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

Choline kinase (CK) catalyses the transfer of the ATP γ‐phosphate to choline to generate phosphocholine and ADP in the presence of magnesium leading to the synthesis of phosphatidylcholine. Of the three isoforms of CK described in humans, only the α isoforms (HsCKα) are strongly associated with cancer and have been validated as drug targets to treat this disease. Over the years, a large number of Hemicholinium‐3 (HC‐3)‐based HsCKα biscationic inhibitors have been developed though the relevant common features important for the biological function have not been defined. Here, selecting a large number of previous HC‐3‐based inhibitors, we discover through computational studies a pharmacophore model formed by five moieties that are included in the 1‐benzyl‐4‐(N‐methylaniline)pyridinium fragment. Using a pharmacophore‐guided virtual screening, we then identified 6 molecules that showed binding affinities in the low μM range to HsCKα1. Finally, protein crystallization studies suggested that one of these molecules is bound to the choline and ATP‐binding sites. In conclusion, we have developed a pharmacophore model that not only allowed us to dissect the structural important features of the previous HC‐3 derivatives, but also enabled the identification of novel chemical tools with good ligand efficiencies to investigate the biological functions of HsCKα1.