The synthesis of potent antibacterial agents, free from side effects and resistant to bacterial enzymes, is the main objective for drug designers. Also, the multi-target drugs have an important role in advanced drug synthesis. The azo-malonate compounds II a & b were prepared from the diazo coupling reaction of aniline derivatives with the acidic methylene group of diethyl malonate. The new azo-malonate derivatives II a–c were reacted with urea or thiourea in the presence of sodium ethoxide, afforded the target new azo-pyrimidine compounds III a & b and IV a & b. The structure of the new compounds was elucidated by using NMR, IR, mass spectroscopy, and elemental analysis. The minimum inhibitory concentration of new azo-compounds III a & b and IV a & b was evaluated for their antibacterial activity. Two new synthesized azo-compounds showed weak (III b) to strong (IV b) antibacterial activity. The molecular operating environment docking program was used for the prediction of the compound IV b action mechanism.
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