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.
-
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. -
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. -
BRD4 inhibitor
BRD4 Inhibitor-30 (Compound 1) is a BRD4 inhibitor with an IC₅₀ value of 415 nM. -
menin-MLL interaction inhibitor
Menin-MLL Inhibitor 20 is an irreversible inhibitor of the menin-MLL interaction with demonstrated antitumor activity. It is referenced as Intermediate 6 in patent WO2020142557A1. -
BRD4/CK2 inhibitor
BRD4/CK2-IN-1 is the first highly potent and orally active dual inhibitor of BRD4 and casein kinase 2 (CK2), with IC₅₀ values of 180 nM and 230 nM, respectively. It exhibits strong anticancer activity with minimal toxicity, and induces apoptosis and autophagy-associated cell death in triple-negative breast cancer (TNBC) cells. -
KIX-KID interaction inhibitor
Naphthol AS-E is a potent, cell-permeable inhibitor of the KIX-KID interaction. It binds directly to the KIX domain of CBP with a Kd of 8.6 μM and inhibits the interaction between the KIX domain and the KID domain of CREB with an IC₅₀ of 2.26 μM. Naphthol AS-E is applicable in cancer research. -
PCAF inhibitor
L-Moses (L-45) dihydrochloride is the first potent, selective, and cell-permeable inhibitor of the p300/CBP-associated factor (PCAF) bromodomain, with a Kd of 126 nM. -
BET inhibitor
JQ1-TCO (JQ1-trans-cyclooctene) is a derivative of JQ1, a BET inhibitor, modified for click chemistry applications. It serves as a molecular probe for in vitro and in vivo studies. -
SPIN1 inhibitor
MS31 is a potent, highly selective fragment-like inhibitor of the methyllysine reader protein spindlin 1 (SPIN1). It strongly inhibits SPIN1 interactions with H3K4me3, with IC50 values of 77 nM (AlphaLISA) and 243 nM (FP). MS31 selectively binds to Tudor domain II of SPIN1 with a Kd of 91 nM and potently blocks binding of trimethyllysine-containing peptides to SPIN1. It exhibits no toxicity toward nontumorigenic cells. -
PRMT7 inhibitor
SGC8158 is a potent inhibitor of PRMT7, useful for investigating PRMT7's cellular functions. It reduces monomethylarginine levels on Hsp70, a key PRMT7 substrate. SGC8158 exhibits growth inhibitory effects in various cancer cells, including multidrug-resistant (MDR) cancer cells, with IC50 values ranging from 2 to 9 μM. -
SP140 Inhibitor
GSK761 is a selective inhibitor of speckled 140 kDa (SP140) protein, with an IC50 of 77.79 nM. It suppresses monocyte-to-inflammatory macrophage differentiation and lipopolysaccharide (LPS)-induced inflammatory activation. Additionally, GSK761 promotes the production of CD206+ regulatory macrophages by inhibiting SP140. -
ATAD2 bromodomain inhibitor
AZ13824374 is a highly potent and selective ATAD2 bromodomain inhibitor, demonstrating cellular target engagement and antiproliferative activity in various breast cancer models. It inhibits ATAD2 with pIC50 values of 8.2 in the ATAD2 FRET assay and 6.2 in the ATAD2 NanoBRET assay. -
BET inhibitor
Amredobresib (BI894999) is an orally active BET inhibitor that potently blocks the binding of BRD4-BD1 and BRD4-BD2 bromodomains to acetylated histones, with IC50 values of 5 nM and 41 nM, respectively. It demonstrates anticancer activity against acute myeloid leukemia (AML) and NUT carcinoma. -
BET/BRD4 bromodomain inhibitor
AZD5153 is a bivalent, selective, and orally active BET/BRD4 bromodomain inhibitor with an IC50 of 5 nM for full-length BRD4 (FL-BRD4). It simultaneously binds both bromodomains of BRD4, enhancing its inhibitory potency. AZD5153 is applicable for research into cancers, including acute myeloid leukemia, multiple myeloma, and diffuse large B-cell lymphoma. -
BET family bromodomain inhibitor
NHWD-870 is a potent, orally active, and selective BET family bromodomain inhibitor, specifically targeting BRD2, BRD3, BRD4 (IC50 = 2.7 nM), and BRDT. It exhibits strong tumor-suppressive effects, enhances tumor apoptosis, inhibits tumor proliferation, and disrupts cancer cell-macrophage interactions. -
Menin-MLL inhibitor
BMF-219 (Menin-MLL inhibitor 21) is a specific, irreversible inhibitor of the Menin-MLL interaction, suitable for research into autoimmune diseases, heteroimmune diseases, cancer, and other menin-MLL-dependent conditions. -
CECR2 inhibitor
NVS-CECR2-1 is a potent and selective non-BET family bromodomain (BRD) inhibitor targeting cat eye syndrome chromosome region, candidate 2 (CECR2). It binds CECR2 BRD with high affinity (IC50 = 47 nM; KD = 80 nM). NVS-CECR2-1 exhibits cytotoxic activity and induces apoptosis in various cancer cells through both CECR2-dependent and CECR2-independent mechanisms. -
ENL/AF9 YEATS domain inhibitor
SR-0813 is a potent and selective inhibitor of the ENL and AF9 YEATS domains. It exhibits IC50 and EC50 values of 25 nM and 205 nM, respectively, for the ENL YEATS domain, and 311 nM and 76 nM (CETSA) for the AF9 YEATS domain. SR-0813 binds MAP3K19 with significantly lower affinity (Kd = 3.5 μM) compared to ENL YEATS (Kd = 30 nM), demonstrating over 100-fold selectivity. It is suitable for research into acute leukemia. -
BPTF inhibitor
BPTF-IN-BZ1 is a highly potent BPTF inhibitor with a Kd of 6.3 nM. -
PBRM1 Bromodomain inhibitor
PBRM1-BD2-IN-8 (compound 34) is a potent inhibitor of the PBRM1 bromodomain, with a Kd of 4.4 μM and an IC50 of 0.16 μM for PBRM1-BD2, and a Kd of 25 μM for PBRM1-BD5. It exhibits anti-cancer activity.
