A simple, mild, and efficient protocol has been developed for the synthesis of 3,3′-bis(indolyl)methanes (BIMs) using prolinium hydrogen sulfate (ProHSO4) as a catalyst under solvent-free and support-free conditions. This mechanochemical method undergoes electrophilic substitution reaction of indole with diverse aldehydes to afford the desired BIMs in high yields at room temperature. Due to diverse pharmacological utility, the synthesized BIMs were subjected to in silico studies. The structure activity analysis of BIMs revealed their ability to bind Eg5 kinesin, Human p38 α MAP Kinase, and Human 3 alpha HSD type 3 as a potential protein target for anticancer activity. The compounds exhibited higher binding affinities with Eg5 kinesin having hydrophobic interactions with α2, α3 helices and loop5 amino acid residues. Moreover, molecular docking with Human p38 α MAP Kinase protein depicted compounds as ATP-competitive molecules interacting with hydrophobic region I, II and allosteric DFG motif. A total of 13 derivatives were synthesized and subjected for in silico screening for predicting potential biological activity. Among them,3b, 3d, 3f, 3 g, 3i, 3j, and 3 k compoundswere identified as potential inhibitors of Eg5 kinesin, Human p38 α MAP Kinase, and Human 3 alpha HSD type 3, and their evaluation in the biological experimental system is warranted.