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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PKC inhibitor
Staurosporine is a natural product originally isolated in 1977 from the bacterium Streptomyces staurosporeus. The main biological activity of staurosporine is the inhibition of protein kinases through the prevention of ATP binding to the kinase. This is achieved through the stronger affinity of staurosporine to the ATP-binding site on the kinase.- Lisa M Kim, .et al. , Cancer Res, 2022, Sep 2;82(17):3045-3057 PMID: 35792658
- Jacobs CL, .et al. , Nat Methods, 2018, Jul;15(7):523-526 PMID: 29967496
- Birte Plitzko, .et al. , J Biol Chem, 2017, Dec 22; 292(51): 21102-21116 PMID: 29074620
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PKC inhibitor
Sotrastaurin is a protein kinase C inhibitor for the prevention of transplant rejection and treatment of psoriasis. -
PKC inhibitor
Ruboxistaurin (LY333531) is a potent, selective inhibitor of Protein Kinase C isozymes, PKC β I(IC50=4.7 nM) and PKC β II (IC50=5.9 nM). -
PKC activator
(-)-Indolactam V is a protein kinase C activator, which strongly directs human ES cell-derived definitive endoderm into pancreatic endoderm.- Manuel Mendoza, .et al. , Tetrahedron, 2019, May
- alpha-Amyloid Precursor Protein Modulator is a cell-permeable benzolactam derived PKC activator (Ki = 11.9 nM for PKCα) that efficiently enhances non-amyloidogenic α-processing of amyloid precursor protein (APP) even at 100 nM in human fibroblas.
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PKC inhibitor
GF 109203X is a potent and selective inhibitor of protein kinase C, selective for the α and β1 isoforms (IC50 values are 0.0084, 0.0180, 0.210, 0.132, and 5.8 μM for α, β1, δ, ε and ζ isoforms respectively). Selective over MLCK, PKG and PKA (IC50 values are 0.6, 4.6, and 33 μM respectively). Potent antagonist at the 5-HT3 receptor (Ki = 29.5 nM). -
PKC inhibitor
Ro 31-8220 mesylate is a PKC-inhibitor, which inhibits stimulated fluid pinocytosis of human PMNs induced by the PKC-activators phorbol myristate acetate (PMA, IC50 = 1.35 x 10(-6) M) or diacylglycerols (OAG, diC8) by 95%.- Dao-Lai Zhang, .et al. , eLife, 2018, 7: e33432 PMID: 29393851
- Valrubicin is a semisynthetic derivative of the antineoplastic anthracycline antibiotic doxorubicin.
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PKC activator
12-O-tetradecanoyl phorbol-13-acetate is a diester of phorbol and is a tumor promoting compound extracted from croton oil. It is a reversible, highly potent protein kinase C (PKC) activator in vitro and in vivo at nM concentrations. - Protein Kinase C (19-31), this peptide derived from the pseudo-substrate regulatory domain of PKCa (residues 19-31) with a serine at position 25 replacing the wild-type alanine, it was used as protein kinase C substrate peptide for testing the protein kinase C activity.
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PKC inhibitor
Bisindolylmaleimide X hydrochloride (BIM-X hydrochloride) is a potent and selective protein kinase C (PKC) inhibitor. -
PKs inhibitor
HA-100 is an isoquinoline compound with an added piperazinylsulfonyl group that acts as an inhibitor of protein kinases (PKs), including PKA, PKC, and PKG (IC50s = 8, 12, and 4 ?M, respectively). -
PKC activating agent
Decursinol angelate, a cytotoxic and protein kinase C (PKC) activating agent from the root of Angelica gigas, possesses anti-tumor and anti-inflammatory activities.
