Argininamide-type neuropeptide Y Y1 receptor antagonists: the nature of Nω-carbamoyl substituents determines Y1R binding mode and affinity

Abstract

The recently resolved crystal structure of the neuropeptide Y Y₁ receptor (Y₁R), co-crystallized with the high-affinity (pK_i: 10.11), argininamide-type Y₁R antagonist UR-MK299 (2), revealed that the N^ω-carbamoyl substituent (van der Waals volume: 139 ų) is deeply buried in the receptor, occupying a hydrophobic pocket. We synthesized and characterized a series of argininamides, structurally related to 2. Y₁R affinity decreased with increasing size of the carbamoyl residue (minimal pK_i: 5.67). Exceeding a critical size of the substituent (van der Waals volume: 212 ų), the ligands bound in an inverted mode with the carbamoyl side chain located at the surface of the receptor, as suggested by induced-fit docking and MD simulations.