Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule
Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule
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DOI：
10.1007/s10822-019-00208-w
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发表时间：
2019-07-01
影响因子：
3.5
通讯作者：
Gago, Federico
中科院分区：
文献类型：
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作者：
Sanchez-Murcia, Pedro A.;Mills, Alberto;Gago, Federico
许多天然产物以哺乳动物微管蛋白为靶标，但只有少数能形成共价键，从而不可逆转地影响微管功能。其中，赞帕内酯(ZMP)和塔卡洛内酯AJ(TAJ)脱颖而出，不仅因为它们是非常有效的抗肿瘤药物，而且因为它们与β-微管蛋白形成的加合物已经在原子细节上进行了结构表征。通过应用建模技术、分子轨道计算、分子动力学模拟和QM/MM混合方法，我们深入研究了His229和Asp226在β-微管蛋白紫杉烷结合部位与ZMP和Taj的1，2和1，4-加成反应。实验上无法接触的预共价络合物强烈表明，ZMP加合物的形成是以水为媒介的质子穿梭机制，以及Asp226的羧酸盐对TAJ中C22R，C23R环氧化物的C22进行直接亲核攻击。M-环对于原丝间的相互作用至关重要，在这两种类型的络合物中都被结构成一个短螺旋，这主要是由于Tyr283的苯酚环和Arg284的胍基的固定造成的。作为一个附带的好处，我们获得了证据支持在β-微管蛋白中Cys241和Cys356之间存在一个通常被忽视的分子内二硫键，该键有助于蛋白质致密性，并且在与紫杉烷和其他药物耐药相关的β(III)同型中不存在。
Many natural products target mammalian tubulin but only a few can form a covalent bond and hence irreversibly affect microtubule function. Among them, zampanolide (ZMP) and taccalonolide AJ (TAJ) stand out, not only because they are very potent antitumor agents but also because the adducts they form with beta-tubulin have been structurally characterized in atomic detail. By applying model building techniques, molecular orbital calculations, molecular dynamics simulations and hybrid QM/MM methods, we have gained insight into the 1,2- and 1,4-addition reactions of His229 and Asp226 to ZMP and TAJ, respectively, in the taxane-binding site of beta-tubulin. The experimentally inaccessible precovalent complexes strongly suggest a water-mediated proton shuttle mechanism for ZMP adduct formation and a direct nucleophilic attack by the carboxylate of Asp226 on C22 of the C22R,C23R epoxide in TAJ. The M-loop, which is crucially important for interprotofilament interactions, is structured into a short helix in both types of complexes, mostly as a consequence of the fixation of the phenol ring of Tyr283 and the guanidinium of Arg284. As a side benefit, we obtained evidence supporting the existence of a commonly neglected intramolecular disulfide bond between Cys241 and Cys356 in beta-tubulin that contributes to protein compactness and is absent in the beta(III) isotype associated with resistance to taxanes and other drugs.