Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.
Research paper by
Jiangdong J Huo, Audrey A Le Bas, Reinis R RR Ruza, Helen M E HME Duyvesteyn, Halina H Mikolajek, Tomas T Malinauskas, Tiong Kit TK Tan, Pramila P Rijal, Maud M Dumoux, Philip N PN Ward, Jingshan J Ren, Daming D Zhou, Peter J PJ Harrison, Miriam M Weckener, Daniel K DK Clare, Vinod K VK Vogirala, Julika J Radecke, Lucile L Moynié, Yuguang Y Zhao, Javier J Gilbert-Jaramillo, Michael L ML Knight, Julia A JA Tree, Karen R KR Buttigieg, Naomi N Coombes, Michael J MJ Elmore, Miles W MW Carroll, Loic L Carrique, Pranav N M PNM Shah, William W James, Alain R AR Townsend, David I DI Stuart, Raymond J RJ Owens, James H JH Naismith
The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naive llama single-domain antibody library and PCR-based maturation, we have produced two closely related nanobodies, H11-D4 and H11-H4, that bind RBD (K of 39 and 12 nM, respectively) and block its interaction with ACE2. Single-particle cryo-EM revealed that both nanobodies bind to all three RBDs in the spike trimer. Crystal structures of each nanobody-RBD complex revealed how both nanobodies recognize the same epitope, which partly overlaps with the ACE2 binding surface, explaining the blocking of the RBD-ACE2 interaction. Nanobody-Fc fusions showed neutralizing activity against SARS-CoV-2 (4-6 nM for H11-H4, 18 nM for H11-D4) and additive neutralization with the SARS-CoV-1/2 antibody CR3022.