Structural Evidence ofN6-Isopentenyladenosine As a New Ligand of Farnesyl Pyrophosphate Synthase

Abstract

N6-isopentenyladenosine (i6A), a modified nucleoside belonging to the cytokinin family, has shown in humans many biological actions, including antitumoral effects through the modulation of the farnesyl pyrophosphate synthase (FPPS) activity. To investigate the relationship between i6A and FPPS, we undertook an inverse virtual screening computational target searching, testing i6A on a large panel of 3D protein structures involved in cancer processes. Experimentally, we performed an NMR investigation of i6A in the presence of FPPS protein. Both inverse virtual screening and saturation transfer difference (STD) NMR outcomes provided evidence of the structural interaction between i6A and FPPS, pointing to i6A as a valuable lead compound in the search of new ligands endowed with antitumoral potential and targeting FPPS protein.

The isoprenoid derivative N6‐benzyladenosine CM223 exerts antitumor effects in glioma patient‐derived primary cells through the mevalonate pathway

“…The mean K D value calculated for the single protons of CM223 (Figure B) was 0.19 mM. This value, which is fivefold lower than the K D value for the i6A‐FPPS interaction (Scrima et al, ), indicates a stronger binding to the FPPS target for CM223 and suggests that the benzyl substituent at N 6 may lead to more potent FPPS inhibitors.…”

“…To confirm that the i6A analogues bound to the active site of FPPS and not to an allosteric binding site (Jahnke et al, ), the FPPS‐ligand complexes were titrated with increasing concentrations of the known allosteric modulator. 3‐carboxymethyl‐5,7‐dichloro‐1H‐indole‐2‐carboxylic acid (IC 50 = 6.0 μM) (Jahnke et al, ) or zoledronic acid, high‐affinity FPPS inhibitor (data not shown) (Scrima et al, ). The quantitative evaluation of STD data confirmed that the compound CM223 interacted with the FPPS binding site with a consistent contribution from the N 6 substituent.…”

“…We then carried out molecular docking calculations (AutoDock 4.2 software) (Morris et al, ), using the interprotonic distances calculated on the basis of STD NMR experiments, as restraints. Compounds CM223 and FP13, respectively representing the strongest and weakest binding to FPPS, were subjected to molecular docking simulations against the 3D FPPS protein model (PDB code: 1ZW5), selected in inverse virtual screening procedure in our previous work (Kavanagh et al, ; Scrima et al, ). For an exhaustive exploration of conformational space, iterative docking calculations consisting of 250 runs were executed, yielding 1500 structures.…”

“…However, as it is involved in many cancer‐related pathways, and appears deregulated in many tumours (Thurnher et al, ), it has attracted the interest of pharmaceutical companies and has led to the identification of new, specific, anticancer compounds (Fournier et al, ; Jahnke et al, ). In our search for the molecular targets of i6A, using in silico inverse virtual screening (Chen and Zhi, ; Lauro et al, ; Wang et al, ), we recently gained additional evidence that FPPS is an important molecular target for i6A (Scrima et al, ). Saturation transfer difference (STD) NMR experiments and enzymic assays indicated that i6A bound to the active site of FPPS, exerting a moderate inhibition of its enzymic activity ( vide infra ) (Laezza et al, ; Ciaglia et al, ).…”

“…Saturation transfer difference (STD) NMR experiments and enzymic assays indicated that i6A bound to the active site of FPPS, exerting a moderate inhibition of its enzymic activity ( vide infra ) (Laezza et al, ; Ciaglia et al, ). Indeed, molecular docking calculations showed that i6A was able to occupy the FPPS active site, with a significant contribution from the isopentenyl portion of the molecule (Scrima et al, ).…”