I. INTRODUCTION
Edoxaban tosylate monohydrate is an anticoagulant (under the brand names Lixiana®, Savaysa®, and others), used for treatment of deep vein thrombosis and pulmonary embolism. It functions as an anticoagulant, a coagulant factor Xa inhibitor, and a platelet aggregation inhibitor. Edoxaban tosylate monohydrate was developed by Daiichi Sankyo and approved in Japan in 2011. The systematic name (CAS Registry number 1229194-11-9) is N-(5-chloropyridin-2-yl)-N′-((1S,2R,4S)-4-(N,N-dimethylcarbamoyl)-2-(5-methyl-4,5,6,7-tetrahydrothiazolo(5,4-c)pyridine-2-carboxamido)cyclohexyl)ethanediamide p-toluenesulfonate monohydrate. The molecular structure of edoxaban tosylate monohydrate is illustrated in Figure 1.
Figure 1. Two-dimensional diagram of the molecular structure of edoxaban tosylate monohydrate.
Edoxaban was first claimed in US Patent 7,365,205 (Ohta et al., Reference Ohta, Komoriya, Yoshino, Nagamochi and Ono2008). European Patent Applications EP1405852 A1 (Ohta et al., Reference Ohta, Komoriya, Yoshino, Uoto, Nakamoto, Naito, Mochizuki, Nagata, Kanno, Haginoya, Yoshikawa, Nagamochi, Kobayashi and Ono2004) and EP 2371830 A1 (Koyama, Reference Koyama2011), as well as US Patent Application US 2017/0022220 A1 (Kawanami and Kitani, Reference Kawanami and Kitani2017), among others, disclose processes for the preparation of edoxaban tosylate monohydrate, but no powder diffraction data are provided. Canadian Patent Application CA 2793413 (Suzuki and Ono, Reference Suzuki and Ono2011) reported powder patterns for both Form I and Form II of edoxaban tosylate monohydrate. European Patent Application EP 3318568 A1 (Berenguer Maimó et al., Reference Berenguer Maimó, Racamonde Villanueva and Winter2018) claims a process for preparing edoxaban tosylate monohydrate and included a high-quality powder pattern of “edoxaban tosylate monohydrate reference standard” used for characterizing the products of the invention.
This work was carried out as part of a project (Kaduk et al., Reference Kaduk, Crowder, Zhong, Fawcett and Suchomel2014) to determine the crystal structures of large-volume commercial pharmaceuticals and include high-quality powder diffraction data for these pharmaceuticals in the Powder Diffraction File (Gates-Rector and Blanton, Reference Gates-Rector and Blanton2019).
II. EXPERIMENTAL
The sample was a commercial reagent, purchased from Sigma (Lot #A100306-001), and was used as-received. The white powder was packed into a 1.5-mm diameter Kapton capillary and rotated during the measurement at ~50 Hz. The powder pattern was measured at 295 K at beamline 11-BM (Lee et al., Reference Lee, Shu, Ramanathan, Preissner, Wang, Beno, Von Dreele, Ribaud, Kurtz, Antao, Jiao and Toby2008; Wang et al., Reference Wang, Toby, Lee, Ribaud, Antao, Kurtz, Ramanathan, Von Dreele and Beno2008) of the Advanced Photon Source at Argonne National Laboratory using a wavelength of 0.457899 Å from 0.5° to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s step−1.
The pattern was indexed on a primitive monoclinic unit cell with a = 7.5521, b = 7.0904, c = 32.8086 Å, β = 94.26°, V = 1745.06 Å3, and Z = 2 using DICVOL14 (Louër and Boultif, Reference Louër and Boultif2014) through the PreDICT interface (Blanton et al., Reference Blanton, Papoular and Louër2019). Analysis of the systematic absences using EXPO2014 (Altomare et al., Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013) suggested the space group P21, which was confirmed by successful solution and refinement of the structure. A reduced cell search in the Cambridge Structural Database (Groom et al., Reference Groom, Bruno, Lightfoot and Ward2016) yielded 3 hits, but no structures for edoxaban derivatives.
An edoxaban molecule was downloaded from PubChem as ConformerD_CID_10280735.sdf. It was converted to a .mol2 file using Materials Studio (Dassault, 2020), and converted into a Fenske-Hall Z-matrix using OpenBabel (O'Boyle et al., Reference O'Boyle, Banck, James, Morley, Vandermeersch and Hutchison2011). A p-toluenesulfonate anion was built using Spartan ‘18 (Wavefunction, 2020), saved as a .mol2 file, and converted to a Fenske-Hall Z-matrix using the same tools. The structure was solved by Monte Carlo simulated annealing techniques as implemented in DASH (David et al., Reference David, Shankland, van de Streek, Pidcock, Motherwell and Cole2006). An edoxaban molecule, a tosylate, and an O atom (water molecule) were used as fragments. A 001 preferred orientation coefficient was also included.
Rietveld refinement was carried out using GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 0.5–25.0° portion of the pattern was included in the refinement (d min = 1.057 Å). All non-H bond distances and angles were subjected to restraints, based on a Mercury/Mogul Geometry Check (Bruno et al., Reference Bruno, Cole, Kessler, Luo, Motherwell, Purkis, Smith, Taylor, Cooper, Harris and Orpen2004; Sykes et al., Reference Sykes, McCabe, Allen, Battle, Bruno and Wood2011) of the model. The Mogul average and standard deviation for each quantity were used as the restraint parameters. The restraints contributed 7.6% to the final χ 2. The y-coordinate of Cl1 was fixed to define the origin. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault, 2020). The U iso were grouped by chemical similarity. The U iso of the hydrogen atoms were constrained to be 1.3× that of the heavy atoms to which there are attached. The background was modeled using a 6-term shifted Chebyshev polynomial, along with two peaks at 1.71° and 5.89° to model the scattering from the Kapton capillary and any amorphous component of the sample. The peak profiles were described using the generalized microstrain model, and a second-order spherical harmonic preferred orientation model was included. N10⋯O80 was the only N⋯A distance < 3.2 Å, so we assumed that N10 was protonated, and added the remaining hydrogen atom there.
The final refinement of 186 variables using 25 340 observations and 124 restraints yielded the residuals R wp = 0.0826 and GOF = 1.52. The largest peak (1.73 Å from C28) and hole (1.63 Å from C35) in the difference Fourier map were 0.51 and −0.43(11) eÅ−3, respectively. The largest errors in the fit (Figure 2) are in the positions and shapes of some of the low-angle peaks, and may indicate subtle changes in the beam during the measurement.
Figure 2. The Rietveld plot for the refinement of edoxaban tosylate monohydrate. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot. The vertical scale has been multiplied by a factor of 10× for 2θ > 9.5°.
A density functional geometry optimization (fixed experimental unit cell) was carried using CRYSTAL14 (Dovesi et al., Reference Dovesi, Orlando, Erba, Zicovich-Wilson, Civalleri, Casassa, Maschio, Ferrabone, De La Pierre, D-Arco, Noël, Causà and Kirtman2014). The basis sets for the H, C, N, and O atoms were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994), and those for Cl and S were those of Peintinger et al. (Reference Peintinger, Vilela Oliveira and Bredow2013). The calculation was run on eight 2.1 GHz Xeon cores (each with 6 GB RAM) of a 304-core Dell Linux cluster at IIT, using 8 k-points and the B3LYP functional, and took ~102 h.
III. RESULTS AND DISCUSSION
The synchrotron pattern from this study (Figure 3) of edoxaban tosylate monohydrate matches those of Berenguer Maimó et al. (Reference Berenguer Maimó, Racamonde Villanueva and Winter2018) and Suzuki and Ono (Reference Suzuki and Ono2011) well enough to conclude that the material studied here is indeed Form I. The refined atom coordinates of edoxaban tosylate monohydrate Form I and the coordinates from the density functional theory (DFT) optimization are reported in the CIFs deposited with ICDD.
Figure 3. Comparison of the synchrotron pattern from this study (black) of edoxaban tosylate monohydrate to the patterns of form I reported by Berenguer Maimó et al. (Reference Berenguer Maimó, Racamonde Villanueva and Winter2018) (red) and Suzuki and Ono (Reference Suzuki and Ono2011) (green). The published patterns were digitized using UN-SCAN-IT (Silk Scientific, 2013) and scaled to the synchrotron wavelength of 0.457899 Å using MDI JADE Pro (MDI, 2020).
The root-mean-square (rms) Cartesian displacement of the non-hydrogen atoms in the Rietveld-refined and DFT-optimized structures is 0.196 Å (Figure 4), within the normal range for correct structures (van de Streek and Neumann, Reference van de Streek and Neumann2014). The maximum difference is 0.685 Å, at N10, and reflects a difference in the conformation of the tetrahydropyridine ring. The conformation difference will be discussed below. This discussion concentrates on the DFT-optimized structure, as we believe it is more reliable. The asymmetric unit (with atom numbering) is illustrated in Figure 5, and the crystal structure is presented in Figure 6.
Figure 4. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the edoxaban cation in edoxaban tosylate monohydrate. The rms Cartesian displacement of the cations is 0.196-Å.
Figure 5. The asymmetric unit of edoxaban tosylate monohydrate Form I, with the atom numbering. The atoms are represented by 50% probability spheroids.
Figure 6. The DFT-optimized crystal structure of edoxaban tosylate monohydrate Form I, viewed down the b-axis.
The crystal structure consists of alternating layers of edoxaban cations and tosylate anions along the c-axis (Figure 6). The water molecules lie near the sulfonate end of the tosylate anions. The phenyl rings of the tosylates and the chloropyridine rings lie near each other.
Almost all of the bond distances, angles, and torsion angles fall within the normal ranges indicated by a Mercury/Mogul Geometry check (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020). The C27–S2–C23 (87.2°, average = 91.4(4)°, Z-score = 9.2), C30–N10–C29 (119.1°, average = 111.5(19)°, Z-score = 3.8), and C29–C27–S2 (127.2°, average = 121.7(10)°, Z-score = 5.3) angles are flagged as unusual. The standard uncertainties on these averages are fairly small, but the differences may represent a weakness in the calculation of the environment around S2. The N10–C29–C27–C26–C28–C30 ring is flagged as unusual in the DFT-optimized structure, but not in the Rietveld-refined structure.
Quantum chemical geometry optimization of the edoxaban cation (DFT/B3LYP/6-31G*/water) using Spartan ‘18 (Wavefunction, 2020) indicated that the local minimum of the DFT configuration is only 0.6 kcal mol−1 lower in energy than that of the Rietveld configuration, even though the rms Cartesian displacement is 0.638 Å (Figure 7). The two conformations are, thus, equivalent in energy. The largest differences are in the conformation of the tetrahydropyridine ring at N10. The DFT conformation leads to a much more reasonable hydrogen-bonding geometry, so it is tempting to conclude that the solid-state interactions determine the conformation of the edoxaban cation. Molecular mechanics conformational analysis indicated that the global minimum-energy conformation is much more compact than the observed one, confirming that intermolecular ring–ring interactions are important to determining the observed conformation.
Figure 7. Comparison of the local minimum-energy conformations for the Rietveld-refined cation (orange) and the DFT-optimized cation (green) in edoxaban tosylate monohydrate.
Analysis of the contributions to the total crystal energy using the Forcite module of Materials Studio (Dassault, 2020) suggests that angle deformation terms are the dominant contributions to the intramolecular deformation energy. The intermolecular energy is dominated by electrostatic repulsions (which in this force-field-based analysis include hydrogen bonds) and van der Waals attractions. The hydrogen bonds are better analyzed using the results of the DFT calculation.
Hydrogen bonds are significant in the crystal structure (Table I). As expected, the protonated nitrogen atom N10 forms a strong N–H⋯O hydrogen bond to one of the tosylate oxygens. The energy was calculated using the correlation of Wheatley and Kaduk (Reference Wheatley and Kaduk2019). Only one of the water molecule hydrogens acts as a donor in an O–H⋯O hydrogen bond. The energy was calculated using the correlation of Rammohan and Kaduk (Reference Rammohan and Kaduk2018). The tosylate oxygens act as acceptors in a number of C–H⋯O hydrogen bonds. The amide nitrogens N12 and N7 act as donors to carbonyl oxygens, and the amino nitrogen N8 forms bifurcated hydrogen bonds to two carbonyl oxygens, one intra- and the other intermolecular. The chlorine Cl1 and sulfur S2 both act as acceptors in C–H⋯A hydrogen bonds. There are also several C–H⋯O hydrogen bonds to the carbonyl oxygens.
Table I. Hydrogen bonds (CRYSTAL14) in edoxaban tosylate monohydrate.
* indicates intramolecular.
The volume enclosed by the Hirshfeld surface (Figure 8; Hirshfeld, Reference Hirshfeld1977; Turner et al., Reference Turner, McKinnon, Wolff, Grimwood, Spackman, Jayatilaka and Spackman2017) is 860.02 Å3, 98.60% of half the unit cell volume. The molecules are, thus, not tightly packed. All of the significant-close contacts (red in Figure 8) involve the hydrogen bonds. The volume/non-hydrogen atom is 17.8 Å3.
Figure 8. The Hirshfeld surface of edoxaban tosylate monohydrate. Intermolecular contacts longer than the sums of the van der Waals radii are colored blue, and contacts shorter than the sums of the radii are colored red. Contacts equal to the sums of radii are white.
The Bravais–Friedel–Donnay–Harker (Bravais, Reference Bravais1866; Friedel, Reference Friedel1907; Donnay and Harker, Reference Donnay and Harker1937) morphology suggests that we might expect platy morphology for edoxaban tosylate monohydrate, with {001} as the principal faces. A second-order spherical harmonic model for preferred orientation was incorporated into the refinement. The texture index was only 1.023(0), indicating that preferred orientation was slight in this rotated capillary specimen. The powder pattern of edoxaban tosylate monohydrate from this synchrotron data set has been submitted to ICDD for inclusion in the Powder Diffraction File.
IV. DEPOSITED DATA
The Crystallographic Information Framework (CIF) files containing the results of the Rietveld refinement (including the raw data) and the DFT geometry optimization were deposited with the ICDD. The data can be requested at info@icdd.com.
ACKNOWLEDGEMENTS
Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This work was partially supported by the International Centre for Diffraction Data. We thank Lynn Ribaud and Saul Lapidus for their assistance in the data collection, and Andrey Rogachev for the use of computing resources at IIT.
CONFLICTS OF INTEREST
The authors have no conflicts of interest to declare.
