Laboratório de Modelagem Computacional - LaModel, Instituto de Ciências Exatas - ICEx, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas Minas Gerais, Brazil.
Facultad de Psicología, Universidad Nacional Autónoma de México, Avenida Universitaria N°3004 Distrito Federal, Mexico.
Comput Biol Chem. 2019 Dec;83:107157. doi: 10.1016/j.compbiolchem.2019.107157. Epub 2019 Nov 2.
Leishmaniosis, caused by intracellular parasites of the genus Leishmania, has become a serious public health problem around the world, and for which there are currently extensive limitations. In this work, a theoretical model was proposed for the development of a multi-epitope vaccine. The protein GP63 of the parasite was selected for epitopes prediction, due to its important biological role for the infection process and abundance. IEDB tools were used to determine epitopes B and T in Leishmania braziliensis; besides, other conserved epitopes in three species were selected. To improve immunogenicity, 50S ribosomal protein L7 / L12 (ID: P9WHE3) was used as a domain of adjuvant in the assembly process. The folding arrangement of the vaccine was obtained through homologous modeling multi-template with MODELLER v9.21, and a Ramachandran plot analysis was done. Furthermore, physicochemical properties were described with the ProtParam tool and secondary structure prediction combining GOR-IV and SOPMA tools. Finally, a molecular dynamics simulation (50 ns) was performed to establish flexibility and conformational changes. The analysis of the results indicates high conservancy in the epitopes predicted among the four species. Moreover, Ramachandran plot, physicochemical parameters, and secondary structure prediction suggest a stable conformation of the vaccine, after a minimum conformational change that was evaluated with the free energy landscape. The conformational change does not drive any substantial change for epitope exposition on the surface. The vaccine proposed could be tested experimentally to guide new approaches in the development of pan-vaccines; vaccines with regions conserved in multiple species.
利什曼病是由利什曼原虫属的细胞内寄生虫引起的，已成为全球严重的公共卫生问题，目前存在广泛的局限性。在这项工作中，针对多表位疫苗的开发提出了一个理论模型。选择寄生虫的 GP63 蛋白进行表位预测，因为它对感染过程和丰度具有重要的生物学作用。使用 IEDB 工具来确定 Leishmania braziliensis 中的 B 和 T 表位；此外，还选择了三种物种中的其他保守表位。为了提高免疫原性，将 50S 核糖体蛋白 L7/L12（ID：P9WHE3）用作组装过程中佐剂的结构域。使用同源建模多模板（MODELLER v9.21）获得疫苗的折叠排列，并进行 Ramachandran 图谱分析。此外，使用 ProtParam 工具描述理化性质，并结合 GOR-IV 和 SOPMA 工具进行二级结构预测。最后，进行了 50ns 的分子动力学模拟以建立灵活性和构象变化。结果分析表明，四种物种之间预测的表位具有高度保守性。此外，Ramachandran 图谱、理化参数和二级结构预测表明，在经过最小构象变化（通过自由能景观评估）后，疫苗具有稳定的构象。构象变化不会导致表面表位暴露发生实质性变化。可以对所提出的疫苗进行实验测试，以指导针对多种物种中保守区域的泛疫苗开发的新方法。
