ArticleBMC bioinformatics2014
Designing of peptides with desired half-life in intestine-like environment.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 104 citations in OpenAlex.
- In silico design and In Vitro validation of WK15: a promising antimicrobial peptide for aquaculture applications.World journal of microbiology & biotechnology · 2026Article
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- Rational designing and synthesizing an antimicrobial peptide from bovine milk casein and evaluating its biological properties.Amino acids · 2025Article
- A Computational Approach for Designing a Peptide-Based Acetyl-CoA Synthetase 2 Inhibitor: A New Horizon for Anticancer Development.Cell biochemistry and biophysics · 2025Article
- Alzheimer's Disease Immunotherapy and Mimetic Peptide Design for Drug Development: Mutation Screening, Molecular Dynamics, and a Quantum Biochemistry Approach Focusing on Aducanumab::Aβ2-7 Binding Affinity.ACS chemical neuroscience · 2024Article
- A Novel Workflow for In Silico Prediction of Bioactive Peptides: An Exploration ofBiomolecules · 2024Article
- Introducing enzymatic cleavage features and transfer learning realizes accurate peptide half-life prediction across species and organs.Briefings in bioinformatics · 2024Article
- Machine learning for antimicrobial peptide identification and design.Nature reviews bioengineering · 2024Article
- Antibacterial activity of a short de novo designed peptide against fish bacterial pathogens.Amino acids · 2024Article
- Derivation of a novel antimicrobial peptide from the Red Sea Brine Pools modified to enhance its anticancer activity against U2OS cells.BMC biotechnology · 2024Article
- In silico molecular and functional characterization of a dual function antimicrobial peptide, hepcidin (GIFT-Hep), isolated from genetically improved farmed tilapia (GIFT, Oreochromis niloticus).Journal, genetic engineering & biotechnology · 2023Article
- New Bioactive Peptides from the Mediterranean SeagrassInternational journal of molecular sciences · 2023Article
- Article
- Computer simulation approach to the identification of visfatin-derived angiogenic peptides.PloS one · 2023Article
- Network Science and Group Fusion Similarity-Based Searching to Explore the Chemical Space of Antiparasitic Peptides.ACS omega · 2022Article
- A Novel Peptide with Antifungal Activity from Red Swamp CrayfishAntibiotics (Basel, Switzerland) · 2022Article
- Recent Progress in the Discovery and Design of Antimicrobial Peptides Using Traditional Machine Learning and Deep Learning.Antibiotics (Basel, Switzerland) · 2022Review
- Anti-Microbial Peptides: Strategies of Design and Development and Their Promising Wound-Healing Activities.Molecular biology reports · 2022Review
- Designing of a bispecific antibody against SARS-CoV-2 spike glycoprotein targeting human entry receptors DPP4 and ACE2.Human immunology · 2022Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn past, a number of peptides have been reported to possess highly diverse properties ranging from cell penetrating, tumor homing, anticancer, anti-hypertensive, antiviral to antimicrobials. Owing to their excellent specificity, low-toxicity, rich chemical diversity and availability from natural sources, FDA has successfully approved a number of peptide-based drugs and several are in various stages of drug development. Though peptides are proven good drug candidates, their usage is still hindered mainly because of their high susceptibility towards proteases degradation. We have developed an in silico method to predict the half-life of peptides in intestine-like environment and to design better peptides having optimized physicochemical properties and half-life.
resultsIn this study, we have used 10mer (HL10) and 16mer (HL16) peptides dataset to develop prediction models for peptide half-life in intestine-like environment. First, SVM based models were developed on HL10 dataset which achieved maximum correlation R/R2 of 0.57/0.32, 0.68/0.46, and 0.69/0.47 using amino acid, dipeptide and tripeptide composition, respectively. Secondly, models developed on HL16 dataset showed maximum R/R2 of 0.91/0.82, 0.90/0.39, and 0.90/0.31 using amino acid, dipeptide and tripeptide composition, respectively. Furthermore, models that were developed on selected features, achieved a correlation (R) of 0.70 and 0.98 on HL10 and HL16 dataset, respectively. Preliminary analysis suggests the role of charged residue and amino acid size in peptide half-life/stability. Based on above models, we have developed a web server named HLP (Half Life Prediction), for predicting and designing peptides with desired half-life. The web server provides three facilities; i) half-life prediction, ii) physicochemical properties calculation and iii) designing mutant peptides.
conclusionIn summary, this study describes a web server 'HLP' that has been developed for assisting scientific community for predicting intestinal half-life of peptides and to design mutant peptides with better half-life and physicochemical properties. HLP models were trained using a dataset of peptides whose half-lives have been determined experimentally in crude intestinal proteases preparation. Thus, HLP server will help in designing peptides possessing the potential to be administered via oral route (http://www.imtech.res.in/raghava/hlp/).
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