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Nature. 2017 Oct 5;550(7674):74-79. doi: 10.1038/nature23912. Epub 2017 Sep 27.

Massively parallel de novo protein design for targeted therapeutics.

Author information

1
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
2
Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
3
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA.
4
Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México City 04510, Mexico.
5
Department of Microbiology, University of Washington, Seattle, Washington 98109, USA.
6
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
7
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
8
State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.
9
Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
10
Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
11
Department of Urology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
12
Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA.
13
Virvio Inc., Seattle, Washington 98195, USA.

Abstract

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

PMID:
28953867
PMCID:
PMC5802399
DOI:
10.1038/nature23912
[Indexed for MEDLINE]
Free PMC Article

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