Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing
作者:David Zanuy、Francisco J. Sayago、Guillem Revilla-López、Gema Ballano、Lilach Agemy、Venkata Ramana Kotamraju、Ana I. Jiménez、Carlos Cativiela、Ruth Nussinov、April M. Sawvel、Galen Stucky、Erkki Ruoslahti、Carlos Alemán
DOI:10.1007/s10822-012-9623-5
日期:2013.1
We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg-Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932–936, 2007) with improved ability to inhibit tumor growth. Computer modeling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bioactive conformation of CREKA. Because this conformation presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids α-methyl and N-methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incorporated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabilization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can converge and lead to useful biomedical advances.
CREKA(Cys-Arg-Glu-Lys-Ala)能与肿瘤血管中的纤维蛋白和纤维蛋白相关凝血浆蛋白结合(Simberg 等人,发表于 Proc Natl Acad Sci USA 104:932-936, 2007),具有更强的抑制肿瘤生长的能力。我们采用模拟退火和分子动力学相结合的方法进行了计算机建模,以设计有针对性的替代物,从而提高 CREKA 生物活性构象的稳定性。由于这种构象呈现出类似口袋的形状,Arg、Glu 和 Lys 的带电基团指向外侧,因此我们选择了 Arg、Glu 和 Lys 的非蛋白源氨基酸 α-甲基和 N-甲基衍生物,并对其进行了合理设计,将其加入到 CREKA 类似物中。根据建模预测,不同 CREKA 类似物的生物活性构象的稳定性与肿瘤荧光结果相吻合,肿瘤蓄积量随着稳定性的增加而增加。在此,我们报告了建模、合成过程以及用于测试类似物疗效和实用性的新生物检测方法。我们的研究结果综合展示了基于多学科合作的研究如何汇聚在一起,并带来有用的生物医学进步。