Synthesis of some new pyrazolo[3,4-d]pyrimidine derivatives using readily available starting materials are described. A one-pot multi component cyclocondensation reaction was used to prepare the novel 3-methyl-4 aryl-1-phenyl-1H-pyrazolo[3,4-d]pyrimidine-6-thiol which served as a new starting material for all new compounds in this research. The anti-microbial activities of the selective synthesized compounds have been evaluated. Some of the newly prepared compounds were found to have moderate to strong anti-microbial activity, e.g., compound 4a, 6a, and 8, in comparison to the reference drugs. Molecular modeling of the most three biologically active new compounds 4a, 6a, and 8 compared to the reference drugs tobramycin and fluconazole was carried out using Fieldalign 2.0 software.