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.

Static and dynamic quenching of Ru(II) polypyridyl excited states by iodide.

The metal-to-ligand charge-transfer (MLCT) excited states of Ru(bpy)(2)(deeb)(PF(6))(2), where bpy is 2,2-bipyridine and deeb is 4,4'-(CO(2)CH(2)CH(3))(2)-2,2'-bipyridine, in dichloromethane were found to be efficiently quenched by iodide at room temperature. The ionic strength dependence of the UV-visible absorption spectra gave evidence for ion pairing. Iodide was found to quench the excited states by static and dynamic mechanisms. Stern-Volmer and Benesi-Hildebrand analysis of the spectral data provided a self-consistent estimate of the iodide-Ru(bpy)(2)(deeb)(2+) adduct in dichloromethane, K = 59 700 M(-1). Transient absorption studies clearly demonstrated an electron-transfer quenching mechanism with transient formation of I(2)(*)(-) in high yield, phi = 0.25 for 355 or 532 nm excitation. For Ru(bpy)(2)(deeb)(PF(6))(2) in acetonitrile, similar behavior could be observed at higher iodide concentrations than that required in dichloromethane. The parent Ru(bpy)(3)(2+) compound also ion pairs with iodide in CH(2)Cl(2), and light excitation gave a higher I(2)(*)(-) yield, phi = 0.50. X-ray crystallographic, IR, and Raman data gave evidence for interactions between iodide and the coordinated deeb ligand in the solid state.