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

Abstract

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.

Design, synthesis, crystallization and biological evaluation of new symmetrical biscationic compounds as selective inhibitors of human Choline Kinase α1 (ChoKα1)

“…Among all the compounds, those belonging to the families of pyridinium and quinolinium offered similar or better IC 50 ChoKα1 than did the lead compounds MN58b and RSM932A . In fact, the best inhibitors were 10a and 10l , and the crystal structure of ChoKα1/ 10a showed that the compound binds to the choline binding site, indicating the accuracy of the theoretical predictions, wherein the first one-benzyl- 4- (dimethylamino) pyridinium represents the appropriate fragment to inhibit the enzyme 33 .…”

“…Compound 10a showed good Hs ChoKα1 inhibition (IC 50 = 1.0 μM), thanks to the presence of the 1-benzyl-4-(dimethylamino)pyridinium fragment, which performs a strong π-cation interaction with the Cho binding site ( Fig. 3C ), this having been described as one of the most efficient moieties for ChoKα1 inhibition 33 . Compound 10b showed a reduced ChoKα1 inhibition (IC 50 = 9.56 μM) attributable to the volume of the 4-(pyrrolidin-1-yl)pyridinium cationic head, causing a decrease in the π-cation interaction ( Figure S2A ).…”

“…Deep modeling and virtual screening studies 32 33 34 have suggested the interaction with the choline binding site in the ChoKα1/ 4 complex while keeping the biscationic structure unchanged. Thus a classical bioisosteric exchange between carbon and oxygen atoms could increase, on one hand, the polarity and the solubility of these compounds and, on the other hand, the affinity for the enzyme due to the synclinal conformation of the linker of these molecules.…”

Recent advances in the design of choline kinase α inhibitors and the molecular basis of their inhibition

“…This strategy has been used for the discovery of new hChoKα1 binders based on the chemical structure of previous HC-3-derived inhibitors and the X-ray crystal structure of hChoKα1 in complex with HC-3 (PDB ID: 3G15). 78 The identified pharmacophore model is formed by five moieties (three aromatic rings, a nitrogen atom and a positive charge; Figure 11) that are included in the 1-benzyl-4-(N-methylaniline)pyridinium fragment. This allowed the dissection of common structural features that were important for the binding mechanism and biological activity of the previous HC-3 derivatives (Figure 11 (PDB ID: 5AFV) binds to both the Cho and ATP binding sites, which suggests that this particular molecule has a dual mechanism in which it competes with both ATP/Mg +2 and Cho.…”

“…This allowed the dissection of common structural features that were important for the binding mechanism and biological activity of the previous HC-3 derivatives (Figure 11 (PDB ID: 5AFV) binds to both the Cho and ATP binding sites, which suggests that this particular molecule has a dual mechanism in which it competes with both ATP/Mg +2 and Cho. 78 According to the Kd values, this pharmacophore model is efficient at discovering new hChoKα1 binders that can lead to a new generation of simpler and potent inhibitors by optimization of their chemical properties.…”