头孢西丁与金属β-内酰胺酶BcⅡ相互作用的光谱分析及分子动力学模拟

doi:10.7503/cjcu20170702

摘要/Abstract

摘要：

利用同步荧光光谱、三维荧光光谱及分子动力学模拟方法研究了β-内酰胺类抗生素头孢西丁(CFX)与金属β-内酰胺酶BcⅡ之间的相互作用机制. 荧光光谱分析表明, CFX与BcⅡ在结合过程中可诱导BcⅡ构象发生改变. 分子动力学模拟结果表明, 上述构象变化是BcⅡ在CFX的诱导下通过改变其结合口袋附近Loop 构象, 使二者达到完美匹配的一个诱导契合过程, 并最终形成一个洞穴状疏水口袋以利于CFX的结合及催化水解.

关键词: 金属β-内酰胺酶;, 头孢西丁, 相互作用, 荧光光谱, 分子动力学模拟

Abstract:

The interaction mechanism between cefoxitin(CFX) and metal β-lactamase BcⅡ was studied by synchronous fluorescence spectroscopy, three-dimensional fluorescence spectroscopy and molecular dynamics simulation. The results of fluorescence spectra show that CFX could induce the conformation changes of BcⅡ during their binding. The simulation results show that the conformational change of BcⅡ is an induction-fit process. Under the induction of CFX, the loops near the binding pocket of BcⅡ match perfectly with the substrate by changing their conformation, and eventually form a cave-like hydrophobic pocket to facilitate the binding process and catalyze hydrolysis. This study may provide some valuable reference and inspiration for the development of new antibiotics to resist the hydrolysis of metal β-lactamases.

Key words: Metal β-lactamase;, Cefoxitin, Interaction, Fluorescence spectroscopy, Molecular dynamics simulation

中图分类号:

O641

TrendMD:

史鹏辉, 边六交. 头孢西丁与金属β-内酰胺酶BcⅡ相互作用的光谱分析及分子动力学模拟. 高等学校化学学报, 2018, 39(5): 971.

SHI Penghui,BIAN Liujiao. Mechanism Study on the Interaction Between Cefoxitin and Metal β-Lactamase BcⅡ Based on Spectroscopic Methods and Computional Simulations^†. Chem. J. Chinese Universities, 2018, 39(5): 971.

图/表 9

Fig.1 Synchronous fluorescence spectra of BcⅡ-CFX complex Note：n(CFX)/n(BcⅡ): a—f. 0, 25, 50, 100, 150, 200; c(BcⅡ)=1.0×10-6 mol/L, Δλ=60 nm, T=277 K.

Fig.2 Three-dimensional fluorescence spectra of BcⅡ(A) and BcⅡ-CFX complex(B) Note：c(BcⅡ)=1.0×10-6 mol/L, c(CFX)=0 for (A) and 2×10-4 mol/L for (B), T=277 K.

Fig.3 RMSD of the backbone atoms of BcⅡ-CFX complex in 20 ns MD simulation

Fig.4 Snapshot of active site residues Note：Binding mode of BcⅡ-CFX complex obtained after MD simulation.

Fig.5 RMSF of the backbone atoms of apo BcⅡ and BcⅡ-CFX complex

Fig.6 RMSD of loop of BcⅡ-CFX complex in 20 ns MD simulation

Fig.7 Molecular surface of BcⅡ-CFX complex before(A) and after(B) dynamic equilibrium

Fig.8 Molecular surface of BcⅡ-CFX complex in 20 ns MD simulation Note：(A)—(J) correspond to average structure of BcⅡ-CFX complex in 0—2, 2—4, 4—6, 6—8, 8—10, 10—12, 12—14, 14—16, 16—18 and 18—20 ns, respectively; Loop 1: green; Loop 2: blue; CFX are not shown.

Fig.9 Distance of Phe28 to Asn174 along the simulation trajectories for BcⅡ-CFX complex

参考文献 29

[1]	Walsh T.R., Toleman M. A., Poirel L., Nordmann P., Clin. Microbiol. Rev., 2005, 18(2), 306—325
[2]	Helfand M.S., Bonomo R. A., Curr. Drug Targets Infect. Disord., 2003, 3(1), 9—23
[3]	Ambler R.P., Phil. Trans. Roy. Soc. Ser. B, 1980, 289(1036), 321—331
[4]	Palzkill T., Ann. N. Y. Acad. Sci., 2013, 1277, 91—104
[5]	Kumarasamy K.K., Toleman M. A., Walsh T. R., Bagaria J., Butt F., Balakrishnan R., Chaudhary U., Doumith M., Giske C. G., Irfan S., Krishnan P., Kumar A. V., Maharjan S., Mushtaq S., Noorie T., Paterson D. L., Pearson A., Perry C., Pike R., Rao B., Ray U., Sarma J. B., Sharma M., Sheridan E., Thirunarayan M. A., Turton J., Upadhyay S., Warner M., Welfare W., Livermore D. M., Woodford N., Lancet Infect. Dis., 2010, 10(9), 597—602
[6]	Yong D., Toleman M.A., Giske C. G., Cho H. S., Sundman K., Lee K., Walsh T. R., Antimicrob. Agents Chemother., 2009, 53(12), 5046—5054
[7]	Karsisiotis A.I., Damblon C. F., Roberts G. C. K., Metallomics, 2014, 6(7), 1181—1197
[8]	Widmann M., Pleiss J., Oelschlaeger P., Antimicrob. Agents Chemother., 2012, 56(7), 3481—3491
[9]	Pleiss J., The Metallo-β-Lactamase Engineering Database(MBLED),
[10]	Dong L., Yi Z.S., Wu Z. W., Wang H. Y., Zhang A. Q., Chem. [J]. Chinese Universities, 2015, 36(3), 516—522
	(董露, 易忠胜, 伍智蔚, 王海洋, 张爱茜. 高等学校化学学报, 2015, 36(3), 516—522)
[11]	Song S.M., Ma X. W., Zhou Y. H., Xu M. T., Shuang S. M., Dong C., Chem. Res. Chinese Universities, 2016, 32(2), 172—177
[12]	Li X., Li C.H., Jiang J. H., Gu H. W., Wei D. L., Ye L. J., HuJ. L., Xiao S. X., Zhang H., Li X., Li Q. G., Chem. Res. Chinese Universities, 2017, 33(2), 166—171
[13]	Senapati S., Bui J.M., McCammon J. A., [J]. Med. Chem., 2005, 48(26), 8155—8162
[14]	Stella L., Nicotra M., Ricci G., Rosato N., Di Iorio E.E., Proteins: Structure, Function, and Bioinformatics, 1999, 37(1), 1—9
[15]	Shi P.H., Qiao P., Zhang Y. L., Li S. H., Feng X., Bian L. J., [J]. Pharm. Biomed. Anal., 2017, 138, 206—214
[16]	Moali C., Anne C., Lamotte-Brasseur J., Groslambert S., Devreese B., Van Beeumen J., Galleni M., Frère J.M., Chem. Biol., 2003, 10(4), 319—329
[17]	Sanner M.F., [J]. Mol. Graph. Model., 1999, 17(1), 57—61
[18]	Huey R., Morris G.M., Olson A. J., Goodsell D. S., [J]. Comput. Chem., 2007, 28(6), 1145—1152
[19]	Case D.A., Berryman J. T., Betz R. M., Cerutti D. S., CheathamⅢ T. E., Darden T. A., Duke R. E., Giese T. J., Gohlke H., Goetz A. W., Homeyer N., Izadi S., Janowski P., Kaus J., Kovalenko A., Lee T. S., LeGrand S., Li P., Luchko T., Luo R., Madej B., Merz K. M., Monard G., Needham P., Nguyen H., Nguyen H. T., Omelyan I., Onufriev A., Roe D. R., Roitberg A., Salomon-Ferrer R., Simmerling C. L., Smith W., Swails J., Walker R. C., Wang J., Wolf R. M., Wu R., York D. M., Kollman P. A., AMBER 2015, University of California, San Francisco, 2015
[20]	Maier J.A., Martinez C., Kasavajhala K., Wickstrom L., Hauser K. E., Simmerling C., [J]. Chem. Theory Comput., 2015, 11(8), 3696—3713
[21]	Bayly C.I., Cieplak P., Cornell W., Kollman P. A., [J]. Phys. Chem., 1993, 97(40), 10269—10280
[22]	Pang Y.P., Proteins, 2001, 45(3), 183—189
[23]	Pang Y.P., Xu K., Yazal J. E., Prendergast F. G., Protein Sci., 2000, 9(10), 1857—1865
[24]	Meng E.C., Pettersen E. F., Couch G. S., Huang C. C., Ferrin T. E., BMC Bioinformatics, 2006, 7(1), 339—349
[25]	Dal Peraro M., Vila A.J., Carloni P., Klein M. L., [J]. Am. Chem. Soc., 2007, 129(10), 2808—2816
[26]	Zheng M., Xu D., J. Phys. Chem. B, 2013, 117(39), 11596—11607
[27]	Xu D., Guo H., Cui Q., [J]. Am. Chem. Soc., 2007, 129(35), 10814—10822
[28]	Karsisiotis A.I., Damblon C. F., Roberts G. C., Biochem. J., 2013, 456(3), 397—407
[29]	Valdez C.E., Sparta M., Alexandrova A. N., [J]. Chem. Theory Comput., 2012, 9(1), 730—737