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

Both agonists and antagonists of the UDP-activated P2Y(6) receptor (P2Y(6)R) have been proposed for therapeutic use, in conditions such as cancer, inflammation, neurodegeneration and diabetes. Uracil nucleotides containing a south-bicyclo[3.1.0] hexane ((S)-methanocarba) ring system in place of the ribose ring were synthesized and shown to be potent P2Y(6)R agonists in a calcium mobilization assay. The (S)-methanocarba modification was compatible with either a 5-iodo or 4-methoxyimino group on the pyrimidine, but not with a alpha,beta-methylene 5'-diphosphate. (S)-Methanocarba dinucleotide potency was compatible with a N-4-methoxy modification on the proximal nucleoside that is assumed to bind at the P2Y(6)R similarly to UDP; (N)-methanocarba was preferred on the distal nucleoside moiety. This suggests that the distal dinucleotide P2Y(6)R binding site prefers a ribose-like group that can attain a (N) conformation, rather than (S). Dinucleotide binding was modeled by homology modeling, docking and molecular dynamics simulations, which suggested the same ribose conformational preferences found empirically.