ArticleJournal of the American Chemical Society2017
Targeting Unoccupied Surfaces on Protein-Protein Interfaces.
Article in Journal of the American Chemical Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- From Concepts to Inhibitors: A Blueprint for Targeting Protein-Protein Interactions.Chemical reviews · 2025Review
- Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations.Nature communications · 2024Article
- What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.Journal of molecular biology · 2023Article
- Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023Review
- Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase.Molecules (Basel, Switzerland) · 2023Article
- Rational peptide design for inhibition of the KIX-MLL interaction.Scientific reports · 2023Article
- Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability.Organic letters · 2022Article
- Optimizing CSP1 analogs for modulating quorum sensing inRSC chemical biology · 2022Article
- Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery.Journal of the American Chemical Society · 2022Article
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS).RSC chemical biology · 2021Article
- A Dual-Site Inhibitor of CBP/p300 KIX is a Selective and Effective Modulator of Myb.Journal of the American Chemical Society · 2021Article
- Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics.ACS chemical biology · 2021Article
- A Fungal Defensin Targets the SARS-CoV-2 Spike Receptor-Binding Domain.Journal of fungi (Basel, Switzerland) · 2021Article
- Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.Nature communications · 2021Article
- A Sos proteomimetic as a pan-Ras inhibitor.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins.Journal of hematology & oncology · 2021Review
- High-throughput determination of protein affinities using unmodified peptide libraries in nanomolar scale.iScience · 2021Article
- Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.Chemical science · 2021Article
- An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators.Bioorganic & medicinal chemistry · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
The use of peptidomimetic scaffolds to target protein-protein interfaces is a promising strategy for inhibitor design. The strategy relies on mimicry of protein motifs that exhibit a concentration of native hot spot residues. To address this constraint, we present a pocket-centric computational design strategy guided by AlphaSpace to identify high-quality pockets near the peptidomimetic motif that are both targetable and unoccupied. Alpha-clusters serve as a spatial representation of pocket space and are used to guide the selection of natural and non-natural amino acid mutations to design inhibitors that optimize pocket occupation across the interface. We tested the strategy against a challenging protein-protein interaction target, KIX/MLL, by optimizing a single helical motif within MLL to compete against the full-length wild-type MLL sequence. Molecular dynamics simulation and experimental fluorescence polarization assays are used to verify the efficacy of the optimized peptide sequence.
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Registered trials
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