jm060903o_si_001.pdf (4.26 MB)
Molecular Modeling of the Human P2Y2 Receptor and Design of a Selective Agonist, 2‘-Amino-2‘-deoxy-2-thiouridine 5‘-Triphosphate
journal contributionposted on 2007-03-22, 00:00 authored by Andrei A. Ivanov, Hyojin Ko, Liesbet Cosyn, Savitri Maddileti, Pedro Besada, Ingrid Fricks, Stefano Costanzi, T. Kendall Harden, Serge Van Calenbergh, Kenneth A. Jacobson
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 π−π complex with conserved Phe3.32. Selectivity-enhancing 2‘-amino-2‘-deoxy substitution interacted through π-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 γ position to the δ 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.
model validationcompound 8Selective AgonistMolecular ModelingMonte CarloP 2YSynthesized nucleotides1321 N 1 astrocytoma cellsdinucleotide agonist4 riboseP 2Y receptorHuman P 2Y ReceptorAminoP 2Y receptor recognitionEC 508 nMcationic Arg 3.29Phe 6.51P 2Y potencyδ positionTyr 3.33.4UUTP γ positionP 2Y receptors