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Supplementary Crystallographic Information for

“Towards understanding P-gp resistance: a case study of the antitumour drug cabazitaxel”

Ulrich Baisch 1,2 and Liana Vella-Zarb*,1,2

1Department of Chemistry, University of Malta, Msida, Malta MSD2080. 2School of Chemistry, Bedson Building, Newcastle University, NE1 7RU, Newcastle-upon-Tyne,

United Kingdom.

E-mail: liana.vella-zarb@um.edu.mt and ulrich.baisch@um.edu.mt

The following tables contain methods and crystallographic information as well as atom coordinates and the main inter- and intramolecular interactions of various cabazitaxel structures. Scheme 1 shows the common numbering scheme applied to each of the cabazitaxel molecules. Where two molecules are situated in the asymmetric unit, the corresponding number plus 100 was used (e.g. atom C22 in one molecule is atom C122 in the other molecule in the asymmetric unit).

Electronic Supplementary Material (ESI) for CrystEngComm.This journal is © The Royal Society of Chemistry 2014

mailto:liana.vella-zarb@um.edu.mtmailto:ulrich.baisch@um.edu.mt

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Scheme S1: Numbering scheme for cabazitaxel

Figure S1: Structure figure for anhydrous cabazitaxel (CCDC structure 940083). The probability for non-hydrogen spheroids is 50%. Hydrogen atoms were refined isotropically and are depicted with a radius of 0.07 Å.

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Figure S2: Structure figure for cabazitaxel hemihydrate (CCDC structure 940084). The probability for

non-hydrogen spheroids is 50%. Hydrogen atoms were refined isotropically and are depicted with a radius of 0.07 Å.

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Figure S3: Structure figure for cabazitaxel hemihydrate ethanol solvate (CCDC structure 940085). The probability for non-hydrogen spheroids is 50%. Hydrogen atoms were refined isotropically and are depicted with a radius of 0.07 Å.

Figure S4: Structure figure for cabazitaxel THF solvate (CCDC structure 940086). The probability for non-hydrogen spheroids is 50%. Hydrogen atoms were refined isotropically and are depicted with a radius of 0.07 Å.

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Figure S5: Structure figure for cabazitaxel acetone solvate (CCDC structure 940087). The probability for non-hydrogen spheroids is 50%. Hydrogen atoms were refined isotropically and are depicted with a radius of 0.07 Å.

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Methods

In order to obtain suitable single crystals, 0.020g of cabazitaxel were dissolved in about 1 ml of solvent at room temperature. 1 ml of water was then added carefully, ensuring that cabazitaxel remained completely dissolved. This was repeated with a variety of solvents and solvent mixtures. In six of the samples, slow evaporation of the solvent mixture over a number of days resulted in the formation of crystals suitable for data collection.

Single crystal X-ray diffraction data were collected at Station I19 at Diamond Light Source on a Rigaku Saturn724+ diffractometer at a temperature of 120K. SADABS-2008/119 was used for absorption correction. The structure was solved by direct methods and refined on all unique F2 values, with anisotropic non-H atoms and constrained riding isotropic H atoms. Even though all compounds crystallised in the non-centrosymmetric space group P21, Flack parameters did not result in meaningful values because of the short wavelength used to collect the data (synchrotron radiation, λ = 0.6889Å) and the absence of heavy atoms in the structure. The crystal structure of cabazitaxel hemihydrate ethanol solvate (CCDC 940085) can also be refinement in the orthorhombic space group P212121. However, the original monoclinic cell setting was retained because of the following reasons: i) the R(int) is lower for the monoclinic cell setting, ii) standard deviation of the β angle of the cell parameters is too low to add up to 90°, ii) the heavily disordered ethanol solvent molecules refine better in the monoclinic cell setting.The software used was Rigaku CrystalClear for data collection, APEX220 for integration and absorption correction, OLEX221or SHELXTL22 for structure solution and refinement, and DIAMOND23 for graphics.

Temperature-resolved X-ray powder diffraction measurements were carried out on a STOE Stadi P diffractometer equipped with a position sensitive detector. Temperatures ranged from 50oC to 130oC at 20o increments. Each measurement covered a range of 2˚ to 70˚ along 2θ in steps of 0.010˚ over 6 hours.

Structure refinement of powder data was carried out using the programs TOPAS 4.124 and DASH 3.3.125. Powder diffraction patterns were indexed independently with the singular value decomposition method as implemented within TOPAS26. The peak profile and precise lattice parameters were determined by Le Bail fits27 using the fundamental parameter (FP) approach of TOPAS28. The crystal structure of cabazitaxel ethanol solvate was refined against the single crystal structure obtained from synchrotron data using DASH25. For the final Rietveld refinement, all profile and lattice parameters were released and all atomic positions were subjected to refinement using soft bond and angle constraints.

Final agreement factors (R-values) and full crystallographic experimental details are provided in the following tables, together with a list of bond distances and angles.

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Table S1: Numerical differences arising from Hirshfeld surface analyses.

Compound Curvedness Shape IndexMolecularVolume /Å3 Min Max Mean Min Max Mean

Paclitaxel 1141.5 -4.1519 0.438 -1.0127 -0.999 0.9989 0.1543Docetaxel 1060.74 -4.4925 0.506 -1.018 -0.995 0.996 0.1512Cabazitaxel 1010.97 -3.5757 0.504 -0.9653 -0.999 0.9976 0.1625

Table S2: Selected bond distances and torsion angles.

1 2 3 4 5C17 – C61 /Å C17-C15

···C47-N54 /°C2-C47 /Å O25-C2

···C47-N54 /°Centroids /Å

Cabazi Anh 4.705(2) 7.0(10) 6.932(2) 119.1(10) 8.430(2)Cabazi Anh 4.510(2) -9.0(9) 6.876(2) 101.5(8) 9.509(2)Cabazi Hemi 4.70(2) -8.2(10) 7.041(19) -120.7(10) 8.551(4)Cabazi Hemi 4.80(2) 11.2(9) 7.064(16) -102.2(8) 9.543(4)Cabazi THF 5.66(2) -42.7(5) 6.95(1) 66.1(5) 10.152(3)Cabazi Acet 5.839(6) -43.72(16) 7.020(3) 64.75(15) 10.242 (1)Cabazi EtW 7.49(1) -44.7(3) 7.146(6) 65.1(3) 10.715(1)Cabazi EtW 7.494(9) -44.9(3) 7.146(6) 65.3(3) 10.710(1)

Doce Anh 6.608(1) -28.06(1) 6.856(1) 56.09(1) 8.933(1)Doce EtW 7.524(5) -45.43(17) 7.117(3) 63.91(16) 10.709(2)Doce Tri 7.491(9) -44.8(3) 7.094(5) 64.0(2) 10.720(2)

Pacli Anh -NA- -145(2) 8.26(3) 94(2) 10.576(1)Pacli Anh -NA- -158(4) 7.49(3) 32(2) 5.978(1)Pacli Dihy -NA- -167.3(14) 8.13(2) -52.9(11) 10.720(5)Pacli Dihy -NA- 171(2) 7.53(2) -56.3(14) 5.955(3)Pacli Hemi -NA- -179.2(14) 8.301(15) 37.8(11) 11.079(1)Pacli Hemi -NA- 178(2) 7.565(15) 38.8(13) 6.174(1)

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Table S3: Chemical, crystallographic and refinement parameters of cabazitaxel anhydrous, hemihydrate and hemihydrate ethanol solvate obtained by single-crystal diffraction using synchrotron radiation.

Cabazitaxel anhydrous

Cabazitaxelhemihydrate

CabazitaxelHemihydrate ethanol

CCDC deposition number CCDC 940083 CCDC 940084 CCDC 940085Empirical formula C45H57NO14 C45H57.5NO14.25 C47H63NO15.5Formula weight /g mol-1 835.91 840.42 889.15Data collection

Temperature/K 120.15 120.15 120.15Crystal system monoclinic monoclinic monoclinicSpace group P21 P21 P21a/Å 8.351(3) 8.506(5) 12.542(2)b/Å 44.438(17) 45.16(2) 8.6716(16)c/Å 11.410(4) 11.675(6) 42.090(8)α/° 90 90 90β/° 98.532(5) 98.362(4) 89.987(2)γ/° 90 90 90Volume/Å3 4187(3) 4438(4) 4577.7(14)Z 4 4 4ρcalcmg/mm3 1.326 1.258 1.291m/mm1 0.092 0.088 0.090F(000) 1784.0 1794.0 1904.0Crystal size/mm3 0.1 × 0.03 × 0.001 0.12 × 0.09 × 0.02 0.2 × 0.05 × 0.0012Θ range for data collection 1.776 to 48.442° 5.246 to 49.444° 1.876 to 49.726°

Index ranges-8 ≤ h ≤ 9, -52 ≤ k ≤ 52, -13 ≤ l ≤ 1

-10 ≤ h ≤ 10, -47 ≤ k ≤ 53, -9 ≤ l ≤ 1

-15 ≤ h ≤ 15, -8 ≤ k ≤ 10, -51 ≤ l ≤ 51

RefinementReflections collected 30848 20627 36815

Independent reflections 14114[R(int) = 0.0938] 11168[R(int) = 0.0698]

15163[R(int) = 0.0315]

Data/restraints/parameters 14114/1/1106 11168/1/1118 15163/2/1281Goodness-of-fit on F2 1.051 1.034 1.101

Final R indexes [I>=2σ (I)] R1 = 0.0989, wR2 = 0.2557 R1 = 0.1002, wR2 = 0.2622

R1 = 0.0549, wR2 = 0.1430

Final R indexes [all data] R1 = 0.1306, wR2 = 0.2760 R1 = 0.1349, wR2 = 0.2838

R1 = 0.0575,wR2 = 0.1456

Largest diff. peak/hole / e Å-3 0.53/-0.38 0.41/-0.27 0.37/-0.27

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Table S4 Chemical, crystallographic and refinement parameters of cabazitaxel THF solvate and acetone solvate obtained by single-crystal diffraction using synchrotron radiation.

Cabazitaxel THF solvate

Cabazitaxelacetone solvate

CCDC deposition number CCDC 940086 CCDC 940087Empirical formula C45H57NO14 C48H63NO15Formula weight /g mol-1 908.03 893.99Data collectionTemperature/K 120.15 120.15Crystal system monoclinic monoclinicSpace group P21 P21a/Å 11.778(5) 11.725(2)b/Å 17.208(7) 17.328(3)c/Å 12.339(5) 12.449(2)α/° 90 90β/° 109.747(5) 110.453(2)γ/° 90 90Volume/Å3 2353.6(18) 2369.9(7)Z 2 2ρcalcmg/mm3 1.180 1.253m/mm1 0.082 0.087F(000) 892.0 956.0Crystal size/mm3 0.1 × 0.05 × 0.001 0.2 × 0.05 × 0.0012Θ range for data collection 4.102 to 51.746° 4.08 to 51.318°

Index ranges-14 ≤ h ≤ 14, -21 ≤ k ≤ 17,-14 ≤ l ≤ 15

-14 ≤ h ≤ 14, -19 ≤ k ≤ 21, -15 ≤ l ≤ 15

RefinementReflections collected 17853 20833

Independent reflections 8370[R(int) = 0.0762] 9446[R(int) = 0.0273]

Data/restraints/parameters 8370/1/635 9446/1/612Goodness-of-fit on F2 1.126 1.032

Final R indexes [I>=2σ (I)] R1 = 0.0869, wR2 = 0.1698 R1 = 0.0317, wR2 = 0.0805

Final R indexes [all data] R1 = 0.1093 wR2 = 0.1789 R1 = 0.0334, wR2 = 0.0817

Largest diff. peak/hole / e Å-3 0.28/-0.23 0.26/-0.18

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Table S5: Hydrogen Bonds for anhydrous cabazitaxel.

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°O146 H146 O38 0.84 2.10 2.861(12) 150.7O22 H22 O361 0.84 2.10 2.878(13) 154.8

O122 H122 O1362 0.84 2.05 2.818(10) 152.6

1-1+X,+Y,+Z; 21+X,+Y,+Z

Table S6: Hydrogen Bonds for cabazitaxel hemihydrate.

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°O146 H146 O38 0.84 2.18 2.877(12) 139.7O122 H122 O1361 0.84 2.18 2.893(10) 142.8O46 H46 O902 0.84 2.17 2.91(3) 147.9

11+X,+Y,+Z; 2-1-X,-1/2+Y,-Z

Table S7: Hydrogen Bonds for cabazitaxel hemihydrate ethanol solvate.

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°O46 H46 O83A1 0.84 2.02 2.700(14) 137.6O122 H122 O1361 0.84 2.13 2.897(4) 151.3O93A H93A O146 0.84 2.05 2.673(15) 130.6O101 H10H O24 0.87 1.98 2.596(11) 126.5

1+X,-1+Y,+Z

Table S8: Hydrogen Bonds for cabazitaxel THF solvate.

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°O46 H46 O44 0.84 2.12 2.619(10) 117.0O22 H22 O361 0.84 2.23 2.948(7) 144.0N54 H54 O212 0.88 2.26 3.050(6) 150.0

12-X,-1/2+Y,1-Z; 2X,Y,1+Z

Table S9: Hydrogen Bonds for cabazitaxel Acetone solvate.

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°O46 H46 O44 0.84 2.27 2.676(3) 110.0O46 H46 O100 0.84 2.26 2.970(4) 143.0O22 H22 O361 0.84 2.27 3.009(2) 147.0N54 H54 O212 0.88 2.30 3.098(2) 151.0

11-X,-1/2+Y,-Z; 2X,Y,-1+Z;