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Rapid covalent-probe discovery by electrophile-fragment screening

DOI: 10.1021/jacs.9b02822 DOI Help

Authors: Efrat Resnick (Weizmann Institute of Science) , Anthony Bradley (Structural Genomics Consortium, University of Oxford) , Jinrui Gan (Weizmann Institute of Science) , Alice Douangamath (Diamond Light Source) , Tobias Krojer (Structural Genomics Consortium, University of Oxford) , Ritika Sethi (Structural Genomics Consortium, University of Oxford; VIB; Vrije Universiteit Brussel) , Paul P. Geurink (Leiden University Medical Center) , Anthony Aimon (Diamond Light Source) , Gabriel Amitai (Weizmann Institute of Science) , Dom Bellini (University of Warwick) , James Bennett (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Michael Fairhead (Structural Genomics Consortium, University of Oxford) , Oleg Fedorov (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Ronen Gabizon (Weizmann Institute of Science) , Jin Gan (Leiden University Medical Center) , Jingxu Guo (University College London) , Alexander Plotnikov (Weizmann Institute of Science) , Nava Reznik (Weizmann Institute of Science) , Gian Filippo Ruda (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Laura Diaz-saez (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Verena M. Straub (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Tamas Szommer (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Srikannathasan Velupillai (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Daniel Zaidman (Weizmann Institute of Science) , Yanling Zhang (Peking University) , Alun R. Coker (University College London) , Christopher G. Dowson (University of Warwick) , Haim Barr (Weizmann Institute of Science) , Chu Wang (Peking University) , Kilian V. M. Huber (Structural Genomics Consortium, University of Oxford; Target Discovery Institute) , Paul E. Brennan (Structural Genomics Consortium, University of Oxford; University of Warwick; Alzheimer’s Research UK Oxford Drug Discovery Institute) , Huib Ovaa (Leiden University Medical Center) , Frank Von Delft (Structural Genomics Consortium, University of Oxford; Diamond Light Source; University of Johannesburg) , Nir London (Weizmann Institute of Science)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of The American Chemical Society

State: Published (Approved)
Published: May 2019

Abstract: Covalent probes can display unmatched potency, selectivity and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered non-selective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against ten cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. By contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.

Journal Keywords: covalent fragments; reactivity; electrophiles; covalent probes; fragment screening

Subject Areas: Biology and Bio-materials, Chemistry, Medicine


Instruments: I03-Macromolecular Crystallography , I04-1-Macromolecular Crystallography (fixed wavelength)