open access publication

Article, 2024

Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain

JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 1520-6106, Volume 128, 2, Pages 451-464, 10.1021/acs.jpcb.3c06258


Monti, Michele 0000-0003-3056-5267 (Corresponding author) [1] Milanetti, Edoardo 0000-0002-3046-5170 [1] [2] Frans, Myrthe T. [3] Miotto, Mattia 0000-0002-0043-8921 [1] Di Rienzo, Lorenzo 0000-0003-4114-5049 [1] Baranov, Maksim V. 0000-0002-9903-9495 [3] Giorgio, Gosti 0000-0002-8571-1404 [1] [4] [5] Somavarapu, Arun Kumar 0000-0001-6123-6875 [6] Nagaraj, Madhu [6] Golbek, Thaddeus W. [6] Rossing, Emiel 0000-0002-6381-6475 [7] Moons, Sam J. [7] Boltje, Thomas [7] van den Bogaart, Geert 0000-0003-2180-6735 [3] Weidner, Tobias 0000-0002-7083-7004 [6] Otzen, Daniel E. [6] Tartaglia, Gian Gaetano [1] Ruocco, Giancarlo 0000-0002-2762-9533 [1] [2] Roeters, Steven J. (Corresponding author) [6] [8] [9]


  1. [1] Ist Italiano Tecnol IIT, Ctr Human Technol CHT, RNA Syst Biol, I-16152 Genoa, Italy
  2. [NORA names: Italy; Europe, EU; OECD];
  3. [2] Sapienza Univ, Dept Phys, I-00185 Rome, Italy
  4. [NORA names: Italy; Europe, EU; OECD];
  5. [3] Groningen Biomol Sci & Biotechnol, Mol Immunol, NL-9747 AG Groningen, Netherlands
  6. [NORA names: Netherlands; Europe, EU; OECD];
  7. [4] CNR, Ist Sci Patrimonio Culturale, DHILab, Sede Roma, I-00010 Rome, Italy
  8. [NORA names: Italy; Europe, EU; OECD];
  9. [5] CNR, Ist Sci Patrimonio Culturale, DHILab, Sede Roma, I-00010 Rome, Italy
  10. [NORA names: Italy; Europe, EU; OECD];


It is not well understood why severe acute respiratory syndrome (SARS)-CoV-2 spreads much faster than other beta-coronaviruses such as SARS-CoV and Middle East respiratory syndrome (MERS)-CoV. In a previous publication, we predicted the binding of the N-terminal domain (NTD) of SARS-CoV-2 spike to sialic acids (SAs). Here, we experimentally validate this interaction and present simulations that reveal a second possible interaction between SAs and the spike protein via a binding site located in the receptor-binding domain (RBD). The predictions from molecular-dynamics simulations and the previously-published 2D-Zernike binding-site recognition approach were validated through flow-induced dispersion analysis (FIDA)& horbar;which reveals the capability of the SARS-CoV-2 spike to bind to SA-containing (glyco)lipid vesicles, and flow-cytometry measurements & horbar;which show that spike binding is strongly decreased upon inhibition of SA expression on the membranes of angiotensin converting enzyme-2 (ACE2)-expressing HEK cells. Our analyses reveal that the SA binding of the NTD and RBD strongly enhances the infection-inducing ACE2 binding. Altogether, our work provides in silico, in vitro, and cellular evidence that the SARS-CoV-2 virus utilizes a two-receptor (SA and ACE2) strategy. This allows the SARS-CoV-2 spike to use SA moieties on the cell membrane as a binding anchor, which increases the residence time of the virus on the cell surface and aids in the binding of the main receptor, ACE2, via 2D diffusion.

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