Ábrányi-Balogh, Péter and Bajusz, Dávid and Orgován, Zoltán and Keeley, Aaron Brian and Petri, László and Péczka, Nikolett and Szalai, Tibor Viktor and Pálfy, Gyula and Gadanecz, Márton and Grant, Emma K. and Imre, Tímea and Takács, Tamás and Randelovic, Ivan and Baranyi, Marcell and Marton, András Dénes and Schlosser, Gitta (Vácziné) and Ashraf, Qirat F. and de Araujo, Elvin D. and Karancsi, Tamás and Buday, László and Tóvári, József and Perczel, András and Bush, Jacob T. and Keserű, György Miklós (2024) Mapping protein binding sites by photoreactive fragment pharmacophores. COMMUNICATIONS CHEMISTRY, 7 (1). No. 168. ISSN 2399-3669
|
Text
s42004-024-01252-w.pdf - Published Version Available under License Creative Commons Attribution. Download (3MB) | Preview |
Abstract
Fragment screening is a popular strategy of generating viable chemical starting points especially for challenging targets. Although fragments provide a better coverage of chemical space and they have typically higher chance of binding, their weak affinity necessitates highly sensitive biophysical assays. Here, we introduce a screening concept that combines evolutionary optimized fragment pharmacophores with the use of a photoaffinity handle that enables high hit rates by LC-MS-based detection. The sensitivity of our screening protocol was further improved by a target-conjugated photocatalyst. We have designed, synthesized, and screened 100 diazirine-tagged fragments against three benchmark and three therapeutically relevant protein targets of different tractability. Our therapeutic targets included a conventional enzyme, the first bromodomain of BRD4, a protein-protein interaction represented by the oncogenic KRas G12D protein, and the yet unliganded N -terminal domain of the STAT5B transcription factor. We have discovered several fragment hits against all three targets and identified their binding sites via enzymatic digestion, structural studies and modeling. Our results revealed that this protocol outperforms screening traditional fully functionalized and photoaffinity fragments in better exploration of the available binding sites and higher hit rates observed for even difficult targets.
| Item Type: | Article |
|---|---|
| Additional Information: | Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary Laboratory of Structural Chemistry and Biology & amp; HUN-REN–ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary GlaxoSmithKline, Hertfordshire, United Kingdom MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary Signal Transduction and Functional Genomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary National Tumor Biology Laboratory and Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary KINETO Lab Ltd, Budapest, Hungary Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary Waters Research Center, Budapest, Hungary MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Budapest, Hungary Department of Chemical & amp; Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON, Canada Export Date: 26 August 2024 Correspondence Address: Keserű, G.M.; Medicinal Chemistry Research Group, Hungary; email: keseru.gyorgy@ttk.hu |
| Subjects: | Q Science / természettudomány > QD Chemistry / kémia |
| SWORD Depositor: | MTMT SWORD |
| Depositing User: | MTMT SWORD |
| Date Deposited: | 18 Sep 2025 12:48 |
| Last Modified: | 18 Sep 2025 12:48 |
| URI: | https://real.mtak.hu/id/eprint/224482 |
Actions (login required)
 |
Edit Item |
