Squalene as a Candidate Signalling Molecule: Computational Evidence for a Predicted KEAP1 Interaction and Implications for Stress-Induced Altruistic Stem-Cell Niche Protection

Stem and progenitor cells must protect themselves and their niche when subjected to cytotoxic stress. Our lab has previously found altruistic stem-cell traits and shown squalene's cytoprotective effects in haematopoietic and mesenchymal cells. Recent research links hypoxia-induced squalene buildup with protection from lipid peroxidation, while other studies implicate NRF2 in this protective process.

The exact mechanism by which squalene interacts with the NRF2 pathway is still unclear. To address this, we examined the structural possibility of squalene binding to the KEAP1 Kelch domain using molecular docking on three KEAP1 crystal structures (PDB IDs: 6TYM, 6SP4, and 5CGJ). Our docking process was assessed through native-ligand redocking, resulting in RMSD values of 0.826, 0.277, and 0.303 Å, respectively.

Squalene was found to fit snugly into the KEAP1 Kelch domain's hydrophobic pocket, with docking scores of 7.905, 7.513, and 6.756 kcal/mol. The predicted interaction mainly involved hydrophobic residues such as Arg415, Arg380, and Asn414, without conventional hydrogen bonding. These results suggest that squalene may indeed interact with the KEAP1 Kelch domain, potentially linking stress-responsive squalene metabolism to KEAP1-NRF2 regulation.

However, docking studies alone do not confirm direct binding, physiological accessibility, KEAP1 inhibition, or functional NRF2 activation. Additional biophysical, molecular dynamics, and cellular experiments are needed to determine the biological relevance of this predicted squalene-KEAP1 interaction.