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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cyt-PTPε inhibitor
cyt-PTPε Inhibitor-1 is a potent cytosolic protein tyrosine phosphatase epsilon (cyt-PTPε) inhibitor, binds to the catalytic domain of cyt-PTPε, blocks c-Src activation (dephosphorylation of c-Src), and exhibits anti-osteoclastic activity. -
BET bromodomain inhibitor
(+)-JQ1 PA is a clickable JQ1 for building PROTACs, which acts as a BET bromodomain inhibitor. -
Sirt2 inhibitor
Sirt2-IN-1 (Compound 9) is a sirtuin 2 (Sirt2) inhibitor with an IC50 of 163 nM. -
BPTF ligand
GSK1379725A is a selective BPTF ligand with a Kd of 2.8 uM, showing no binding activity for Brd4. -
Bromodomain inhibitor
BMS-986158 is an inhibitor of the bromodomain and extra-terminal (BET) proteins. -
Aurora A kinase inhibitor
Aurora Kinase Inhibitor 3 is a strong and selective Aurora A kinase inhibitor with an IC50 of 42 nM, and weakly inhibits EGFR with an IC50>10 μM. -
virion mRNA(guanine-7-)-methyltransferase inhibitor
Sinefungin is a potent inhibitor of virion mRNA(guanine-7-)-methyltransferase, mRNA(nucleoside-2'-)-methyltransferase, and viral multiplication. -
EHMT inhibitor
EHMT2-IN-2 is a potent EHMT inhibitor, with IC50s of all <100 nM for EHMT1 peptide, EHMT2 peptide and cellular EHMT2. Used in the research of blood disease or cancer. -
KDM4D inhibitor
KDM4D-IN-1 is a new histone lysine demethylase 4D (KDM4D) inhibitor with an IC50 value of 0.41±0.03 μM. -
Aurora inhibitor
Aurora inhibitor 1 is a potent Aurora inhibitor with an IC50 of ?? 4 nM and ??13 nM for Aurora A and Aurora B kinase, respectively. -
KDM2A/7A inhibitor
KDM2A/7A-IN-1 is a first-in-class, selective and cell-permeable inhibitor of histone lysine demethylases KDM2A/7A, with an IC50 of 0.16?μM for KDM2A, exhibits 75 fold selevtivity over other JmjC lysine demethylases, and is inactive on methyl transferases, and histone acetyl transferases. -
LSD1 inhibitor
Seclidemstat (SP-2577) is a potent and orally bioavailable LSD1 inhibitor, with a mean IC50 of 127 nM. -
BET inhibitor
BET bromodomain inhibitor is a potent BET inhibitor extracted from patent WO/2015/153871A2, compound example 11. -
SIRT5 inhibitor
SIRT5 inhibitor 1 is a potent Human Sirtuin 5 deacylase inhibitor, with an IC50 of 0.11 μM.