A subunit vaccine against pneumonia: targeting S treptococcus pneumoniae and Klebsiella pneumoniae

Md Oliullah Rafi; Khattab Al-Khafaji; Santi M Mandal; Nigar Sultana Meghla; Polash Kumar Biswas; Md Shahedur Rahman

doi:10.1007/s13721-023-00416-3

A subunit vaccine against pneumonia: targeting S treptococcus pneumoniae and Klebsiella pneumoniae

Netw Model Anal Health Inform Bioinform. 2023;12(1):21. doi: 10.1007/s13721-023-00416-3. Epub 2023 Apr 19.

Authors

Md Oliullah Rafi^{1

2}, Khattab Al-Khafaji³, Santi M Mandal⁴, Nigar Sultana Meghla⁵, Polash Kumar Biswas⁶, Md Shahedur Rahman^{1

2}

Affiliations

¹ Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh.
² Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh.
³ College of Dentistry, The University of Mashreq, Baghdad, Iraq.
⁴ Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India.
⁵ Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh.
⁶ Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 South Korea.

Abstract

Community-acquired pneumonia is primarily caused by Streptococcus pneumoniae and Klebsiella pneumoniae, two pathogens that have high morbidity and mortality rates. This is largely due to bacterial resistance development against current antibiotics and the lack of effective vaccines. The objective of this work was to develop an immunogenic multi-epitope subunit vaccine capable of eliciting a robust immune response against S. pneumoniae and K. pneumoniae. The targeted proteins were the pneumococcal surface proteins (PspA and PspC) and choline-binding protein (CbpA) of S. pneumoniae and the outer membrane proteins (OmpA and OmpW) of K. pneumoniae. Different computational approaches and various immune filters were employed for designing a vaccine. The immunogenicity and safety of the vaccine were evaluated by utilizing many physicochemical and antigenic profiles. To improve structural stability, disulfide engineering was applied to a portion of the vaccine structure with high mobility. Molecular docking was performed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptors (TLR2 and 4). Further, the dynamic stabilities of the vaccine and TLRs complexes were investigated by molecular dynamics simulations. While the immune response induction capability of the vaccine was assessed by the immune simulation study. Vaccine translation and expression efficiency was determined through an in silico cloning experiment utilizing the pET28a(+) plasmid vector. The obtained results revealed that the designed vaccine is structurally stable and able to generate an effective immune response to combat pneumococcal infection.

Supplementary information: The online version contains supplementary material available at 10.1007/s13721-023-00416-3.

Keywords: HLA; Immunoinformatics; Klebsiella pneumonia; Molecular docking; Multi-epitope prediction; Streptococcus pneumonia.

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