**4. Stages development of epitope vaccine**

In principle, a material's antigenic nature shows how much the antigen's ability to bind to antibodies and cause different reactions in human immunity formation. Antibodies or immunoglobulins are specialized proteins that are products of differentiated B lymphocytes or plasma cells. The bond between antibodies and antigens induces systemic immunity and activates the complement to process further activate the humoral immune system [9].

Specific antibodies can be made on an individual's body by immunizing selected peptides that present epitopes of these proteins. Epitopes play an essential role in vaccine development. Mapping epitope sequences or antigenic peptides from pathogenic proteins recognized by B cells and T cells is crucial for vaccine development. Epitope mapping provides useful information for designing peptide-based vaccines and as libraries to monitor specific cellular immunity in protected individuals, patients, and vaccines [8].

B cell epitope mapping is divided into linear and nonlinear B cell epitope mapping. Although minor, linear B cell mapping has further attention in vaccine research because linear epitopes are epitopes ready to replace antigens in immunization. There are various epitope mapping method using different approaches and algorithms; for instance Kolaskar and Tongaonkar [10], Bepipred, Preditop, ABCPred, LBtope, and many others [11].

The IEDB (The Immune Epitope Database) maps experiments identify and characterize epitopes and epitope-specific receptors with related details, including host organisms, immune exposures, and induced immune responses. The genes that encode polypeptides are then cloned into pRSETA, a bacterial vector for highlevel expression of proteins, plasmid vectors. Transformation of the recombinant plasmid in *E. coli* host was followed by induction with IPTG (Isopropyl ß-D-1-thiogalactopyranoside), which resulted in a polypeptide expression as observed in SDS-PAGE (Sodium dodecyl sulfate polyacrylamide gel electrophoresis) and Western blot analysis. Purified polypeptides were subjected to step dialysis. The final concentration was quantified and adjusted to 2.5 mg/ml by Lowry's calorimetric assay against BSA (Bovine Serum Albumin) standard [12].

#### **5. In silico experiments as tools to design epitopes for vaccine**

Epitope-based vaccine design using this computational method silico is an effective strategy that can lead to vaccine development to induce the necessary immunogenicity without the emergence of a cytokine storm or immune tolerance. Based on several in vitro studies and in vivo, if scientifically and critically designed, epitopebased vaccines offer several advantages over other types of vaccines, including their fast design and accurate, time/cost effective formulations, and desired immunogenicity with minimal side effects [13].

There is no denying that vaccination is beneficial in promoting a healthy global population. This act has saved countless lives, reduced healthcare costs, and improved the quality of human life. Accidental discoveries in immunology are augmented by knowledge about bioinformatics tools for epitope prediction, resulting in the emergence of a pattern new vaccine design. The art and science of efficient and comprehensive information extraction and analysis of data stored in relevant databases is of increasing importance in research related to immunology [14].

Fortunately, although research in experimental immunology are expensive and highly intensive, usually large amounts of data are generated. Such data can only be analyzed with high precision and high-speed using bioinformatics tools. For example, genome sequencing as well as in vitro T-cell confirmation takes place within a few months. With conventional vaccine designs, computational immunology methods drastically reduce time and labor requirements in epitope screening. With computational immunological techniques, it is possible to find vaccine candidate epitopes only by scanning deep protein sequences of the desired pathogen. Many of these proteins have not been isolated or at least cloned into specific and unique pathogens, and they present a ready candidate in vaccine construction [14].

This in silico strategy also helps in selecting better molecules before testing conditions in vitro or in vivo. In this early stage, the use of in silico methods can direct and thus significantly shorten the next experimental work. Besides, proper use of the silico method can replace, reduce and improve the usage of animal experiments that are often misleading and time-consuming [15].

The position of the in-silico method in the vaccine development process lies at the preclinical development stage. In vaccine development, the first steps are to do is identify a vaccine candidate. The preclinical stage aims to determine the safety profile of the vaccine. During this stage, the researchers will carefully select the appropriate antigen and technology, and in vitro and in vivo will do. The information gathered from this study will be essential to continue with the subsequent clinical trials in humans [16].

There are some advantages of using the In silico method [17]. This technique offers an advantage in giving new drug candidates faster and at a lower cost. It is

#### *In-Silico Approach in the Development of* Salmonella *Epitope Vaccine DOI: http://dx.doi.org/10.5772/intechopen.96313*

also Increases the chances of success in the many stages of the discovery process and facilitates access to the large amount of data generated. In silico experiments, it was also turning massive complex biological data into useful knowledge.

Revolution in information technology and molecular biology, together with growth in genome data storage, has provided the basis for vaccine design using computational and bioinformatics tools. These tools are used for silico mapping of the most precise and immunogenic components for the manufacture of a hypothetical protein. The vaccine that is designed can then be simulated and evaluated prior to experimental validation, enabling the process research and development (R&D) to be carried out efficiently, and leads to the development of vaccines with few adverse effects [13]. Here is some software that can be used to help in silico design of epitope vaccine.

#### **5.1 Mega x™**

Over the last decade, genome sequencing has become an efficient and efficient way to investigate a wide variety of biological systems, ranging from diversity studies large-scale biology to tracking the evolution and origin of pathogenic microbes. The steps needed to gather interpretable and interpretable results actionable from raw sequence data always require a comparative analysis of molecular sequences to find differences in functional and adaptive genomes. The Molecular Evolutionary Genetics Analysis (MEGA) software provides the tools to do that analysis. MEGA includes many programs for assembling sequence alignments, inferring evolutionary trees, estimating genetic distances and diversities, inferring ancestral sequences, computing time trees, and testing selection [18]. MEGA software or other software allows alignment of *salmonella* typhi genome sequences from various countries to determine which sequences are considered sustainable. The selection of sustainable sequences is vital for the manufacture of vaccines so that later the vaccine can be used in many countries.

#### **5.2 IEDB**

The Immune Epitope Database (IEDB, iedb.org) [19] captures experimental data limited in figures, texts, and tables of the scientific literature, making them available online free and easily searchable by the public. The scope of the IEDB includes data on immune epitopes associated with all studied species and includes the antibody binding context, T cells, and MHCs associated with infection, allergy, autoimmune, and related diseases transplant [20]. The IEDB is a website that provides tools computations that focus on the prediction and analysis of B and T cell epitopes. The IEDB maps experiments identify and characterize epitopes and epitope-specific receptors with related details, including host organisms, exposures immunity, and induced immune response. The site associated with the IEDB is the ISDBA Analysis Resource, which is a predictor of various B cell and T cell epitopes. Using a trained and validated algorithm [21]. An antigenicity analysis was carried out using the Kolaskar and Tongaonkar principles followed by epitope mapping using Bepipred. Both are done based on a database owned by IEDB (The Immune Epitope Database).

IEDB web server using some parameters, including Kolaskar-Tongaonkar as the antigenicity scale parameter, which is the standard for epitope prediction [22]. The Kolaskar and Tongaonkar antigenicity scales based on the amino acid residues' physicochemical properties and the known tendency frequency as an experimental epitope have an accuracy of 75% [10]. The BepiPred-2.0 server predicts B cell epitopes from protein sequences, using a Random Forest algorithm trained on epitopes and amino acids non-epitope determined from the crystal structure [21, 23]. The Immune Epitope Database (IEDB) retrieves experimental data through pictures,

texts, and tables of scientific literature, even the scope of the IEDB extends to the immune epitope, where data are linked to all studied species including antibodies, T cells, and the binding context MHC is associated with infections, allergies, autoimmune, and transplant-related diseases [20].
