In-silico modeling of SHLP6: A novel mitochondrial peptide controlling neurodegeneration and cellular aging

Small humanin-like peptide-6 (SHLP6), is derived from the mitochondrial genome. The 3D structure of SHLP6 was evaluated using PEPstr, with homology modeling predicting a Cyt-C structure with a DOPE score of -645.717 and a GA341 score of 0.2832. The analysis showed that 96.5 % of residues were in favored regions in the Ramachandran plot, indicating a stable protein conformation. Molecular docking studies revealed that SHLP6 has binding affinities with apoptotic proteins such as Caspase 8 (-77.6 ± 2.9 kcal/mol), Bcl-2 (39.2 ± 15.3 kcal/mol), Bax (43.6 ± 7.7 kcal/mol), Cyt-C (-53.2 ± 8.7 kcal/mol), and CAT (-62.5 ± 1.3 kcal/mol). The interaction of SHLP6 with DRP1 (-47.7 ± 1.9 kcal/mol) was found to promote apoptosis, while interactions with SIRT1 (-49.1 ± 4.7 kcal/mol), IGF-1 (-58.7 ± 3.6 kcal/mol), and INSR (-66.4 ± 3.4 kcal/mol) suggest a potential role in controlling neurodegeneration. Molecular dynamics simulations confirmed the compact conformation of Caspase-8, high structural stability of SIRT1, and flexibility of DRP1. Treatment with SHLP6 (40 μg/ml) reduced developmental toxicity and improved antioxidant enzyme levels (SOD and CAT) in stress-induced zebrafish larvae. SHLP6 treatment also improved AChE levels in H₂O₂-exposed zebrafish larvae. SHLP6 treatment upregulated SOD, CAT, PRKN, p62, LCIII, SIRT1 and NDUFS4 genes, while modulating inflammation by downregulating TNF-α through IL-10 upregulation. SHLP6 efficiently restored locomotory activity in stress-induced zebrafish larvae. FTIR analysis indicated alterations in the secondary structure of proteins, and Congo red staining showed a 10 % decrease in BSA aggregation with SHLP6 treatment. These findings suggest that SHLP6 can be a promising therapeutic agent in enhancing antioxidant defenses, restoring mitochondrial health, and modulating inflammatory responses to mitigate oxidative stress-induced cellular dysfunction.