Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus

SIMPLE SUMMARY: Infectious diseases are among the problems facing the global aquaculture industry, particularly Vibriosis, a bacterial infection caused by the Vibrio species. In shrimp farming, Vibrio parahaemolyticus causes the disease known as acute hepatopancreatic necrosis disease, which can lead to a 100% mortality rate of the infected shrimp. The use of antibiotics in aquaculture disease management is common; however, the misuse and overuse of antibiotics has led to the emergence of antibiotic resistance, demanding the development of alternative therapeutic agents for disease control and management. This study aimed to develop a potential therapeutic aptamer using a computational biology approach. The aptamer was designed to target the quorum-sensing receptor protein, which is involved in the regulation of bacterial pathogenicity. In this study, the aptamer exhibited anti-quorum-sensing properties and suppressed the flagellum gene expression. The flagellum is crucial in bacterial motility, and it is involved in the adhesion to, and invasion of, the host, causing infection. The findings of this study demonstrated the feasibility of developing the anti-quorum-sensing aptamer as a potential alternative therapeutic agent to control the Vibrio infection in the aquaculture industry. ABSTRACT: (1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (K(d)) of 0.2 and 0.5 micromolar. The aptamer with the lowest K(d) demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.