A new series of bis-benzimidazole clubbed with primary amine (3i-iii) and aromatic aldehydes (4i-ix) were design and synthesize with an intention to search an anticancer lead compound under microwave irradiation in good yields. Further, the spectral characterization of synthetic compounds were done with modern instrumental techniques such as FTIR, NMR (H and C), MS and elemental analysis. Anticancer activities of synthesized compounds were investigated at National Cancer Institute (NCI) against NCI 60 cell line panel, results showed good to notable anticancer activity. With the help of molinspiration, drug like properties and bioactivity score for drug targets of synthetic compounds were predicted and found to obey the Lipinski's rule, result indicates that the derivatives are orally active molecules. Osiris property explorer was used for the prediction of drug relevant properties and toxicity of synthetic compounds. Pre ADMET and Lazar toxicity was also used to estimate ADME and toxicity of synthetic compounds. Two compounds, 4i [(Z)-2-((1H-benzo[d]imidazol-2-yl) methyl)-1-(1H-benzo[d]imidazol-2-yl)-3-(thiophen-2-yl) prop-2-en-1-one] and 4iii [(Z)-2-((1H-benzo[d]imidazol-2-yl) methyl)-1-(1H-benzo [d] imidazol-2-yl)-3-(1H-pyrrol-2-yl)prop-2-en-1-one] were exhibited highest drug score and emerged as lead compounds and motivates for further development of more effective and safer compounds.