Abstract

Bacterial kidney disease (BKD), caused by the Gram-positive intracellular bacterium Renibacterium salmoninarum, remains a major challenge for salmon aquaculture, particularly in Chile, where the lack of an effective vaccine has led to sustained antibiotic use. In this study, we applied an integrative in silico approach combining comparative genomics, reverse vaccinology, immunoinformatics, structural modeling, molecular docking, and molecular dynamics to design a multiantigenic and multiepitope chimeric protein as a vaccine candidate. Comparative analysis of three genomes revealed a highly conserved proteome, supporting the identification of shared immunogenic targets. From proteins associated with virulence, secretion systems, iron acquisition, chaperones, ribosomal functions, magnesium transport, and carbohydrate uptake, 17 proteins were selected after antigenicity and localization screening. Epitope prediction initially identified 154 candidates; after filtering for antigenicity, toxicity, and host homology, 60 epitopes grouped into 26 antigenic regions derived from 15 proteins were retained. Structural models were evaluated using QMEAN and Ramachandran analysis, and docking against Atlantic salmon MHC class I and II alleles identified the best candidates, with HADDOCK scores ranging from -71.2 to -154.6 (MHC I) and -116.5 to -152.0 (MHC II). Twelve antigenic regions were assembled into a 439-amino-acid chimeric protein using GSGSGS linkers. The construct showed a predicted molecular weight of 43.7 kDa, pI of 9.56, aliphatic index of 87.97, moderate solubility (0.43), and no predicted toxicity. Molecular dynamics (100 ns) supported structural stability, with RMSD convergence at similar to 85 ns. Surface analysis identified exposed antigenic regions mainly from DnaK, HmuU, Tpl, and DacB. This approach enabled the rational design of a structurally stable and immunologically promising candidate, providing a basis for future experimental validation.