RESUMEN
Novel chemical biology probes linking a serine hydrolase-directed fluorophosphonate warhead and cereblon-binding pomalidomide were assessed for the degradation of serine hydrolases. A quantitative proteomics approach to detect degraded proteins revealed that, despite the engagement of â¼40 serine hydrolases, degradation was achieved for only a single serine hydrolase, lysophospholipase II (LYPLA2).
Asunto(s)
Colorantes Fluorescentes/química , Hidrolasas/análisis , Fosfatos/química , Proteómica , Serina/análisis , Talidomida/análogos & derivados , Colorantes Fluorescentes/metabolismo , Hidrolasas/metabolismo , Estructura Molecular , Fosfatos/metabolismo , Serina/metabolismo , Talidomida/química , Talidomida/metabolismoRESUMEN
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
Asunto(s)
Descubrimiento de Drogas , Aprendizaje Automático , Proteómica , Bibliotecas de Moléculas Pequeñas , Humanos , Ligandos , Unión Proteica , Proteoma/metabolismo , Proteómica/métodos , Bibliotecas de Moléculas Pequeñas/química , Ubiquitina-Proteína Ligasas/metabolismoRESUMEN
PF-956980 has been used previously as a JAK3-selective chemical probe in numerous cell-based experiments. Here, we report that not only is PF-956980 a pan-JAK ATP-competitive inhibitor but it also causes selective reduction of endogenous JAK2 and JAK3 protein levels in human primary immune cells (in a time-dependent manner), leaving the other JAK family members (JAK1 and TYK2) unchanged. We found that PF-956980 selectively downregulated JAK2 and JAK3 mRNA, corresponding to changes observed at the protein level. This work highlights therapeutic opportunities for the development of pharmacological inhibitors that also modulate the expression of their cognate binding proteins.