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SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution.
Nat Microbiol. 2021 09; 6(9):1188-1198.NM

Abstract

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.

Authors+Show Affiliations

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Paris, France.Viral Populations and Pathogenesis Unit CNRS UMR 3569, Institut Pasteur, Paris, France.Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel. Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel.Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.Bioqual, Rockville, MD, USA.Bioqual, Rockville, MD, USA.Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel. gideon.schreiber@weizmann.ac.il.

Pub Type(s)

Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34400835

Citation

Zahradník, Jiří, et al. "SARS-CoV-2 Variant Prediction and Antiviral Drug Design Are Enabled By RBD in Vitro Evolution." Nature Microbiology, vol. 6, no. 9, 2021, pp. 1188-1198.
Zahradník J, Marciano S, Shemesh M, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol. 2021;6(9):1188-1198.
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Harari, D., Chiaravalli, J., Meyer, B., Rudich, Y., Li, C., Marton, I., Dym, O., Elad, N., Lewis, M. G., Andersen, H., Gagne, M., Seder, R. A., Douek, D. C., & Schreiber, G. (2021). SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nature Microbiology, 6(9), 1188-1198. https://doi.org/10.1038/s41564-021-00954-4
Zahradník J, et al. SARS-CoV-2 Variant Prediction and Antiviral Drug Design Are Enabled By RBD in Vitro Evolution. Nat Microbiol. 2021;6(9):1188-1198. PubMed PMID: 34400835.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. AU - Zahradník,Jiří, AU - Marciano,Shir, AU - Shemesh,Maya, AU - Zoler,Eyal, AU - Harari,Daniel, AU - Chiaravalli,Jeanne, AU - Meyer,Björn, AU - Rudich,Yinon, AU - Li,Chunlin, AU - Marton,Ira, AU - Dym,Orly, AU - Elad,Nadav, AU - Lewis,Mark G, AU - Andersen,Hanne, AU - Gagne,Matthew, AU - Seder,Robert A, AU - Douek,Daniel C, AU - Schreiber,Gideon, Y1 - 2021/08/16/ PY - 2021/06/26/received PY - 2021/07/28/accepted PY - 2021/8/18/pubmed PY - 2021/9/10/medline PY - 2021/8/17/entrez SP - 1188 EP - 1198 JF - Nature microbiology JO - Nat Microbiol VL - 6 IS - 9 N2 - 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. SN - 2058-5276 UR - https://www.unboundmedicine.com/medline/citation/34400835/SARS_CoV_2_variant_prediction_and_antiviral_drug_design_are_enabled_by_RBD_in_vitro_evolution_ L2 - https://doi.org/10.1038/s41564-021-00954-4 DB - PRIME DP - Unbound Medicine ER -