槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

引用本文: 王长生, 刘朋, 于楠. 槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点[J]. 物理化学学报, 2013, 29(06): 1173-1182. doi: 10.3866/PKU.WHXB201303153 shu

Citation: WANG Chang-Sheng, LIU Peng, YU Nan. Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin[J]. Acta Physico-Chimica Sinica, 2013, 29(06): 1173-1182. doi: 10.3866/PKU.WHXB201303153 shu

槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

基金项目:
国家自然科学基金(20973088, 21173109, 21133005) (20973088, 21173109, 21133005)

教育部高等学校博士学科点专项科研基金(20102136110001) (20102136110001)

辽宁省优秀人才基金(LR2012037)资助项目 (LR2012037)

摘要:

深入理解药物分子和核酸碱基间的相互作用机制对合理设计研发新型高效药物有重要意义. 本文运用密度泛函理论B3LYP方法对核酸碱基尿嘧啶和胸腺嘧啶与药物分子槲皮素间的氢键相互作用位点进行了研究. 使用B3LYP/6-31G(d)方法优化得到了30个稳定的氢键复合物结构, 使用B3LYP/6-311++G(3df,2p)方法计算了这些复合物的结合能. 研究结果表明, 槲皮素可以使用5个不同的结合位点与尿嘧啶或胸腺嘧啶形成氢键复合物, 尿嘧啶或胸腺嘧啶可以使用3个不同的结合位点与槲皮素形成氢键复合物. 当槲皮素的结合位点固定时, 槲皮素与尿嘧啶的位点u1或胸腺嘧啶的位点t1形成的氢键作用最强, 与位点u2或位点t2形成的氢键强度最弱; 当尿嘧啶或胸腺嘧啶的作用位点固定时, 二者与槲皮素的位点qu1 形成的氢键作用最强, 与位点qu5 作用强度次之, 与位点qu3的作用强度最弱. 分子中原子(AIM)和自然键轨道(NBO)分析计算结果表明, 轨道作用在氢键中起重要作用.

关键词:

English

Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

1.
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
Received Date: 28 December 2012
Available Online: 17 May 2013
Fund Project:
国家自然科学基金(20973088, 21173109, 21133005)

教育部高等学校博士学科点专项科研基金(20102136110001)

辽宁省优秀人才基金(LR2012037)资助项目

Abstract:

Exploring the binding features between small drug molecules and biomolecules is particularly important because it can provide valuable information for understanding the interaction mechanism and therefore rationally designing, modifying and screening of new drugs. In this paper, the site-preference of the nucleic acid bases uracil and thymine hydrogen bonding to the small medical molecule quercetin is investigated using the density functional theory method. Thirty stable hydrogen-bonded complexes were located at the B3LYP/6-31G(d) level of theory. The binding energies for these complexes were further evaluated at the B3LYP/6-311++G(3df,2p) level of theory with the basis set superposition error corrections. The results indicate that quercetin can interact with uracil or thymine through five binding sites, which herein we refer to as Site qu1, Site qu2, Site qu3, Site qu4, and Site qu5, and uracil (or thymine) can interact with quercetin through three binding sites, which herein we refer to as Site u1, Site u2, and Site u3 (or Site t1, Site t2, and Site t3). We found that once the binding site of quercetin is fixed, the hydrogen bonds formed through uracil Site u1 and thymine Site t1 are the strongest, while those formed through uracil Site u2 and thymine Site t2 are the weakest. When the binding site of uracil or thymine is fixed, the hydrogen bonds formed through the quercetin Site qu1 are the strongest, followed by those formed through quercetin Site qu5, while those formed through quercetin Site qu3 are the weakest. Atoms in molecules (AIM) and natural bond orbital (NBO) analyses were also carried out to explore the interaction nature of these hydrogen-bonded complexes.

Key words:

1. [1]
  
  (1) Trouillas, P.; Marsal, P.; Siri, D.; Lazzaroni, R.; Duroux, J. L.Food Chem. 2006, 97, 679. doi: 10.1016/j.foodchem.2005.05.042
  (1) Trouillas, P.; Marsal, P.; Siri, D.; Lazzaroni, R.; Duroux, J. L.Food Chem. 2006, 97, 679. doi: 10.1016/j.foodchem.2005.05.042
2. [2]
  (2) Lespade, L.; Bercion, S. J. Phys. Chem. B 2010, 114, 921. doi: 10.1021/jp9041809(2) Lespade, L.; Bercion, S. J. Phys. Chem. B 2010, 114, 921. doi: 10.1021/jp9041809
3. [3]
  (3) Guzzo, M. R.; Uemi, M.; Donate, P. M.; Nikolaou, S.; Machado,A. E. H.; Okano, L. T. J. Phys. Chem. A 2006, 110, 10545. doi: 10.1021/jp0613337(3) Guzzo, M. R.; Uemi, M.; Donate, P. M.; Nikolaou, S.; Machado,A. E. H.; Okano, L. T. J. Phys. Chem. A 2006, 110, 10545. doi: 10.1021/jp0613337
4. [4]
  (4) Chakraborty, S.; Biswas, P. K. J. Phys. Chem. A 2012, 116,8775. doi: 10.1021/jp303543z(4) Chakraborty, S.; Biswas, P. K. J. Phys. Chem. A 2012, 116,8775. doi: 10.1021/jp303543z
5. [5]
  (5) Estévez, L.; Mosquera, R. A. J. Phys. Chem. A 2007, 111,11100. doi: 10.1021/jp074941a(5) Estévez, L.; Mosquera, R. A. J. Phys. Chem. A 2007, 111,11100. doi: 10.1021/jp074941a
6. [6]
  (6) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. Theor.Chem. Acc. 2004, 111, 210. doi: 10.1007/s00214-003-0544-1(6) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. Theor.Chem. Acc. 2004, 111, 210. doi: 10.1007/s00214-003-0544-1
7. [7]
  (7) Lee, S.; Shin, S. Y.; Lee, Y.; Park, Y.; Kim, B. G.; Ahn, J. H.;Chong, Y.; Lee, Y. H.; Lim, Y. Bioorg. Med. Chem. Lett. 2011,21, 3866. doi: 10.1016/j.bmcl.2011.05.043(7) Lee, S.; Shin, S. Y.; Lee, Y.; Park, Y.; Kim, B. G.; Ahn, J. H.;Chong, Y.; Lee, Y. H.; Lim, Y. Bioorg. Med. Chem. Lett. 2011,21, 3866. doi: 10.1016/j.bmcl.2011.05.043
8. [8]
  (8) Kang, J.W.; Zhuo, L.; Lu, X. Q.; Liu, H. D.; Zhang, M.;Wu, H.X. J. Inorg. Biochem. 2004, 98, 79. doi: 10.1016/j.jinorgbio.2003.08.015(8) Kang, J.W.; Zhuo, L.; Lu, X. Q.; Liu, H. D.; Zhang, M.;Wu, H.X. J. Inorg. Biochem. 2004, 98, 79. doi: 10.1016/j.jinorgbio.2003.08.015
9. [9]
  (9) Bhuva, H. A.; Kini, S. G. J. Mol. Graph. Model. 2010, 29, 32.doi: 10.1016/j.jmgm.2010.04.003(9) Bhuva, H. A.; Kini, S. G. J. Mol. Graph. Model. 2010, 29, 32.doi: 10.1016/j.jmgm.2010.04.003
10. [10]
  (10) Zhang, M.; Lv, Q. L.; Yue, N. N.;Wang, H. Y. Spectrochim.Acta A 2009, 72, 572. doi: 10.1016/j.saa.2008.10.045(10) Zhang, M.; Lv, Q. L.; Yue, N. N.;Wang, H. Y. Spectrochim.Acta A 2009, 72, 572. doi: 10.1016/j.saa.2008.10.045
11. [11]
  (11) Cornard, J. P.; Merlin, J. C. J. Mol. Struct. 2003, 651-653, 381.(11) Cornard, J. P.; Merlin, J. C. J. Mol. Struct. 2003, 651-653, 381.
12. [12]
  (12) Mukai, K.; Oka,W.;Watanabe, K.; Egawa, Y.; Nagaoka, S. I.J. Phys. Chem. A 1997, 101, 3746. doi: 10.1021/jp9706745(12) Mukai, K.; Oka,W.;Watanabe, K.; Egawa, Y.; Nagaoka, S. I.J. Phys. Chem. A 1997, 101, 3746. doi: 10.1021/jp9706745
13. [13]
  (13) Ni, Y. N.; Du, S.; Kokot, S. Anal. Chim. Acta 2007, 584, 19.doi: 10.1016/j.aca.2006.11.006(13) Ni, Y. N.; Du, S.; Kokot, S. Anal. Chim. Acta 2007, 584, 19.doi: 10.1016/j.aca.2006.11.006
14. [14]
  (14) Ren, J.; Meng, S.; Lekka, C. E.; Kaxiras, E. J. Phys. Chem. B2008, 112, 1845. doi: 10.1021/jp076881e(14) Ren, J.; Meng, S.; Lekka, C. E.; Kaxiras, E. J. Phys. Chem. B2008, 112, 1845. doi: 10.1021/jp076881e
15. [15]
  (15) Leopoldini, M.; Russo, N.; Chiodo, S.; Toscano, M. J. Agric.Food Chem. 2006, 54, 6343. doi: 10.1021/jf060986h(15) Leopoldini, M.; Russo, N.; Chiodo, S.; Toscano, M. J. Agric.Food Chem. 2006, 54, 6343. doi: 10.1021/jf060986h
16. [16]
  (16) Lekka, C. E.; Ren, J.; Meng, S.; Kaxiras, E. J. Phys. Chem. B2009, 113, 6478. doi: 10.1021/jp807948z(16) Lekka, C. E.; Ren, J.; Meng, S.; Kaxiras, E. J. Phys. Chem. B2009, 113, 6478. doi: 10.1021/jp807948z
17. [17]
  (17) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. J. Phys.Chem. A 2004, 108, 4916. doi: 10.1021/jp037247d(17) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. J. Phys.Chem. A 2004, 108, 4916. doi: 10.1021/jp037247d
18. [18]
  (18) Lemańska, K.; Szymusiak, H.; Tyrakowska, B.; Zieliński, R.;Soffers, A. E. M. F.; Rietjens, I. M. C. M. Free Raobc. Med.2001, 7, 869.(18) Lemańska, K.; Szymusiak, H.; Tyrakowska, B.; Zieliński, R.;Soffers, A. E. M. F.; Rietjens, I. M. C. M. Free Raobc. Med.2001, 7, 869.
19. [19]
  (19) Plaper, A.; lob, M.; Hafner, I.; Oblak, M.; Šolmajer, T.;Jerala, R. Biochem. Biophys. Res. Commun. 2003, 306, 530.doi: 10.1016/S0006-291X(03)01006-4(19) Plaper, A.; lob, M.; Hafner, I.; Oblak, M.; Šolmajer, T.;Jerala, R. Biochem. Biophys. Res. Commun. 2003, 306, 530.doi: 10.1016/S0006-291X(03)01006-4
20. [20]
  (20) Solimani, R. Biochim. Biophys. Acta 1997, 1336, 281. doi: 10.1016/S0304-4165(97)00038-X(20) Solimani, R. Biochim. Biophys. Acta 1997, 1336, 281. doi: 10.1016/S0304-4165(97)00038-X
21. [21]
  (21) Zhang, C. S.; Lai, L. H. Acta Phys. -Chim. Sin. 2012, 28 (10),2363. [张长胜, 来鲁华. 物理化学学报, 2012, 28 (10), 2363.]doi: 10.3866/PKU.WHXB201209172(21) Zhang, C. S.; Lai, L. H. Acta Phys. -Chim. Sin. 2012, 28 (10),2363. [张长胜, 来鲁华. 物理化学学报, 2012, 28 (10), 2363.]doi: 10.3866/PKU.WHXB201209172
22. [22]
  (22) Huang, Y. Y.; Yang, X. F.; Li, H. T.; Ji, X. F.; Cheng, H. L.;Zhao, Y. J.; Guo, D. C.; Li, L.; Liu, S. Y. Acta Phys. -Chim. Sin.2012, 28 (10), 2390. [黄阳玉, 阳秀凤, 李昊田, 纪晓峰, 程洪礼, 赵蕴杰, 郭大川, 李林, 刘士勇. 物理化学学报, 2012, 28 (10), 2390.] doi: 10.3866/PKU.WHXB201209111(22) Huang, Y. Y.; Yang, X. F.; Li, H. T.; Ji, X. F.; Cheng, H. L.;Zhao, Y. J.; Guo, D. C.; Li, L.; Liu, S. Y. Acta Phys. -Chim. Sin.2012, 28 (10), 2390. [黄阳玉, 阳秀凤, 李昊田, 纪晓峰, 程洪礼, 赵蕴杰, 郭大川, 李林, 刘士勇. 物理化学学报, 2012, 28 (10), 2390.] doi: 10.3866/PKU.WHXB201209111
23. [23]
  (23) Zhang, M.; Zheng, Y. P.; Jiang, X. N.;Wang, C. S. ActaPhys. -Chim. Sin. 2010, 26 (3), 735. [张敏, 郑艳萍, 姜笑楠, 王长生. 物理化学学报, 2010, 26 (3), 735.] doi: 10.3866/PKU.WHXB20100235(23) Zhang, M.; Zheng, Y. P.; Jiang, X. N.;Wang, C. S. ActaPhys. -Chim. Sin. 2010, 26 (3), 735. [张敏, 郑艳萍, 姜笑楠, 王长生. 物理化学学报, 2010, 26 (3), 735.] doi: 10.3866/PKU.WHXB20100235
24. [24]
  (24) Liu, D. J.;Wang, C. S. Acta Phys. -Chim. Sin. 2012, 28 (12),2809. [刘冬佳, 王长生. 物理化学学报, 2012, 28 (12), 2809.]doi: 10.3866/PKU.WHXB201209263(24) Liu, D. J.;Wang, C. S. Acta Phys. -Chim. Sin. 2012, 28 (12),2809. [刘冬佳, 王长生. 物理化学学报, 2012, 28 (12), 2809.]doi: 10.3866/PKU.WHXB201209263
25. [25]
  (25) Dong, H.; Hua,W. J.; Li, S. H. J. Phys. Chem. A 2007, 111,2941. doi: 10.1021/jp0709860(25) Dong, H.; Hua,W. J.; Li, S. H. J. Phys. Chem. A 2007, 111,2941. doi: 10.1021/jp0709860
26. [26]
  (26) Jiang, X. N.;Wang, C. S. Sci. China Ser. Chem. 2010, 8, 1754.(26) Jiang, X. N.;Wang, C. S. Sci. China Ser. Chem. 2010, 8, 1754.
27. [27]
  (27) Li, Y.;Wang, C. S. Sci. China Ser. Chem. 2011, 54 (11), 1759.doi: 10.1007/s11426-011-4411-y(27) Li, Y.;Wang, C. S. Sci. China Ser. Chem. 2011, 54 (11), 1759.doi: 10.1007/s11426-011-4411-y
28. [28]
  (28) Kobko, R.; Dannenberg, J. J. J. Phys. Chem. A 2003, 107,10389. doi: 10.1021/jp0365209(28) Kobko, R.; Dannenberg, J. J. J. Phys. Chem. A 2003, 107,10389. doi: 10.1021/jp0365209
29. [29]
  (29) Wu, Y. D.; Zhao, Y. L. J. Am. Chem. Soc. 2001, 123, 5313.doi: 10.1021/ja003482n(29) Wu, Y. D.; Zhao, Y. L. J. Am. Chem. Soc. 2001, 123, 5313.doi: 10.1021/ja003482n
30. [30]
  (30) Frish, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gassian 03,Revision D.01; Gaussian Inc.: Pittsburgh, PA, 2003.(30) Frish, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gassian 03,Revision D.01; Gaussian Inc.: Pittsburgh, PA, 2003.
31. [31]
  (31) Biegler, K. F.; Schonbohm, J.; Bayles, D. J. Comput. Chem.2001, 22, 545.(31) Biegler, K. F.; Schonbohm, J.; Bayles, D. J. Comput. Chem.2001, 22, 545.
32. [32]
  (32) Yang, Y. J. Phys. Chem. A 2012, 116, 10150. doi: 10.1021/jp304420c(32) Yang, Y. J. Phys. Chem. A 2012, 116, 10150. doi: 10.1021/jp304420c
33. [33]
  (33) Yang, Y. J. Phys. Chem. A 2011, 115, 9043. doi: 10.1021/jp204531e(33) Yang, Y. J. Phys. Chem. A 2011, 115, 9043. doi: 10.1021/jp204531e
34. [34]
  (34) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B2007, 111, 8940.(34) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B2007, 111, 8940.
35. [35]
  (35) Zhao, G. J.; Han, K. L. Accounts Chem. Res. 2012, 45, 404. doi: 10.1021/ar200135h
  (35) Zhao, G. J.; Han, K. L. Accounts Chem. Res. 2012, 45, 404. doi: 10.1021/ar200135h

扫一扫看文章

计量

PDF下载量: 612
文章访问数: 1467
HTML全文浏览量: 59

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

English

Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

English

Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs