Immunoinformatics Approach to Develop a Novel Chimeric L1/L2 Messenger RNA-based Vaccine Targeting a Broad Spectrum of Human Papillomavirus Species

Papillomaviruses can infect animals and humans, causing benign lesions and cancer. Chimeric vaccines may address the limited coverage of current papillomavirus vaccines by providing cross-type immunity. The present study focused on the in silico design of a chimeric mRNA vaccine targeting a wide range of human papillomaviruses (HPV). The study incorporated 25 amino acid sequences derived from L1 and L2 capsid proteins of 14 high-risk and 11 low-risk HPV strains. These sequences underwent multiple sequence alignment, and the resulting sequences were used to develop consensus sequences. Computational approaches were then applied to predict and identify immunodominant T-cell and B-cell epitopes. The mRNA vaccine structure was designed by merging codon-optimized multi-epitope chimeric peptides with regulatory components that enhance both transcription and translation efficiency. The present study identified 19 T and 6 B cell epitopes, which were evaluated as non-toxic, non-allergenic, highly antigenic, and fully or partially conserved. The final multi-epitope peptide vaccine had a molecular weight of 60,161.29 kDa, a theoretical isoelectric point (pI) of 9.44, a solubility index of 0.451, and an antigenicity score of 0.9178. The mRNA vaccine exhibited a stable mRNA structure with a minimum free energy of -731.10 kcal/mol and an estimated molecular weight of 644.98 kDa. The proposed vaccine demonstrated no cross-affinity with the human genome and attained a worldwide population coverage rate of 86.24%. The vaccine formed a stable docking complex and exhibited strong interactions with major histocompatibility class I and class II molecules, as well as Toll-like receptor 4 (TLR4), Toll-like receptor 9 (TLR9), and the B-cell receptor. Binding affinities were assessed based on free energy (ΔG) values of -34.01 kcal/mol and -20.77 kcal/mol for major histocompatibility complex (MHC) class I and II, respectively, -1377.5 kcal/mol for TLR4, -24.19 kcal/mol for TLR9, and -34.41 kcal/mol for the B-cell receptor. This vaccine triggered both antibody and cell-mediated immune responses and increasing levels of IFN-γ and the interleukins IL-2, IL-10, and IL-12. This vaccine is considered preventive against multiple HPV infections. Nonetheless, in vitro and in vivo investigations are necessary to validate the safety and efficacy of this vaccine.