Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospitals for Children, Department of Surgery, 51 Blossom Street, Boston, MA 02114, United States.
J Mol Graph Model. 2011 Jun;29(7):965-73. doi: 10.1016/j.jmgm.2011.04.001. Epub 2011 Apr 13.
Ligands of the thiazolidinedione (TZD) class of compounds, pioglitazone (Actos™) and rosiglitazone (Avandia™) are currently approved for treatment of type 2 diabetes and are known to bind to the PPAR-γ nuclear receptor subtype. Recent evidence suggesting PPAR-γ independent action of the TZDs led to the discovery of a novel integral outer mitochondrial membrane protein, mitoNEET. In spite of the several reported X-ray crystal structures of the unbound form of mitoNEET, the location and nature of the mitoNEET ligand binding sites (LBS) remain unknown. In this study, a molecular blind docking (BD) method was used to discover potential mitoNEET LBS and novel ligands, utilizing the program AutoDock Vina (v 1.0.2). Validation of BD was performed on the PPAR-γ receptor (PDB ID: 1ZGY) with the test compound rosiglitazone, demonstrating that the binding conformation of rosiglitazone determined by AutoDock Vina matches well with that of the cocrystallized ligand (root mean square deviation of the heavy atoms 1.45Å). The locations and a general ligand binding interaction model for the LBS were determined, leading to the discovery of novel mitoNEET ligands. An in vitro fluorescence binding assay utilizing purified recombinant mitoNEET protein was used to determine the binding affinity of a predicted mitoNEET ligand, and the data obtained is in good agreement with AutoDock Vina results. The discovery of potential mitoNEET ligand binding sites and novel ligands, opens up the possibility for detailed structural studies of mitoNEET-ligand complexes, as well as rational design of novel ligands specifically targeted for mitoNEET.
噻唑烷二酮（TZD）类化合物的配体吡格列酮（Actos）和罗格列酮（Avandia）目前被批准用于治疗 2 型糖尿病，已知它们与 PPAR-γ 核受体亚型结合。最近有证据表明 TZDs 具有 PPAR-γ 非依赖性作用，这导致了一种新型完整的外线粒体膜蛋白，mitoNEET 的发现。尽管已经报道了 mitoNEET 未结合形式的几个 X 射线晶体结构，但 mitoNEET 配体结合位点（LBS）的位置和性质仍然未知。在这项研究中，使用分子盲目对接（BD）方法利用程序 AutoDock Vina（v1.0.2）发现潜在的 mitoNEET LBS 和新型配体。BD 的验证是在 PPAR-γ 受体（PDB ID：1ZGY）上进行的，测试化合物为罗格列酮，证明了 AutoDock Vina 确定的罗格列酮结合构象与共晶配体非常吻合（重原子的均方根偏差为 1.45Å）。确定了 LBS 的位置和一般配体结合相互作用模型，从而发现了新型的 mitoNEET 配体。利用纯化的重组 mitoNEET 蛋白进行体外荧光结合测定，用于测定预测的 mitoNEET 配体的结合亲和力，并且获得的数据与 AutoDock Vina 的结果非常吻合。潜在的 mitoNEET 配体结合位点和新型配体的发现，为 mitoNEET-配体复合物的详细结构研究以及针对 mitoNEET 的新型配体的合理设计开辟了可能性。
