Mind the metal: a fragment library-derived zinc impurity binds the E2 ubiquitin-conjugating enzyme Ube2T and induces structural rearrangements

Morreale, F. E., Testa, A., Chaugule, V. K. , Bortoluzzi, A., Ciulli, A. and Walden, H. (2017) Mind the metal: a fragment library-derived zinc impurity binds the E2 ubiquitin-conjugating enzyme Ube2T and induces structural rearrangements. Journal of Medicinal Chemistry, 60(19), pp. 8183-8191. (doi: 10.1021/acs.jmedchem.7b01071) (PMID:28933844)

Abstract

Efforts to develop inhibitors, activators, and effectors of biological reactions using small molecule libraries are often hampered by interference compounds, artifacts, and false positives that permeate the pool of initial hits. Here, we report the discovery of a promising initial hit compound targeting the Fanconi anemia ubiquitin-conjugating enzyme Ube2T and describe its biophysical and biochemical characterization. Analysis of the co-crystal structure led to the identification of a contaminating zinc ion as solely responsible for the observed effects. Zinc binding to the active site cysteine induces a domain swap in Ube2T that leads to cyclic trimerization organized in an open-ended linear assembly. Our study serves as a cautionary tale for screening small molecule libraries and provides insights into the structural plasticity of ubiquitin-conjugating enzymes.

• Item Type: Articles
• Additional Information: This work was supported by the Medical Research Council (MRC grant number MC_UU_12016/12); the EMBO Young Investigator Programme to H.W.; the European Research Council (ERC-2015-CoG-681582 ICLUb consolidator grant to H.W.; ERC-2012-StG-311460 DrugE3CRLs starting grant to A.C.); the UK Biotechnology and Biological Sciences Research Council (BBSRC BB/G023123/2 David Phillips Fellowship to A.C.); and the Wellcome Trust (strategic awards 100476/Z/ 12/Z for biophysics and drug discovery and 094090/Z/10/Z for structural biology and X-ray crystallography to BCDD).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Chaugule, Dr Viduth and Walden, Professor Helen
• Authors: Morreale, F. E., Testa, A., Chaugule, V. K., Bortoluzzi, A., Ciulli, A., and Walden, H.
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: Journal of Medicinal Chemistry
• Publisher: American Chemical Society
• ISSN: 0022-2623
• ISSN (Online): 1520-4804
• Published Online: 21 September 2017
• Copyright Holders: Copyright © 2017 American Chemical Society
• First Published: First published in Journal of Medicinal Chemistry 60(19):8083-8191
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher.