Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay
Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay
复制标题
DOI：
10.1021/acs.jcim.6b00672
复制
发表时间：
2017-05-01
影响因子：
5.6
通讯作者：
Xie, Xiangqun
中科院分区：
文献类型：
--
作者：
Chen, Si;Feng, Zhiwei;Xie, Xiangqun
肿瘤坏死因子α（TNF-α）在多种疾病中过表达，已成为自身免疫性疾病的有效治疗靶点。目前用于靶向TNF-α的所有治疗剂都是生物大分子，已经报道了有限数量的TNF-α化学抑制剂，这使得迫切需要鉴定小分子替代品。最近的研究主要集中在鉴定直接结合TNF-α或TNF受体-1（TNFR 1）、抑制TNF-α和TNFR 1之间的相互作用和/或调节相关信号通路的小分子。在这项研究中，我们结合了生物物理和细胞为基础的分析，以确定新的拮抗剂结合TNF-α或TNFR 1的计算机方法。应用药效团模型过滤和分子对接来鉴定潜在的TNF-α拮抗剂。关于TNFR 1，我们构建了一个三维模型的TNF-α TNFR 1复合物，并进行了分子动力学模拟样品的构象。已报道在TNF-α TNFR 1复合物中起重要作用的TNF-α中的残基被去除以形成口袋，用于进一步虚拟筛选TNFR 1结合配体。我们获得了20个虚拟命中，并使用基于表面等离子体共振的测定对其进行了测试，这导致了一种与TNFR 1结合的配体和四种具有不同支架的配体与TNF-α结合。T1和R1是两种最具活性的化合物，其对TNF-α和TNFR 1的Kd值分别为H和16 μ M，显示出与已知拮抗剂相似的活性。进一步的基于细胞的测定也表明，与已知的TNF-α拮抗剂C87相比，T1和R1具有相似的活性。我们的工作不仅产生了几种具有新型支架的TNF-α和TNFR 1拮抗剂，用于进一步的结构优化，而且还展示了我们在基于TNF-α和TNFR 1的药物发现中的计算机方法的能力。
Tumor necrosis factor alpha (TNF-alpha) is overexpressed in various diseases, and it has been a validated therapeutic target for autoimmune diseases. All therapeutics currently used to target TNF-alpha are biomacromolecules, limited numbers of TNF-alpha chemical inhibitors have been reported, which makes the identification of small-molecule alternatives an urgent need. Recent studies have mainly focused on identifying small molecules that directly bind to TNF-alpha or TNF receptor-1 (TNFR1), inhibit the interaction between TNF-alpha and TNFR1, and/or regulate related signaling pathways. In this study, we combined in silico methods with biophysical and cell-based assays to identify novel antagonists that bind to TNF-alpha or TNFR1. Pharmacophore model filtering and molecular docking were applied to identify potential TNF-alpha antagonists. In regard to TNFR1, we constructed a threedimensional model of the TNF-alpha TNFR1 complex and carried out molecular dynamics simulations to sample the conformations. The residues in TNF-alpha that have been reported to play important roles in the TNF-alpha TNFR1 complex were removed to form a pocket for further virtual screening of TNFR1-binding ligands. We obtained 20 virtual hits and tested them using surface plasmon resonance-based assays, which resulted in one ligand that binds to TNFR1 and four ligands with different scaffolds that bind to TNF-alpha. T1 and R1, the two most active compounds with Kd values of H and 16 uM for TNF-alpha and TNFR1, respectively, showed activities similar to those of known antagonists. Further cell-based assays also demonstrated that T1 and R1 have similar activities compared to the known TNF-alpha antagonist C87. Our work has not only produced several TNF-alpha and TNFR1 antagonists with novel scaffolds for further structural optimization but also showcases the power of our in silico methods for TNF-alpha- and TNFR1-based drug discovery.