Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Mar 22;50(6):1166-76.
doi: 10.1021/jm060903o. Epub 2007 Feb 16.

Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate

Andrei A Ivanov  1 , Hyojin Ko, Liesbet Cosyn, Savitri Maddileti, Pedro Besada, Ingrid Fricks, Stefano Costanzi, T Kendall Harden, Serge Van Calenbergh, Kenneth A Jacobson
Affiliations

Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate

Andrei A Ivanov et al. J Med Chem. .

Abstract

A rhodopsin-based homology model of the nucleotide-activated human P2Y2 receptor, including loops, termini, and phospholipids, was optimized with the Monte Carlo multiple minimum conformational search routine. Docked uridine 5'-triphosphate (UTP) formed a nucleobase pi-pi complex with conserved Phe3.32. Selectivity-enhancing 2'-amino-2'-deoxy substitution interacted through pi-hydrogen-bonding with aromatic Phe6.51 and Tyr3.33. A "sequential ligand composition" approach for docking the flexible dinucleotide agonist Up4U demonstrated a shift of conserved cationic Arg3.29 from the UTP gamma position to the delta position of Up4U and Up4 ribose. Synthesized nucleotides were tested as agonists at human P2Y receptors expressed in 1321N1 astrocytoma cells. 2'-Amino and 2-thio modifications were synergized to enhance potency and selectivity; compound 8 (EC50 = 8 nM) was 300-fold P2Y2-selective versus P2Y4. 2'-Amine acetylation reduced potency, and trifluoroacetylation produced intermediate potency. 5-Amino nucleobase substitution did not enhance P2Y2 potency through a predicted hydrophilic interaction possibly because of destabilization of the receptor-favored Northern conformation of ribose. This detailed view of P2Y2 receptor recognition suggests mutations for model validation.

PubMed Disclaimer

Figures

Figure 1
Figure 1
a) RMSF of the P2Y2 receptor residues calculated from the 10 ns MD trajectory. b) RMSF of a part of C-terminal region of the P2Y2 receptor. A helical structure of H8 remained stable during the MD simulation.
Figure 2
Figure 2
Superimposition of the initial structure of the human P2Y2 receptor (white) and its structure obtained after MD simulation (colored by residue position: N-terminus in red, TM1 in orange, TM2 in ochre, TM3 – in yellow, TM4 in green, TM5 in cyan, TM6 in blue, TM7 and C-terminus in purple).
Figure 3
Figure 3
Putative electrostatic and disulfide bridges found in the extracellular (a) and intracellular (b) regions of the model of the P2Y2 receptor
Figure 4
Figure 4
The binding modes of various agonists to the human P2Y2 receptor following MCMM calculations. A) UTP 1; B) A 2′-amino-2′-deoxy analogue 8 of UTP. The 2′-amino group is shown in its protonated form, which can be involved in cation-π interactions with F6.51 and can form an additional H-bond with Y3.33; C) 3-Methyl-UTP. The 3-methyl group has an unfavorable position between hydroxyl groups of Y1.39 and S7.43, and backbone oxygen atom of P7.40; D) 5-Methyl-UTP 19. In the model obtained, the 5-methyl group of 19 is unfavorably located between hydroxyl groups of T182 (EL2) and Y1.39. Also, it is close to the methyl groups of V181 (EL2); E) ATP 2; F) Up4U 4a.
Figure 5
Figure 5
Activation by compound 8 of PLC in 1321N1 astrocytoma cells expressing the human P2Y2 receptor or P2Y4 receptor.
Scheme 1
Scheme 1
Preparation of the synthetic intermediate 15, a 2′-amino-2′-deoxy-2-thio nucleoside. Reagents and conditions. (a) NaN3, DMF, 150° C, 15 h; (b) MsCl, pyridine, 0° C, 61%; (c) NaHCO3/EtOH, reflux, 36 h, 57%; (d) H2S, pyridine, 50°C, 250 psi, 24 h, 77%.
Scheme 2
Scheme 2
Synthesis of 2′-amino-2′-deoxy-2-thioUTP 8 and its N-trifluoroacetyl derivative 9. Reagents and conditions. (a) DIEA, ethyl trifluoroacetate, DMF, room temperature, 13 h, 88%; (b) (i) POCl3, PO(OCH3)3, Proton Sponge, 0° C, 2 h, (ii) (Bu3NH+)2P2O7H2, Bu3N, DMF, 10 min, (iii) 0.2 M triethylammonium bicarbonate solution, room temperature, 1 h, 12% (8), 7% (9).
Scheme 3
Scheme 3
Synthesis of 2′-acetylamino-2′-deoxy-2-thioUTP 10. Reagents and conditions. (a) acetic anhydride, H2O, room temperature, 6 h, 57%.
Scheme 4
Scheme 4
Synthesis of Up4-5′-ribose 5. Reagents and conditions. (a) (i) DCC, DMF, room temperature, 1h, (ii) D-ribose-5-phosphate, DMF, room temperature, 48 h, 18%.
Chart 1
Chart 1
Structures of native nucleoside 5′-triphosphate (UTP and ATP) ligands and a dinucleotide (UpnU) ligand of the P2Y2 receptor. EC50 values reported at the human P2Y2 receptor are shown.,,,
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Costanzi S, Mamedova L, Gao ZG, Jacobson KA. Architecture of P2Y nucleotide receptors: Structural comparison based on sequence analysis, mutagenesis, and homology modeling. J Med Chem. 2004;47:5393–5404. - PMC - PubMed
    1. Brunschweiger A, Müller CE. P2 receptors activated by uracil nucleotides--an update. Curr Med Chem. 2006;13:289–312. - PubMed
    1. Jacobson KA, Jarvis MF, Williams M. Purine and pyrimidine (P2) receptors as drug targets. J Med Chem. 2002;45:4057–4093. - PubMed
    1. Jacobson KA, Costanzi S, Ohno M, Joshi BV, Besada P, Xu B, Tchilibon S. Molecular recognition at purine and pyrimidine nucleotide (P2) receptors. Curr Top Med Chem. 2004;4:805–819. - PMC - PubMed
    1. Jacobson KA, Mamedova L, Joshi BV, Besada P, Costanzi S. Molecular recognition at adenine nucleotide (P2) receptors in platelets. Semin Thromb Hemost. 2005;31:205–216. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources