I. INTRODUCTION
Brigatinib (Alunbrig®) is an anticancer drug specified as an anaplastic lymphoma kinase (ALK) inhibitor and tyrosine kinase inhibitor. It is mainly used as treatment in adult patients with metastatic ALK positive non-small cell lung cancer (NSCLC). Brigatinib targets a broad range of ALK mutations and ROS1 rearrangements (Camidge et al., Reference Camidge, Kim, Ahn, Yang, Han, Lee, Hochmair, Li, Chang, Lee and Gridelli2018). It is prescribed as a tablet and can be taken with or without food. The IUPAC name (CAS Registry number 1197953-54-0) is 5-chloro-4-N-(2-dimethylphosphorylphenyl)-2-N-[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]pyrimidine-2,4-diamine. The molecular structure of brigatinib is illustrated in Figure 1.
The 2D molecular structure of brigatinib.
Crystalline Forms A through H and J through K of brigatinib are claimed in International Patent Application WO 2016/065028 A1 (Rozamus, Reference Rozamus2016; Ariad Pharmaceuticals Inc.) Single-phase powder X-ray diffraction (XRD) patterns are claimed for the eight forms A through H, and powder patterns for mixtures of Phase J and Phase A, and Phase K and Phase A are also presented. A small fraction of d-spacings for peaks observed in the powder XRD patterns are reported in WO 2016/065028, and there is no peak intensity data presented. Unit cell and refined crystal structure parameters collected at 150 K are provided for Form A, but no atomic coordinates are reported. Pharmaceutical compositions of brigatinib are claimed in International Patent Application WO 2019/158421 A1 (Martin, Reference Martin2019; Sandoz), and powder diffraction data for Form A are provided as a comparative example.
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 the atomic coordinates and 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 TargetMol (Lot #120474), and was used as-received. The light-yellow 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 0.458119(2) Å from 0.5 to 50° 2θ with a step size of 0.001° and a counting time of 0.1 s per step.
The pattern was indexed on a primitive triclinic unit cell with a = 9.95892, b = 10.93110, c = 14.97764 Å, α = 76.18, β = 79.92, γ = 74.11°, V = 1457.61 Å3, and Z = 2 using JADE Pro (MDI, 2021). This is very close to the unit cell reported by Rozamus (Reference Rozamus2016), so the space group was assumed to be P-1. A reduced cell search in the Cambridge Structural Database (Groom et al., Reference Groom, Bruno, Lightfoot and Ward2016) yielded 1 hit, but no structures for brigatinib derivatives.
A brigatinib molecule was downloaded from PubChem (Kim et al., Reference Kim, Chen, Cheng, Gindulyte, He, He, Li, Shoemaker, Thiessen, Yu, Zaslavsky, Zhang and Bolton2019) as Conformer3D_CID_68165256.sdf. It was converted to a .mol2 fie using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020) and a Fenske–Hall Z-matrix using OpenBabel (O'Boyle et al., Reference O'Boyle, Banck, James, Morley, Vandermeersch and Hutchison2011). The structural model was obtained by Monte Carlo simulated annealing techniques using FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002). Although most of the 200 solutions had cost factors in the range of 700 000 to 900 000 (Figure 2), the best solution had a cost factor of 242 861. The next three solutions (with cost factors of 276 992, 280 553, and 290 793) were also saved. Refinement of the best solution yielded R wp = 0.0781. Although the four molecules from the four lowest cost factor solutions are generally similar (Figure 3), the lowest cost factor solution has a different conformation of the dimethylphosphoryl group. The other three solutions have the P=O oriented more reasonably, to form an intramolecular hydrogen bond to an N–H group (Figure 4). This “other” conformation (which yields a structure lower in energy by 1.5 kcal mol−1) was used to begin the final refinement.
Distribution of the cost factors from 200 FOX structure solutions.
Overlay of the four best solutions from FOX. The lowest cost factor solution has a different orientation of the dimethylphosphoryl group than the next three.
Overlay of the two best solutions, showing the additional intramolecular hydrogen bond in the second-best cost factor solution.
Rietveld refinement was carried out using GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 1.5–25.0° portion of the pattern was included in the refinement (d min = 1.058 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 molecule. The Mogul average and standard deviation for each quantity were used as the restraint parameters. The restraints contributed 9.6% to the final χ 2. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault, 2021). The U iso for the non-hydrogen atoms were grouped by chemical similarity. The U iso of the hydrogen atoms were constrained to be 1.3× that of the U iso of the heavy atoms to which they are attached. The background was modeled using a 4-term shifted Chebyshev polynomial, along with three peaks at 1.70, 5.72, and 22.20° to model the scattering from the Kapton capillary and the amorphous component of the sample. The peak profiles were described using the generalized microstrain model, and a spherical harmonic preferred orientation model was included.
The final refinement of 164 variables using 23 358 observations and 107 restraints yielded the residuals R wp = 0.0572 and GOF = 1.39. The largest peak (2.26 Å from N5) and hole (1.69 Å from O4) in the difference Fourier map were 0.17 and −0.16(4) eÅ−3, respectively. The difference plot in the Rietveld-refined diffraction pattern (Figure 5) is quite flat; the largest errors are subtle ones in peak shape and/or intensity. A density functional geometry optimization (fixed experimental cell) and population analysis were carried out 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 the basis sets for P and Cl 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.
The Rietveld plot for the refinement of brigatinib Form A. 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 > 9.0°.
III. RESULTS AND DISCUSSION
The synchrotron powder pattern of this study matches powder XRD patterns of Rozamus (Reference Rozamus2016) and Martin (Reference Martin2019) well enough (Figure 6) to conclude that all three samples represent brigatinib Form A. The refined atom coordinates of brigatinib Form A and the coordinates from the density functional theory (DFT) optimization are reported in the CIFs which have been deposited with ICDD. The root-mean-square (rms) Cartesian displacement of the non-hydrogen atoms in the Rietveld-refined and DFT-optimized structures is 0.163 Å (Figure 7). The maximum displacement is 0.365 Å, at the methyl group C22. The excellent agreement is evidence that the structure is correct (van de Streek and Neumann, Reference van de Streek and Neumann2014). This discussion concentrates on the DFT-optimized structure. The asymmetric unit (with atom numbering) is illustrated in Figure 8, and the crystal structure is presented in Figure 9.
Comparison of the synchrotron pattern of brigatinib from this study to the patterns of Form A reported by Rozamus (Reference Rozamus2016) and Martin (Reference Martin2019). The published patterns were digitized using UN-SCAN-IT (Silk Scientific, 2013) and scaled to the synchrotron wavelength of 0.458119 Å using MDI JADE Pro (MDI, 2021).
Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of cation 1 of brigatinib Form A. The rms Cartesian displacement is 0.163 Å.
The asymmetric unit of brigatinib Form A, with the atom numbering. The atoms are represented by 50% probability spheroids.
The crystal structure of brigatinib Form A, viewed down the a-axis.
The crystal structure (Figure 9) is characterized by alternating layers of aliphatic and aromatic portions of the molecules along the b-axis. The molecular packing seems relatively loose along the a-axis. Most 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 C32–C36–Cl1 angle of 122.0° is flagged as unusual (average = 119.9(7)°, Z-score = 3.2). The standard uncertainty on the average is very small, inflating the Z-score. The torsion angles involving rotation about the P2–C30 bond lie in broad distributions containing few hits, so it is hard to say if they are truly unusual. The C26–C27–N8–C28 torsion lies on the tail of the distribution of a small population. The torsion angles involving rotation about the C12–N5 bond lie outside of the usual gauche/trans distributions, and are truly unusual. These torsions involve rotation of the two saturated rings with respect to each other.
Quantum chemical geometry optimization of the brigatinib molecule (DFT/B3LYP/6-31G*/water) using Spartan ‘18 (Wavefunction, Inc., 2018) indicated that the observed solid-state conformation is 6.5 kcal mol–1 higher in energy than the local minimum (Figure 10). The rms Cartesian displacement is 0.701 Å, and the differences in conformation are mainly in the orientation of the dimethylphosphoryl group and the saturated rings. The minimum energy conformation (Figure 11) is 3.5 kcal mol–1 lower in energy. The rms Cartesian displacement is 1.403 Å, and the differences are spread throughout the molecule, particularly in the saturated rings. The differences show that solid-state interactions play a role in determining the observed conformation.
Comparison of the observed (blue) and DFT-optimized local minimum (orange) conformations of brigatinib in Form A.
Comparison of the observed (blue) and global minimum-energy (Green) conformations of brigatinib in Form A.
Analysis of the contributions to the total crystal energy using the Forcite module of Materials Studio (Dassault, 2021) suggests that angle distortion terms dominate the intramolecular deformation energy. The intermolecular energy is dominated by electrostatic attractions, which in this force-field-based analysis include cation coordination and hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculation.
Hydrogen bonds are significant in the crystal structure (Table I). Strong N8–H64⋯N10 hydrogen bonds link the molecules into pairs, with a graph set R2,2(8) (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Shields et al., Reference Shields, Raithby, Allen and Motherwell2000). There is a strong intramolecular N11–H68⋯O4 hydrogen bond to the phosphoryl group, which determines the orientation of this group. The energy of this hydrogen bond was calculated using the correlation of Wheatley and Kaduk (Reference Wheatley and Kaduk2019). Several C–H⋯O, C–H⋯N, C–H⋯Cl, and N–H⋯Cl hydrogen bonds also contribute to the crystal energy. Several axial–axial and axial–methyl H⋯H interactions in the methylpiperazine ring seem to be significant.
Hydrogen bonds (CRYSTAL14) in brigatinib Form A
a Intramolecular.
The volume enclosed by the Hirshfeld surface (Figure 12; Hirshfeld, Reference Hirshfeld1977; Turner et al., Reference Turner, McKinnon, Wolff, Grimwood, Spackman, Jayatilaka and Spackman2017) is 719.15 Å3, 98.62% of half the unit cell volume. The packing density is thus fairly typical. All of the significant close contacts (red in Figure 12) involve the hydrogen bonds. The volume/non-hydrogen atom is 18.2 Å3.
The Hirshfeld surface of brigatinib Form A. 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 brigatinib Form A, with {001} as the principal faces. A second-order spherical harmonic model for preferred orientation was incorporated into the refinement. The texture index was 1.031(0), indicating that preferred orientation was slight for this rotated capillary specimen. The powder pattern of brigatinib 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
The 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 Illinois Institute of Technology.
CONFLICTS OF INTEREST
The authors have no conflicts of interest to declare.
