Mapping protein binding sites by photoreactive fragment pharmacophores
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 KRasG12D 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.
Ábrányi-Balogh Péter, Bajusz Dávid, Orgován Zoltán, Keeley Aaron B., Petri László, Péczka Nikolett, Szalai Tibor Viktor, Pálfy Gyula, Gadanecz Márton, Grant Emma K., Imre Tímea, Takács Tamás, Ranđelović Ivan, Baranyi Marcell, Marton András, Schlosser Gitta, Ashraf Qirat F., de Araujo Elvin D., Karancsi Tamás, Buday László, Tóvári József, Perczel András, Bush Jacob T., Keserű György M.
2024
COMMUNICATIONS CHEMISTRY 2399-3669 2399-3669 7 (1) Paper: 168 , 13 p. 2024