(S)-N-[(4-{(S)-1-[2-(4-Meth­oxy­benz­amido)-2-methyl­propano­yl]pyrrolidine-2-carboxamido}-3,4,5,6-tetra­hydro-2H-pyran-4-yl)carbon­yl]proline dimethyl sulfoxide monosolvate (4-MeBz-Aib-Pro-Thp-Pro-OH)

Svetlana A Stoykova; Anthony Linden; Heinz Heimgartner

doi:10.1107/S1600536813004546

. 2013 Feb 20;69(Pt 3):o419–o420. doi: 10.1107/S1600536813004546

(S)-N-[(4-{(S)-1-[2-(4-Methoxybenzamido)-2-methylpropanoyl]pyrrolidine-2-carboxamido}-3,4,5,6-tetrahydro-2H-pyran-4-yl)carbonyl]proline dimethyl sulfoxide monosolvate (4-MeBz-Aib-Pro-Thp-Pro-OH)

Svetlana A Stoykova ^a, Anthony Linden ^a,^*, Heinz Heimgartner ^a

PMCID: PMC3588532 PMID: 23476594

Abstract

The asymmetric unit of the title compound, C₂₈H₃₈N₄O₈·C₂H₆OS, contains one tetrapeptide and one disordered dimethyl sulfoxide (DMSO) molecule. The central five-membered ring (Pro²) of the peptide molecule has a disordered envelope conformation [occupancy ratio 0.879 (2):0.121 (2)] with the envelope flap atom, the central C atom of the three ring methylene groups, lying on alternate sides of the mean ring plane. The terminal five-membered ring (Pro⁴) also adopts an envelope conformation with the C atom of the methylene group closest to the carboxylic acid function as the envelope flap, and the six-membered tetrahydropyrane ring shows a chair conformation. The tetrapeptide exists in a helical conformation, stabilized by an intramolecular hydrogen bond between the amide N—H group of the heterocyclic α-amino acid Thp and the amide O atom of the 4-methoxybenzoyl group. This interaction has a graph set motif of S(10) and serves to maintain a fairly rigid β-turn structure. In the crystal, the terminal hydroxy group forms a hydrogen bond with the amide O atom of Thp of a neighbouring molecule, and the amide N—H group at the opposite end of the molecule forms a hydrogen bond with the amide O atom of Thp of another neighbouring molecule. The combination of both intermolecular interactions links the molecules into an extended three-dimensional framework.

Related literature

For the azirine/oxazolone method, see: Heimgartner (1991 ▶); Altherr et al. (2007 ▶); Stamm & Heimgartner (2004 ▶). For the synthesis of Thp-containing peptides via the azirine/oxazolone method and their crystal structures, see: Suter et al. (2000 ▶). For the synthesis of Aib-Pro containing peptides via azirine coupling, see: Luykx et al. (2003 ▶); Stamm & Heimgartner (2006 ▶); Pradeille et al. (2012 ▶); Stoykova et al. (2012 ▶). For the insertion of Xaa-Pro units (Xaa = heterocyclic α-amino carboxylic acid) into peptides, see: Suter et al. (2000 ▶); Stamm et al. (2003 ▶). For the conformation of peptides containing α,α-disubstituted α-amino acids, see: Prasad & Balaram (1984 ▶); Toniolo & Benedetti (1991 ▶); Schweitzer-Stenner et al. (2007 ▶); Aravinda et al. (2008 ▶); Demizu et al. (2012 ▶). For crystal structures of peptaibols, see: Whitmore & Wallace (2004 ▶), authors of The Peptaibol Database http://www.cryst.bbk.ac.uk/peptaibol. For graph-set theory, see: Bernstein et al. (1995 ▶). graphic file with name e-69-0o419-scheme1.jpg

Experimental

Crystal data

C₂₈H₃₈N₄O₈·C₂H₆OS
M _r = 636.76
Orthorhombic,
a = 10.8594 (1) Å
b = 13.7414 (2) Å
c = 21.1929 (3) Å
V = 3162.48 (7) Å³
Z = 4
Mo Kα radiation
μ = 0.16 mm⁻¹
T = 160 K
0.28 × 0.20 × 0.18 mm

Data collection

Nonius KappaCCD area-detector diffractometer
53400 measured reflections
9238 independent reflections
7711 reflections with I > 2σ(I)
R _int = 0.044

Refinement

R[F ² > 2σ(F ²)] = 0.042
wR(F ²) = 0.103
S = 1.02
9231 reflections
433 parameters
21 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.28 e Å⁻³
Δρ_min = −0.33 e Å⁻³
Absolute structure: Flack & Bernardinelli (1999 ▶, 2000 ▶), 4115 Friedel pairs
Flack parameter: −0.02 (8)

Data collection: COLLECT (Nonius, 2000 ▶); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997 ▶); data reduction: DENZO-SMN and SCALEPACK (Otwinowski & Minor, 1997 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEPII (Johnson, 1976 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Supplementary Material

Click here for additional data file.^{(45.6KB, cif)}

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536813004546/nc2305sup1.cif

e-69-0o419-sup1.cif^{(45.6KB, cif)}

Click here for additional data file.^{(451.5KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813004546/nc2305Isup2.hkl

e-69-0o419-Isup2.hkl^{(451.5KB, hkl)}

Click here for additional data file.^{(5.2KB, cdx)}

Supplementary material file. DOI: 10.1107/S1600536813004546/nc2305Isup3.cdx

Click here for additional data file.^{(12.5KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536813004546/nc2305Isup4.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯O7ⁱ	0.87 (2)	1.81 (3)	2.6669 (17)	168 (2)
N6—H6⋯O13	0.87 (2)	2.19 (2)	3.0468 (17)	169.5 (18)
N12—H12⋯O4ⁱⁱ	0.80 (2)	2.37 (2)	3.1247 (18)	156 (2)

Open in a new tab

Symmetry codes: (i) Inline graphic ; (ii) .

supplementary crystallographic information

Comment

Peptaibols are naturally occurring peptides containing high proportions of α-aminoisobutyric acid (Aib) and occasionally other 2,2-disubstituted glycines (Whitmore & Wallace, 2004). As a result of the presence of α,α-disubstituted α-amino acids, these peptides adopt fairly rigid helical structures, the preferred conformation being the 3₁₀-helix as a sequence of β-turns (Prasad & Balaram, 1984; Toniolo & Benedetti, 1991; Schweitzer-Stenner et al., 2007; Aravinda et al., 2008; Demizu et al., 2012). In the past we have elaborated the 'azirine/oxazolone method' as a convenient protocol for the introduction of α,α-disubstituted α-amino acids into peptide chains in solution (Heimgartner, 1991; Altherr et al., 2007) as well as on solid phase (Stamm & Heimgartner, 2004). In addition, it has been shown that the dipeptide unit Aib-Pro, which frequently appears in natural peptaibols (Whitmore & Wallace, 2004), can be inserted conveniently into a peptide chain via 'azirine coupling' with methyl N-(2,2-dimethyl-2H-azirin-3-yl)prolinate (Luykx et al., 2003; Pradeille et al., 2012; Stoykova et al., 2012). In a similar manner, dipeptide segments consisting of a heterocyclic α-amino carboxylic acid and proline have been inserted into peptides via 'azirine coupling' (Suter et al., 2000; Stamm et al., 2003). In all cases, the heterocyclic α-amino carboxylic acid behaves in a similar way to other α,α-disubstituted α-amino acids, that is they induce helical conformations of the peptide. The synthesis of the title tetrapeptide was carried out with the aim of further testing the scope of the 'azirine coupling' with a combination of two different Xaa-Pro synthons.

The crystals of the title compound are enantiomerically pure and the expected absolute configuration, S at C2 and C8 of the two proline residues, has been confirmed by the diffraction experiment. The asymmetric unit contains one molecule of the peptide plus one molecule of DMSO. The S atom of the DMSO molecule is disordered over two sites (details in the Experimental section). The peptide molecule exists in a β-turn conformation stabilized by an intramolecular hydrogen bond between N6—H of the heterocyclic amino acid Thp and the O atom of the amide C=O group of the 4-methoxybenzoyl group (Fig. 1; Table 1). This interaction has a graph set motif (Bernstein et al., 1995) of S(10). The central five-membered ring of Pro2 is disordered in that the ring has an envelope conformation in which atom C23 as the envelope flap is located on alternate sides of the mean ring plane with the major conformation found in 72.0 (10)% of the molecules. The other 5-membered ring (Pro4) also has an envelope conformation with atom C14 as the envelope flap. The six-membered tetrahydropyrane ring (Thp) exists in a chair conformation. All four amide groups are quite planar.

Classical intermolecular hydrogen bonds of the O—H···O and N—H···O type link the molecules into a three-dimensional framework (Fig. 2). This network is built from two substructures. In the first substructure, the carboxylic acid group, O2—H, forms an intermolecular hydrogen bond with one of the central amide O atoms, O7, of a neighbouring molecule, thereby linking the peptide molecules into extended chains which run parallel to the [100] direction and have a graph set motif of C(10). In the second substructure, the amide N—H group, N12—H, at the opposite end of the molecule forms an intermolecular hydrogen bond with the first amide O atom, O4, in the backbone of a different neighbouring molecule. This interaction links the peptide molecules into extended chains which run parallel to the [001] direction and have a graph set motif of C(11).

Experimental

The title compound was prepared in analogy to earlier described procedures (Suter et al., 2000; Stoykova et al., 2012) by treatment of (S)-N-[N-(4-methoxyphenyl)-2-methylalanyl]proline (4-MeOBz-Aib-Pro-OH; Stoykova et al., 2012) with two mol-equivalents of methyl (S)-N-(1-aza-6-oxaspiro[2.5]oct-1-en-2-yl)prolinate (Suter et al., 2000) in dry THF at room temperature for 48 h. After removing the solvent under reduced pressure, the residue was purified by column chromatography (silica gel, CH₂Cl₂/MeOH; gradient 110:1 to 20:1). Saponification of the resulting tetrapeptide ester was achieved by treatment with 4 mol-equivalents of LiOH.H₂O in THF/MeOH/H₂O 3:1:1 at room temperature for 25 h. After completion of the reaction, 1M HCl was added until pH 1 was reached, and the organic solvent was evaporated. The residue was extracted with CH₂Cl₂, the combined organic phase was dried over MgSO₄, and the solvent evaporated to give the title compound in 74% yield (over two steps). Colourless crystals suitable for an X-ray crystal structure analysis were grown from DMSO at ca 278 K.