Prediction of cell-penetrating potential of modified peptides containing natural and chemically modified residues

Vinod Kumar, Piyush Agrawal, Rajesh Kumar, Sherry Bhalla, Salman Sadullah Usmani, Grish C. Varshney, Gajendra P.S. Raghava

Research output: Contribution to journalArticlepeer-review

34 Scopus citations

Abstract

Designing drug delivery vehicles using cell-penetrating peptides is a hot area of research in the field of medicine. In the past, number of in silico methods have been developed for predicting cell-penetrating property of peptides containing natural residues. In this study, first time attempt has been made to predict cell-penetrating property of peptides containing natural and modified residues. The dataset used to develop prediction models, include structure and sequence of 732 chemically modified cell-penetrating peptides and an equal number of non-cell penetrating peptides. We analyzed the structure of both class of peptides and observed that positive charge groups, atoms, and residues are preferred in cell-penetrating peptides. In this study, models were developed to predict cell-penetrating peptides from its tertiary structure using a wide range of descriptors (2D, 3D descriptors, and fingerprints). Random Forest model developed by using PaDEL descriptors (combination of 2D, 3D, and fingerprints) achieved maximum accuracy of 95.10%, MCC of 0.90 and AUROC of 0.99 on the main dataset. The performance of model was also evaluated on validation/independent dataset which achieved AUROC of 0.98. In order to assist the scientific community, we have developed a web server "CellPPDMod" for predicting the cell-penetrating property of modified peptides.

Original languageEnglish
Article number725
JournalFrontiers in Microbiology
Volume9
Issue numberAPR
DOIs
StatePublished - 12 Apr 2018
Externally publishedYes

Keywords

  • Antimicrobial peptide
  • Chemical descriptors
  • In silico method
  • Machine learning
  • Modified cell-penetrating peptides
  • Random Forest
  • SVM

Fingerprint

Dive into the research topics of 'Prediction of cell-penetrating potential of modified peptides containing natural and chemically modified residues'. Together they form a unique fingerprint.

Cite this