Stereoselective synthesis of Gly-Gly-type (E)-methylalkene and (Z)-chloroalkene dipeptide isosteres and their application to 14-mer RGG peptidomimetics

Racemization-free peptide bond formation via 2-nitrobenzensulfonyl strategy for diastereoselective synthesis of (Z)-fluoroalkene-type peptidomimetics

The Xaa-Pro-type (Z)-fluoroalkene dipeptide isostere (FADI) serves as a versatile surrogate for peptide bonds, effectively restricting cis-trans isomerization of the prolyl amide bond and offering advantages in the development of conformationally constrained peptide analogues. However, the diastereoselective synthesis of tripeptidomimetics incorporating Xaa-Pro-type FADIs is challenging due to the high susceptibility to racemization of the α-stereogenic center during peptide bond formation. Here, we introduce a racemization- and epimerization-free coupling strategy for the stereoselective synthesis of fluoroalkene-type peptidomimetics by reacting Xaa-Pro-type FADIs with amino acid benzyl esters or peptides. This approach leverages the unique properties of the 2-nitrobenzenesulfonyl (Ns) group as an N-terminal protecting group, which promotes sulfonamide anion formation, effectively suppressing α-deprotonation and thereby preventing racemization or epimerization. Our findings highlight the pivotal role of the N-Ns group in peptide synthesis and provide a robust platform for expanding the utility of FADIs in peptidomimetic designing.

Amide-to-chloroalkene substitution for overcoming intramolecular acyl transfer challenges in hexapeptidic neuromedin U receptor 2 agonists

CPN-116 is a peptidic agonist that activates human neuromedin U receptor type 2 (NMUR2) but suffers from chemical instability due to inherent backbone isomerization on the Dap residue. To address this, a Leu-Dap-type (Z)-chloroalkene dipeptide isostere was synthesized diastereoselectively as a surrogate of the Leu-Dap peptide bond to develop a (Z)-chloroalkene analogue of CPN-116. The synthesized CPN-116 analogue is stable in 1.0 M phosphate buffer (pH 7.4) without backbone isomerization and can activate NMUR2 with similar potency to CPN-116 at nM concentrations (EC50 = 1.0 nM).

Substitution Effects of Alkene Dipeptide Isosteres on Adjacent Peptide Bond Rotation

Alkene dipeptide isosteres (ADIs) are promising surrogates of peptide bonds that enhance the bioactive peptide resistance to enzymatic hydrolysis in medicinal chemistry. In this study, we investigated the substitution effects of an ADI on the energy barrier of cis-trans isomerization in the acetyl proline methyl ester (Ac-Pro-OMe) model. The (E)-alkene-type proline analog, which favors a cis-amide conformation, exhibits a lower rotational barrier than native Ac-Pro-OMe. A van't Hoff analysis suggests that the energy barrier is primarily reduced by enthalpic repulsion. It was concluded that although carbon-carbon double bonds and pyrrolidine rings individually increase the rigidity of the incorporation site, their combination can provide structural flexibility and disrupt bioactive conformations. This work provides new insights into ADI-based drug design.

Synthesis and Structural Characterization of β-Turn Mimics Containing (Z)-Chloroalkene Dipeptide Isosteres

Described here is the synthetic, spectroscopic, crystallographic, and computational analysis of a series of peptidomimetics containing l-Xaa-d-Yaa-type (Z)-chloroalkene dipeptide isosteres (CADIs) that were measured in an investigation of the β-turn mimicry of this peptide bond surrogate. We found that the 1,3-allylic strain across the chloroalkene moiety engenders the hyperconjugative interactions between the chloroalkene moiety and the C-H bonding or antibonding orbitals of the C-H bonds in allylic positions. These effects contribute significantly to the stabilization of β-turn structures.

Chloroalkene dipeptide isosteres as peptidomimetics

To date various biologically active peptides have been discovered, characterized and modified for drug discovery. However, the utilization of peptides as therapeutics involves some limitation due to several factors, including low metabolic stability owing to proteolysis and non-specific interactions with multiple off-target molecules. Hence, the development of "peptidomimetics," in which a part or whole of a molecule is modified, is a desirable strategy to enhance the stability or bioactivity of peptide-based drugs. In this situation, we have designed and developed a synthetic method for chloroalkene dipeptide isosteres (CADIs), which involves replacement of an amide bond in peptides with a chloroalkene structure and are classified as peptidomimetics. By a developed synthetic method, an N-tert-butylsulfonyl protected CADI can be obtained utilizing diastereoselective allylic alkylation with organocopper reagents as a key reaction. This CADI can be transformed into an N-fluorenylmethoxycarbonyl protected CADI in short steps. In addition, CADIs are used in Fmoc-based solid-phase peptide synthesis and introduced into a bioactive peptide. Protocols for practical preparation of some CADIs and peptide mimetics containing a CADI are described as detailed recipes.