Molecular Docking, QSAR and Molecular Dynamics Simulation on Spiro-oxindoles as MDM2 Inhibitors

doi:10.6023/A13040375

Acta Chimica Sinica ›› 2013, Vol. 71 ›› Issue (10): 1396-1403.DOI: 10.6023/A13040375 Previous Articles Next Articles

Article

螺环吲哚类MDM2抑制剂的分子对接、定量构效关系和分子动力学模拟

李博^a, 周锐^a, 何谷^a,b, 郭丽^a, 黄维^c

a 四川大学华西药学院成都 610041;
b 四川大学华西医院生物治疗国家重点实验室成都 610041;
c 成都中医药大学药学院成都 611137

投稿日期:2013-04-06 发布日期:2013-08-25
通讯作者: 何谷,E-mail:heguscu@163.com;郭丽,E-mail:rosaguoli2000@yahoo.com.cn E-mail:heguscu@163.com;rosaguoli2000@yahoo.com.cn
基金资助:
项目受国家自然科学基金(Nos. 81001357, 81273471)和中药资源系统研究与开发利用省部共建国家重点实验室培育基地开放课题资助.

Molecular Docking, QSAR and Molecular Dynamics Simulation on Spiro-oxindoles as MDM2 Inhibitors

Li Bo^a, Zhou Rui^a, He Gu^a,b, Guo Li^a, Huang Wei^c

a West China School of Pharmacy, Sichuan University, Chengdu 610041;
b State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041;
c School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137

Received:2013-04-06 Published:2013-08-25
Supported by:
Project supported by the National Natural Science Foundation of China (Nos. 81001357, 81273471) and the Open Research Fund of State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine.

Inhibition of the MDM2-p53 interaction is considered to be a new therapeutic strategy to activate wild-type p53 in tumors. Recently, a series of potent and specific small-molecule spiro-oxindole inhibitors of the MDM2 were reported. In the current study, the interaction modes between 21 spiro-oxindole MDM2 inhibitors and the protein were studied by using the combination of molecular docking, molecular dynamics simulation and three-dimensional quantitative structure-activity relationships (3D-QSAR). The QSAR predictive models were established by using comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) techniques. The predictive power of the 3D-QSAR models were determined from external test sets that were excluded during model development. The inhibitors in test sets were given exactly the same pretreatment as the inhibitors in the corresponding training sets. The correlation between the experimental and predicted activity for all models was calculated as a predictive r² value. With the CoMFA model, the cross-validated value (q²) was 0.573, the non-cross-validated value (r²) was 0.948. And with the CoMSIA model, the corresponding q² and r² were 0.651 and 0.98, respectively. The interaction mode obtained by molecular docking was in agreement with the results of molecular dynamics simulations, the interaction mode revealed that the hydrophobic interaction and H-bond played an important role in the binding of spiro-oxindole derivatives and MDM2. Compounds designed by our group were synthesized and tested their in vitro cytotoxic activities against the MDM2 positive prostatic carcinoma LNCaP cell line. Two compounds, namely 5 and 6, with favorable scores from the CoMFA and CoMSIA models, showed potent cytotoxic activities with IC₅₀ values lower than 1.0 μg·mL^-¹. The result was corresponding with that in experiment. And it was very significance to discover novel spiro-oxindole inhibitors which are mainly aimed at the MDM2-p53 interaction. It was expected that the information provided here was helpful for the study toward more accurate structure based on 3D-QSAR modeling and anti-tumor drug design and discovery.

Key words: Spiro spiro-oxindole derivatives, Molecular molecular docking, Molecular molecular dynamics, Comparative comparative molecular field analysis, Comparative comparative molecular similarity indices analysis

Cite this article

Li Bo, Zhou Rui, He Gu, Guo Li, Huang Wei. Molecular Docking, QSAR and Molecular Dynamics Simulation on Spiro-oxindoles as MDM2 Inhibitors[J]. Acta Chimica Sinica, 2013, 71(10): 1396-1403.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

References

[1] Kubbutat, M. H.; Jones, S. N.; Vousden, K. H. Nature 1997, 387, 299.

[2] Ashcroft, M.; Taya, Y.; Vousden, K. H. Mol. Cell. Biol. 2000, 20, 3024.

[3] Lai, Z. H.; Yang, T.; Kim, Y. B.; Sielecki, T. M.; Diamond, M. A.; Strack, P.; Rolfe, M.; Caligiuri, M.; Benfield, P. A.; Auger, K. R.; Copeland R. A. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 14734.

[4] Yang, Y.; Ludwig, R. L.; Jensen, J. P.; Pierre, S. A.; Medaglia, M. V.; Davydov, I. V.; Safiran, Y. J.; Oberoi, P.; Kenten, J. H.; Phillips, A. C.; Weissman, A. M.; Vousden, K. H. Cancer Cell 2005, 7, 547.

[5] Vassilev, L. T.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C.; Fotouhi, N.; Liu, E. A. Science 2004, 303, 844.

[6] Chène, P.; Fuchs, J.; Bohn, J.; García-Echeverría, C.; Furet, P.; Fabbro, D. J. Mol. Biol. 2000, 299, 245.

[7] Parks, D. J.; Lafrance, L. V.; Calvo, R. R.; Milkiewicz, K. L.; Gupta, V.; Lattanze, J.; Ramachandren, K.; Carver, T. E.; Petrella, E. C.; Cummings, M. D.; Maguire, D.; Grasberger, B. L.; Lu, T. Bioorg. Med. Chem. Lett. 2005, 15, 765.

[8] Hu, C. Q.; Hu, Y. Z. Curr. Med. Chem. 2008, 15, 1720.

[9] Stoll, R.; Renner, C.; Hansen, S.; Palme, S.; Klein, C.; Belling, A.; Zeslawski, W.; Kamionka, M.; Rehm, T.; Mühlhahn, P.; Schumacher, R.; Hesse, F.; Kaluza, B.; Voelter, W.; Engh, R. A.; Holak, T. A. Biochemistry 2001, 40, 336.

[10] Wang, W. S.; Hu, Y. Z. Med. Res. Rev. 2012, 32, 1159.

[11] Zhuang, C. L.; Miao, Z. Y.; Sheng, C. Q.; Yao, J. Z.; Zhang, W. N. Chin. J. Med. Chem. 2010, 20, 403.[(庄春林, 缪震元, 盛春泉, 姚建忠, 张万年., 中国药物化学杂志, 2010, 20, 403.)]

[12] Macchiarulo, A.; Giacche, N.; Carotti, A.; Baroni, M.; Cruciani, G.; Pellicciari, R. J. Chem. Inf. Model. 2008, 48, 1999.

[13] Chen, J. Z.; Wang, J. N.; Xu, B. S.; Zhu, W. L.; Li, G. H. J. Mol. Graphics Modell. 2011, 30, 46.

[14] Fu, T.; Min, H.; Xu, Y.; Chen, J.; Li, G. Int. J. Mol. Sci. 2012, 13, 9709.

[15] Barakat, K.; Mane, J.; Friesen, D.; Tuszynski, J. J. Mol. Graphics Modell. 2010, 28, 555.

[16] Cheng, W. Y.; Chen, J. Z.; Liang, Z. Q.; Li, G. H.; Yi, C. H.; Wang, W.; Wang, K. Y. Comput. Theoret. Chem. 2012, 984, 43.

[17] Lu, S. Y.; Jiang, Y. J.; Zou, J. W.; Wu, T. X. J. Mol. Graphics Modell. 2011, 30, 167.

[18] Wang, F. F.; Li, Y.; Ma, Z.; Wang, X.; Wang, Y. H. J. Mol. Model. 2012, 18, 295.

[19] Ding, K.; Lu, Y.; Nikolovska-Coleska, Z.; Qiu, S.; Ding, Y.; Gao, W.; Stuckey, J.; Krajewski, K.; Roller, P. P.; Tomita, Y.; Parrish, D. A.; Deschamps, J. R.; Wang, S. J. Am. Chem. Soc. 2005, 127, 10130.

[20] Ding, K.; Lu, Y.; Nikolovska-Coleska, Z.; Wang, G.; Qiu, S.; Shangary, S.; Gao, W.; Qin, D.; Stuckey, J.; Krajewski, K.; Roller, P. P.; Wang, S. J. Med. Chem. 2006, 49, 3432.

[21] Yu, S.; Qin, D.; Shangary, S.; Chen, J.; Wang, G.; Ding, K.; McEachern, D.; Qiu, S.; Nikolovska-Coleska, Z.; Miller, R.; Kang, S.; Yang, D.; Wang, S. J. Med. Chem. 2009, 52, 7970.

[22] Shangary, S.; Wang, S. Clin. Cancer Res. 2008, 14, 5318.

[23] Canner, J. A.; Sobo, M.; Ball, S.; Hutzen, B.; DeAngelis, S.; Willis, W.; Studebaker, A. W.; Ding, K.; Wang, S.; Yang, D.; Lin, J. Brit. J.

[23]Cancer 2009, 101, 774.

[24] Popowicz, G. M.; Domling, A.; Holak T. A. Angew. Chem., Int. Ed. 2011, 50, 2680.

[25] Kubinyi, H. Drug Discovery Today 1997, 11, 457.

[26] Kubinyi, H. Drug Discovery Today 1997, 12, 538.

[27] Xie, X.; Peng, C.; He, G.; Leng, H. J.; Wang, B.; Huang, W.; Han, B. Chem. Commun. 2012, 48, 10487.

[28] Wu, G. S.; Ouyang, L.; Liu, J.; Zeng, S.; Huang, W.; Han, B.; Wu, F. B.; He, G.; Xiang, M. L. Mol. Divers. 2013, 17, 271.

[29] Clark, M.; Cramer, R. D.; Jones, D. M.; Patterson, D. E.; Simeroth, P. E. Tetrahedron Comput. Method 1990, 3, 47.

[30] He, G.; Qiu, M. H.; Li, R.; Ouyang, L.; Wu, F. B.; Song, X. R.; Cheng, L.; Xiang, M. L.; Yu, L. T. Chem. Biol. Drug Des. 2012, 79, 960.

[31] Ouyang, L.; He, G.; Huang, W.; Song, X. R.; Wu, F. B.; Xiang, M. L. Int. J. Mol. Sci. 2012, 13, 5348.

[32] SYBYL Molecular Modeling Software, Tripos Inc., St. Louis, MO, USA, 2002.

[33] http://www. rcsb. Org.

[34] Discovery Studio, version 3.5, Accelrys Inc.: San Diego, CA, USA, 2012.

[35] Zhu, R. X.; Wang, F.; Liu, Q.; Kang, T. G. Acta Chim. Sinica 2011, 69, 1731. (朱瑞新, 王飞, 刘琦, 康廷国, 化学学报, 2011, 69, 1731.)

[36] McIntosh, A. R.; Bookstein, F. L.; Haxby, J. V.; Grady, C. L. Neuroimage 1996, 3, 143.

[37] Cramer, R. D. Perspect. Drug Discovery Des. 1993, 1, 269.

[38] Qiao, K.; Zeng, L. X.; Jin, H. W.; Liu, Z. M.; Zhang, L. R. Acta Phys.-Chim. Sin. 2012, 28, 1509.[(乔康, 曾凌晓, 金宏威, 刘振明, 张亮仁, 物理化学学报, 2012, 28, 1509.].)

[39] Tropsha, A.; Golbraikh, A. J. Mol. Graphics Modell. 2002, 20, 269.

[40] van der Spoel, D.; van Buuren, A. R.; Tieleman, D. P.; Berendsen, H. J. C. J. Biomol. NMR 1996, 8, 229.

[41] van Aalten, D. M. F.; Bywater, R.; Findlay, J. B. C.; Hendlich, M.; Hooft, R. W. W.; Vriend, G. J. Comput. Aided Mol. Des. 1996, 10, 255.

[42] Niu, C.; Xu, Y.; Xu, Y.; Luo, X. J. Phys. Chem. B 2005, 109, 23730.

[43] Zhan, D.-L.; Wang, S.; Han, W.-W.; Liu, J.-S. Acta Chim. Sinica 2012, 70, 217. (詹冬玲, 王嵩, 韩葳葳, 刘景圣, 化学学报, 2012, 70, 217.)

[44] Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.

[45] Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.

螺环吲哚类MDM2抑制剂的分子对接、定量构效关系和分子动力学模拟

Molecular Docking, QSAR and Molecular Dynamics Simulation on Spiro-oxindoles as MDM2 Inhibitors

PDF

Knowledge

Cited

Abstract

Cite this article

share this article

References

Related Articles 0

Recommended Articles

Metrics

Comments