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9 protocols using natural product library

1

Screening L1 Mimetic Compounds for Cell Viability

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Media and reagents for cell culture were from Gibco. The L1 mimetic compounds 6,7-dichloro-1,5-dihydroimidazo (2,1-b) quinazolin-2(3H)-one (anagrelide; CAS 68475-42-3), 5-fluoro-1H-pyrimidin-2-one (2-hydroxy-5-fluoropyrimidine; CAS 2022-78-8), and (8R,9S,13S,14S,17R)-17-ethynyl-3-methoxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-ol (mestranol; CAS 72-33-3) were from Sigma-Aldrich (St. Louis, MO, USA). Ortho-phenylenediamine dihydrochloride (OPD, CAS 615-28-1), calcein-AM (CAS 148504-34-1), and propidium iodide (CAS 25535-16-4) were from Thermo Fisher Scientific (Waltham, MA, USA). The NIH Clinical Collection libraries 1 and 2 were from Evotec (San Francisco, CA, USA) and the Natural Product Library was from Selleckchem (Houston, TX, USA). The rat anti-mouse L1 monoclonal antibody 324 (CAS MAB5272) was from Sigma-Aldrich, and secondary donkey anti-rat IgG antibodies coupled to horseradish peroxidase (HRP) were from Jackson ImmunoResearch (West Grove, PA, USA). Recombinant mouse L1CAM-Fc (L1-Fc) chimera (CAS 5674-NC-050) was from R&D Systems (Minneapolis, MN, USA). Human IgG1-Fc tag free protein (CAS FCC-H5214) was from ACROBiosystems (Newark, DE, USA). L1CAM (clone UJ127; catalog# sc-533386) was from Santa Cruz (Dallas, TX, USA). GAPDH (Cat# 60004-1-Ig was from Proteintech (Rosemont, IL, USA)).
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2

Screening Natural Compounds for Cardioprotection

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Natural Product Library and OA were purchased from Selleck (Houston, United States). H9c2 cells (104 cells per well) were seeded on 96-well plates and cultured in the incubator (95% air, 5% CO2) at 37°C for 24 h. Subsequently, 2,661 natural compounds were added into each well at a final concentration of 10 μM at the initiation of OGD/R. At the end of the experiment, the cell viability was detected by Cell Counting Kit-8 (CCK-8, Biosharp, China) according to the manufacturer’s instructions and the screened candidate compound, which was OA. To determine the optimal concentration of OA administration, H9c2 cells were treated by different concentrations, which were 5 μM, 10 μM, 100 μM, and 1,000 μM, respectively. Finally, 10 μM was used as the optimal concentration for subsequent experiments. The cells were randomly assigned either into the Control group, the OGD/R group, or the OGD/R + OA group. The latter group represents those cells that were treated with 10 µM OA and subjected to OGD/R procedure.
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3

Marine Natural Product Library Screening

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The Marine Natural Product Library containing 103 compounds was obtained from the Natural Product Library (Cat #L1400; Selleck, Shanghai, China) by searching the Dictionary of Marine Natural Products in the ChemNetBase website (https://dmnp.chemnetbase.com/faces/chemical/ChemicalSearch.xhtml) and applied for preliminary screens against T. gondii. Estradiol benzoate (Cat #S4110; Selleck) and octyl gallate (Cat #S9338; Selleck) were also obtained from Selleck. These compounds were dissolved with dimethyl sulfoxide (DMSO) into a 10 mM solution and stored at −20°C. Pyrimethamine (Cat # 46706, Sigma-Aldrich, Shanghai, China) was used as a reference drug. All information of compounds is listed in Supplementary Table S1.
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4

Natural Compound Library Protocol

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The Natural Product Library was purchased from Selleck Chemicals (Houston, TX, USA). This library contains a collection of 139 natural compounds supplied as solutions dissolved in DMSO.
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5

Compound Libraries for Screening

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A small molecule library containing 424 FDA approved compounds provided as 10 mM stock solutions in DMSO, and a natural product library containing 146 compounds provided as 10 mM stock solutions in DMSO were purchased from SelleckChem. See Tables S1 and S2 for details.
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6

Screening for SARS-CoV-2 Main Protease Inhibitors

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Potential inhibitors against SARS-CoV-2 M pro were screened by an enzymatic inhibition assay. When the different compounds were added into the enzymatic reaction mixture, the change of initial rates was calculated to evaluate their inhibitory effect. Five drug librariesthe Approved Drug Library (Target Mol), Clinic Compound Library (Target Mol), FDA-approved Drug Library (Selleck), Natural Product Library (Selleck), and Anti-virus Drug Library (Shanghai Institute for Advanced Immunochemical Studies)-that together comprised about 10,000 compounds were used. The preliminary screening reaction mixture included 0.2 μM protein, 20 μM substrate and 50 μM compounds. The compounds of interest were defined as those with a percentage of inhibition over 60% compared with the reaction in the absence of inhibitor. IC 50 values of 7 drug leads were measured using 0.2 μM protein, 20 μM substrate and 11 different inhibitor concentrations. To exclude inhibitors possibly acting as aggregators, a detergent-based control was performed by adding 0.001% or 0.01% freshly made up Triton X-100 to the reaction at the same time 25 . All experimental data was analysed using GraphPad Prism. All experiments were performed in triplicate.
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7

Analyzing Necroptosis Signaling Pathways

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Natural Product Library (Selleck Chemicals, Houston, TX; L1400), piperlongumine (Selleck Chemicals, S7551, CAS: 20069-09-4), Necrostatin-1 (Nec-1, Selleck Chemicals, S8037), Z-VAD-fmk (Selleck Chemicals, S7023); recombinant murine/human TNF-α (Sino Biological, Beijing, China; 50349-MNAE); SMAC mimetic (SM-164, Beyotime Biotechnology, Jiangsu, China; C0114-10 mM); dimethyl sulfoxide (DMSO; Sigma-Aldrich, St. Louis, MO). Anti-RIPK1 and anti-human phosphorylated RIPK1 antibodies for Western blotting were purchased from BD Biosciences (Franklin Lakes, NJ) and Cell Signaling Technology (Danvers, MA), respectively.
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8

Estrogen Receptor Activation Assay

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According to the manufacturer's instructions, the transfection of cells with plasmids was performed using Lipofectamine 2000 (ThermoFisher, catalog number: 116680300). HeLa cells were transfected with the indicated expression plasmids. The natural product library was purchased from Selleckchem (catalog number: L1440). After 24 h, phenol red-free Dulbecco's minimum essential medium (DMEM) containing 10% charcoal-stripped fetal bovine serum (FBS) was added to the cells. Estradiol (10−8 M) and estradiol (10−8 M) plus natural product (10−8 M) were added to the cells 24 h after the medium was changed and incubated for another 24 h. The cells were harvested, and the luciferase activity was determined and normalized against the total input protein levels.
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9

Proteomic Analysis of Androgen Receptor Pathways

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Chemicals: natural product library (#L1400), rutaecarpine (#S2349), parecoxib (#S4656), bortezomib (#S1013), MG132 (#S2619), enzalutamide (#S1250), and bicalutamide (#S1190) were obtained from Selleckchem (Houston, TX). Antibodies: anti-AR-V7 (#19672), anti-AR (#5153), anti-K48-ubiquitin (#12805), anti-IgG (#3900), anti-MDM2 (#86934), anti-CDK2 (#2546), anti-CDK4 (#12790), anti-CDK6 (#13331), anti-cyclinD1 (#2978), anti-p21 (#2947), anti-p27 (#3686), anti-p15 (#4822), anti-COX2 (#12282), anti-HA-tag (#2367), anti-FLAG-tag (#8146), anti-GAPDH (#5174), anti-GRP94 (#20292), anti-HSP90 (#4877), and anti-lamin B1(#13435) were obtained from Cell Signaling Technology (Beverly, MA); anti-GRP78 (#ab21685), anti-HSP7C (#ab51052), anti-SIAH2 (#ab230532), anti-STUB1 (#ab134064), anti-AR-V7 (#ab198394, for IHC), and anti-Ki67 (#ab15580) were obtained from Abcam (Cambridge, MA).
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