Physicochemical characteristics of sunitinib malate and its process-related impurities

Article abstract of DOI:10.1002/jps.23412

In this article, details of crystal and molecular structures of sunitinib malate (SUM), an anticancer therapeutic, and its key synthetic intermediate are presented. Both these compounds were also characterized spectroscopically and thermally. SUM crystallizes in the monoclinic P2₁ space group with two molecules in the asymmetric part of the unit cell, whereas the intermediate crystallises in the triclinic P-1 space group with four independent molecules in the asymmetric unit. The three-dimensional structure of SUM consists of two different layers of molecules. The first one is built of the malic anions, whereas the other layer consists of more hydrophobic sunitinib molecules. This layer is formed by two types of molecules creating a herring bond-like pattern with pairs of neighboring cations forming the V-shape arrangement of molecules. The V-shaped pairs of molecules form ribbons by fitting into two neighboring V shapes. The characteristic V-shape assemble of the moieties is hold together with three C-H...F weak interactions. Besides, process-related impurities of SUM were identified and their structures confirmed by separate synthesis. These impurities were fully characterized by spectroscopic and crystallographic methods as well as by differential scanning calorimetry and thermogravimetric analysis. The H-, ¹³C-, and ¹⁵N-nuclear magnetic resonance signals were fully assigned structurally and the resulting structures were confirmed by Fourier-transformed infrared spectroscopy. It was the herein elaborated synthesis of impurity-free SUM that allowed for growing of its single crystals suitable for X-ray crystallographic studies. Comparison of the powder X-ray diffraction pattern for SUM with that derived from single-crystal X-ray crystallographic analysis indicated that SUM formed the polymorph I crystal phase, which is also encountered in its pharmaceutical formulation.

Full text of DOI:10.1002/jps.23412

Physicochemical Characteristics of Sunitinib Malate and its
Process-Related Impurities
1
2
1
1
1
´
´
KATARZYNA SIDORYK, MAURA MALINSKA, KRZYSZTOF BANKOWSKI, MAREK KUBISZEWSKI, MARTA ŁASZCZ,
MAGDALENA BODZIACHOWSKA-PANFIL,1 MAGDALENA KOSSYKOWSKA,1 TOMASZ GILLER,2 ANDRZEJ KUTNER,1
2
´
KRZYSZTOF WOZNIAK
1Pharmaceutical Research Institute, Warszawa 01-793, Poland
2Department of Chemistry, The University of Warsaw, Warszawa 02-093, Poland
Received 8 August 2012; revised 5 November 2012; accepted 15 November 2012
Published online 11 December 2012 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/jps.23412
ABSTRACT: In this article, details of crystal and molecular structures of sunitinib malate
(SUM), an anticancer therapeutic, and its key synthetic intermediate are presented. Both these
compounds were also characterized spectroscopically and thermally. SUM crystallizes in the
monoclinic P21 space group with two molecules in the asymmetric part of the unit cell, whereas
the intermediate crystallises in the triclinic P-1 space group with four independent molecules
in the asymmetric unit. The three-dimensional structure of SUM consists of two different lay-
ers of molecules. The first one is built of the malic anions, whereas the other layer consists of
more hydrophobic sunitinib molecules. This layer is formed by two types of molecules creating a
herring bond-like pattern with pairs of neighboring cations forming the V-shape arrangement
of molecules. The V-shaped pairs of molecules form ribbons by fitting into two neighboring
V shapes. The characteristic V-shape assemble of the moieties is hold together with three
C H. . .F weak interactions. Besides, process-related impurities of SUM were identified and
their structures confirmed by separate synthesis. These impurities were fully characterized by
spectroscopic and crystallographic methods as well as by differential scanning calorimetry and
thermogravimetric analysis. The H-, 13C-, and 15N-nuclear magnetic resonance signals were
fully assigned structurally and the resulting structures were confirmed by Fourier-transformed
infrared spectroscopy. It was the herein elaborated synthesis of impurity-free SUM that allowed
for growing of its single crystals suitable for X-ray crystallographic studies. Comparison of the
powder X-ray diffraction pattern for SUM with that derived from single-crystal X-ray crys-
tallographic analysis indicated that SUM formed the polymorph I crystal phase, which is also
encountered in its pharmaceutical formulation. © 2012 Wiley Periodicals, Inc. and the American
Pharmacists Association J Pharm Sci 102:706–716, 2013
Keywords: sunitinib malate; structure; physicochemical characteristics; process-related im-
purities; crystallization; thermal analysis
drug discovery and development. However, a com-
plete physicochemical characteristic not only for an
active pharmaceutical ingredient (API), but also of
its key synthetic intermediates, has recently become
required by both the U.S. Food and Drug Adminis-
tration (FDA) and by the European Medicine Agency
(EMA). In addition to the purity characteristics of
API, it is now necessary to characterize an impurity
profile by identification and physicochemical charac-
terization of both impurities, that is, process-related
and degradation impurities.
INTRODUCTION
Crystal structure knowledge, at both the molecu-
lar and supramolecular levels, is crucial for rational
Correspondence to: Krzysztof Woz´niak (Telephone: +48-22-
8220211x212; Fax: +48-22-8220211x212; E-mail: kwozniak@
chem.uw.edu.p); Andrzej Kutner (E-mail: a.kutner@ifarm.eu)
Presented in part (by A.K.) at the 12th International Conference
on Pharmacy and Applied Physical Chemistry (PhandTA 12), Karl-
Franzens-University Graz, Austria; May 6–9, 2012 and (by K.B.)
at the VIIth Multidisciplinary Conference on Drug Research, Rawa
Mazowiecka, Poland; May 30–June 1, 2012.
Katarzyna Sidoryk and Maura Malin´ska have contributed
equally to this work.
Sunitinib malate [N-[2-(diethylamino)ethyl]-5-
[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-
methyl] -2,4 -dimethyl -1H -pyrrole -3 -carboxamide
Journal of Pharmaceutical Sciences, Vol. 102, 706–716 (2013)
© 2012 Wiley Periodicals, Inc. and the American Pharmacists Association
706
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PHYSICOCHEMICAL CHARACTERISTICS OF SUNITINIB MALATE AND ITS PROCESS-RELATED IMPURITIES
707
L-malate (SUM)] is the first in the class of orally
active, multitargeted tyrosine kinase and angio-
and
N-hydroxybenzotriazole
(2.01
g,
13.16
mmol) in N,N-dimethylformamide (10 mL). N,N-
Diisopropylethylamine (4.5 mL, 26 mmol) was added,
and the mixture was stirred at room temperature for
30 min. N-Ethyl-ethylenediamine (2.78 mL, 26 mmol)
was then added, and the resulting dark red solution
was stirred overnight. Hydrochloric acid (1 M, 10
mL) was added, and the mixture was stirred for 1 h.
Water (10 mL) and dichloromethane (150 mL) was
then added, and the organic phase was separated.
The saturated solutions of NaHCO3 (30 mL), brine
(30 mL), and 10% NaOH (to reach pH 13) were
added to aqueous phase, and the resulting mixture
was extracted with 10% methanol/dichloromethane
(3 × 30 mL). The organic extracts were combined,
dried over anhydrous MgSO4, and evaporated to
give crude product as a dark oil. The crude material
(4 g) was purified on silica gel column (150 g) with
methanol. The combined fractions were evaporated to
give N-[2-(ethylamino)ethyl]-5-formyl-2,4-dimethyl-
1H-pyrrole-3-carboxy-amide [SU-5; Electrospray
ionization mass spectroskopy (ESI–MS): calcd. for
R
genesis inhibitors.1–2 The Sutentꢀ, drug containing
SUM as API, originally developed by Sugen and
acquired by Pfizer, was approved by the FDA and
the EMA in 2006. Since then, it was administered
for the treatment of imatinib-resistant gastrointesti-
nal stromal cell tumors and metastatic renal cell
carcinoma.3–5 Moreover, it was approved by FDA
and EMA in 2011 for the treatment of pancreatic
neuroendocrine tumors.6–8 Although the drug has
been marketed several years now, so far neither
SUM nor its process-related impurities have been
fully characterized physicochemically. Therefore,
there was a need for a complete physicochemical
characterization not only for this API but also its
impurities and key synthetic intermediates to comply
with the current FDA and EMA requirements.9–10
Herein, we identified the process-related impuri-
ties of SUM and the origin of its formation. Struc-
ture of this impurity was determined by spectroscopic
methods and confirmed by a separate synthesis. Quite
unexpectedly, the impurity appeared identical with
the primary metabolite of SUM.11 Moreover, we devel-
oped a procedure of removal of the precursor of this
impurity from the key synthetic intermediate at an
early step of SUM synthesis. Single crystal of this in-
termediate was obtained and its X-ray structure was
first solved. We synthesized the impurity-free SUM
and optimized conditions of its single-crystal growth.
The major challenge was to select an appropriate sol-
vent system and the crystallization procedure. For the
first time to our knowledge, we succeeded in obtaining
a nonsolvated single crystal of SUM suitable for X-ray
determination, thus giving an unequivocal proof of
its structure for a better understanding of its molec-
ular function. Furthermore, SUM and its synthetic
key intermediate as well as the process-related impu-
rity were characterized by high-performance liquid
(M+H)+: 238.30, found 238.3; purity: 96.34%, tR
=
9.0 min (by HPLC)].
N-(2-Ethylaminoethyl)-5-[(Z)-(5-Fluoro-2-oxo-1H-Indol-
3-ylidene)Methyl]-2,4-Dimethyl-1H-Pyrrole-3-
Carboxamide
A solution of SU-5 (2.05 g, 8.64 mmol), 5-fluoro-1,3-
dihydro-2H-indol-2-one (SU-2; 1.31 g, 8.64 mmol),
and pyrrolidine (58 :L) in ethanol (5 mL) was heated
to reflux for 3 h. Upon cooling to room temperature,
crude N-(2-ethylaminoethyl)-5-[(Z)-(5-fluoro-2-oxo-
1H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-
3-carboxamide (SU-6) was filtered off and dried. The
crude SU-6 (2.0 g) was purified on silica gel column
with CHCl3–CH3OH–25% NH3 (49:8.1:0.6, v/v). The
combined fractions were evaporated to give pure
SU-6 [1.45 g; ESI–MS: calcd. for (M+H)+: 371.4,
found 371.2; purity: 95.36% tR = 12.8 min by HPLC].
1
chromatography (HPLC); H-, 13C-, and 15N-nuclear
magnetic resonance (NMR); Fourier-transformed in-
frared (FTIR) spectroscopy; powder X-ray diffraction
(PXRD); and thermal analyses, including differential
scanning calorimetry (DSC) and thermogravimetric
analysis (TGA).
Crystallization of N-[2-(Diethylamino)Ethyl]-5-Formyl-
2,4-Dimethyl-1H-Pyrrole-3-Carboxy
Amide
The suspension of N-[2-(diethylamino)ethyl]-5-
formyl-2,4-dimethyl-1H-pyrrole-3-carboxy
amide
(SU-1; 1.0 g, purity: 99.50%; and 0.33% SU-5 by
HPLC) in ethanol (5 mL) was heated at reflux for 15
min with stirring to obtain the clear solution. The
solution was slowly cooled down to room temperature
and left overnight. The crystals of SU-1 were filtered
off and dried [0.75 g, purity: 99.75% SU-1; and 0.08%
SU-5 (by HPLC)].
MATERIALS AND METHODS
Syntheses
N-[2-(Ethylamino)Ethyl]-5-Formyl-2,4-Dimethyl-1H-
Pyrrole-3-Carboxy-Amide
5-Formyl-2,4-dimethyl-1H-pyrrole-3-carboxylic acid
(SU-4; 2.0 g, 11.96 mmol) was added to a solution
Crystallization of SUM
of
2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyl-
The suspension of SUM (1.0 g; purity: 99.62% SUM;
and 0.09% SU-6 by HPLC) in water (4.65 mL) was
uronium tetrafluoroborate (4.23 g, 13.16 mmol)
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SIDORYK ET AL.
heated with stirring to 85◦C to get a clear solution.
Stirring was continued for 20 min, then methanol
(32 mL) was added and the mixture was cooled down
to room temperature. After 4 days, the crystals of
SUM were filtered off and dried.
carried out with the Oxford Diffraction Ltd. suit of
programs.12 Whereas the X-ray diffraction data for
SUM were collected using a KAPPA APEXII ULTRA
diffractometer (Bruker AXS GmbH, Karlsruhe, Ger-
many) controlled by APEXII software (Bruker AXS),13
equipped with MoK" rotating-anode X-ray source (λ =
Nuclear Magnetic Resonance
˚
0.71073 A, 50.0 kV, 22.0 mA) with the radiation
Nuclear magnetic resonance spectra were acquired
on a Varian 600 spectrometer (Agilent Technologies,
Santa Clara, California) at the 600 MHz transmitter
frequency for the 1H. Spectra were measured at 298 K
in DMSO-d6 solution relatively to tetramethylsilane.
signal as the 1H and 13C chemical shift standard. The
15N-NMR spectrum was calibrated to CH3NO2 as a
chemical shift standard.
monochromatized by multilayer optics, and APEX-II
CCD detector. The data collection for both compounds
was carried out at 100 K using the Oxford Cryostream
cooling device. The crystal was mounted on Mounted
CryoLoop with a droplet of Pantone-N oil and imme-
diately cooled down. Indexing, integration, and initial
scaling were performed with SAINT14 and SADABS15
software. The crystal was positioned at 50 mm from
the CCD camera. Three thousand and seven hundred
frames were measured at 0.5◦ intervals with a count-
ing time of 10–20 s.
The structures were solved by direct methods using
the SHELXS-97 16 program (Bruker AXS) and refined
with the SHELXL-97 (Bruker AXS).16 The multiscan
absorption correction was applied in the scaling pro-
cedure. The refinement was based on F2 for all re-
flections except those with the negative intensities.
Weighted R factors (wR) and all goodness-of-fit S val-
ues were based on F2, whereas the conventional R fac-
tors were based on the amplitudes, with F set to zero
for negative F2. The F2 > 2σ (F2) criterion was applied
only for the R factors calculation and was not relevant
to the choice of reflections for the refinement. The R
factors based on F2 are for all structures about twice
as large as those based on F. Scattering factors were
taken from Tables 4.2.6.8 and 6.1.1.4 from the Inter-
national Crystallographic Tables Vol.C.17 The crystal
data and other important parameters related to data
collection are summarized in Table 1.
Infrared Spectroscopy
The infrared spectra were recorded on the
PerkinElmer FT-IR BX spectrometer (Perkin Elmer,
Waltam, Massachustts) in the range from 4000 to
400 cm−1. A spectral resolution of 4 cm−1 was used.
The solid samples were measured in KBr pellets.
Powder X-ray Diffraction
Powder X-ray diffraction was performed on a Mini-
Flex diffractometer (Rigaku Corporation, Tokyo,
Japan) using CuK"1 radiation. Samples were pressed
on a glass plate. The instrument was operated in the
range from 3◦ to 40◦ with the scan rate of 0.02◦/min.
The simulated powder pattern of SUM was gener-
ated from X-ray structural data with the use of the
CCDC Mercury 3.0 program (Cambridge Crystallo-
graphic Data Centre, Cambridge, United Kingdom).
Thermal Analysis (DSC and TGA)
Thermal analyses were carried out on a differential
scanning calorimeter DSC 822 with IntraCooler and
on the thermogravimeter TGA/SDTA 851 cells (Met-
tler Toledo GmBH, Schwerzenbach, Switzerland) un-
der nitrogen atmosphere. Accurately weighed sam-
ples (4–7 mg) were packed in aluminum pans with
pierced lids. TGA measurements were blank-curve
corrected.
RESULTS AND DISCUSSION
Synthesis of Impurity-Free Crystalline SUM
Convergent synthesis of SUM from key synthetic in-
termediates (Scheme 1) is well documented.18–19 How-
ever, in our hands, the crude product (SUM) obtained
by the known method resisted the formation of crys-
tals of the quality required for X-ray study. There-
fore, we anticipated that our product might slightly
be contaminated with an unknown process-related
impurity. Herein, this impurity was identified by a
combined liquid chromatography–mass spectrometry
(MS). Molecular ion at m/z 371.2 and its fragmenta-
tion ions at 326.2, 283, and 255 (the same as for SUM),
as well as the lack of ions at m/z 100 and 117 (char-
acteristic for diethylamine moiety), in the impurity
spectrum indicated the structure of some des-ethyl
analog, most likely SU-6 (Scheme 2; and Figure S1
and Scheme S1, the Supporting Information).
X-ray Crystallography
The X-ray diffraction data collection for a single crys-
tal of SU-1 was performed on a Kuma KM4CCD
four-axis diffractometer (Agilent Technologies) with
the graphite-monochromated MoK" radiation. The
diffractometer was equipped with a nitrogen gas-flow
apparatus (Oxford Cryosystems Ltd, Oxford, United
Kingdom). A single crystal was positioned at 50 mm
from the KM4CCD camera. Six hundred forty four
frames were measured at 1◦ intervals with a counting
time of 30 s. The data were corrected for Lorentz and
polarization effects. The multiscan absorption correc-
tion was applied. Data reduction and analysis were
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PHYSICOCHEMICAL CHARACTERISTICS OF SUNITINIB MALATE AND ITS PROCESS-RELATED IMPURITIES
709
Table 1. Summary of Crystallographic Data and Structure Refinement for SUM and SU-1
Identification Code
SUM
SU-1
Chemical formula
Molecular weight
Temperature
C26H33FN4O7
532.56 g/mol
100(2) K
C14H23N3O2
265.35 g/mol
100(2) K
˚
˚
Wavelength
0.71073 A
0.71073 A
Crystal system, Space group
Unit cell dimensions
Monoclinic, P21
Triclinic, P-1
˚
˚
a = 7.5404(16) A
a = 10.0256(3) A
α = 90◦
α = 72.030(3)◦
˚
˚
b = 8.3349(18) A
b = 14.2161(3) A
β = 98.352(11)∞
β = 86.223(3)◦
˚
˚
c = 20.286(4) A
c = 21.7536(7) A
γ = 90◦
γ = 87.753(7)∞
2942.2(1) A3
8, 1.198 mg/m3
0.081 mm−1
1152
Volume
1261.4(5) A3
2, 1.402 mg/m3
0.107 mm−1
564
Z, Calculated density
Absorption coefficient
F(000)
Crystal size
Theta range for data collection
Limiting indices
Reflections collected/unique
Completeness to Thmax
Absorption correction
Maximum and minimum transmission 0.9841 and 0.9644
Refinement method
0.34 × 0.26 × 0.15 mm3
0.30 × 0.10 × 0.02 mm3
1.01◦–30.64◦
1.97◦–25.68◦
−10 ≤ h ≤ 10, −11 ≤ k ≤ 11, −28 ≤ l ≤ 28 −12 ≤ h ≤ 12, −17 ≤ k ≤ 7, −26 ≤ l ≤ 26
57,330/4109 [R(int) = 0.0427]
99.30%
44,637/11,176 [R(int) = 0.0440]
100%
Semiempirical from equivalents
Semiempirical from equivalents
0.9984 and 0.9760
Full matrix least squares on F2
4109/1/349
1.140
Full matrix least squares on F2
11,176/1/764
Data/restraints/parameters
Goodness-of-fit on F2
1.018
Final R indices [I > 2sigma(I)]
R indices (all data)
Largest diff. peak and hole
R1 = 0.0319, wR2 = 0.0879
R1 = 0.0339, wR2 = 0.0897
0.368 and −0.323 eA−3
R1 = 0.0481, wR2 = 0.1318
R1 = 0.0830, wR2 = 0.1643
0.414 and −0.435 eA−3
In order to confirm this structure, we synthesized20
SU-6 by a coupling of an acid SU-4 with N-ethyl-
ethylenediamine, followed by condensation of crude
SU-5 with SU-2 (Scheme 2). For identification, SU-6
was purified by column chromatography and charac-
Apparently, purity of SU-1 is crucial for preparation
of SUM of a pharmaceutical grade. During condensa-
tion with SU-2, the presence of even a small amount
of the SU-5 impurity in SU-1 leads to formation of
N-des-ethyl-sunitinib (SU-6). This impurity is very
difficult to remove from SUM by repetitive solvent
crystallization.
Although strictly regulated as an impurity, N-des-
ethyl-sunitinib (SU-6) is known as primary active
metabolite of SUM.21–22
Sunitinib malate prepared from SU-1, free from
the process-related impurity SU-5, was crystallized
in an optimized solvent system (water/methanol) to
give single crystals suitable for X-ray crystallographic
studies. The solubility of SUM in the most of the
1
terized by MS spectrometry, H-, 13C-, and 15N-NMR
and FTIR spectroscopy (see Experimental). Further,
we concluded that the presence of the process-related
impurity SU-6 in SUM might originate from contam-
ination of the key synthetic intermediate SU-1 with
N-des-ethyl analog SU-5 (Scheme 2). This might be
the reason why commercially available key interme-
diate SU-1 usually contains the N-des-ethyl impurity
SU-5 (Scheme 2), in a substantial amount of up to
0.5% (by HPLC).
Scheme 1. Convergent synthesis of sunitinib malate (SUM): N-[2-(diethylamino)ethyl]-
5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-
carboxamide L-malate.
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SIDORYK ET AL.
Scheme 2. Synthesis of N-des-ethyl-sunitinib (SU-6): N-(2-diethylaminoethyl)-5-[(Z)-(5-
fluoro-2-oxo-1H-indol-3-ylidene)methyl] -2,4-dimethyl-1H-pyrrole-3-carboxamide.
organic solvents is very poor; however, the compound
is quite soluble in water. To obtain single crystals
of SUM, we investigated different mixtures of water
containing organic solvent such as ethanol, acetone,
tetrahydrofuran, acetonitrile, n-propanol, t-butanol,
isopropanol, methanol, and water alone. We tested a
number of mixtures of different ratio of water and or-
ganic solvent and various temperature of cooling. We
found that crystals of the quality required for X-ray
crystallographic study were obtained from the mix-
ture of water and methanol (1:7, v/v).
We also investigated different solvent systems to
obtain of SU-1 crystals suitable for X-ray crystallo-
graphic studies. We have found that crystallization
from ethanol or ethanol/water gave SU-1 with a high
purity of 99.75% and with a very low level of SU-5
(0.08% by HPLC). Crystals of SU-1 thus obtained
were suitable for X-ray crystallographic studies.
FTIR Spectroscopy
The structures of all the compounds obtained were
confirmed by FTIR spectroscopy (Table 3S, Support-
ing Information). However, because of the low concen-
tration of SU-6 in SUM in our samples, the method did
not allowed to determine the presence of the process-
related impurity SU-6 in SUM. The bands originated
from the same functional groups in the spectra of
all the compounds were observed. Additional band
at 2695 cm−1 indicates the hydrogen bonds of the salt
in the spectrum of SUM.
Powder X-ray Diffraction
Polymorphism of SUM was reported up to now only in
the patent literature by pharmaceutical companies.
Originally, SUM was described to exist in two poly-
morphic forms I and II.23 Recently, SUM has been
reported in two patent applications to exist also as
the other polymorphs [III (Ref. 24) and III, IV (Ref.
25)]. However, our crystallizations from various wa-
ter–methanol mixtures resulted exclusively in the
polymorph I. Moreover, it was the polymorph I that we
Structures Elucidation by NMR and FTIR Spectroscopy
NMR Spectroscopy
R
observed in capsules of Sutentꢀ, containing 25 mg of
All signals in the 1H-, 13C-, and 15N-NMR spectra
of SUM, key intermediates SU-2, SU-1, and process-
related impurity SU-6 as well as of its precursor SU-5
were assigned to the respective atoms using one- and
two-dimensional techniques (Nuclear Overhauser Ef-
fect Spectroscopy, Correlation Spectroscopy, Gradi-
ent Heteronuclear Single Quantum Correlation, and
Gradient Heteronuclear Multiple Bond Coherence;
1H–13C and 1H–15N). A comparison of spectra of SUM
with the ones of SU-6 (Table S1, the Supporting In-
formation) and spectra of SU-1 with the ones of SU-5
(Table S2, the Supporting Information) shows that
these pairs of compounds have a very similar skeletal
system. The number of the NMR signals is the same
for these pairs of compounds and their spectra differ
only in the region of the ethyl group. As expected, the
NMR spectra of SUM contained signals from both,
sunitinib and the ones from malic acid in the 1:1 ra-
tio. However, the techniques we used did not allow
to determine the exact position of each carbonyl from
malic acid moiety.
SUM. Direct comparison (Fig. 1) of the PXRD pattern
R
of Sutentꢀ with the experimental one and the one
simulated from the single-crystal X-ray structure23
indicated clearly the signals originated from SUM
(11.90◦, 13.16◦, 15.92◦, 17.18◦, 19.40◦, 22.13◦, 24.17◦,
25.46◦, 26.96◦, and 27.56◦) in addition to signals
from mannitol (10.53◦, 11.46◦, 14.64◦, 16.80◦, 18.74◦,
20.33◦, 21.08◦, 21.70◦, 23.33◦, 24.70◦, 25.90◦, 26.51◦,
28.32◦, and29.47◦) as the main excipient. The reflec-
tions are summarized in Table 4S (see the Supporting
Information).
Thermal Characteristics
Sunitinib malate and its impurities were character-
ized by DSC (Fig. 2). SUM melts at 197.91◦C (onset)
with an accompanying decomposition (a visible exo
effect at about 225◦C) coming from the elimination
of carboxy group. The melting point of SUM agrees
well,23 with the data for form I (about 196◦C). The
TGA curve of SUM shows no significant mass loss
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PHYSICOCHEMICAL CHARACTERISTICS OF SUNITINIB MALATE AND ITS PROCESS-RELATED IMPURITIES
711
Figure 1. (a) Simulated (black) and experimental (green) PXRD pattern of SUM (form I), (b)
PXRD pattern of SutentꢀR 25 mgꢀ(black) and mannitol (red). Peaks originated from form I of
SUM, present in PXRD of SutentR 25 mg, are marked with arrows.
(0.2%) up to the melting point, indicating the lack
of solvent included in the crystal lattice. Both start-
ing materials, SU-2 and SU-1, melt at 143.35◦C and
151.08◦C, respectively. The DSC curve of SU-6 shows
two endotherms at 190.12◦C and 259.83◦C. The TGA
proved that the first effect is connected with evapo-
ration of the residual solvents (mass loss 1.7%). The
SU-5 curve also shows two endotherms at 105.62◦C
and 125.59◦C. The thermogravimetric profile shows
a mass loss equal to 6.1% in the temperature range
of the first endothermic effect. The second endotherm
comes from the melting with an accompanying de-
composition proved by decreasing line of TGA curve
(Figs. S2–S5 in the Supporting Information).
molecules in the asymmetric unit (Fig. 3). There is a
pseudotranslation in the crystal lattice of this com-
pound. Each SU-1 molecule consists of a substituted
pyrrole ring with two methyl groups attached, the
aldehyde group, and a chain with tertiary amine
and amide groups. The geometrical features of
the corresponding bonds in the four independent
molecules are generally reproduced within the 3σ
(F-standard uncertainty) for a given structural
parameter. However, a significant difference is a
disorder in the ethyl substituent present in two
molecules. For clarity of the description, only the
geometrical parameters for one molecule are shown
and discussed. The C(1) N(1) and C(4) N(1) bond
˚
length are equal to 1.380(3) and 1.349(2) A, respec-
Single-Crystal X-ray Crystallography
tively. The C(1)–N(1)–C(4) valence angle is equal to
110.2(2)◦. The bond length for the carbonyl group
N-[2-(Diethylamino)ethyl]-5-formyl-2,4-dimethyl-
1H-pyrrole-3-carboxy amide crystallizes in the
triclinic P-1 space group with four independent
˚
in the aldehyde and amide groups are 1.231(2) A
˚
[C(7) O(1)] and 1.241(2) A [C(8) O(2)], respectively.
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SIDORYK ET AL.
Figure 2. DSC profiles of SUM, process-related impurity SU-6, its precursor SU-5, and key
synthetic intermediates SU-2 and SU-1.
The torsion angle between the aldehyde group and
the pyrrole ring is 0.2(3)◦ [O(1)–C(7)–C(1)–N(1)]. The
Sunitinib Malate
Sunitinib malate (Fig. 5) crystallizes in the monoclinic
P21 space group with two moieties (a cation with pro-
tonated tertiary amine and an anion of the malic acid)
in the asymmetric part of the unit cell. The cation has
the indolyl group substituted with fluorine atom and
the pyrrole ring with two methyl groups. These rings
are lying on the same plane and they are connected
by methylene bridge. The C(17) F(1) bond length is
˚
amid C(8) N(2) bond is equal to 1.342(3) A, and the
O(2)–C(8)–N(2)–H(2) torsion angle is 167(2)◦. For all
structural parameters of this and SUM structures,
see the Supporting Information.
A proper conformation of the pyrrole ring and
the aldehyde group enables formation of dimers con-
nected by two hydrogen bonds (see Fig. 4a). These
hydrogen bonds are due to the following short con-
tacts between the non-hydrogen atoms: N(8)···O(5),
N(4)···O(1), N(5)···O(7), and N(1)···O(3). For geomet-
rical details, see Table 2. The tertiary amine groups
from the neighboring molecules interact with each
other and form a layer by hydrophobic interactions.
These interactions arrange molecule into layer with
alternate hydrophilic and hydrophobic contacts. A
three-dimensional (3D) structure is created also by
other hydrogen bonds between the amide groups from
the neighboring molecules (see Fig. 4b); N(11)···O(2),
N(2)···O(4), N(9)···O(6), and N(6)···O(8) (Table 2). Be-
tween the layers of molecules, there is also a C–H···π
interaction between the hydrogen atom from the
methyl group and the carbon atom from the pyr-
role ring with the H(6A)···C(18) distance equal to
˚
1.368(2) A, and the length of the carbonyl bond in
˚
the indolyl group is equal to 1.238(2) A [O(5) C(21)].
The distances between the carbon atoms in the pyr-
role ring are close to 1.40 A, which are of standards
˚
values. The bonds between the N(4) nitrogen atom
and the C(12) and C(22) vicinal carbons are shorter,
˚
˚
1.385(2) A and 1.345(2) A, respectively. The amide
bond connects the pyrrole ring with the amine. The
˚
C(9) O(7) and C(9) N(2) bond lengths are 1.238(2) A
˚
and 1.385(2) A, respectively. The nitrogen N(1) atom
from the amine group is substituted with three ethyl
groups and the hydrogen atom from the malic acid.
The anion of the malic acid has two different car-
boxyl groups: one with and the other one without hy-
drogen atom. The one with the H atom has the car-
˚
bonyl O(1) C(1) bond, which is 1.218(2) A long, and
˚
2.682(2) A.
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PHYSICOCHEMICAL CHARACTERISTICS OF SUNITINIB MALATE AND ITS PROCESS-RELATED IMPURITIES
713
Figure 3. The four independent molecules in the structure of SU-1 and the labelling of the
non-hydrogen atoms. Thermal displacement ellipsoids are drawn at the 50% probability level
[ORTEP-3 (26)]. The hydrogen atoms have been omitted for clarity.
˚
tions with tyrosine kinases receptor and helps to form
the 3D crystal lattice.
formally a single C(1) O(4) bond of 1.307(2) A. The
second carboxyl group has similar bond lengths be-
In the 3D structure of SUM, two layers of moieties
(see Fig. 6) can be distinguished. The first one is built
of the malic anions, whereas the other layer consists
of more hydrophobic sunitinib molecules. This layer is
formed by two types of molecules creating a herring
bond-like pattern with pairs of neighboring cations,
thus forming the V-shape arrangement of molecules.
tween the oxygen and carbon atoms [O(3) C(4) =
˚
˚
1.252(2) A and O(2) C(4) is 1.259(2) A]. This is due
to the fact that the hydrogen atom is not present and
the character of the carbon oxygen bonds is becoming
very similar. This molecule contains many acceptors
and donors of hydrogen bonds, which enables interac-
Figure 4. The view of crystal packing along the x-axis (a) and crystal packing along the y-axis
(b). Hydrogen bond marked by orange dashed line.
Table 2. Selected Hydrogen-Bond Parameters for SU-1
DH···A
DH (A)
H···A (A)
D···A (A)
DH···A (◦)
˚
˚
˚
N1 H1···O3a
N2 H2···O4
N4 H4···O1a
N5 H5···O7b
N6 H6···O8c
N8 H8···O5b
N9 H9···O6
N11 H11···O2d
0.86 (2)
0.83 (2)
0.87 (2)
0.86 (2)
0.85 (2)
0.88 (2)
0.87 (2)
0.85 (3)
2.03 (2)
2.07 (3)
1.99 (2)
2.00 (2)
2.17 (2)
2.00 (2)
2.04 (2)
2.08 (3)
2.863 (2)
2.816 (2)
2.838 (2)
2.832 (2)
2.936 (2)
2.848 (2)
2.856 (2)
2.871 (2)
165 (2)
149 (2)
167 (2)
162 (2)
149 (2)
163 (2)
155 (2)
155 (2)
Symmetry codes: a−x,−y + 1,−z + 1; b−x + 1,−y,−z + 1; cx + 1,y,z; dx − 1,y,z.
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SIDORYK ET AL.
Figure 5. The molecular structure of SUM and labeling of atoms. Thermal displacement
ellipsoids are drown at the 50% probability level [ORTEP-3 26].
The V-shaped pairs of molecules form ribbons by fit-
ting into two neighboring V-shapes. The characteris-
tic V-shape assemble of the moieties is hold together
with three C H. . .F weak interactions (see Fig. 6).
The parameters of these interactions are shown in
Table 2. The shortest intermolecular contact be-
tween F(1)#5 and C(16) fluorine and carbon atoms is
The closest intermolecular contacts within the an-
ionic layers are shorter than the ones in the other lay-
ers. This indicates that such interactions are stronger
there. The number of acceptor and donor atoms is sig-
nificant, and the wide variety of arrangement should
be possible. The most flexible part of this structure
is interactions between the SUM cations. This can
lead to a possible occurrence of polymorphism for this
drug.
˚
3.389(2) A.
In the parallel direction (along the y-axis), SUM
forms flat chains within this layer. This shape is
formed by the N(3) H(3). . .O(7)#3 hydrogen bonds
and the distance between the acceptor and donor
CONCLUSIONS
˚
atoms is 2.802(2) A. Moreover, the intermolecular hy-
Herein, we solved and refined the crystal structure
of SUM, an active ingredient of anticancer therapeu-
tics. For that, first, we identified the process-related
impurity and then fully characterized it physicochem-
ically. The impurity was identified as N-des-ethyl
sunitinib, also known as the primary metabolite of
SUM. A method of removal of the impurity precursor
from the key synthetic intermediate was developed.
The structure of the key synthetic intermediate and
that of the process-related impurity was fully con-
firmed by spectroscopic methods. Additionally, X-ray
crystal structure was solved of the key synthetic in-
termediate. The comparison of simulated and exper-
imental PXRD data revealed that SUM obtained by
our synthesis formed a polymorph I phase, which is
maintained in commercial drug formulation. The pu-
rity of the key synthetic intermediate appeared cru-
cial for the preparation of SUM of the pharmaceutical
grade. Identification of process-related impurities and
removal of their precursors, at the steps of their for-
mation, might be a successful approach to the efficient
purification of API and growing of its single crystals
suitable for X-ray crystal structural determination.
Sunitinib malate crystallizes in the monoclinic P21
space group with two molecules in the asymmetric
drogen bonds N(4) H(4A). . .O(5) enforces the copla-
narity of the indole and pyrrole rings. The distance
between the oxygen O(5) atom and the nitrogen
˚
N(4) atom is 2.674(2) A. In the second layer, also
some strong hydrogen bonds are present. The an-
ion of the malic acid contains five oxygen atoms
and each of them can either be an acceptor of hy-
drogen, and two hydrogen atoms in hydroxyl group
can donate the hydrogen atom. Those donors form
bonds with the carbonyl oxygens from another anions:
O(4) H(4). . .O(3)#2 and O(6) H(6). . .O(2)#1 (see
Table 3). The O(4) H(4). . .O(3)#2 hydrogen bond is
˚
the shortest in the structure [2.494(2) A]. The oxygen
O(2) and O(1) atoms are the acceptors of the hydrogen
atoms from the cationic amino groups. The distances
˚
between: N(1) and O(2)#1 is 2.750(2) A, and between
˚
N(2) and O(1)#4 is 2.943(2) A. The oxygen atoms from
the malic anion participate also in the C H. . .O weak
interactions, and the appropriate distances between
the oxygen and carbon atoms are in the range from
˚
3.230(2) to 3.442(2) A. The hydrogen bonds N(1) to
O(2)#1, N(2) to O(1)#4, and C H. . .O weak interac-
tions connects the herring bond-like pattern with the
one containing anions.
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PHYSICOCHEMICAL CHARACTERISTICS OF SUNITINIB MALATE AND ITS PROCESS-RELATED IMPURITIES
715
Figure 6. The view of crystal packing along the y-axis (a) and crystal packing along the x-axis
(b). Hydrogen bond marked by orange dashed line and the C H. . .F interactions marked with
green dashed line.
Table 3. The List of the Shortest Interactions and Their Properties for the
SUM Structure
Hydrogen Bond
DH
H. . .A
D. . .A
<(DHA)
O6 H6. . .O2#1
O4 H4. . .O3#2
N1 H1. . .O2#1
N2 H2. . .O1#4
N4 H4A. . .O5
N3 H3. . .O7#3
0.84
0.84
0.93
0.88
0.88
0.88
1.94
1.65
1.83
2.15
1.89
1.96
2.758(2)
2.493(2)
2.750(2)
2.943(2)
2.674(2)
2.802(2)
165.6
176.8
168.9
150.4
147.3
160.0
C
H. . .F
C23 H23A. . .F1#5
C13 H13A. . .F1#6
C16 H16. . .F1#7
0.98
0.95
0.95
2.58
2.59
2.50
3.432(2)
3.498(2)
3.39(2)
145.3
159.6
155.3
O. . .H
C
O3. . .H8 C8
0.99
0.99
0.99
0.99
0.98
0.98
0.98
0.98
2.34
2.37
2.46
2.50
2.50
2.52
2.55
2.64
3.310(2)
3.188(2)
3.442(2)
3.329(2)
3.238(2)
3.303(2)
3.385(2)
3.269(2)
175.6
139.2
169.2
141.0
131.6
136.6
143.2
122.4
O1. . .H24B#8 C24#8
O4. . .H6B#9 C6#9
O5. . .H7B#3 C7#3
O1. . .H26A#2 C26#2
O2. . .H25C#9 C25#9
O6. . .H5#2 C5#2
O5. . .H23C#4 C23#4
N. . .H
C
N2. . .H25B#7 C25#7
0.98
2.75
3.588(3)
143.7
#1, −x + 1,y + 1/2,−z + 1.
#2, x + 1,y,z
#3, x − 1,y,z
#4, x − 1,y − 1,z
#5, x,1 + y,z
#6, 1 − x,1/2 + y,2 − z
#7, x,−1 + y,z
#8, z,x + 1,z
#9, −1 + y,z,1 − x,−1/2 + y,1 − z
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716
SIDORYK ET AL.
part of the unit cell. The intermediate crystallises
in the triclinic P-1 space group with four indepen-
dent molecules in the asymmetric unit. The 3D struc-
ture of SUM has a layered character. It consists of
two different layers of molecules repeated in 3D. The
first layer is created by the malic anions, whereas the
other one consists of more hydrophobic SUM cations.
Two types of SUM molecules create a herring bond-
like pattern with pairs of neighboring cations forming
the V-shape arrangement of molecules. The V-shaped
pairs of molecules form ribbons by fitting into two
neighboring V-shapes. The V-shape assemble of the
moieties is hold together with three C H. . .F weak
interaction.
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This work was supported by The Ministry of Science
and Higher Education, Information Processing In-
stitute, Poland (grant number UDA-POIG 01.03.01-
14-069/08-00). M.M. thanks for a financial support
within the Polish National Science Centre (project
number UMO-2011/01/N/ST4/03616).
The authors declare no competing financial
interest.
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