Mechanistic In-Silico Insights into the Anti-quorum Sensing Potential of Coumaric Acid and Syringic Acid in Serratia marcescens with Invitro Analysis.

Abstract

Antibiotic resistance presents a major global health threat, especially with ESKAPE pathogens like Serratia marcescens, which exhibit resistance to all known antibiotics. Quorum sensing (QS) is key to its virulence and resistance, emphasizing the need for novel natural antimicrobial agents. This study investigates two plant-derived phenolic compounds, coumaric acid and syringic acid, targeting QS proteins of S. marcescens using in silico molecular docking, molecular dynamics simulations, and in vitro biochemical assays. Validated homology models of eight QS-associated proteins-BsmA, FimA, FimC, FlhD, LuxS, PigP, RsmA, and RssB-were employed for molecular docking studies, ADME (absorption, distribution, metabolism, and excretion) profiling, and 100-ns molecular dynamics (MD) simulations to evaluate ligand-binding stability. Coumaric acid displayed more desirable physicochemical properties (logP 1.79; TPSA 57.53 Ų) compared to syringic acid (logP 1.04; TPSA 75.99 Ų). Binding energy calculations indicated a stronger affinity of coumaric acid for six of the proteins, with the LuxS-coumaric acid complex showing the most significant interaction (ΔGbind - 21.74 ± 3.01 kcal/mol). Analysis of the MD trajectory revealed that coumaric acid enhanced protein stability, as shown by reductions in RMSF (root mean square fluctuation), a more compact Rg (radius of gyration), decreased SASA (solvent-accessible surface area), alterations in the Dictionary of secondary structure of protein (DSSP), and consistent hydrogen bonding. Conversely, syringic acid induced increased conformational flexibility and destabilized alpha-helices and beta-sheets in specific proteins. Principal component analysis (PCA) confirmed tighter conformational clustering in coumaric acid complexes, consistent with improved stabilization. Furthermore, antibacterial assays demonstrated strong inhibitory effects, with MIC values of 700 µg/mL for coumaric acid and 1000 µg/mL for syringic acid. Coumaric acid displayed a bactericidal effect, whereas syringic acid was bacteriostatic. Additionally, time-kill assays revealed a dose-dependent reduction in bacterial growth over 48 h following treatment with varying concentrations of these phenolic acids . Interestingly, qPCR analysis of QS-specific gene expression showed significant downregulation of key QS-regulated genes in response to both compounds, highlighting their potential as quorum-sensing inhibitors and supporting their development as alternative antimicrobial agents against antibiotic-resistant S. marcescens.