Arshad Fizza, Pervaiz Rania, Sarfraz Asifa, Ejaz Hasan, Alotaibi Amal, Ullah Riaz, Nishan Umar, Ali Abid, Khan Muhammad Umer, Shah Mohibullah
Department of Biochemistry, Bahauddin Zakariya University, Multan, Multan, 66000, Punjab, Pakistan.
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, 72388, Sakaka, Saudi Arabia.
Mol Genet Genomics. 2025 Sep 6;300(1):92. doi: 10.1007/s00438-025-02288-w.
Moraxella catarrhalis is a Gram-negative diplococcus bacterium and a common respiratory pathogen, implicated in 15-20% of otitis media (OM) cases in children and chronic obstructive pulmonary disease (COPD) in adults. The rise of drug-resistant Moraxella catarrhalis has highlighted the urgent need for the potent vaccine strategies to reduce its clinical burden. Despite a mortality rate of 13%, there is no FDA-approved vaccine for this pathogen. The aim of this study was to computationally identify novel antigens and design a multi-epitope peptide-based vaccine candidate against M. catarrhalis using an immunoinformatics-driven subtractive proteomics and reverse vaccinology approaches. The core proteome of 12 M. catarrhalis genomes were analyzed, identifying 360 host non-homologous proteins. Subsequent screening revealed 30 metabolic pathway-dependent and 7 independent drug targets, along with 7 membrane and extracellular proteins as potential vaccine candidates. A prioritized protein target (WP_081569984.1) was selected for vaccine design. The predicted B-cell, MHC-I, and MHC-II epitopes were linked using adjuvants and linkers to construct four vaccine candidates (V1-V4). These constructs were assessed for physicochemical properties, allergenicity, antigenicity, secondary structures, and immune receptor interactions. As a result, V1 emerged as the most promising candidate. Molecular docking and molecular dynamics (MD) simulations evaluated the interactions of V1 with human toll-like receptors (TLR2 and TLR3). MD trajectories including RMSD, RMSF, Radius of gyration (Rg), SASA, binding free energy (MM-PBSA), PCA, free energy landscapes, and DCCM, showed a strong interaction of vaccine with the TLR recptors. Immune simulations predicted significant immune responses against the proposed vaccine. Additionally, the vaccine construct was in-silico tested in an E. coli plasmid vector (pET-28a(+) for its cloning potential. These findings highlight the potential of the proposed multi-epitope vaccine V1 as a safe and effective preventive strategy against M. catarrhalis-associated infections, and additionally laid the groundwork for future in vitro, in vivo, and clinical studies to validate its immunogenicity and protective efficacy.
卡他莫拉菌是一种革兰氏阴性双球菌，是常见的呼吸道病原体，在儿童中耳炎（OM）病例的15%-20%以及成人慢性阻塞性肺疾病（COPD）中起作用。耐药卡他莫拉菌的出现凸显了迫切需要有效的疫苗策略来减轻其临床负担。尽管死亡率为13%，但尚无FDA批准的针对该病原体的疫苗。本研究的目的是利用免疫信息学驱动的减法蛋白质组学和反向疫苗学方法，通过计算鉴定新型抗原并设计一种基于多表位肽的卡他莫拉菌疫苗候选物。分析了12个卡他莫拉菌基因组的核心蛋白质组，鉴定出360种宿主非同源蛋白。随后的筛选揭示了30个代谢途径依赖性和7个独立的药物靶点，以及7种膜蛋白和细胞外蛋白作为潜在的疫苗候选物。选择了一个优先的蛋白质靶点（WP_081569984.1）用于疫苗设计。使用佐剂和接头连接预测的B细胞、MHC-I和MHC-II表位，构建了四种疫苗候选物（V1-V4）。评估了这些构建体的物理化学性质、致敏性、抗原性、二级结构和免疫受体相互作用。结果，V1成为最有前景的候选物。分子对接和分子动力学（MD）模拟评估了V1与人 toll样受体（TLR2和TLR3）的相互作用。包括均方根偏差（RMSD）、均方根波动（RMSF）、回转半径（Rg）、溶剂可及表面积（SASA）、结合自由能（MM-PBSA）、主成分分析（PCA）、自由能景观和动态相关矩阵（DCCM）的MD轨迹显示疫苗与TLR受体有强烈相互作用。免疫模拟预测了针对所提出疫苗的显著免疫反应。此外，在计算机上测试了疫苗构建体在大肠杆菌质粒载体（pET-28a(+)）中的克隆潜力。这些发现突出了所提出的多表位疫苗V1作为一种安全有效的预防卡他莫拉菌相关感染策略的潜力，并为未来验证其免疫原性和保护效力的体外、体内和临床研究奠定了基础。
