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 PanDaniel C. Gray, Roy M. Pollock, Andrew M. Fry, Richard D. Klausner, Sharon A. Townson, Gregory L. Verdine

Research output: Contribution to journalArticlepeer-review

36 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)17195-17203
Number of pages9
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number29
DOIs
StatePublished - Jul 21 2020

Keywords

  • FK506-binding protein
  • Genome mining
  • Natural products

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