A series of piperazine-based phthalimide derivatives 5 (a-l) were synthesized and extensively characterized using a variety of spectrum methods, including LC-MS, 1H-NMR, 13C-NMR, and FT-IR. All the derivatives were examined for their physicochemical, pharmacokinetic, bio-activity score, and PASS analysis. The 5e piperazine-based phthalimide derivative demonstrated promising antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) in the in vitro antibacterial studies. In comparison to streptomycin and bacitracin (10 µg/mL), the minimum inhibitory concentration of 5e against MRSA was discovered to be 45±0.15 micro g/ml. The anti-MRSA activity was validated with membrane damage studies by using SEM, and in silico docking studies were against 3VMT and 6FTB proteins of MRSA. In the toxicity study, 5e derivatives were evaluated against L6 cell lines. The results of the studies show the synthesized 2-(2-(4-((4-chlorophenyl) sulfonyl) piperazin-1-yl) ethyl) isoindoline-1,3-dione (5e) can be used for the development of anti-MRSA drugs.