Thienopyrimidines are one of the emerging classes among fused pyrimidines owing to their broad spectrum of pharmacological properties, including antimicrobial, anti-inflammatory, antimalarial, anticancer, etc. The anticancer activity of these compounds is mechanistically proven via the inhibition of validated drug targets such as EGFR, VEGFR-2, PI3K, and c-kit. In this research article, we designed and attempted synthesis of new 4-amino substituted 2-(4-bromobenzyl)-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines to explore their anticancer potential further. These heterocycles were designed based on pharmacophoric features of the core heterocycle, varying its C-4 substitution with a variety of amines and considering cancer protein-ligand interactions aiming to get potent lead molecules. The target compound-protein interaction complexes were analyzed, and lead compounds were identified based on their better binding affinity in molecular docking studies.