Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine

Abstract

Vaccines are an upcoming medical intervention for breast cancer. By targeting the tumor antigen, cancer vaccines can be designed to train the immune system to recognize tumor cells. Therefore, along with technological advances, the vaccine design process is now starting to be carried out with more rational methods such as designing epitope-based peptide vaccines using immunoinformatics methods. Immunoinformatics methods can assist vaccine design in terms of antigenicity and safety. Common protocols used to design epitope-based peptide vaccines include tumor antigen identification, protein structure analysis, T cell epitope prediction, epitope characterization, and evaluation of protein‒epitope interactions. Tumor antigen can be divided into two types: tumor associated antigen and tumor specific antigen. We will discuss the identification of tumor antigens using high-throughput technologies. Protein structure analysis comprises the physiochemical, hydrochemical, and antigenicity of the protein. T cell epitope prediction models are widely available with various prediction parameters as well as filtering tools for the prediction results. Epitope characterization such as allergenicity and toxicity can be done in silico as well using allergenicity and toxicity predictors. Evaluation of protein‒epitope interactions can also be carried out in silico with molecular simulation. We will also discuss current and future developments of breast cancer vaccines using an immunoinformatics approach. Finally, although prediction models have high accuracy, the opposite can happen after being tested in vitro and in vivo. Therefore, further studies are needed to ensure the effectiveness of the vaccine to be developed. Although epitope-based peptide vaccines have the disadvantage of low immunogenicity, the addition of adjuvants can be a solution.

Integration: Gospel for immune bioinformatician on epitope-based therapy

“…GalaxyRefine performs repeated structure perturbation and subsequent overall structural relaxation by molecular dynamics simulation ( 48 ). The integration of I-TASSER and GalaxyRefine server allows the molecular structure to be rebuilt and optimized, providing an overall intuitive molecular structure ( 8 , 49 ).…”

Peptide Vaccines as Therapeutic and Prophylactic Agents for Female-Specific Cancers: The Current Landscape

“…The multi-epitope vaccine construct is an acceptable choice for future research [ 205 ]. Epitopes can also be designed based on the sequence of TAA or TSA that are encoded by mutated cancer genes [ 42 , 206 , 207 ]. In the case of viral induced cancers, the viral antigens can serve as a guide for epitope-based vaccine design [ 208 , 209 , 210 ].…”

Designing a Conserved Immunogenic Peptide Construct from the Nucleocapsid Protein of Puumala orthohantavirus

“…In recent years, significant progress has been made in identifying potentially immunogenic peptides using the immunoinformatic approach, which has shown promising results in various experimental systems [15]. Various immunoinformatic methods were employed to identify immunogenic peptides containing multiple epitopes of SARS-CoV-2 [16], DENV [17], Ebola virus [18], H1N1 influenza virus [19,20], CanineCV [21], Zika virus [22], and hantavirus [23].…”