Crystal structure of a 1:1 co-crystal of quabodepistat (OPC-167832) with 2,5-dihydroxybenzoic acid using microcrystal electron diffraction

A co-crystal of quabodepistat and 2,5-dihydroxybenzoic acid was obtained and the crystal structure was solved from microcrystal electron diffraction (MicroED) data.


Chemical context
Quabodepistat (OPC-167832), discovered by Otsuka Pharmaceutical Co., Ltd. as an anti-tuberculosis drug (Hariguchi et al., 2020), has a mode of action that involves inhibiting the DprE1 enzyme of M. tuberculosis.2,5-dihydroxybenzoic acid (2,5DHBA) -a derivative of benzoic acid or salicylic acid -is one of the hepatic metabolites of acetylsalicylic acid (aspirin) (Levy & Tsuchiya, 1972).In the pharmaceutical industry, crystal-engineering approaches such as co-crystallization have been useful techniques for modifying the physicochemical properties [e.g., solubility (Yoshimura et al., 2017) or tabletability (Wang et al., 2021)] of an active pharmaceutical ingredient.We obtained the quabodepistat co-crystal with 2,5DHBA by the anti-solvent crystallization method and then attempted to solve its crystal structure using a conventional X-ray diffractometer; however, the crystal size was too small (1 � 0.2 � 0.2 mm).Therefore, we used MicroED (XtaLAB Synergy-ED, Rigaku Corporation, Tokyo, Japan), which is a powerful tool to solve crystal structures when the crystal size is smaller than 1 mm (Ito et al., 2021).Here, we report the crystal structure of the 1:1 co-crystal between quabodepistat and 2,5DHBA, solved using MicroED.

Supramolecular features
Intermolecular interactions via hydrogen bonds are observed between quabodepistat and 2,5DHBA.One of the interactions is between a carboxylic group and an amide.As shown in Fig. 1, they form the common synthon: (amide of quabo-depistat) N7-H7� � �O40 C38 (carboxylic group of 2,5DHBA) and (amide of quabodepistat) C8 O12� � �H39-O39 (carboxylic group of 2,5DHBA).Moreover, the C8 O12 of the amide interacts with a hydroxyl group of a neighboring quabodepistat (O12� � �H22-O22), and the H22-O22 interacts with another hydroxyl of quabodepistat (O22� � �H21-O21).These interactions form a three-dimensional network (Figs. 2 and 3, Table 1).It is worth mentioning that the C-O:C O bond-length ratio of the carboxylic group in 2,5DHBA is 1.08 (1.34A ˚/1.24 A ˚), which suggests that protonation has not occurred for complex binding.Therefore, this material is a co-crystal instead of a salt.The compound TAK-020 has also been reported as a cocrystal with 2,5DHBA (Kimoto et al., 2020).Therein, a carboxylic group of 2,5DHBA interacts with an amide moiety of the triazolinone of TAK-020, which is similar to the synthon observed in the compound reported in this contribution.

Database survey
A search for co-crystals with 2,5-dihydroxybenzoic acid (or gentisic acid) in the Cambridge Structural Database (WebCSD, accessed June 2023; Groom et al., 2016) gave a total of 55 hits.In contrast, a search for co-crystals of quabodepistat with 2,5DHBA in the SciFinder database gave a total of two hits (Sakamoto & Miyata, 2021).

Figure 1
The molecular structure of the quabodepistat:2,5DHBA co-crystal showing the carboxylic group and amide hydrogen bond synthon.Displacement ellipsoids are drawn at the 50% probability level.

Figure 3
Crystal packing viewed down the a axis of the quabodepistat:2,5DHBA co-crystal.

Synthesis and crystallization
Quabodepistat was synthesized at Otsuka Pharmaceutical Co., Ltd.(Tokushima, Japan).Tetrahydrofuran (THF) and hexane were purchased from FUJIFILM Wako Pure Chemical Corporation (Osaka, Japan).2,5DHBA was purchased from Tokyo Kasei Kogyo Co., Ltd.(Tokyo, Japan).Quabodepistat (5 g) and 2,5DHBA (16.9 g, stoichiometric ratio 1:10) were dissolved in 100 mL of THF.250 mL of hexane were added while stirring.Precipitation occurred as soon as hexane was added.The THF/hexane was stirred at room temperature (approximately 298 K) for three days.After filtration, it was dried at room temperature for 24 h, then heated at 383 K for 20 h.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. Two data sets were merged to obtain 93.1% data completeness to 0.9 A ˚resolution.Crystals were illuminated at an electron dose rate of �0.01 e À A ˚À 2 s À 1 .Contiguous diffraction frames were collected every 0.5 � from each crystal by continuously rotating the sample stage at a goniometer rotation speed of 1 � s À 1 ; the sample stage was rotated from À 40 � to 40 � for the first crystal (crystal 1) and from À 60 � to 60 � for the second crystal (crystal 2).The structure was refined kinematically.Refinement with SHELXL was carried out using the scattering factors for electron diffraction (Saha et al., 2022).Pseudo-merohedric twinning was identified and refined as described by Parkin (2021).For absolute structure determination, dynamical refinement is required.However, it was not performed since the absolute configuration of quabodepistat, which has two stereocenters, is known.Extinction was high because of the dynamical effects of electron diffraction (Saha et al., 2022).In spite of the presence of some unusual bond lengths and angles, no unusual intermolecular contacts are observed.This indicates that the structural model presented is correct.Extinction coefficient: 368 (31) Absolute structure: All f" are zero, so absolute structure could not be determined

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.

Table 2
Experimental details.