Department of Basic Sciences, Touro University-California, Vallejo, California 94592, USA.
J Am Chem Soc. 2009 Mar 4;131(8):2821-3. doi: 10.1021/ja8094558.
The development of nonpeptide fusion inhibitors through rational drug design has been hampered by the limited accessibility of the gp41 coiled coil target, which is highly hydrophobic, and the absence of structural data defining details of small molecule interactions. Here we describe a new approach for obtaining structural information on small molecules bound in the hydrophobic pocket of gp41, using a paramagnetic probe peptide which binds adjacent to the pocket along an extended coiled coil. Ligand binding in the pocket leads to paramagnetic relaxation effects or pseudocontact shifts of ligand protons. These effects are distance and/or orientation dependent, permitting determination of ligand pose in the pocket. The method is demonstrated with a fast-exchanging ligand. Multiple measurements at different coiled coil and probe peptide ratios enabled accurate determination of the NMR parameters. Use of a labeled probe peptide stabilizes an otherwise aggregation-prone coiled coil and also enables modulation of the paramagnetic effect to study ligands of various affinities. Ultimately, this technique can provide essential information for structure-based design of nonpeptide fusion inhibitors.
通过合理药物设计开发非肽类融合抑制剂受到 gp41 卷曲螺旋靶标的有限可及性的阻碍，该靶标具有高度疏水性，并且缺乏定义小分子相互作用细节的结构数据。在这里，我们描述了一种使用与口袋相邻结合的顺磁探针肽获得结合在 gp41 疏水口袋中的小分子的结构信息的新方法。沿着扩展的卷曲螺旋。口袋中的配体结合导致顺磁弛豫效应或配体质子的赝接触位移。这些效应是距离和/或方向依赖性的，允许确定口袋中配体的姿势。该方法通过快速交换配体进行了演示。在不同的卷曲螺旋和探针肽比例下进行多次测量，可准确确定 NMR 参数。标记探针肽的使用稳定了原本易于聚集的卷曲螺旋，并且还能够调节顺磁效应以研究各种亲和力的配体。最终，该技术可以为非肽类融合抑制剂的基于结构的设计提供必要的信息。
