Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

Abstract

A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens. In silico designing and developing a safe and novel vaccine construct involves knowledge of reverse vaccinology, various vaccine databases, and high throughput techniques. The computational tools and techniques directly associated with vaccine research are extremely effective, economical, precise, robust, and safe for human use. Many vaccine candidates have entered clinical trials instantly and are available prior to schedule. In light of this, the present article provides researchers with up-to-date information on various approaches, protocols, and databases regarding the computational designing and development of potent multi-epitope-based peptide vaccines that can assist researchers in tailoring vaccines more rapidly and cost-effectively.

Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.)

“…By default, the top 10 models of the docked complexes were displayed. Herein, the first model of OSLM0467, OSLM2629, and OSPM4294 binding with homodimeric TLR4 receptor providing the lowest docking score (indicated high-affinity binding and molecular interaction) 37 was chosen, and the docked structure was observed on the Pymol program (Fig. 6 A–C).…”

Immunoinformatics, molecular docking and dynamics simulation approaches unveil a multi epitope-based potent peptide vaccine candidate against avian leukosis virus

“…The GPGPG linkers were applied to facilitate immune processing and merge the B-cells and T-helper cell epitopes. The YAA linkers ameliorated the immunogenicity of a vaccine by impacting protein stability and epitope presentation capacity and were used to fuse the cytotoxic T-cells 24 , 79 . As an adjuvant, the β-defensin was added via an EAAAK linker at the N terminus of the vaccine construct to improve the immunogenicity of the vaccine.…”

“…As an adjuvant, the β-defensin was added via an EAAAK linker at the N terminus of the vaccine construct to improve the immunogenicity of the vaccine. EAAAK are helical linkers used to control the distance and decrease the interference between the domains 24 , 79 . As a 45amino acids peptide with a relatively small size, the β-defensin was used for its immune modulation and antimicrobial features 44 .…”

“…On the other hand, common traditional vaccines might use inactivated or attenuated forms of microorganism, which might provide adverse effects and autoimmune diseases in infected hosts. Also the development of traditional vaccines candidate such as chimeric virus vaccines, live attenuated vaccines, virus-like particles (VLPs), subunit vaccines and nucleic acid vaccines is complex process, expensive, time consuming, need complicated in vitro and in vivo studies for evaluating their potential efficacy 24 , 25 .…”

In silico design and analysis of a multiepitope vaccine against Chlamydia

“…Traditional vaccine development approaches are facing logistical challenges and safety concerns, prompting a transition towards exploring alternative vaccination methods (Madewell et al 2021 ). Epitope-based vaccines stand out for their ability to trigger targeted immune responses and streamline vaccine development through advancements in immunoinformatics (Shawan et al 2023 ). Contrasting conventional approaches, epitope-based vaccines offer advantages such as cost-effectiveness, safety, and customization, rendering them particularly appealing in the fight against infectious diseases (Excler et al 2021 ).…”