葡萄糖苷酶抑制剂作用机理的分子动力学模拟和自由能计算

doi:10.3866/PKU.WHXB201207063

Abstract

Abstract:

Sulfonium ion glucosidase inhibitors such as kotalanol (SK) and de-O-sulfonated kotalanol (DSK) are potential drug candidates for the treatment of type II diabetes, with no serious toxicity or side effects. Experimental binding assays against glucosidase show that the activity of DSK is slightly higher than that of SK, while the activity of the nitrogen analogue of de-O-sulfonated kotalanol (DSN) is ~1500-fold higher than that of the nitrogen analog of kotalanol (SN). Here, the binding mechanisms of four representative inhibitors of glucoamylase, SK, DSK, and their two nitrogen analogues, were explored in an integrated modeling study combining molecular dynamics (MD) simulations, binding free energy calculations, and binding free energy decomposition analysis. Our simulations highlight the significant impact of the combination of nitrogen substitution and sulfate anion group. Nitrogen substitution in the five-membered ring leads to the overturning of the polyhydroxylated chain, originating from the shorter bond length of N―C compared with S ― C, while the sulfate anion group restrains the freedom of the polyhydroxylated chain. These cumulative effects are able to significantly change the binding conformation of the inhibitor and substantially impair interactions between the inhibitor and glucosidase. The structural insights obtained in this study are expected to be valuable for increased understanding of the binding mechanism of sulfonium ion glucosidase inhibitors and future design of more potent glucosidase inhibitors.

Key words: Sulfonium ion, Glucoamylase inhibitor, Molecular dynamic simulation, Free energy calculation, Free energy decomposition

MSC2000:

O641

LUO Fang, GAO Jian, CHENG Yuan-Hua, CUI Wei, JI Ming-Juan. Interaction Mechanisms of Inhibitors of Glucoamylase by Molecular Dynamics Simulations and Free Energy Calculations[J].Acta Phys. -Chim. Sin., 2012, 28(09): 2191-2201.

References

(1) Nichols, B. L.; Avery, S.; Sen, P.; Swallow, D. M.; Hahn, D.;Sterchi, E. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 1432. doi: 10.1073/pnas.0237170100
(2) Auricchio, S.; Semenza, G.; Rubino, A. Biochim. Biophys. Acta1965, 96, 498.
(3) Semenza, G.; Auricchio, S.; Rubino, A. Biochim. Biophys. Acta1965, 96, 487.
(4) Holman, R. R.; Cull, C. A.; Turner, R. C. Diabetes Care 1999,22, 960. doi: 10.2337/diacare.22.6.960
(5) Silva, C. H.; Taft, C. A. J. Biomol. Struct. Dyn. 2004, 22, 59.doi: 10.1080/07391102.2004.10506981
(6) Withers, S. G.; Namchuk, M.; Mosi, R. Potent GlycosideInhibitors: Transition State Mimics or Simply FortuitousBinders? In Iminosugars as Glycosidase Inhibitors; Arnold, E.S. Ed.;Wiley: New York, 2004; p 188.
(7) Matsuda, H.; Murakami, T.; Yashiro, K.; Yamahara, J.;Yoshikawa, M. Chem. Pharm. Bull. 1999, 47, 1725. doi: 10.1248/cpb.47.1725
(8) Wang, P. Y.; Kaneko, T.;Wang, Y.; Sato, A. Hepatology 1999,29, 161. doi: 10.1002/hep.510290109
(9) Yoshikawa, M.; Xu, F. M.; Nakamura, S.;Wang, T.; Matsuda,H.; Tanabe, G.; Muraoka, O. Heterocycles 2008, 75, 1397. doi: 10.3987/COM-07-11315
(10) Yoshikawa, M.; Murakami, T.; Shimada, H.; Matsuda, H.;Yamahara, J.; Tanabe, G.; Muraoka, O. Tetrahedron Lett. 1997,38, 8367. doi: 10.1016/S0040-4039(97)10270-2
(11) Matsuda, H.; Li, Y.; Murakami, T.; Matsumura, N.; Yamahara,J.; Yoshikawa, M. Chem. Pharm. Bull. 1998, 46, 1399. doi: 10.1248/cpb.46.1399
(12) Muraoka, O.; Xie,W. J.; Tanabe, G.; Amer, M. F. A.;Minematsu, T.; Yoshikawa, M. Tetrahedron Lett. 2008, 49,7315. doi: 10.1016/j.tetlet.2008.10.036
(13) Minami, Y.; Kurlyarna, C.; Ikeda, K.; Kato, A.; Takebayashi, K.;Adachi, I.; Fleet, G.W. J.; Kettawan, A.; Karnoto, T.; Asano, N.Bioorg. Med. Chem. 2008, 16, 2734. doi: 10.1016/j.bmc.2008.01.032
(14) Mohan, S.; Pinto, B. M. Carbohydr. Res. 2007, 342, 1551. doi: 10.1016/j.carres.2007.05.014
(15) Sim, L.; Jayakanthan, K.; Mohan, S.; Nasi, R.; Johnston, B. D.;Pinto, B. M.; Rose, D. R. Biochemistry-Us 2010, 49, 443. doi: 10.1021/bi9016457
(16) Mohan, S.; Jayakanthan, K.; Nasi, R.; Kuntz, D. A.; Rose, D.R.; Pinto, B. M. Org. Lett. 2010, 12, 1088. doi: 10.1021/ol100080m
(17) Yuasa, H.; Izumi, M.; Hashimoto, H. Curr. Top. Med. Chem.2009, 9, 76. doi: 10.2174/156802609787354270
(18) Case, D.; Darden, T. A.; Cheatham, T. E.; Simmerling, C.;Wang, J.; Duke, R.; Luo, R.; Crowley, M.;Walker, R.; Zhang,W.; Merz, K. M.;Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.;Kolossváry, I.;Wong, K. F.; Paesani, F.; Vanicek, J.;Wu, X.;Brozell, S.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.;Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M.G.; Sagui, C.; Babin, V.; Kollman, P. Amber 11; University ofCalifornia: San Francisco, 2010.
(19) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03,Revision B.03; Gaussian Inc.:Wallingford, CT, 2004.
(20) Bayly, C. I.; Cieplak, P.; Cornell,W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269. doi: 10.1021/j100142a004
(21) Wang, J. M.;Wolf, R. M.; Caldwell, J.W.; Kollman, P. A.; Case,D. A. J. Comput. Chem. 2004, 25, 1157. doi: 10.1002/jcc.20035
(22) Duan, Y.;Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.;Zhang,W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.;Wang, J. M.; Kollman, P. J. Comput. Chem. 2003, 24, 1999. doi: 10.1002/jcc.10349
(23) Jorgensen,W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R.W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926. doi: 10.1063/1.445869
(24) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
(25) Eslami, H.; Mojahedi, F.; Moghadasi, J. J. Chem. Phys. 2010,133, 084105. doi: 10.1063/1.3474951
(26) Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327. doi: 10.1016/0021-9991(77)90098-5
(27) Wang, J.; Hou, T.; Xu, X. Curr. Comput. Aided. Drug. Des.2006, 2, 287. doi: 10.2174/157340906778226454
(28) Kuhn, B.; Kollman, P. A. J. Med. Chem. 2000, 43, 3786. doi: 10.1021/jm000241h
(29) Huo, S.;Wang, J.; Cieplak, P.; Kollman, P. A.; Kuntz, I. D.J. Med. Chem. 2002, 45, 1412. doi: 10.1021/jm010338j
(30) Hou, T.; Yu, R. J. Med. Chem. 2007, 50, 1177. doi: 10.1021/jm0609162
(31) Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. J. Med. Chem.2005, 48, 4040. doi: 10.1021/jm049081q
(32) Hou, T.;Wang, J.; Li, Y.;Wang,W. J. Comput. Chem. 2011, 32,866. doi: 10.1002/jcc.21666
(33) Hou, T. J.; Xu, Z.; Zhang,W.; McLaughlin,W. A.; Case, D. A.;Xu, Y.;Wang,W. Mol. Cell. Proteomics 2009, 8, 639. doi: 10.1074/mcp.M800450-MCP200
(34) Hou, T. J.; Zhang,W.; Case, D. A.;Wang,W. J. Mol. Biol. 2008,376, 1201. doi: 10.1016/j.jmb.2007.12.054
(35) Hou, T. J.; Zhang,W.; Xu, X. J. J. Phys. Chem. B 2001, 105,5304. doi: 10.1021/jp0044476
(36) Hou, T. J.; Zhu, L. L.; Chen, L. R.; Xu, X. J. J. Chem. Inf. Comp. Sci. 2003, 43, 273. doi: 10.1021/ci025552a
(37) Wang, J. M.; Morin, P.;Wang,W.; Kollman, P. A. J. Am. Chem. Soc. 2001, 123, 5221. doi: 10.1021/ja003834q
(38) Hou, T.;Wang, J.; Li, Y.;Wang,W. J. Chem. Inf. Model. 2011,51, 69. doi: 10.1021/ci100275a
(39) Still,W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T.J. Am. Chem. Soc. 1990, 112, 6127. doi: 10.1021/ja00172a038
(40) Zhang,W.; Hou, T. J.; Qiao, X. B.; Xu, X. J. Acta Phys. -Chim. Sin. 2003, 19, 289. [章威, 侯廷军, 乔学斌, 徐筱杰. 物理化学学报, 2003, 19, 289.] doi: 10.3866/PKU.WHXB20030401
(41) Weiser, J.; Shenkin, P. S.; Still,W. C. J. Comput. Chem. 1999,20, 217. doi: 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
(42) Onufriev, A.; Bashford, D.; Case, D. A. Proteins 2004, 55, 383.doi: 10.1002/prot.20033
(43) Gohlke, H.; Kiel, C.; Case, D. A. J. Mol. Biol. 2003, 330, 891.doi: 10.1016/S0022-2836(03)00610-7
(44) Sim, L.; Quezada-Calvillo, R.; Sterchi, E. E.; Nichols, B. L.;Rose, D. R. J. Mol. Biol. 2008, 375, 782. doi: 10.1016/j.jmb.2007.10.069
(45) Hou, T.; Qiao, X.; Zhang,W.; Xu, X. J. Phys. Chem. B 2002,106, 11295. doi: 10.1021/jp025595u
(46) Brady, G. P.; Sharp, K. A. J. Mol. Biol. 1995, 254, 77. doi: 10.1006/jmbi.1995.0600
(47) Yuasa, H.; Saotome, C.; Kanie, O. Trends Glycosci. Glycotechnol. 2002, 14, 231.
(48) Eskandari, R.; Jones, K.; Rose, D. R.; Pinto, B. M. Chem. Commun. 2011, 47, 9134. doi: 10.1039/c1cc13052h
(49) Rejto, P. A.; Verkhivker, G. M. Proteins 1997, 28, 313. doi: 10.1002/(SICI)1097-0134(199707)28:3<313::AID-PROT2>3.0.CO;2-D
(50) Pujadas, G.; Palau, J. Protein Sci. 2001, 10, 1645. doi: 10.1110/ps.8201

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Interaction Mechanisms of Inhibitors of Glucoamylase by Molecular Dynamics Simulations and Free Energy Calculations

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