Fragment-based Drug Discovery (FBDD) is an expanding and efficient method of developing compounds that bind to specific protein targets for use as therapeutics or biological tools.1 This is true even for difficult targets like protein-protein interaction sites. The prerequisites for this method are: (1) Sensitive and efficient screen for fragment detection (2) A robust assay for fragment binding and affinity (3) Atomic resolution structures of the protein-ligand complexes to support compound optimisation. A combination of protein and ligand observed NMR techniques, SPR and X-ray crystallography offers relatively high sensitivity for detection towards weak/small ligands and proteins with shallow binding pockets.2 However not all the targets are amenable to protein NMR or X-Ray crystallography. In those cases the use of appropriate ligand detected NMR techniques can be employed to detect site of protein binding for small molecules. This presentation will discuss NMR based fragment detection and binding studies in order to develop modulators for a cytokine signalling (JAK- STAT-SOCS) pathway2,3 by FBDD. We have used a combination of site specific and competition based CPMG and STD experiments as well as protein NMR experiment i.e. HSQC (where feasible) to obtain maximized binding site information for fragments those binds to therapeutically relevant protein-protein interaction sites (SOCS3-STAT and JAK2-SOCS3) in cytokine signalling pathway.
Abbreviations
SOCS: suppressor of cytokine signaling, JAK: Janus kinase, STAT: Signal Transducer and Activator of Transcription, CPMG: Carr-Purcell-Meiboom-Gill sequence, STD: Saturation Transfer Difference, HSQC: Heteronuclear Single Quantum Coherence