In Silico Evaluation of Bioactive Compounds from Shipworm (Spathoteredo obtusa) Extract Against PirA/PirB Toxins of Vibrio parahaemolyticus as Antibacterial Candidates

Abstract

Acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio species encoding PirA and PirB toxins, induces hepatopancreatic pore formation and massive mortality in shrimp ponds. The rising prevalence of antimicrobial resistance (AMR) in aquaculture urgently requires sustainable therapeutic alternatives. This study aims to evaluate the molecular interactions of bioactive compounds derived from the shipworm (Spathoteredo obtusa) extract with the PirA and PirB toxins using an in-silico molecular docking approach. LC-HRMS analysis of the extract revealed five major constituents. Ligands were evaluated using Lipinski's Rule of Five, revealing zero violations across all compounds. Molecular docking simulations against PirA and PirB demonstrated that the screened natural compounds successfully established stable complexes. The results showed distinct target specificities; DL-Stachydrine exhibited optimal binding affinity against the PirA toxin (-4.3 kcal/mol), whereas L-Norleucine demonstrated the strongest interaction with the PirB toxin (-5.0 kcal/mol). Mechanistically, L-Norleucine utilizes a flexible aliphatic chain for deep receptor penetration, while DL-Stachydrine attains high structural stability through a rigid pyrrolidine ring, a dense hydrogen bond network, and potent electrostatic attractive charges. Although L-Norleucine showed optimal binding, its practical application is constrained by an extremely low yield of 1.10%. Conversely, DL-Stachydrine constitutes 24.89% of the total extract. Integrating molecular docking profiles and quantitative yields highlights DL-Stachydrine as a realistic and sustainable natural therapeutic agent for mitigating AHPND outbreaks in shrimp aquaculture