Pharmacophore-Based Virtual Screening to Discover New Active Compounds for Human Choline Kinase α1

C holine kinase (CK) catalyses the transfer of the ATP g-phosphate to choline to generate phosphocholine and ADP in the presence of magnesium leading to the syn- thesis of phosphatidylcholine. Of the three isoforms of CK described in humans, only the a isoforms (HsCKa )a re strongly associated with cancer and have been validated as drug targets to treat this disease. Over the years, al arge number of Hemicholinium-3 (HC-3)-based HsCKa biscation- ic inhibitors have been developed though the relevant common features important for the biological function have not been defined. Here, selecting al arge number of previous HC-3-based inhibitors, we discover through com- putational studies ap harmacophore model formed by five moieties that are included in the 1-benzyl-4-(N-methylanili- ne)pyridinium fragment. Using ap harmacophore-guided virtual screening, we then identified 6m olecules that showed binding affinities in the low m Mr ange to HsCKa1. Finally ,p rotein crystallization studies suggested that one of these molecules is bound to the choline and ATP-binding sites. In conclusion, we have developed ap harmacophore model that not only allowed us to dissect the structural im- portant features of the previous HC-3 derivatives, but also enabled the identification of novel chemical tools with good ligand efficiencies to investigate the biological func- tions of HsCKa1.