Kyle D J, Chakravarty S, Sinsko J A, Stormann T M
Scios Nova Inc., Baltimore, Maryland 21224.
J Med Chem. 1994 Apr 29;37(9):1347-54. doi: 10.1021/jm00035a015.
A putative model of bradykinin bound to the rat B2 receptor was generated using a combination of homology modeling (from the known transmembrane structure of bacteriorhodopsin), energy minimization, molecular dynamics, and a two-stage conformational search as a docking simulation. Overall, the proposed bound ligand adopts a twisted "S" shape, wherein a C-terminal beta-turn is buried in the receptor just below the extracellular boundary of the cell membrane and the N-terminus is interacting with negatively charged residues in extracellular loop 3 of the receptor (most notably Asp268 and Asp286). Mutagenesis experiments describing mutations which result in both a loss of bradykinin affinity as well as those which have no effect on bradykinin affinity are in good agreement with the proposed structure. In short, the mutagenesis results and the computational simulations each point to the same region of the receptor as likely to bind bradykinin. A double mutation, predicted as being likely to have a dramatic effect on bradykinin binding affinity, was confirmed experimentally, adding some validation to the proposed complex. Moreover, a new pseudopeptide bradykinin receptor antagonist (D-Arg0-Arg1-[12-aminododecanoyl]2- Ser3-D-Tic4-Oic5-Arg6) was designed on the basis of the model, and found to have good receptor affinity. Speculation regarding other possible sites for mutagenesis are also described.
利用同源建模（基于已知的细菌视紫红质跨膜结构）、能量最小化、分子动力学以及作为对接模拟的两阶段构象搜索相结合的方法，构建了缓激肽与大鼠B2受体结合的推测模型。总体而言，所提出的结合配体呈扭曲的“S”形，其中C末端β-转角埋在细胞膜细胞外边界正下方的受体中，N末端与受体细胞外环3中的带负电荷残基相互作用（最显著的是Asp268和Asp286）。描述导致缓激肽亲和力丧失的突变以及对缓激肽亲和力无影响的突变的诱变实验与所提出的结构高度一致。简而言之，诱变结果和计算模拟均指向受体中可能结合缓激肽的同一区域。预测可能对缓激肽结合亲和力有显著影响的双突变经实验证实，为所提出的复合物增添了一些验证。此外，基于该模型设计了一种新的假肽缓激肽受体拮抗剂（D-Arg0-Arg1-[12-氨基十二烷酰基]2-Ser3-D-Tic4-Oic5-Arg6），并发现其具有良好的受体亲和力。还描述了关于其他可能诱变位点的推测。
