人类NEET蛋白,例如NAF-1和mitoneet,是同型二聚体,以三半胱氨酸和一个组氨酸配位的[2Fe-2S]簇表征的氧化还原铁硫蛋白。它们以氧化和还原状态存在。集群的异常释放与多种疾病有关,包括癌症和神经变性.从药物的角度来看,影响簇释放的配体的计算机辅助和基于结构的设计至关重要。不幸的是,到目前为止,实验结构信息仅限于一种配体/蛋白质复合物。这是与氧化的有丝分裂细胞结合的呋塞米的X射线结构。在这里,我们采用了增强的抽样方法,基于局部体积的元动力学,我们中的一些人开发的,鉴定呋塞米与溶液中人mitoNEET蛋白的结合状态。结合模式显示在X射线结构中鉴定的蛋白质表面上的相同浅结合袋内的高可变性。在不同的结合构象中,其中一个与晶体结构一致。由于存在晶体堆积相互作用,这种构象可能在后者中过度稳定,不存在于溶液中。计算的结合亲和力与实验数据相容。我们的方案可以以直接的方式用于针对该药学上重要的蛋白质家族的药物设计活动。
Human NEET proteins, such as NAF-1 and mitoNEET, are homodimeric, redox iron-sulfur proteins characterized by triple cysteine and one histidine-coordinated [2Fe-2S] cluster. They exist in an oxidized and reduced state. Abnormal release of the cluster is implicated in a variety of diseases, including cancer and neurodegeneration. The computer-aided and structure-based design of ligands affecting cluster release is of paramount importance from a pharmaceutical perspective. Unfortunately, experimental structural information so far is limited to only one ligand/protein complex. This is the X-ray structure of furosemide bound to oxidized mitoNEET. Here we employ an enhanced sampling approach, Localized Volume-based Metadynamics, developed by some of us, to identify binding poses of furosemide to human mitoNEET protein in solution. The binding modes show a high variability within the same shallow binding pocket on the protein surface identified in the X-ray structure. Among the different binding conformations, one of them is in agreement with the crystal structure\'s one. This conformation might have been overstabilized in the latter because of the presence of crystal packing interactions, absent in solution. The calculated binding affinity is compatible with experimental data. Our protocol can be used in a straightforward manner in drug design campaigns targeting this pharmaceutically important family of proteins.