We investigated the effect of both electron donating group and e//lectron withdrawing group on biological activity of pyrimidine-based compounds as metalloproteinase-7 inhibitors and predicting a library of drug-like compounds with potent cytotoxicity using in silico approach. The selected compounds were optimized and subjected to both docking as well as absorption, distribution, metabolism, excretion and toxicity (ADMET) analyzes. We observed that the addition of electron withdrawing group (–CF3) to the predicted pyrimidine-based compound induced a radical improvement in the hydrogen bond strength with Leu181 and Ala182 in matrix metalloproteinase-7. Also, communal orientation of 2-mercapto-4-(3-(trifluoromethyl)phenyl)-6-((4-(trifluoromethyl)phenyl)amino) pyrimidine-5-carbonitrile (PC10) and matrix metalloproteinase-7 showed improved binding tendency with calculated binding affinity value of -10.2 kcal mol−1 than other studied compounds. Our findings may open door for the design and development of library of efficient pyrimidine-based drug-like compounds as potential anti-cancer agents.

The equilibrium geometries of α,α-ditert-butyl-4H-cyclopenta[2,1-b,3;4-b']dithiophene (DBDT) and α,α-ditert-butyl-4H-cyclopenta[2,1-b,3;4-b']dithiophene S-oxide (DBDTO) were studied at the DFT level of theory with a standard 6-311G* basis set. The molecular structures of the DBDT series were more planar than the corresponding DBDTO series, as revealed by dihedral angles. The UV-visible absorption calculated at TD-DFT/6-311G* showed two absorption peaks for all the molecules except C=S and C=O bridged molecules. In DBDTOs, C=S and C=O bridged molecules showed three and four absorption peaks, respectively. The DBDTOs had lower band gaps and longer wavelengths compared to the corresponding DBDTs.