Home This molecule targets at type 2 diabetes - a single crystal study on (2R,3S,5R)-2-(2,5-difluorophenyl)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl] tetrahydro-2H-pyran-3-amine (Omarigliptin), C17H20F2N4O3S
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This molecule targets at type 2 diabetes - a single crystal study on (2R,3S,5R)-2-(2,5-difluorophenyl)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl] tetrahydro-2H-pyran-3-amine (Omarigliptin), C17H20F2N4O3S

  • Kun-Yan Wang EMAIL logo and Xiao-Li Yang
Published/Copyright: April 7, 2016

Abstract

C17H20F2N4O3S, triclinic, P1 (no. 1), a = 6.0020(12) Å, b = 6.7650(14) Å, c = 11.831(2) Å, α = 89.39(3)°, β = 86.29(3)°, γ = 66.50(3)°, V = 439.55(15) Å3, Z = 1, Rgt(F) = 0.0543, wRref(F2) = 0.1568, T = 293(2) K.

CCDC no.:: 1463122

Tables 13 contain details of the methods used and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colorless, block, size 0.10×0.20×0.30 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:2.32 cm−1
Diffractometer, scan mode:Nonius CAD4, ω/2Θ
2θmax:50.74°
N(hkl)measured, N(hkl)unique:1784, 1784
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 1595
N(param)refined:244
Programs:CAD4 programs [3, 4], Abbsortion correction [5], SHELX [6]
Table 2:

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

AtomSitexyzUiso
H(1A)1a0.99310.9626−0.03110.051
H(1B)1a0.84411.0953−0.12170.051
H(1C)1a0.11471.2489−0.13680.048
H(3B)1a0.20191.6789−0.35150.056
H(14A)1a0.18810.38100.47250.044
H(4B)1a0.49311.7073−0.24010.056
H(7A)1a0.48921.29940.07160.038
H(8A)1a0.58370.9268−0.06240.036
H(9A)1a0.80870.72320.08160.038
H(9B)1a0.75520.93210.15400.038
H(10A)1a0.39980.77950.09840.036
H(11A)1a0.11771.07780.20230.042
H(11B)1a0.32351.15760.22480.042
H(12A)1a0.85740.54640.27690.041
H(12B)1a0.74640.46790.17740.041
H(16A)1a0.17500.70410.24710.048
H(16B)1a0.17910.82650.35980.048
H(17A)1a0.8027−0.02650.69810.089
H(17B)1a0.63740.21210.66950.089
H(17C)1a0.89420.09650.60560.089
Table 3:

Fractional coordinates and atomic displacement parameters (Å2).

AtomSitexyzU11U22U33U12U13U23
S1a0.6234(2)−0.0161(2)0.5349(1)0.0432(9)0.0330(8)0.0380(8)−0.0121(7)−0.0014(7)0.0166(6)
O(1)1a0.2259(7)1.1988(6)0.0659(3)0.036(2)0.034(2)0.033(2)−0.008(2)−0.001(2)0.015(2)
F(1)1a−0.0338(9)1.4463(8)−0.3177(4)0.058(3)0.103(4)0.055(3)−0.037(3)−0.027(2)0.037(3)
N(1)1a0.855(1)1.0226(9)−0.0607(5)0.033(3)0.051(3)0.043(3)−0.017(3)0.000(2)0.021(3)
C(1)1a0.192(1)1.340(1)−0.1559(5)0.035(3)0.046(3)0.041(3)−0.019(3)−0.006(3)0.017(3)
F(2)1a0.6462(7)1.5111(6)−0.0587(3)0.055(2)0.042(2)0.051(2)−0.030(2)−0.001(2)−0.002(2)
O(2)1a0.398(1)−0.0143(9)0.5767(5)0.062(4)0.063(3)0.065(3)−0.032(3)−0.008(3)0.039(3)
N(2)1a0.4984(9)0.7395(7)0.2593(4)0.034(3)0.031(2)0.028(2)−0.012(2)−0.004(2)0.013(2)
C(2)1a0.140(1)1.461(1)−0.2533(5)0.032(3)0.051(4)0.037(3)−0.008(3)−0.001(3)0.012(3)
N(3)1a0.551(1)0.1840(8)0.4401(5)0.036(3)0.031(3)0.037(3)−0.008(2)0.001(2)0.015(2)
O(3)1a0.801(1)−0.2031(7)0.4835(4)0.064(3)0.038(2)0.048(3)−0.014(2)−0.004(2)0.011(2)
C(3)1a0.245(1)1.599(1)−0.2861(6)0.045(4)0.039(3)0.043(3)−0.004(3)0.001(3)0.022(3)
C(14)1a0.337(1)0.360(1)0.4354(5)0.040(4)0.039(3)0.034(3)−0.018(3)−0.002(3)0.013(3)
C(4)1a0.416(2)1.616(1)−0.2198(6)0.061(4)0.025(3)0.048(4)−0.014(3)0.014(4)0.011(3)
C(5)1a0.472(1)1.4953(9)−0.1215(5)0.042(4)0.027(3)0.039(3)−0.014(3)0.005(3)0.003(2)
C(6)1a0.361(1)1.3578(8)−0.0875(5)0.027(3)0.023(3)0.035(3)−0.005(2)0.003(2)0.007(2)
C(7)1a0.435(1)1.2218(9)0.0175(5)0.039(4)0.026(3)0.031(3)−0.014(3)−0.001(3)0.008(2)
C(8)1a0.641(1)1.0010(9)−0.0077(5)0.033(3)0.030(3)0.027(3)−0.014(3)−0.004(2)0.007(2)
C(9)1a0.689(1)0.8676(9)0.0996(5)0.035(3)0.028(3)0.033(3)−0.013(3)−0.005(3)0.011(2)
C(10)1a0.459(1)0.8549(9)0.1515(5)0.033(3)0.033(3)0.025(3)−0.015(3)−0.003(2)0.008(2)
C(11)1a0.269(1)1.0827(9)0.1707(5)0.042(3)0.032(3)0.028(3)−0.011(3)0.000(3)0.011(2)
C(12)1a0.713(1)0.531(1)0.2532(5)0.028(3)0.036(3)0.037(3)−0.010(3)−0.007(3)0.016(2)
C(13)1a0.630(1)0.4010(9)0.3350(5)0.033(3)0.031(3)0.032(3)−0.011(3)−0.001(3)0.009(2)
N(4)1a0.745(1)0.2078(8)0.3785(4)0.034(3)0.036(3)0.042(3)−0.006(2)0.005(2)0.016(2)
C(15)1a0.389(1)0.498(1)0.3653(5)0.031(3)0.038(3)0.031(3)−0.016(3)−0.005(2)0.011(2)
C(16)1a0.276(1)0.711(1)0.3066(6)0.034(3)0.038(3)0.043(3)−0.009(3)0.000(3)0.020(3)
C(17)1a0.754(2)0.077(1)0.6387(7)0.064(5)0.053(4)0.053(4)−0.012(4)−0.018(4)0.003(3)

Source of material

The title compound was prepared by a literature method [1]. 16.5 g (50.4 mmol) of tert-butyl [(2R,3S)-5-oxo-2-(2,5-difluorophenyl)tetrahydro-2H-pyran-3-yl]carbamate, 19.6 g (56.8 mmol) of pyrazole salt (benzenesulfonic acid and 2-(methylsulfonyl)-2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole) and 250 mL of dimethylacetamide were mixed while stirring. The resulting homogeneous solution was cooler to 268 K and 14 g (66 mmol) of sodium triacetoxyborohydride was added portionwise. The mixture was stirred for 2 h and quenched by the slow addition of a mixture of NH4OH (17 mL) and water (35 mL). The slurry was heated to 323 K and then cooled to 295 K and filtered. The wet cake was washed with 5:1 dimethylacetamide/water (135 mL) and then water (130 mL) and dried under vacuum/N2 sweep to afford (22 g, 96%) of the title compound as a white solid. The primary product 22 g (42 mmol) 65 mL of dimethylacetamide, and 85 mL of water were mixed, than 25 mL of H2SO4 in 45 mL of water were added and stirred for 20 h at room temperature. NH4OH was added until the pH was 10.2. The slurry was filtered and washed with water (2 × 30 mL) and dried under vacuum/N2 to give the title compound (14.1 g, 92%). Crystallization from ethyl acetate gave a product with greater than 99% purity. Prism-shaped crystals were obstained by slow evaporation of an ethyl acetate solution at room temperature for about 20 d.

Experimental details

The hydrogen atoms were placed on calculated positions (SHELX: AFIX 13, 23, 33, 43 and 93 option) [6]. The Flack-parameter refines to a value near zero, which verifys the absolute configuration of the title molecule (see the figure).

Discussion

Experimental, clinical, and epidemiological studies have shown that type 2 diabetes mellitus is a growing epidemic affecting approximately 220 million people worldwide [1, 2]. Commercial proof of concept for DPP-4 inhibitors has been established with sitagliptin, Merck's lead DPP-4 inhibitor; Omarigliptin, which was the first DPP-4 inhibitor, approved by the FDA in October 2006. Omarigliptin (MK-3102) prolong the circulating half-life of glucagonlike peptide 1 (GLP-1) and glucose-dependant insulinotropic polypeptide (GIP), incretin hormones that stimulate insulin secretion in a glucose-dependent manner. Additionally, GLP-1 has been shown to inhibit glucagon release, decrease gastric emptying, and promote the regeneration and differentiation of islet b-cells. By increasing the circulating concentration GLP-1 and GIP, DPP-4 inhibitors improve glucose control in patients with type 2 diabetes.

The molecular structure of the title compound (drug name: Omarigliptin) is shown in the Figure. All bond lengths and angles are within normal ranges. The title molecule consists of four rings, A(C1—C2—C3—C4—C5—C6), B(C7—C8—C9—C10—C11—O1), C(C12—C13—C15—C16—N2) and D(C13—C15—C14—N3—N4). The dihedral angle between C and D is 2.3(3)°. The six-members ring B is in the typical chair conformation. In the molecular structure of the title compound, there are three chiral carbon atoms, C7, C8 and C10. The configuration of the chiral carbon atoms can be obtained directly from the crystal structure: C7, C8 and C10 are R, S, and R, respectively. In the crystal there are no classical intermolecular hydrogen bonds. Surprisingly, the F2 atom is close to one of the hydrogen atoms of the NH2 group as well as to the adjacent CH group. Thus a very weak bifurcated intramolecular N—H⋯ F and a C—H⋯F hydrogen bond seem to be very effective in the stabilization of the crystal structure. In the crystal structure, there are no π−π stacking interactions, as the centroid to centroid distance between the two nearest furan rings is larger than 5 Å.

Acknowledgements:

This work is supported by PhD Research Startup Foundation of Jinling Institute of Technology (JIT-B-201323). We also thank the Center of Testing and Analysis, Nanjing University. The authors thank the responsible editor for supplying the figure.

References

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Received: 2015-11-18
Accepted: 2016-3-11
Published Online: 2016-4-7
Published in Print: 2016-9-1

©2016 Kun-Yan Wang et al., published by De Gruyter.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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  57. Crystal structure of 6-hydroxy-5-((2-hydroxy-6-oxocyclohex-1-en-1-yl)(phenyl)methyl)-1,3-dimethylpyrimidine-2,4(1H,3H)-dione, C19H20N2O5
  58. Crystal structure of 2-(4-(4-bromophenyl)thiazol-2-yl)isoindoline-1,3-dione, C17H9BrN2O2S
  59. Crystal structure of 2-(4-methylbenzoyl)pyrene, C24H16O
  60. Crystal structure of N-(5-bromo-4-(p-tolyl)thiazol-2-yl)-4-chlorobutanamide, C14H14BrClN2OS
  61. Crystal structure of 4,5-diphenylthiazol-2-amine, C15H12N2S
  62. Crystal structure of poly[bis(μ2-4-(3-(pyridin-3-yl)-1H-1,2,4-triazol-5-yl)benzoato-κ3N:O,O′)-lead(II)], C28H18O4N8Pb
  63. Crystal structure of (Z)-4-(4-oxopent-2-en-2-ylamino)benzenesulfonamide, C11H14N2O3S
  64. Crystal structure of poly[(μ2-2-methyl-1-(4-(2-methyl-2H-benzo[d] imidazol-1(7aH)-yl)butyl)-1H-benzo[d]imidazole-κ2N:N′)bis(μ3-5-tert-butylbenzene-1,3-dicarboxylato-κ4O:O,O′:O′′,O′′′)dicadmium(II)] tetrahydrate, C44H54Cd2N4O12
  65. Crystal structure of catena-poly-[aqua(μ2-4,4′-bipyridine-κ2N:N′)bis(3′,5,5′-tricarboxybiphenyl-2-carboxylato-κ2O,O′)cadmium(II)], C42H28N2O17Cd
  66. Crystal structure of (2RS,3RS)-1-(4-chlorophenyl)-4,4-dimethyl-2-(1H-1,2,4-triazol-1-yl)pentan-3-ol, C15H20ClN3O
  67. Crystal structure of N′-(4-(dimethylamino)benzylidene)-5-phenyl-1H-pyrazole-3-carbohydrazide, C19H19N5O
  68. Crystal structure of 3-(benzofuran-2-yl)-5-(4-fluorophenyl)-4,5-dihydro-1Hpyrazole-1-carbothioamide, C18H14FN3OS
  69. Crystal structure of ent-1β-acetoxy-7α,14α-di-hydroxy-7β,20-epoxykaur-16-en-15-one, C22H30O6
  70. Crystal structure of 1α,7β-dihydroxy-11β-acetoxy-ent-7β,20-epoxykaur-16-en-15-one, C22H30O6
  71. Crystal structure of 7β,14β,15β-trihydroxy-1α-acetoxy-7α,20-epoxy-ent-kaurane, C22H32O6
  72. Crystal structure of ent-1β,7α,11α-trihydroxy-7β,20-epoxykaur-16-en-15-one, C20H28O5
  73. Crystal structure of poly-[tetraaquabis(μ8-benzene-1,2,4,5-tetracarboxylato-1κ3O4:O6:O8:2κ4O2:O2:O5:O5:3κ4O1:O3:O5:O7)(di-μ3-hydroxido)-pentazinc(II)] decahydrate, C20H34O32Zn5
  74. Crystal structure of 1-(4-methylthiazol-2-yl)-3-propylthiourea, C8H13N3S2
  75. Crystal structure of 2-((dimethylamino)methylene)-5,5-Dimethylcyclohexane-1,3-dione, C11H17NO2
  76. Crystal structure of poly[1,4-bis(2-methylbenzimidazol)butane-κ2N:N′)bis(4,4′-oxybis(benzoato-κ4O,O′:O′′,O′′′)dicadmium] monohydrate, C48H38Cd2N4O10
  77. Crystal structure of 2-(3-(benzofuran-2-yl)-5-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl)-4-(4-chlorophenyl)thiazole, C26H17ClFN3OS
  78. Crystal structure of bis(μ3-isophthalato-κ3O:O′:O′′)(μ2-1,4-\ bis((2-propyl-1H-benzo[d]imidazol-1-yl)methyl)benzene-κ2N:N′)dizinc(II), C22H19N2O4Zn
  79. Crystal structure of poly[bis(adipate-κ4O,O′:O′′, O′′′)(1,4-bis(2-methyl-1H-benzo[d]imidazol-1-yl)benzene-κ2N:N′)dizinc(II), C36H38N4O8Zn2
  80. Crystal structure of N-(2-(2-oxoindolin-4-yl)ethyl)-N-propylpropan-1-aminium tetraphenylborate, C40H45BN2O
  81. Crystal structure of 1-(2,3-dihydro-4-methyl-3-phenyl-2-thioxothiazol-5-yl)-1-ethanone, C12H11NOS2
  82. Crystal structure of 3-(adamantan-1-yl)-1-[(4-benzylpiperazin-1-yl)methyl]-4-[(E)-(2,6-difluorobenzylidene)amino]-1H-1,2,4-triazole-5(4H)-thione, C31H36F2N6S
  83. Crystal structure of 6-(4-chlorophenyl)-3-(thiophen-2-yl)-[1,2,4]triazolo[3,4-b][1,3,4]-thiadiazole, C13H7ClN4S2
  84. Crystal structure of bis(ethanaminium) poly[bis(hexaselenido-κ2Se1,Se6)palladate(II)], C4H16N2PdSe12
  85. Crystal structure of 2-(3-(benzofuran-2-yl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl)-4-phenylthiazole, C26H19N3OS
  86. Crystal structure of poly-[bis(μ3-5-hydroxyisophtalato-κ3O:O′:O′′)(μ2-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)dizinc(II)], C40H30N4O5Zn2
  87. Crystal structure of poly-[(μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ4-2,2′-(1,3-phenylene)diacetate-κ4O:O′:O′′:O′′′)dizinc(II)], C44H38N4O8Zn2
  88. Crystal structure of 5,17-bis-cyano-25,26,27,28-tetrapropyloxy-calix[4]arene, C42H46N2O4
  89. Crystal structure of poly-[μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ3-5-hydroxyisophthalate(2–)-κ3O,O′:O′′)dicadmium(II)] monohydrate, C64H54N8O11Cd2
  90. Crystal structure of poly-[μ-1,4-bis(2-ethylbenzimidazol-1-ylmethyl)benzene-κ2N:N′)-bis(μ4-4,4′-sulfonyldibenzoato-κ4O:O′:O′′:O′′′)dicadmium(II)] monohydrate, C52H42N4O14Cd2
  91. Crystal structure of poly-[bis(μ4-adipato-κ4O:O′:O′′:O′′′)(μ2-1,4-bis((2-ethyl-1H-benzo[d]imidazol-1-yl)methyl)benzene-κ2N:N′)dizinc(II)], C38H42N4O8Zn2
  92. Crystal structure of (2-(2-chlorophenyl)-5-methyl-1,3-dioxan-5-yl)methanol, C12H15ClO3
  93. Crystal structure of 2-(4-Bromophenyl)-5-ethyl-1,3-dioxane-5-carboxylic acid, C13H15BrO4
  94. Crystal structure of (2-(4-bromophenyl)-5-ethyl-1,3-dioxan-5-yl)methanol, C13H17BrO3
  95. Crystal structure of 3-((1,3,5,7-tetraoxo-6-(pyridin-3-ylmethyl)-3,3a,4,4a,5,6,7,7a,8,8a-decahydro-4,8-ethenopyrrolo[3,4-f]isoindol-2(1H)-yl)methyl)pyridin-1-ium-κN-trichloridocobalt(II) hemihydrate, C24H22Cl3CoN4O4.5
  96. Crystal structure of 4-chloro-4′,6′-dichloro-2,2′-[propane-1,3-diyldioxybis(nitrilomethylidyne)]-diphenol, C17H14Cl3N2O4
  97. Crystal structure of 2-amino-4-(3-trifluoromethylphenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile, C17H13F3N2O2
  98. Crystal structure of bis(benzoato-κO)bis(4,4′-((1H-1,2,4-triazol-1-yl)methylene)dibenzonitrile-κN)zinc(II), C48H32N10O4Zn
  99. Crystal structure of 3-methyl-2H-chromen-2-one, C10H8O2
  100. Crystal structure of catena-poly-[aqua-(2-carboxy-5-(3-carboxy-5-carboxylatophenoxy)benzoato-κO)(μ2-4,4′-di(1H-imidazol-1-yl)-1,1′-biphenyl-κ2N:N′)cobalt(II)], C34H24N4O10Co
  101. Crystal structure of 4,4′-di(1H-imidazol-1-yl)-1,1′-biphenyl, C36H28N8
  102. Crystal structure of 1-(3-chloropropyl)piperidin-1-ium tetraphenylborate, C32H37BClN
  103. Crystal structure of dimethyl 5-(benzylamino)isophthalate, C17H17NO4
  104. Crystal structure of dimethyl 5-(dibenzylamino)isophthalate, C24H23NO4
  105. Crystal structure of N-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioamide, C21H29N3S
  106. Crystal structure of (2,2′(cyclohexane-1,2-diylbis(nitrilo(E)methylylidene))diphenolato-κ4O,O′,N,N′)dimethanolmanganese(III) bromide, C22H28BrMnN2O4
  107. Crystal structure of 3,5,7-tris(morpholinomethyl)tropolone·0.67 hydrate, C22H33N3O5·0.67H2O
  108. Crystal structure of biphenyl-2,3′,5,5′-tetracarboxylic acid – 4,4′-biphenyl-4,4′-diyldipyridine (3/2), C49H34N3O8
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