ArticlePLoS computational biology2013
Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 107 citations in OpenAlex.
- Molecular Interplay of Small Molecules and Calcium Ions with α-Synuclein Revealed by NMR and Molecular Dynamics Simulations.ACS chemical neuroscience · 2026Article
- Sequence-Directed Transcriptional Silencing Using Gamma Peptide Nucleic Acids.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Direct detection of an NH-π hydrogen bond in an intrinsically disordered peptide.Nature communications · 2025Article
- Article
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- DIRseq: a method for predicting drug-interacting residues of intrinsically disordered proteins from sequences.bioRxiv : the preprint server for biology · 2025Article
- Article
- Ensemble Docking for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2025Article
- Evidence of α-Synuclein/Glucocerebrosidase Dual Targeting by Iminosugar Derivatives.ACS chemical neuroscience · 2025Article
- Article
- Comparison of Methodologies for Absolute Binding Free Energy Calculations of Ligands to Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2024Article
- Picosecond Dynamics of a Small Molecule in Its Bound State with an Intrinsically Disordered Protein.Journal of the American Chemical Society · 2024Article
- Antitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor.Cell reports. Medicine · 2024Article
- Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition.Nature plants · 2023Article
- Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins.Nature communications · 2023Article
- How aberrant N-glycosylation can alter protein functionality and ligand binding: An atomistic view.Structure (London, England : 1993) · 2023Article
- Review
- Splice-switch oligonucleotide-based combinatorial platform prioritizes synthetic lethal targets CHK1 and BRD4 against MYC-driven hepatocellular carcinoma.Bioengineering & translational medicine · 2023Article
- More is simpler: Decomposition of ligand-binding affinity for proteins being disordered.Protein science : a publication of the Protein Society · 2022Article
- Functional inhibition of c-Myc using novel inhibitors identified through "hot spot" targeting.The Journal of biological chemistry · 2022Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Intrinsically disordered proteins (IDPs) were found to be widely associated with human diseases and may serve as potential drug design targets. However, drug design targeting IDPs is still in the very early stages. Progress in drug design is usually achieved using experimental screening; however, the structural disorder of IDPs makes it difficult to characterize their interaction with ligands using experiments alone. To better understand the structure of IDPs and their interactions with small molecule ligands, we performed extensive simulations on the c-Myc₃₇₀₋₄₀₉ peptide and its binding to a reported small molecule inhibitor, ligand 10074-A4. We found that the conformational space of the apo c-Myc₃₇₀₋₄₀₉ peptide was rather dispersed and that the conformations of the peptide were stabilized mainly by charge interactions and hydrogen bonds. Under the binding of the ligand, c-Myc₃₇₀₋₄₀₉ remained disordered. The ligand was found to bind to c-Myc₃₇₀₋₄₀₉ at different sites along the chain and behaved like a 'ligand cloud'. In contrast to ligand binding to more rigid target proteins that usually results in a dominant bound structure, ligand binding to IDPs may better be described as ligand clouds around protein clouds. Nevertheless, the binding of the ligand and a non-ligand to the c-Myc₃₇₀₋₄₀₉ target could be clearly distinguished. The present study provides insights that will help improve rational drug design that targets IDPs.
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