the surface of a protein for possible binding sites and scores them
according to size, degrees of enclosure and exposure, tightness,
hydrophobic and hydrophilic character, and physical description of
hydrogen-bond donors and acceptors.
Korea (NRF) funded by the Ministry of Education, Science and
Technology (2103R1A1A2013610), Republic of Korea.
References and notes
19. Ligand docking: We used
a docking method with Glide 5.5
(SchrÖdinger Inc.). Glide is based on grids for energy scoring and ligand
matching. One starts with receptor grid generation in which a grid is
generated that conforms to the shape and properties of the receptor.
Conformational search in Glide is done in a hierarchical way. Rough
matching of ligand atom positions and grid points generates a set of
1. Zhang, C.; Zhang, X.; Chen, X. -H. Clinic. Rev. Allerg. Immunol. 2014,
47,163.
2. Hunter, C. A.; Jones, S. A. Nat. Immunol. 2015, 16, 448.
3. Yao, X.; Huang, J.; Zhong, H.; Shen, N.; Faggioni, R.; Fung, M.; Yao, Y.
Pharmacol. Ther. 2014, 141, 125.
4. Rossi, J. -F.; Lu, Z. –Y.; Jourdan, M.; Klein, B. Clin. Cancer Res. 2015,
21, 1248.
5. Hashizume, M.; Mihara, M. Arthritis (Egypt) 2011, 2011, 765624.
6. Brahn, E.; Banquerigo, M. L.; Firestein, G. S. D.; Boyle, L.; Salzman, A.
L.; Szabo´, C. J. Rheumatol. 1998, 25, 1785.
possible ligand poses, which are refined through
optimization procedure.
a successive
20. Saleh , A. Z. M.; Greenman, K. L.; Billings, S.; Vranken, D. L. V.;
Krolewski, J. J. Biochemistry 2005, 44, 10822.
21. Li, H.; Xiao, H.; Lin, L.; Jou, D.; Kumari, V.; Lin, J.; Li, C. J. Med.
Chem. 2014, 57, 632.
22. Surface plasmon resonance analysis: To examine the direct binding
between compound 4d and the extracellular domain of gp130, gp130
V93A, and gp130 C6A (ANRT, Daejeon, Korea), we performed surface
plasmon resonance (SPR) analysis using BIAcore T200 model (GE
7. Nawata, Y.; Eugui, E. M.; Lee, S. W.; Allison, A. C. Ann. N. Y. Acad.
Sci. 1989, 557, 230.
8. Zyromski, N., Murr, M. M. Surgery 2003, 133, 235.
9. Norman, J., Franz, M.; Messina, J.; Riker, A.; Fabri, P. J.; Rosemurgy, A.
S.; Gower, Jr. W. R. Surgery 1995, 117, 648.
Healthcare) at 25 ̊C with buffer HBS-EP+ (10 mM HEPES, pH 7.4, 150
mM NaCl, 3 mM EDTA, and 0.05% surfactant P-20) containing 5%
DMSO (Sigma-Aldrich). The pH scouting for immobilization was
performed in 10 mM acetate buffer at pH 4.0, 4.5, 5.0, 5.5. gp130, V93A,
or C6A was immobilized on a CM5 sensor chip to the 3970 response unit
(RU), 4113 RU, or 4271 RU respectively with standard amine coupling
at pH 4.5. Compound 4d was injected into the gp130 or mutants-
immobilized flow cell at concentrations of 200, 100, 50, 25, 12.5, 0.78,
0.39, and 0.19 mM with a flow rate of 30 ml/min for 240 s and allowed
to dissociate for 900 s. T-200 BIAevaluation software was used to obtain
RU and subtract references.
10. Tanaka, T.; Narazaki, M.; Kishimoto, T. Molecular Biology of B Cells
(2nd Edition); Honjo, T., Reth, M., Radbruch, A., Alt, F., Eds.;
ACADEMIC PRESS, 2015, pp 515-525.
11. Mintz, C. S.; Crea, R. Bioprocess Int. 2013, 11, 40.
12. Terstegen, L.; Gatsios, P.; Bode, J. G.; Schaper, F.; Heinrich, P. C.;
Graeve. L. J. Biol. Chem. 2000, 275, 18810.
13. Hayashi, M., Rho, M. -C.; Enomoto, A.; Fukami, A.; Kim, Y.-P.;
Kikuchi, Y.; Sunazuka, T.; Hirose, T.; Komiyama, K.; Omura, S. Proc.
Natl. Acad. Sci. USA, 2002, 99, 14728.
14. Hong, S. -S.; Choi, J. H.; Lee, S. Y.; Park, Y. -H., Park, K. -Y.; Lee, J.
Y.; Kim, J.; Gajulapati, V.; Goo, J. -I.; Singh, S.; Lee, K.; Kim, Y. -K.;
Im, S. H.; Ahn, S. -H.; Rose-John, S.; Heo, T. -H.; Choi, Y. J. Immunol.
2015, 195, 237.
Supplementary Material
15. Walker, M. A.; Heathcock, C. H. J. Org. Chem. 1991, 56, 5747.
16. Procedure for the synthesis of (S)-3-((2S,3S)-3-hydroxy-2-methyl-4-
methylenenonanoyl)-4-isopropyloxazolidin-2-one (4d): Aqueous
formaldehyde solution (0.434 ml, 5.8 mmol, 37%) was mixed with 1d
(662 mg, 5.8 mmol). The mixture was stirred at room temperature for 5
minutes, followed by the addition of dimethylamine hydrochloride (440
mg, 5.0 mmol). The solution was refluxed for 48 h at 70oC. Then water
(10 mL) was added and the mixture steam distilled. The distillate was
extracted with diethyl ether (3x30 mL) and the whole organic phases
were washed with saturated NaCl solution and dried over MgSO4. The
solvent was evaporated to get crude product 2d which was used for
Experimental details for the synthesis and characterization of all
compounds
1
next step without any purification (crude yield 85%): H NMR (CDCl3,
500 MHz): δ 9.52 (s, 1H), 6.23 (s, 1H), 5.97 (s, 1H), 2.21 (t, 2H, J =
7.8 Hz), 1.31-1.25 (m, 6H), 0.87 (t, 3H, J = 6.8 Hz). To the stirred
solution of 4-oxazolidinone (3a) (2.5g, 13.5 mmol) in CH2Cl2 (60 ml)
was added to Bu2BOTf (16.37 ml, 16.37 mmol) and
diisopropylethylamine (3.31 ml, 19.0 mmol) at 0°C. After stirring for
50 min, 2d (3.53 g, 28.0 mmol) was added to the enolate reaction
mixture at -78°C. The reaction mixture was stirred at -78°C for 20 min
and then was allowed to warm at 0°C. After 1 hour of stirring at 0°C,
pH 7 buffer solution (1 mL) and MeOH (2 mL) were added to the
reaction mixture, followed by continuous addition of H2O2 (2 mL) and
MeOH (2 mL) at the same temperature. After stirring the reaction
mixture for 1 hour at 0°C, the solvent was removed in vacuo, followed
by addition of water to the remaining mixture. The mixture was then
extracted with CH2Cl2 (3 × 50 ml). The combined organic layer were
dried over anhydrous MgSO4, filtered, and concentrated in vacuo. The
organic residue was purified by column chromatography on silica gel
(using 14 % ethyl acetate in hexane as eluting solvents) to afford (3.58
g, 84 %) of 4d; Colorless oil; IR-FT (neat): ν 3527.5, 2960.0, 2929.8,
2873.4, 1773.8, 1696.8, 1685.4, 1457.6 cm-1; 1H-NMR (CDCl3, 500
MHz): δ 5.18 (1H, s), 4.99 (1H, s), 4.50-4.47 (1H, m), 4.42 (1H, brs),
4.28 (1H, dd, J = 17.4, 9.0 Hz), 4.22 (1H, dd, J = 9.3, 2.9 Hz), 3.95 (1H,
dq, J = 7.3, 2.9 Hz), 3.15 (1H, brs), 2.39 - 2.33 (1H, m), 2.04 - 1.90 (2H,
m), 1.49 - 1.43 (2H, m), 1.34 - 1.28 (4H, m), 1.18 (3H, d, J = 7.3 Hz),
0.93 (3H, d, J = 7.1 Hz, 0.88 (3H, d, J = 7.1 Hz), 0.87 (3H, t, J = 5.4
Hz);
13C NMR (CDCl3, 125 MHz): δ 177.7, 153.4, 147.9, 110.5, 72.7, 63.3,
58.3, 40.1, 32.7, 31.6, 28.3, 27.6, 22.5, 17.9, 14.6, 14.0, 10.5; HRMS
(ES+) C17H29NO4, m/z 312.2261 [M + H]+
17. Schrodinger, Inc.: Maestro v9.5, 2013.
18. Binding Site Prediction: Although the hexameric complex interaction of
IL-6/GP130 (PDB ID : 1P9M) is known, but in order to study more
detailed binding sites, we used a binding site prediction tool called
“SiteMap” (SchrÖdinger Inc., Portland, OR, U.S.A.). SiteMap searches