Elfadil Mayada M, Samhoon Samah Omer A, Saadaldin Moaaz M, Ibrahim Sabah A E, Mohamed Ahmed Abdelghyoum M, Suliman Omnia H, Mohamed Osama, Damiri Nadzirah, Firdaus-Raih Mohd, Mohamed Sofia B, M Ali Qurashi
Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan.
Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan; Al Neelain University Faculty of Medicine Biochemistry and Molecular Biology Department, Sudan; Al-Neelain Institute for Medical Research, Sudan.
J Genet Eng Biotechnol. 2025 Sep;23(3):100510. doi: 10.1016/j.jgeb.2025.100510. Epub 2025 May 23.
Klebsiella pneumoniae (K. pneumoniae), a Gram-negative pathogen, is a leading cause of hospital-acquired infections in Sudan and worldwide. The emergence of multidrug-resistant (MDR) strains has severely limited treatment options, underscoring the urgent need for an effective vaccine. In this study, we employed reverse vaccinology and immunoinformatics to design a novel multi-epitope vaccine targeting the hypervirulent NUBRI-K strain. Two conserved, non-host homologous iron acquisition proteins, IucA/IucC and FyuA, were prioritized as targets. The vaccine construct integrates six B-cell, six cytotoxic T lymphocyte (CTL), and six helper T lymphocyte (HTL) epitopes, linked by optimized spacers and fused to a β-defensin adjuvant. Computational analyses confirmed strong antigenicity (1.0429), non-allergenicity, and favorable solubility (0.477). Molecular docking revealed high-affinity binding to Toll-like receptor 4 (TLR4) (-278.22 kcal/mol), stabilized by eight hydrogen bonds and two salt bridges. Structural validation showed that 91 % of residues were located in favored regions of the Ramachandran plot. Additionally, CABSflex 2.0 dynamics analysis confirmed stable vaccine-TLR4 interactions, with minimal residue-level fluctuations (RMSF <1.5 Å), indicating conformational stability of the complex. In silico immune simulations predicted potent humoral and cellular responses, including elevated IgG/IgM titers, T-cell proliferation, and IFN-γ secretion. The construct was further optimized for mammalian expression, achieving an ideal GC content (48.27 %) and a codon adaptation index (CAI) of 1.0, facilitating efficient in silico cloning into the pcDNA3 vector. By targeting conserved iron acquisition systems, this vaccine candidate presents a promising strategy to combat antibiotic-resistant K. pneumoniae while minimizing selective pressure. Future in vitro and in vivo studies are warranted to validate its immunogenicity and protective efficacy.
肺炎克雷伯菌（K. pneumoniae）是一种革兰氏阴性病原体，是苏丹和全球医院获得性感染的主要原因。多重耐药（MDR）菌株的出现严重限制了治疗选择，凸显了对有效疫苗的迫切需求。在本研究中，我们采用反向疫苗学和免疫信息学方法设计了一种针对高毒力NUBRI-K菌株的新型多表位疫苗。两种保守的、非宿主同源的铁摄取蛋白IucA/IucC和FyuA被优先作为靶点。疫苗构建体整合了六个B细胞表位、六个细胞毒性T淋巴细胞（CTL）表位和六个辅助性T淋巴细胞（HTL）表位，通过优化的间隔区连接，并与β-防御素佐剂融合。计算分析证实了其强抗原性（1.0429）、无致敏性和良好的溶解性（0.477）。分子对接显示与Toll样受体4（TLR4）具有高亲和力结合（-278.22 kcal/mol），由八个氢键和两个盐桥稳定。结构验证表明91%的残基位于拉氏图的有利区域。此外，CABSflex 2.0动力学分析证实了疫苗与TLR4之间稳定的相互作用，残基水平波动最小（RMSF<1.5 Å），表明复合物的构象稳定性。计算机免疫模拟预测了强大的体液和细胞反应，包括IgG/IgM滴度升高、T细胞增殖和IFN-γ分泌。该构建体进一步针对哺乳动物表达进行了优化，实现了理想的GC含量（48.27%）和密码子适应指数（CAI）为1.0，便于在计算机上高效克隆到pcDNA3载体中。通过靶向保守的铁摄取系统，这种候选疫苗为对抗耐抗生素肺炎克雷伯菌提供了一种有前景的策略，同时将选择压力降至最低。未来有必要进行体外和体内研究以验证其免疫原性和保护效果。
