A new series of 1,3,4-thiadiazole were synthesized under microwave irradiation. Confirmation of the chemical structure of synthesized compounds was substantiated by IR, NMR and Mass spectroscopy. The derivatives with potent antibacterial activity were subjected to molecular docking studies to investigate the interactions between the active derivatives and amino acid residues existing in the active site to assess their antibacterial potential which docked against receptor crystal structure of Rhodostomin ARLDDL mutant (PDB Code-3UCI). The docking results highlight that fact that the compounds code 3b exhibited good docking score. All the synthesized compounds were screened for antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus and Staphylococcus aureus by disc diffusion method. Some of the compounds exhibited good antibacterial activity as compared to standard drug. This study provides valuable directions to our ongoing endeavor of rationally designing more potent antimicrobial agents.