In Silico Evaluation of Betaine, DL-Stachydrine, and Choline from Shipworm (Spathoteredo obtusa) Extract as Antibacterial Agents Candidates Against Vibrio alginolyticus via LuxR Targeting

Abstract

Bacterial infections caused by Vibrio alginolyticus represent a major challenge in aquaculture, leading tosignificant economic losses and increasing concerns regarding antibiotic resistance. This study aimed to evaluatethe potential of bioactive compounds from shipworm (Spathoteredo obtusa) as antibacterial and quorum sensinginhibitory agents through an in silico approach targeting the LuxR protein. Active compound screening using LC-HRMS identified three dominant compounds, namely betaine, DL-stachydrine, and choline. Molecular dockinganalysis was performed using PyRx, while ligand–protein interactions were visualized using Discovery Studio2021. The docking results showed that all tested compounds were able to interact with the LuxR protein withvarying binding affinity values. DL-stachydrine exhibited the best binding affinity among the tested compounds(-4.5 kcal/mol), followed by betaine (-3.9 kcal/mol) and choline (-3.8 kcal/mol), whereas the control quercetinshowed a substantially stronger binding affinity (-7.8 kcal/mol). Interaction analysis revealed the involvement ofhydrogen bonding, π-interactions, hydrophobic interactions, and van der Waals interactions within the LuxRbinding pocket. Several compounds also showed consistent interactions with key amino acid residues, suggestingbiologically relevant binding regions. These findings indicate that the tested compounds possess potential asantibacterial and quorum sensing inhibitory agents by targeting LuxR. However, further in vitro and in vivostudies are required to validate their biological activity and therapeutic potential.