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Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants

The recent Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola and Zika virus outbreaks exemplify the continued threat of (re-)emerging viruses to human health, and our inability to rapidly develop effective therapeutic countermeasures. Many viruses, including MERS-CoV and the Crimean-Con...

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Autores principales: Zhang, Wei, Bailey-Elkin, Ben A., Knaap, Robert C. M., Khare, Baldeep, Dalebout, Tim J., Johnson, Garrett G., van Kasteren, Puck B., McLeish, Nigel J., Gu, Jun, He, Wenguang, Kikkert, Marjolein, Mark, Brian L., Sidhu, Sachdev S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451084/
https://www.ncbi.nlm.nih.gov/pubmed/28542609
http://dx.doi.org/10.1371/journal.ppat.1006372
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author Zhang, Wei
Bailey-Elkin, Ben A.
Knaap, Robert C. M.
Khare, Baldeep
Dalebout, Tim J.
Johnson, Garrett G.
van Kasteren, Puck B.
McLeish, Nigel J.
Gu, Jun
He, Wenguang
Kikkert, Marjolein
Mark, Brian L.
Sidhu, Sachdev S.
author_facet Zhang, Wei
Bailey-Elkin, Ben A.
Knaap, Robert C. M.
Khare, Baldeep
Dalebout, Tim J.
Johnson, Garrett G.
van Kasteren, Puck B.
McLeish, Nigel J.
Gu, Jun
He, Wenguang
Kikkert, Marjolein
Mark, Brian L.
Sidhu, Sachdev S.
author_sort Zhang, Wei
collection PubMed
description The recent Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola and Zika virus outbreaks exemplify the continued threat of (re-)emerging viruses to human health, and our inability to rapidly develop effective therapeutic countermeasures. Many viruses, including MERS-CoV and the Crimean-Congo hemorrhagic fever virus (CCHFV) encode deubiquitinating (DUB) enzymes that are critical for viral replication and pathogenicity. They bind and remove ubiquitin (Ub) and interferon stimulated gene 15 (ISG15) from cellular proteins to suppress host antiviral innate immune responses. A variety of viral DUBs (vDUBs), including the MERS-CoV papain-like protease, are responsible for cleaving the viral replicase polyproteins during replication, and are thereby critical components of the viral replication cycle. Together, this makes vDUBs highly attractive antiviral drug targets. However, structural similarity between the catalytic cores of vDUBs and human DUBs complicates the development of selective small molecule vDUB inhibitors. We have thus developed an alternative strategy to target the vDUB activity through a rational protein design approach. Here, we report the use of phage-displayed ubiquitin variant (UbV) libraries to rapidly identify potent and highly selective protein-based inhibitors targeting the DUB domains of MERS-CoV and CCHFV. UbVs bound the vDUBs with high affinity and specificity to inhibit deubiquitination, deISGylation and in the case of MERS-CoV also viral replicative polyprotein processing. Co-crystallization studies further revealed critical molecular interactions between UbVs and MERS-CoV or CCHFV vDUBs, accounting for the observed binding specificity and high affinity. Finally, expression of UbVs during MERS-CoV infection reduced infectious progeny titers by more than four orders of magnitude, demonstrating the remarkable potency of UbVs as antiviral agents. Our results thereby establish a strategy to produce protein-based inhibitors that could protect against a diverse range of viruses by providing UbVs via mRNA or protein delivery technologies or through transgenic techniques.
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spelling pubmed-54510842017-06-09 Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants Zhang, Wei Bailey-Elkin, Ben A. Knaap, Robert C. M. Khare, Baldeep Dalebout, Tim J. Johnson, Garrett G. van Kasteren, Puck B. McLeish, Nigel J. Gu, Jun He, Wenguang Kikkert, Marjolein Mark, Brian L. Sidhu, Sachdev S. PLoS Pathog Research Article The recent Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola and Zika virus outbreaks exemplify the continued threat of (re-)emerging viruses to human health, and our inability to rapidly develop effective therapeutic countermeasures. Many viruses, including MERS-CoV and the Crimean-Congo hemorrhagic fever virus (CCHFV) encode deubiquitinating (DUB) enzymes that are critical for viral replication and pathogenicity. They bind and remove ubiquitin (Ub) and interferon stimulated gene 15 (ISG15) from cellular proteins to suppress host antiviral innate immune responses. A variety of viral DUBs (vDUBs), including the MERS-CoV papain-like protease, are responsible for cleaving the viral replicase polyproteins during replication, and are thereby critical components of the viral replication cycle. Together, this makes vDUBs highly attractive antiviral drug targets. However, structural similarity between the catalytic cores of vDUBs and human DUBs complicates the development of selective small molecule vDUB inhibitors. We have thus developed an alternative strategy to target the vDUB activity through a rational protein design approach. Here, we report the use of phage-displayed ubiquitin variant (UbV) libraries to rapidly identify potent and highly selective protein-based inhibitors targeting the DUB domains of MERS-CoV and CCHFV. UbVs bound the vDUBs with high affinity and specificity to inhibit deubiquitination, deISGylation and in the case of MERS-CoV also viral replicative polyprotein processing. Co-crystallization studies further revealed critical molecular interactions between UbVs and MERS-CoV or CCHFV vDUBs, accounting for the observed binding specificity and high affinity. Finally, expression of UbVs during MERS-CoV infection reduced infectious progeny titers by more than four orders of magnitude, demonstrating the remarkable potency of UbVs as antiviral agents. Our results thereby establish a strategy to produce protein-based inhibitors that could protect against a diverse range of viruses by providing UbVs via mRNA or protein delivery technologies or through transgenic techniques. Public Library of Science 2017-05-18 /pmc/articles/PMC5451084/ /pubmed/28542609 http://dx.doi.org/10.1371/journal.ppat.1006372 Text en © 2017 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Zhang, Wei
Bailey-Elkin, Ben A.
Knaap, Robert C. M.
Khare, Baldeep
Dalebout, Tim J.
Johnson, Garrett G.
van Kasteren, Puck B.
McLeish, Nigel J.
Gu, Jun
He, Wenguang
Kikkert, Marjolein
Mark, Brian L.
Sidhu, Sachdev S.
Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title_full Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title_fullStr Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title_full_unstemmed Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title_short Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
title_sort potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451084/
https://www.ncbi.nlm.nih.gov/pubmed/28542609
http://dx.doi.org/10.1371/journal.ppat.1006372
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