Development of new antimicrobial agents is a better solution to rectify drug resistance problems in society. In this circumstances new functionalized sulphur bearing heterocyclic moiety were designed, synthesized and evaluated for their in vitro antibacterial activity. The present work encompasses the designing novel series of thiophene substituted analogous linked to para amino acetophenone and different aldehydes were successfully synthesized and biological activity was predicted using various computational software's such as Chemsketch, Molinspiration, and admetSAR. Among the synthesized thiophene substituted chalcones T-IV-I and thiophene T-IV-B displayed significant activity against Streptococcus auresis. Compounds T-IV-J, T-IV-H and T-IV-C bearing sulphur moiety possess better activity against Staphylococcus aureus. Moreover T-IV-C and T-IV-J exhibits good antibacterial activity against E. coli and Pseudomonas aeruginosa. In general, most of the synthesized compounds exhibited remarkable antibacterial activity due to the presence of sulphur atom in the heterocyclic moieties as well as its lipophilic characters. Molecular docking studies indicated that the synthesized compounds are potent inhibitor of microsomal enzyme Glutathione-S-transferases (PDB ID: 1GNW) also find the different interacting residues, bond distanceand nature of bondingbetween the target and the ligand molecules. The results provide important information for the future design of more effective antibacterial agents.