ArticleProteins2010
Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Programmable protein degraders enable selective knockdown of pathogenic β-catenin subpopulations in vitro and in vivo.Science advances · 2026Article
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- Efficient exploration of peptide libraries using active learning with AlphaFold-based screening.bioRxiv : the preprint server for biology · 2026Article
- Rational molecular design of novel class-III peptidic antagonists to competitively disrupt human PPARδ self-binding peptide.Journal of computer-aided molecular design · 2025Article
- Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics.Chemical reviews · 2025Review
- CDK2 Allosteric Modulators: The New Route in the Design of New Drugs as Anticancer and Non-hormonal Contraceptives.Current medicinal chemistry · 2025Review
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.Current medicinal chemistry · 2024Article
- Analysis, Modeling, and Target-Specific Predictions of Linear Peptides Inhibiting Virus Entry.ACS omega · 2023Article
- A Comprehensive Technology Platform for the Rapid Discovery of Peptide Inhibitors against SARS-CoV-2 Pseudovirus Infection.International journal of molecular sciences · 2023Article
- Chimeric Peptides fromToxins · 2023Article
- Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions.PLoS computational biology · 2023Article
- PD1 CD44 antiviral peptide as an inhibitor of the protein-protein interaction in dengue virus invasion.Peptides · 2022Article
- Fibronectin containing alternatively spliced extra domain A interacts at the central and c-terminal domain of Toll-like receptor-4.Scientific reports · 2022Article
- PepNN: a deep attention model for the identification of peptide binding sites.Communications biology · 2022Article
- Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design.Pathogens (Basel, Switzerland) · 2021Review
- Covalent flexible peptide docking in Rosetta.Chemical science · 2021Article
- Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors.Cell systems · 2021Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
In this study, we assess on a large scale the possibility of deriving self-inhibitory peptides from protein domains with globular architectures. Such inhibitory peptides would inhibit interactions of their origin domain by mimicking its mode of binding to cognate partners, and could serve as promising leads for rational design of inhibitory drugs. For our large-scale analysis, we analyzed short linear segments that were cut out of protein interfaces in silico in complex structures of protein-protein docking Benchmark 3.0 and CAPRI targets from rounds 1-19. Our results suggest that more than 50% of these globular interactions are dominated by one short linear segment at the domain interface, which provides more than half of the original interaction energy. Importantly, in many cases the derived peptides show strong energetic preference for their original binding mode independently of the context of their original domain, as we demonstrate by extensive computational peptide docking experiments. As an in depth case study, we computationally design a candidate peptide to inhibit the EphB4-EphrinB2 interaction based on a short peptide derived from the G-H loop in EphrinB2. Altogether, we provide an elaborate framework for the in silico selection of candidate inhibitory molecules for protein-protein interactions. Such candidate molecules can be readily subjected to wet-laboratory experiments and provide highly promising starting points for subsequent drug design.
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Registered trials
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