Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments.Becker, D., Kaczmarska, Z., Arkona, C., Schulz, R., Tauber, C., Wolber, G., Hilgenfeld, R., Coll, M., Rademann, J.
(2016) Nat Commun 7: 12761-12761
- PubMed: 27677239
- DOI: 10.1038/ncomms12761
- PubMed Abstract:
Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their pot ...
Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors. A protein-binding nucleophile reacts reversibly with a bis-electrophilic warhead, thereby positioning the second electrophile in close proximity of the active site of a viral protease, resulting in the covalent de-activation of the enzyme. The concept is implemented for Coxsackie virus B3 3C protease, a pharmacological target against enteroviral infections. Using an aldehyde-epoxide as bis-electrophile, active fragment combinations are validated through measuring the protein inactivation rate and by detecting covalent protein modification in mass spectrometry. The structure of one enzyme-inhibitor complex is determined by X-ray crystallography. The presented warhead activation assay provides potent non-peptidic, broad-spectrum inhibitors of enteroviral proteases.
Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany.,Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel Site, University of Lübeck, 23562 Lübeck, Germany.,Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.