Peptide candidates and host-pathogen protein interactions against WSSV and Vibrio spp. in farmed penaeid shrimp: A scoping review of CADD strategies.

Abstract

This scoping review highlights the advancements in the computational discovery of peptide candidates and the modeling of host-pathogen protein interactions, spanning from the discovery of physiological AMPs to rational design mediated by computational tools, which have become a pivotal asset in addressing major shrimp farming pathogens such as WSSV and virulent Vibrio spp. strains. In this context, biocomputational studies hold strategic potential for mitigating sanitary crises in modern aquaculture. By analyzing 23 articles (2015-2026), a transition from traditional biochemical isolation to in silico prospecting was identified. The results also reveal a marked concentration of this output in Asia (22/23; 95.7% of the corpus), led by India and China (7/23; 30.4% each). Methodological convergence toward protein-protein docking (HADDOCK/ClusPro) combined with Molecular Dynamics simulations (GROMACS) was also observed. Notably, envelope proteins (VP28, VP26, and VP39) prevail as antiviral targets, while membrane lysis and the blockade of PirA/PirB toxins dominate antibacterial strategies. A consistent gap was identified: none of the 23 included studies reported electronic reactivity (DFT), QSAR-based toxicity prediction or ecotoxicological analyses, so that the chemical stability of these candidates in aquatic environments and their effects on the associated microbiota were not assessed in this literature. We conclude that the future of the field depends on the integration of drug delivery systems (e.g., chitosan), thermodynamic rigor via MM-PBSA, and the expansion of methods that ensure environmental biosafety and translational viability, aiming to consolidate these compounds as viable pharmacological agents.

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