Targeting SARS-CoV-2 variants with Bromelain: an in-silico study of Spike-ACE2 inhibition using docking, molecular...

SARS-CoV-2, responsible for COVID-19, continue to pose a significant global health challenge due to its high transmissibility and ability to evolve through mutations. The SARS-CoV-2 spike protein mediates viral entry by binding to the ACE2 receptor, making it a crucial target for therapeutics, with efforts focused on blocking this interaction to develop effective treatments against the virus and its evolving variants. Our study investigates the potential of Bromelain, a plant-derived protease, as a competitive inhibitor of ACE2 binding. We analysed the receptor-binding domain (RBD) of spike proteins from variants prevalent in the Indian subregion, including Wuhan, Delta, Omicron, JN.1.1, and JN.1.4. Sequence analysis revealed several mutations in emerging variants, with JN.1.1 and JN.1.4 exhibiting the highest levels of variation. Docking studies showed that Bromelain occupied ACE2 binding sites within the RBD at varying levels 57.89% for Wuhan, 42.1% for Delta, 47.36% for Omicron, 52.6% for JN.1.1, and 68.42% for JN.1.4, suggesting a competitive inhibition mechanism. Molecular dynamics simulations confirmed stable interactions across the variants. MM/PBSA calculations further validated Bromelain's interactions, supported by Principal Component analysis and Free Energy Landscape studies, with JN.1.4 demonstrating the strongest binding affinity. These findings align with prior studies demonstrating Bromelain's antiviral properties, including its ability to degrade viral proteins. Our findings highlight Bromelain as a promising antiviral candidate against emerging SARS-CoV-2 variants, particularly JN.1.1 and JN.1.4. Further in-vitro and in-vivo studies are suggested to explore Bromelain's therapeutic efficacy.

The online version contains supplementary material available at 10.1007/s40203-025-00446-x.