Du Qingqing, Qian Yan, Xue Weiwei
Department of Pharmacy, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, China.
Front Mol Biosci. 2020 Mar 4;7:29. doi: 10.3389/fmolb.2020.00029. eCollection 2020.
Therapeutics targeting cytokines such as the oncostatin M (OSM)-mediated inflammation represent a potential strategy for the treatment of inflammatory bowel disease (IBD). Despite the investigation of the specific role of the interactions between OSM and the receptor (OSMR) in IBD pathogenesis, the 3D structure of the OSM-OSMR complex remains elusive. In this work, the interaction mode between OSM and OSMR at atomic level was predicted by computational simulation approach. The interaction domain of the OSMR was built with the homology modeling method. The near-native structure of the OSM-OSMR complex was obtained by docking, and long-time scale molecular dynamics (MD) simulation in an explicit solvent was further performed to sample the conformations when OSM binds to the OSMR. After getting the equilibrated states of the simulation system, per-residue energy contribution was calculated to characterize the important residues for the OSM-OSMR complex formation. Based on these important residues, eight residues (OSM: Arg100, Leu103, Phe160, and Gln161; OSMR: Tyr214, Ser223, Asp262, and Trp267) were identified as the "hot spots" through computational alanine mutagenesis analysis and verified by additional MD simulation of R100A (one of the identified "hotspots") mutant. Moreover, six cavities were detected at the OSM-OSMR interface through the FTMap analysis, and they were suggested as important binding sites. The predicted 3D structure of the OSM-OSMR complex and the identified "hot spots" constituting the core of the binding interface provide helpful information in understanding the OSM-OSMR interactions, and the detected sites serve as promising targets in designing small molecules to block the interactions.
靶向细胞因子(如抑瘤素M(OSM)介导的炎症)的疗法是治疗炎症性肠病(IBD)的一种潜在策略。尽管对OSM与受体(OSMR)之间相互作用在IBD发病机制中的具体作用进行了研究,但OSM - OSMR复合物的三维结构仍不清楚。在这项工作中,通过计算模拟方法预测了OSM与OSMR在原子水平上的相互作用模式。采用同源建模方法构建了OSMR的相互作用结构域。通过对接获得了OSM - OSMR复合物的近天然结构,并在显式溶剂中进行了长时间尺度的分子动力学(MD)模拟,以对OSM与OSMR结合时的构象进行采样。在获得模拟系统的平衡态后,计算每个残基的能量贡献以表征形成OSM - OSMR复合物的重要残基。基于这些重要残基,通过计算丙氨酸诱变分析确定了八个残基(OSM:Arg100、Leu103、Phe160和Gln161;OSMR:Tyr214、Ser223、Asp262和Trp267)为“热点”,并通过对R100A(已鉴定的“热点”之一)突变体的额外MD模拟进行了验证。此外,通过FTMap分析在OSM - OSMR界面检测到六个空腔,它们被认为是重要的结合位点。预测的OSM - OSMR复合物三维结构以及构成结合界面核心的已鉴定“热点”为理解OSM - OSMR相互作用提供了有用信息,并且检测到的位点有望成为设计小分子以阻断相互作用的靶点。