ArticleBiophysical journal2019
β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking.RSC medicinal chemistry · 2026Article
- StrEAMM-Thioether: Efficient Structure Prediction for Thioether-Linked Cyclic Peptides.The journal of physical chemistry. B · 2026Article
- Asymmetric Mannich Reaction of α-(2-Nitrophenylsulfenyl)imino Acetamide: A Cyclization-Driven Process.Molecules (Basel, Switzerland) · 2026Article
- Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.Journal of chemical theory and computation · 2025Article
- Computational Design of a Bicyclic Peptide Inhibitor Targeting the ICOS/ICOS-L Protein-Protein Interaction.Chemical biology & drug design · 2025Article
- Unsupervised learning of collective variables for conformational sampling of cyclic peptides.Methods in enzymology · 2025Article
- Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides.The journal of physical chemistry. B · 2024Article
- One-pot chemoenzymatic syntheses of non-canonical amino acids.Journal of industrial microbiology & biotechnology · 2024Review
- Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders.Journal of chemical information and modeling · 2023Article
- Training Neural Network Models Using Molecular Dynamics Simulation Results to Efficiently Predict Cyclic Hexapeptide Structural Ensembles.Journal of chemical theory and computation · 2023Article
- Structure prediction of cyclic peptides by molecular dynamics + machine learning.Chemical science · 2021Article
- Stapled β-Hairpins Featuring 4-Mercaptoproline.Journal of the American Chemical Society · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Cyclic peptides: backbone rigidification and capability of mimicking motifs at protein-protein interfaces.Physical chemistry chemical physics : PCCP · 2021Article
- Conformation and Permeability: Cyclic Hexapeptide Diastereomers.Journal of chemical information and modeling · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that β-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.
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Registered trials
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