Ud-Din Miraj, Albutti Aqel, Ullah Asad, Ismail Saba, Ahmad Sajjad, Naz Anam, Khurram Muhammad, Haq Mahboob Ul, Afsheen Zobia, Bakri Youness El, Salman Muhammad, Shaker Bilal, Tahir Ul Qamar Muhammad
Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan.
Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia.
Int J Environ Res Public Health. 2022 May 4;19(9):5568. doi: 10.3390/ijerph19095568.
Antibiotic resistance (AR) is the result of microbes' natural evolution to withstand the action of antibiotics used against them. AR is rising to a high level across the globe, and novel resistant strains are emerging and spreading very fast. is a multidrug resistant Gram-negative bacteria, responsible for causing severe nosocomial infections that are treated with several broad spectrum antibiotics: carbapenems, β-lactam, aminoglycosides, tetracycline, gentamicin, impanel, piperacillin, and amikacin. The genome is superplastic to acquire new resistant mechanisms and, as there is no vaccine in the development process for this pathogen, the situation is more worrisome. This study was conducted to identify protective antigens from the core genome of the pathogen. Genomic data of fully sequenced strains of were retrieved from the national center for biotechnological information (NCBI) database and subjected to various genomics, immunoinformatics, proteomics, and biophysical analyses to identify potential vaccine antigens against . By doing so, four outer membrane proteins were prioritized: TonB-dependent siderphore receptor, OmpA family protein, type IV pilus biogenesis stability protein, and OprD family outer membrane porin. Immuoinformatics predicted B-cell and T-cell epitopes from all four proteins. The antigenic epitopes were linked to design a multi-epitopes vaccine construct using GPGPG linkers and adjuvant cholera toxin B subunit to boost the immune responses. A 3D model of the vaccine construct was built, loop refined, and considered for extensive error examination. Disulfide engineering was performed for the stability of the vaccine construct. Blind docking of the vaccine was conducted with host MHC-I, MHC-II, and toll-like receptors 4 (TLR-4) molecules. Molecular dynamic simulation was carried out to understand the vaccine-receptors dynamics and binding stability, as well as to evaluate the presentation of epitopes to the host immune system. Binding energies estimation was achieved to understand intermolecular interaction energies and validate docking and simulation studies. The results suggested that the designed vaccine construct has high potential to induce protective host immune responses and can be a good vaccine candidate for experimental in vivo and in vitro studies.
抗生素耐药性（AR）是微生物自然进化以抵御针对它们使用的抗生素作用的结果。全球范围内，AR正上升到很高水平，新型耐药菌株不断出现且传播迅速。[具体细菌名称]是一种多重耐药革兰氏阴性菌，可导致严重的医院感染，需用多种广谱抗生素治疗：碳青霉烯类、β-内酰胺类、氨基糖苷类、四环素类、庆大霉素、亚胺培南、哌拉西林和阿米卡星。[具体细菌名称]的基因组具有高度可塑性，能够获得新的耐药机制，而且由于目前尚无针对该病原体的疫苗处于研发阶段，情况更加令人担忧。本研究旨在从该病原体的核心基因组中鉴定保护性抗原。从美国国立生物技术信息中心（NCBI）数据库检索[具体细菌名称]全测序菌株的基因组数据，并对其进行各种基因组学、免疫信息学、蛋白质组学和生物物理分析，以鉴定针对[具体细菌名称]的潜在疫苗抗原。通过这样做，确定了四种外膜蛋白的优先级：依赖TonB的铁载体受体、OmpA家族蛋白、IV型菌毛生物合成稳定性蛋白和OprD家族外膜孔蛋白。免疫信息学预测了这四种蛋白的B细胞和T细胞表位。将抗原表位连接起来，使用GPGPG接头和佐剂霍乱毒素B亚基设计多表位疫苗构建体，以增强免疫反应。构建了疫苗构建体的三维模型，进行环优化，并进行广泛的误差检查。为提高疫苗构建体的稳定性进行了二硫键工程。对疫苗与宿主MHC-I、MHC-II和Toll样受体4（TLR-4）分子进行了盲对接。进行分子动力学模拟以了解疫苗与受体的动力学和结合稳定性，以及评估表位向宿主免疫系统的呈递情况。通过估计结合能来了解分子间相互作用能，并验证对接和模拟研究。结果表明，设计出的疫苗构建体具有诱导宿主产生保护性免疫反应的高潜力，可作为体内和体外实验研究的良好疫苗候选物。
