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Crystal structure of camptothecin, C20H16N2O4

  • Zhuo-Jie Tan , Yun-Bo Wang , Quan-Nu Yang , Yao-Lan Li , Guo-Cai Wang , Yong-Zhong Ouyang and Guo-Qiang Li EMAIL logo
Published/Copyright: February 16, 2018

Abstract

C20H16N2O4, monoclinic, P21 (no. 4), a = 8.0094(5) Å, b = 6.7689(3) Å, c = 29.577(2) Å, β = 95.809(6)°, V =1595.27(16) Å3, Z = 4, Rgt(F) = 0.0457, wRref(F2) = 0.1209, T = 293 K.

CCDC no.: 1558968

The asymmetric unit of the title crystal structure (systematic name: (S-)4-Ethyl-4-hydroxy-1H-pyrano[3′,4′:6,7]indolizino[1,2-b]chinolin-3,14-(4H,12H)-dion) is shown in the figure. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Needle, clear light yellow
Size:0.3 × 0.22 × 0.1 mm
Wavelength:Cu Kα radiation (1.54178 Å)
μ:0.85 mm−1
Diffractometer, scan mode:Gemini S Ultra, ω-scans
θmax, completeness:63.3°, >98%
N(hkl)measured, N(hkl)unique, Rint:10754, 4004, 0.053
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3089
N(param)refined:473
Programs:CrysAlisPRO [1], SHELX [2]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

AtomxyzUiso*/Ueq
N1−0.0325(5)0.4660(6)0.23580(13)0.0461(10)
N1′0.3623(5)0.5509(6)0.74856(12)0.0441(9)
N40.2024(5)0.0847(5)0.29496(13)0.0440(9)
N4′0.5932(5)0.9503(5)0.80164(12)0.0424(9)
O10.5247(5)0.2263(6)0.43384(12)0.0660(10)
O1′0.7023(5)0.9753(5)0.96206(10)0.0530(9)
O20.5591(6)0.5453(7)0.44316(19)0.0998(16)
O2′0.5583(5)0.7590(5)0.99745(12)0.0640(10)
O30.2495(5)0.6425(5)0.40474(12)0.0637(10)
H30.30710.68340.38540.096*
O3′0.5380(4)0.4948(5)0.92857(10)0.0491(8)
H3′0.53040.46250.95500.074*
O40.3506(5)−0.1684(5)0.32979(12)0.0588(9)
O4′0.7326(5)1.2176(5)0.83315(11)0.0546(9)
C20.0467(6)0.3025(7)0.24926(16)0.0452(11)
C2′0.4406(6)0.7161(7)0.75967(15)0.0413(10)
C30.1358(6)0.2713(6)0.29446(15)0.0412(11)
C3′0.5281(6)0.7618(6)0.80417(14)0.0378(10)
C50.1631(7)−0.0208(7)0.25146(15)0.0486(12)
H5A0.0984−0.13950.25550.058*
H5B0.2646−0.05570.23800.058*
C5′0.5510(6)1.0440(7)0.75692(15)0.0458(11)
H5′A0.65111.07640.74260.055*
H5′B0.48471.16260.75940.055*
C60.0619(6)0.1291(7)0.22312(16)0.0456(11)
C6′0.4504(6)0.8836(7)0.73125(16)0.0452(11)
C7−0.0086(6)0.1272(7)0.17966(16)0.0492(12)
H70.00180.01760.16120.059*
C7′0.3750(7)0.8776(7)0.68805(16)0.0506(12)
H7′0.38150.98360.66830.061*
C8−0.0996(6)0.2981(8)0.16277(17)0.0496(12)
C8′0.2856(6)0.7025(8)0.67425(15)0.0461(11)
C9−0.1794(6)0.3104(9)0.11811(17)0.0572(14)
H9−0.17700.20280.09860.069*
C9′0.2005(7)0.6808(9)0.63060(17)0.0578(14)
H9′0.19960.78480.61000.069*
C10−0.2603(7)0.4798(10)0.10330(18)0.0623(15)
H10−0.31260.48620.07380.075*
C10′0.1200(7)0.5110(10)0.61814(18)0.0665(16)
H10′0.06320.50000.58920.080*
C11−0.2655(7)0.6420(9)0.13166(18)0.0635(15)
H11−0.31870.75710.12070.076*
C11′0.1213(7)0.3530(9)0.64804(17)0.0596(14)
H11′0.06840.23560.63860.072*
C12′0.1988(7)0.3676(8)0.69093(16)0.0530(13)
H12′0.19540.26210.71100.064*
C12−0.1939(7)0.6353(8)0.17519(17)0.0544(13)
H12−0.20290.74350.19420.065*
C13−0.1049(6)0.4640(7)0.19204(16)0.0476(11)
C13′0.2848(6)0.5429(7)0.70522(15)0.0429(11)
C140.1587(6)0.3917(7)0.33114(15)0.0457(11)
H140.11370.51840.33040.055*
C14′0.5490(6)0.6563(6)0.84340(13)0.0376(10)
H14′0.51050.52700.84470.045*
C150.2527(6)0.3187(7)0.37031(16)0.0461(12)
C15′0.6307(5)0.7495(6)0.88193(14)0.0375(10)
C160.3204(6)0.1326(7)0.37061(16)0.0473(12)
C16′0.6924(6)0.9371(6)0.87931(15)0.0402(11)
C170.4281(7)0.0652(7)0.41236(19)0.0593(14)
H17A0.35730.00910.43380.071*
H17B0.5039−0.03730.40400.071*
C17′0.7678(7)1.0402(7)0.92075(16)0.0524(12)
H17C0.88821.01920.92370.063*
H17D0.74801.18100.91710.063*
C180.1983(13)0.4798(17)0.4934(2)0.128(4)
H18A0.18870.62000.48890.192*
H18B0.30910.44860.50700.192*
H18C0.11710.43690.51300.192*
C18′0.8763(7)0.4715(8)0.98215(16)0.0590(14)
H18D0.98470.41010.98350.088*
H18E0.79300.37350.98670.088*
H18F0.87670.57041.00540.088*
C190.1671(8)0.3769(10)0.44853(17)0.0672(16)
H19A0.05160.40010.43650.081*
H19B0.18060.23590.45350.081*
C19′0.8359(6)0.5671(7)0.93602(16)0.0465(11)
H19C0.85360.47090.91270.056*
H19D0.91350.67530.93310.056*
C200.2829(7)0.4418(7)0.41269(16)0.0510(13)
C20′0.6552(6)0.6468(6)0.92751(14)0.0393(10)
C210.4662(7)0.4127(8)0.43145(19)0.0621(15)
C21′0.6320(6)0.7988(7)0.96485(16)0.0467(11)
C220.2960(6)0.0031(7)0.33232(16)0.0455(11)
C22′0.6776(6)1.0495(7)0.83776(16)0.0438(11)

Source of material

The dry fruit of Camptotheca acuminata was purchased from Guangzhou qingping medicine market, Guangdong, China. The powdered fruit of C. acuminata (25 kg) was extracted three times with 95% ethanol at room temperature. The solution was concentrated in vacuum to get a residue (2.8 kg), which was suspended in water and partitioned with petroleum ether and then ethyl acetate to yield the ethyl acetate extract (432 g). The ethyl acetate extract was subjected to a silica gel column chromatography (12 × 120 cm, 4000 g) using the petroleumether-ethyl acetate solvent system (100:0, 95:5, 90:10, 80:20, 70:30, 60:40, 50:50, 0:100) to afford eight fractions (Fr. A-H). Fraction E (30.50 g) was further subjected to a silica gel column chromatography (6 × 60 cm, 500 g) eluted with CHCl3—CH3OH (100:0, 90:10, 80:20, 70:30, 50:50, 0:100), which provided six subfractions (Fr.E1—E6). Subfraction Fr.E4 (400 mg) was purified by Sephadex LH-20 column chromatography (CH3OH) and the title compound was crystallized from the eluent.

Experimental details

The C-bound H atoms were positioned geometrically and were included in the refinement in the riding-model approximation. The crystal structure was solved by direct method and refined by full-matrix least-squares refinement with SHELX program [2]. The Flack paramter was found to be 0.1(3) based on 740 quotients [2].

Discussion

Camptotheca acuminata (Chinese happy tree), a tree native to mainland China, belongs to the Nyssaceae family [3], [4]. The dried ripe fruit of C. acuminata has long been used in traditional Chinese medicine for the treatment of cancer [5], and the title compound, camptothecin (CPT), is the main active constituent [6]. It is a quinoline alkaloid originally isolated from C. acuminata [7] and well-known as a topoisomerase inhibitor possessing a proven anti-cancer activity against various cancer cell lines [8, 9] . The phase of clinical trials of CPT have been completed, and it is now used as a chemotherapeutic reagent [4]. Moreover, some modern studies revealed that CPT also has insecticidal activity [10], and the derivatives of CPT were designed, synthesized as well due to its biological activities [11], such as the 5-aryl-(20S)-camptothecin derivatives [12]. In addition, the crystal of camptothecin iodoacetate was obtained and its crystal structure was analysed, which has defined the constitution and absolute stereochemistry of CPT [13]. However, there was still no report on the crystal structure of CPT.

There are two crystallographically independent molecules in the asymmetric unit (cf. the figure). Both molecules are almost identical concerning their geometric parameters. To keep it simple, only one molecule is described in detail. The title compound is composed of five rings, one quinoline moiety, one indolizino moiety and a pyrano ring. The carbon atoms C(8), C(9), C(10), C(11), C(12), C(13) are coplanar constructing the phenyl ring (plane 1, mean deviation 0.009 Å) and the atoms N(1), C(2), C(6), C(7), C(8), C(13) are also coplanar (plane 2, mean deviation 0.008 Å). Plane 1 and plane 2 of which dihedral angle is 0.6° form the quinoline moiety by fusing the atoms of C(8) and C(13). The indolizino moiety consists of plane 3 [atoms: N(4), C(5), C(6), C(2), C(3), mean deviation 0.002 Å] and plane 4 [atoms: N(4), C(3), C(14), C(15), C(16), C(22), mean deviation 0.005 Å] in which the dihedral angle is 0.4°. The atoms C(15), C(16), C(17), O(1), C(21), C(20) form the pyrano ring adopting a Boat conformation with the puckering parameters [14] Q = 0.5492(2) Å, θ = 83.08°, φ = 245.0776°.

Acknowledgements

This work was supported financially by grants from the national Natural Science Foundation of China (no. 21405013), the Fundamental Research Funds for the Central Universities (Grant gg040971), the Natural Science Foundation of Guangdong Province (Grant 2016A030310079).

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Received: 2017-10-7
Accepted: 2018-1-30
Published Online: 2018-2-16
Published in Print: 2018-5-24

©2018 Zhuo-Jie Tan et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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  43. Synthesis and crystal structure of poly[aqua{μ3-(1S,2S)-1-((7-hydroxy-3-(4-hydroxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)pyrrolidin-1-ium-2-carboxylato-κ4O,O′:O′′:O′′′}sodium(I)] monohydrate, C21H22NNaO11S
  44. Halogen bonds in the crystal structure of 1,4-diiodotetrafluorobenzene–1,2-bis(4-pyridyl)propane (1/1), C19H14F4I2N2
  45. Crystal structure of bis(μ-N-i-propyl-N-n-propyldithiocarbamato-κ2S:S′) bis(N-i-propyl-N-n-propyldithiocarbamato-κ2S,S′)dizinc(II), C28H56N4S8Zn2
  46. Crystal structure of bis(μ-N-i-propyl-N-n-propyldithiocarbamato-κ3S,S′:S)bis(N-i-propyl-N-n-propyldithiocarbamato-κ2S,S′)dicadmium(II), C28H56Cd2N4S8
  47. Crystal structure of bis(μ2-di-n-butyldithiocarbamato-κ3S,S′:S3S:S:S′)-hexacarbonyl-di-rhenium(I), C24H36N2O6Re2
  48. Crystal structure of 7-(4-methylphenyl)imidazo[1,2-a][1,3,5]triazin-4-amine, C12H11N5
  49. Crystal structure of the co-crystal O-isopropyl phenylcarbamothioate – 4,4′-bipyridine (2/1), C15H17N2OS
  50. Crystal structure of the coordination polymer catena-poly[chlorido-{μ2-2-(((3,5-dimethyl-1H-pyrazol-1-yl)methyl)amino)-3-hydroxybutanoato-κ4N,N,O:O′}copper(II)], C11H16ClCuN2O3
  51. Synthesis and crystal structure of bis(μ2-acetato-κ2O:O′)-di(ethanol)-bis{μ2-5-(N,N′-diethylamine)-5′-methoxyl-2,2′-[ethylenediyldioxybis(nitrilomethylidyne)]diphenolato-κ6O:O,N,N,O′:O′}trinickel(II) – ethanol – acetonitrile (1/2/2), C58H86Ni3N8O18
  52. Crystal structure of the bis((E)-O-ethyl-N-phenylthiocarbamate) – 4,4′-bipyridine co-crystal (2/1), C28H30N4O2S2
  53. Crystal structure of the (E)-O-methyl-N-phenyl-thiocarbamate – 4,4′-bipyridine (1/1), C18H17N3OS
  54. Crystal structure of bis(μ2-diethyldithiocarbamato-κ3S,S′:S′)-bis(tricyclohexylphosphane-κP)dicopper(I), C46H86Cu2N2P2S4
  55. Crystal structure of N-(3-chlorophenyl)ethoxycarbothioamide, C9H10ClNOS
  56. Crystal structure of bis(μ2-pyrrolidine-1-carbodithioato-κ3S,S′:S;κ3S:S:S′)-bis(tricyclohexylphosphane-P)-di-copper(I), C46H82Cu2N2P2S4
  57. Crystal structure of N-(2-chlorophenyl)methoxycarbothioamide, C8H8ClNOS
  58. Crystal structure of chlorido-methanol-(N-(2-(oxy)-3-methoxybenzylidene)pyridine-4-carbohydrazonato-κ3O,N,O′)-(4-methylphenyl)methyl-tin(IV), C23H24ClN3O4Sn
  59. Crystal structure of N-(3-chlorophenyl)(propan-2-yloxy)carbothioamide, C10H12ClNOS
  60. Crystal structure of 1-[(Z)-[4-(4-methoxyphenyl)butan-2-ylidene]amino]-3-phenylurea, C18H21N3O2
  61. A triclinic polymorph of bis(μ-N,N-bis(2-hydroxyethyl)dithiocarbamato-κ3S,S′:S′) bis(N,N-bis(2-hydroxyethyl)dithiocarbamato-κ2S:S′)zinc(II), C20H40N4O8S8Zn2
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