Citation: SUN Wei-Qi, ZHANG Ji-Long, ZHENG Qing-Chuan, SUN Zhi-Wei, ZHANG Hong-Xing. Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II[J]. Acta Physico-Chimica Sinica doi: 10.3866/PKU.WHXB201301183 shu

Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II

1.
1 School of Public Health, Jilin University, Changchun 130021, P. R. China;
2 State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China;
3 School of Public Health, Beihua University, Jilin 132013, P. R. China;
4 School of Public Health and Family Medicine, Capital Medical University, Beijing 100069, P. R. China

Received Date: 8 November 2012
Available Online: 18 January 2013
Fund Project: 国家自然科学基金(21273095, 20903045, 21203072) (21273095, 20903045, 21203072) 高等学校博士点学科专项基金(20070183046)与吉林大学基本科研业务费(201003044)资助项目 (20070183046)与吉林大学基本科研业务费(201003044)

Molecular dynamics (MD) simulations and free energy calculations were integrated to investigate substrate-enzyme dynamic interactions during the unbinding of phenylsulfonamide from carbonic anhydrase II (CA II). The potential of mean force (PMF) along the unbinding pathway shows that a special ligand-binding state exists, and the electrostatic interaction dominates the ligand?s binding with CA II. The analysis of trajectories reveals that, apart from the zinc ion, the key residues in the unbinding pathway, Leu198, Thr199, and Thr200, prevent the substrate?s unbinding from the enzyme by hydrogen bonding with the sulfanilamide group of the substrate. The present results are of direct significance for the in-depth understanding of the sulfonamide-CA II binding process and related drug design.
- Molecular dynamics simulation,
- Free energy,
- Phenylsulfonamide,
- Carbonic anhydrase II,
- Substrate’s binding
1. [1]
  
  (1) Krishnamurthy, V. M.; Kaufman, G. K.; Urbach, A. R.; Gitlin,I.; Gudiksen, K. L.;Weibel, D. B.; Whitesides, G. M. Chem.Rev. 2008, 108, 946. doi: 10.1021/cr050262p
2. [2]
  (2) Sanyal, G.; Maren, T. H. J. Biol. Chem. 1981, 256, 608.
3. [3]
  (3) Stabenau, E. K.; Heming, T. Comp. Biochem. Physiol. Part A:Mol. Integr. Physiol. 2003, 136, 271. doi: 10.1016/S1095-6433(03)00177-6
4. [4]
  (4) Shah, G. N.; Ulmasov, B.;Waheed, A.; Becker, T.; Makani, S.;Svichar, N.; Chesler, M.; Sly,W. S. Proc. Natl. Acad. Sci. U. S.A. 2005, 102, 16771. doi: 10.1073/pnas.0508449102
5. [5]
  (5) Gay, C. V.;Weber, J. A. Crit. Rev. Eukaryotic Gene Expression2000, 10, 213.
6. [6]
  (6) Henry, R. P. Ann. Rev. Physiol. 1996, 58, 523. doi: 10.1146/annurev.ph.58.030196.002515
7. [7]
  (7) Svastova, E.; Hulikova, A.; Rafajova, M.; Zatovicova, M.;Gibadulinova, A.; Casini, A.; Cecchi, A.; Scozzafava, A.;Supuran, C. T.; Pastorek, J.; Pastorekova, S. FEBS Lett. 2004,577, 439. doi: 10.1016/j.febslet.2004.10.043
8. [8]
  (8) Sun, M. K.; Alkon, D. L. Trends Pharm. Sci. 2002, 23, 83. doi: 10.1016/S0165-6147(02)01899-0
9. [9]
  (9) Scoozzafava, A.; Mastrolorenzo, A; Supuran, C. T. Expert Opin.Ther. Pat. 2006, 16, 1627. doi: 10.1517/etp.2006.16.issue-12
10. [10]
  (10) Pastorekova, S.; Parkkila, S.; Pastorek, J.; Supuran, C. T.J. Enzyme Inhib. Med. Chem. 2004, 19, 199. doi: 10.1080/14756360410001689540
11. [11]
  (11) Khalifah, R. G. J. Biol. Chem. 1971, 246, 2561.
12. [12]
  (12) Wistrand, P. J.; Schenholm, M.; Lonnerholm, G. Invest.Ophthalmol. Vision Sci. 1986, 27, 419.
13. [13]
  (13) Alward,W. L. M. N. Engl. J. Med. 1998, 339, 1298. doi: 10.1056/NEJM199810293391808
14. [14]
  (14) Borthwick, K. J.; Kandemir, N.; Topaloglu, R.; Kornak, U.;Bakkaloglu, A.; Yordam, N.; Ozen, S.; Mocan, H.; Shah, G. N.;Sly,W. S.; Karet, F. E. J. Med. Genet. 2003, 40, 115. doi: 10.1136/jmg.40.2.115
15. [15]
  (15) Güzel, Ö.; Innocenti, A.; Scozzafava, A.; Salman, A.; Supuran,C. T. Bioorg. Med. Chem. Lett. 2009, 19, 3170. doi: 10.1016/j.bmcl.2009.04.123
16. [16]
  (16) Zhang, J. L.; Zheng, Q. C.; Li, Z. Q.; Zhang, H. X. PLoS ONE2012, 7, e39546.
17. [17]
  (17) Dong, X. Y.; Du,W. J.; Liu, F. F. Acta Phys. -Chim Sin. 2012,28, 2735. [董晓燕, 都文婕, 刘夫锋. 物理化学学报, 2012,28, 2735.] doi: 10.3866/PKU.WHXB201207162
18. [18]
  (18) Zhao, Y. S.; Zheng, Q. C.; Zhang, H. X.; Chu, H. Y.; Sun, C. C.Acta Phys. -Chim. Sin. 2009, 25, 417. [赵勇山, 郑清川, 张红星, 楚慧郢, 孙家钟. 物理化学学报, 2009, 25, 417.] doi: 10.3866/PKU.WHXB20090304
19. [19]
  (19) Zhang, J. L.; Zheng, Q. C.; Zhang, H. X. Comput. Biol. Chem.2011, 35, 50. doi: 10.1016/j.compbiolchem.2011.01.001
20. [20]
  (20) Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14,33. doi: 10.1016/0263-7855(96)00018-5
21. [21]
  (21) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
22. [22]
  (22) Hoover,W. G. Phys. Rev. A 1985, 31, 1695. doi: 10.1103/PhysRevA.31.1695
23. [23]
  (23) Hénin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904. doi: 10.1063/1.1773132
24. [24]
  (24) Zhang, J. L.; Zheng, Q. C.; Zhang, H. X. J. Phys. Chem. B 2010,114, 7383. doi: 10.1021/jp9113078
25. [25]
  (25) Zhang, J. L.; Zheng, Q. C.; Li, Z. Q.; Zhang, H. X. PLoS ONE2013, 8, e53811.
26. [26]
  (26) Zhang, J. L.; Zheng, Q. C.; Zhang, H. X. Chem. Phys. Lett.2010, 484, 338. doi: 10.1016/j.cplett.2009.12.022
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