Dipeptides, cyclic, conformations

Funasaki, N., Hada, S., and Neya, S., Conformational effects in reversed-phase liquid chromatographic separation of diastereomers of cyclic dipeptides, Anal. Chem., 65, 1861, 1993. 

The three prototype mixed p agonist/S antagonists described in this chapter have excellent potential as analgesics with low propensity to produce tolerance and dependence. The pseudotetrapeptide DIPP-NH2[ ] has already been shown to produce a potent analgesic effect, less tolerance than morphine, and no physical dependence upon chronic administration. In preliminary experiments, the tetrapeptides DIPP-NH2 and DIPP-NH2[T] were shown to cross the BBB to some extent, but further structural modifications need to be performed in order to improve the BBB penetration of these compounds. The Tyr-Tic dipeptide derivatives can also be expected to penetrate into the central nervous system because they are relatively small, lipophilic molecules. In this context, it is of interest to point out that the structurally related dipeptide H-Dmt-D-Ala-NH-(CH2)3-Ph (SC-39566), a plain p-opioid agonist, produced antinociception in the rat by subcutaneous and oral administration [72], As indicated by the results of the NMR and molecular mechanics studies, the conformation of the cyclic p-casomorphin analogue H-Tyr-c[-D-Orn-2-Nal-D-Pro-Gly-] is stabilized by intramolecular hydrogen bonds. There-... 

Conformationally restricted cyclic dipeptides have several advantages over their linear counterparts ... 

The conformations and molecular structures of cyclic dipeptides containing the DKP ring have been studied by a... 

Riva and coworkers obtained conformationally restricted cyclic peptidomimetics 13a and b by a tandem Ugi-4CR/RCM procedure as reported before (Scheme 13). The initial A-alkylated dipeptide moiety was formed in the Ugi reaction of A-Boc... 

S. Oishi, K. Miyamoto, A. Niida, M. Yamamoto, K. Ajito, H. Tamamura, A. Otaka, Y. Kuroda, A. Asai, N. Fujii, Application of tri- and tetrasubstituted alkene dipeptide mimetics to conformational studies of cyclic ROD peptides. Tetrahedron 62 (2006) 1416-1424. 

Cyclic dipeptides, especially when N-alkylated, undergo extremely fast epimerization (79JA1885). For example, cyclo(L-Pro-L-Phe) is rapidly converted to its diastereomer, cyclo(D-Pro-L-Phe) (80% conversion), by treatment with 0.5 N NaOH at 25°C for 15 min. This diastereomer is the one in which the proline residue has epimerized and not the more activated phenylalanine. CNDO/2 calculations seem to provide a rationale for this. It is not yet completely clear why such base-catalyzed epimerizations of piperazinediones are so easy the conformation of the molecule may play a role in this (79MI1). It is also worth noting that even in linear peptides, rm-amides of N-alkyl-amino acids, which consist of s-trans and s-cis rotamers of almost equal energy, are more prone to racemization than the sec-amides, which exist only in the s-trans configuration. Of course, the amide functions of piperazine-2,5-diones are obliged to assume the s-cis conformation. 

We have been more concerned with the nature of the water around proteins and peptides. To this end we have investigated the structure and energetics of the solvent, both ordered and disordered around the enzyme lysozyme, in the triclinic crystal[l7d]. In addition to lysozyme, we have characterized the water structure and fluctuations in the crystal of a cyclic hexapeptide, (L-Ala-L-Pro-D-Phe)9[20]. and studied the effect of solvent on the conformation of the dipeptide of alanine[2l] and on the equilibria between extended and helical alanine polypeptides such as those discussed in the previous section[22]. The latter systems simulate aqueous solution conditions rather than crystalline environment. 

Figure 38 Representation of the equilibrium between the cyclic and acyclic forms of a hexapeptide. The N- and C-terminal blocking groups, CH3CO— and —NHCH3, respectively, are not shown.233 The standard free energy change for this process depends on the intrinsic chemistry to form a disulfide bond from two sulfhydryl groups, the tendency of Pro-Giy (or any other dipeptide in this position) to form a P turn, and the tendencies of residues X and Y to adopt the extended conformation (and interact with each other). Table 5 of Reference 234 illustrates the range of standard free energy changes for a family of such hexapeptides.

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