Home Crystal structure of 3-(2-chloro-benzyl)-7-[4-(2-chloro-benzyl)-piperazin-1-yl]-5,6,8-trifluoro-3H-quinazolin-4-one, C26H21Cl2F3N4O
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Crystal structure of 3-(2-chloro-benzyl)-7-[4-(2-chloro-benzyl)-piperazin-1-yl]-5,6,8-trifluoro-3H-quinazolin-4-one, C26H21Cl2F3N4O

  • Shu-Fen Fang , Wen-Wen Peng , Yuan-Zhen Xiong , Xu-Liang Nie ORCID logo EMAIL logo and Jian-Ping Huang ORCID logo EMAIL logo
Published/Copyright: May 3, 2021

Abstract

C26H21Cl2F3N4O, monoclinic, Pc (no. 7), a = 21.218(6) Å, b = 5.9599(16) Å, c = 9.439(3) Å, β = 99.295(3)°, V = 1177.9(5) Å3, Z = 2, Rgt(F) = 0.0471, wRref(F2) = 0.1282, T = 296(2) K.

CCDC no.: 2074197

The molecular structure is shown in the Figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colourless plate
Size:0.22 × 0.18 × 0.15 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.33 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:25.5°, 99%
N(hkl)measured, N(hkl)unique, Rint:4178, 4178,
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3955
N(param)refined:326
Programs:Bruker [1], SHELX [2], [3], Diamond [4]
Table 2:

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

AtomxyzUiso*/Ueq
C10.8915 (2)0.6189 (9)0.8761 (6)0.0331 (12)
C20.8280 (3)0.6519 (9)0.8191 (6)0.0331 (11)
C30.7920 (2)0.8327 (9)0.8544 (6)0.0331 (12)
C40.8257 (3)0.9890 (9)0.9485 (7)0.0365 (13)
C50.8876 (3)0.9633 (9)1.0078 (6)0.0366 (12)
C60.9234 (2)0.7797 (10)0.9737 (6)0.0326 (11)
C70.9902 (3)0.7459 (10)1.0329 (6)0.0378 (13)
C80.9818 (3)0.4122 (10)0.8826 (7)0.0429 (14)
H81.0030840.2886970.8530460.051*
C91.0849 (3)0.5096 (11)1.0308 (7)0.0469 (16)
H9A1.0947020.3596161.0008630.056*
H9B1.0928000.5133331.1348530.056*
C101.1286 (3)0.6738 (10)0.9749 (6)0.0372 (12)
C111.1092 (3)0.8280 (12)0.8659 (7)0.0461 (15)
H111.0666130.8295370.8222170.055*
C121.1510 (3)0.9779 (13)0.8211 (8)0.0535 (17)
H121.1364451.0807490.7490890.064*
C131.2146 (3)0.9760 (13)0.8827 (8)0.0555 (18)
H131.2431091.0773680.8530460.067*
C141.2351 (3)0.8227 (13)0.9883 (8)0.0519 (17)
H141.2779010.8197571.0299720.062*
C151.1936 (3)0.6746 (11)1.0328 (7)0.0426 (14)
C160.7070 (3)1.0529 (9)0.7135 (7)0.0399 (13)
H16A0.7108461.0116980.6157980.048*
H16B0.7344261.1811590.7407170.048*
C170.6388 (3)1.1135 (9)0.7215 (7)0.0407 (13)
H17A0.6356551.1628910.8179900.049*
H17B0.6254981.2364480.6561660.049*
C180.6175 (3)0.7401 (10)0.7851 (7)0.0403 (13)
H18A0.5892030.6124270.7635630.048*
H18B0.6150310.7895650.8819690.048*
C190.6854 (3)0.6704 (9)0.7757 (8)0.0454 (15)
H19A0.6985650.5494290.8427490.054*
H19B0.6880280.6177170.6796370.054*
C200.5302 (3)0.9790 (10)0.6826 (7)0.0414 (14)
H20A0.5221131.1264030.6399990.050*
H20B0.5222870.9874930.7809030.050*
C210.4841 (2)0.8151 (10)0.6017 (6)0.0343 (12)
C220.5035 (3)0.6552 (11)0.5107 (7)0.0418 (13)
H220.5463060.6487830.5002480.050*
C230.4610 (4)0.5058 (12)0.4354 (8)0.0569 (18)
H230.4751460.4000800.3751990.068*
C240.3971 (4)0.5145 (13)0.4503 (8)0.0569 (19)
H240.3682280.4136520.4004280.068*
C250.3765 (3)0.6708 (12)0.5380 (8)0.0504 (16)
H250.3335900.6767700.5479290.061*
C260.4193 (3)0.8193 (10)0.6117 (6)0.0390 (13)
N10.9225 (2)0.4344 (8)0.8302 (6)0.0385 (11)
N21.0166 (2)0.5573 (8)0.9795 (6)0.0399 (11)
N30.7270 (2)0.8641 (8)0.8104 (6)0.0401 (12)
N40.5969 (2)0.9218 (8)0.6840 (5)0.0360 (10)
O11.0225 (2)0.8669 (9)1.1194 (5)0.0544 (12)
Cl11.22141 (8)0.4830 (4)1.16859 (19)0.0615 (5)
Cl20.39223 (8)1.0155 (3)0.72358 (19)0.0603 (5)
F10.91514 (17)1.1193 (7)1.0997 (4)0.0510 (10)
F20.79463 (16)1.1701 (6)0.9887 (4)0.0493 (9)
F30.79970 (16)0.5028 (6)0.7220 (4)0.0437 (8)

Source of material

To a stirred solution of 5,6,8-trifluoro-7-piperazin-1-yl-3H-quinazolin-4-one (28.42 g, 0.10 mol) in ethanol (140 mL) was in turn added 1-bromomethyl-2-chloro-benzene (41.10 g, 0.20 mol) and sodium hydroxide (8.00 g, 0.20 mol), and then the reaction mixture was refluxed for about 5 h. After the reaction was found to be completed (monitored by TLC), the ethanol was distillated under reduced pressure to give the crude product. The crude product was poured into water (30 mL) and extracted with EtOAc (50 mL * 3). The EtOAc solvent was evaporated to provide the title compound as crystals suitable for X-ray diffraction analysis in 95.3% yield. 1H NMR (400 MHz, CDCl3) δ 2.44–2.468 (t, J = 4.8 Hz, 4 H, PhN(CH2)2), 3.230–3.254 (t, J = 4.8, Hz, 4 H, BnN(CH2)2), 3.476 (s, 2 H, NCH2), 5.014 (s, 2 H, OCNCH2), 6.987–7.298 (m, 8 H, PhH), 7.934 (s, 1 H, NCHN) ppm. 13C NMR (100 MHz, CDCl3) δ = 156.30, 146.58, 133.77, 132.98, 131.80, 130.58, 130.22, 129.19, 128.84, 127.73, 126.69, 125.99, 101.28, 58.52, 52.67, 49.97, 46.74, 28.97 ppm.

Experimental details

All H atoms were included in calculated positions and refined as riding atoms, with O–H = 0.82 Å with Uiso(H) = 1.2 Ueq(O), C–H = 0.93–0.98 Å with Uiso (H) = 1.2–1.5 Ueq(C) [3].

Comment

KRAS mutations have been ubiquitous in human cancers [5]. Because of the missense mutation of KRAS at codon 12, the protein are aberrantly activated into a hyperexcitable state by attenuating its GTPase activity resulting in accretion of GTP-bound activated KRAS and activation of downstream signaling pathways [6], [7], [8], [9]. KRAS p.G12C mutations are dominant in NSCLC and existent in 11–16% of lung adenocar-cinomas (45–50% of mutant KRAS is p.G12C), as well as 1–4% of pancreatic and colorectal adenocarcinomas respectively [10], [11], [12], [13]. KRAS G12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S–IIP). As accessibility of the S–IIP being restricted only to the GDP-bound state, the success of abovementioned approach requires active cycling of KRAS G12C between its active–GTP and inactive–GDP conformations [14]. The active cycling has been realized by these compounds, which possess a quinazoline core as a versatile lead scaffold following systematic optimization of substituent around the scaffold to achieve rapid and sustained in vitro and in vivo target occupancy to induce tumor regression [14, 15]. Recently, an impactful and high-yielding method for the synthesis of quinazolines is developed in our group, and crystals of several key compounds have been achieved. Herein, the synthesis and crystal structure of a key compound 3-(2-chloro-benzyl)-7-(4-(2-chloro-benzyl)-piperazin-1-yl)-5,6,8-trifluoro-3H-quinazolin-4-one is disclosed.

There is one molecule in the asymmtric unit (shown in the figure). In the crystal structure of the title compound bond lengths and angles are very similar to those given in the literature for 3-benzyl-7-chloro-2-isobutylquinazolin-4(3H)-one [16].

The molecule consists of four moieties: quinoline, piperazin ring and two chlorobenzyl groups. The quinoline ring is connected to the nitrogen atom (N3) of piperazin ring. Two benzyls are connected to the nitrogen atom (N4) of piperazin ring and the nitrogen atom (N2) of the quinoline ring, respectively. The atoms of the quinoline and the two chlorobenzyl moieties are coplanar, and piperazin ring is in a typical chair configuration. The torsion angles of C21–C20–N4–C18 and C20–N4–C18–C19 are 76.6(6)° and 175.3(5)°, respectively.


Corresponding authors: Xu-Liang Nie, Key Laboratory of Chemical Utilization of Plant Resources of Nanchang/Department of Chemistry, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China; and Jian-Ping Huang, Key Laboratory of Chemical Utilization of Plant Resources of Nanchang/Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources/Department of Chemistry, Jiangxi Agricultural University, Nanchang 330031, People’s Republic of China, E-mail: (X.-L. Nie), (J.-P. Huang). https://orcid.org/0000-0002-9449-8932 (X.-L. Nie). https://orcid.org/0000-0001-9708-6856 (J.-P. Huang)

Funding source: Natural Science Foundation of Science and Technology

Award Identifier / Grant number: 20151BBF60081

Award Identifier / Grant number: 20171BBE50027

Award Identifier / Grant number: 20171BBG70029

Award Identifier / Grant number: 20202BBEL53028

Funding source: Natural Science Foundation of Education

Award Identifier / Grant number: GJJ170275

Award Identifier / Grant number: GJJ200404

Funding source: Natural Science Foundation of Nanchang City

Award Identifier / Grant number: 2018CXTD014

Funding source: Natural Science Foundation of Jiangxi Agriculture University

Award Identifier / Grant number: 201610410007

Award Identifier / Grant number: 201610410079

Acknowledgements

X-ray data were collected at Instrumental Analysis Center Nanchang Hangkong University, Nanchang, 330063, People’s Republic of China.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: Natural Science Foundation of Science and Technology Department of Jiangxi Province (No. 20151BBF60081; 20171BBE50027; 20171BBG70029; 20202BBEL53028), Natural Science Foundation of Education Department of Jiangxi Province (No. GJJ170275; GJJ200404), Natural Science Foundation of Nanchang City (2018CXTD014), and Natural Science Foundation of Jiangxi Agriculture University (No. 201610410007; 201610410079).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2021-03-09
Accepted: 2021-03-30
Published Online: 2021-05-03
Published in Print: 2021-07-27

© 2021 Shu-Fen Fang et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  46. The crystal structure of catena-poly[diaqua-bis(μ2-2-((2-(2-phenylacetyl)hydrazineylidene)methyl)benzoato-κ2O:O')zinc(II)], C32H30N4O8Zn
  47. The crystal structure of 2-(3,4-dimethoxyphenyl)-2,3-dihydro-1H-naphtho [1,8-de][1,3,2]diazaborinine, C18H17BN2O2
  48. The crystal structure of hexakis(1-ethylimidazole-κ1N)nickel(II) dichloride – 1-ethylimidazole (1/2), C40H64Cl2NiN16
  49. Crystal structure of diaqua-bis(2,4-dinitrophenolato-κ2O,O′)copper(II) 1.5 hydrate, C12H13CuN4O13.5
  50. Crystal structure of N′,N‴-((1E,1′E)-((decane-1,10-diylbis(oxy))bis(2,1-phenylene)) bis(methaneylylidene))di(isonicotinohydrazide), C36H40N6O4
  51. The crystal structure of 2-[(R)-1-(naphthalen-1-yl)ethyl]-2,3,7,7a-tetrahydro-3a,6-epoxyisoindol-1(6H)-one, C19H20NO2
  52. Synthesis and crystal structure of (1E,2E)-3-(anthracen-9-yl)-1-(4-methoxyphenyl)prop-2-en-1-one oxime, C24H19NO2
  53. Synthesis and crystal structure of (2E,2′E)-3,3′-(1,3-phenylene)bis(1-(3-bromophenyl)prop-2-en-1-one), C24H16Br2O2
  54. The crystal structure of catena-poly[bis(µ2-1,2-bis((1H-imidazol-1-yl)methyl)benzene- κ2N:N′)-bis(nitrato-κO)copper(II)], C28H28N10O6Cu
  55. Synthesis and crystal structure of the novel chiral acetyl-3-thiophene-5-(9-anthryl)-2-pyrazoline, C23H18N2OS
  56. Crystal structure of (E)-3-(dimethylamino)-1-(thiophen-3-yl)prop-2-en-1-one, C9H11NOS
  57. Crystal structure of catena-poly[aqua-(4-iodopyridine-2,6-dicarboxylato-κ3N,O,O′)-(μ2-4-amino-4H-1,2,4-triazole-κ2N:N′) copper(II)], C9H8N5O5CuI
  58. Crystal structure of cyclopropane-1,2,3-triyltris(phenylmethanone), C24H18O3
  59. Crystal structure of bis(amino(thioureido)methaniminium) terephthalate, C12H18N8O4S2
  60. A three-dimensional Eu(III) framework in the crystal structure of dimethylaminium poly[dimethylformamide-κ1N)bis(μ4-terephthalato-κ4O:O′:O′′:O′′′)europium(III)] monohydrate, C21H25EuN2O10
  61. Crystal structure of 2-methoxyphenyl 2-(6-methoxynaphthalen-2-yl)propanoate, C21H20O4
  62. The crystal structure of Hexakis(diethylamido)dimolybdenum, Mo2(NEt2)6
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