Design and synthesis of bombykol analogues for probing pheromone-binding protein–ligand interactions

Mono-, difluorinated, and thioanalogues of Bombyx mori female sex pheromones (bombykol, 1) were designed according to the ab initio calculations. These rationally designated analogues were synthesized using hydroboration and Sonogashira coupling strategy via (5E,7Z)-undecadien-1-ol (10) as a common intermediate. A new simplified binding assay based on nanoLC-linear ion trap ESI-MS for quantifying complexation of the B. mori pheromone-binding protein (BmPBP) with native (1) and prepared analogues was developed. The binding properties of native 1 and thioanalogue 4 with PBP were studied in detail. The dissociation constant (KD) of 1 and 4 was determined to be 2.1×10−6 M and 2.4×10−6 M, respectively. The similar values for both ligands correlated with ab initio calculations. The new binding assay could be used to determine the KD of other PBPs.