Motamedi Hamid, Ari Marzie Mahdizade, Shahlaei Mohsen, Moradi Sajad, Farhadikia Parisa, Alvandi Amirhoushang, Abiri Ramin
Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
BMC Bioinformatics. 2023 Feb 24;24(1):65. doi: 10.1186/s12859-023-05197-0.
It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage.
In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4 and CD8) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy.
A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4 T and CD8 cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ.
Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.
肠道微生物群的几个成员，如牛链球菌、脆弱拟杆菌、幽门螺杆菌、具核梭杆菌、粪肠球菌、大肠杆菌、厌氧消化链球菌，似乎可被视为结直肠癌（CRC）的致病因素。本研究采用生物信息学和免疫信息学方法，设计一种基于潜在表位的多表位疫苗，以预防CRC，并实现最佳人群覆盖。
在本研究中，从NCBI数据库检索了10个CRC相关病原体的氨基酸序列。使用三个在线服务器ABCpred、BCPREDS和LBtope进行B细胞预测，使用IEDB服务器进行T细胞（CD4和CD8）预测。然后，使用网络服务器对所有序列进行验证、致敏性、毒性和理化分析。总共使用了三种接头AAY、GPGPG和KK分别连接CTL、HTL和BCL表位。此外，对最终构建体进行二硫键工程、分子对接、免疫模拟和密码子优化，以设计有效的疫苗生产策略。
总共获得了19个不同长度的线性B细胞表位序列，19个和18个序列分别被视为CD4 T细胞和CD8细胞的表位。预测的表位通过合适的接头连接，因为它们在产生延伸构象和蛋白质折叠中起重要作用。通过分子对接评估最终的多表位构建体和Toll样受体4（TLR4），结果显示它们之间存在稳定且强烈的结合相互作用。疫苗的免疫模拟显示免疫球蛋白、辅助性T细胞、细胞毒性T细胞和INF-γ水平显著升高。
最后，结果表明设计的多表位疫苗可作为预防CRC相关病原体的优秀候选疫苗，但需要进行体外和动物研究来证实我们的发现，以证明其作为一种可能的预防措施的用途。
