1,916
Views
8
CrossRef citations to date
0
Altmetric
Research Article

In silico identification and experimental validation of cellular uptake and intracellular labeling by a new cell penetrating peptide derived from CDN1

, , , , , , , ORCID Icon & ORCID Icon show all
Pages 1722-1736 | Received 24 Jun 2021, Accepted 26 Jul 2021, Published online: 31 Aug 2021

References

  • Amit C, Muralikumar S, Janaki S, et al. (2019). Designing and enhancing the antifungal activity of corneal specific cell penetrating peptide using gelatin hydrogel delivery system. Int J Nanomedicine 14:605–22.
  • Bachmair A, Finley D, Varshavsky A. (1986). In vivo half-life of a protein is a function of its amino-terminal residue. Science 234:179–86.
  • Calis JJ, Maybeno M, Greenbaum JA, et al. (2013). Properties of MHC class I presented peptides that enhance immunogenicity. PLOS Comput Biol 9:e1003266.
  • Carver T, Bleasby A. (2003). The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics 19:1837–43.
  • Colovos C, Yeates TO. (1993). Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–9.
  • Desale K, Kuche K, Jain S. (2021). Cell-penetrating peptides (CPPs): an overview of applications for improving the potential of nanotherapeutics. Biomater Sci 9:1153–88.
  • Ding Y, Zhao X, Geng J, et al. (2019). Intracellular delivery of nucleic acid by cell-permeable hPP10 peptide. J Cell Physiol 234:11670–8.
  • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. (2004). PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665–7.
  • Eiríksdóttir E, Konate K, Langel U, et al. (2010). Secondary structure of cell-penetrating peptides controls membrane interaction and insertion. Biochim Biophys Acta 1798:1119–28.
  • Eisenberg D, Lüthy R, Bowie JU. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404.
  • Elmquist A, Hansen M, Langel U. (2006). Structure-activity relationship study of the cell-penetrating peptide pVEC. Biochim Biophys Acta 1758:721–9.
  • England CG, Luo H, Cai W. (2015). HaloTag technology: a versatile platform for biomedical applications. Bioconjug Chem 26:975–86.
  • Feger G, Angelov B, Angelova A. (2020). Prediction of amphiphilic cell-penetrating peptide building blocks from protein-derived amino acid sequences for engineering of drug delivery nanoassemblies. J Phys Chem B 124:4069–78.
  • Gautam A, Chaudhary K, Kumar R, et al. (2013). In silico approaches for designing highly effective cell penetrating peptides. J Transl Med 11:74.
  • Geng J, Guo X, Wang L, et al. (2020). Intracellular delivery of DNA and protein by a novel cell-permeable peptide derived from DOT1L. Biomolecules 10:217.
  • Holehouse AS, Das RK, Ahad JN, et al. (2017). CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins. Biophys J 112:16–21.
  • Hu G, Miao Y, Luo X, et al. (2020). Identification of a novel cell-penetrating peptide derived from the capsid protein of chicken anemia virus and its application in gene delivery. Appl Microbiol Biotechnol 104:10503–13.
  • Ishida T, Kinoshita K. (2007). PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 35:W460–4.
  • Kardani K, Bolhassani A. (2021). Exploring novel and potent cell penetrating peptides in the proteome of SARS-COV-2 using bioinformatics approaches. PLoS One 16:e0247396.
  • Kardani K, Milani A, S HS, Bolhassani A. (2019). Cell penetrating peptides: the potent multi-cargo intracellular carriers. Expert Opin Drug Deliv 16:1227–58.
  • Klausen MS, Jespersen MC, Nielsen H, et al. (2019). NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning. Proteins 87:520–7.
  • Laskowski RA, Macarthur MW, Moss DS, Thornton JM. (1993). Procheck – a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–91.
  • Liu H, Zeng F, Zhang M, et al. (2016). Emerging landscape of cell penetrating peptide in reprogramming and gene editing. J Control Release 226:124–37.
  • Liu S, Kondo N, Long Y, et al. (2010). Membrane topology analysis of HIV-1 envelope glycoprotein gp41. Retrovirology 7:100.
  • Lomize AL, Pogozheva I. (2018). Modeling of peptide folding and translocation across membranes. Biophys J 114:267a.
  • Lomize MA, Pogozheva ID, Joo H, et al. (2012). OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res 40:D370–6.
  • Manavalan B, Subramaniyam S, Shin TH, et al. (2018). Machine-learning-based prediction of cell-penetrating peptides and their uptake efficiency with improved accuracy. J Proteome Res 17:2715–26.
  • Mészáros B, Erdos G, Dosztányi Z. (2018). IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res 46:W329–37.
  • Park SE, Sajid MI, Parang K, Tiwari RK. (2019). cyclic cell-penetrating peptides as efficient intracellular drug delivery tools. Mol Pharm 16:3727–43.
  • Pleschke JM, Kleczkowska HE, Strohm M, Althaus FR. (2000). Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 275:40974–80.
  • Qiang X, Zhou C, Ye X, et al. (2018). CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning. Brief Bioinform 21:11–23.
  • Ramachandran GN, Ramakrishnan C, Sasisekharan V. (1963). Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–9.
  • Reid LM, Verma CS, Essex JW. (2019). The role of molecular simulations in understanding the mechanisms of cell-penetrating peptides. Drug Discov Today 24:1821–35.
  • Schmidt S, Adjobo-Hermans MJ, Kohze R, et al. (2017). Identification of short hydrophobic cell-penetrating peptides for cytosolic peptide delivery by rational design. Bioconjug Chem 28:382–9.
  • Shen L, Hillebrand A, Wang DQ, Liu M. (2012). Isolation and primary culture of rat hepatic cells. J Vis Exp 64:e3917.
  • Toyohara D, Yokoi Y, Inoue G, et al. (2019). Abiotic factors promote cell penetrating peptide permeability in enterobacteriaceae models. Front Microbiol 10:2534.
  • Vacic V, Uversky VN, Dunker AK, Lonardi S. (2007). Composition profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinf 8:211.
  • Vivès E, Richard JP, Rispal C, Lebleu B. (2003). TAT peptide internalization: seeking the mechanism of entry. Curr Protein Pept Sci 4:125–32.
  • Wang H, Li X, Nakane S, et al. (2014). Co-expression of foreign proteins tethered to HIV-1 envelope glycoprotein on the cell surface by introducing an intervening second membrane-spanning domain. PLoS One 9:e96790.
  • Wang H, Ma J, Yang Y, et al. (2016a). Highly efficient delivery of functional cargoes by a novel cell-penetrating peptide derived from SP140-like protein. Bioconjug Chem 27:1373–81.
  • Wang H, Ma JL, Yang YG, et al. (2016b). Efficient therapeutic delivery by a novel cell-permeant peptide derived from KDM4A protein for antitumor and antifibrosis. Oncotarget 7:49075–90.
  • Wang H, Zhang M, Zeng F, Liu C. (2016c). Hyperosmotic treatment synergistically boost efficiency of cell-permeable peptides. Oncotarget 7:74648–57.
  • Wang H, Zhong CY, Wu JF, et al. (2010). Enhancement of TAT cell membrane penetration efficiency by dimethyl sulphoxide. J Control Release 143:64–70.
  • Wang S, Li W, Liu S, Xu J. (2016). RaptorX-property: a web server for protein structure property prediction. Nucleic Acids Res 44:W430–5.
  • Wei HH, Yang W, Tang H, Lin H. (2019). The development of machine learning methods in cell-penetrating peptides identification: a brief review. Curr Drug Metab 20:217–23.
  • Wei L, Tang J, Zou Q. (2017a). SkipCPP-pred: an improved and promising sequence-based predictor for predicting cell-penetrating peptides. BMC Genomics 18:742.
  • Wei L, Xing P, Su R, et al. (2017b). CPPred-RF: a sequence-based predictor for identifying cell-penetrating peptides and their uptake efficiency. J Proteome Res 16:2044–53.
  • Wilkins MR, Gasteiger E, Bairoch A, et al. (1999). Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 112:531–52.
  • Wu J, Li J, Wang H, Liu CB. (2018). Mitochondrial-targeted penetrating peptide delivery for cancer therapy. Expert Opin Drug Deliv 15:951–64.
  • Yang J, Zhang Y. (2015). I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43:W174–181.
  • Zhang M, Zhao X, Geng J, et al. (2019). Efficient penetration of Scp01-b and its DNA transfer abilities into cells. J Cell Physiol 234:6539–47.
  • Zhang P, Monteiro da Silva G, Deatherage C, et al. (2018). Cell-penetrating peptide mediates intracellular membrane passage of human papillomavirus L2 protein to trigger retrograde trafficking. Cell 174:1465–76.
  • Zhou N, Wu J, Qin YY, et al. (2017). Novel peptide MT23 for potent penetrating and selective targeting in mouse melanoma cancer cells. Eur J Pharm Biopharm 120:80–8.