Cancer has scrolled up to the second position and has become the leading cause of deaths worldwide responsible for 9.6 million of deaths in 2018 across the globe. Colon cancer is the cancer of alimentary canal that starts with the development of abnormal projection of tissue or mucous membrane surrounding the inner lining of the colon and rectum called as polyps. These polyps may be malignant or benign and over time can develop into cancers, which further invade to inner layers resulting in cancerous lesions. The designed methodology is proposed for the design and synthesis to of anti-cancer agents to target colon cancer with the help of heterocyclic fragments to design a clubbed pharmacophoric lead molecule. The two heterocycles reported for anti-cancer activity: thioquinazolinone and benzothiazole were clubbed together to form a new lead molecule which were decorated with different substituents. The designed set of molecules were virtually screened for drug-like properties, toxicity and docking. The synthesized compounds were tested for pharmacological activity with cell viability testing assay with Trypan Blue Exclusion method against Colon Cancer HT29 cell lines of which the compounds C3 and C7 showed highest inhibitory activity compared to others and standard anti-cancer drug. Thus, the study involves design and development of ligands targeting colon cancer parallel with in-silico computational approaches to tackle cancer with fragment-based drug design method rational way towards drug design and development with promising results