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. Carmofur is a pyrimidine analogue used as an antineoplastic agent. It is a derivative of fluorouracil.
  2. HCV NS3/4A protease inhibitor

    Danoprevir is a potent inhibitor of the HCV NS3/4A serine protease.
  3. Disulfiram blocks the processing of alcohol in the body by inhibiting acetaldehyde dehydrogenase thus causing an unpleasant reaction when alcohol is consumed.
  4. Ivermectin is a broad-spectrum antiparasitic avermectin medicine.
  5. Lamivudine is a potent nucleoside analog reverse transcriptase inhibitor (nRTI).
  6. HIV Protease inhibitor

    Lopinavir is an inhibitor of the HIV protease.
  7. Mitoxantrone is a synthetic antineoplastic anthracenedione (IC50 = 0.42 mM).
  8. Mitoxantrone Dihydrochloride is an antiviral, antibacterial, antiprotozoal, immunomodulating, and antineoplastic cytostatic anthraquinone derivative.
  9. serine protease inhibitor

    Nafamostat is an anticoagulant. Broad spectrum serine protease inhibitor. Reduces eosinophil infiltration, mast cell activation and airway responsiveness in a murine model of asthma.
  10. HMG-CoA reductase inhibitor

    Pitavastatin Calcium is a competitive inhibitor of the enzyme HMGCR (HMG-CoA reductase) results in a reduction in LDL cholesterol synthesis.
  11. Praziquantel is a highly effective anthelmintic against all Schistosoma species.
  12. HIV Protease inhibitor

    Ritonavir is a protease inhibitor with activity against Human Immunodeficiency Virus Type 1 (HIV-1). Protease inhibitors block the part of HIV called protease.Ritonavir inhibits the HIV viral proteinase enzyme which prevents cleavage of the gag-pol polyprotein, resulting in noninfectious, immature viral particles.
  13. HMG-CoA reductase inhibitor

    Rosuvastatin (Crestor) is a member of the drug class of statins, used to treat high cholesterol and related conditions, and to prevent cardiovascular disease. Rosuvastatin is a competitive inhibitor of the enzyme HMG-CoA reductase, having a mechanism of action similar to that of other statins.
  14. HCV NS3-4A protease inhibitor

    Telaprevir (VX-950) is known as protease inhibitors that inhibits the hepatitis C virus NS3.4A serine protease.
  15. HIV reverse transcriptase inhibitor

    Tenofovir is in a class of medications called nucleoside reverse transcriptase inhibitors (NRTIs). It works by decreasing the amount of HIV in the blood.
  16. nucleotide reverse transcriptase inhibitor

    Tenofovir Disoproxil Fumarate is employed as an anti-HIV agend and a reverse transcriptase inhibitor.
  17. HMG-CoA reductase inhibitor

    Rosuvastatin is a member of the drug class of statins, used to treat high cholesterol and related conditions, and to prevent cardiovascular disease.
  18. Proteasome inhibitor

    PR-171 (Carfilzomib) is a tetrapeptide epoxyketone and a selective proteasome inhibitor. It is an analog of epoxomicin.
  19. HCV Protease Inhibitor

    Boceprevir is a protease inhibitor used as a treatment for hepatitis C genotype 1.
  20. Histamine Receptor antagonist

    Bepotastine Beslilate (Bepreve) is a histamine H1 receptor anatagonist.
  21. HIV-1 protease inhibitor

    Nelfinavir is a potent and orally bioavailable human immunodeficiency virus HIV-1 protease inhibitor (Ki=2 nM) and is widely prescribed in combination with HIV reverse transcriptase inhibitors for the treatment of HIV infection.
  22. viral RNA polymerase inhibitor

    T-705, a substituted pyrazine compound, has been found to exhibit potent anti-influenza virus activity in vitro and in vivo.

  23. GSK-3 Inhibitor

    Tideglusib is a GSK-3 inhibitor currently in phase II clinical trials for the treatment of Alzheimer disease and progressive supranuclear palsy
  24. Prulifloxacin is an older synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Like other fluoroquinolones, Prulifloxacin prevents bacterial DNA replication, transcription, repair and recombination through inhibition of bacterial DNA gyrase.
  25. Moexipril hydrochloride is a potent orally active non-sulfhydryl angiotensin converting enzyme inhibitor (ACE) which is used for the treatment of hypertension and congestive heart failure.
  26. Camostat mesylate is an orally active protease inhibitor. Known to inhibit trypsin and various inflammatory proteases including plasmin, kallikrein and thrombin.
  27. Azithromycin is an azalide antibiotic, which inhibits the growth of gram negative bacteria, such as Haemophilus influenza.
  28. HIV protease inhibitor

    Darunavir Ethanolate (Prezista) is an HIV protease inhibitor.
  29. Indinavir sulfate is a novel hydroxyaminopentane amide class of HIV-1 protease inhibitors.
  30. GSK-3 Inhibitor

    TDZD-8 protects the brain against I/R injury by inhibiting GSK-3beta activity
  31. Bepotastine is a non-sedating, selective antagonist of the histamine 1 (H1) receptor.
  32. NS5A inhibitor

    Ledipasvir is an inhibitor of the hepatitis C virus HCV NS5A protein
  33. Atovaquone is an anti-protozoal mitochondrial electron transport inhibitor.
  34. Trx-1 inhibitor

    PX 12 inhibits hypoxia-induced HIF-1a transcriptional activity (IC50 11 nM) and proliferation of HT29 and MCF-7 tumor cells (IC50 1.9 and 0.9 uM, respectively).
  35. HMG-CoA reductase inhibitor

    Pitavastatin Lactone is an HMG-CoA reductase inhibitor.
  36. Hydroxychloroquine Sulfate is an antimalarial agent used for the treatment of systemic lupus erythematosus, rheumatoid arthritis and other autoimmune, inflammatory and dermatologic conditions. Also acts as an inhibitor of autophagy and toll-like receptor (TLR) 7/9.
  37. HIV protease inhibitor

    Nelfinavir Mesylate is a potent HIV protease inhibitor with Ki of 2 nM.
  38. Ciclesonide is a glucocorticoid used to treat obstructive airway diseases.
  39. Azithromycin Dihydrate is an acid stable orally administered macrolide antimicrobial drug, structurally related to erythromycin.
  40. Chloroquine phosphate is a 4-aminoquinoline anti-malarial and anti-rheumatoid agent, also acting as an ATM activator.
  41. HIV-1 integrase Inhibitor

    Bictegravir, also known as GS-9883, is a potent, unboosted, once-Daily HIV-1 Integrase Strand Transfer Inhibitor (INSTI) (IC50 - 1.6 nM) with improved pharmacokinetics and in vitro resistance profile.
  42. antiviral

    Remdesivir, also known as GS-5734, inhibits murine hepatitis virus (MHV) with an EC50 of 30 nM, and blocks SARS-CoV and MERS-CoV in HAE cells with EC50s of both 74 nM in HAE cells after treatment for 24 h.
  43. HCV NS5A inhibitor

    Velpatasvir, also known as GS-5816, is a potent and selective Hepatitis C virus NS5A inhibitor.
  44. HCV NS5A inhibitor

    Ledipasvir acetone is the active pharmaceutical ingredient of Ledipasvir. Ledipasvir is an inhibitor of the hepatitis C virus NS5A, with EC50 values of 34 pM against GT1a and 4 pM against GT1b replicon.
  45. PF-07321332 is an orally bioavailable 3C-like protease (3CLPRO) inhibitor.
  46. serine protease inhibitor

    Nafamostat is an anticoagulant. Broad spectrum serine protease inhibitor. Reduces eosinophil infiltration, mast cell activation and airway responsiveness in a murine model of asthma.
  47. serine protease inhibitor

    Nafamostat hydrochloride is an anticoagulant. Broad spectrum serine protease inhibitor. Reduces eosinophil infiltration, mast cell activation and airway responsiveness in a murine model of asthma.
  48. HIV protease inhibitor

    Darunavir is an HIV protease inhibitor
  49. HIV-1 capsid CTD dimerization inhibitor

    Ebselen (SPI-1005) is an inhibitor of HIV-1 capsid CTD dimerization. Ebselen can permeate the blood-brain barrier and inhibit inositol monophosphatase (IMPase). Ebselen is a non-toxic seleno-organic drug with anti-inflammatory and antioxidant properties. Ebselen inhibits QSOX1 enzymatic activity and has anticancer activity .
  50. Plpro inhibitor

    PLpro inhibitor is a potent inhibitor of papain-like protease (PLpro) with IC50 of 2.6 uM.

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