Immunoinformatics: Multiepitope Vaccine Designing
What is a Vaccine?
A vaccine contains weakened, dead, or fragmented germs or toxins that are introduced into your body to prevent illness. Additionally, it may consist of other biological materials, such as messenger RNA (mRNA), white blood cells, or antibodies. This process instructs and trains your immune system to recognize and combat germs, thereby safeguarding you from future infections. Vaccines trigger both humoral and cell-mediated immune responses and, in the body, provide strong protection against diseases. When vaccines are introduced, the body responds similarly to real germs, effectively preparing itself to combat future infections. The primary goal of administering vaccines is to prompt the body to develop immunity to potential threats using harmless versions of pathogens that cannot cause illness or allergies.
What are Multiepitope Vaccines?
Although there are many different types of vaccines, I will concentrate on multiepitope vaccines in my blog and how researchers use different bioinformatic methods to build them. Multiepitope vaccines contain multiple small antigenic epitopes that the immune system can recognize. These epitopes can stem from diverse pathogens or different regions within a single pathogen. By combining multiple epitopes, multiepitope vaccines aim to generate an effective and strong immune response, potentially enhancing effectiveness and guarding against a wide range of microorganisms. This approach can potentially boost the vaccine's capacity to stimulate T- and B-cells, thereby fortifying overall immunity against various illnesses.
Epitope and Paratope:
An epitope, also referred to as an antigenic determinant, is a specific portion of an antigen that the immune system can identify. It is recognized by antibodies, T cells, and B cells. On the other hand, the paratope is the binding site that exists between an antibody and an antigen.
Insilico Multiepitope Vaccine Designing:
1.Pathogenic Microorganisms and virulence factors detection: The initial step involves selecting a disease-causing microorganism based on specific criteria. Choose a bacteria or virus with the highest mortality rate, highest morbidity, antibiotic resistance, no previous vaccine availability, low infectious dose, highest prevalence in the community, and biofilm production. First, it's important to search for virulence factors of pathogens. You can utilize existing literature and the VFDB database for this step.
2.Protein Sequence Retrieval: Remember to shortlist the virulence factors and obtain the protein sequences. Next, perform a BLAST search against the human proteome. Select only the proteins with no significant similarity. Utilize the Uniprot KB database for protein sequences and NCBI's BLASTp for homology. This step is critical to avoid potential cross-reactivity that could arise from using similar proteins.
3.Protein Evaluation: In the screening process, only proteins that are highly antigenic, non-toxic, and non-allergenic should be selected. To determine antigenicity, vaxigen can be used, while toxin pred can be used for toxicity analysis. To assess whether a protein is a potential allergen or not, allertop v.2.0 should be used.
4.MHC class 1 (T h ), MHC Class 2 (T c ), and B cell Epitopes Prediction: To identify the epitopes of the antigens, utilize the IEDB database to retrieve T and B cell epitopes. It's also possible to derive T cell epitopes from a sequence of B cell epitopes, as there are two pathways for B cell activation in the body - T dependent and T independent. Additionally, consider employing ABC pred for the detection of B cell epitopes.
5.Epitope Evaluation: Just like proteins evaluation, select only those epitopes that are highly antigenic, non-allergenic, and non-toxic.
6.Population Coverage Analysis: Conduct a population coverage analysis worldwide for each chosen epitope and consider only those epitopes with a coverage of over 90%. For this utilize IEDB analysis resource.
7.Vaccine construct: During the vaccine construction process, B cell and T cell epitopes are meticulously combined using linkers, and an adjuvant is introduced to the construct. Upon combining all the epitope sequences, a protein sequence ensues. This protein will serve as the antigen and is designed to effectively stimulate an immune response in the recipient. Evaluate the vaccine construct in a manner similar to how proteins and epitopes are evaluated. It's important to thoroughly review relevant literature to determine the most suitable adjuvants and linkers for connecting epitopes in order to create a vaccine construct.
8.Physio Chemical Properties: Use Expasy Protparam to determine the vaccine construct's physiochemical characteristics and assess the solubility. Soluprot can be used to assess the protein's soluble expression in E. coli.
9.Structure Modeling, refinement and Validation: For structural modeling from the construct sequence, utilize Alphafold2, I-TASSER, and PHYRE 2.0. For refinement, employ GalaxyWEB. Validate the structure using the Ramachandran plot, ensuring that at least 90% of amino acids are present in the favorable region.
10.Molecular Docking and molecular dynamic simulation: Ensure you select receptors with the highest binding affinity for molecular docking, particularly those resulting from the expression of different HLA alleles. When performing manual docking, use Autodock Vina. For automated docking, utilize Cluspro, and subsequently, conduct molecular interaction analysis using the PDsum server and then proceed with molecular dynamic simulation.
11.Codon Optimization and in-silico cloning: By aligning the gene's codon usage with the host’s translational machinery codon optimization enhances the efficacy of recombinant protein synthesis in the host organism . We will utilize J-cat for this purpose. For in silico cloning utilize Snapgene. The combination of in silico cloning and gel electrophoresis will yield crucial insights into vaccine production in the host organism. Through this analysis, we will be able to pinpoint the optimal vector materials and restriction enzymes for use in wet laboratory vaccine production.
12.Immune simulation: C-immsim is an outstanding program for immunological simulation, enabling us to monitor the populations of B and T cells over time in response to different dosages.
Map for vaccine Designing:
Conclusion:
In conclusion, combining multiple epitopes from various antigens in a multiepitope vaccine is a highly effective strategy for eliciting a powerful immune response. This strategy effectively boosts immunity and enhances the efficacy of vaccinations, positioning them as crucial weapons in the battle against complex and constantly mutating microorganisms.
