UCB Celltech, 216 Bath Road, Slough, United Kingdom.
UCB Pharma, Chemin du Foriest 1, B-1420 Braine-l'Alleud, Belgium.
Sci Rep. 2017 Jan 27;7:41306. doi: 10.1038/srep41306.
Therapeutic and diagnostic applications of monoclonal antibodies often require careful selection of binders that recognize specific epitopes on the target molecule to exert a desired modulation of biological function. Here we present a proof-of-concept application for the rational design of an epitope-specific antibody binding with the target protein Keap1, by grafting pre-defined structural interaction patterns from the native binding partner protein, Nrf2, onto geometrically matched positions of a set of antibody scaffolds. The designed antibodies bind to Keap1 and block the Keap1-Nrf2 interaction in an epitope-specific way. One resulting antibody is further optimised to achieve low-nanomolar binding affinity by in silico redesign of the CDRH3 sequences. An X-ray co-crystal structure of one resulting design reveals that the actual binding orientation and interface with Keap1 is very close to the design model, despite an unexpected CDRH3 tilt and V/V interface deviation, which indicates that the modelling precision may be improved by taking into account simultaneous CDR loops conformation and V/V orientation optimisation upon antibody sequence change. Our study confirms that, given a pre-existing crystal structure of the target protein-protein interaction, hotspots grafting with CDR loop swapping is an attractive route to the rational design of an antibody targeting a pre-selected epitope.
单克隆抗体的治疗和诊断应用通常需要仔细选择能够识别靶分子上特定表位的结合物，以对生物功能进行所需的调节。在这里，我们提出了一个概念验证应用，用于通过将天然结合伴侣蛋白 Nrf2 的预定义结构相互作用模式嫁接到一组抗体支架的几何匹配位置，来合理设计与靶蛋白 Keap1 特异性结合的表位抗体。设计的抗体以表位特异性方式与 Keap1 结合并阻断 Keap1-Nrf2 相互作用。通过对 CDRH3 序列的计算机重新设计，进一步优化了一种产生的抗体以实现低纳摩尔亲和力。一个结果设计的 X 射线共晶结构表明，实际的结合方向和与 Keap1 的界面非常接近设计模型，尽管存在意想不到的 CDRH3 倾斜和 V/V 界面偏差，这表明通过考虑同时的 CDR 环构象和 V/V 方向优化，在抗体序列改变时，建模精度可以得到提高。我们的研究证实，在给定靶蛋白-蛋白相互作用的预先存在的晶体结构的情况下，热点嫁接与 CDR 环交换是针对预先选择的表位设计抗体的有吸引力的途径。
