A number of 2-(aryl/alkyl) thio-3-chloro-l, 4-naphthoquinones (3a-g) and 2,3-( aryl/alkyl) thio-l, 4-naphthoquinones (4a-d, 4f-g) were obtained by the reactions of 2,3-dichloro-1,4naphthoquinone (1) with some various thiols and subsequently used as building blocks for the synthesis of 2-(arylthio)-3-amino-1,4-naphthoquinone (5a-c, 5f) derivatives. The substituted naphthoquinones were reacted with sodium azide in dimethylformamide and 2-arylthio-3-amino-1,4naphthoquinone derivatives were obtained as the sole identifiable products except one cyclized compound. PASS prediction results and their analysis provided by PharmaExpert software were used for the studied compounds to explore pharmacotherapeutic potential, possible mechanism of action and drug-metabolising enzyme inhibition. Furthermore, in vitro antimicrobial potential was evaluated against seven bacterial strains (Gram-positive and Gram-negative bacteria) and one fungi. Among the tested compounds, 3c was found to have the best level of antibacterial activity against S. aureus (MIC = 39.06 mu g/mL). Molecular docking studies were applied to better clarify the action and binding modes.