Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

Koenig PA, Das H, Liu H, Kümmerer BM, Gohr FN, Jenster LM, Schiffelers LDJ, Tesfamariam YM, Uchima M, Wuerth JD, Gatterdam K, Ruetalo N, Christensen MH, Fandrey CI, Normann S, Tödtmann JMP, Pritzl S, Hanke L, Boos J, Yuan M, Zhu X, Schmid-Burgk JL, Kato H, Schindler M, Wilson IA, Geyer M, Ludwig KU, Hällberg BM, Wu NC, Schmidt FI

Science 371 (6530) eabe6230 [2021-01-12; online 2021-01-12]

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to spread with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. Here, we generated four neutralizing nanobodies that target the receptor-binding domain of the SARS-CoV-2 spike protein. We defined two distinct binding epitopes using x-ray crystallography and cryo-electron microscopy. Based on the structures, we engineered multivalent nanobodies with more than 100-fold improved neutralizing activity than monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor-binding competition, while other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion, and rendered the virions non-infectious.

Category: Biochemistry

Category: Imaging

Category: Proteins

Funder: H2020

Funder: VR

Type: Journal article

PubMed 33436526

DOI 10.1126/science.abe6230

Crossref 10.1126/science.abe6230

PDB: 7KN5 Crystal structure of SARS-CoV-2 RBD complexed with nanobodies VHH E and U
PDB: 7KN6 Crystal structure of SARS-CoV-2 RBD complexed with nanobody VHH V and antibody Fab CC12.3
PDB: 7KN7 Crystal structure of SARS-CoV-2 RBD complexed with nanobody VHH W and antibody Fab CC12.3
PDB: 7KSG SARS-CoV-2 spike in complex with nanobodies E
PDB: 7B14 Nanobody E bound to Spike-RBD in a localized reconstruction.
PDB: 7B11 SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs
PDB: 7B18 SARS-CoV-spike bound to two neutralising nanobodies
PDB: 7B17 SARS-CoV-spike RBD bound to two neutralising nanobodies

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