Selective UBC 13 Inhibitors

Robert Ardecky  1 ,  Charitha Madiraju ,  Shu-ichi Matsuzawa ,  Jiwen Zou  1 ,  Santhi Ganji  1 ,  Ian Pass  1 ,  Tram A. Ngo  1 ,  Anthony B. Pinkerton  1 ,  Eduard Sergienko  1 ,  Ying Su  1 ,  Derek Stonich  1 ,  Arianna Mangravita-Novo  2 ,  Michael Vicchiarelli  2 ,  Danielle McAnally  2 ,  Layton H. Smith  2 ,  Jena Diwan  1 ,  Thomas D.Y. Chung  1 ,  Yasuko Matsuzawa ,  Carina Wimer ,  Paul W. Diaz  3 ,  John C. Reed  3
Affiliations
  • 1. Sanford-Burnham Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA.
  • 2. Sanford-Burnham Center for Chemical Genomics at Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827, USA.
  • 3. Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
PMID: 23762936
Abstract

This probe report describes the identification and development of a potent, sub-micromolar (IC50 = 781 nM), first-in-class, small molecule inhibitor of Ubc13 enzyme activity, ML307. The activity of the probe compound was assessed by its ability to suppress Ubc13-mediated formation of heteropolymeric poly-ubquitination chains comprised of a mix of terbium-labeled and fluorescein-labeled ubiquitin molecules, as monitored by a reduction of the time-resolved fluorescent resonance energy transfer (TR-FRET) signal arising from this chains when synthesized in vitro in collaboration with the Ubc13 cofactor UEV1a. ML307 has excellent solubility and stability in buffer and is not a general cysteine protease inhibitor as it is >128-fold selective against Caspase-3, nor a TR-FRET artifact as it is not inhibitory a TR-FRET assay for Bfl-1, an out of class target. ML307 resulted from an extensive elucidation of the structure-activity relationship (SAR) through the purchase and synthesis of over 90 compounds representing 5 related scaffolds. The level of in vitro potency achieved is unprecedented in the current state of art, thus representing a significant advance and providing a chemical tool for assessing the biological roles and biochemical mechanisms of Ubc13.

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