Earthworm as a Sustainable Bioreactor: Biotransformed Nigella sativa Metabolites as Potential Dual Modulators of HDAC2 and BCL2 for HIV Latency: An Integrated Computational and Zebrafish Study

Abstract

Earthworm-mediated biotransformation offers a sustainable strategy to enhance the biological potential of natural products through the generation of structurally modified bioactive metabolites. In this study, Eisenia fetida was employed as a living bioreactor to biotransform Nigella sativa (black cumin), and the resulting methanolic extracts were evaluated using integrated experimental and computational approaches. GC–MS profiling revealed distinct alterations in the metabolite composition of the black cumin-fed earthworm extract compared with the kitchen waste-fed control, indicating the formation of biotransformed metabolites. The biotransformed extract exhibited enhanced antioxidant, anti-inflammatory and erythrocyte membrane-stabilizing activities, together with selective antibacterial activity against Staphylococcus aureus and antifungal activity against Aspergillus niger. Zebrafish (Danio rerio) embryo toxicity assays demonstrated concentration-dependent developmental toxicity, with the bio-transformed extract exhibiting a higher median lethal concentration (LC₅₀ = 229.89 µg/mL) than the control extract (LC₅₀ = 147.10 µg/mL), indicating improved embryonic biocompatibility following earthworm-mediated biotransformation. Network pharmacology identified HDAC2 and BCL2 as key host proteins associated with HIV latency, epigenetic regulation and apoptosis. Molecular docking predicted favourable interactions of Benzoic acid, 3-formyl-2,4-dihydroxy-6-methyl-, methyl ester, identified as the prominent bio-transformed metabolite, exhibited favourable binding to HDAC2 (− 8.16 kcal mol⁻¹) and BCL2 (− 6.75 kcal mol⁻¹), supporting it as a putative as a dual-target candidate and provide a hypothesis for further experimental investigation, rather than demonstrating direct target modulation. Collectively, these findings indicate that earthworm-mediated biotransformation enhances both the biological activity and safety profile of N. sativa, highlighting the potential of earthworms as sustainable living bioreactors for generating novel metabolites with promising therapeutic applications in HIV latency and associated pathways.

Graphical Abstract