Microtubules, composed of α- and β-tubulin subunits are crucial for cell division with their dynamic tissue-specificity which is dictated by expression of isotypes. These isotypes differ in carboxy-terminal tails (CTTs), rich in negatively charged acidic residues in addition to the differences in the composition of active site residues. 2-Methoxy estradiol (2-ME) is the first antimicrotubule agent that showed less affinity toward hemopoietic-specific β1 isotype consequently preventing myelosuppression toxicity. The present study focuses on the MD-directed conformational analysis of 2-ME and estimation of its binding affinity in the colchicine binding pocket of various β-tubulin isotypes combined with the α-tubulin isotype, α1B. AlphaFold 2.0 was used to predict the 3D structure of phylogenetically divergent human β-tubulin isotypes in dimer form with α1B. The dimeric complexes were subjected to induced-fit docking with 2-ME. The statistical analysis of docking showed differences in the binding characteristics of 2-ME with different isotypes. The replicas of atom-based molecular dynamic simulations of the best conformation of 2-ME provided insights into the molecular-level details of its binding pattern across the isotypes. Furthermore, the MM/GBSA analyses revealed the specific binding energy profile of 2-ME in β-tubulin isotypes. It also highlighed, 2-ME exhibits the lowest binding affinity toward the β1 isotype as supported by experimental study. The present study may offer useful information for designing next-generation antimicrotubule agents that are more specific and less toxic.

中文翻译：

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瞄准癌症的宿敌：从分子动力学角度揭示 2-甲氧基雌二醇与人类 β-微管蛋白同种型的特异性结合性质


由 α- 和 β- 微管蛋白亚基组成的微管对于细胞分裂至关重要，其动态组织特异性由同种型的表达决定。这些同种型的不同之处在于羧基末端尾部 (CTT)，除了活性位点残基的组成不同之外，还富含带负电的酸性残基。 2-甲氧基雌二醇 (2-ME) 是第一种抗微管药物，它对造血特异性 β1 同种型的亲和力较低，因此可防止骨髓抑制毒性。本研究的重点是 2-ME 的 MD 定向构象分析，并评估其在各种 β-微管蛋白同种型与 α-微管蛋白同种型 α1B 的秋水仙碱结合袋中的结合亲和力。 AlphaFold 2.0 用于预测系统发育上不同的人类 β-微管蛋白同种型与 α1B 的二聚体形式的 3D 结构。将二聚体复合物与 2-ME 进行诱导拟合对接。对接统计分析显示2-ME与不同同种型的结合特征存在差异。 2-ME 最佳构象的基于原子的分子动力学模拟的复制品提供了对其跨同种型结合模式的分子水平细节的见解。此外，MM/GBSA 分析揭示了 2-ME 在 β-微管蛋白同种型中的特异性结合能谱。它还强调，根据实验研究的支持，2-ME 对 β1 同种型表现出最低的结合亲和力。本研究可能为设计更具特异性和毒性更低的下一代抗微管药物提供有用的信息。