Chemoselectivity of chlorine versus methylthio (–SCH3), methylsulfinyl (–SOCH3), or methylsulfonyl [–S (O) 2CH3] in either functionalization or substitution of pyridopyrimidinone and pyrimidopyrimidinone was studied. Utilization to prepare final targets for accelerated SAR studies via two-dimensional array syntheses has been demonstrated in both systems.