Research Article
Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study
Table 1
List of CPPs included in the study.
| | CPP type | CPP name | Amino acid sequence (underlined residues are positively charged) | Residue count | Nominal charge (charge per residue) |
| | Cationic cell penetrating peptides | Penetratin [44, 45] | RQIKIWFQNRRMKWKK | 16 | +7 (0.44) | | HIV-TAT (47–57) [46, 47] | YGRKKRRQRRR | 11 | +8 (0.72) | | R10 [48, 49] | RRRRRRRRRR | 10 | +10 (1.00) | | CCMV Gag (7–25) [49–51] | KLTRAQRRAAARKNKRNTRGC | 21 | +9 (0.43) | | Chimeric dermaseptin S4 and SV40 ‘S413-PV’ [11, 34] | ALWKTLLKKVLKAPKKKRKVC | 21 | +9 (0.43) |
| | Amphipathic cell penetrating peptides | Transportan [52] | GWTLNSAGYLLGKINLKALAALAKKIL | 27 | +4 (0.15) | | pVEC (vascular endothelial cadherin) [53–56] | LLIILRRRIRKQAHAHSK | 18 | +6 (0.33) | | MPG [57, 58] | GALFLGFLGAAGSTMGAWSQPKKKRKV | 27 | +5 (0.16) | | CADY [59, 60] | GLWRALWRLLRSLWRLLWRA | 20 | +5 (0.25) | | sC18 [61] | GLRKRLRKFRNKIKEK | 16 | +8 (0.50) | | C6 [62] | RLLRLLLRLWRRLLRLLR | 18 | +7 (0.39) |
| | Hydrophobic cell penetrating peptides | K-FGF (Kaposi’s sarcoma fibroblast growth factor) [63] | AAVALLPAVLLALLAP | 16 | 0 (0.00) | | Integrin β3-fragment [64, 65] | VTVLAGALAGVGVG | 14 | 0 (0.00) | | Hepatitis B virus translocation motif [66] | PLSSIFSRIGDP | 12 | 0 (0.00) | | Grb2 (SH2 domain) [67] | AAVLLPVLLAAP | 12 | 0 (0.00) | | Fusion sequence HIV-1 gp41(1–23) [46, 68] | GALFLGFLGAAGSTMGA | 17 | 0 (0.00) | | C105Y [69] | CSIPPEVKFNKPFVYLI | 17 | +1 (0.06) |
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