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Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface.

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posted on 06.08.2020, 08:48 by Uddhav K Shigdel, Seung-Joo Lee, Mathew E Sowa, Brian R Bowman, Keith Robison, Minyun Zhou, Khian Hong Pua, Dylan T Stiles, Joshua AV Blodgett, Daniel W Udwary, Andrew T Rajczewski, Alan S Mann, Siavash Mostafavi, Tara Hardy, Sukrat Arya, Zhigang Weng, Michelle Stewart, Kyle Kenyon, Jay P Morgenstern, Ende Pan, Daniel C Gray, Roy M Pollock, Andrew M Fry, Richard D Klausner, Sharon A Townson, Gregory L Verdine
The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of "undruggability" for an intracellular target. Structural studies reveal extensive protein-WDB002 and protein-protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise "undruggable" targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

Funding

This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. Use of the Life Sciences Collaborative Access Team Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (Grant 085P1000817). We thank Proteros BioStructures GmbH for determining the structure.

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Citation

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. Uddhav K. Shigdel, Seung-Joo Lee, Mathew E. Sowa, Brian R. Bowman, Keith Robison, Minyun Zhou, Khian Hong Pua, Dylan T. Stiles, Joshua A. V. Blodgett, Daniel W. Udwary, Andrew T. Rajczewski, Alan S. Mann, Siavash Mostafavi, Tara Hardy, Sukrat Arya, Zhigang Weng, Michelle Stewart, Kyle Kenyon, Jay P. Morgenstern, Ende Pan, Daniel C. Gray, Roy M. Pollock, Andrew M. Fry, Richard D. Klausner, Sharon A. Townson, Gregory L. Verdine. Proceedings of the National Academy of Sciences Jul 2020, 117 (29) 17195-17203; DOI: 10.1073/pnas.2006560117

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VoR (Version of Record)

Published in

Proceedings of the National Academy of Sciences (PNAS)

Volume

117

Issue

29

Pagination

17195-17203

Publisher

National Academy of Sciences

issn

0027-8424

eissn

1091-6490

Copyright date

2020

Available date

06/08/2020

Spatial coverage

United States

Language

eng

Publisher version

https://www.pnas.org/content/117/29/17195/

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