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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CARM1 inhibitor
SGC2085 hydrochloride is a potent and selective inhibitor of coactivator associated arginine methyltransferase 1 (CARM1) with IC50 of 50 nM. -
SHP2 allosteric inhibitor
IACS-13909 is a selective, potent and orally active SHP2 allosteric inhibitor with an IC50 of 15.7 nM and a Kd of 32 nM. -
pan-PIM/FLT3 inhibitor
SEL24-B489 is a potent, type I, orally active dual inhibitor of PIM kinases and FLT3-ITD. It exhibits high affinity for PIM family members, with Kd values of 2 nM for PIM1, 2 nM for PIM2, and 3 nM for PIM3, making it a promising candidate for targeted cancer therapy. -
NAD+ competitive inhibitor of PARP7
RBN-2397 is a potent, accross species and orally active NAD+ competitive inhibitor of PARP7 (IC50<3 nM). -
peptidylarginine deminase (PAD) inhibitor
Cl-amidine TFA is an orally active peptidylarginine deminase (PAD) inhibitor, with IC50 values of 0.8 μM, 6.2 μM and 5.9 μM for PAD1, PAD3, and PAD4, respectively. -
epigenetic modifier
L-2-Hydroxyglutaric acid disodium ((S)-2-Hydroxyglutaric acid disodium, L-2-Hydroxyglutarate disodium, LGA, L-2HG) is an epigenetic modifier and a putative oncometabolite in kidney cancer that inhibits histone demethylases and hence promotes histone methylation. -
EZH2 inhibitor
Gambogenic acid is an active ingredient in gamboge, with anticancer activity. Gambogenic acid acts as an effective inhibitor of EZH2, specifically and covalently binds to Cys668 within the EZH2-SET domain, and induces EZH2 ubiquitination. -
anticancer agent
5,7,4'-Trimethoxyflavone is isolated from Kaempferia parviflora (KP) that is a famous medicinal plant from Thailand. 5,7,4'-Trimethoxyflavone induces apoptosis, as evidenced by increments of sub-G1 phase, DNA fragmentation, annexin-V/PI staining, the Bax/Bcl-xL ratio, proteolytic activation of caspase-3, and degradation of poly (ADP-ribose) polymerase (PARP) protein.5,7,4'-Trimethoxyflavone is significantly effective at inhibiting proliferation of SNU-16 human gastric cancer cells in a concentration dependent manner. -
HDAC6 inhibitor
Tubastatin A is a potent HDAC6 inhibitor with an IC50 value of 15 nM. -
antidepressant agent
Gardenia yellow is an active member of crocin, increases mRNA expression of SIRT3, and acts as an orally active antidepressant agent. -
pan-HDAC inhibitor
Quisinostat dihydrochloride (JNJ-26481585 dihydrochloride) is an orally available, potent pan-HDAC inhibitor with IC50s of 0.11 nM, 0.33 nM, 0.64 nM, 0.46 nM, and 0.37 nM for HDAC1, HDAC2, HDAC4, HDAC10 and HDAC11, respectively. Quisinostat dihydrochloride has a broad spectrum antitumoral activity. -
Pdia3/ERp57 activator, STAT3 inhibitor
Diosgenin palmitate, also known as Diosgenin hexadecanoate, is the hexadecanoic ester of Diosgenin. Diosgenin, a phytosteroid sapogenin, is the product of hydrolysis by acids, strong bases, or enzymes of saponins, extracted from the tubers of Dioscorea wild yam, such as the Kokoro. -
Menin-MLL inhibitor
SNDX-5613 is a potent and specific Menin-MLL inhibitor. -
HDAC1 and HDAC3 inhibitor
Suberoyl bis-hydroxamic acid (Suberohydroxamic acid; SBHA) is a competitive and cell-permeable HDAC1 and HDAC3 inhibitor with ID50 values of 0.25 μM and 0.30 μM, respectively. -
SIRT1/SIRT3 inhibitor
4'-bromo-Resveratrol is a potent inhibitor of the deacetylases sirtuin 1 (SIRT1) and 3 (SIRT3).
- Phoenixin-20 (PNX-20) is a bioactive peptide with hormone-like actions in vertebrates, and can stimulates hypothalamo-pituitary-gonadal hormones and regulate reproductive processes in mammals. Phoenixin-20 promotes neuronal mitochondrial biogenesis via CREB-PGC-1α pathway. Phoenixin-20 has anxiolytic effect.
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histone acetyltransferase Gcn5 inhibitor
Butyrolactone 3 (MB-3) is a specific small-molecule inhibitor of the histone acetyltransferase Gcn5, exhibiting an IC₅₀ of 100 μM and binding affinity comparable to that of its natural substrate, histone H3. It displays weak inhibitory activity against CBP (IC₅₀ = 0.5 mM), indicating high selectivity for Gcn5. By modulating histone acetylation and epigenetic regulation, Butyrolactone 3 serves as a valuable research tool for exploring the roles of Gcn5 in cancer, metabolic disorders, autoimmune diseases, and neurological conditions. -
KDM4D Inhibitor
Zavondemstat (QC8222; TACH 101) is an inhibitor of histone lysine demethylase 4D (KDM4D) with demonstrated antineoplastic activity. It is under investigation for its potential use in cancer therapy by targeting epigenetic regulation mechanisms. - Tz-Thalidomide is a tetrazine-tagged thalidomide derivative that functions as a ligand for E3 ligases. It exhibits binding affinity for BRD4, with IC₅₀ values of 46.25 μM for BRD4-1 and 62.55 μM for BRD4-2. As a click chemistry reagent, Tz-Thalidomide contains a tetrazine moiety capable of undergoing inverse electron demand Diels–Alder (iEDDA) reactions with trans-cyclooctene (TCO)-containing molecules, enabling bioorthogonal labeling and conjugation applications.
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HDAC inhibitor
Nullscript is an inactive analog of Scriptaid and serves as a negative control for Scriptaid, a representative histone deacetylase (HDAC) inhibitor. Despite its inactivity as an HDAC inhibitor, Nullscript inhibits the growth of *Cryptosporidium parvum* with an IC₅₀ value of 2.1 μM. -
SMARCA4/SMARCA2 ATPase inhibitor
FHD-286 is a selective, orally active inhibitor of the SMARCA4/SMARCA2 (BRG1/BRM) ATPase. It holds potential for research into BAF (BRG1/BRM-associated factor)-related disorders, including acute myeloid leukemia. -
p300/CBP inhibitor
NEO2734 (EP31670) is an orally active dual inhibitor of p300/CBP and BET bromodomains, with IC₅₀ values of <30 nM for both targets. It is effective in both SPOP-mutant and wild-type prostate cancer models. -
SMARCA4/SMARCA2 ATPase Inhibitor
FHT-1015 is a selective allosteric inhibitor of SMARCA4 (BRG1) and SMARCA2 (BRM), with IC₅₀ values of 4 nM and 5 nM, respectively. It binds to an allosteric site, inducing conformational changes that inhibit the ATPase activity of BRG1/BRM. FHT-1015 disrupts tumor cell growth and migration and is applicable in research on uveal melanoma and hematologic malignancies. -
ATAD2 bromodomain inhibitor
GSK8814 is a potent and selective chemical probe and inhibitor of the ATAD2 bromodomain, with an IC₅₀ of 0.059 μM, a pK\_d of 8.1, and a pK\_i of 8.9 in BROMOscan. It binds to ATAD2 and BRD4 BD1 with pIC₅₀ values of 7.3 and 4.6, respectively, demonstrating over 500-fold selectivity for ATAD2. GSK8814 is suitable for research in cancers associated with ATAD2 bromodomain activity. - NICE-01 (AP1867-PEG2-JQ1; AP-PEG2-JQ1) is a bifunctional compound designed to induce nuclear import of cytosolic proteins. It functions by binding proteins in distinct cellular compartments and leveraging nuclear-localized BRD4 as a “carrier” to facilitate co-import and nuclear retention of cytosolic cargoes.
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Menin inhibitor
BN-104 (BNM-1192) is an orally active and selective brain-penetrant menin inhibitor that disrupts the menin-MLL interaction, leading to degradation of the menin protein. It exhibits antitumor activity and is applicable in cancer research, including studies on acute myeloid leukemia. BN-104 is a weak hERG inhibitor, with an IC₅₀ greater than 100 μM. -
Menin inhibitor
Enzomenib is an inhibitor of menin, a protein encoded by the multiple endocrine neoplasia (MEN) gene. It disrupts the interaction between menin and mixed lineage leukemia (MLL) fusion proteins and is applicable in the study of hematological malignancies. -
BET/EP300 inhibitor
XP-524 is a potent dual inhibitor of BET and EP300, exhibiting strong antitumor activity in vivo. It prevents KRAS-induced neoplastic transformation and prolongs survival in two transgenic mouse models of aggressive pancreatic ductal adenocarcinoma (PDAC). XP-524 also enhances self-peptide presentation and promotes tumor infiltration by cytotoxic T lymphocytes, supporting its potential for PDAC research. -
CBP/p300 inhibitor
CBP/p300-IN-8 is a potent inhibitor of the CBP/p300 family of bromodomains, with an IC₅₀ of 0.01–0.1 µM for CBP. It also inhibits BRD4 activity with significantly lower potency (IC₅₀ = 1–1000 µM). -
p300/CBP inhibitor
CBP/p300-IN-12 is a potent and selective covalent inhibitor of the histone acetyltransferases p300 and CBP, with an IC₅₀ of 166 nM for p300. It reduces H3K27Ac levels in PC-3 cells with an EC₅₀ of 37 nM and forms a covalent adduct with cysteine residue C1450. -
BRD4/NAMPT inhibitor
BRD4/NAMPT-IN-1 (Compound A2) is a dual inhibitor of NAMPT and BRD4, with IC₅₀ values of 35 nM and 58 nM, respectively. It suppresses the growth and migration of hepatocellular carcinoma cells and induces apoptosis. In the HCCLM3 xenograft mouse model, BRD4/NAMPT-IN-1 exhibits potent anticancer activity without apparent toxicity. -
BET BD1 inhibitor
LT052 is a highly selective BET BD1 inhibitor with an IC₅₀ of 87.7 nM. It demonstrates nanomolar potency against BRD4 BD1 and exhibits 138-fold selectivity over BRD4 BD2 (IC₅₀ = 12.130 μM). LT052 possesses anti-inflammatory activity and is applicable in acute gout arthritis research.
