In the present study, total fifteen compounds of 1,2,4,5-tetraoxane derivatives were docked. Two series of 1,2,4,5-tetraoxane derivatives were taken for molecular docking studies, one tetraoxaquines, a hybrid of two pharmacophores such as 4-aminoquinoline & 1,2,4,5-tetraoxane, and other dispirotetraoxanes. The docking studies were performed into the binding pocket of a falcipain-3 protein (pdb: 3bwk - hydrolase) by using the Ligand fit module within docking server. The results showed a better binding affinity of hybrid tetraoxaquines compared to dispirotetraoxanes at the active site of falcipain-3 because of very low binding energies for falcipain-3 protein (pdb: 3bwk - hydrolase). Therefore, hybrid tetraoxaquines are better Cysteine proteases (falcipains) inhibitors. They would be potent antimalarial agents. So the proposed inhibitors in the future could be more effective to treat malaria.