CPPsite 2.0 is the updated version of cell penetrating peptides database (CPPsite). It is a manually curated database and holds 1855 entries, including more than 1000 new entries. Data was collected and compiled from research articles and patents. In the updated version, additional fields were incorporated that provide information on (i) diverse chemical modifications, (ii) in vitro/in vivo model systems and (iii) different cargoes delivered by CPPs. CPPsite 2.0 covers different types of CPPs that includes linear, cyclic, and CPPs with various non-natural residues. In addition, it provides structural information of CPPs.
CPPsite 2.0 is the only platform for complete & relevant information for large number of CPPs. It has following applications:
CPPsite 2.0 provides different datasets for the development of various prediction tools. For example, one of the major drawbacks of CPP-based drug delivery system is the poor bioavailability. After internalization, CPP-cargo complexes are entrapped into the vesicular compartments (endosomes) and subsequently degrade into the lysosomes and thus the bioavailability is severely reduced. Therefore, different types of chemically modified CPPs have been developed over the years to improve the endosomal escape of CPP-cargo complexes in order to enhance the bioavailability. CPPsite 2.0 provides comprehensive information of such type of chemical modifications. User can collect this information from the database and can develop datasets for the prediction of endosmolytic peptide, which can easily escape from endosomes before being degraded into the lysosomes. Similarly, user can develop datasets for prediction tools for non-natural CPPs.
Data was collected from research articles and patents. In order to collect the comprehensive information on CPPs, research articles were retrieved from PubMed using various combinations of key words like “cell-penetrating peptides”, “membrane transduction peptides”. From these articles, only research papers, providing information of experimentally validated CPPs and their analogs, were selected. Information of CPP sequences, their family, names, and other relevant experimental information like uptake efficiency, sub-cellular localization, terminal modifications, in vitro/in vivo model systems (cell lines or animal models), etc. were extracted manually. Finally, CPPsite 2.0 contains total 1855 entries (843 from previous version and 1012 new entries).
CPPsite 2.0 provides the users a comprehensive information of the CPPs giving details like their sequence, length, origin, chirality, nature, N-terminal modifications, C-terminal modifications, uptake efficiency, uptake mechanism, in vitro/in vivo models systems used for CPP evaluation and various cargoes delivered by CPPs. Also, various tools like BLAST, Smith-waterman, Mapping and alignment have been integrated to make it more user friendly.
|ID||All the cell penetrating peptides have been assigned a unique id number which is constant throughout the database.||1025|
|PMID||It is a PubMed identification number for further reference.||20374250|
|SEQUENCE||It provides the amino acid sequence of peptide||RRRRRGADFASDLF|
|CATEGORY||It represents the one of the three categories (Protein derived, synthetic, Chimeric) to which it belongs.||Protein Derived|
|CHIRALITY||It represents the chirality of peptide.||D|
|PEPTIDE NAME||It represents name of the peptide used in literature.||Tat|
|NATURE||It represents the nature of peptide.||Cationic|
|SUB-CELLULAR LOCALIZATION||This field gives information about the sub-cellular localization of peptide inside the cell.||Nucleus|
|UPTAKE EFFICIENCY||It gives the information about the relative efficiency of peptide.||High|
|N-TERMINAL MODIFICATION||This field contains the information about N-terminal modification of peptide.||FITC labeling|
|C-TERMINAL MODIFICATION||This field contains the information about N-terminal modification of peptide.||Amidation|
|CHEMICAL MODIFICATION||This field contains the information about any chemical modification within the sequence of peptide.||Ornithine insertion|
|UPTAKE MECHANISM||It gives the information about the mechanism of CPP uptake.||Endocytosis|
|IN VITRO/IN VIVO||It gives the information about the model systems in which CPPs were tested.||In Vivo|
|CELL LINE USED||It tells about the cell line used for validation of CPP.||HeLa|
|Animal model||It tells about the animal model used for testing of CPP.||BALB/C Mice|
|Cargo Types||It tells about the entity used as cargo for delivery in various model systems using CPPs.||Nucleic Acids|
|PATENT||It provides the patent information.||US 20100168034|
|STRUCTURE||This field represents the structure of CPPs predicted by PEPstr, a webserver developed by our group. Due to the limitation of the PEPstr, we only predicted the structure of peptides containing natural amino acids.||3D structure|
|NET CHARGE||Represents the net charge on the peptide.||+1|
|HYDROPHOBICITY||Represents the overall hydrophobicity of the peptide.||33.33|
|MOLECULAR WEIGHT||Represents the molecular weight of peptide.||1025.32|
|pI||Represents the isoelectric point of the CPP.||4|
|AA FREQUENCY||Represents the frequency of each amino acid present on the peptide.||5|
|AA COMPOSITION||Represents the percentage composition of each amino acid present in the peptide.||50.00|
|SECONDARY STRUCTURE INFORMATION||Represents the secondary structure conformational state of each amino acid present in the peptide.||Helix, Coil, Strand|
Answer: CPPsite 2.0 is the updated version of cell penetrating peptide database (CPPsite).Q2. Is CPPsite 2.0 a curated database?
Answer: Yes, it is a manually curated database and data was collected from research articles and patents.Q3. How is CPPsite 2.0 different from previous version?
Answer: A major update was performed on CPP data in CPPsite 2.0. The first version (CPPsite) contains total 843 entries and provides structures of only CPPs having natural amino acids. CPPsite 2.0 holds total 1855 entries with 1012 new recent entries. Three additional fields (i) chemical modifications, (ii) in vitro/in vivo model systems used for CPP evaluation, and (iii) cargoes types (fluorophore, nanoparticles, protein, peptide, nucleic acid, etc) delivered by CPPs has been incorporated in the updated version, which was not available in the pervious version. Also, CPPsite 2.0, provides structure of CPPs having natural as well as non-natural residues.Q4. Does CPPsite 2.0 provide information of chemically modified CPPs?
Answer: Yes, CPPsite 2.0 contains information of diverse types of chemical modifications, including end modifications (acylation, amidation, stearylation, biotinylation), non-natural residues (ornithine, beta-alanine,), side chain modifications, peptide backbone modifications, and linkers (amino hexanoic acid).Q5. Does CPPsite 2.0 give information of peptide structures?
Answer: Yes, CPPsite 2.0 provides information of predicted secondary and tertiary structures of CPPs including structure of CPPs having D-amino acids and few modified residues like ornithine and beta-alanine.Q6. Is CPPsite website compatible for smartphone?
Answer: Yes, we have built user-friendly responsive website, which is compatible for desktop, tablet and smartphone.