Center for Bioinformatics, Saarbruecken, Germany.
J Mol Model. 2012 May;18(5):2031-42. doi: 10.1007/s00894-011-1217-y. Epub 2011 Aug 30.
Protein-protein interactions are abundant in signal transduction pathways and thus of crucial importance in the regulation of apoptosis. However, designing small-molecule inhibitors for these potential drug targets is very challenging as such proteins often lack well-defined binding pockets. An example for such an interaction is the binding of the anti-apoptotic BIR2 domain of XIAP to the pro-apoptotic caspase-3 that results in the survival of damaged cells. Although small-molecule inhibitors of this interaction have been identified, their exact binding sites on XIAP are not known as its crystal structures reveal no suitable pockets. Here, we apply our previously developed protocol for identifying transient binding pockets to XIAP-BIR2. Transient pockets were identified in snapshots taken during four different molecular dynamics simulations that started from the caspase-3:BIR2 complex or from the unbound BIR2 structure and used water or methanol as solvent. Clustering of these pockets revealed that surprisingly many pockets opened in the flexible linker region that is involved in caspase-3 binding. We docked three known inhibitors into these transient pockets and so determined five putative binding sites. In addition, by docking two inactive compounds of the same series, we show that this protocol is also able to distinguish between binders and nonbinders which was not possible when docking to the crystal structures. These findings represent a first step toward the understanding of the binding of small-molecule XIAP-BIR2 inhibitors on a molecular level and further highlight the importance of considering protein flexibility when designing small-molecule protein-protein interaction inhibitors.
蛋白质-蛋白质相互作用在信号转导途径中很丰富，因此对细胞凋亡的调控至关重要。然而，设计这些潜在药物靶点的小分子抑制剂非常具有挑战性，因为这些蛋白质通常缺乏明确的结合口袋。这种相互作用的一个例子是抗凋亡 BIR2 结构域的 XIAP 与促凋亡 caspase-3 的结合，导致受损细胞的存活。尽管已经鉴定出这种相互作用的小分子抑制剂，但由于其晶体结构没有合适的口袋，因此不知道它们在 XIAP 上的确切结合位点。在这里，我们应用我们之前开发的用于识别瞬态结合口袋的方案来研究 XIAP-BIR2。在从 caspase-3:BIR2 复合物或未结合的 BIR2 结构开始的四个不同分子动力学模拟中，瞬态口袋在快照中被识别出来，并使用水或甲醇作为溶剂。这些口袋的聚类表明，在涉及 caspase-3 结合的柔性连接区中，出乎意料地有许多口袋打开。我们将三种已知抑制剂对接入这些瞬态口袋中，从而确定了五个可能的结合位点。此外，通过对接同一系列的两种非活性化合物，我们表明该方案还能够区分结合物和非结合物，而对接晶体结构时则不可能。这些发现代表了在分子水平上理解小分子 XIAP-BIR2 抑制剂结合的第一步，进一步强调了在设计小分子蛋白质-蛋白质相互作用抑制剂时考虑蛋白质灵活性的重要性。
