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Selection for constrained peptides that bind to a single target protein

Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a...

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Autores principales: King, Andrew M., Anderson, Daniel A., Glassey, Emerson, Segall-Shapiro, Thomas H., Zhang, Zhengan, Niquille, David L., Embree, Amanda C., Pratt, Katelin, Williams, Thomas L., Gordon, D. Benjamin, Voigt, Christopher A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8566587/
https://www.ncbi.nlm.nih.gov/pubmed/34732700
http://dx.doi.org/10.1038/s41467-021-26350-4
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author King, Andrew M.
Anderson, Daniel A.
Glassey, Emerson
Segall-Shapiro, Thomas H.
Zhang, Zhengan
Niquille, David L.
Embree, Amanda C.
Pratt, Katelin
Williams, Thomas L.
Gordon, D. Benjamin
Voigt, Christopher A.
author_facet King, Andrew M.
Anderson, Daniel A.
Glassey, Emerson
Segall-Shapiro, Thomas H.
Zhang, Zhengan
Niquille, David L.
Embree, Amanda C.
Pratt, Katelin
Williams, Thomas L.
Gordon, D. Benjamin
Voigt, Christopher A.
author_sort King, Andrew M.
collection PubMed
description Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards “molecular glues” for therapeutics and diagnostics.
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spelling pubmed-85665872021-11-15 Selection for constrained peptides that bind to a single target protein King, Andrew M. Anderson, Daniel A. Glassey, Emerson Segall-Shapiro, Thomas H. Zhang, Zhengan Niquille, David L. Embree, Amanda C. Pratt, Katelin Williams, Thomas L. Gordon, D. Benjamin Voigt, Christopher A. Nat Commun Article Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards “molecular glues” for therapeutics and diagnostics. Nature Publishing Group UK 2021-11-03 /pmc/articles/PMC8566587/ /pubmed/34732700 http://dx.doi.org/10.1038/s41467-021-26350-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
King, Andrew M.
Anderson, Daniel A.
Glassey, Emerson
Segall-Shapiro, Thomas H.
Zhang, Zhengan
Niquille, David L.
Embree, Amanda C.
Pratt, Katelin
Williams, Thomas L.
Gordon, D. Benjamin
Voigt, Christopher A.
Selection for constrained peptides that bind to a single target protein
title Selection for constrained peptides that bind to a single target protein
title_full Selection for constrained peptides that bind to a single target protein
title_fullStr Selection for constrained peptides that bind to a single target protein
title_full_unstemmed Selection for constrained peptides that bind to a single target protein
title_short Selection for constrained peptides that bind to a single target protein
title_sort selection for constrained peptides that bind to a single target protein
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8566587/
https://www.ncbi.nlm.nih.gov/pubmed/34732700
http://dx.doi.org/10.1038/s41467-021-26350-4
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