Epigenetics

Epigenetics research delves into the molecular mechanisms that control gene expression and cellular traits without altering the underlying DNA sequence. One crucial aspect of this field is the role of small molecules, which act as powerful regulators of epigenetic modifications. These small compounds, typically comprising a few dozen to a few hundred atoms, have emerged as essential tools in understanding and manipulating the epigenome.

  • DNA Methylation Inhibitors: Small molecules like 5-azacytidine and 5-aza-2'-deoxycytidine are DNA methyltransferase inhibitors. They block the addition of methyl groups to DNA, leading to DNA demethylation. This can reactivate silenced genes, potentially offering therapeutic avenues for conditions like cancer.
  • HDAC inhibitors: HDACs remove acetyl groups from histone proteins, contributing to gene repression. Small molecule HDAC inhibitors, such as Vorinostat and Romidepsin, can reverse this process by increasing histone acetylation, allowing genes to be more accessible for transcription. These inhibitors are being explored for cancer therapy and other conditions.
  • Histone Methyltransferase Inhibitors: Small molecules like GSK126 inhibit specific histone methyltransferases, affecting histone methylation patterns. This can alter gene expression, making them promising candidates for cancer and other diseases with epigenetic dysregulation.
  • RNA Modulators: Small molecules can also target non-coding RNAs involved in epigenetic regulation. For instance, small molecules called small interfering RNAs (siRNAs) can be designed to target and degrade specific long non-coding RNAs, influencing gene expression.
  • Epigenetic Reader Domain Inhibitors: These small molecules target proteins that recognize and bind to specific epigenetic marks. Examples include inhibitors of bromodomain-containing proteins (BET inhibitors), which can disrupt gene regulation by interfering with protein-DNA interactions.

Small molecules in epigenetics research not only provide insights into the fundamental biology of gene regulation but also hold immense promise for developing novel therapeutics. Their ability to selectively modulate specific epigenetic marks and pathways has led to ongoing clinical trials and drug development efforts for various diseases, including cancer, neurological disorders, and inflammatory conditions. Understanding and harnessing the power of these small molecules is at the forefront of modern epigenetics research, offering new hope for precision medicine and targeted therapies.


3 key components involved in the regulation of epigenetic modifications

Epigenetics Writer

Epigenetics writers are enzymes responsible for adding chemical marks or modifications to DNA or histone proteins. These marks include DNA methylation (addition of methyl groups to DNA) and histone modifications (such as acetylation, methylation, phosphorylation, etc.).

Epigenetics Reader

Function: Epigenetics readers are proteins that can recognize and bind to specific epigenetic marks on DNA or histones. These reader proteins interpret the epigenetic code and facilitate downstream cellular processes, such as gene activation or repression.

Epigenetics Eraser

Function: Epigenetics erasers are enzymes responsible for removing or reversing epigenetic marks on DNA or histones. This process allows for the dynamic regulation of gene expression and the resetting of epigenetic states during various stages of development and in response to environmental changes.

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  1. Mdm2 antagonist

    MDM2 antagonist nutlin-3 is a potent inducer of apoptosis.
  2. MDMX Inhibitor

    NSC207895 is a cell-permeable benzofuroxan compound that downregulates the p53 negative regulator MDMX protein level in MCF-7, LNCaP, and A549 cells (1 to 10 µM for 16 to 24 h) by suppressesing MDMX promoter transcription activity (IC50 = 2.5 µM in HT1080 cells), leading to enhanced p53 stabilization and activation.

  3. MDM2 inhibitor

    Nutlin 3a is a potent inhibitor of MDM2 (mouse double minute 2) binding to p53 that induces the expression of p53 regulated genes, and shows potent antiproliferative activity in cells expressing functional p53.
  4. MDM2 inhibitor

    Nutlin 3b is a p53/MDM2 antagonist or inhibitor with IC50 value of 13.6 uM, 150-fold less potent (+)-enantiomer of Nutlin-3 as in comparison with opposite (-)-enantiomer Nutlin-3a.
  5. selective p53-MDM2 inhibitor

    RG7112 is the first clinical small-molecule MDM2 inhibitor designed to occupy the p53-binding pocket of MDM2.
  6. MDM2 inhibitor

    APG-115 (AA-115) is an orally active MDM2 protein inhibitor binding to MDM2 protein with IC50 and Ki values of 3.8 nM and 1 nM, respectively.
  7. dual MDM2/NFAT1 inhibitor

    MA242 is a dual inhibitor of murine double minute 2 (MDM2) and nuclear factor of activated T cells 1 (NFAT1) for Pancreatic Cancer Therapy.
  8. MDM2 inhibitor

    MDM2 Inhibitor is a cell-permeable boranyl-chalcone exhibiting strong binding to MDM2 and irreversibly disrupts the MDM2/p53 protein complex.
  9. Kevetrin (thioureidobutyronitrile), is a water-soluble, small molecule and activator of the tumor suppressor protein p53, with potential antineoplastic activity.
  10. MDM2/MDMX inhibitor

    WK23 is an inhibitor based on four aromatic groups and able to efficiently fill the binding pockets of MDM2/MDMX, its median inhibitory concentration (IC50) values to MDM2/MDMX are 1.17 and 36 uM, respectively
  11. Mdm2 inhibitor

    YH239-EE is a potent p53-MDM2 antagonist and an apoptosis inducer.
  12. MDM2/p53 Inhibitor

    Idasanutlin is a potent and selective p53-MDM2 inhibitor.
  13. MDM2 inhibitor

    AMG 232 is a highly potent, selective and orally bioavailable piperidinone inhibitor of the MDM2-p53 interaction((SPR KD= 0.045 nM, SJSA-1 EdU IC50=9.1 nM).
  14. Mdm2 inhibitor

    MI-773 is a new small molecule inhibitor of the MDM2-p53 interaction, binds to MDM2 with high affinity (Ki=0.88 nM) and blocks the p53-MDM2 interaction.
  15. p53-MDM2 interaction inhibitor

    p53 and MDM2 proteins-interaction-inhibitor chiral is an inhibitor of the interaction between p53 and MDM2 proteins.
  16. p53-MDM2 interaction inhibitor

    p53 and MDM2 proteins-interaction-inhibitor racemic is an inhibitor of the interaction between p53 and MDM2 proteins.
  17. MDMX inhibitor

    SJ 172550 is the first MDMX inhibitor with EC50 of 0.84 uM; binds reversibly to MDMX and effectively kills retinoblastoma cells in which the expression of MDMX is amplified.
  18. P53/p21waf-1/MDM2 activator

    WR 1065, a dephosphorylated metabolite of amifostine (Ethyol), can protect against the immediate and delayed effects of radiation exposure.
  19. MDM2 inhibitor

    MI-773 is an orally available MDM2 antagonist with Ki of 0.88 nM.
  20. MDM2 inhibitor

    NVP-CGM097 is a potent and selective MDM2 inhibitor; an orally bioavailable HDM2 antagonist with potential antineoplastic activity.
  21. MDM2/XIAP inhibitor

    MX-69 is the MDM2/XIAP inhibitor, used for cancer treatment.
  22. MDM2 inhibitor

    HDM201 is a novel, highly potent and selective inhibitor of the p53-Mdm2 interaction with affinity constant for Mdm2 in the picomolar range and a selectivity ratio greater than 10000-fold vs Mdm4.
  23. MDM2 inhibitor

    MI-1061 is a potent, orally bioavailable, and chemically stable MDM2 (MDM2-p53 interaction) inhibitor (IC50=4.4 nM; Ki=0.16 nM). MI-1061 potently activates p53, induces apoptosis, and has anti-tumor activity.
  24. MDM2 degrader

    MD-224 is a first-in-class and highly potent small-molecule human murine double minute 2 (MDM2) degrader based on the proteolysistargeting chimera (PROTAC) concept. MD-224 has the potential to be a new class of anticancer agent.
  25. MDM2/MDMX inhibitor

    RO-5963 is an inhibitor of the interaction of both MDM2 and MDMX with p53 with IC50s of ~17 nM and ~24 nM, respectively.
  26. MDM2 inhibitor

    PROTAC MDM2 Degrader-4 is a MDM2 degrader based on PROTAC technology. PROTAC MDM2 Degrader-4 composes of a potent MDM2 inhibitor, linker, and the MDM2 ligand for E3 ubiquitin ligase.
  27. MDM2 degrader

    PROTAC MDM2 Degrader-3 is a MDM2 degrader based on PROTAC technology. PROTAC MDM2 Degrader-3 composes of a potent MDM2 inhibitor, linker, and the MDM2 ligand for E3 ubiquitin ligase.
  28. MDM2 inhibitor

    PROTAC MDM2 Degrader-2 is a MDM2 degrader based on PROTAC technology. PROTAC MDM2 Degrader-2 composes of a potent MDM2 inhibitor, linker, and the MDM2 ligand for E3 ubiquitin ligase.
  29. MDM2 degrader

    PROTAC MDM2 Degrader-1 is a MDM2 degrader based on PROTAC technology. PROTAC MDM2 Degrader-1 composes of a potent MDM2 inhibitor, linker, and the MDM2 ligand for E3 ubiquitin ligase.
  30. Nutlin 3-based MDM2 ligand

    Nutlin carboxylic acid (MDM2 ligand 1) is the Nutlin 3-based MDM2 ligand. Nutlin carboxylic acid (MDM2 ligand 1) can be connected to the ligand for protein by a linker to form PROTACs.
  31. Nutlin 3-based MDM2 ligand

    (4R,5S)-nutlin carboxylic acid (MDM2 ligand 2) is the Nutlin 3-based MDM2 ligand. (4R,5S)-nutlin carboxylic acid can be connected to the ligand for protein by a linker to form PROTACs.
  32. MDM2 inhibitor

    Mliademetan is a specific MDM2 inhibitor, a pharmaceutical composition for use in treating acute myeloid leukemia (AML).
  33. Dual MDM2/TSPO Inhibitor

    PK 11195 is a 2?Phenylindolylglyoxylyldipeptide Murine Double Minute (MDM)2/Translocator Protein (TSPO) Dual Inhibitor, and is potentially useful for the Treatment of Gliomas.
  34. MDM2-p53 inhibitor

    BI-0252 is an orally active, selective MDM2-p53 inhibitor with an IC50 of 4 nM.
  35. MDM2 inhibitor

    RO8994 is a highly potent and selective series of spiroindolinone small-molecule MDM2 inhibitor, with IC50 of 5 nM (HTRF binding assays) and 20 nM (MTT proliferation assays).
  36. HIF-1α inhibitor

    Minocycline hydrochloride is a broad-spectrum tetracycline antibiotic, acting by binding to the bacterial 30S ribosomal subunit and inhibiting protein synthesis.

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