Crystal structures of two alanylpiperidine analogues

The crystal structures of ethyl 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylate and 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylic acid, two analogues studied as potentiators of Ubiquitin C-terminal hydrolase-L1 (UCH-L1), have been determined. Despite being analogues, different crystal packings are observed. A polymorph risk assessment was carried out to study interactions in the second compound.


Chemical context
Ubiquitin C-terminal Hydrolase-L1 is a deubiquitinase that represents 2% of the neuronal soluble proteins in the brain and is involved in the neuropathogenesis of neurodegenerative diseases. Studies have shown that several mutations have an impact on the hydrolase activity of UCH-L1 (Leroy et al., 1998;Maraganore et al., 1999) and that its down-regulation is associated with idiopathic Parkinson's disease (Choi et al., 2004). Finding potentiators of UCH-L1 could be a therapeutic pathway for these diseases (Mitsui et al., 2010). Ethyl 1-[N-(methylsulfonyl)-N-(p-tolyl)-alanyl]piperidine-4-carboxylate was discovered through in silico drug screening as an activator of UCH-L1, with a hydrolase activity up to 111% at 63 mM (Mitsui et al., 2010). We studied the only known activator in the literature, compound I. Derivatives of compound I were then investigated as potential activators and compound II was obtained after a saponification. Compound II bears a carboxylic acid group, which opens up the possibility for co-crystallization and salification in order to modulate the physicochemical properties, such as the solubility. We report the crystal structures of these two compounds as well as a survey of the interactions observed in compound II.

Structural commentary
Both compounds crystallize as colorless plate-like crystals but in different space groups. Compound I crystallizes in the ISSN 2056-9890

Supramolecular features
As compound I does not have any strong hydrogen-bond acceptors, only weak hydrogen bonds are observed in the crystal structure (see Table 1). The amide oxygen atom O1 participates in the formation of two intramolecular hydrogen bonds [S 1 1 (7) motifs; Etter et al., 1990]. The oxygen atom O4 is inter-connected with atom H12C of the sulfonyl methyl of an adjacent molecule [d(HÁ Á ÁO) 2.44 Å ; Table 1], forming an R 2 2 (8) hydrogen bond motif along the a-axis direction (Fig. 2). As compound I bears a tolyl moiety,interactions were expected but were not observed in this crystal packing.
Compound II bearing a carboxylic moiety instead of an ester has an impact on the hydrogen bonds and thus on the  Table 1 Hydrogen-bond geometry (Å , ) for compound I. Symmetry code: (i) Àx; Ày; Àz þ 1.

Figure 2
Crystal packing of I with hydrogen bonds highlighted in green (a) showing one layer of molecules, viewed down the a axis and (b) showing adjacent layers of molecules.

Figure 3
Crystal packing of II showing the tubular arrangement viewed down the a axis. Hydrogen bonds are highlighted in green.

Figure 1
The asymmetric units of compounds I and II, with displacement ellipsoids drawn at the 50% probability level.
crystal packing. In compound II, a tubular arrangement (Fig. 3) can be observed, which is different from that of compound I. In compound II, a hydrogen-bonded ring with an R 2 2 (24) motif is formed by a strong hydrogen bond between H3 of the carboxylic acid group and O5 from an adjacent molecule [d(HÁ Á ÁO) 1.88 (3) Å ; Table 2]. In addition, two intramolecular [S 1 1 (7) motifs] and one intermolecular [R 2 2 (10) motif] weak hydrogen bonds are detected. As in compound I, nointeractions are noticed in the crystal structure. A dimer synthon is observed in the crystal packing in both cases, but for compound I it is ensured by weak hydrogen bonds in contrast to compound II where the dimer is based on strong hydrogen bonds.

Database survey
Searches of the Cambridge Structural Database (CSD, version 5.42, update September 2021;Groom et al. 2016) were carried out with the exact structures of compounds I and II and with substructures containing the significant fragments (alanylpiperidine with and without the sulfonyl methyl and tolyl group). No comparable structures came out of this survey.
A polymorph risk assessment based on the hydrogen bonds in the CSD was carried out. This statistical analysis allows us to estimate which atoms are the donors and the acceptors for hydrogen bonds in the crystal structure (Chemburkar et al., 2000;Galek et al., 2007). This quantifies the probability of hydrogen-bond formation and thus the different probable polymorphs that can arise from a specific compound. The results are summarized in Table 3. A hydrogen-bonding interaction between two carboxylic groups is predicted with the highest probability. We did not observe the carboxylic dimer but rather this group interacting with one oxygen of the sulfonyl methyl. The analysis also predicts other plausible hydrogen-bonded networks (Fig. 4), one that is statistically slightly more likely to be formed than the current one. This suggests that another potential polymorph could be obtained. Thus, we undertook a polymorph screening by several crystallization experiments of compound II. The recrystallization solvents that we tested were cyclohexane, toluene, ethyl acetate, chloroform, dichloromethane, acetone, acetonitrile, 2propanol, ethanol and methanol. They all lead to the same polymorph.

Synthesis and crystallization
Compound I: This was purchased from Evotech (Hamburg, Germany). The product was crystallized by slow evaporation from non-anhydrous ethyl acetate, which provided colorless plate-like crystals suitable for SCXRD. M.p. 442.2 K Compound II: In a round-bottom flask, compound I (405.1 mg, 1.02 mmol, 1.0 eq) dissolved in 8 mL of THF was added to a solution of LiOH (81.9 mg, 3.40 mmol, 3.4 eq) dissolved in 5 mL of water. The mixture was stirred at room temperature for 8 h. The resulting mixture was washed with ether. The aqueous phase was then acidified with HCl 37% to a pH of 2 and extracted with dichloromethane. The combined organic phases were dried over anhydrous Na 2 SO 4 and concentrated under vacuum to yield a white solid (351.0 mg, 93%). The product was crystallized by slow evaporation from methanol, which provided colorless plate-like crystals suitable for SCXRD. 1 168.7, 138.2, 133.5, 132.0, 129.4, 53.3, 44.5, 41.3, 28.5, 20.7, 16.8. M.p. 496.2 K

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 4. All H atoms, except one of the -OH group in II, were refined using a riding model, with C-H = 0.93 (aromatic), 0.96 (methyl) or 0.98 Å (tertiary carbon). Coordinates of the hydrogen atom of the -OH group were refined. The isotropic atomic displacement parameters of the H atoms were set at 1.5U eq of the parent atom for the methyl and alcohol groups, and at 1.2U eq otherwise. Table 3 Hydrogen-bond propensity calculation for compound II.

Donor
Acceptor Propensity

Figure 4
Hydrogen-bond propensity chart for compound II.   For both structures, data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).  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.

1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylic acid (II)
Crystal data 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.