Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
ChemMedChem. 2018 Jan 8;13(1):20-24. doi: 10.1002/cmdc.201700530. Epub 2017 Nov 23.
Regulation of microtubule assembly by antimitotic agents is a potential therapeutic strategy for the treatment of cancer, parasite infections, and neurodegenerative diseases. One of these agents is nocodazole (NZ), which inhibits microtubule polymerization by binding to β-tubulin. NZ was recently co-crystallized in Gallus gallus tubulin, providing new information about the features of interaction for ligand recognition and stability. In this work, we used state-of-the-art computational approaches to evaluate the protonation effects of titratable residues and the presence of water molecules in the binding of NZ. Analysis of protonation states showed that residue E198 has the largest modification in its pK value. The resulting E198 pK value, calculated with pH-REMD methodology (pK =6.21), was higher than the isolated E amino acid (pK =4.25), thus being more likely to be found in its protonated state at the binding site. Moreover, we identified an interaction between a water molecule and C239 and G235 as essential for NZ binding. Our results suggest that the protonation state of E198 and the structural water molecules play key roles in the binding of NZ to β-tubulin.
抗有丝分裂药物调节微管组装是治疗癌症、寄生虫感染和神经退行性疾病的潜在治疗策略。其中一种药物是诺考达唑（NZ），它通过与β-微管蛋白结合来抑制微管聚合。最近 NZ 与鸡β-微管蛋白共结晶，为配体识别和稳定性的相互作用特征提供了新的信息。在这项工作中，我们使用了最先进的计算方法来评估可质子化残基的质子化效应和 NZ 结合中水分子的存在。质子化状态分析表明，残基 E198 的 pK 值变化最大。用 pH-REMD 方法计算得到的 E198 pK 值（pK =6.21）高于分离的 E 氨基酸（pK =4.25），因此在结合部位更有可能处于质子化状态。此外，我们发现一个水分子与 C239 和 G235 之间的相互作用对于 NZ 与β-微管蛋白的结合是必不可少的。我们的结果表明，E198 的质子化状态和结构水分子在 NZ 与β-微管蛋白的结合中起关键作用。
