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
Chelerythrine affects translocation of PKC from cytosol to plasma membrane. Shown to prevent neurite growth. Induces apoptosis in a concentration- and schedule-dependent manner.
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PKC inhibitor
Bryostatin 1 is a macrolactone isolated from the marine bryozoan, Bugula neritina, that modulates protein kinase C (PKC) activity. Bryostain 1 induces an initial rapid activation and autophosphorylation of PKC that results in the translocation of the PKC enzyme to the membrane. -
EGFR, PKA,PKC inhibitor
Daphnetin is a coumarin analog that acts as an inhibitor of several protein kinases. It inhibits EGFR kinase (IC50 = 7.67 μM), PKA (IC50 = 9.33 μM), and PKC (IC50 = 25 μM), in vitro. The inhibition of EGFR kinase by daphnetin was competitive to ATP and non-competitive to the peptide substrate. Also acts as a potent antioxidant and anti-malarial agent. -
PKCβ inhibitor
LY317615 (Enzastaurin) is a potent and selective inhibitor of PKCβ with antiproliferative activity (IC50= ~6 nM). - Myricitrin is the 3-O-rhamnoside of myricetin. Myricitrin is used by several beetle species in their communication system.
- Ayumi Yamamoto, .et al. , Nutrients, 2022, Mar 4;14(5):1078 PMID: 35268053
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MAO-B inhibitor
Quercetin inhibits many enzyme systems including tyrosine protein kinase, phospholipase A2, phosphodiesterases, mitochondrial ATPase, PI 3-kinase and protein kinase C. -
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
Verbascoside is isolated from Lantana camara, acts as an ATP-competitive inhibitor of PKC, with an IC50 of 25 μM, and has antitumor, anti-inflammatory and antineuropathic pain activity. -
p32-kinase activator
D-erythro-Sphingosine (Erythrosphingosine) is a very potent activator of p32-kinase with an EC50 of 8 μM, and inhibits protein kinase C (PKC). D-erythro-Sphingosine (Erythrosphingosine) is also a PP2A activator. -
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 inhibitor
PKC 412 is a broad spectrum protein kinase inhibitor. Inhibits conventional PKC isoforms α/β/γ, PDFRβ, VEGFR2, Syk, Flk-1, Flt3, Cdk1/B, PKA, c-Kit, c-Fgr, c-Src, VEGFR1 and EGFR. Displays potent antitumor activity. -
δ-protein kinase C (δPKC) inhibitor
Delcasertib (KAI-9803) is a potent and selective δ-protein kinase C (δPKC) inhibitor. - Ingenol mebutate is a substance found in the sap of the plant Euphorbia peplus and an inducer of cell death.
- Yao-Yu Hsieh, .et al. , Toxicol Appl Pharmacol, 2022, Aug 15;449 PMID: 35724704
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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
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PKC activator
Prostratin is a protein kinase C activator found in the bark of the mamala tree of Samoa, Homalanthus nutans. -
PKC inhibitor
GO6983 is a potent protein kinase C (PKC) inhibitor. It reduces polymorphonuclear leukocyte adherence and infiltration following myocardial ischemia/reperfusion injury.- Kouki Kawakami, .et al. , Nat Commun, 2022, 13: 487 PMID: 35078997
- 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. -
PKC inhibitor
PKC (19-36), pseudosubstrate peptide inhibitor of protein kinase C (IC50 = 0.18 uM). - 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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antiviral agent
Daphnoretin (Dephnoretin), isolated from Wikstroemia indica, possesses antiviral activity. Daphnoretin likes PMA, may direct activation of protein kinase C which in turn activated NADPH oxidase and elicited respiratory burst. -
PKCβ1 and PKCβ2 inhibitor
LY333531 is a β-specific protein kinase C inhibitor. It competitively and reversibly inhibits PKCβ1 and PKCβ2 with IC50 values of 4.7 and 5.9 nM respectively. -
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 (IC50 = 8, 12, and 4 μM, respectively). -
PKCθ inhibitor
PKC-theta inhibitor 1 is the PKCθ inhibitor with an Ki value of 6 nM, inhibits IL-2 production in vivo with an IC50 of 0.19 μM. -
PKC-θ inhibitor
PKC-theta inhibitor is a selective PKC-θinhibitor, with an IC50 of 12 nM. -
PKC activator
Phorbol 12,13-dibutyrate (Phorbol dibutyrate) is a PKC activator and a potent skin tumor promoter. -
PKC inhibitor
Ro 31-8220 is a potent PKC inhibitor, with IC50s of 5, 24, 14, 27, 24 and 23 nM for PKCα, PKCβI, PKCβII, PKCγ, PKCε and rat brain PKC, respectively. -
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).