Pseudomonas aeruginosa is an opportunistic pathogen, having complicated quorum sensing (QS) system utilizing multiple signals and receptors to coordinate virulence and pathogenicity. N-acyl-homoserine-lactones (AHLs) are the most common autoinducers responsible for regulation of QS-mediated virulence gene expression. There are four QS systems in P. aeruginosa among which the LasI/R and RhlI/R systems are regulated by 3-oxo-C₁₂-HSL and C₄-HSL respectively. They play a major role in host-associated pathogenesis. The LasR and RhlR binding specificity to cognate or non-cognate HSLs influences the QS-mediated responses. Here, we used computational approaches to consolidate the interaction of different types of HSLs produced by P. aeruginosa with LasR and RhlR receptors. To explore the binding affinity, fourteen different AHLs were subjected for molecular docking analysis with LasR and RhlR receptors. The RhlR was modelled using MMseqs2 in ColabFold: Alpha fold 2. Further, to validate the stability and interaction mechanism, molecular dynamic simulations was performed with the top docked six HSLs for 100 ns. In docking results, apart from 3-oxo-C₁₂-HSL and C₄-HSL, other HSLs such as C₁₆-HSL and C₆-HSL showed better binding affinity towards LasR and RhlR proteins, respectively. Further validation by molecular dynamic simulations showed that 3-oxo-C₁₀-HSL and 3-oxo-C₆-HSL formed stable complex with LasR and RhlR, respectively. Our comprehensive in silico study results may provide promising targets for development of anti-QS drugs against Las/Rhl QS systems.