ArticleACS omega2022
Insights into Rational Design of a New Class of Allosteric Effectors with Molecular Dynamics Markov State Models and Network Theory.
Article in ACS omega, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Restoration of the Y220C p53 Full-Length Mutant by PK11000: a Molecular Dynamics Study of an Intrinsically Disordered Protein.ACS omega · 2026Article
- Network Theory Analysis of Allosteric Drug-Rescue Mechanisms in the Tumor Suppressor Protein p53 Y220C Mutant.International journal of molecular sciences · 2025Article
- MD Multi-Sector Selector: Recursive Extraction and Refinement of Molecular Dynamics Based Sectors Yields Two Sectors in p53 Tumor Suppressor Protein.The journal of physical chemistry. B · 2025Article
- Navigating the complexity of p53-DNA binding: implications for cancer therapy.Biophysical reviews · 2024Review
- Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein.ACS omega · 2024Article
- Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis.The journal of physical chemistry. B · 2023Article
- Article
- Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction.The journal of physical chemistry. B · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The development of drugs to restore protein function has been a major advance facilitated by molecular medicine. Allosteric regulation, a phenomenon widely observed in nature, in which a molecule binds to control a distance active site, holds great promise for regulating proteins, yet how to rationally design such a molecule remains a mystery. Over the past few years, we and others have developed several techniques based on molecular dynamics (MD) simulations: MD-Markov state models to capture global conformational substates, and network theory approach utilizing the interaction energy within the protein to confer local allosteric control. We focus on the key case study of the p53 Y220C mutation restoration by PK11000, a compound experimentally shown to reactivate p53 native function in Y220C mutant present tumors. We gain insights into the mutation and allosteric reactivation of the protein, which we anticipate will be applicable to de novo design to engineer new compounds not only for this mutation, but in other macromolecular systems as well.
Identifiers
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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.