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

• Published in: Proceedings of the National Academy of Sciences - PNAS 2021-12, Vol.118 (50), p.1-10
• Main Authors: Valero, Julián, Civit, Laia, Dupont, Daniel M., Selnihhin, Denis, Reinert, Line S., Idorn, Manja, Israels, Brett A., Bednarz, Aleksandra M., Bus, Claus, Asbach, Benedikt, Peterhoff, David, Pedersen, Finn S., Birkedal, Victoria, Wagner, Ralf, Paludan, Søren R., Kjems, Jørgen
• Format: Article
• Language: English
• Subjects: ACE2; Affinity; Angiotensin-converting enzyme 2; Angiotensin-Converting Enzyme 2 - metabolism; Aptamers; Aptamers, Nucleotide - chemistry; Aptamers, Nucleotide - metabolism; Aptamers, Nucleotide - pharmacology; Binding; Biological Sciences; Cell culture; Coronaviruses; COVID-19; Fluorescence; Fluorescence microscopy; Humans; Interferometry; Mutation; Neutralization Tests; New technology; Nucleic Acid Conformation; Pandemics; Protein Binding - drug effects; Protein Interaction Domains and Motifs; Receptors; Ribonucleic acid; RNA; SARS-CoV-2 - drug effects; SARS-CoV-2 - physiology; SELEX Aptamer Technique; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - metabolism; Spike protein; Viral diseases; Virus Internalization - drug effects; Virus-like particles
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2112942118

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 2′-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.