Home Crystal structure of (3aR,4R,5R,7R,8S,9R,9aS,12R)-7-ethyl-5-(1-hydroxy-2-((R)-3-hydroxypyrrolidin-1-yl)ethoxy)-4,7,9,12-tetramethyldecahydro-4,9a-propanocyclopenta[8]annulene-3,8-diol – a pleuromutilin derivative, C26H41NO5
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Crystal structure of (3aR,4R,5R,7R,8S,9R,9aS,12R)-7-ethyl-5-(1-hydroxy-2-((R)-3-hydroxypyrrolidin-1-yl)ethoxy)-4,7,9,12-tetramethyldecahydro-4,9a-propanocyclopenta[8]annulene-3,8-diol – a pleuromutilin derivative, C26H41NO5

  • Yan Liang , Yun-Xing Fu and Jian-Ping Liang EMAIL logo
Published/Copyright: July 20, 2018

Abstract

C26H41NO5, orthorhombic, P212121 (no. 19), a = 9.6178(8) Å, b = 13.3335(11) Å, c = 19.0758(16) Å, V = 2446.3(4) Å3, Z = 4, Rgt(F) = 0.0389, wRref(F2) = 0.0888, T = 296(2) K.

CCDC no.: 1829225

The crystal structure 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:Colourless block
Size:0.30 × 0.20 × 0.20 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.08 mm−1
Diffractometer, scan mode:Bruker APEXII, ω
θmax, completeness:25.0°, 99%
N(hkl)measured, N(hkl)unique, Rint:12437, 4283, 0.024
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3728
N(param)refined:295
Programs:Bruker [11], SHELX [12], [13]
Table 2:

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

AtomxyzUiso*/Ueq
C10.1974(3)0.36665(19)0.92354(13)0.0398(6)
C20.1420(3)0.3988(2)0.99625(14)0.0522(8)
H2A0.08000.45580.99180.063*
H2B0.09160.34411.01810.063*
C30.2688(3)0.4267(3)1.03976(15)0.0567(8)
H3A0.25370.48961.06410.068*
H3B0.28880.37491.07400.068*
C40.3861(3)0.4363(2)0.98822(15)0.0508(7)
C50.3245(3)0.4372(2)0.91382(13)0.0356(6)
H50.28710.50470.90620.043*
C60.4252(3)0.4161(2)0.85228(13)0.0399(6)
C70.4755(3)0.3064(2)0.85957(16)0.0572(8)
H70.52680.30320.90390.069*
C80.3540(4)0.2338(2)0.86710(19)0.0669(10)
H8A0.39020.16660.87400.080*
H8B0.30070.23380.82390.080*
C90.2569(4)0.2596(2)0.92816(17)0.0611(9)
H9A0.30760.25260.97180.073*
H9B0.18060.21200.92890.073*
C100.0823(3)0.3743(2)0.86717(14)0.0402(6)
H100.11900.34360.82430.048*
C110.0435(3)0.4843(2)0.84899(14)0.0403(6)
H110.08250.52670.88610.048*
C120.1012(3)0.5245(2)0.77815(15)0.0465(7)
C130.2615(3)0.5287(2)0.77546(15)0.0437(7)
H13A0.28670.56080.73160.052*
H13B0.29150.57310.81280.052*
C140.3486(3)0.4327(2)0.78127(13)0.0373(6)
H140.29000.37430.77100.045*
C15−0.0470(4)0.3135(3)0.88878(19)0.0662(9)
H15A−0.01960.24670.90140.099*
H15B−0.11110.31070.85020.099*
H15C−0.09100.34530.92810.099*
C160.0486(3)0.4603(3)0.71855(15)0.0671(10)
H160.09050.39790.71360.081*
C17−0.0474(5)0.4817(5)0.6736(2)0.129(2)
H17A−0.09310.54310.67590.155*
H17B−0.07090.43560.63890.155*
C180.5481(3)0.4905(3)0.85622(17)0.0608(9)
H18A0.61040.47850.81780.091*
H18B0.59690.48120.89970.091*
H18C0.51350.55790.85370.091*
C190.5763(4)0.2693(3)0.8027(2)0.0869(14)
H19A0.62130.20910.81850.130*
H19B0.64500.31990.79380.130*
H19C0.52550.25570.76040.130*
O1−0.1043(2)0.4990(2)0.84987(12)0.0638(6)
H1−0.13500.49340.81000.096*
C210.4415(3)0.3962(2)0.66600(14)0.0422(6)
C220.5640(3)0.4203(2)0.62004(14)0.0497(7)
H22A0.55830.49010.60580.060*
H22B0.64860.41210.64700.060*
C240.6124(4)0.2545(2)0.57249(17)0.0609(9)
H24A0.53100.21420.58300.073*
H24B0.67520.25180.61220.073*
C250.6844(4)0.2158(2)0.50649(17)0.0577(8)
H250.62930.16250.48460.069*
C260.6915(4)0.3072(2)0.45888(17)0.0640(9)
H26A0.77940.30960.43410.077*
H26B0.61630.30650.42500.077*
C270.6775(3)0.3943(2)0.50793(15)0.0504(7)
H27A0.76480.40880.53130.061*
H27B0.64590.45390.48350.061*
N10.5721(2)0.35805(17)0.55788(11)0.0409(5)
C500.0541(4)0.6337(3)0.7714(2)0.0854(13)
H50A−0.04570.63660.77170.128*
H50B0.08840.66120.72820.128*
H50C0.08990.67190.81010.128*
O20.5069(2)0.4398(2)1.00501(12)0.0818(8)
O30.45818(19)0.44112(16)0.72783(9)0.0473(5)
O40.3434(2)0.34720(19)0.64994(11)0.0665(7)
O50.8156(3)0.1788(2)0.52774(13)0.0787(8)
H5A0.86370.16790.49310.118*

Source of material

To a solution of 22-O-tosyl-pleuromutilin (0.49 g, 1 mmol) in 10 mL methanol, 3-pyrrolidinol (0.26 g, 3 mmol) was added and stirred for 7 h at room temperature, followed by evaporation under reduced pressure to dryness. The obtained crude product was extracted with a solution of ethyl acetate (30 mL) and water (10 mL) and further with saturated NaHCO3. The target compound was then precipitated and purified by flash silica column chromatography (petroleum ether:ethyl acetate = 1:10–1:3 v/v). Crystals were obtained by slow evaporation from methanol solution at room temperature.

Experimental details

Hydrogen atoms were added using the standard procedures of the SHELX program system. The absolute structure was estimated from the synthesis.

Comment

Pleuromutilin was isolated from Pleurotus mutilus and P. passeckerianus in 1951 [1]. Its chemical structure includes a rather rigid 5-6-8 tricyclic carbon skeleton and a C-14 side chain [2], [3]. Pleuromutilin and its derivatives selectively inhibit bacterial protein synthesis via binding to the 50S subunit of ribosomes at the A-site and P-site [4], [5]. Preliminary studies showed that the modification of pleuromutilin C-14 side chain improved its biological activity [2], and there are three drugs, tiamulin, valnemulin and retapamulin, which are presently used in therapy [6]. Nabriva’s lefamulin received FDA fast-track status to treat community-acquired bacterial pneumonia (CABP) and acute bacterial skin and skin structure (ABSSS) [7], [8].

The crystal structure of the title compound is built up of C26H41NO5 molecules containing the well known 5-6-8 tricyclic carbon skeleton and a pyrrolidinol group, in which all bond lengths and angles are in normal ranges. The eight-membered ring (C14—C13—C12—C11—C10) exhibits a boat conformation. The six-membered ring (C6—C7—C8—C9—C1—C5) exhibits a chair conformation. The tricyclic carbon skeleton exhibits similar conformation with reported pleuromutilin derivatives [9], [10]. The side chain of pleuromutilin exhibits zigzag conformation. The torsion angles are 167.11° and 177.25° for O3—C21—C22—N1 and C22—C21—O3—C14, respectively (cf. the figure).

References

Kavanagh, F.; Hervey, A.; Robbins, W.: Antibiotic substances from basidiomycetes: VIII. Pleurotus Multilus (Fr.) Sacc. and Pleurotus Passeckerianus Pilat. Proc. Natl. Acad. Sci. USA 37 (1951) 570–574.10.1073/pnas.37.9.570Search in Google Scholar PubMed PubMed Central

Riedl, K.: Studies on pleuromutilin and some of its derivatives. J. Antibiot. 29 (1976) 132–139.10.7164/antibiotics.29.132Search in Google Scholar PubMed

Egger, H.; Reinshagen, H.: New pleuromutilin derivatives with enhanced antimicrobial activity. II. Structure-activity correlations. J. Antibiot. 29 (1976) 923–927.10.7164/antibiotics.29.923Search in Google Scholar PubMed

Eyal, Z.; Matzov, D.; Krupkin, D.; Paukner, S.; Riedl, R.; Rozenberg, H.; Zimmerman, E.; Bashan, A.; Yonath, A.: A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism. Sci. Rep. 6 (2016) 39004.10.1038/srep39004Search in Google Scholar PubMed PubMed Central

Davidovich, C.; Bashan, A.; Auerbach-Nevo, T.; Yaggie, R. D.; Gontarek, R. R.; Yonath, A.: Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proc. Natl. Acad. Sci. USA 104 (2007) 4291–4296.10.1073/pnas.0700041104Search in Google Scholar PubMed PubMed Central

Novak, R.; Shlaes. D. M.: The pleuromutilin antibiotics: a new class for human use. Curr. Opin. Investig. Drugs 11 (2010) 182–191.Search in Google Scholar

Zeitlinger, M.; Schwameis, R.; Burian, A.; Burian, B.; Matzneller, P.; Muller, M.; Wicha, W. W.; Strickmann, D. B.; Prince, W.: Simultaneous assessment of the pharmacokinetics of a pleuromutilin, lefamulin, in plasma, soft tissues and pulmonary epithelial lining fluid. J. Antimicrob. Chemother. 71 (2016) 1022–1026.10.1093/jac/dkv442Search in Google Scholar PubMed

Wang, X.; Ling, Y.; Wang, H.; Yu, J.; Tang, J.; Zheng, H.; Zhao, X.; Wang, D.; Chen, G.; Qiu, W.; Tao. J.: Novel pleuromutilin derivatives as antibacterial agents: synthesis, biological evaluation and molecular docking studies. Bioorg. Med. Chem. Lett. 22 (2012) 6166–6172.10.1016/j.bmcl.2012.08.021Search in Google Scholar PubMed

Shang, R.; Yi, Y.; Liang, J.: Crystal structure of 14-((1-(benzyloxycarbonyl-amino)-2-methylpropan-2-yl)sulfanyl) acetate Mutilin, C34H49NO6S. Z. Kristallogr. NCS 231 (2016) 465–467.10.1515/ncrs-2015-0142Search in Google Scholar

Zhao, F.; Wang, G.: Crystal structure of 14-O-[(4-chlorobenzamide-2-methylpropane-2-yl)-thioacetate] mutilin diethanol solvate, C37H58ClNO7S. Z. Kristallogr. NCS 228 (2013) 422–424.10.1524/ncrs.2013.0154Search in Google Scholar

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Received: 2018-04-15
Accepted: 2018-06-27
Published Online: 2018-07-20
Published in Print: 2018-08-28

©2018 Yan Liang 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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  66. Crystal structure of (3aR,4R,5R,7R,8S,9R,9aS,12R)-7-ethyl-5-(1-hydroxy-2-((R)-3-hydroxypyrrolidin-1-yl)ethoxy)-4,7,9,12-tetramethyldecahydro-4,9a-propanocyclopenta[8]annulene-3,8-diol – a pleuromutilin derivative, C26H41NO5
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  69. Crystal structure of methyl 4-(3,5-ditrifluoromethylphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate — water (2/1), C22H21F6NO3
  70. Crystal structure of 2-(4-bromophenyl)-2,3-dihydro-1H-perimidine, C17H13BrN2
  71. Crystal structure of (5-ethyl-2-(4-methoxyphenyl)-1,3-dioxan-5-yl)methanol, C14H20O4
  72. Crystal structure of (E)-N-(4-bromo-2-(1-(hydroxyimino)ethyl)phenyl)benzamide, C15H13BrN2O2
  73. Crystal structure of caffeinium triiodide – caffeine (1/1), C16H21I3N8O4
  74. Crystal structure of methyl 2-methyl-4-(3-methoxyphenyl)-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C19H21NO4
  75. Crystal structure of (E)-3-(3,5-di-tert-butyl-4-hydroxyphenyl)-1-phenylprop-2-en-1-one, C23H28O2
  76. Crystal structure of 1,4-bis(2-azidoethyl)piperazine-1,4-diium dichloride, C8H18N8Cl2
  77. The crystal structure of dichlorido-(1,3-bis(2,6-dimethylphenyl)-1H-imidazol-2(3H)-ylidene)-(morpholine-κ1N)palladium(II), C23H29Cl2N3OPd(II)
  78. The crystal structure of 1-((5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-yl)methyl)-1,3-diphenylurea, C24H21ClN4O
  79. Crystal structure of 6-(2-bromoacetamido)tetrahydro-2H-pyran-2,3,4,5-Tetrayl tetraacetate, C16H22BrNO10
  80. Crystal structure of 5-methylpyrazine-2-carbohydrazide, C6H8N4O
  81. Crystal structure of catena-poly[(μ2-5-(tert-butyl)isophthalato-κ4O,O′:O′′,O′′′)(-4′-(pyridin-4-yl)-2,2′:6′,2′′-terpyridine-κ3N,N′,N′′)manganese(II)], C32H28N4O5Mn
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