Title

設計與合成十一異戊二烯焦磷酸合成酶的抑制劑及其生物活性探討

Translated Titles

Design and Synthesis of the Undecaprenyl Pyrophosphate Synthase Inhibitors to Study Biological Activity

DOI

10.6342/NTU.2007.02392

Authors

劉維民

Key Words

十一異戊二烯焦磷酸酶法呢基焦磷酸 ; 嵌合模擬評比篩選 ; 靶標導向合成 ; Undecaprenyl pyrophosphate synthase ; farnesyl pyrophosphate ; isopyrophosphate ; docking ; target- guided synthesis

PublicationName

臺灣大學化學研究所學位論文

Volume or Term/Year and Month of Publication

2007年

Academic Degree Category

碩士

Advisor

陳昭岑

Content Language

繁體中文

Chinese Abstract

十一異戊二烯焦磷酸酶(undecaprenyl pyrophosphate synthase, UPPs)所縮合成的55個碳產物十一異戊二烯焦磷酸(undecaprenyl pyrophosphate, UPP)在細菌細胞壁生合成過程中扮演者重要的角色。如果能有效地抑制UPPs的生物活性,進而能抑制細菌細胞壁的生合成,達到抑制細菌生長的功效。本論文的研究方向主要分為兩個部份,目的在發展可能具有抑制UPPs生物活性的小分子。 第一部分是依據UPPs和其天然受質法呢基焦磷酸(farnesyl pyrophosphate, FPP)的X-ray共結晶圖,利用苯環當作中間骨架和Cu(I)-catalyzed [3+2] cycloaddition 發展設計了L型及Y型兩種不同形狀的分子,進行生物活性的測試及探討。此外亦利用化學計算軟體Discovery Studio 1.7做L型及Y型分子和UPPs的嵌合(Docking)模擬評比篩選。計算結果顯示L型分子和目標酵素具有較好的結合能力,而所進行的酵素抑制實驗結果顯示L型分子也同樣使酵素具有較低的殘餘活性。 第二部份則是利用靶標導向合成(target-guided synthesis,TGS)的概念,依據UPPs活性中心位置的特性,設計並成功地合成出八個具有疊氮官能基團的疏水性分子片段及五個具有炔基的親水性的分子片段,以目標酵素UPPs當做模版一次進行四十組篩選,並使用質譜儀監測是否有反應的發生,篩選可能具有生物活性的前導藥物。此外也利用化學合成方法成功地合成出具有質譜訊號的化合物,進行生物活性的測試。

English Abstract

Undecaprenyl pyrophosphate synthase (UPPs) catalyzes eight consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopyrophosphate (IPP) to form a 55-carbon long-chain product, which is a lipid carrier for peptidoglycan synthesis of bacterial cell wall. In this study, we used two strategies to develop potential molecules which can inhibit UPPs. The first strategy is to design Y-shaped and L-shaped molecules based on the X-ray crystal structure analysis of UPPs. Both of biological assay and molecular modeling results show that L-shaped molecules have better binding affinity towards UPPs resulting in inhibitory effect. Among all the compounds investigated, L-shaped compound 22 exhibits the best inhibitory properties decrease 28 % activity of UPPs at 100 μM. The second strategy is to develop potential inhibitors by “target- guided synthesis”. It is hoped that the energy itself serves as a template to promote “1,3-dipolar“ cyclization to form the product with proper geometric and electronic fitness for the active site. To provide the necessary functionalities for the reaction and complement electronic properties of UPPs active site, two types of molecular fragments were designed and synthesized. Different combination of there two types of molecular fragments were mixed in the presence of UPPs and evaluated the possibility of forming the cycliztion compounds with the aid of eletrospray mass spectrometry.

Topic Category 基礎與應用科學 > 化學
理學院 > 化學研究所
Reference
  1. 2. Walsh, C. Nature, 2000, 406, 775-781.
    連結:
  2. 6. Suzuki, H., Nishimura, Y., Hirota, Y. Proc. Natl. Acad. Sci. U. S. A. 1978, 75, 664-668.
    連結:
  3. 7. Tamaki, S., Nakajima, S., Matsuhashi, M. Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 5472-5476.
    連結:
  4. 8. Chang, S. Y.; Ko, T. P.; Liang, P. H.; Wang, A. H. J. J. Biol. Chem. 2003, 278, 29298-29307.
    連結:
  5. 9. Ko, T. P.; Chen, Y. K.; Robinson, H. Tsai, P. C.; Gao, Y. G.; Chen, A. P.-C.; Wang, A. H.-J.; Liang, P. H. J. Biol. Chem. 2001, 276, 47474-47482.
    連結:
  6. 10. Chang, S. Y.; Chen, Y. K.; Wang, A. H.-J.; Liang, P. H. Biochemistry 2003, 42, 14452-14459.
    連結:
  7. 11. Chang, S. Y.; Ko, T. P.; Chen, A. P. C.; Wang, A. H.-J.; Liang, P. H. Protein Science 2004, 13, 971-978.
    連結:
  8. 12. Guo, R. T.; Ko, T. P.; Chen, A. P. C.; Kuo, C. J.; Wang, A. H. J; Liang, P. H. J. Biol. Chem. 2005, 280, 20762-20774.
    連結:
  9. 13. Chang, S. Y.; Ko, T. P.; Liang, P. H.; Wang, A. H.-J. J. Biol. Chem. 2003, 278, 29298-29307.
    連結:
  10. 14. Chen, A. P. C.; Chang, S. Y.; Lin, Y. C.; Sun, Y. S.; Chen, C. T.; Wang, A. H. J.; Liang, P. H. Biochem. J. 2005, 386, 169-176.
    連結:
  11. 15. Chen, Y. H.; Chen, A. P. C.; Chen, C. T.; Liang, P. H. J. Biol. Chem. 2002, 277, 7369-7376.
    連結:
  12. 16. Pan, J. J.; Yang, L. W.; Liang, P. H. Biochemistry 2000, 39, 13856-13861.
    連結:
  13. 17. DiMasi, J. A.; Bryant, N. R.; Lasagna, L. Clin. Pharmacol. Ther. 1991, 50, 471-487
    連結:
  14. 20.章仲偉, 發展類別最佳化之高解析度之配體受體交互作用評分函數, 2006, 7月
    連結:
  15. 21.Lyne, P. D. Structure-based virtual screening: an overview. Drug Discov Today 2002, 7, 1047-1055.
    連結:
  16. 22.蘇芳玉, 發展具潛力的法呢基轉移酶抑制劑:虛擬嵌合與篩選研究, 2004, 7月.
    連結:
  17. 23.Schulz-Gaxsch, T.; Stahl, M. Drug Discovery Today, Technol. 2004, 1, 231-239.
    連結:
  18. 24.Kenny B. Lipkowitz, Donald B. Boyd Reviews in Computational Chemistry Volume 17. 2001, Wiley
    連結:
  19. 25.Böhm, H. J. J. Comput. Aided Mol. Des. 1994, 8, 243-256.
    連結:
  20. 26.Wang, R.; Lu, Y.; Wang, S. J. Med. Chem. 2003, 46, 2287-2303.
    連結:
  21. 27.Martin, Y. C.; Muegge, I. J. Med. Chem. 1999, 42. 791-804.
    連結:
  22. 30.Klei, A. Van der, Jong, R. L. P. de, Lugtenburg, J. Tielens, A. G. M. Eur. J. Org. Chem. 2002, 3015-3023.
    連結:
  23. 38.Holton, R. A.; Zoeller, J. R. J. Am. Chem. Soc. 1985, 107, 2124-2131.
    連結:
  24. 46. Lewis, W. G.; Green, L. G.; Grynszpan, F.; Radić, Z.; Carlier, P. R.; Taylor, P.; Finn, M. G.; Sharpless, K. B. Angew. Chem. Int. Ed. 2002, 41, 1053-1057.
    連結:
  25. 47. Rideout, D. Science 1986, 233, 561-563.
    連結:
  26. 48. Huc, I.; Lehn, J. M. Proc. Natl. Acad. Sci. USA 1997, 94, 2106-2110.
    連結:
  27. 50. Maly, D. J.; Choong, I. C.; Ellman, J. A. Proc. Natl. Acad. Sci. USA 2000, 97, 2419-2424.
    連結:
  28. 51. Nguyen, R.; Huc, I. Angew. Chem., Int. Ed. 2001, 40, 1774-1776.
    連結:
  29. 57. 李育瑾, 以法呢焦磷酸酯螢光類似物探測十一異戊二烯焦磷酸合成酶的活性中心和反應構形變化, 2004, 七月
    連結:
  30. 58. Silverman, D. N; Lindskog, S. Acc. Chem. Res., 1988, 21, 30-36.
    連結:
  31. 60. Coppola, G. M. Synthesis, 1980, 505-536.
    連結:
  32. 61. Venuti, M. C. Synthesis, 1982, 266-268.
    連結:
  33. 63. Chen, C. T.; Chiang. C. L.; Lin, Y. C.; Chan, L. H.; Huang, C. H.; Tsai, Z. W.; Chen. C. T. Org. Lett. 2003, 5, 1261-1264.
    連結:
  34. 64. Chou, P. T.; Huang, C. H.; Pu, S. C.; Cheng, Y. M.; Liu, Y. H., Wang, Y. Chen, C. T. J. Phy. Chem. A 2004, 108, 6452-6454.
    連結:
  35. 65. Hsu, H. J.; Liang, M. R.; Chen, C. T.; Chung, B. C. Nature 2006, 439, 480-483.
    連結:
  36. 67. Greenidge, P. A.; Mérette, S. A. M.; Beck, R.; Dodson, G.; Goodwin, C. A.; Scully, M. F.; Spencer, J.; Weiser, J.; Deadman, J. J. J. Med. Chem. 2003, 46, 1293-1305.
    連結:
  37. 1. Patrick, G. L. An Introduction to Medicinal Chemistry3th, 2005, Oxford
  38. 3. Rogers, H. J., Perkin, H. R., and Ward, J. B. Microbial Cell Walls and Membranes 1980, Champman and Hall, London, U. K.
  39. 4. Kahne, D., Leimkuhler, C., Lu, W., Walsh, C. Chem. Rev. 2005, 105, 425-448.
  40. 5. (a). van Heijenoort, J. Nat. Prod. Rep. 2001, 18, 503-519. (b) Bugg, T. D. In Comprehensive Natural Products Chemistry; Pinto, B. M., Ed.; Elsevier: Oxford, 1999; Vol. 3.
  41. 18. 李冠漢Chemistry ( The Chinese Chem. Soc., Taipei ) 2003, 61, 655-670.
  42. 19. 陳香惠、陳基旺, 後基因體時代之生物技術 第二十章 電腦虛擬篩選。
  43. 28.Gaon, I.; Turek, T. C.; Weller, V. A.; Edelstein, R. L.; Singh, S. K.; Distefano, M. D. J. Org. Chem. 1996, 61, 7738-7745.
  44. 29.Ackerley, N.; Brewster, A. G.; Brown, G. R.; Clarke, D. S.; Foubister, A. J. Griffin, S. J.; Hudson, J. A.; Smithers, M. J. Whittamore, P. R. O. J. Med. Chem. 1995, 38, 1608-1628.
  45. 31.Berg, E. I.; Robinson, M. K.; Warnock, R. A.; Butcher, E. C. J. Cell Biol. 1991, 114, 343-349.
  46. 32.Mikami, K.; Azuma, K. I.; Nakai, T. Tetrahedron 1984, 40, 2303-2308.
  47. 33.Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. Angew. Chem. Int. Ed. 2002, 41, 2596-2599.
  48. 34.Chen, A. P. -C.; Chen, Y. H.; Liu, H. P.; Li, Y. C.; Chen, C. T.; Liang, P. H. J. Am. Chem. Soc. 2002, 124, 15217-15224.
  49. 35.Volkert, M.; Uwai, K.; Tebbe, A.; Popkirova, B.; Wagner, M.; Kuhlmann, J.; Waldmann, H. J. Am. Chem. Soc. 2003, 125, 12749-12758.
  50. 36.Davisson, V. J.; Woodside, A. B.; Neal, T. R.; Stremler, K. E.; Poulter, C. D. J. Org. Chem. 1986, 51, 4768-4779.
  51. 37.Rao Rama, A. V.; Chakraborty, T. K.; Joshi, S. P. Tetrahedron Lett. 1992, 33, 4045-4048.
  52. 39.Gibson, F. S.; Park, M. S.; Rapoport, H. J. Org. Chem. 1994, 59, 7503-7507.
  53. 40.Kolb, H. C; Finn, M. G.; Sharpless, K. B. Angew. Chem. Int. Ed. 2001, 40, 2004-2021.
  54. 41.Husigen, R. In 1,3-Dipolar Cycloaddition Chemistry Wiley- Interscience, New York, 1984.
  55. 42. Himo, F.; Lovell, T.; Hilgraf, R.; Rostovtsev, V. V.; Noodleman, L.; Sharpless, K. B.; Fokin, V. V. J. Am. Chem. Soc. 2005, 127, 210-216.
  56. 43. Chan, T. R.; Hilgraf, R.; Sharpless, K. B.; Fokin, V. V. Org. Lett. 2004, 6, 2853-2855.
  57. 44. Krasiński, A.; Fokin, V. V.; Sharpless, K. B. Org. Lett. 2004, 6, 1237-1240.
  58. 45. (a) Kolb, H. C.; Sharpless, K. B. Drug discovery Today 2003, 8, 1128-1137. (b) Sawa, M.; Hsu, T. L.; Itoh, T.; Sugiyama, M.; Hanson, S. R.; Vogt, P. K.; Wong, C. H. Proc. Natl. Acad. Sci. USA 2006, 103, 12371-12376.
  59. 49. Lenh, J. M. Chem. Eur. J. 1999, 5, 2455-2463.
  60. 52. (a) Mock, W. L.; Irra, T. A.; Wepsiec, J. P.; Manimaran, T. L. J. Org. Chem. 1983, 48, 3619-3620. (b) Mock, W. L.; Irra, T. A.; Wepsiec, J. P.; Adhya, M. J. Org. Chem. 1989, 54, 5302-5308.
  61. 53. Krasińskí, A.; Radić, Z.; Manetsch, R.; Raushel, J.; Taylor, P.; Sharpless, K. B.; Kolb, H. C. J. Am. Chem. Soc. 2005, 127, 6686-6692.
  62. 54. Mocharla, V. P.; Colasson, B.; Lee, L. V.; Röper S.; Sharpless, K. B. Wong, C. H.; Kolb, H. C. Angew. Chem. Int. Ed. 2005, 44, 116-120.
  63. 55. Whiting, M.; Muldoon, J. Lin, Y. C.; Silverman, S. M.; Lindstrom, W.; Olson, A. J.; Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Elder, J. H.; Fokin, V. V. Angew. Chem. Int. Ed. 2006, 45, 1435-1439.
  64. 56. (a) Bourne, Y.; Kolb, H. C.; Radić, Z.; Sharpless, K. B.; Taylor, P.; Marchot, P. Proc. Natl. Acad. Sci. USA 2004, 101, 1449-1454. (b) Manetsch, R.; Krasiński, A.; Radić, Z.; Raushel, J.; Taylor, P.; Sharpless, K. B.; Kolb, H. C. J. Am. Chem. Soc. 2004, 126, 12809-12818.
  65. 59. Carboni, B.; Benalil, A.; Vaultier. M.; J. Org. Chem. 1993, 58, 3736-3741.
  66. 62. González-Gómez, J. C.; Santana, L.; Uria, E. Tetrahedron 2003, 59, 8171-8176.
  67. 66. Frédrérik, R.; Charlier, C.; Robert, S.; Wouters, J., Masereel, B.; Pochet, L. Bioorg. Med. Chem. Lett. 2006, 16, 2017-2021.
  68. 68. Okuda, Y.; Lakshmikantham, M. V.; Cava, M. P. J. Org. Chem. 1991, 56, 6024-6026.
  69. 69. Brink, H. T. ten; Rijkers, D. T. S.; Liskamp, R. M. J. J. Org. Chem. 2006, 71, 1817-1824.
  70. 70. Takaoka, Y.; Tsutsumi, H.; Kasagi, N.; Nakata, E.; Hamahi, I. J. Am. Chem. Soc. 2006, 128, 3273-3280.
  71. 71. (a) Haugland, R. P. Handbook of fluorescent Probes and Research Products, 9th ed, Molecular Probes Inc., 2002. (b) Hiratsuka, T. J. Biol. Chem. 1982, 257, 13354-13358.
Times Cited
  1. 張皓晴(2009)。螢光發報之原位適配接合反應應用於異戊二烯焦磷酸合成酶抑制劑的開發。臺灣大學化學研究所學位論文。2009。1-98。 
  2. 詹孟學(2009)。設計及合成針對十一異戊二烯焦磷酸合成酶的抑制劑。臺灣大學化學研究所學位論文。2009。1-123。