An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation.

BioRxiv : the Preprint Server for Biology
Michael SchoofAashish Manglik

Abstract

Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri...Continue Reading

Citations

Jan 14, 2021·The Biochemical Journal·George M Burslem
Jan 19, 2021·3 Biotech·Naun Lobo-GaloEduardo Ruiz-Bustos
Feb 8, 2021·Stem Cell Research·Gangyu SunZhizhi Wang
Nov 7, 2020·Science·Thomas W LinskyDaniel-Adriano Silva
Apr 24, 2021·Microbial Cell Factories·Norma A Valdez-CruzMauricio A Trujillo-Roldán
Apr 25, 2021·Nature Communications·Jung-Eun ShinDebora S Marks

Methods Mentioned

BETA
fluorescence-activated cell sorting
fluorescence activated cell sorting
Flow
surface plasmon resonance
electron microscopy
footprinting
X-ray
chip
circular dichroism
Size exclusion chromatography

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