SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution.
Angiotensin-Converting Enzyme 2
/ chemistry
Animals
Antiviral Agents
/ administration & dosage
COVID-19
/ genetics
Cricetinae
Drug Design
Evolution, Molecular
Female
Humans
Male
Mesocricetus
Molecular Dynamics Simulation
Mutation
Protein Binding
/ drug effects
Protein Domains
Receptors, Virus
/ genetics
SARS-CoV-2
/ chemistry
Spike Glycoprotein, Coronavirus
/ chemistry
Virus Internalization
/ drug effects
COVID-19 Drug Treatment
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
09 2021
09 2021
Historique:
received:
26
06
2021
accepted:
28
07
2021
pubmed:
18
8
2021
medline:
10
9
2021
entrez:
17
8
2021
Statut:
ppublish
Résumé
SARS-CoV-2 variants of interest and concern will continue to emerge for the duration of the COVID-19 pandemic. To map mutations in the receptor-binding domain (RBD) of the spike protein that affect binding to angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, we applied in vitro evolution to affinity-mature the RBD. Multiple rounds of random mutagenic libraries of the RBD were sorted against decreasing concentrations of ACE2, resulting in the selection of higher affinity RBD binders. We found that mutations present in more transmissible viruses (S477N, E484K and N501Y) were preferentially selected in our high-throughput screen. Evolved RBD mutants include prominently the amino acid substitutions found in the RBDs of B.1.620, B.1.1.7 (Alpha), B1.351 (Beta) and P.1 (Gamma) variants. Moreover, the incidence of RBD mutations in the population as presented in the GISAID database (April 2021) is positively correlated with increased binding affinity to ACE2. Further in vitro evolution increased binding by 1,000-fold and identified mutations that may be more infectious if they evolve in the circulating viral population, for example, Q498R is epistatic to N501Y. We show that our high-affinity variant RBD-62 can be used as a drug to inhibit infection with SARS-CoV-2 and variants Alpha, Beta and Gamma in vitro. In a model of SARS-CoV-2 challenge in hamster, RBD-62 significantly reduced clinical disease when administered before or after infection. A 2.9 Å cryo-electron microscopy structure of the high-affinity complex of RBD-62 and ACE2, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.
Identifiants
pubmed: 34400835
doi: 10.1038/s41564-021-00954-4
pii: 10.1038/s41564-021-00954-4
doi:
Substances chimiques
Antiviral Agents
0
Receptors, Virus
0
Spike Glycoprotein, Coronavirus
0
Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1188-1198Subventions
Organisme : Israel Science Foundation (ISF)
ID : 3814/19
Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Nature Limited.
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