Consensus bioactive conformation of cyclic GnRH antagonists defined by NMR and molecular modeling

Little is known of the conformation of peptide hormones as they interact with their receptors for a number of reasons: peptide hormones are notoriously flexible in solution, their receptors are particularly complex, and there is strong evidence that receptor-ligand interaction leading to activation is a dynamic process. Insights into the active conformation of the decapeptide gonadotropin releasing hormone (GnRH) have been obtained previously from the solution structures of four constrained GnRH antagonists {cyclo(1-10)[Ac-Delta(3)-Pro(1),DCpa(2),DTrp(3,6),- NMeLeu(7),beta Ala(10)]GnRH (1), cyclo(4-10)[Ac-Delta(3)pro(1),DFpa(2),DTrp(3),Asp(4),DNal(6),Dpr(10)] GnRH (2), dicyclo(4-10/5-8)[Ac-DNal(1),DCpa(2),DTrp(3),Asp(4),Glu(5),DArg(6),Lys(8),Dpr(10)]GnRH (3), and dicyclo(4-10/5-5'-8)[Ac-DNal(1),DCpa(2),DPal(3),Asp(4),Glu(5)(Gly),DArg(6),Dbu(8),Dpr(10)]GnRH(4)}. However, the precise location of the N-terminal tripeptide in the highly potent (K-i < 0.4 nM) 2-4 remained unclear due to the lack of constraints in this region. The NMR structure of the newly discovered and potent (K-i = 0.24 nM) dicyclo(1-1'-5/4-10)[Ac-Glu(1)(Gly),DCpa(2),DTrp(3),Asp(4),Dbu(5),DNal(6), Dpr(10)]GnRH (5) now allows the definition of the conformation of this region. A combined computational analysis (consensus forcing) of compounds 2-5, designed to explore the common conformations available to them that are simultaneously consistent with the NMR data corresponding to each compound, leads to a consensus structural model for the GnRH pharmacophore. This model shares some common features with the structure of the nonpeptidic GnRH mimetic T-98475. In the course of that comparative study, two additional contact points to those proposed by the authors are identified, suggesting that this model has predictive value.