Synthesis and crystal structure of peptide dimethyl biphenyl hybrid C52H60N6O10·0.25H2O

The crystal structure of the title compound shows a disorder of the methyl and methoxycarbonyl groups of one alanine residue. Compared to previously reported peptide biphenyl hybrids, the backbone torsion angles are different.


Chemical context
Since the first application in 1922 of peptides in the treatment of diabetes with insulin (Banting et al., 1922), the chemistry of peptides has become a very important domain in the search of new therapeutic drugs. From 2011 to 2018, the global market of drugs has increased from US $ 14.1 to 24.4 billion. With more than 140 peptides in clinical trials, the number of peptide-based drugs is expected to grow significantly (Fosgerau et al., 2015). Despite their tremendous potential, applications of peptides for pharmaceutical purposes are limited by their instability toward enzymatic systems, short half-life, rapid renal clearance, and formulation challenges (Otvos et al., 2014). These problems can be overcome by modifying the linear peptide to enhance the stability and therefore the selectivity and affinity. The biphenyl structure is present in numerous pharmaceuticals and bioactive compounds, as illustrated by the glycopeptide antibiotic vancomycin, the proteasome inhibitor TMC-95A (Kaiser et al., 2004) and arylomycins (Schimana et al., 2002). A statistical analysis of NMR data indicates that compounds containing the biphenyl structure can bind a wide range of proteins with high levels of specificity (Hajduk et al., 2000). Coupling of a small protein chain to the biphenyl structure is a strategy to create a new family of peptidomimetic compounds, which can be used in medicinal chemistry because of its specific conformation and its particular hydrogen-bonding interactions.
The synthesis and biological activity as calpain inhibitor of peptide-biphenyl hybrids type I have been reported by Montero and Mann (Montero et al., 2004a,b;Mann et al., 2002). Amine et al. (2002) synthesized a bis amido-copper(II) complex from N-containing tetradentate ligands having two amido groups with a biphenyl skeleton, which is used as a DNA cleaving agent. Recently, we have reported crystal- ISSN 2056-9890 lographic studies of a peptide-biphenyl hybrid A ( Fig. 1) with tripeptide Pro-Phe-Ala (Le et al., 2020).
We report herein the synthesis and crystallographic study of a peptide-2,2 0 -biphenyl B (Fig. 1) with the introduction of two methyl groups at the 6-6 0 positions to prevent free rotation around the central aryl-aryl bond.
The backbone conformation of the two tripeptide fragments is characterized by the torsion angles !, ', (see Table 1). The torsion angles ' and of amino acids Ala1, Ala2, Phe2 correspond with the usual -helix (right-handed) region of the Ramachandran plot, and only the torsion angles of amino acid Phe1 fall into the corresponding type -sheet Ramachandran plot region. For both prolines, the related torsion angles lie in the region of the Ramachandran plot for proline.
There are six intramolecular hydrogen bonds formed in the structure of the title compound (Table 2). Two hydrogen bonds are formed between the NH and CO groups with HÁ Á ÁO distances of 2.07 Å for N5-H5 Á Á ÁO5 and 2.42 Å for N6-H6Á Á ÁO6. The latter value is noticeably longer than the values observed (from 2.04 to 2.29 Å ) in other reported peptides (Ranganathan et al., 1997;Le et al., 2020). Four other intramolecular bonds are formed between CH and CO groups with distances from 2.35 to 2.59 Å .

Supramolecular features
In the crystal, the packing is characterized by N-HÁ Á ÁO, O-HÁ Á ÁO and C-HÁ Á ÁO hydrogen bonding (see Table 2, Fig. 3). The strongest intermolecular interaction is formed between NH and CO groups of two neighboring peptide residues [N1-H1Á Á ÁO4 i , with d = 2.01 Å ; symmetry code: (i) 1 2 À x, 1 2 + y, 1 À z]. Furthermore, there are six additional hydrogen bonds linking the molecules. Two contacts are established between the water molecule and two tripeptides (O11-H11AÁ Á ÁO8; C13-H13Á Á ÁO11). Four C-HÁ Á ÁO C contacts with HÁ Á ÁO distances ranging from 2.39 to 2.60 Å further consolidate the crystal packing. In addition, the molecules are linked by two intermolecular C-H Á Á Á interactions, one between a proline H atom and the phenyl ring of a phenylalanine residue, the other between a H atom of the disordered methyl group and a phenyl ring of the central biphenyl fragment.  Table 1 Backbone torsion angles !, ', ( ) for the two tripeptide fragments.

Figure 2
A view of the molecular structure of the title compound showing displacement ellipsoids drawn at the 50% probability level and hydrogen bonds (dashed lines) within the asymmetric unit. H atoms are shown as small circles of arbitrary radii.

Figure 1
Peptide-biphenyl hybrids A and B.  (Weigand & Feigel, 1998), PITSUJ (Linden et al., 2018d) and NIKJOI (Samadi et al., 2013). For these structures the dihedral angles between the dimethyl biphenyl rings varies from 82.0 to 95.8 o , larger than the corresponding angle of the title compound.

Synthesis and crystallization
To a round-bottom flask was added 6,6 0 -dimethyl-[1,1 0biphenyl]-2,2 0 -dicarboxylic acid (1 eq.) and SOCl 2 (3 eq.) respectively under a nitrogen atmosphere. The mixture was heated under reflux for 4 h and was then evaporated under vacuum. The acid chloride was used in the next step without further purification.
To a round-bottom flask was added amine HN-prolinephenylalanine-alanine-COOMe (1 eq.), Et 3 N (2 eq.) and anhydrous CH 2 Cl 2 (50mL). To this solution was added a solution of (6,6 0 -dimethyl-[1,1 0 -biphenyl]-2,2 0 -dicarbonyl dichloride in CH 2 Cl 2 at 273 K under an N 2 atmosphere. After completion of the reaction, the mixture was washed with 1 N HCl solution, water and a solution of brine, respectively. The organic phase was dried over Na 2 SO 4 , filtered and evaporated under reduced pressure. The crude product was then purified by flash chromatography (AcOEt/hexane 3:2) to give a white solid (60% yield). The compound was recrystallized by slow evaporation in methanol to give crystals suitable for X-ray diffraction.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. The methyl and methoxycarbonyl groups of alanine show two conformations with refined occupancy factors converging to 0.502 (6) Table 2 Hydrogen-bond geometry (Å , ).

Figure 3
Crystal packing of the title compound, indicating some intermolecular hydrogen bonds (dashed lines).

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.