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An In Silico Multi-epitopes Vaccine Ensemble and Characterization Against Nosocomial Proteus penneri

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Abstract

Proteus penneri (P. penneri) is a bacillus-shaped, gram-negative, facultative anaerobe bacterium that is primarily an invasive pathogen and the etiological agent of several hospital-associated infections. P. penneri strains are naturally resistant to macrolides, amoxicillin, oxacillin, penicillin G, and cephalosporins; in addition, no vaccines are available against these strains. This warrants efforts to propose a theoretical based multi-epitope vaccine construct to prevent pathogen infections. In this research, reverse vaccinology bioinformatics and immunoinformatics approaches were adopted for vaccine target identification and construction of a multi-epitope vaccine. In the first phase, a core proteome dataset of the targeted pathogen was obtained using the NCBI database and subjected to bacterial pan-genome analysis using bacterial pan-genome analysis (BPGA) to predict core protein sequences which were then used to find good vaccine target candidates. This identified two proteins, Hcp family type VI secretion system effector and superoxide dismutase family protein, as promising vaccine targets. Afterward using the IEDB database, different B-cell and T-cell epitopes were predicted. A set of four epitopes “KGSVNVQDRE, NTGKLTGTR, IIHSDSWNER, and KDGKPVPALK” were chosen for the development of a multi-epitope vaccine construct. A 183 amino acid long vaccine design was built along with “EAAAK” and “GPGPG” linkers and a cholera toxin B-subunit adjuvant. The designed vaccine model comprised immunodominant, non-toxic, non-allergenic, and physicochemical stable epitopes. The model vaccine was docked with MHC-I, MHC-II, and TLR-4 immune cell receptors using the Cluspro2.0 web server. The binding energy score of the vaccine was − 654.7 kcal/mol for MHC-I, − 738.4 kcal/mol for MHC-II, and − 695.0 kcal/mol for TLR-4. A molecular dynamic simulation was done using AMBER v20 package for dynamic behavior in nanoseconds. Additionally, MM-PBSA binding free energy analysis was done to test intermolecular binding interactions between docked molecules. The MM-GBSA net binding energy score was − 148.00 kcal/mol, − 118.00 kcal/mol, and − 127.00 kcal/mol for vaccine with TLR-4, MHC-I, and MHC-II, respectively. Overall, these in silico-based predictions indicated that the vaccine is highly promising in terms of developing protective immunity against P. penneri. However, additional experimental validation is required to unveil the real immune response to the designed vaccine.

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Acknowledgements

The authors extend their appreciation to the Researchers Supporting Project number (RSPD2023R632), King Saud University, Riyadh, Saudi Arabia.

Funding

The authors extend their appreciation to the Researchers Supporting Project number (RSPD2023R632), King Saud University, Riyadh, Saudi Arabia.

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Authors and Affiliations

  1. Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan

    Asad Ullah, Riaz Muhammad & Sajjad Ahmad

  2. Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan

    Asad Ullah

  3. Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan

    Bushra Rehman & Saifullah Khan

  4. Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia

    Taghreed N. Almanaa

  5. Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, 44000, Pakistan

    Yasir Waheed

  6. Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, 1401, Lebanon

    Yasir Waheed

  7. Department of Pharmacy, Bacha Khan University, Charsadda, 24461, Pakistan

    Muhammad Hassan

  8. Department of Chemical and Life Sciences, Qurtuba University of Science and Technology, Peshawar, Pakistan

    Tahira Naz

  9. Department of Pharmacy, Abasyn University, Peshawar, 25000, Pakistan

    Mehboob ul Haq

  10. Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran

    Samira Sanami

  11. Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32611, USA

    Muhammad Irfan

  12. Department of Natural Sciences, Lebanese American University, P.O. Box 36, Beirut, Lebanon

    Sajjad Ahmad

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  1. Asad Ullah
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Contributions

AU, BR, MH, and SK (data curation, manuscript writing), TNA, YW, and MH (manuscript review, analyses validation), TN, RM, SS, and BR (manuscript proofread, resources, visualization), and MI and SA (supervision, conceptualization and final manuscript review).

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Correspondence to Sajjad Ahmad.

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Ullah, A., Rehman, B., Khan, S. et al. An In Silico Multi-epitopes Vaccine Ensemble and Characterization Against Nosocomial Proteus penneri. Mol Biotechnol (2023). https://doi.org/10.1007/s12033-023-00949-y

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