3.10 Cell-penetrating peptide sequence in IRX4 homeodomain
TFs were considered as undruggable targets. Several approaches to target these TFs, such as inhibiting the protein-protein interactions and TF-DNA binding have been demonstrated in recent years80. DNA has been the target for various antiviral, anti-cancer and antimicrobial drugs wherein ligands bind to the major groove for inhibiting DNA-protein interactions 81. Interactions of short peptides with DNA and their effectiveness as anti-tumour, antibacterial or anti-inflammatory have recently been gaining attention. These peptides despite being an attractive entity, need work for improving their stability and their ability to penetrate the cells 82. Cell penetrating peptides (CPPs) have shown to be a potential therapeutic delivery agent entering cells via endocytosis. These CPPs have been found to be positively charged due to presence of several Arginine/lysine residues83. To check the efficacy of the homeodomain penetrating the cell membrane, we used different tools and databases including CPP site2.084, a database of cell-penetrating peptides and SkipCPP-Pred61. Using the CPP site2.0, we found more than 50% similarities in the C-terminal sequence, residues from 184-204 (MTLTQVSTWFANARRRLKKEN) of IRX4. The presence of positively charged amino acids in the C-terminal region highlights the potential of this region to be effective in cell penetration.
Additionally, this sequence from C-terminal homeodomain was subjected to SkipCPP-Pred to predict the effectiveness of this sequence (Table 6). The full-length 62 amino acid homeodomain had a low prediction confidence of 0.57 compared to the C-terminal residues, highlighting their potential to be in the class of cell penetrating peptides. The C-terminal sequence of IRX4 shares similarity with other IRXs. However, N-terminal of the homeodomain in all the IRX proteins offer specificity to these peptides.