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Crystal structure of ribociclib hydrogen succinate, (C23H31N8O)(HC4H4O4)

Published online by Cambridge University Press:  27 May 2024

James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Anja Dosen Open the ORCID record for Anja Dosen [Opens in a new window]  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616, USA North Central College, 131 S. Loomis St., Naperville, IL 60540, USA
Anja Dosen
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: [email protected]
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Abstract

The crystal structure of ribociclib hydrogen succinate (commonly referred to as ribociclib succinate) has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Ribociclib hydrogen succinate crystallizes in space group P-1 (#2) with a = 6.52215(4), b = 12.67120(16), c = 18.16978(33) Å, α = 74.0855(8), β = 82.0814(4), γ = 88.6943(1)°, V = 1430.112(6) Å3, and Z = 2 at 295 K. The crystal structure consists of alternating layers of cations and anions parallel to the ab-plane. The protonated N in each ribociclib cation acts as a donor in two strong N–H⋯O hydrogen bonds to two different succinate anions. Strong O–H⋯O hydrogen bonds link the hydrogen succinate anions into chains parallel to the a-axis. N–H⋯N hydrogen bonds link the cations into dimers, with a graph set R2,2(8). The result is a three-dimensional hydrogen bond network. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Keywords

ribociclibKisqali®powder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , First View , pp. 1 - 8
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Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited
Copyright
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

I. INTRODUCTION

Ribociclib succinate (marketed under the trade names Kisqali® and Kryxana®) is used to treat selected types of advanced or metastatic breast cancer in premenopausal or postmenopausal women. The systematic name (CAS Registry Number 1374639-75-4) is 7-cyclopentyl-N,N-dimethyl-2-[(5-piperazin-1-ylpyridin-2-yl)amino]pyrrolo[2,3-d]pyrimidine-6-carboxamide butanedioic acid. A two-dimensional molecular diagram of ribociclib hydrogen succinate is shown in Figure 1.

Figure 1. The two-dimensional structure of ribociclib hydrogen succinate.

Ribociclib succinate is claimed, and a powder pattern is provided, in International Patent Application WO 2012/064805 A1 (Calienni et al., Reference Calienni, Chen, Gong, Kapa and Saxena2012; Novartis and Astex Therapeutics); however, a crystal structure was not reported. Novel forms of ribociclib succinate are claimed in US Patent 9,193,732 B2 (Calienni et al., Reference Calienni, Chen, Gong, Kapa and Saxena2015; Novartis and Astex Therapeutics). Crystalline forms SRS-I and SRS-II of ribociclib succinate, as well as an amorphous form, are claimed in International Patent Application WO 2019/123364 A1 (Rampalli et al., Reference Rampalli, Upalla, Cherukuvada, Needi, Dasari and Seshagiri2019; Shilpa Medicare Ltd.). Crystalline forms C-2, C-3, C-4, C-5, C-6, C-7, C-8, C-9, and C-10 are claimed in International Patent Application WO 2019/167068 A1 (Pathi et al., Reference Pathi, Rao, Malhotra, Chennuru, Bollineni, Ashwathanarayana, Pullela and Mithun2019; Cipla Ltd.). Crystalline form APO-I is claimed in US Patent 10,611,772 B2 (Souza and Khalili, Reference Souza and Khalili2020; Apotex). Crystalline forms M10, M11, M12, M14, and M15 are claimed in International Patent Application WO 2020/225827 (Jetti et al., Reference Jetti, Bhatraju, Golivi, Manukonda, Jayachandra and Khanduri2020; Mylan Laboratories Ltd.). Novel crystalline and amorphous forms are claimed in US Patent 11,111,250 B2 (Rampalli et al., Reference Rampalli, Upalla, Cherukuvada, Patneedi, Dasari and Seshagiri2021; Shilpa Medicare Ltd.).

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 them in the Powder Diffraction File (Gates-Rector and Blanton, Reference Gates-Rector and Blanton2019).

II. EXPERIMENTAL

Ribociclib succinate was a commercial reagent, purchased from TargetMol (Batch #144117), 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 (Antao et al., Reference Antao, Hassan, Wang, Lee and Toby2008; 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 0.459744(2) Å from 0.5 to 40° 2θ with a step size of 0.001° and a counting time of 0.1 s per step. The high-resolution powder diffraction data were collected using twelve silicon crystal analyzers that allow for high angular resolution, high precision, and accurate peak positions. A mixture of silicon (NIST SRM 640c) and alumina (NIST SRM 676a) standards (ratio Al2O3:Si = 2:1 by weight) was used to calibrate the instrument and refine the monochromatic wavelength used in the experiment.

The pattern was indexed using both N-TREOR (Altomare et al., Reference Altomare, Cuocci, Giacovazzo, Moliterni, Rizzi, Corriero and Falcicchio2013) and DICVOL14 (Louër and Boultif, Reference Louër and Boultif2014) through the PreDICT interface (Blanton et al., Reference Blanton, Papoular and Louër2019) on a primitive triclinic unit cell with a = 6.5192, b = 12.6781, c = 18.1671 Å, α = 74.105, β = 81.996, γ = 88.675°, V = 1429.95 Å3, and Z = 2. The space group was assumed to be P-1, which was confirmed by successful solution and refinement of the structure. A reduced cell search of the Cambridge Structural Database (Groom et al., Reference Groom, Bruno, Lightfoot and Ward2016) yielded no hits.

The ribociclib molecule was downloaded from PubChem (Kim et al., Reference Kim, Chen, Cheng, Gindulyte, He, He, Li, Shoemaker, Thiessen, Yu, Zaslavsky, Zhang and Bolton2023) as Conformer3D_CID_44631912.sdf. It was converted to a *.mol2 file using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020). A succinate anion was built using Spartan ‘20 (Wavefunction, 2022) and saved as a .mol2 file. The crystal structure was solved using Monte Carlo simulated annealing techniques as implemented in DASH (David et al., Reference David, Shankland, van de Streek, Pidcock, Motherwell and Cole2006), using ribociclib and succinate molecules as the fragments. Examination of close intermolecular contacts (potential hydrogen bonds) indicated that N7 and O70 were protonated, and thus, the compound is correctly named ribociclib hydrogen succinate.

Rietveld refinement was carried out with GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). Only the 1.0–25.0° portion of the pattern was included in the refinements (d min = 1.062 Å). The region 1.58–1.89° 2θ, which contained a moderately sharp peak from the Kapton capillary, was excluded. 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). The Mogul average and standard deviation for each quantity were used as the restraint parameters. The pyridine ring and the fused ring system were restrained to be planar. The restraints contributed 4.1% to the final χ 2. The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault, 2022). The U iso of the C, N, and O atoms were grouped by chemical similarity. The U iso for the H atoms were fixed at 1.3× the U iso of the heavy atoms to which they are attached. The peak profiles were described using a uniaxial microstrain model, with 100 as the unique axis.

The final refinement of 159 variables using 23 731 observations and 104 restraints yielded the residuals R wp = 0.12521 and GOF = 1.52. The largest peak (0.09 Å from C10) and hole (1.61 Å from N3) in the difference Fourier map were 0.57(10) and −0.46(10) eÅ−3, respectively. The final Rietveld plot is shown in Figure 2. The largest features in the normalized error plot represent a subtle error in peak shapes, the result of using a simple profile model.

Figure 2. The Rietveld plot for the refinement of ribociclib hydrogen succinate. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot, and the red line is the background curve. The vertical scale has been multiplied by a factor of 20× for 2θ > 9.5°.

The crystal structure of ribociclib hydrogen succinate was optimized (fixed experimental unit cell) with density functional techniques using VASP (Kresse and Furthmüller, Reference Kresse and Furthmüller1996) through the MedeA graphical interface (Materials Design, 2016). The calculation was carried out on 16 2.4 GHz processors (each with 4 Gb RAM) of a 64-processor HP Proliant DL580 Generation 7 Linux cluster at North Central College. The calculation used the GGA-PBE functional, a plane wave cutoff energy of 400.0 eV, and a k-point spacing of 0.5 Å−1 leading to a 2 × 2 × 1 mesh, and took ~8.7 h. Single-point density functional calculations (fixed experimental cell) and population analysis were carried out using CRYSTAL23 (Erba et al., Reference Erba, Desmarais, Casassa, Civalleri, Donà, Bush, Searle, Maschio, Daga, Cossard, Ribaldone, Ascrizzi, Marana, Flament and Kirtman2023). The basis sets for the H, C, N, and O atoms in the calculation were those of Gatti et al. (Reference Gatti, Saunders and Roetti1994). The calculations were run on a 3.5 GHz PC using 8 k-points and the B3LYP functional, and took ~3.6 h.

III. RESULTS AND DISCUSSION

The agreement between the powder pattern of ribociclib hydrogen succinate of this study and the pattern reported by Calienni et al. (Reference Calienni, Chen, Gong, Kapa and Saxena2012) is good enough to conclude that the material in this study is the same as that patented by Novartis (Figure 3). The intensities in the patent pattern differ from those observed here, probably indicating some preferred orientation and/or granularity. There are also a few weak extra peaks, perhaps indicating the presence of an impurity.

Figure 3. Comparison of the synchrotron pattern of ribociclib hydrogen succinate (black) from this study to that reported by Calienni et al. (Reference Calienni, Chen, Gong, Kapa and Saxena2012; green). The literature pattern (measured using Cu Kα radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013) and converted to the synchrotron wavelength of 0.459744(2) Å using JADE Pro (MDI, 2023). Image generated using JADE Pro (MDI, 2023).

The asymmetric unit (Figure 4) contains one ribociclib cation and one hydrogen succinate anion, showing that the compound is properly described as ribociclib hydrogen succinate. The root-mean-square (rms) Cartesian displacement of the non-H atoms in the Rietveld-refined and VASP-optimized cation is 0.088 Å (Figure 5) and in the succinate anion is 0.102 Å (Figure 6). The agreement is within the normal range for correct structures (van de Streek and Neumann, Reference van de Streek and Neumann2014), and provides confirmation that the structure is correct. The remainder of this discussion will emphasize the VASP-optimized structure.

Figure 4. The asymmetric unit of ribociclib hydrogen succinate, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 5. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the ribociclib cation ribociclib hydrogen succinate. The rms Cartesian displacement is 0.088 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 6. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the hydrogen succinate anion in ribociclib hydrogen succinate. The rms Cartesian displacement is 0.102 Å. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Almost all of the bond distances, bond 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 torsion angles involving rotation about the C65–C66 bond in the succinate anion are flagged as unusual. They lie on long tails of peaked distributions, and indicate that the succinate anion conformation is unusual.

Quantum chemical geometry optimization of the isolated cation (DFT/B3LYP/6-31G*/water) using Spartan ‘20 (Wavefunction, 2022) indicated that the solid-state conformation is 6.6 kcal mol−1 higher in energy than a local minimum, which is the global minimum-energy conformation. A similar optimization indicated that the solid-state conformation of the anion is 6.0 kcal mol−1 higher in energy than a local minimum, which has different orientations of the carboxyl groups. The global minimum-energy conformation of the anion has a similar backbone, but again different orientations of the carboxyl groups. Apparently, the hydrogen bonding affects the solid-state conformation.

The crystal structure (Figure 7) consists of alternating layers of cations and anions parallel to the ab-plane. As discussed below, hydrogen bonding is important in the structure. Analysis of the contributions to the total crystal energy of the structure using the Forcite module of Materials Studio (Dassault Systèmes, 2022) suggests that angle distortion terms are the most important contributors to the intramolecular energy, as expected from a fused ring system. The intermolecular energy is dominated by electrostatic attractions, which in the force-field analysis include hydrogen bonds. The hydrogen bonds are better analyzed using the results of the DFT calculation.

Figure 7. The crystal structure of ribociclib hydrogen succinate, viewed down the a-axis. Image generated using Diamond (Crystal Impact, 2023).

Hydrogen bonds (Table I) are important in the structure. The protonated N7 in each ribociclib acts as a donor in two strong N–H⋯O hydrogen bonds to two different succinate anions (Figure 8). Strong O–H⋯O hydrogen bonds link the hydrogen succinate anions into chains parallel to the a-axis. N–H⋯N hydrogen bonds link the cations into dimers, with a graph set (Etter, Reference Etter1990; Bernstein et al., Reference Bernstein, Davis, Shimoni and Chang1995; Shields et al., Reference Shields, Raithby, Allen and Motherwell2000) R2,2(8) (Figure 9). The result is a three-dimensional hydrogen bond network. The energies of the O–H⋯O hydrogen bonds were calculated using the correlation of Rammohan and Kaduk (Reference Rammohan and Kaduk2018), and those of the N–H⋯O hydrogen bonds using the correlation of Wheatley and Kaduk (Reference Wheatley and Kaduk2019). A variety of C–H⋯O, C–H⋯N, and C–H⋯C hydrogen bonds link the cations and anions, also contributing to the lattice energy.

Table I. Hydrogen bonds (CRYSTAL23) in ribociclib hydrogen succinate.

a Intramolecular.

Figure 8. The hydrogen bonds (light blue dotted lines) of the ribociclib cation connect to two succinate anions. The dotted red lines indicate other hydrogen bonds. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Figure 9. The hydrogen-bonded dimer of ribociclib cations (light blue lines). The dark red dotted lines indicate cation–anion hydrogen bonds. Image generated using Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

The volume enclosed by the Hirshfeld surface of ribociclib hydrogen succinate (Figure 10; Hirshfeld, Reference Hirshfeld1977; Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021) is 704.73 Å3, 98.55% of the unit cell volume. The packing density is thus fairly typical. The only significant close contacts (red in Figure 10) involve the hydrogen bonds. The volume/non-hydrogen atom is typical, at 17.9 Å3.

Figure 10. The Hirshfeld surface of ribociclib hydrogen succinate. 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. Image generated using CrystalExplorer (Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021).

The Bravais–Friedel–Donnay–Harker (Bravais, Reference Bravais1866; Friedel, Reference Friedel1907; Donnay and Harker, Reference Donnay and Harker1937) morphology suggests that we might expect elongated morphology for ribociclib hydrogen succinate, with <100> as the long axis, or platy morphology with {001} as the major faces. A fourth-order spherical harmonic model was included in the refinement. The texture index was 1.0066(1), indicating that the preferred orientation was not significant in this rotated capillary specimen.

IV. DEPOSITED DATA

The powder pattern of ribociclib hydrogen succinate from this synchrotron data set has been submitted to ICDD for inclusion in the Powder Diffraction File. 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

ACKNOWLEDGMENTS

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 Saul Lapidus for his assistance in the data collection.

CONFLICTS OF INTEREST

The authors have no conflicts of interest to declare.

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Figure 0

Figure 1. The two-dimensional structure of ribociclib hydrogen succinate.

Figure 1

Figure 2. The Rietveld plot for the refinement of ribociclib hydrogen succinate. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot, and the red line is the background curve. The vertical scale has been multiplied by a factor of 20× for 2θ > 9.5°.

Figure 2

Figure 3. Comparison of the synchrotron pattern of ribociclib hydrogen succinate (black) from this study to that reported by Calienni et al. (2012; green). The literature pattern (measured using Cu Kα radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013) and converted to the synchrotron wavelength of 0.459744(2) Å using JADE Pro (MDI, 2023). Image generated using JADE Pro (MDI, 2023).

Figure 3

Figure 4. The asymmetric unit of ribociclib hydrogen succinate, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., 2020).

Figure 4

Figure 5. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the ribociclib cation ribociclib hydrogen succinate. The rms Cartesian displacement is 0.088 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 5

Figure 6. Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of the hydrogen succinate anion in ribociclib hydrogen succinate. The rms Cartesian displacement is 0.102 Å. Image generated using Mercury (Macrae et al., 2020).

Figure 6

Figure 7. The crystal structure of ribociclib hydrogen succinate, viewed down the a-axis. Image generated using Diamond (Crystal Impact, 2023).

Figure 7

Table I. Hydrogen bonds (CRYSTAL23) in ribociclib hydrogen succinate.

Figure 8

Figure 8. The hydrogen bonds (light blue dotted lines) of the ribociclib cation connect to two succinate anions. The dotted red lines indicate other hydrogen bonds. Image generated using Mercury (Macrae et al., 2020).

Figure 9

Figure 9. The hydrogen-bonded dimer of ribociclib cations (light blue lines). The dark red dotted lines indicate cation–anion hydrogen bonds. Image generated using Mercury (Macrae et al., 2020).

Figure 10

Figure 10. The Hirshfeld surface of ribociclib hydrogen succinate. 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. Image generated using CrystalExplorer (Spackman et al., 2021).