Intestinal Permeability of Cyclic Peptides: Common Key Backbone Motifs Identified

Insufficient oral bioavailability is considered as a key limitation for the widespread development of peptides as therapeutics. While the oral bioavailability of small organic compounds is often estimated from simple rules, similar rules do not apply to peptides, and even the high oral bioavailability that is described for a small number of peptides is not well understood. Here we present two highly Caco-2 permeable template structures based on a library of 54 cyclo­(-d-Ala-Ala₅-) peptides with different <i>N</i>-methylation patterns. The first (all-<i>trans</i>) template structure possesses two β-turns of type II along Ala⁶-d-Ala¹ and Ala³-Ala⁴ and is only found for one peptide with two <i>N</i>-methyl groups at d-Ala¹ and Ala⁶ [<b>(</b><i><b>N</b></i><b>Me­(1,6)</b>]. The second (single-<i>cis</i>) template possesses a characteristic <i>cis</i> peptide bond preceding Ala⁵, which results in type VI β-turn geometry along Ala⁴-Ala⁵. Although the second template structure is found in seven peptides carrying <i>N</i>-methyl groups on Ala⁵, high Caco-2 permeability is only found for a subgroup of two of them [<i><b>N</b></i><b>Me­(1,5)</b> and <i><b>N</b></i><b>Me­(1,2,4,5)</b>], suggesting that <i>N</i>-methylation of d-Ala¹ is a prerequisite for high permeability of the second template structure. The structural similarity of the second template structure with the orally bioavailable somatostatin analog cyclo­(-Pro-Phe-<i>N</i>Me-d-Trp-<i>N</i>Me-Lys-Thr-<i>N</i>Me-Phe-), and the striking resemblance with both β-turns of the orally bioavailable peptide cyclosporine A, suggests that the introduction of bioactive sequences on the highly Caco-2 permeable templates may result in potent orally bioavailable drug candidates