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In this study, due to the importance of dipeptide compounds in diagnosis of disease or as drug compounds, new dipeptide compounds were synthesized using pyrimidine derivatives of thymine and uracil. The reaction of Methyl 2- (5-methyl-2,4-dioxo-4,3-dihydropyrimidine-1 (2 H) -yl) acetate and methyl 2-2,4-dioxo-4,3-dihydropyrimidine -1 (2H) -Il) acetate with diamine derivatives lead to the production of dipeptide derivatives in good yield. Then, using the computational design of the drug by the molecular docking method, the inhibitory effect of synthetic compounds on the LasR regulatory protein of Pseudomonas aeruginosa quorum sensing system, which plays an important role in regulating the expression of pathogenic genes in bacteria, were investigated. The results of the study showed that synthetic compounds have a significant inhibitory effect on the LasR protein.