Rapamycin

Manufactured by Merck Group

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Rapamycin is a macrolide compound isolated from the bacterium Streptomyces hygroscopicus. It functions as an immunosuppressant and has anti-proliferative effects.

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Lab products found in correlation

Fetal bovine serum (fbs), by Thermo Fisher Scientific (121 mentions) Dimethyl sulfoxide (dmso), by Merck Group (92 mentions) Bafilomycin a1, by Merck Group (91 mentions) Chloroquine, by Merck Group (84 mentions) Ly294002, by Merck Group (74 mentions) 3 methyladenine 3 ma, by Merck Group (56 mentions) Cycloheximide (chx), by Merck Group (56 mentions) Lipofectamine 2000, by Thermo Fisher Scientific (49 mentions) Dulbecco modified eagle medium (dmem), by Thermo Fisher Scientific (43 mentions) 3 methyladenine, by Merck Group (43 mentions) Penicillin streptomycin, by Thermo Fisher Scientific (39 mentions) Wortmannin, by Merck Group (39 mentions) Mg132, by Merck Group (32 mentions) Torin1, by Bio-Techne (29 mentions) Tunicamycin, by Merck Group (27 mentions) Rpmi 1640 medium, by Thermo Fisher Scientific (27 mentions) Streptomycin, by Thermo Fisher Scientific (27 mentions) Penicillin, by Thermo Fisher Scientific (27 mentions) Metformin, by Merck Group (25 mentions) Lipopolysaccharides (lps), by Merck Group (23 mentions)

Spelling variants of this product

Rapamycin (Rapa) (37 citations) Rapamycin (RAP) (22 citations) Rapamycin (R8781) (10 citations) Rapamycin (R0395) (9 citations) Rapamycin (Rap; V900930) (4 citations) Rapamycin powder (4 citations) Rapamycin Ready Made Solution (3 citations) Rapamycin (RP) (2 citations) Rapamycin for p70S6K (2 citations) Rapamycin (Sirolimus, (2 citations)

1 486 protocols using rapamycin

Cellular Dynamics Modulation Protocols

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Transiently transfected cells in 35-mm glass-bottom dishes were starved with FBS-free media (DMEM [Invitrogen] supplemented by 1 mM penicillin/streptomycin [Invitrogen] and 1 mM GlutaMAX [Invitrogen]) for 7 h prior to imaging. At 27 h after transient transfection, MβCD (Sigma; 10 mg/ml) was added to the culture media. After 10 min, cells were treated with rapamycin (Toronto Research; 2 µM) for 30 min. For the experiments with actin cytoskeleton perturbation, LatB (Sigma; 5 µM) was added to the culture media for 10 min before 20 min of rapamycin. For cluster motility assays, applying drugs indicated in transfected cells were transferred into Hank’s balanced salt solution (HBSS) supplemented with 0.5% BSA prior to chemical treatments. Cells were then treated for 20 min with LatB, blebbistatin S or R (50 µM; Toronto Research), or CK666 or CK869 (100 µM; Millipore) after 20 min of rapamycin treatment. For peripheral cluster formation assays, cells were treated for 10 min of MβCD followed by 10 min of rapamycin. For Src inactivation experiments, cells were treated with PP2 (Sigma; 20 µM) as follows: 1) <1 min of rapamycin followed by 10 min of PP2, 2) <1 min of PP2 followed by 10 min of rapamycin, or 3) 10 min of rapamycin followed by 30 min of PP2.

Kim S., Kalappurakkal J.M., Mayor S, & Rosen M.K. (2019). Phosphorylation of nephrin induces phase separated domains that move through actomyosin contraction. Molecular Biology of the Cell, 30(24), 2996-3012.

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Rapamycin and Artesunate Treatment Protocols

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For rapamycin treatment, a stock solution of rapamycin (catalog no. R0395; Sigma Aldrich) was prepared by dissolving rapamycin in pure ethanol (25 mg/ml). For treatment of mice, which weighed approximately 20 g in these studies, the stock rapamycin solution was diluted in a solution of 5% polyethylene glycol 400 (Sigma), 4% ethanol, and 5% Tween 80 for a final concentration of rapamycin of 1 mg/ml. Mice were injected intraperitoneally with 1 mg/kg rapamycin every day starting on day 1, 4, or 5 p.i., unless otherwise noted. For artesunate treatment, 60 mg of artesunate (catalog no. A3731; Sigma) was dissolved in 1 ml of 5% sodium bicarbonate, to which 4 ml of 5% dextrose was added for a final concentration of 12 mg/ml. One hundred milligrams per kilogram was administered i.p. to mice on the specified days.

Gordon E.B., Hart G.T., Tran T.M., Waisberg M., Akkaya M., Skinner J., Zinöcker S., Pena M., Yazew T., Qi C.F., Miller L.H, & Pierce S.K. (2015). Inhibiting the Mammalian Target of Rapamycin Blocks the Development of Experimental Cerebral Malaria. mBio, 6(3), e00725-15.

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Modulating Corneal Autophagy with Exosomes

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The autophagy activator (AA) Rapamycin (V900930, Sigma Aldrich) and the autophagy inhibitor (AI) dorsomorphin/Compound C (P5499, Sigma Aldrich) were dissolved and stored at 4 C. Group designs and schematic protocol of in vitro and in vivo experiments are shown as follows (Figure 1).
HCECs in the control group were treated with PBS; HCECs in the Exo group were treated with 1 × 10⁶/μl hucMSC-Exos; HCECs in the AA group were treated with 50 nM Rapamycin; HCECs in the AI group were treated with 5 μM Compound C; HCECs in the Exo + AA group were treated with 1 × 10⁶/μl hucMSC-Exos and 50 nM Rapamycin; and HCECs in the Exo + AI group were treated with 1 × 10⁶/μl hucMSC-Exos and 5 μM Compound C.
Normal corneas in the control group were treated with PBS; injured corneas in the CI + PBS group were treated with PBS; injured corneas in the CI + L-Exo group were treated with 1 × 10⁵/μl hucMSC-Exos; injured corneas in the CI + M-Exo group were treated with 1 × 10⁶/μl hucMSC-Exos; injured corneas in the CI + H-Exo group were treated with 1 × 10⁷/μl hucMSC-Exos; injured corneas in the CI + Exo + AA group were treated with 1 × 10⁶/μl hucMSC-Exos and 10 μM Rapamycin; and injured corneas in the CI + Exo + AI group were treated with 1 × 10⁶/μl hucMSC-Exos and 50 μM Compound C.

Ma S., Yin J., Hao L., Liu X., Shi Q., Diao Y., Yu G., Liu L., Chen J, & Zhong J. (2022). Exosomes From Human Umbilical Cord Mesenchymal Stem Cells Treat Corneal Injury via Autophagy Activation. Frontiers in Bioengineering and Biotechnology, 10, 879192.

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Immunoblotting Analysis of Signaling Pathways

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For immunoblotting analysis, rabbit anti-phospho-p70S6K (S371), rabbit anti-phospho- p70S6K (T389), rabbit anti-GSK-3β, rabbit anti-phospho-GSK-3β (S9), rabbit anti-phospho-GS (S641), rabbit-anti-p38, rabbit-anti-phospho-p44/42 (T202/Y204), rabbit anti-phospho-p38 (T180/Y182) (Cell Signaling, Danvers, MA, USA), mouse anti-actin (Sigma-Aldrich, St. Louis, MO, USA), and horseradish peroxidase-conjugate secondary anti-mouse and anti-rabbit Abs (Santa Cruz Biotechnology) were used. Rapamycin (0.2 µM, Sigma-Aldrich) or Torin 1 (0.5 µM Tocris, Bristol, UK) were added to DC culture 4 h after Mtb-infection for studying mammalian target of Rapamycin complex 1 (mTORC1) and mTOR inhibition respectively. For the selective inhibition of GSK-3β and p70S6K1 respectively, SB216763 (5 µM, Sigma-Aldrich) and PF4708671 (0.1 µM, Sigma-Aldrich) were used to treat DC 30 min before infection and Rapamycin treatment. To evaluate Rapamycin bystander effect, DC were treated for 30 min before infection and Rapamycin treatment with SB203580 (10 µM, Sigma-Aldrich) or SB202129 (10 µM, Sigma-Aldrich) to inhibit p38 or with PD980509 (0.1 µM, Sigma-Aldrich) to block p44/42.

Etna M.P., Severa M., Licursi V., Pardini M., Cruciani M., Rizzo F., Giacomini E., Macchia G., Palumbo O., Stallone R., Carella M., Livingstone M., Negri R., Pellegrini S, & Coccia E.M. (2021). Genome-Wide Gene Expression Analysis of Mtb-Infected DC Highlights the Rapamycin-Driven Modulation of Regulatory Cytokines via the mTOR/GSK-3β Axis. Frontiers in Immunology, 12, 649475.

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Modulation of Platelet Oxidative Stress

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The washed platelets were divided into 8 groups in equal volumes: the Control group (platelets treated with the vehicle, dimethyl sulfoxide (DMSO) (Sigma-Aldrich, USA)); ox-LDL group (platelet suspension treated with 50 μg/ml ox-LDL for 5 min) [27] ; N-acetylcysteine (NAC) group; Rapamycin group; 3-methyladenine (3-MA) group; NAC + Rapamycin group; NAC + 3-MA group; and Rapamycin + 3-MA group. The suspended platelets in each group were pre-treated with a 1-mM dose of the ROS scavenger N-acetylcysteine (NAC) (Sigma-Aldrich, USA) [28] , a 0.2-μM dose of the mTOR inhibitor Rapamycin (Sigma-Aldrich, USA) [16] or a 1-mM dose of the autophagy inhibitor 3-MA (Sigma-Aldrich, USA) [16] for 30 min, and then 50 μg/ml ox-LDL was added to platelets and incubated for 10 min.

Wang X., Fu Y.F., Liu X., Feng G., Xiong D., Mu G.F, & Chen F.P. (2018). ROS Promote Ox-LDL-Induced Platelet Activation by Up-Regulating Autophagy Through the Inhibition of the PI3K/AKT/mTOR Pathway. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 50(5).

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Modulating Autophagy in Ischemia-Reperfusion Injury

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The stock solution of chloroquine diphosphate (CQ) (Sigma, C6628) was prepared in PBS and stored at −20°C until it was used. To block autophagosome clearance, cells in 6-well plates were treated with 50 μM CQ (Pivtoraiko, et al., 2010 (link)) at the beginning of OGD or at the corresponding time point for the control group. After the OGD, cells were incubated with CQ at 37°C until they were used for Western blot or LDH assay.
To study the role of autophagy activation, cells were pretreated with rapamycin for 24 h. The final concentration of rapamycin (Sigma, R0395) was 0.2 μM (final concentration of DMSO that was used to dissolve rapamycin was 0.1% v/v) (Xiong, et al., 2011 ). DMSO was added to the culture medium in other groups. rapamycin was present until the cells were harvested for assay.
To investigate the effect of autophagy inhibition, 3-methyladenine (3-MA, Sigma, M9281) was dissolved in PBS at 55°C, stored at −20°C and completely dissolved by warming to 55°C just prior to use. The final concentration of 3-MA was 5 mM (Deng, et al., 2013 (link)). 3-MA was added 1 h prior to OGD and present until cells were harvested for assy.

Cheng A., Lu Y., Huang Q, & Zuo Z. (2019). Attenuating oxygen-glucose deprivation-caused autophagosome accumulation may be involved in sevoflurane postconditioning-induced protection in human neuron-like cells. European journal of pharmacology, 849, 84-95.

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Antifungal Susceptibility Assay

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Exponentially growing cells were dissolved in fresh, preheated YPD medium to OD₆₀₀ 0.1 in glass flasks. Cultures were incubated with agitation (200 rpm) and growth curves were performed by measuring optical density at absorbance 600 nm hourly. Exponentially growing cells were treated with five times the AmB MIC and viability was determined as CFUs. Rapamycin-induced target of Rapamycin (TOR) inhibition was performed by exposing exponential growing populations to 1 μg/ml Rapamycin (R0395, Sigma) prior to AmB treatment. AmB was added after four hours of Rapamycin pre-exposure.

Bojsen R., Regenberg B., Gresham D, & Folkesson A. (2016). A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations. Scientific Reports, 6, 21874.

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Starvation and Rapamycin Response in 3T3-L1 Preadipocytes

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3T3-L1 preadipocytes were subjected to starvation for 0, 2, 4, 12, and 24 h by culturing cells in Hank’s balanced salt solution (HBSS). To investigate the response to refeeding starving cells, a set of cells undergoing 12 h of starvation was fed with fresh growth medium for an additional 12 h (Fig. 3a). For rapamycin stimulation, preadipocytes were treated with 20 ng/ml rapamycin (Sigma), for 2, 4, 12, and 24 h. A set of cells kept in rapamycin for 12 h was cultured in fresh growth medium for the following 12 h (Fig. 3b). To quantify cell survival, 3T3-L1 cells and transfected cells were seeded in six-well plates at 86,000 cells per well. Two days later, the cells were starved in HBSS. At 0, 2, 4, 6, 12, and 24 h, the cells were collected and 100 μl of the cell suspension samples was added to an equal volume of trypan blue (Life Technologies). The mixture was loaded into an automated cell counter (Cellometer Mini, Nexcelom Bioscience), and viable cell numbers were measured. Cell death rates were calculated by subtracting the number of viable cells at 6 h from cell numbers at 0 h and dividing the result by the cell numbers at 6 h.

Minster R.L., Hawley N.L., Su C.T., Sun G., Kershaw E.E., Cheng H., Buhule O.D., Lin J., Reupena M.S., Viali S., Tuitele J., Naseri T., Urban Z., Deka R., Weeks D.E, & McGarvey S.T. (2016). A thrifty variant in CREBRF strongly influences body mass index in Samoans. Nature genetics, 48(9), 1049-1054.

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Rat Cardiomyocyte H9C2 Cell Culture

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Rat cardiomyocyte H9C2 cells were purchased from the American Type Culture Collection. The Cells were cultured in DMEM (Invitrogen) and supplemented with heat-inactivated 10% FBS (Invitrogen), 5% horse serum, and antibiotics (100 units/ml penicillin, 100 μg/ml streptomycin). They were then incubated in a humidified atmosphere containing 5% CO₂ at 37°C. Based on our previous study, the cells were treated with rapamycin (100 nM), bFGF (40 ng/ml), bFGF with rapamycin or the autophagy inhibitor 3-methyladenine (3-MA, 5 mM; Sigma-Aldrich) with rapamycin. All experiments were performed in triplicate.

Wang Z.G., Wang Y., Huang Y., Lu Q., Zheng L., Hu D., Feng W.K., Liu Y.L., Ji K.T., Zhang H.Y., Fu X.B., Li X.K., Chu M.P, & Xiao J. (2015). bFGF regulates autophagy and ubiquitinated protein accumulation induced by myocardial ischemia/reperfusion via the activation of the PI3K/Akt/mTOR pathway. Scientific Reports, 5, 9287.

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Rapamycin Preparation and Dilution

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Rapamycin (Sigma-Aldrich) was
dissolved in DMSO at a concentration of 1 mM. Before stimulation,
Rapamycin in DMSO was diluted in media at a 10× final concentration
and an appropriate volume of Rapamycin/media solution was added to
the cell media to achieve a 1× final concentration.

Verbič A., Lebar T., Praznik A, & Jerala R. (2024). Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins. ACS Synthetic Biology, 13(3), 792-803.

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