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Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit
Published on: June 28, 2013
Integrated computational approaches assisted development of a novel multi-epitope vaccine against MDR Streptococcus
1University of Jeddah, Faculty of Science, Department of Biology, Jeddah, Saudi Arabia.
Abstract:
The emergence of antibiotic resistance (AR) in bacteria is becoming an alarming health concern because it allows them to adapt themselves to changing environments. It is possible to prevent the spread of AR in many ways, such as reducing antibiotic misuse in human and veterinary medicine. Streptococcus pseudopneumoniae is one of these AR bacterial species that can cause pneumonia in humans and is responsible for high mortality and morbidity rates. It is oval shaped gram-positive bacterium that shows resistance to several antibiotics like penicillin, tetracycline, ciprofloxacin, erythromycin, and co-trimoxazale and no approved vaccine is available to overcome diseases of the pathogen. Thus, substantial efforts are necessary to select protective antigens from a whole genome of pathogens that are easily tested experimentally. The in silico designed vaccine was safe and potent in immunizing individuals against the aforementioned pathogens. Herein, we utilized a subtractive genomic approach to identify potential epitope-based vaccine candidates against S. pseudopneumoniae. In total, 50850 proteins were retrieved from the NCBI, representing the complete genome of S. pseudopneumoniae. Out of the total, CD-HIT analysis identified 1022 proteins as non-redundant and 49828 proteins as redundant and further subjected for subcellular localization in which bulk of proteins was located in the cytoplasm, with seven extracellular proteins (penicillin-binding protein, alpha-amylase, solute-binding protein, hypothetical protein, CHAP domain-containing protein, polysaccharide deacetylase family protein, hypothetical protein). Six immune cells epitopes (SNLQSENDRL, RNDSLQKQAR, NPTTTSEGF, KVKKKNNKK, AYSQGSQKEH, and SVVDQVSGDF) were predicted with the help of the IEDB server. To design a multi-epitopes vaccine these immune cell epitopes were together by GPGPG and adjuvant linker to enhance immune response efficacy. The 3D structure of the designed vaccine was modeled and conducted molecular docking and dynamic simulation studies were to check the binding efficacy with immune cells receptor and dynamic behavior of the docked complex. Finally, we concluded that the designed vaccine construct can provoke a proper and protective immune response against S. pseudopneumoniae.
Insights
This study developed a novel in silico vaccine against antibiotic-resistant Streptococcus pseudopneumoniae. The designed multi-epitope vaccine shows potential for a protective immune response against this dangerous pathogen.
Area of Science:
- Microbiology and Immunology
- Bioinformatics and Computational Biology
- Vaccine Development
Background:
- Antibiotic resistance (AR) in bacteria, including Streptococcus pseudopneumoniae, poses a significant global health threat.
- Streptococcus pseudopneumoniae causes pneumonia with high mortality and morbidity, and lacks an approved vaccine.
- Developing new vaccines is crucial to combat AR pathogens and reduce disease burden.
Purpose of the Study:
- To identify potential vaccine candidates against Streptococcus pseudopneumoniae using a subtractive genomic approach.
- To design and computationally evaluate a multi-epitope vaccine construct targeting S. pseudopneumoniae.
Main Methods:
- Retrieved and analyzed the complete genome of S. pseudopneumoniae to identify non-redundant proteins.
- Predicted extracellular proteins and identified potential T-cell epitopes using the IEDB server.
- Constructed a multi-epitope vaccine by linking epitopes with GPGPG and adjuvant linkers, followed by 3D modeling, molecular docking, and dynamic simulations.
Main Results:
- Identified seven extracellular proteins and six T-cell epitopes from the S. pseudopneumoniae genome.
- Successfully designed a multi-epitope vaccine construct with favorable 3D structure.
- Molecular docking and dynamic simulations indicated effective binding affinity and stability of the vaccine construct with immune cell receptors.
Conclusions:
- The in silico designed multi-epitope vaccine construct demonstrates potential for eliciting a protective immune response against Streptococcus pseudopneumoniae.
- This computational approach offers a promising strategy for developing vaccines against antibiotic-resistant bacteria.
- Further experimental validation is warranted to confirm the efficacy of the designed vaccine.
