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.
- Calcineurin inhibitory peptide is a selective inhibitor of Ca2+-calmodulin-dependent protein phosphatase (calcineurin) (IC50 ~ 10 uM). Does not inhibit PP1, PP2A or CaM kinase II (IC50 > 100 mM).
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PTPMT1 inhibitor
Alexidine is an alkyl bis(biguanide) antiseptic which has been used in mouthwashes to eliminate plaque forming microorganisms. -
HDAC6 inhibitor
TCS HDAC6 20b, selective inhibitor of histone deacetylase 6 (HDAC6). Inhibits HCT116 growth in combination with taxol. Also inhibits growth of MCF-7 cells stimulated by estrogen. -
PTP1B Inhibitor
TCS 401 is a selective inhibitor of protein-tyrosine phosphatase 1B (PTP1B) (Ki values are 0.29, 59, 560, 1100, > 2000, > 2000 and > 2000 μM for PTP1B, CD45 D1D2, PTPβ, PTPε D1, SHP-1, PTPα D1 and LAR D1D2 respectively). -
Calcineurin inhibitor
Cyclosporine is a calcineurin phosphatase pathway inhibitor, used as an immunosuppressant drug to prevent rejection in organ transplantation. -
HDAC inhibitor
R306465 is a novel hydroxamate-based histone deacetylase (HDAC) inhibitor with broad-spectrum antitumour activity against solid and haematological malignancies in preclinical models.- Mari Ishigami-Yuasa, .et al. , Biol Pharm Bull, 2019, 42, 448-452 PMID: 30828077
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G9a/GLP inhibitor
UNC0642 is a potent and selective G9a and GLP histone lysine methyltransferase inhibitor (IC50 < 2.5 nM). It reduces H3K9 dimethylation levels in MDA-MB-231 cells (IC50 = 110 nM). Displays modest brain penetration in vivo.- Afifa Yaqub, .et al. , Pakistan Journal of Zoology, 2022, 54(6)
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TNKS inhibitor
G007-LK displays high selectivity toward tankyrases 1 and 2 with biochemical IC50 values of 46 nM and 25 nM, respectively, and a cellular IC50 value of 50 nM combined with an excellent pharmacokinetic profile in mice,- Dominic B. Bernkopf, .et al. , Nat Commun, 2019, 10:4251 PMID: 31534175
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LSD1 inhibitor
GSK2879552 is an orally available, irreversible, inhibitor of lysine specific demethylase 1 (LSD1), with potential antineoplastic activity.- Nicolas A Fraunhoffer, .et al. , EBioMedicine, 2023, Jun;92:104602 PMID: 37148583
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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. -
HDAC/ACE inhibitor
Sinapinic acid (Sinapic acid) is a phenolic compound isolated from Hydnophytum formicarum Jack. Rhizome, acts as an inhibitor of HDAC, with an IC50 of 2.27 mM, and also inhibits ACE-I activity. Sinapinic acid posssess potent anti-tumor activity, induces apoptosis of tumor cells. -
MEK/Aurora Inhibitor
BI-847325 is an orally bioavailable, and selective dual MEK/Aurora kinase inhibitor with IC50 of 3 nM, 25 nM, 15 nM, 25 nM, and 4 nM for Xenopus laevis Aurora B, human Aurora A and Aurora C, as well as human MEK1 and MEK2, respectively. Phase 1.- Hilda Samimi, .et al. , Cancer Cell Int, 2022, Dec 8;22(1):388 PMID: 36482411
- Hilda Samimi, .et al. , Thyroid Res, 2021, Dec 3;14(1):27 PMID: 34861882
- Hilda Samimi, .et al. , DARU J Pharm Sci, 2019, 1-7 PMID: 31077090
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TNKS2 inhibitor
NVP-TNKS656 is a highly potent, selective, and orally active TNKS2 inhibitor with IC50 of 6 nM; > 300 fold selectivity against PARP1 and PARP2. -
Calcineurin/PP2B inhibitor
Ascomycin is an ethyl analog of tacrolimus (FK506) with strong immunosuppressant properties. It has been researched for the treatment of autoimmune diseases and skin diseases, and to prevent rejection after an organ transplant. -
CBP/beta-catenin antagonist
PRI-724 is the second-generation, potent and specific inhibitor of CBP/β-Catenin complex, and a modulator of the β-Catenin dependent canonical Wnt signaling pathway in cancer stem cells.
- Paul Mark Medina, .et al. , Transl Oncol, 2021, Jan;14(1):100940 PMID: 33221682
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LSD1 Inhibitor
ORY-1001 is an orally active and selective lysine-specific demethylase LSD1/KDM1A inhibitor with IC50 of <20 nM, with high selectivity against related FAD dependent aminoxidases. Phase 1. -
Selective SIRT2 inhibitor
SirReal2 is a potent and selective Sirt2 inhibitor with IC50 of 140 nM.- Yang Li, .et al. , Neoplasia, 2018, Jul; 20(7): 745-756 PMID: 29925042
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WDR5 antagonist
WDR5-0103 is a small molecule that binds a peptide-binding pocket on WDR5 (Kd = 450 nM), inhibiting the catalytic activity of the MLL core complex in vitro (IC50 = 39 M).- Nicolas A Fraunhoffer, .et al. , EBioMedicine, 2023, Jun;92:104602 PMID: 37148583