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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  1. Aurora A Kinase inhibitor

    MLN8237 (Alisertib) is a selective Aurora A inhibitor with IC50 of 1.2 nM in a cell-free assay. It has >200-fold higher selectivity for Aurora A than Aurora B. Phase 3..
  2. Antioxidant, antiangiogenic, antitumor agent

    (-)-Epigallocatechin gallate is a potent anti-oxidant polyphenol flavonoid isolated from green tea.
  3. PARP1 inhibitor

    A-966492 displayed high potency against the poly(ADP-ribose) polymerase-1 (PARP-1) enzyme with a K(i) of 1 nM and an EC(50) of 1 nM in a whole cell assay.
  4. PARP inhibitor

    ABT-888(Veliparib) is a potential anti-cancer drug acting as a PARP inhibitor.
  5. PARP inhibitor

    AG-014699 (Rucaparib) is a PARP inhibitor that inhibits poly(ADP-ribose) polymerase (PARP) is a key enzyme in DNA repair.
  6. PARP inhibitor

    AG14361 is a potent PARP inhibitor, enhanced TMZ cytotoxicity in MMR(mismatch repair)-proficient / deficient cells.
  7. EGFR inhibitor

    AG 490 is a selective inhibitor of EGF receptor tyrosine kinase (IC50 values are 2 and 13.5 μM for EGFR and ErbB2 respectively). Also inhibits JAK2 with no activity to Lck, Lyn, Btk, Syk and Src.
  8. Aurora/JAK inhibitor

    AT9283 inhibits aurora kinase A and B and targets other tyrosine and serine/threonine kinases associated with myeloid cell proliferation.
  9. Aurora A Inhibitor

    Aurora A Inhibitor I is a potent and selective inhibitor of Aurora A kinase (AurA), with IC50 values to be 3.4 nM (Aurora A) and unusually high selectivity 1000 fold against Aurora B; a useful tool compound for investigating the cellular role of Aurora A kinases.

  10. JAK2inhibitor

    AZ-960 is a potent, selective and ATP competitive JAK2 inhibitor that inhibits JAK2 kinase with a Ki of 0.45 nM in vitro and induces growth arrest and apoptosis in adult T-cell leukemia (ATL) cell.
  11. DNMT inhibitor

    Azacitidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA that is mainly used in the treatment of myelodysplastic syndrome (MDS).
  12. Aurora Kinase B inhibitor

    AZD 1152-HQPA is a highly potent and selective inhibitor of Aurora B, with Ki values to be 0.36 (Aurora B) and 1369 nM (Aurora A) respectively and has a high specificity versus a panel of 50 other kinases.
  13. JAK Inhibitor

    AZD1480 is a novel potent small JAK2 inhibitor with an IC50 of 0.26 nM.
  14. PARP inhibitor

    Olaparib (AZD2281) is an inhibitor of poly ADP ribose polymerase (PARP), an enzyme involved in DNA repair.
  15. HDAC inhibitor

    Belinostat (PXD101) is a HDAC inhibitor that inhibits HDAC activity in HeLa cell extracts with an IC50 of 27 nM.
  16. PARP inhibitor

    BSI-201 is a potent inhibitor of PARP-1 and has been shown to cross the blood-brain barrier.
  17. Aurora Inhibitor

    CCT129202 is a representative of a structurally novel series of imidazopyridine small-molecule inhibitors of Aurora kinase activity. It shows high selectivity for the Aurora kinases over a panel of other kinases tested and inhibits proliferation in multiple cultured human tumor cell lines.

  18. JAK3 inhibitor

    CP-690550 (Tofacitinib citrate) is an orally available, highly selective inhibitor of the Janus kinase (JAK) family of enzymes.
  19. HDAC inhibitor

    CUDC-101 is a novel compound which inhibits multiple targets, which is designed to inhibit HDAC, EGFR and Her2.
  20. JAK2 inhibitor

    Curcumol induces apoptosis via caspases-independent mitochondrial pathway in human lung adenocarcinoma ASTC-a-1 cells.
  21. Aurora Kinase inhibitor

    Aurora kinase/VEGFR 2 inhibitor CYC116 inhibits Aurora kinases A and B and vascular endothelial growth factor receptor 2 (VEGFR2), resulting in disruption of the cell cycle, rapid cell death, and the inhibition of angiogenesis.
  22. JAK inhibitor

    CYT387 is an inhibitor of Janus kinases JAK1 and JAK2, acting as an ATP competitor with IC50 values of 11 and 18 nM, respectively.
  23. DNA Methyltransferase Inhibitors

    Decitabine is a hypomethylating agent.It hypomethylates DNA by inhibiting DNA methyltransferase.
  24. HDAC inhibitor

    Droxinostat is a selective inhibitor of HDAC3, HDAC6, and HDAC8 that shows comparable inhibition of HDAC6 and HDAC8 with IC50 = 2.47 and 1.46 μmol/L, respectively.
  25. Aurora A / FLT3 Inhibitor

    ENMD-2076 has selective activity against Aurora A and Flt3 with IC50 of 14 nM and 1.86 nM, 25-fold selective for Aurora A than over Aurora B and less potent to VEGFR2/KDR and VEGFR3, FGFR1 and FGFR2 and PDGFRα. Phase 2.
  26. SIRT1 inhibitor

    EX 527 is a potent and selective SIRT1 class III histone deacetylase enzyme inhibitor with IC50 of 38 nM in a cell-free assay.
  27. Fisetin is a flavonol, a structurally distinct chemical substance that belongs to the flavonoid group of polyphenols. It can be found in many plants, where it serves as a colouring agent. Possible anti-aging, anti-inflammatory, anti-cancer, and anti-viral properties of fisetin are under active scientific investigation.
  28. mTOR inhibitor

    FK-506 is an immunosuppressive drug that is mainly used after allogeneic organ transplant to reduce the activity of the patient's immune system and so lower the risk of organ rejection. It reduces interleukin-2 (IL-2) production by T-cells.
  29. Aurora B Kinase inhibitor

    Hesperadin is a human Aurora B inhibitor with an IC50 of 40 nM for the prevention of the phosphorylation of substrate. It markedly reduces the activity of AMPK, Lck, MKK1, MAPKAP-K1, CHK1 and PHK while it does not inhibit MKK1 activity in vivo.
  30. PARP Inhibitor

    3-Aminobenzamide is a novel PARP inhibitor, known to sensitize cells to radiation in vitro by inhibiting the repair of DNA damage.
  31. HDAC inhibitor

    ITF2357 (Givinostat) is a HDACs inhibitor with potential anti-inflammatory, anti-angiogenic, and antineoplastic activities.
  32. HDAC inhibitor

    JNJ-26481585 (Quisinostat) is a pan-HDAC inhibitor with marked potency toward HDAC1 (IC(50), 0.16 nmol/L).
  33. CDK/Aurora A/B Inhibitor

    JNJ-7706621 is pan-CDK inhibitor with the highest potency on CDK1/2 with IC50 of 9 nM/4 nM and showing >6-fold selectivity for CDK1/2 than CDK3/4/6 in cell-free assays. It also potently inhibits Aurora A/B and has no activity on Plk1 and Wee1.
  34. FLT3/FGFR/Bcr-Abl/Aurora Inhibitor

    KW-2449 is a multikinase inhibitor of FLT3, ABL, ABL-T315I, and Aurora kinase.
  35. HDAC Inhibitor

    LAQ824 (NVP-LAQ824) is a potent novel histone deacetylase inhibitor with significant activity against multiple myeloma.
  36. HDAC Inhibitor

    LBH589 is a hydroxamic acid and acts as a non-selective HDAC inhibitor with IC5o of HDAC1 to be 0.23 nM.
  37. JAK inhibitor

    LY2784544 is identified as being highly selective for JAK2-V617F and has advanced into human clinical trials for the treatment of several myeloproliferative disorders.
  38. HDAC Inhibitor

    MC1568 is a member of HDAC inhibitors that inhibits the histone deacetylase class II by modifying the genetic expression of various important genes of cell cycle mostly at G1 phase, resulting in the death of breast cancer cells by apoptosis.
  39. HDAC Inhibitor

    MGCD0103 (Mocetinostat) is a benzamide histone deacetylase inhibitor by inhibiting mainly histone deacetylase 1 (HDAC1), but also HDAC2, HDAC3, and HDAC11.
  40. Aurora A Inhibitor

    MLN8054 is an inhibitor of Aurora A kinase, induces senescence in human tumor cells both in vitro and in vivo.
  41. HDAC inhibitor

    MS-275 (Entinostat) is a potent HDAC inhibitor with IC50 of 0.3 and 8uM for HDAC1 and HDAC3, respectively.
  42. Parthenolide ((-)-Parthenolide) is a sesquiterpene lactone which occurs naturally in the plant feverfew (Tanacetum parthenium).
  43. HDAC Inhibitor

    PCI-24781 is a broad-spectrum phenyl hydroxamic acid HDAC inhibitor.
  44. Aurora inhibitor

    PHA-680632 is potent inhibitor of Aurora A, Aurora B and Aurora C with IC50 of 27 nM, 135 nM and 120 nM, respectively. It has 10- to 200-fold higher IC50 for FGFR1, FLT3, LCK, PLK1, STLK2, and VEGFR2/3.
  45. Aurora inhibitor

    Danusertib (PHA-739358) is an Aurora kinase inhibitor for Aurora A/B/C with IC50 of 13 nM/79 nM/61 nM in cell-free assays, modestly potent to Abl, TrkA, c-RET and FGFR1, and less potent to Lck, VEGFR2/3, c-Kit, CDK2, etc. Phase 2
  46. HDAC Inhibitor

    Pyroxamide (NSC 696085) is a potent inhibitor of affinity-purified HDAC1 and causes the accumulation of acetylated core histones in MEL cells cultured with the agent.
  47. HDAC inhibitor

    SB939 is an oral inhibitor of HDAC, selective for class I, II and IV HDACs and displays an IC50 value of 77 nM in an in vitro HDAC1 activity assay.
  48. PIM1 Inhibitor

    SGI-1776 free base is a novel ATP competitive inhibitor of Pim1 with IC50 of 7 nM in a cell-free assay, 50- and 10-fold selective versus Pim2 and Pim3, also potent to Flt3 and haspin. Phase 1.
  49. Aurora inhibitor

    SNS-314 Mesylate is a potent and selective inhibitor of Aurora A, Aurora B and Aurora C with IC50 of 9 nM, 31 nM, and 3 nM, respectively. It is less potent to Trk A/B, Flt4, Fms, Axl, c-Raf and DDR2. Phase 1.
  50. HDAC inhibitor

    Sodium butyrate (NaB, Butanoic acid sodium salt), sodium salt of butyric acid, is a histone deacetylase inhibitor and competitively binds to the zinc sites of class I and II histone deacetylases (HDACs).

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