Division of Bioinformatics , Bose Institute , P-1/12 C.I.T. Scheme VII M , Kolkata 700054 , India.
J Chem Inf Model. 2019 May 28;59(5):2274-2286. doi: 10.1021/acs.jcim.8b00538. Epub 2018 Dec 24.
The α,β-tubulin is the building block of microtubules, which is associated with and dissociated from the microtubular architecture complying with the dynamic instability of the microtubules. This dynamic instability has a direct relation with the spindle formation by the microtubules and cell division kinetics. E7010 is one of the promising ligands of an α,β-tubulin protein that binds at the core of this protein and can diminish the protein's ability to fit to a growing microtubule, thus frustrating cell division. Although X-ray crystallography has reported a specific binding conformation of E7010 in PDB, molecular dynamics (MD) simulations have revealed two other conformational states of the ligand capable of binding to tubulin with stabilities close to that state reported in PDB. To rationalize this quasidegeneracy of ligand binding modes, MD simulations have further revealed that the understanding of the mechanism of E7010-tubulin binding remains incomplete unless the role of water molecules to bridge this interaction is taken into consideration, a very critical insight that was not visible from the PDB structure. Further, these water molecules differ from the standard examples of "bridging" waters which generally exist as isolated water molecules between the receptor and the ligand. In the present case, the water molecules sandwiched between ligand and protein, sequestered from the bulk solvent, integrate with each other by an H-bonds network forming a group, which appear as microclusters of water. The structural packing with the ligand binding pocket and the bridging interactions between protein and ligand take place through such clusters. The presence of this microcluster of water is not just cosmetic, instead they have a crucial impact on the ligand binding thermodynamics. Only with the explicit consideration of these water clusters in the binding energy calculations (MMGBSA) is the stability of the native mode of ligand binding reported in PDB rationalized. At the same time, two other binding modes are elucidated to be quasi-degenerate with the native state and that indicates the further possibility in gaining more entropic stabilization of the complex. The role of such "bridging" water clusters to enhance the protein-ligand interaction will be insightful for designing the next generation prospective compounds in the field of cancer therapeutics.
α、β-微管蛋白是微管的结构单元，它与微管结构相关联并与之脱离，符合微管的动态不稳定性。这种动态不稳定性与微管的纺锤体形成和细胞分裂动力学直接相关。E7010 是一种有前途的 α、β-微管蛋白配体，它结合在该蛋白的核心部位，可以降低该蛋白与生长中的微管结合的能力，从而阻碍细胞分裂。尽管 X 射线晶体学已经在 PDB 中报告了 E7010 的特定结合构象，但分子动力学（MD）模拟揭示了配体的另外两种构象状态，它们能够与微管蛋白结合，稳定性接近 PDB 中报告的状态。为了使配体结合模式的这种准简并合理化，MD 模拟进一步表明，除非考虑到水分子在桥接这种相互作用中的作用，否则对 E7010-微管蛋白结合机制的理解仍然不完整，这是一个非常关键的见解，从 PDB 结构中无法看出。此外，这些水分子与通常作为受体和配体之间孤立水分子存在的“桥接”水的标准例子不同。在这种情况下，夹在配体和蛋白质之间的水分子被隔离在溶剂之外，通过氢键网络相互整合形成一个群，这些水分子表现为微团簇。配体结合口袋的结构包装和蛋白质与配体之间的桥接相互作用通过这些簇发生。这些水分子的存在不仅仅是表面上的，相反，它们对配体结合热力学有至关重要的影响。只有在结合能计算（MMGBSA）中明确考虑这些水分子簇，才能合理化 PDB 中报告的配体结合的天然模式的稳定性。同时，还阐明了另外两种结合模式与天然状态准简并，这表明复杂体系的熵稳定性有进一步提高的可能。这种“桥接”水分子簇增强蛋白质-配体相互作用的作用将为设计癌症治疗领域的下一代前瞻性化合物提供有价值的见解。
