Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
PLoS Comput Biol. 2011 Jun;7(6):e1002083. doi: 10.1371/journal.pcbi.1002083. Epub 2011 Jun 23.
P-glycoprotein (P-gp) is an ATP-dependent transport protein that is selectively expressed at entry points of xenobiotics where, acting as an efflux pump, it prevents their entering sensitive organs. The protein also plays a key role in the absorption and blood-brain barrier penetration of many drugs, while its overexpression in cancer cells has been linked to multidrug resistance in tumors. The recent publication of the mouse P-gp crystal structure revealed a large and hydrophobic binding cavity with no clearly defined sub-sites that supports an "induced-fit" ligand binding model. We employed flexible receptor docking to develop a new prediction algorithm for P-gp binding specificity. We tested the ability of this method to differentiate between binders and nonbinders of P-gp using consistently measured experimental data from P-gp efflux and calcein-inhibition assays. We also subjected the model to a blind test on a series of peptidic cysteine protease inhibitors, confirming the ability to predict compounds more likely to be P-gp substrates. Finally, we used the method to predict cellular metabolites that may be P-gp substrates. Overall, our results suggest that many P-gp substrates bind deeper in the cavity than the cyclic peptide in the crystal structure and that specificity in P-gp is better understood in terms of physicochemical properties of the ligands (and the binding site), rather than being defined by specific sub-sites.
P-糖蛋白（P-gp）是一种 ATP 依赖性转运蛋白，选择性地表达于外源性物质进入的敏感器官的入口处，作为外排泵，它可防止这些物质进入敏感器官。该蛋白在许多药物的吸收和血脑屏障穿透中也起着关键作用，而其在癌细胞中的过度表达与肿瘤的多药耐药性有关。最近发表的小鼠 P-gp 晶体结构揭示了一个大而疏水的结合腔，没有明确界定的亚部位，支持“诱导契合”配体结合模型。我们采用了柔性受体对接来开发一种新的 P-gp 结合特异性预测算法。我们使用 P-gp 外排和钙黄绿素抑制测定中一致测量的实验数据来测试该方法区分 P-gp 结合物和非结合物的能力。我们还在一系列肽类半胱氨酸蛋白酶抑制剂上对模型进行了盲测，证实了预测更有可能成为 P-gp 底物的化合物的能力。最后，我们使用该方法预测了可能是 P-gp 底物的细胞代谢物。总的来说，我们的结果表明，许多 P-gp 底物在结合腔内的结合位置比晶体结构中的环肽更深，并且 P-gp 的特异性在配体（和结合部位）的物理化学性质方面得到了更好的理解，而不是由特定的亚部位来定义。
