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Epoxomicin

Epoxomicin is a natural product isolated from Actinomycetes that functions as a potent and specific inhibitor of the proteasome, a key enzymatic complex involved in protein degradation.
This highly selective proteasome inhibitor has been extensively studied for its potential therapeutic applications, particularly in the treatment of various cancers and inflammatory disorders.
PubCompare.ai, an AI-driven platform, can help researchers streamline their work on Epoxomicin by providing insighful comparisons of protocols from literature, pre-prints, and patents, thereby enhancing reproducibility and accuracy in their research efforts.

Most cited protocols related to «Epoxomicin»

1
Cardiac Tissue Harvesting and Analysis
Cited 6 times

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Publication 2009
Abdominal Cavity Ascending Aorta Biopsy Cold Temperature epoxomicin Freezing Heart Heart Arrest, Induced Heparin Institutional Animal Care and Use Committees Isoflurane Left Ventricles Males Normal Saline Rattus norvegicus Thoracotomy Tissues Vena Cavas, Inferior Venae Cavae Viaspan
2
Inhibitors and Antibodies for Alzheimer's Research
Cited 5 times
ALLN (Ac-Leu-Leu-Nle-al), Epoxomicin (Epox), CA-074Me, cathepsin G inhibitor I, cathepsin L inhibitor II, synthetic cell-permeable calpastatin peptide, and scrambled peptide were purchased from Millipore. MDL28170, E-64D, cathepsin L inhibitor III, and proteasome substrate Suc-LLVY-AMC were purchased from Enzo life sciences. MG132, cycloheximide, pepstatin A, and L-685,458 were purchased from Sigma-Aldrich. MK-0822 (Odanacatib) was purchased from ChemieTek. The anti-Myc antibody (9B11) was obtained from Cell Signaling. The anti-APP C-terminal antibody C1/6.1 and anti-β-amyloid (1–16) antibody 6E10 were purchased from Covance. The G12A antibody for APP (rabbit polyclonal, clone C7 targeting amino acid residues 732–751 of APP751, custom-manufactured by Thermo Fisher Scientific Inc.) has been previously described.17 (link) The anti-Talin antibody (TA205) and protease inhibitor cocktail were purchased from Millipore. The mouse anti-β-actin antibody was purchased from Sigma-Aldrich. The anti-BACE1 antibody (PA1–757) was purchased from Thermo Scientific. The APP695-Myc construct in pcDNA3.1 was a generous gift from B. T. Hyman at Harvard University.
Wang H., Sang N., Zhang C., Raghupathi R., Tanzi R.E, & Saunders A. (2015). Cathepsin L Mediates the Degradation of Novel APP C-Terminal Fragments. Biochemistry, 54(18), 2806-2816.
Publication 2015
acetylleucyl-leucyl-norleucinal Actins aloxistatin Amino Acids Amyloid anti-c antibody Antibodies, Anti-Idiotypic BACE1 protein, human CA-074Me calpastatin Cathepsin L Clone Cells Cycloheximide epoxomicin Immunoglobulins L 685458 MDL 28170 MG 132 MK-0822 Multicatalytic Endopeptidase Complex Mus odanacatib pepstatin Peptides Permeability Protease Inhibitors Rabbits Talin Z-Phe-Gly-NHO-Bz
3
Investigating Tau Protein Modifications
Cited 4 times
Methylthionine (AC), tetramethylthionine (MB), thionin (TN) and myricetin were purchased from Sigma and suspended in dimethylsulfoxide (DMSO). The dihydropyrimidines 115-7c and SW02 were synthesized as described (Wisen et al., 2008 (link)). Epoxomicin and 17-AAG were acquired from A.G. Scientific. All clones were in the pcDNA3.1 vector. SiRNAs (Qiagen) were transfected at 20 nM. All antibodies were diluted in 5% NFDM in TBST at 1:1000 with the exception of pS396/S404 tau, which was used at 1:100. Where pTau is indicated, pS396/S404 was the antibody used. PHF1 (pS396/S404 tau) was provided by Dr. Peter Davies. 12E8 (pS262/S356 tau) was provided by Dr. Peter Seubert. The following antibodies were purchased from the company indicated in parentheses; α-synuclein (Cell Signaling), TDP43 (Protein Tech), Hsp70 and HSF1 (Assay Designs), HA (Roche), Actin (Sigma Aldrich), Hsp40 (BD Transduction Labs), Hsp27 and total tau (Santacruz Biotech). All cell lines were maintained according to ATCC guidelines. Stably transfected HeLa cells over-expressing wildtype 4R0N human tau were generated by clonal selection with G418 (Invitrogen).
Jinwal U.K., Miyata Y., Koren J I.I.I., Jones J.R., Trotter J.H., Chang L., O'Leary J., Morgan D., Lee D.C., Shults C.L., Rousaki A., Weeber E.J., Zuiderweg E.R., Gestwicki J.E, & Dickey C.A. (2009). Chemical Manipulation of Hsp70 ATPase Activity Regulates Tau Stability. The Journal of Neuroscience, 29(39), 12079-12088.
Publication 2009
Actins alpha-Synuclein antibiotic G 418 Antibodies Biological Assay Cell Lines Clone Cells Cloning Vectors epoxomicin Heat-Shock Proteins 70 HeLa Cells Homo sapiens HSP40 Heat-Shock Proteins HSPB1 protein, human Immunoglobulins myricetin PHF1 protein, human Proteins protein TDP-43, human RNA, Small Interfering Sulfoxide, Dimethyl tanespimycin Thionins
4
Investigating Nrf2 Activation and Protein Aggregation in Neuroblastoma
Cited 4 times
SH-SY5Y human neuroblastoma (ECACC, Salisbury, Wiltshire, UK) and HeLa (JCRB, Osaka, Japan) cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum and antibiotics. Cells were treated with epoxomicin (Calbiochem, San Diego, CA, USA), MG132 (Calbiochem), bortezomib (Cell Signaling Technology, Inc., Danvers, MA, USA), bafilomycin A (Wako, Osaka, Japan), and amyloid β peptide 1–40 or 1–42 (Aβ40 or Aβ42) (Peptide Institute Inc., Osaka, Japan). For activation of the Nrf2 system, diethyl maleate (DEM) was used at 100 μM. At the indicated times, the cultures were washed with phosphate-buffered saline (PBS) (pH 7.4), harvested and used as samples for further studies.
Human p62 cDNA was prepared as previously described [23 (link)]. p62 cDNA was subcloned into pcDNA3 (Invitrogen, Carlsbad, CA, USA) tagged with hemagglutinin (HA) or pEGFP-N1 (Invitrogen). Mutagenesis was performed according to the manufacturer’s instructions (Takara, Otsu, Japan), followed by sequencing to confirm the mutation site. Serine (S) was changed into glutamic acid (E) for a phosphorylation-mimetic mutant, or into alanine (A) for a phosphorylation-deficient mutant. Cells were transfected using Fugene 6 (Roche Molecular Biochemicals, Indianapolis, IN, USA) or Lipofectamine 2000 (Invitrogen). siRNAs were purchased from Dharmacon (Lafayette, CO, USA). The siRNAs (final concentration 20 nM) for p62 (5’-GCA TTG AAG TTG ATA TCG A-3’), Keap1 (M-012453-00-0005), and Nrf2 (M-003755-02-0005) were performed using Lipofectamine RNAi MAX (Invitrogen). After 24 h, the cells were treated with an inhibitor for an additional 24 h. Cells were subsequently harvested and lysed with lysis buffer [75 mM Tris–HCl, pH 6.8, 4% sodium dodecyl sulphate (SDS), 25% glycerol, 5% β-mercaptoethanol].
Tanji K., Miki Y., Ozaki T., Maruyama A., Yoshida H., Mimura J., Matsumiya T., Mori F., Imaizumi T., Itoh K., Kakita A., Takahashi H, & Wakabayashi K. (2014). Phosphorylation of serine 349 of p62 in Alzheimer’s disease brain. Acta Neuropathologica Communications, 2, 50.
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Publication 2014
2-Mercaptoethanol Alanine Amyloid beta-Peptides Antibiotics bafilomycin A Bortezomib Buffers Cells diethyl maleate DNA, Complementary Eagle epoxomicin Fetal Bovine Serum FuGene Glutamic Acid Glycerin HeLa Cells Hemagglutinin Homo sapiens KEAP1 protein, human Lipofectamine lipofectamine 2000 MG 132 Mutagenesis Mutation Neuroblastoma NFE2L2 protein, human Peptides Phosphates Phosphorylation RNA, Small Interfering RNA Interference Saline Solution Serine Sulfate, Sodium Dodecyl Tromethamine
5
Docking and Binding Analysis of Immunoproteasome and Constitutive Proteasome
Cited 3 times
After the homology models were built, the docking study was performed to explore the best possible modes of ligand binding with LMP2 (i.e. β1i) subunit of immunoproteasome and β5 subunit of constitutive proteasome using the Glide. Glide (Grid-Based Ligand Docking with Energetics) approximates a systematic search of positions, orientations, and conformations of the ligand in the receptor binding site using a series of hierarchical filters.34 (link),38 (link) The shape and properties of the receptor are represented on a grid by several different sets of fields that provide progressively more accurate scoring of the ligand pose.
To facilitate the definition of the center of the active site for docking, the crystal structure complex of regular proteasome with epoxomicin (PDB code: 1G65) was used, as neither the X-ray crystal structure of regular proteasome β5 subunit (PDB code: 1IRU-L) nor the homology modeled LMP2 subunit have a ligand bound in the active site. First, the two covalent bonds between Thr 1 and epoxomicin were broken and the missing atoms of epoxomicin were added. Then, the complex (1G65-KL) with waters removed was minimized in vacuum using Amber program (version 8) with all the residues fixed except the ligand in order to mimic the conformation of the ligand before reactions. After that, the minimized complex substructure 1G65-K was aligned to 1IRU-L and LMP2 by superimposing the backbone atoms in order to transfer the epoxomicin into 1IRU-L and LMP2 to get a reference ligand for docking. The RMSD values of the alignments for the 1IRU-L and LMP2 are 1.28 and 1.25 Å, respectively. After alignments, the coordinates of epoxomicin were transferred into 1IRU-LM and LMP2/MECL1. For the histidine residues, hydrogens were placed at the ε-position for His 35 in LMP2, His 66, His 97, and His 185 in MECL1; His 36 and His 58 in 1IRU-M; and at the δ-position for His 66, His 93, His 114, and His 116 in LMP2; His 38 in MECL1; His 10, His 178, and His 196 in 1IRU-L; His 77 and His 163 in 1IRU-M. Then, the two complexes (1IRU-LM and LMP2/MECL1 with epoxomicin in the active site) were minimized in vacuum with all the residues fixed except the ligand to get the best position of the ligand.
The proteins were imported into Maestro and prepared in the presence of ligand in the active site using Pprep in Glide. The grid midpoint was defined by the center of the bound epoxomicin. Geometries of both ligands were optimized at Hartree-Fock (HF) level with 6–31G* basis set using Gaussian program (03 version)37 and were docked with Glide in extra-precision mode with up to thirty poses saved per molecule. For each molecule, the best scoring pose was selected for the subsequent molecular dynamics simulations and binding free energy calculations.
Lei B., AbdulHameed M.D., Hamza A., Wehenkel M., Muzyka J.L., Yao X.J., Kim K.B, & Zhan C.G. (2010). Molecular Basis of the Selectivity of the Immunoproteasome Catalytic Subunit LMP2-Specific Inhibitor Revealed by Molecular Modeling and Dynamics Simulations. The journal of physical chemistry. B, 114(38), 12333-12339.
Publication 2010
Amber Binding Sites epoxomicin Hydrogen Ligands Mental Orientation Multicatalytic Endopeptidase Complex Proteins Protein Subunits PSMB5 protein, human Vacuum Vertebral Column

Most recents protocols related to «Epoxomicin»

1
Heat Shock and Proteasome Inhibition
Not available on PMC !
Before subjected to heat shock, the ISRIB treatment group cells were pre-treated with 200 nM ISRIB (Merk) for 30 minutes. After heat shock, 100 nM epoxomicin (Sigma) was added for 4 hours. To test the effect of ISRIB on sodium arsenate-induced stress, cells were first pretreated with 200 nM ISRIB for 30 min followed by incubation with 50 µM sodium arsenate (Sigma) for 4 hours. For the proteasome inhibitor titration experiments, Ub-YFP MelJuSo cells were treated with the indicated epoxomicin concentration for 4 hours.
Xu S., Gierisch M.E., Barchi E., Poser I., Alberti S., Salomons F.A., & Dantuma N.P. (2024). Chemical inhibition of the integrated stress response impairs the ubiquitin-proteasome system.
Publication 2024
2
Proteasome Inhibition and FLAG-SOCS7 Expression
Epoxomicin (Sigma, Cat#E3652) was used at 0.8 μM for 20 h in the proteasome inhibition experiments. Doxycyline (Sigma, Cat#D9891) was used to induce the expression of FLAG-K19-SOCS7 or FLAG-K19dm-SOCS7 from the TLCV2 lentivector.
Cornebois A., Sorbara M., Cristol M., Vigne E., Cordelier P., Desrumeaux K, & Bery N. (2024). Discovery of SOCS7 as a versatile E3 ligase for protein-based degraders. iScience, 27(5), 109802.
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Publication 2024
3
Ectopic Expression and Protein Stability
HEK293T cells were transfected with HA-tagged WT, Q402* or E82K using Effectene (QIAGEN) according to the manufacturer’s instructions. After 16 to 18 hours of incubation, cells were treated with Cycloheximide (10 μg/mL, Sigma-Aldrich) alone or together with Epoxomicin (100 nM, Sigma-Aldrich) or Bortezomib (50 nM, Selleckchem) for additional 8 hours. Cells were lysed and subjected to the immunoblotting using anti-HA (Cell signaling technology, Cat. 2999S) and anti-Vinculin (Santa Cruz Biotechnology, Cat. sc-73614).
Kuehn H.S., Sakovich I.S., Niemela J.E., Gil Silva A.A., Stoddard J.L., Polyakova E.A., Esteve Sole A., Aleshkevich S.N., Uglova T.A., Belevtsev M.V., Vertelko V.R., Shman T.V., Kupchinskaya A.N., Walter J.E., Fleisher T.A., Notarangelo L.D., Peng X.P., Delmonte O.M., Sharapova S.O, & Rosenzweig S.D. (2024). Disease-associated AIOLOS variants lead to immune deficiency/dysregulation by haploinsufficiency and redefine AIOLOS functional domains. The Journal of Clinical Investigation, 134(3), e172573.
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Publication 2024
4
Antibody Purification and Inhibitor Compounds
Anti-Tks5 and anti-MT1-MMP polyclonal antibodies were raised by immunizing rabbits with purified recombinant His-tagged human Tks5 (aa 817–1118) and MT1-MMP (aa 280–520), respectively, and then the antisera were affinity-purified. Commercially available antibodies are listed in Table S6. Secondary antibodies labeled with horseradish peroxidase (HRP) and fluorochrome were purchased from Bio-Rad Laboratories and Life Technologies, respectively. The following inhibitors were purchased: latrunculin A (Sigma-Aldrich), nocodazole (Sigma-Aldrich), MG132 (Sigma-Aldrich), epoxomicin (Peptide Institute), bortezomib (FujiFilm Wako), bafilomycin A1 (Millipore), chloroquine (Sigma-Aldrich), leupeptin (Peptide Institute), and wortmannin (Sigma-Aldrich).
Inoue H., Kanda T., Hayashi G., Munenaga R., Yoshida M., Hasegawa K., Miyagawa T., Kurumada Y., Hasegawa J., Wada T., Horiuchi M., Yoshimatsu Y., Itoh F., Maemoto Y., Arasaki K., Wakana Y., Watabe T., Matsushita H., Harada H, & Tagaya M. (2024). A MAP1B–cortactin–Tks5 axis regulates TNBC invasion and tumorigenesis. The Journal of Cell Biology, 223(3), e202303102.
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Publication 2024
5
Synergistic Drug Combination Analysis
Synergy of drug combinations was analyzed by the SynergyFinder package [140 (link)] using the Loewe additivity model [141 (link)] to calculate synergy scores. Each drug concentration combination had three replicates which were used to fit dose-response curves. For compounds NCGC00347424 (pladienolide B), NCGC00389337 (epoxomicin), and NCGC00386288 (AZD2858), the top-three concentrations were removed from analysis, as a dose-response curve could not be fit due to toxicity at higher concentrations. A response matrix and corresponding synergy score matrix were generated for each combination. In general, negative, zero, and positive scores in the synergy matrix indicate antagonistic, additive, and synergistic interactions between drugs, respectively.
Williams D., Glasstetter L.M., Jong T.T., Kapoor A., Zhu S., Zhu Y., Gehrlein A., Vocadlo D.J., Jagasia R., Marugan J.J., Sidransky E., Henderson M.J, & Chen Y. (2024). Development of quantitative high-throughput screening assays to identify, validate, and optimize small-molecule stabilizers of misfolded β-glucocerebrosidase with therapeutic potential for Gaucher disease and Parkinson’s disease. bioRxiv.
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Publication Preprint 2024

Top products related to «Epoxomicin»

1
Epoxomicin by Merck Group
Sourced in United States, Germany, United Kingdom, Ireland
Epoxomicin is a proteasome inhibitor, a type of laboratory equipment used to study and inhibit the proteasome, a cellular complex responsible for the degradation of proteins. Epoxomicin is a potent and selective inhibitor of the proteasome, making it a useful tool for researchers investigating protein metabolism and turnover.
2
Mg132 by Merck Group
Sourced in United States, Germany, China, United Kingdom, Macao, Sao Tome and Principe, France, Canada, Italy, Switzerland, Morocco, Belgium, Japan, Sweden, Australia, Austria, Israel, Spain
MG132 is a proteasome inhibitor, a type of laboratory reagent used in research applications. It functions by blocking the activity of the proteasome, a complex of enzymes responsible for the degradation of proteins within cells. MG132 is commonly used in cell biology and biochemistry studies to investigate the role of the proteasome in various cellular processes.
3
Cycloheximide (chx) by Merck Group
Sourced in United States, Germany, United Kingdom, China, Italy, Sao Tome and Principe, France, Macao, Japan, Spain, Canada, Switzerland, India, Israel, Brazil, Poland, Portugal, Australia, Morocco, Sweden, Austria, Senegal, Belgium
Cycloheximide is a laboratory reagent commonly used as a protein synthesis inhibitor. It functions by blocking translational elongation in eukaryotic cells, thereby inhibiting the production of new proteins. This compound is often utilized in research applications to study cellular processes and mechanisms related to protein synthesis.
4
Epoxomicin by Enzo Life Sciences
Sourced in Germany
Epoxomicin is a proteasome inhibitor, a class of compounds that primarily target the 20S proteasome. The 20S proteasome is a multi-subunit protease complex responsible for the degradation of misfolded or damaged proteins within cells. Epoxomicin functions by irreversibly binding to and inhibiting the activity of the 20S proteasome, thereby disrupting cellular protein homeostasis.
5
Epoxomicin by Peptide Institute
Sourced in Japan
Epoxomicin is a laboratory reagent used for the inhibition of the proteasome, a large protein complex responsible for the degradation of proteins within cells. It functions by irreversibly binding to and inhibiting the chymotrypsin-like activity of the proteasome. Epoxomicin is commonly used in research applications to investigate the role of the proteasome in various cellular processes.
6
Dimethyl sulfoxide (dmso) by Merck Group
Sourced in United States, Germany, United Kingdom, China, Italy, Sao Tome and Principe, France, Macao, India, Canada, Switzerland, Japan, Australia, Spain, Poland, Belgium, Brazil, Czechia, Portugal, Austria, Denmark, Israel, Sweden, Ireland, Hungary, Mexico, Netherlands, Singapore, Indonesia, Slovakia, Cameroon, Norway, Thailand, Chile, Finland, Malaysia, Latvia, New Zealand, Hong Kong, Pakistan, Uruguay, Bangladesh
DMSO is a versatile organic solvent commonly used in laboratory settings. It has a high boiling point, low viscosity, and the ability to dissolve a wide range of polar and non-polar compounds. DMSO's core function is as a solvent, allowing for the effective dissolution and handling of various chemical substances during research and experimentation.
7
Chloroquine by Merck Group
Sourced in United States, Germany, United Kingdom, China, France, Macao, Sao Tome and Principe, Switzerland, Italy, Canada, Japan, Spain, Belgium, Israel, Brazil, India
Chloroquine is a laboratory chemical primarily used as a research tool in biochemical and cell biology applications. It is a white, crystalline solid that is soluble in water. Chloroquine is commonly used in experiments to study cellular processes, such as autophagy and endocytosis, by inhibiting the function of lysosomes. Its core function is to serve as a research reagent for scientific investigations, without making any claims about its intended use.
8
Epoxomicin by Apexbio
Sourced in United States
Epoxomicin is a laboratory reagent that functions as a proteasome inhibitor. It is a cyclic epoxyketone compound that selectively and irreversibly binds to and inhibits the chymotrypsin-like activity of the 20S proteasome complex. Epoxomicin is commonly used in research applications to study the role of the proteasome in cellular processes.
9
Suc llvy amc by Enzo Life Sciences
Sourced in United States
Suc-LLVY-AMC is a fluorogenic substrate used for detecting and measuring the activity of the proteasome, a multi-subunit protein complex responsible for the degradation of cellular proteins. The substrate contains the amino acid sequence Suc-LLVY, which is specifically cleaved by the chymotrypsin-like activity of the proteasome, releasing the fluorescent molecule AMC (7-amino-4-methylcoumarin). The resulting fluorescence can be measured to quantify proteasome activity.
10
Lipofectamine 2000 by Thermo Fisher Scientific
Sourced in United States, China, Germany, United Kingdom, Canada, Japan, France, Italy, Switzerland, Australia, Spain, Belgium, Denmark, Singapore, India, Netherlands, Sweden, New Zealand, Portugal, Poland, Israel, Lithuania, Hong Kong, Argentina, Ireland, Austria, Czechia, Cameroon, Taiwan, Province of China, Morocco
Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.

More about "Epoxomicin"

Epoxomicin, a natural product isolated from Actinomycetes, is a potent and specific inhibitor of the proteasome - a key enzymatic complex involved in protein degradation.
This highly selective proteasome inhibitor has been extensively studied for its potential therapeutic applications, particularly in the treatment of various cancers and inflammatory disorders.
Epoxomicin is often compared to other proteasome inhibitors like MG132 and Cycloheximide, as well as compounds like DMSO and Chloroquine that can influence cellular processes.
Researchers also utilize Suc-LLVY-AMC, a fluorogenic substrate, to measure proteasome activity.
PubCompare.ai, an AI-driven platform, can enhance reproducibility and accuracy in Epoxomicin research by providing insightful comparisons of protocols from literature, pre-prints, and patents.
This helps researchers identify the optimal experimental approaches, streamlining their work and unlocking new discoveries around this important proteasome inhibitor.
Lipofectamine 2000 is a common transfection reagent used in conjunction with Epoxomicin to study its cellular effects.
By leveraging PubCompare.ai, scientists can confidently navigate the complexities of Epoxomicin research and accelerate their progress towards potential therapeutic applications.