bind	118
Nummer	50
Antal sider	10
ISSN	0027-8424
DOI	https://doi.org/10.1073/pnas.2112942118
Status	Udgivet - dec. 2021

Adgang til dokumentet

10.1073/pnas.2112942118Licens: CC BY

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

Andre filer og links

Link to publication in Scopus

Citationsformater

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), Artikel 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",

}

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, bind 118, nr. 50, e2112942118. https://doi.org/10.1073/pnas.2112942118

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

UR - http://www.scopus.com/inward/record.url?scp=85121034006&partnerID=8YFLogxK

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

Abstract

Adgang til dokumentet

Andre filer og links

Fingeraftryk

Citationsformater