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.
-
PARP inhibitor
Rucaparib Camsylate is an inhibitor of PARP with a Ki of 1.4 nM for PARP1, and also shows binding affinity to eight other PARP domains. -
PARP1 and PARP2 inhibitor
Niraparib hydrochloride (MK-4827 hydrochloride) is a highly potent and orally bioavailable PARP1 and PARP2 inhibitor with IC50s of 3.8 and 2.1 nM, respectively. -
JAK1 Inhibitor
Upadacitinib (ABT-494) is a potent and selective Janus kinase (JAK) 1 inhibitor being developed for the treatment of several autoimmune disorders with an IC50 of 43 nM. IC50 & Target: IC50: 43 nM (JAK1), 200 nM (JAK2) -
JAK1 inhibitor
Abrocitinib (PF-04965842) is a potent, orally active and selective JAK1 inhibitor, with IC50s of 29 and 803 nM for JAK1 and JAK2, respectively. Abrocitinib (PF-04965842) exhibits less active effect on TYK2 (IC50, 1.253 μM), and inhibits phosphorylation of STAT1, STAT3 and STAT5 after stimulation. Effective in autoimmune disease. -
JAK3 inhibitor
JAK3-IN-2 is a potent and highly selective JAK3 inhibitor with IC50 of 0.15 nM. dispalys >4,300-fold selectivity over JAK1, JAK2 and TYK2, and other kinases BMX, EGFR, ITK and BTK; blocks cytokine signaling through JAK3, but not through other JAK family enzymes; inhibits IL-7 induced pSTAT5 in CD3+, CD8+ T cells with IC50 of 280 nM; sufficiently blocks the development of inflammation in a rat model of rheumatoid arthritis, while sparing hematopoiesis. -
LSD1 inhibitor
T-3775440 (hydrochloride) is an irreversible lysine-specific histone demethylase (LSD1) inhibitor with an IC50 value of 2.1 nM. -
HDAC inhibitor
EDO-S101 is a pan HDAC inhibitor; inhibits HDAC1, HDAC2 and HDAC3 with IC50 values of 9, 9 and 25 nM, respectively. -
selective BET inhibitor
PLX51107 is a potent and selective BET inhibitor, with Kds of 1.6, 2.1, 1.7, and 5 nM for BD1 and 5.9, 6.2, 6.1, and 120 nM for BD2 of BRD2, BRD3, BRD4, and BRDT, respectively; PLX51107 also interacts with the bromodomains of CBP and EP300 (Kd, in the 100 nM range). -
p300/CBP histone acetyltransferase inhibitor
P300/CBP-IN-3, a p300/CBP histone acetyltransferase inhibitor. -
SMYD3 inhibitor
SMYD3-IN-1 (compound 29) is an irreversible and selective inhibitor of SMYD3 (SET and MYND domain containing 3), with an IC50 of 11.7 nM. -
PARP14 inhibitor
PARP14 inhibitor H10, compound H 10, is a selective inhibitor against PARP14 (IC50=490 nM), over other PARPs (??24 fold over PARP1). PARP14 inhibitor H10 induces caspase-3/7-mediated cell apoptosis. -
SUV39H2 inhibitor
OTS186935 is a protein methyltransferase SUV39H2 inhibitor with an IC50 of 6.49 nM.- Jennings Luu, .et al. , Hum Mol Genet, 2020, Jul 21;ddaa158 PMID: 32691052
-
BRD4-BD1 inhibitor
BRD4 Inhibitor-10 is a potent BRD4-BD1 inhibitor extracted from patent WO2015022332A1, Compound II-25, has an IC50 of 8 nM. -
TYK2 Inhibitor
BMS-986165 is a Highly Potent and Selective Allosteric Inhibitor of TYK2. BMS-986165 Blocks Il-12, IL-23 and type I Interferon Signaling and Provides for Robust Efficacy in Preclinical Models of Inflammatory Bowel Disease. -
Bromodomain inhibitor
Bromodomain IN-1 is a Bromodomain inhibitor extracted from patent WO2016069578A1, compound 4 . -
HDAC inhibitor
CHDI-390576, a potent, cell permeable and CNS penetrant class IIa histonedeacetylase (HDAC) inhibitor with IC50s of 54 nM, 60 nM, 31 nM, 50 nM for class IIa HDAC4, HDAC5, HDAC7, HDAC9, respectively, shows >500-fold selectivity over class I HDACs (1, 2, 3) and ~150-fold selectivity over HDAC8 and the class IIb HDAC6 isoform. -
JAK3 covalent inhibitor
JAK3 covalent inhibitor-1 is a potent and selective janus kinase 3 (JAK3) covalent inhibitor with an IC50 of 11 nM and shows 246-fold selectivity vs other JAKs. -
pan-PAD inhibitor
Streptonigrin (Bruneomycin), a natural product produced by Streptomyces flocculus, possesses both anti-tumor and anti-bacterial activity. Streptonigrin acts as a pan-PAD inhibitor with IC50s of 48.3??34.2 ?M, 26.1??0.3 ?M, 0.43??0.03 ?M, and 2.5??0.4 ?M for PAD1, PAD2, PAD3, and PAD4, respectively. -
HDAC inhibitor
MPT0E028 is an orally active and selective HDAC inhibitor with IC50s of 53.0 nM, 106.2 nM, 29.5 nM for HDAC1, HDAC2 and HDAC6, respectively. -
TYK2 inhibitor
Ropsacitinib (PF-06826647) is a selective TYK2 inhibitor, which binds to TYK2 catalytically active JH1 domain with an IC50 of 17 nM, used in the treatment of psoriasis.
-
BRM/BRG1 ATP Inhibitor
BRM/BRG1 ATP Inhibitor-1 is an allosteric dual brahma homolog (BRM)/SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily A member 2 (SMARCA2) and brahma related gene 1 (BRG1)/SMARCA4 ATPase activity inhibitor, both IC50s are below 0.005 ?M. -
Tankyrase inhibitor
Tankyrase-IN-2 (compound 5k) is a potent, selective, and orally active tankyrase inhibitor (IC50s of 10, 7, and 710 nM for TNKS1, TNKS2 as well as PARP1, respectively).
