Various novel heterocyclic compounds containing pyrimidine nuclei 5H-chromeno[4,3-d]pyrimidine (4a-c, e-h, l-r, t) and pyrimidine-5-yl-(2-hydroxyphenyl)methanone (5a, c, d, f-k, m-o, r, s, u) were synthesized from the reaction of guanylhydrazones (2a-u) and 3-formylchromone (3). These compounds were tested against human liver hepatocellular carcinoma cell line (HepG2) and human breast adenocarcinoma cell line (MDA-MB-231) using the MTT assay method. Furthermore, molecular docking calculations were performed to compare the biological activities of various novel heterocyclic compounds against cancer proteins. In these calculations, the protein used are crystal structure of the BRCT repeat region from the breast cancer associated protein, 1JNX, crystal structure of VEGFR kinase (liver cancer) protein, 3WZE, and crystal structure of an allosteric Eya2 phosphates inhibitor (lung cancer) protein, 5ZMA, respectively. After molecular docking calculations, absorption, distribution, metabolism, and excretion/toxicity analysis was performed to examine the properties of various novel heterocyclic compounds for their future use as drugs.