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.
-
multi-kinase inhibitor
Lestaurtinib (CEP-701;KT-5555) is a multi-kinase inhibitor with potent activity against the Trk family of receptor tyrosine kinases. Lestaurtinib inhibits JAK2, FLT3 and TrkA with IC50s of 0.9, 3 and less than 25 nM, respectively. -
miR-544 inhibitor
SID 3712249 (MiR-544 Inhibitor 1) is an inhibitor of the biogenesis of microRNA-544 (miR-544). - Trifloxystrobin (CGA 279202) is a fungicide, with EC50s of 23.0 μg/L and 1.7 μg/L for Daphnia magna neonate and embryos, respectively, after treatment for 48 h.
-
endothelial barrier enhancer
Ginsenoside Rk1, one of the main elements of Sung Ginseng, has been confirmed as a new endothelial barrier enhancer recently and has anti-cancer activity. -
DOT1L inhibitor
EPZ004777 hydrochloride is a potent, selective DOT1L inhibitor with IC50 of 0.4 nM. -
HDAC inhibitor
Sulforaphane activates Nrf2 and inhibits high glucose-induced progression of pancreatic cancer via AMPK dependent signaling. Sulforaphane has shown anti-cancer and anti-inflammatory activities.- Satoshi Endo, .et al. , J Biochem, 2021, Mar 17 PMID: 33729485
-
Aloe emodin is a anthraquinone present in aloe latex, an exudate from the aloe plant. It has a strong stimulant-laxative action.
- Flunisolide is a corticosteroid often used to treat allergic rhinitis.The principal mechanism of action of Flunisolide is to activate glucocorticoid receptors, meaning it has an anti-inflammatory action.
-
nonsteroidal anti-inflammatory agent
Flurbiprofen is a nonsteroidal anti-inflammatory agent (NSAIA) with antipyretic and analgesic activity. -
nitroimidazole antibiotic medication
Metronidazole is a nitroimidazole antibiotic medication used particularly for anaerobic bacteria and protozoa. -
anticancer and radioprotection agent
Geniposidic acid is an effective anticancer and radioprotection agent. - TPEN is a heavy metal chelator. Reacts with both Zn-proteome and Zn-metallothionein (MT) in LLC-PK1 cells; acts as an intracellular chelator of proteomic Zn2+.
- Arctigenin is an antioxidant, anti-inflammatory, antiproliferative and antiviral agent. It inhibits LPS-induced iNOS expression via inhibition of IκBα phosphorylation and p65 nuclear translocation (IC50 = 10 nM)
- Clofilium tosylate, a potassium channel blocker, induces apoptosis of human promyelocytic leukemia (HL-60) cells via Bcl-2-insensitive activation of caspase-3. Antiarrhythmic agent.
-
PINK1 activator
Kinetin riboside is an activator of the Parkinson's Disease-associated PTEN-induced Putative Kinase 1 (PINK1), and acts independently from mitochondrial depolarization. -
Caspase/apoptosis activator
Ubiquitin Isopeptidase Inhibitor I, G5 (NSC 144303) is an apoptosome-independent caspase and apoptosis activator with IC50 values of 1.76 and 1.6 μM in E1A and E1A/C9DN cells, respectively. - Trabectedin (Ecteinascidin-743 or ET-743) is a novel antitumour agent of marine origin with potent antitumour activity both in vitro and in vivo.
-
Cdc42 GTPase inhibitor
CASIN is a novel and potent Cdc42 inhibitor.- Yongru Xu, .et al. , Int J Mol Sci, 2017, Mar; 18(3): 586 PMID: 28282856
-
antitumor agent
2-Methoxycinnamaldehyde (o-Methoxycinnamaldehyde) is a natural compound of Cinnamomum cassia, with antitumor activity. -
HO-1 inhibitor
Zinc Protoporphyrin (Zn(II)-protoporphyrin IX) is a competitive heme oxygenase-1 (HO-1) inhibitor, markedly attenuates the protective effects of Phloroglucinol (PG) against H2O2. - Ecabet sodium is a widely employed mucoprotective agent for the treatment of gastric ulcers.
-
osteoblast differentiation inducer
Asperosaponin VI, A saponin component from Dipsacus asper wall, induces osteoblast differentiation through BMP?\2/p38 and ERK1/2 pathway. Asperosaponin ?? inhibits apoptosis in hypoxia-induced cardiomyocyte by increasing the Bcl-2/Bax ratio and decreasing active caspase-3 expression, as well as enhancing of p-Akt and p-CREB. -
elastogenesis inhibitor
L-Ascorbic acid (L-Ascorbate), an electron donor, is an endogenous antioxidant agent. L-Ascorbic acid inhibits selectively Cav3.2 channels with an IC50 of 6.5 μM. L-Ascorbic acid is also a collagen deposition enhancer and an elastogenesis inhibitor. -
anti-cancer agent
Falcarindiol (FAD, (3R,8S)-Falcarindiol, FaDOH) is a natural polyacetylene compound found rich in many plants of the Umbelliferae family. Falcarindiol suppresses LPS-stimulated expression of inducible nitric oxide synthase (iNOS), tumor necrosis factor alpha (TNFα), interleukin-6 (IL-6), and interleukin-1 beta (IL-1β). Falcarindiol attenuates the LPS-induced activation of JNK, ERK, STAT1, and STAT3 signaling molecules. Falnidamol is a pyrimido-pyrimidine compound with anti-cancer activity. -
anti-bacterial agent
Pogostone is isolated from patchouli with anti-bacterial and anti-cancer activities. Pogostone inhibits both gram negative and gram positive bacteria, also show inhibitory effect on corynebacterium xerosis with a MIC value of 0.098 ?g/ml . Pogostone induces cell apoptosis and autophagy. -
anti-inflammatory agent
Neobavaisoflavone, a flavonoid, is isolated from the seeds of Psoralea corylifolia. Neobavaisoflavone exhibits anti-inflammatory, anti-cancer and anti-oxidation activities. Neobavaisoflavone inhibits DNA polymerase at moderate to high concentrations. Neobavaisoflavone also inhibits platelet aggregation. -
antitumor agent
Methyl protodioscin(NSC-698790) is a furostanol bisglycoside with antitumor properties; shows to reduce proliferation, cause cell cycle arrest. -
micronutrient
Thiamine hydrochloride (Thiamine chloride hydrochloride) is an essential micronutrient needed as a cofactor for many central metabolic enzymes. - Cetrimonium bromide is an amine based cationic quaternary surfactant, is one of the components of the topical antiseptic Cetrimide.
-
iron-chelating drug
Deferiprone is the only orally active iron-chelating drug to be used therapeutically in conditions of transfusional iron overload. -
iodinated radiocontrast agent
Diatrizoic acid (Diatrizoate) is an iodinated radiocontrast agent and has the potential for radiographic imaging of the airways. Diatrizoic acid induces mitochondrial turnover and oxidative stress, and activating apoptosis by dysregulating calcium. -
nonsteroidal, anti-inflammatory antiarthritic agent
Fenoprofen Calcium hydrate is a nonsteroidal, anti-inflammatory antiarthritic agent. -
GGTase I inhibitor
GGTI298 Trifluoroacetate is a CAAZ peptidomimetic geranylgeranyltransferase I (GGTase I) inhibitor, which can inhibit Rap1A with IC50 of 3 μM; little effect on Ha-Ras with IC50 of >20 μM. -
CYP51 inhibitor
Tebuconazole is a triazole fungicide used agriculturally to treat plant pathogenic fungi. -
X-ray agent
Diatrizoate Sodium is an X-ray contrast agent. Diatrizoate sodium blocks X-rays which lets body structures with iodine to be delineated in comparison to the structures that do not have iodine. -
nuclear transport receptor importin-β inhibitor
Importazole is a cell-permeable inhibitor of importin-β. It specifically inhibits the function of importin-β, likely by altering its interaction with RanGTP.