NMR spectroscopy and computational analysis of interaction between Serratia marcescens chitinase B and a dipeptide derived from natural-product cyclopentapeptide chitinase inhibitor argifin
NMR spectroscopy and computational analysis of interaction between Serratia marcescens chitinase B and a dipeptide derived from natural-product cyclopentapeptide chitinase inhibitor argifin
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粘质沙雷氏菌几丁质酶 B 与天然产物环五肽几丁质酶抑制剂精氨酸衍生的二肽之间相互作用的核磁共振波谱和计算分析
DOI：
10.1016/j.bmc.2010.06.093
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发表时间：
2010
期刊：
影响因子：
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通讯作者：
Shuichi Hirono
中科院分区：
文献类型：
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作者：
Hiroaki Gouda;Toshiaki Sunazuka;Tomoyasu Hirose;Kanami Iguchi;Noriyuki Yamaotsu;Akihiro Sugawara;Yoshihiko Noguchi;Yoshifumi Saito;Tsuyoshi Yamamoto;Takeshi Watanabe;Kazuro Shiomi;Satoshi Omura;Shuichi Hirono
N-乙酰基-Arg{Nω-（N-甲基氨基甲酰基）}-N-甲基-苯丙氨酸（2）是天然产物环肽几丁质酶抑制剂argifin（1）的一部分，它对粘质沙雷氏菌几丁质酶B（SmChiB）有抑制作用，其半数抑制浓度（IC 50）为3.7μM。尽管2的大小相对较小，但其抑制活性与1相当（IC 50 =6.4μM）。为了阐明这一有趣现象的基础，我们研究了2和SmChiB之间的相互作用，使用核磁共振光谱和计算方法相结合。转移核Overhauser效应（TRNOE）实验获得的SmChiB结合构象2的结构信息。2和SmChiB的结合模式由我们实验室提出的新的分子对接方法建模，该方法可以明确地考虑蛋白质-配体界面中水介导的氢键相互作用。在所得模型中2的SmChiB结合构象满足来自TRNOE实验的所有质子-质子距离约束，表明我们的2-SmChiB复合物的模型结构是合理的。分子动力学（MD）模拟检查了所得复合物结构的稳定性，并表明2与SmChiB的结合方式与argifin-SmChiB复合物晶体结构中1的Nω-（N-甲基氨基甲酰基）-Arg（1）和N-甲基-Phe（2）观察到的结合模式相似。最后，1和2与SmChiB的结合自由能通过分子力学Poisson-Boltzmann表面积（MM-PBSA）方法使用MD轨迹估计。MM-PBSA计算表明，1和2以相似的亲和力与SmChiB结合，这与它们的实验IC 50值一致。能量分析表明，2与SmChiB的货车德瓦尔斯相互作用远小于1，但完全被溶质熵和总静电分量的更有利贡献所补偿.改进的总静电分量来自更有利的静电相互作用。因此，我们得出结论，从静电的角度来看，二肽2也比1更好地针对SmChiB进行了优化。
The dipeptide N-acetyl-Arg{Nω-(N-methylcarbamoyl)}-N-methyl-Phe(2), which is a part of the natural-product cyclopentapeptide chitinase inhibitor argifin (1), inhibits chitinase B from Serratia marcescens (SmChiB) with a half-maximal inhibitory concentration (IC50) of 3.7μM. Despite the relatively small size of 2, its inhibitory activity is comparable with that of 1 (IC50=6.4μM). To elucidate the basis for this interesting phenomenon, we investigated the interaction between 2 and SmChiB using a combination of nuclear magnetic resonance spectroscopy and computational methods. The transferred nuclear Overhauser effect (TRNOE) experiment obtained structural information on the SmChiB-bound conformation of 2. The binding mode of 2 and SmChiB was modeled by the novel molecular-docking approach proposed in our laboratory, which can explicitly consider water-mediated hydrogen-bonding interactions in protein-ligand interfaces. The SmChiB-bound conformation of 2 in the resulting model satisfied all proton-proton distance constraints derived from the TRNOE experiment, indicating that our model structure of the 2-SmChiB complex is reasonable. A molecular dynamics (MD) simulation examined the stability of the resultant complex structure and suggested that 2 binds to SmChiB in a similar fashion to the binding mode observed for Nω-(N-methylcarbamoyl)-Arg(1) and N-methyl-Phe(2) of 1 in the crystal structure of the argifin–SmChiB complex. Finally, the binding free energies of 1 and 2 with SmChiB were estimated by the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method using the MD trajectory. The MM-PBSA calculation suggested that both 1 and 2 bind to SmChiB with similar affinities, which is consistent with their experimental IC50values. Energetic analysis revealed that the van der Waals interaction of 2 with SmChiB is much less than that of 1, but is completely compensated by the more favorable contribution of solute entropy and the total electrostatic component. The improved total electrostatic component was derived from more favorable electrostatic interactions. Therefore, we conclude that dipeptide 2 was also better optimized against SmChiB than 1 in an electrostatic point of view.