Immunoinformatics-Driven Design of Malaria Protein-Based Multi-Epitope Vaccine

Background Plasmodium falciparum accounts for over 90% of global malaria-related mortalities, posing a great challenge to public health. Conventional control measures, such as the use of insecticides and antimalarial drugs, have proven less effective owing to parasite resistance. Additionally, many promising malaria vaccine candidates have encountered reduced efficacy at different stages of preclinical and clinical studies. The complicated biology of Plasmodium parasites, including their genomic size and multiple stages of the life cycle, impedes the development of an effective malaria vaccine. Therefore, this study aimed to design a vaccine candidate capable of eliciting immune responses across multiple stages of the P. falciparum lifecycle using immunogenic regions from the Kelch Protein (KP), Erythrocyte Binding Antigen 175 (EBA-175), and Liver Stage-Specific Antigen 1 (LSA1). Methods ABCPred, CTLPred, and Immune Epitope Database (IEDB) and NetMHCII-2.3 were used to predict B-cell, cytotoxic T-cell lymphocyte (CTL), and helper T-cell lymphocyte (HTL) epitopes, respectively. The VaxiJen v.2.0 and AllergenFP v.1.0 databases were used to predict antigenicity and allergenicity, respectively. Population coverage analysis was performed using IEDB. The vaccine was constructed using immunogenic B- and T-cell epitopes, with flagellin as an adjuvant. The vaccine was modeled using the Iterative Threading ASSEmbly Refinement server, refined using GalaxyRefine, and docked with toll-like receptors (TLR5 and TLR8) using Cluspro v.2.0. The docked complexes were subjected to molecular dynamics simulation using the Desmond package in Schrodinger. The Java Codon Adaptation Tool was used for codon optimization, and SnapGene was used for in silico cloning. The C-IMMSIM server was used to simulate the immune response. Results Forty-five B-cell, thirteen CTL, and twenty-two HTL epitopes were antigenic and non-allergenic. The HTL epitope-associated human leukocyte antigen (HLA) alleles were expressed globally. The vaccine construct demonstrated good expression potential and was cloned into the pET-28a (+) expression vector. Furthermore, the docked complexes demonstrated strong binding interactions, and molecular dynamics simulation underscored the stability of the vaccine-TLR8 complex. Conclusions The immune response simulations affirmed that the vaccine can induce an effective immune reaction against malaria. Further immunological experimental validations are needed to prove the functionality of this vaccine.