Molecular Modeling of the Human P2Y2 Receptor and Design of a Selective Agonist, 2‘-Amino-2‘-deoxy-2-thiouridine 5‘-Triphosphate

• Published in: Journal of medicinal chemistry 2007-03, Vol.50 (6), p.1166-1176
• Main Authors: Ivanov, Andrei A, Ko, Hyojin, Cosyn, Liesbet, Maddileti, Savitri, Besada, Pedro, Fricks, Ingrid, Costanzi, Stefano, Harden, T. Kendall, Van Calenbergh, Serge, Jacobson, Kenneth A
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphate - chemistry; Binding Sites; Biological and medical sciences; Cell Line, Tumor; Drug Design; Humans; Medical sciences; Models, Molecular; Monte Carlo Method; Neuropharmacology; Neurotransmitters. Neurotransmission. Receptors; Peptidergic system (neuropeptide, opioid peptide, opiates...). Adenosinergic and purinergic systems; Pharmacology. Drug treatments; Protein Conformation; Purinergic P2 Receptor Agonists; Quantitative Structure-Activity Relationship; Receptors, Purinergic P2 - chemistry; Receptors, Purinergic P2Y2; Uridine Triphosphate - analogs & derivatives; Uridine Triphosphate - chemical synthesis; Uridine Triphosphate - chemistry; Uridine Triphosphate - pharmacology
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm060903o

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.