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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IGF-1R, Aurora, FGFR, ABL, SRC inhibitor
XL228 is a protein kinase inhibitor targeting IGF1R, the AURORA kinases, FGFR1-3, ABL and SRC family kinases. XL228 is an Aurora A inhibitor (IC50, f3 nmol/L) that has shown potent biochemical activity against ABL1 (Ki, 5 nmol/L), as well as the BCR-ABL1 T315I (Ki, 1.4 nmol/L) kinases. -
Src/Abl inhibitor
Saracatinib (AZD0530) is a highly selective, orally available, dual-specific Src/Abl kinase inhibitor with IC50 of 2.7 and 30 nM for c-Src and Abl kinase, respectively.- Andromachi Lambrianidou, .et al. , Cell Signal, 2021, Apr;80:109912 PMID: 33388443
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Src inhibitor
Bosutinib (SKI-606) is a tyrosine kinase inhibitor undergoing research for use in the treatment of cancer.- Li Li, .et al. , Leukemia Res, 2019, 78:12-20 PMID: 30660961
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Abl-Src inhibitor
Dasatinib (BMS-354825) is an oral multi- BCR/ABL and Src family tyrosine kinase inhibitor. The main targets of dasatinib, are BCR/ABL, Src, c-Kit, ephrin receptors, and several other tyrosine kinases, but not erbB kinases such as EGFR or Her2.- Hiroto Kataoka, .et al. , Anal Biochem, 2023, Oct 1;678 PMID: 37541642
- Vijaya Bharti, .et al. , Cell Rep, 2022, Dec 20;41(12):111826 PMID: 36543138
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EphB4 inhibitor
NVP-BHG712 is a selective inhibitor of EphB4 kinase that exhibits selectivity for EphB4 over more than 40 other kinases in vitro, including FGFR3.- Y Kaibori, .et al. , the FASEB Journal, 2019, Jan 22:fj201801519RR PMID: 30668924
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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. -
Src inhibitor
KX2-391 2Hcl is the first clinical Src inhibitor (peptidomimetic class) that targets the peptide substrate site of Src, with GI50 of 9-60 nM in cancer cell lines. - Scutellarin, a main active ingredient extracted from Erigeron breviscapus (Vant.) Hand-Mazz, has been wildly used to treat acute cerebral infarction and paralysis induced by cerebrovascular diseases.
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Src tyrosine kinase inhibitor
Src Inhibitor 1 is a potent and selective dual site Src tyrosine kinase inhibitor with IC50 values of 44 nM for Src and 88nM for Lck. - MLR 1023 is a selective allosteric activator of Lyn kinase (EC50 = 63 nM)
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Src Inhibitor
PP1 is a potent inhibitor of Src-family tyrosine kinases. Inhibits p56lck and p59fynT (IC50 values are 5 and 6 nM respectively). Displays > 8000-fold selectivity over ZAP-70 and JAK2. Also moderately inhibits p38, CSK, PDGF receptors, RET-derived oncoproteins, c-Kit and Bcr-Abl - PP1 Analog II, 1NM-PP1 is a cell-permeable PP1 analog that acts as a potent and selective inhibitor of mutant kinases over their wild-type progenitors.
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Src inhibitor
Dasatinib hydrochloride is a potent and dual Abl/ Src inhibitor IC50 of <1 nM/0.8 nM respectively; also inhibit c-Kit (WT)/c-Kit (D816V) with IC50 of 79 nM/37 nM. -
Lck Inhibitor
TC-S 7003 is a new class of compounds that are potent inhibitors of Lck with an IC50 value of 7 nM. -
Lck inhibitor
Lck inhibitor 2 is a bis-anilinopyrimidine inhibitor of tyrosine kinases including LCK, BTK, LYN, SYK, and TXK. The IC50 values are 13nM, 9nM, 3nM, 26nM and 2nM for Lck, Btk, Lyn, Btk and Txk respectively . -
VEGFR2/Src kinase inhibitor
TG 100572 is a multi-targeted kinase inhibitor that inhibit select growth factor receptor tyrosine kinases and Src familt kinases with IC50 values of 2/7/2/1/0.5 nM for VEGFR1/VEGFR2/FGFR1/Src/Fyn kianse respectively. -
Src inhibitor
T338C Src-IN-1 is a potent mutant-Src T338C inhibitor; exhibited the most potent inhibition of T338C(IC50=111 nM) relative to WT c-Src (10-fold increase). -
Src inhibitor
T338C Src-IN-2 is a potent mutant c-Src T338C kinase inhibitor with IC50 of 317 nM; also inhibits T338C/V323A and T338C/V323S with IC50 of 57 nM/19 nM. -
Lck inhibitor
KIN001-051 is a potent and selective inhibitor of lck. Lymphocyte-speci?c protein tyrosine kinase (Lck) is a member of the Src-family of non-receptor protein tyrosine kinases and plays a critical role in the initial steps of T cell receptor signaling that trigger the production of cytokines. -
SRC inhibitor
CSF1R-IN-2 (compound 5) is an oral-active inhibitor of SRC, MET and c-FMS, with IC50 values of 0.12 nM, 0.14 nM and 0.76 nM for SRC, MET and c-FMS respectively. -
Src inhibitor
WEHI-345 analog is a Src inhibitor, extracted from patent WO/2012003544A1, compound example 71. -
Src inhibitor
Tirbanibulin Mesylate (KX2-391 Mesylate) is an inhibitor of Src that targets the peptide substrate site of Src, with GI50 of 9-60 nM in cancer cell lines. -
Src/c-Abl inhibitor
1-Naphthyl PP1 hydrochloride is a selective inhibitor of src family kinases v-Src and c-Fyn as well as the tyrosine kinase c-Abl (IC50 values are 1.0, 0.6, 0.6, 18 and 22 μM for v-Src, c-Fyn, c-Abl, CDK2 and CAMK II respectively).