ArticleJournal of chemical information and modeling2023
Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Toward the Engineering of Chameleonicity: Quantum Mechanical Prediction for the Octanol/Water Distributions of Large Flexible Triazine Macrocycles.Journal of chemical information and modeling · 2026Article
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- Linker Engineering in Stapled Peptides for Enhanced Membrane Permeability: Screening and Optimization Strategies.International journal of molecular sciences · 2026Review
- Article
- Flexible molecular chameleons: structural adaptability and therapeutic applications.Frontiers in chemistry · 2026Review
- Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents.Journal of chemical information and modeling · 2024Article
- Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.PloS one · 2024Article
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Authors and funding
6 authors.
Funding
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Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
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