Vaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii

Miraj Ud-Din, Aqel Albutti, Asad Ullah, Saba Ismail, Sajjad Ahmad, Anam Naz, Muhammad Khurram, Mahboob ul Haq, Zobia Afsheen, Youness El Bakri, Muhammad Salman, Bilal Shaker and Muhammad Tahir ul Qamar
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Miraj Ud-Din: Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Aqel Albutti: Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
Asad Ullah: Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Saba Ismail: Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
Sajjad Ahmad: Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Anam Naz: Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore 54590, Pakistan
Muhammad Khurram: Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
Mahboob ul Haq: Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
Zobia Afsheen: Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Youness El Bakri: Department of Theoretical and Applied Chemistry, South Ural State University, Lenin Prospect 76, 454080 Chelyabinsk, Russia
Muhammad Salman: Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Bilal Shaker: Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Korea
Muhammad Tahir ul Qamar: Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan

IJERPH, 2022, vol. 19, issue 9, 1-26

Abstract: 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. Acinetobacter baumannii 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 A. baumannii 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 A. baumannii 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 A. baumannii . 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.

Keywords: Acinetobacter baumannii; pan-genomics; core genomics; epitope vaccine; molecular dynamics simulations (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2022
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