F chemical library and F-NMR for a weakly bound complex structure.

Fragment-based drug discovery (FBDD), which involves small compounds <300 Da, has been recognized as one of the most powerful tools for drug discovery. In FBDD, the affinity of hit compounds tends to be low, and the analysis of protein-compound interactions becomes difficult. In an effort to overcome such difficulty, we developed a F-NMR screening method optimizing a F chemical library focusing on highly soluble monomeric molecules. Our method was successfully applied to four proteins, including protein kinases and a membrane protein. For FKBP12, hit compounds were carefully validated by protein thermal shift analysis, H-N HSQC NMR spectroscopy, and isothermal titration calorimetry to determine dissociation constants and model complex structures. It should be noted that the H and F saturation transfer difference experiments were crucial to obtaining highly precise model structures. The combination of F-NMR analysis and the optimized F chemical library enables the modeling of the complex structure made up of a weak binder and its target protein.