DNA Damage

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  1. HDAC2/HDAC3 inhibitor

    MI-192 is a selective inhibitor of histone deacetylases HDAC2 and HDAC3, with IC₅₀ values of 30 nM and 16 nM, respectively. It demonstrates high selectivity for HDAC2/3 over other HDAC isoforms. MI-192 induces apoptosis in myeloid leukemia cells and exhibits both anticancer and neuroprotective activities, making it a valuable compound for research in oncology and neurodegenerative diseases.
  2. HDAC inhibitor

    Pivanex (AN-9) is an orally active histone deacetylase (HDAC) inhibitor derived from butyric acid. It downregulates BCR-ABL protein expression and promotes apoptosis, contributing to its antitumor effects. In addition, Pivanex exhibits antimetastatic and antiangiogenic properties, making it a promising candidate for research in hematologic malignancies and solid tumors.
  3. HDAC inhibitor

    BRD4884 is a potent histone deacetylase (HDAC) inhibitor that selectively targets class I HDACs. It exhibits IC₅₀ values of 29 nM for HDAC1, 62 nM for HDAC2, and 1.09 µM for HDAC3. Its differential potency across HDAC isoforms makes BRD4884 a valuable tool for investigating HDAC1/2-mediated epigenetic regulation and their roles in disease pathogenesis.
  4. HDAC inhibitor

    FNDR-20123 is a first-in-class, orally active histone deacetylase (HDAC) inhibitor developed for antimalarial therapy. It demonstrates potent inhibitory activity against both Plasmodium and human HDACs, with IC₅₀ values of 31 nM and 3 nM, respectively. FNDR-20123 effectively targets multiple stages of *Plasmodium falciparum*, with IC₅₀ values of 41 nM for the asexual blood stage and 190 nM for male gametocytes. It inhibits HDAC1, HDAC2, HDAC3, HDAC6, and HDAC8 with IC₅₀ values of 25, 29, 2, 11, and 282 nM, respectively, and also exhibits nanomolar-level inhibition of Class III HDAC isoforms. FNDR-20123 shows a favorable safety profile, supporting its potential as a novel antimalarial agent targeting epigenetic regulation.
  5. HDAC inhibitor

    Pomiferin (NSC 5113) is a natural compound that functions as a dual inhibitor of histone deacetylases (HDACs) and the mammalian target of rapamycin (mTOR). It exhibits an IC₅₀ of 1.05 μM for HDAC inhibition and an IC₅₀ of 6.2 μM for mTOR. With its dual-targeting activity, Pomiferin holds potential for anticancer research, particularly in pathways involving epigenetic regulation and cell growth signaling.
  6. HDAC inhibitor

    m-Carboxycinnamic acid bishydroxamide is a potent histone deacetylase (HDAC) inhibitor, demonstrating in vitro ID₅₀ values of 10 nM for HDAC1 and 70 nM for HDAC3. It effectively induces apoptosis and suppresses tumor growth, making it a promising candidate for epigenetic cancer therapy and research focused on HDAC1/3-regulated pathways.
  7. HPB

    HDAC6 inhibitor

    HPB is a selective histone deacetylase 6 (HDAC6) inhibitor with an IC₅₀ of 31 nM. It demonstrates over 30-fold selectivity for HDAC6 compared to HDAC1, making it a valuable tool for studying HDAC6-specific biological functions and a promising candidate for the development of targeted therapies in diseases involving HDAC6 dysregulation.

  8. HDAC6 inhibitor

    SelSA is a selective and orally active histone deacetylase 6 (HDAC6) inhibitor with an IC₅₀ of 56.9 nM. It also inhibits ERK1/2 phosphorylation, contributing to its anticancer effects. SelSA suppresses the proliferation of breast cancer and hepatocellular carcinoma cells with IC₅₀ values ranging from 0.58 to 2.6 μM, inhibits migration and invasion of Huh7 cells, and induces apoptosis. In vivo, SelSA demonstrates significant antitumor activity, supporting its potential as a therapeutic agent for solid tumors.
  9. HDAC inhibitor

    KH16 is a potent histone deacetylase (HDAC) inhibitor with low nanomolar activity, selectively targeting class I HDACs—HDAC1, HDAC2, and HDAC3—with IC₅₀ values ranging from 6 to 34 nM. It effectively induces apoptosis and exhibits broad-spectrum antitumor activity across cancer cells with diverse gene expression profiles, making it a promising candidate for epigenetic cancer therapy research.
  10. HDAC11 inhibitor

    PB94 is a selective inhibitor of histone deacetylase 11 (HDAC11), with an IC₅₀ of 108 nM. It can be radiolabeled as [¹¹C]-PB94 for positron emission tomography (PET) imaging, enabling in vivo assessment of brain uptake and metabolic properties. PB94 has demonstrated efficacy in alleviating neuropathic pain in mouse models and holds potential as a research tool for investigating HDAC11-related mechanisms in neurological disorders.
  11. HDAC6 inhibitor

    AES-350 is a potent and orally bioavailable histone deacetylase 6 (HDAC6) inhibitor, with an IC₅₀ of 0.0244 μM and a Kᵢ of 0.035 μM. It also exhibits inhibitory activity against HDAC3 and HDAC8, with IC₅₀ values of 0.187 μM and 0.245 μM, respectively. AES-350 induces apoptosis in acute myeloid leukemia (AML) cells through HDAC inhibition, making it a promising compound for AML research and the development of epigenetic-based cancer therapies.
  12. HDAC6 inhibitor

    ITF 3756 is a potent and selective inhibitor of histone deacetylase 6 (HDAC6). In vitro, it effectively reduces the expression of PD-L1 on human monocytes and CD8⁺ T cells, suggesting immunomodulatory potential. ITF 3756 also exhibits antitumor activity, making it a promising candidate for cancer immunotherapy and epigenetic modulation research.
  13. HDAC inhibitor

    HL23 is a histone deacetylase (HDAC) inhibitor with demonstrated efficacy against hepatocellular carcinoma (HCC). It enhances acetylation at the TXNIP promoter, leading to upregulation of TXNIP expression and modulation of potassium channel activity, ultimately inducing TXNIP-dependent potassium deprivation. HL23 effectively suppresses HCC progression and metastasis, and exhibits a synergistic antitumor effect when combined with Sorafenib, outperforming the combination of Sorafenib and Vorinostat in preclinical models.
  14. POLA1-HDAC11 Inhibitor

    GEM144 is a potent and orally bioavailable dual inhibitor of DNA polymerase α (POLA1) and histone deacetylase 11 (HDAC11). It promotes p53 acetylation, induces p21 activation, and triggers G1/S cell cycle arrest followed by apoptosis. GEM144 exhibits significant antitumor efficacy in human orthotopic malignant pleural mesothelioma xenograft models, highlighting its potential as a targeted therapeutic agent for aggressive thoracic malignancies.
  15. HDAC inhibitor

    F-SAHA is a histone deacetylase inhibitor (HDACi) structurally derived from suberoylanilide hydroxamic acid (SAHA). Its fluorine-18 (^18F) labeled derivative enables non-invasive imaging of HDAC expression and activity, making F-SAHA a valuable tool for tumor imaging research and the assessment of epigenetic modulation in vivo.
  16. POLA1/HDAC 11 Inhibitor

    MIR002 is a potent, orally bioavailable dual inhibitor targeting DNA polymerase α (POLA1) and histone deacetylase 11 (HDAC11). It induces p53 acetylation, upregulates p21 expression, and triggers G1/S cell cycle arrest followed by apoptosis. MIR002 demonstrates significant antitumor efficacy in vivo, highlighting its potential as a therapeutic agent for cancers driven by POLA1 and HDAC11 dysregulation.
  17. HDAC1 and HDAC2 inhibitor

    KPZ560 is a potent inhibitor of histone deacetylases HDAC1 and HDAC2, with IC₅₀ values of 12 nM and 68 nM, respectively. It has been shown to enhance dendritic spine density in granule neurons of mice, indicating potential neurotrophic effects. Additionally, KPZ560 inhibits the proliferation of MCF breast cancer cells, supporting its potential application in both neurobiological and oncological research.
  18. HDAC6 inhibitor

    MPI_5a is a potent and selective inhibitor of histone deacetylase 6 (HDAC6), with an IC₅₀ of 36 nM. It exhibits minimal activity against other HDAC isoforms, demonstrating high isoform selectivity. In cellular assays, MPI_5a effectively inhibits acylated tubulin accumulation with an IC₅₀ of 210 nM, highlighting its utility in modulating HDAC6-dependent processes for potential therapeutic applications.
  19. HDAC1 substrate

    MOCPAC is an HDAC1 specific substrate.
  20. HDAC6 inhibitor

    QTX125 is a potent and highly selective inhibitor of histone deacetylase 6 (HDAC6), demonstrating excellent specificity over other HDAC isoforms. It exhibits significant antitumor activity through selective inhibition of HDAC6-mediated pathways. Both the salt and free base forms of QTX125 display comparable biological activity at equivalent molar concentrations, ensuring consistent pharmacological effects across different formulations.
  21. VDR agonist

    Triciferol is a multifunctional small molecule that acts as both a vitamin D receptor (VDR) agonist and a histone deacetylase (HDAC) antagonist. It binds directly to VDR with an IC₅₀ of 87 nM and exhibits 1,25-dihydroxyvitamin D₃ (1,25D)-like potency in activating multiple VDR target genes. In addition to its transcriptional effects, Triciferol induces significant tubulin hyperacetylation and enhances histone acetylation, contributing to its antiproliferative and cytotoxic activities. This dual mechanism highlights its potential as a therapeutic agent in cancer and epigenetic modulation.
  22. HDAC3/8 PROTAC degrader

    YX968 is a potent and selective PROTAC degrader targeting histone deacetylases HDAC3 and HDAC8, with DC₅₀ values of 1.7 nM and 6.8 nM, respectively. By inducing degradation of these epigenetic regulators, YX968 promotes apoptosis and exhibits significant antitumor activity, representing a promising therapeutic strategy for cancers driven by aberrant HDAC3/8 activity.
  23. FFAR3 agonist

    AR420626 is a selective agonist of free fatty acid receptor 3 (FFAR3, also known as GPR41), with an IC₅₀ of 117 nM. It demonstrates anti-inflammatory, antitumor, and antidiabetic activities. AR420626 improves neurogenic diarrhea by modulating neural pathways mediated by nicotinic acetylcholine receptors (nAChRs). In cancer models, it suppresses the growth of HepG2 xenografts and inhibits hepatoma cell proliferation through apoptosis induction. Additionally, AR420626 mitigates allergic asthma and eczema and enhances glucose uptake by activating FFAR3-mediated Ca²⁺ signaling, offering potential therapeutic benefits in metabolic disorders such as diabetes.
  24. HDAC Degrader

    JPS016 is a benzamide-based PROTAC that recruits the Von Hippel-Lindau (VHL) E3 ligase to selectively degrade class I histone deacetylases (HDACs). It is a potent degrader of HDAC1/2, leading to broad transcriptional changes and enhanced apoptosis in HCT116 cells, supporting its application in epigenetic and cancer research.
  25. PARP1 Degrader

    SK-575 is a highly potent and selective PROTAC degrader of PARP1, with an IC₅₀ of 2.30 nM. It effectively inhibits the proliferation of cancer cells harboring BRCA1/2 mutations, making it a valuable agent for targeted cancer research.
  26. eIF4A Inhibitor

    Zotatifin is a highly selective inhibitor of eIF4A, targeting the assembly of the eIF4F initiation complex. With an IC50 of 2 nM, it promotes eIF4A binding to specific mRNA recognition motifs in the 5’-UTRs. Zotatifin exhibits significant antiviral properties, effectively reducing the infectivity of SARS-CoV-2 by inhibiting the biogenesis of its NP protein (IC90 = 37 nM) and also induces apoptosis in cancer cells. This compound is valuable for studies related to viral infections and translational control mechanisms.
  27. Fluorometric HDAC Substrate

    Boc-Lys(Ac)-AMC is a cell-permeable fluorometric substrate for histone deacetylases (HDACs). When cleaved by HDAC enzymes, it releases a fluorescent signal with excitation and emission maxima at 355 nm and 460 nm, respectively. This compound is valuable for studying HDAC activity in various biological contexts and can be utilized in high-throughput screening assays to evaluate enzyme inhibitors.
  28. PARP1 Degrader

    iRucaparib-AP6 is a potent PROTAC compound that selectively targets PARP1 for degradation. This non-trapping degrader inhibits both the catalytic activity and scaffolding functions of PARP1, effectively disrupting its role in DNA repair pathways. iRucaparib-AP6 is useful in studying the biology of PARP1 and its implications in cancer research, particularly in understanding resistance mechanisms to PARP inhibitors.
  29. VUBI1 Analogue

    VUBI1 analogue-1 is an analogue of VUBI1, functioning as a selective activator of the SOS1 pathway with a Kd of 44 nM. This compound is valuable for studying SOS1 activation mechanisms and provides a basis for the synthesis of (4S)-PROTAC SOS1 degrader-1. Its applications include investigations into targeted degradation and modulation of cellular pathways involving SOS1, offering insights into cellular signaling and potential therapeutic strategies.
  30. PROTAC PARP1 Degrader

    PROTAC PARP1 Degrader functions as a targeted protein degradation agent that specifically targets PARP1 through the MDM2 E3 ligase. This compound effectively induces PARP1 cleavage and promotes apoptosis in cancer cells, making it valuable for research in cancer therapies. The structure includes the MDM2 ligand, the PARP1 ligand, and a PEG-based linker, facilitating efficient delivery and degradation of the target protein.
  31. RNA RIBOTAC Degrader

    Dovitinib-RIBOTAC TFA is a targeted RNA RIBOTAC degrader that specifically binds to and degrades pre-miR-21. This compound demonstrates significant anti-tumor activity and effectively inhibits breast cancer metastasis. It serves as a valuable tool for research involving RNA-targeted degradation and its implications in cancer biology.
  32. SIRT2 Inhibitor

    SIRT2-IN-8 is a selective inhibitor of SIRT2 (Sirtuin 2), a member of the sirtuin family of proteins implicated in various cellular processes. This compound exhibits strong inhibition of SIRT2 activity, making it a valuable tool for investigating the role of SIRT2 in neurodegenerative diseases, particularly Huntington's and Parkinson's diseases. Its use in research can contribute to a better understanding of the molecular mechanisms underlying these conditions and aid in the development of therapeutic strategies.
  33. HDAC Inhibitor

    HC-Toxin is a potent histone deacetylase (HDAC) inhibitor with an IC50 of 30 nM. This cyclic tetrapeptide effectively induces apoptosis in tumor cells, demonstrating significant anticancer activity. Its mechanism of action makes it valuable for research in cancer therapy and the modulation of gene expression.
  34. HIV Reverse Transcriptase Inhibitor

    β-Rubromycin is a selective inhibitor of HIV-1 reverse transcriptase, exhibiting a Ki of 0.27 μM. Additionally, it demonstrates potent telomerase inhibition with an IC50 of 3 μM. β-Rubromycin effectively inhibits the proliferation of K-562 and HeLa cell lines, showing IC50 values of 19.5 µM and 22.7 µM, respectively, making it a valuable tool for research in HIV and telomerase-related studies.
  35. DNA Stain

    7-Aminoactinomycin D (7-AAD) is a cell-impermeant fluorescent DNA stain that primarily targets and binds to GC-rich regions of DNA. This compound is often utilized in flow cytometry and fluorescence microscopy to assess cell viability and apoptosis. Additionally, 7-AAD exhibits antibacterial properties, expanding its utility in various biological research applications.
  36. SIRT Inhibitor

    Nicotinamide is a form of vitamin B3 or niacin. Nicotinamide Hydrochloride inhibits SIRT2 activity (IC50: 2 μM). Nicotinamide also inhibits SIRT1. Nicotinamide increases cellular NAD+, ATP, ROS levels. Nicotinamide inhibits tumor growth and improves survival. Nicotinamide also has anti-HBV activity.
  37. Alkaloid

    Berberine (Natural Yellow 18) is an alkaloid isolated from the Chinese herbal medicine Huanglian, as an antibiotic. Berberine (Natural Yellow 18) induces reactive oxygen species (ROS) generation and inhibits DNA topoisomerase. Berberine (Natural Yellow 18) has antineoplastic properties. 

  38. Pre-mRNA Splicing Inhibitor

    Herboxidiene (GEX1A) is a potent phytotoxic polyketide from Streptomyces sp. A7847 with a diverse range of activities, including herbicidal, anti-cholesterol, anti-tumor effects. Herboxidiene inhibits the pre-mRNA splicing process by binding to spliceosome-associated protein (SAP) 155, a subunit of SF3b, in the splicesome.
  39. Cyanotoxin

    Cylindrospermopsin, a cyanotoxin, is a polycyclic uracil derivative containing guanidine and sulfate groups, which can inhibit protein synthesis and covalently modify DNA or RNA. Cylindrospermopsin induces hepatocellular hypertrophy, renal cellular hypertrophy, intracellular reactive oxygen species (ROS), DNA strand breaks, mitochondrial hyperpolarisation, ultrastructural damage, and altered gene expression in liver, kidney, and intestinal cells. Cylindrospermopsin can be used in research including hepatocellular carcinoma and water quality testing.
  40. Fluorochrome

    Propidium Iodide (PI) is a nuclear staining agent that stains DNA. Propidium Iodide is an analogue of ethidine bromide that emits red fluorescence upon embedding in double-stranded DNA. Propidium Iodide cannot pass through living cell membranes, but it can pass through damaged cell membranes to stain the nucleus. Propidium Iodide has a fluorescence wavelength of 493/617 nm and a wavelength of 536/635 nm after Mosaic with DNA. Propidium Iodide is commonly used in the detection of apoptosis (apoptosis) or necrosis (necrosis), and is often used in flow cytometry analysis.
  41. Antibiotic

    Erythromycin is a macrolide antibiotic that targets bacterial 50S ribosomal subunits, effectively inhibiting RNA-dependent protein synthesis by obstructing transpeptidation and translocation reactions. This compound demonstrates a broad spectrum of antimicrobial activity against various bacteria, making it valuable in microbiological research. Additionally, erythromycin has been shown to possess antitumor and neuroprotective properties, contributing to its usefulness in diverse areas of biomedical research.
  42. Skin Depigmenting Agent

    Monobenzone is a potent skin depigmenting agent that primarily targets the enzyme ribonucleotide reductase (RNR) by inhibiting its regulatory subunit, RRM2. It effectively induces depigmentation, making it a valuable compound in vitiligo research. Additionally, Monobenzone demonstrates significant anti-leukemic properties, inhibiting the proliferation and DNA synthesis of acute myeloid leukemia (AML) cells, and promoting cell cycle arrest and apoptosis. These dual functionalities position Monobenzone as a critical reagent in both dermatological and oncology studies.
  43. PDE Inhibitor

    Theophylline, a potent phosphodiesterase (PDE) inhibitor, primarily targets PDE3, leading to relaxation of airway smooth muscle and enhanced bronchodilation. This compound also functions as an adenosine receptor antagonist and exhibits anti-inflammatory properties by elevating IL-10 levels and inhibiting NF-κB translocation into the nucleus. Additionally, Theophylline has been shown to induce apoptosis in certain cell types. Its applications are particularly relevant in the research of asthma and chronic obstructive pulmonary disease (COPD).
  44. Topoisomerase IV Inhibitor

    Ciprofloxacin is a potent topoisomerase IV inhibitor that demonstrates significant antibacterial activity as a fluoroquinolone antibiotic. It induces both mitochondrial and nuclear DNA damage, leading to mitochondrial dysfunction and increased reactive oxygen species (ROS) production. Ciprofloxacin exhibits anti-proliferative properties and triggers apoptotic pathways, making it a valuable tool for research applications focused on bacterial infections, oxidative stress, and cancer biology.
  45. Anti-microbial Agent/Kir3.2 Blocker

    3,6-Diaminoacridine hemisulfate is an acridine compound that functions primarily as a broad-spectrum antimicrobial agent and a Kir3.2 potassium channel blocker. Its mechanism involves insertion into bacterial DNA, thereby disrupting replication and transcription, which ultimately leads to bacterial lysis. Additionally, this compound is utilized in research to investigate the neurological phenotype associated with Down syndrome. Due to its ability to penetrate the stratum corneum and accumulate in the cell nucleus, prolonged exposure warrants caution due to potential oncogenic effects.
  46. Topoisomerase I Inhibitor

    Irinotecan hydrochloride is a potent inhibitor of topoisomerase I, an enzyme crucial for DNA replication and transcription. This compound exhibits significant anti-tumor activity, primarily in the treatment of colorectal cancers. Its mechanism involves the stabilization of the enzyme-DNA complex, leading to apoptosis in cancer cells. Irinotecan hydrochloride is widely utilized in cancer research to elucidate cellular response mechanisms and to develop novel therapeutic strategies.
  47. DNA Dye

    DAPI (4',6-Diamidino-2-phenylindole) is a fluorescent DNA dye that selectively binds to the AT base pairs in the minor groove of double-stranded DNA, enhancing fluorescence intensity approximately 20-fold upon binding. This property makes DAPI suitable for applications in fluorescence microscopy, allowing for quantification of DNA based on fluorescence intensity. Additionally, DAPI's ability to penetrate intact cell membranes enables its use in staining both live and fixed cells. DAPI also acts as an inhibitor of acid-sensing ion channel 3 (ASIC3), potentially contributing to research in chronic pain treatment (Ex/Em = 356/451 nm).
  48. DNA Structure Probe

    2-Aminopurine is a fluorescent analog of guanosine and adenosine, functioning as a DNA structure probe. Its insertion into oligonucleotides results in significant fluorescence quenching due to stacking interactions with adjacent natural bases. This property makes 2-Aminopurine an invaluable tool for investigating nucleic acid structure and dynamics in various research applications.
  49. Fluorescent Dye

    CellTracker Blue CMF2HC Dye is a fluorescent dye primarily used for visualizing and tracking live cells. It emits a blue fluorescence when excited at wavelengths between 450-460 nm, making it suitable for applications such as two-channel nucleic acid sequencing. Additionally, this dye facilitates the rapid assessment of microbial antibiotic sensitivity, providing valuable insights for microbiological research.
  50. DNA Fluorescent Dye

    Methyl Green is a non-intercalating fluorescent dye that targets DNA by selectively binding to the major groove. It exhibits high affinity, resistance to photobleaching, and stable fluorescence emission, making it suitable for various applications. Methyl Green can be utilized for fluorescent labeling of nuclei in embryonic tissues or cells, as well as for DNA staining and assessing cell activity in gel electrophoresis. Its fluorescence peaks are observed at 633 nm and 677 nm, enabling direct measurement through microscopy and flow cytometry.

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