5-OMe-UDP is a Potent and Selective P2Y₆-Receptor Agonist

Abstract

P2Y nucleotide receptors (P2Y-Rs) play important physiological roles. However, most of the P2Y-R subtypes are still lacking potent and selective agonists and antagonists. Based on data mining analysis of binding interactions in 44 protein-uridine nucleos(t)ides complexes, we designed uracil nucleotides, substituted at the C5/C6 position. All C6-substituted derivatives were inactive at the P2Y(2,4,6)-Rs, while out of the C5-substituted analogues, only 5-OMe-UD(T)P showed activity. To rationalize the data, the ionization and conformation of these analogues were evaluated. The pK(a) values of most analogues substituted at the C5/C6 positions were unaltered compared to UTP (pK(a) 9.42), except for 5-F-UTP nucleotide (pK(a) 7.85). C6-substituted analogues adopt the syn or high-syn conformations, which are disfavored by the receptors, while 5-OMe-UD(T)P adopt the favored anti conformation. Furthermore, 5-OMe-UDP adopts the S sugar puckering, which is the conformation preferred by the P2Y(6)-R, but not the P2Y(2)- or P2Y(4)-Rs. 5-OMe-UDP fulfills the conformational and H-bonding requirements of P2Y(6)-R, thus, making a potent P2Y(6)-R agonist (EC(50) 0.08 microM), more than UDP (EC(50) 0.14 microM).

Synthesis and structure–activity relationship of uracil nucleotide derivatives towards the identification of human P2Y 6 receptor antagonists

“…51 The loss of activity of compound 23, bearing a methyl moiety on N3, at hP2Y 6 -R may be due to a loss of a significant H-bond present in 98% of the complexes of uracil-nucleotides and proteins, between the uracil N3-H and a protein H-bond acceptor. 8,32 At 100 µM, compounds 21 and 22, bearing a phosphonomethylene-sulfonate moiety, neither activated P2Y 6 -R nor inhibited its activity. Analogue 19, bearing a phosphosulfate moiety, although partially hydrolysable by NPP1/3, proved to be a very poor P2Y 6 -R agonist and caused an apparent inhibition of P2Y 6 -R with an IC 50 value of 112 µM (Fig.…”

“…In the present study we have established SAR of several series of UDP derivatives at recombinant hP2Y 6 -R stably expressed in 1321N1 cells. P α ,P ß -CH 2 modification 48 of P2Y 6 -R agonist 5-OMe-UDP, 8 i.e. analogue 9, resulted in reduced agonist activity.…”

“…5-OMe-UDP and 5-F-UDP scaffolds, which are a selective P2Y 6 -R agonist / partial agonist, respectively, 8,31 or 5-alkyl/aryl-UDP scaffold, where C5-substituent is expected to improve the fit of the ligand to P2Y 6 -R hydrophobic pocket. 8,32 Specifically, UDP analogues 6-11 were obtained from nucleosides 32 and 33. The latter were prepared by ribosylation of uracil derivatives 24 and 25 (Scheme 1).…”

“…): δ 11.02 (d, J = 16.0 Hz, P α ),8.58 (d, J = 16.0 Hz, P ß ) ppm 19. F NMR (D 2 O, 188 MHz): δ -165.08 (d, J = 6.1 Hz, F-5) ppm.…”

Pyrimidine nucleotides containing a (S)-methanocarba ring as P2Y6 receptor agonists

“…16–17,18,19,20,21,22,23,24,25,26 Also, a few P2Y 6 R antagonists have reported, but none approaching nM affinity. 2,27,28 Both mononucleotides (mainly UDP and its analogues, e.g.…”