Integrative In vitro and In Silico analysis of marine Actinobacterium, Streptomyces rubrogriseus-derived metabolites as quorum sensing inhibitors against Chromobacterium violaceum.

Abstract

Quorum-sensing (QS), a bacterial communication mechanism regulating virulence, biofilm formation, and environmental adaptation, represents a promising target for antivirulence therapies. Unlike conventional antibiotics, QS inhibition disrupts bacterial coordination without promoting antimicrobial resistance. Marine actinobacteria, well adapted to extreme habitats, are a rich source of bioactive quorum-sensing inhibitors (QSI). This study evaluates the QSI activity of ethyl acetate (EA) extract from a marine actinobacterium, Streptomyces rubrogriseus, against Chromobacterium violaceum 12472, a QS model organism. Marine actinobacteria were isolated from Kochi coastal sediments, and the most potent strain was identified via 16S rDNA sequencing. Crude extract was prepared through solid-state fermentation and solvent extraction. Antivirulence assays included MIC determination, violacein inhibition, biofilm suppression, AHL quantification, and swarming motility tests. Gene expression changes were analyzed by RT-qPCR, while bioactive metabolites were fractionated using silica gel chromatography and characterized by HR-LC-MS. In silico approaches, including molecular docking and molecular dynamics (MD) simulations, were applied to predict compound-receptor interactions. The extract showed a MIC of 128 μg/mL. At 64 μg/mL (sub-MIC), it inhibited biofilm formation (92%), violacein production (78%), and AHL levels (74%), while impairing motility. RT-qPCR confirmed downregulation of the QS-regulated cviR gene. HR-LC-MS profiling identified several metabolites, among which 3-dehydrosphinganine exhibited the highest docking affinity for the CviR receptor (Glide score - 9.688 kcal/mol). MD simulations further validated binding stability of 3-dehydrosphinganine and hexadecasphinganine. These findings highlight marine actinobacteria-derived metabolites as potent QS inhibitors with significant antivirulence potential.