ArticleInternational journal of molecular sciences2023
Design of Cyclic Peptides Targeting Protein-Protein Interactions Using AlphaFold.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 42 citations in OpenAlex.
- Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking.RSC medicinal chemistry · 2026Article
- Peptide Aptamers: Innovative Design and Applications in Pathogen Detection.Chembiochem : a European journal of chemical biology · 2026Review
- Cyclic Peptides as Modulators of Protein-Protein Interactions: A Survival Guide from Discovery Platforms to AI-Driven Design.International journal of molecular sciences · 2026Review
- The MDM2-p53 Axis in Osteosarcoma: Current Understanding of Regulatory Mechanisms and Targeted Therapeutic Strategies.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Mapping targetable sites on the human surfaceome for the design of novel binders.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tumor Targeting with Peptide-Drug Conjugates: Showcasing Key Progress and Hurdles.Drug design, development and therapy · 2026Review
- Differential Self-Assembly Behaviors and Proteolytic Stability of Bicyclic Peptides Compared to Monocyclic Peptides.Chemistry, an Asian journal · 2026Article
- An Integrated Meta-QTL and Transcriptome Analysis Provides Candidate Genes Associated with Drought Tolerance in Rice Seedlings.Plants (Basel, Switzerland) · 2025Article
- Predicted peptide scaffolds for drug screening in endometrial cancer organoids.Scientific reports · 2025Article
- Discovery of a Novel Anticoagulant Cystine Knot Peptide from Spider Venom Gland Transcriptome.International journal of molecular sciences · 2025Article
- Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.Journal of chemical theory and computation · 2025Article
- Deep active optimization for complex systems.Nature computational science · 2025Article
- Selective disruption of DNMT1/ELK1 interactions induces DGKI re-expression and promotes temozolomide sensitivity of MGMTClinical epigenetics · 2025Article
- Design of linear and cyclic peptide binders from protein sequence information.Communications chemistry · 2025Article
- Quadratic unconstrained binary optimization and constraint programming approaches for lattice-based cyclic peptide docking.Scientific reports · 2025Article
- Chemical Protein Engineering: Backbone Cyclization Rescues Folding of a 183-Residue Truncated Domain of Malaria Parasite Protein PfAMA1.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Emerging frontiers in protein structure prediction following the AlphaFold revolution.Journal of the Royal Society, Interface · 2025Review
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer.Frontiers in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
More than 930,000 protein-protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting PPIs, but it is difficult to predict the structure of a target protein-cyclic peptide complex or to design a cyclic peptide sequence that binds to the target protein using computational methods. Recently, AlphaFold with a cyclic offset has enabled predicting the structure of cyclic peptides, thereby enabling de novo cyclic peptide designs. We developed a cyclic peptide complex offset to enable the structural prediction of target proteins and cyclic peptide complexes and found AlphaFold2 with a cyclic peptide complex offset can predict structures with high accuracy. We also applied the cyclic peptide complex offset to the binder hallucination protocol of AfDesign, a de novo protein design method using AlphaFold, and we could design a high predicted local-distance difference test and lower separated binding energy per unit interface area than the native MDM2/p53 structure. Furthermore, the method was applied to 12 other protein-peptide complexes and one protein-protein complex. Our approach shows that it is possible to design putative cyclic peptide sequences targeting PPI.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.