York Centre for Complex Systems Analysis (YCCSA), University of York, York, UK.
Cell Cycle. 2013 Feb 1;12(3):394-404. doi: 10.4161/cc.23511. Epub 2013 Jan 16.
The interaction of p53 with its regulators MDM2 and MDMX plays a major role in regulating the cell cycle. Inhibition of this interaction has become an important therapeutic strategy in oncology. Although MDM2 and MDMX share a very high degree of sequence/structural similarity, the small-molecule inhibitor nutlin appears to be an efficient inhibitor only of the p53-MDM2 interaction. Here, we investigate the mechanism of interaction of nutlin with these two proteins and contrast it with that of p53 using Brownian dynamics simulations. In contrast to earlier attempts to examine the bound states of the partners, here we locate initial reaction events in these interactions by identifying the regions of space around MDM2/MDMX, where p53/nutlin experience associative encounters with prolonged residence times relative to that in bulk solution. We find that the initial interaction of p53 with MDM2 is long-lived relative to nutlin, but, unlike nutlin, it takes place at the N- and C termini of the MDM2 protein, away from the binding site, suggestive of an allosteric mechanism of action. In contrast, nutlin initially interacts with MDM2 directly at the clefts of the binding site. The interaction of nutlin with MDMX, however, is very short-lived compared with MDM2 and does not show such direct initial interactions with the binding site. Comparison of the topology of the electrostatic potentials of MDM2 and MDMX and the locations of the initial encounters with p53/nutlin in tandem with structure-based sequence alignment revealed that the origin of the diminished activity of nutlin toward MDMX relative to MDM2 may stem partly from the differing topologies of the electrostatic potentials of the two proteins. Glu25 and Lys51 residues underpin these topological differences and appear to collectively play a key role in channelling nutlin directly toward the binding site on the MDM2 surface and are absent in MDMX. The results, therefore, provide new insight into the mechanism of p53/nutlin interactions with MDM2 and MDMX and could potentially have a broader impact on anticancer drug optimization strategies.
p53 与其调节因子 MDM2 和 MDMX 的相互作用在调节细胞周期中起着重要作用。抑制这种相互作用已成为肿瘤学中一种重要的治疗策略。尽管 MDM2 和 MDMX 具有非常高的序列/结构相似性，但小分子抑制剂 nutlin 似乎仅能有效地抑制 p53-MDM2 相互作用。在这里，我们使用布朗动力学模拟研究了 nutlin 与这两种蛋白相互作用的机制，并将其与 p53 进行了对比。与早期尝试检查这些伙伴的结合状态不同，我们通过确定 MDM2/MDMX 周围的空间区域，识别出 p53/nutlin 与之具有延长的停留时间的缔合相遇的区域，从而定位了这些相互作用中的初始反应事件。我们发现，p53 与 MDM2 的初始相互作用比 nutlin 更持久，但与 nutlin 不同，它发生在 MDM2 蛋白的 N 端和 C 端，远离结合位点，提示存在别构作用机制。相比之下，nutlin 最初直接在结合位点的裂隙处与 MDM2 相互作用。然而，nutlin 与 MDMX 的相互作用非常短暂，与 MDM2 相比，它没有与结合位点直接发生初始相互作用。与结构基序比对相结合，比较 MDM2 和 MDMX 的静电势拓扑和与 p53/nutlin 的初始相互作用的位置表明，与 MDM2 相比，nutlin 对 MDMX 的活性降低可能部分源于两种蛋白静电势拓扑的不同。Glu25 和 Lys51 残基构成了这些拓扑差异的基础，并且似乎共同在将 nutlin 直接引导到 MDM2 表面的结合位点方面发挥关键作用，而在 MDMX 中则不存在。因此，这些结果为 p53/nutlin 与 MDM2 和 MDMX 的相互作用机制提供了新的见解，并可能对癌症药物优化策略产生更广泛的影响。
