A cyclic carbo-isosteric penta-depsipeptide: cyclo(Phe(1)-d-Ala(2)-Gly(3)-Phe(4)-APO(5)).

The title compound, cyclo(Phe(1)-d-Ala(2)-Gly(3)-Phe(4)-APO(5)), C26H32N4O5, is the minor diastereoisomer of a cyclic penta-peptidomimetic analogue containing a novel 2-amino-propyl lactone (APO) motif, which displays the same number of atoms as the native amino acid glycine and has a methyl group in place of the carbonyl O atom. The crystal structure presented here allows the analysis of the secondary structure of this unprecedented cyclic carbo-isosteric depsipeptide. The conformation of the central ring is stabilized by an intra-molecular N-H⋯O hydrogen bond between the carbonyl O atom of the first residue (Phe(1)) and the amide group H atom of the fourth residue (Phe(4)). Based on the previously reported hydrogen bond and on the values of the torsion angles ϕ and ψ, the loop formed by the first, second, third and fourth residues (Phe(1), d-Ala(2), Gly(3) and Phe(4)) can be classified as a type II' β-turn. The loop around the new peptidomimetic motif, on the other hand, resembles an open γ-turn containing a weak N-H⋯O hydrogen bond between the carbonyl group O atom of the fourth residue (Phe(4)) and the amide unit H atom of the first residue (Phe(1)). In the crystal, the peptidomimetic mol-ecules are arranged in chains along the b-axis direction. Within such a chain, the mol-ecules of the structure are linked via N-H⋯O hydrogen bonds between the amide group H atom of the secondary residue (d-Ala(2)) and the carb-oxy unit O atom of the fourth residue (Phe(4)) in a neighboring mol-ecule. The newly formed methyl stereocentre of the APO peptidomimetic motif (APO(5)) was obtained as the minor diastereoisomer in a ring-closing reductive amination reaction and adopts an R configuration.

The title compound, cyclo(Phe 1 -d-Ala 2 -Gly 3 -Phe 4 -APO 5 ), C 26 H 32 N 4 O 5 , is the minor diastereoisomer of a cyclic penta-peptidomimetic analogue containing a novel 2-aminopropyl lactone (APO) motif, which displays the same number of atoms as the native amino acid glycine and has a methyl group in place of the carbonyl O atom. The crystal structure presented here allows the analysis of the secondary structure of this unprecedented cyclic carbo-isosteric depsipeptide. The conformation of the central ring is stabilized by an intramolecular N-HÁ Á ÁO hydrogen bond between the carbonyl O atom of the first residue (Phe 1 ) and the amide group H atom of the fourth residue (Phe 4 ). Based on the previously reported hydrogen bond and on the values of the torsion angles ' and , the loop formed by the first, second, third and fourth residues (Phe 1 , d-Ala 2 , Gly 3 and Phe 4 ) can be classified as a type II 0 -turn. The loop around the new peptidomimetic motif, on the other hand, resembles an open -turn containing a weak N-HÁ Á ÁO hydrogen bond between the carbonyl group O atom of the fourth residue (Phe 4 ) and the amide unit H atom of the first residue (Phe 1 ). In the crystal, the peptidomimetic molecules are arranged in chains along the b-axis direction. Within such a chain, the molecules of the structure are linked via N-HÁ Á ÁO hydrogen bonds between the amide group H atom of the secondary residue (d-Ala 2 ) and the carboxy unit O atom of the fourth residue (Phe 4 ) in a neighboring molecule. The newly formed methyl stereocentre of the APO peptidomimetic motif (APO 5 ) was obtained as the minor diastereoisomer in a ring-closing reductive amination reaction and adopts an R configuration.

Chemical context
Cyclic peptidomimetics, with their ability to mimic the secondary structure of peptides, represent a very attractive class of macrocycles. While still being modular and promising a strong affinity for a broad range of biological targets, they have improved pharmacological properties and bioavailability compared to linear peptides.
During our research, we have developed a highly selective cyclization method to access a new class of cyclic carbo-isos- ISSN 2056-9890 teric depsipeptides (Gué ret et al., 2014). Our strategy allowed the formation of a novel APO motif which is believed to mimic the glycine amino-acid structure. In order to study the secondary structure of our peptidomimetic motifs, we have started crystallization trials for various analogues. The first compound for which we obtained crystals suitable for single crystal structure determination was the title compound cyclo(Phe 1 -d-Ala 2 -Gly 3 -Phe 4 -APO 5 ).

Structural commentary
The cyclic carbo-isosteric depsipeptide cyclo(Phe 1 -d-Ala 2 -Gly 3 -Phe 4 -APO 5 ) was obtained as the minor diastereoisomer in a ring-closing reductive amination reaction between the Cterminal methyl ketone and the N-terminal amine of phenylalanine 1 of the linear precursor H 2 N-Phe 1 -d-Ala 2 -Gly 3 -Phe 4 -CO 2 CH 2 COCH 3 . The two natural amino acids, Phe 1 and Phe 4 are in an l-configuration, whereas the unnatural alanine unit, Ala 2 is in a d-configuration, following the Cahn-Ingold-Prelog priority rules or CORN rules (Cahn et al., 1966). Based on the known stereochemistry of the backbone amino acids, the absolute configuration of the newly formed methyl stereocentre to the secondary amine (N9) of the minor diastereoisomer could be unambiguously assigned as C19R. The result is supported by a Flack x parameter of 0.10 (11), calculated using the quotient method (Parsons & Flack, 2004) as implemented in the 2013 version of SHELXL (Sheldrick, 2008). The structure of the title compound in the crystal, including the residue-labelling scheme, is shown in Fig. 1.
The secondary structure of the cyclic peptidomimetic, in which all peptidic bonds adopt a trans conformation, is stabilized by a -turn containing an intramolecular hydrogen bond (Table 1, Fig. 2) between the carbonyl oxygen O23 of the first residue (Phe 1 ) and the amide hydrogen N15-H15 of the residue located three residues after the first residue (Phe 4 ). The related torsion angle values fall into the corresponding type II 0 -turn Ramachandran plot area (Ramachandran et al., 1963). The APO peptidomimetic motif adopts an open -turn with a loose hydrogen bond between the carbonyl oxygen of the lactone unit (O25) of the first residue (Phe 4 ) and the secondary amine (N9) of the residue located two residues after the first (Phe 1 ). Selected backbone torsion angles are given in Table 2 and a review on the secondary structure of peptides and proteins is given by Smith et al. (1980). The structure of the title compound in the crystal, including the residuelabelling scheme. Non-H atoms are represented by displacement ellipsoids drawn at the 50% probability level. H atoms are represented as small spheres of arbitrary radius. The atom labelling has been omitted for clarity but is displayed in Fig. 2.

Figure 2
The atom-and residue-labelling scheme of the title compound, showing the intramolecular hydrogen bond. All atoms are represented as small spheres of arbitrary radius. Table 1 Hydrogen-bond geometry (Å , ).
Within each chain, the peptide molecules are linked via hydrogen bonds between O25 and N21-H21 (blue). The individual chains are loosely connected via hydrogen bonds between O34 and N18-H18 (orange).

Synthesis and crystallization
Step 1 The linear precursor H 2 N-Phe 1 -d-Ala 2 -Gly 3 -Phe 4 -CO 2 CH 2 COCH 3 (90.7 mg, 152 mmol) was stirred in hydrogen chloride (4 M in 1,4-dioxane, 20.0 ml) at 0 C for 1 h, then at room temperature for 2 h. The reaction mixture was concentrated under reduced pressure and the resulting amine was used in the following step without further purification.
Step 2 The previously obtained crude amine was dissolved in DMF (15.2 ml) and acetic acid (152 ml, 2.66 mmol) was added. The reaction mixture was stirred at room temperature for 1.5 h.

Figure 3
Packing diagram along the face diagonal of the plane defined by the a and c axes, showing the hydrogen-bonded chains parallel to b. Hydrogen bonds are indicated as green (intramolecular)

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. The C-bound H atoms were calculated in idealized positions (C-H = 0.98-1.00 Å ) and refined using a riding model with U iso (H) = 1.2U eq (parent atom). The hydrogen atoms of the amide groups and the hy-droxy group were located in a difference Fourier map and allowed to refine freely. A cyclic carbo-isosteric penta-depsipeptide: cyclo(Phe 1 -D-Ala 2 -Gly 3 -Phe 4 -

Special details
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.