This paper deals with the study on the effects of a novel epoxy steroid (NES) extracted from the parotid gland of the Indian toad (Bufo melanostictus) on the liver, kidney, and colon. NES is a new chemical compound and it is first time reported with potential protective effects on organ toxicities from Indian toad venom. The Indian toad parotid secretion-derived chemical was isolated, identified as NES and tested for its potential of protective effect. NES was identified by using infrared, 1D, and 2D approaches. The in-silico investigations showed that it has a higher affinity for TNF-α and IL-6. By exposing mice to organ toxicity induced by Dextran Sodium Sulphate and Bisphenol A in the colon, kidneys, and liver, NES was able to target the production of IL-6 and TNF-α. NES significantly suppressed the IL-6 and TNF-α level in all selected organ toxicities in a dose a dependent manner and revealed prominent protection by inhibiting TNF-α. It was further confirmed by the histo-pathological recovery of the damaged cells and immunohistology suppression of CD 68 expression when compared to the induced groups. Further, the structural parameters of the new compound NES were determined from the optimized molecular geometry, approaching the quantum chemical computations employing density functional theory (DFT) using Becke's hybrid functional (B3LYP) along with 6–311++G(d,p) basis set. HOMO-LUMO energy gap was performed to assess the chemical reactivity and biological activity.