Constrained NBMPR analogue synthesis, pharmacophore mapping and 3D-QSAR modeling of equilibrative nucleoside transporter 1 (ENT1) inhibitory activity

Abstract

Conformationally constrained analogue synthesis was undertaken to aid in pharmacophore mapping and 3D QSAR analysis of nitrobenzylmercaptopurine riboside (NBMPR) congeners as equilibriative nucleoside transporter 1 (ENT1) inhibitors. In our previous study (Zhu et al., J. Med. Chem. 46, 831-837, 2003), novel regioisomeric nitro-1, 2, 3, 4-tetrahydroisoquinoline conformationally constrained analogues of NBMPR were synthesized and evaluated as ENT1 ligands. 7-NO 2 -1, 2, 3, 4-tetrahydroisoquino-2-yl purine riboside was identified as the analogue with the nitro group in the best orientation at the NBMPR binding site of ENT1. In the present study, further conformational constraining was introduced by synthesizing 5′-O, 8-cyclo derivatives. The flow cytometrically determined binding affinities indicated that the additional 5′-O, 8-cyclo constraining was unfavorable for binding to the ENT1 transporter. The structure-activity relationship (SAR) acquired was applied to pharmacophore mapping using the PHASE program. The best pharmacophore hypothesis obtained embodied an anti-conformation with three H-bond acceptors, one hydrophobic center, and two aromatic rings involving the 3′-OH, 4′-oxygen, the NO 2 group, the benzyl phenyl and the imidazole and pyrimidine portions of the purine ring, respectively. A PHASE 3D-QSAR model derived with this pharmacophore yielded an r 2 of 0.916 for four (4) PLS components, and an excellent external test set predictive r 2 of 0.78 for 39 compounds. This pharmacophore was used for molecular alignment in a comparative molecular field analysis (CoMFA) 3D-QSAR study that also afforded a predictive model with external test set validation predictive r 2 of 0.73. Thus, although limited, this study suggests that the bioactive conformation for NBMPR at the ENT1 transporter could be anti. The study has also suggested an ENT1 inhibitory pharmacophore, and established a predictive CoMFA 3D-QSAR model that might be useful for novel ENT1 inhibitor discovery and optimization.

The Antiepileptic Potential of Nucleosides

“…5B) as ENT1 inhibitors. The most suitable substitution position of the nitro group was explored by varying its position on the aromatic ring of the tetrahydroisoquinone moiety [332,333]. In addition, novel fluorescent substrates have also been produced for probing transporter activity [334].…”

Computer-Aided Drug Design and Discovery, Screening and Synthesis of Small Molecule Inhibitors of Nucleoside Transporters

“…hCNT2 seemed to involve primarily H-bond interactions while hCNT1 utilized electrostatic and steric interactions as well. 63 Two studies 64,65 described 3D QSAR results of NBMPR analogues and their interaction with hENT1 which not only agreed with prior research, but correlated with an NMR study 66 which demonstrated an anti-configuration rather than the syn configuration seen in X-ray diffraction and X-ray crystals of NBMPR. 67,68 Ho et al did a study on hENT4 in which they looked at substrate and inhibitor structure-activity relationships at physiological pH.…”

“…Considering NBMPR possesses a nitro group, and dipyridamole and its potent analogues lack such a highly polar and strong hydrogen bond acceptor group, this prediction correlates with the chemical functionality. As the position of the nitro substituent greatly effected potency, 64 this suggested that steric interaction played a more important role in NBMPR analogue potency compared to the dipyridamole analogues, suggesting that this portion of the molecules may occupy the non-overlapping regions of the binding sites for hENT1.…”

Regulation of hepatic glucose production and AMPK by AICAR but not by metformin depends on drug uptake through the equilibrative nucleoside transporter 1 (ENT1)

“…Therefore, we used a highly selective inhibitor of ENT1, NBMPR, to demonstrate that ENT1 inhibition is sufficient to block the effect of AICAR on HGP and AMPK signalling. Molecular docking data are unavailable for 8CPT‐cAMP analogues docking to ENT1 but in contrast, robust 3D‐Quantitative Structure‐Activity Relationship analysis is available for NBMPR/ENT1 interaction 30, 31, 32. NBMPR did not alter the effects of metformin on AMPK and HGP.…”