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96 protocols using bafilomycin a1

1

Comprehensive Compound Acquisition Protocol

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Sorafenib (#T0093L) was purchased from TargetMol (Shanghai, China); lenvatinib (#S1164), brivanib (#S1084) and bafilomycin A1 (#S1413) were purchased from Selleck (Shanghai, China); cisplatin (#P4394), doxorubicin (#D1515), N-acetyl-l-cysteine (NAC, #A7250), and Hoechst (#94403) were purchased from Sigma‒Aldrich (Shanghai, China); canagliflozin (#A11100) was purchased from AdooQ Bioscience (Nanjing, China); and oligomycin (#HY-N6782), antimycin A (#HY-105755), phloretin (#HY-N0142), z-VAD-FMK (#HY-16658B), necrostatin-1 (#HY-15760), and ferrostatin-1 (#HY-100579) were purchased from MedChemExpress (Shanghai, China).
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2

Cardiomyocyte Hypoxia-Reoxygenation Model

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The HR injury model was mimicked in vitro by 45 min of hypoxia and 6 h of reoxygenation. The primary cardiomyocytes were isolated from WT and CK2αCKO mice according to our previous study [44 (link)]. To inhibit the mitophagy, siRNA against FUNDC1 was transfected to cardiomyocytes isolated from WT mice. To observe the autophagic flux, Bafilomycin-A1 (0.5 μM, Selleck Chemicals) was used 12 h before treatment. Details on MTT assay, TUNEL staining and caspase3/9 activities are described in the supplemental methods. The siRNAs specific against the expression of CK2α and FUNDC1 or control siRNAs were purchased Santa Cruz Biotechnology. The siRNA transfection was based on our previous study [45 (link)], and the transfection efficiency was confirmed by western blots.
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3

Mitochondrial Dysfunction Modulation Protocol

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Zalcitabine (S1719), erastin (S7242), sulfasalazine (S1576), IKE (S8877), MitoQ (S8978), bafilomycin A1 (S1413), staurosporine (S1421), and CCCP (S6494) were purchased from Selleck Chemicals. MitoTEMPO (SML0737) was purchased from Sigma-Aldrich. The antibodies to STING1 (13647), TOMM20 (42406), MFN1 (14739), OPA1 (67589), PINK1 (6946), PRKN (4211), ACTB (3700), CALR (12238), and MAP1LC3B (3868) were purchased from Cell Signaling Technology. The antibody to MFN2 (ab205236) was purchased from Abcam. The antibody to mitHsp70 (MA3-028) was purchased from Thermo Fisher Scientific.
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4

Elaiophylin Biosynthesis from Deep-Sea Streptomyces

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Elaiophylin was prepared from the deep-sea-derived Streptomyces sp. SCSIO 1934 [44 (link)]. Rapamycin, torin1, bafilomycin A1, compound C, STO-609, and rosiglitazone were purchased from Selleck. Insulin, IBMX, and dexamethasone were purchased from Sigma-Aldrich. Antibodies recognizing phospho-AMPKα (#2535), AMPKα (# 2532), phospho-ACC (#3661), ACC (#3662), phospho-AKT (#4060), phospho-S6K (#9204), S6K (#9202), 4EBP1 (#9644), phospho-ERK (#4370), phospho-c-JUN (#3270), and LC3B (#3868) were procured from Cell Signaling. Other antibodies included anti-AKT (Proteintech, 60203-2-Ig), anti-GST (Proteintech, 10000-0-AP), anti-TXNIP (Abcam, ab188865), and anti-ACTIN (Genescript, A00702).
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5

Pharmacological Modulation of Proteostasis

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DMSO was used as vehicle control. The proteasome inhibitor MG132 was obtained from Merck/Millipore and used at the final concentration of 20 μM for 3 h. PHD inhibitors IOX2 and FG-4592 were purchased from Selleckchem. VHL inhibitors VH032, VH298, and nonbinding epimer cisVH298 were synthesized by a group member of our laboratory (13 (link), 14 (link)). Compounds were added to cells for indicated length of time. Chloroquine (Merck) and bafilomycin A1 (Selleckchem) were added to cells for 3 h at 50 μM and 50 nM, respectively.
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6

Autophagy Signaling Pathway Analysis

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Antibodies against LC3 I/II, p70S6 K, ULK, and beclin 1 were purchased from Cell Signaling Technology. Antibodies against GAPDH and His-Tag were purchased from Beyotime. Antibodies against TLR2 and TLR4 were purchased from Abcam. Antibody against p-mTOR was purchased from Santa Cruz. Protein-G coupled agarose beads and RapidStep™ ECL Reagent were purchased from Millipore. Ni2+-NTA column was purchased from GE lifesciences. DMEM High glucose culture medium was purchased from Hyclone. Cell lysis buffer for Western and IP and Nitric Oxide Synthase Assay Kit was purchased from Beyotime. Protease Inhibitor Cocktail is purchased from Bimake. Red Cell Lysis Buffer was purchase from Tiangen. Rapamycin and Bafilomycin A1 were purchased from Selleck. Clodronate Liposome was purchased from Liposoma.
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7

Macrophage Nitric Oxide Regulation

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The macrophages were treated with PepO or pre-treated with Bafilomycin A1 (Selleck) before PepO treatment, and then the cells were treated with NOS assay kit (Beyotime) according to the instruction of the manufacturer.
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8

Seriniquinone and Analogues Evaluation

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Unless noted, all compounds were prepared as stocks in DMSO (Synth, Diadema, SP, Brazil). Seriniquinone (SQ1) and its synthetic analogues SQ2, SQ3, SQ4, and SQ5 (Figure 1A) were obtained as described in [2 (link)] and were used with ≥98% purity. All other compounds were obtained from commercial sources, as follows: doxorubicin (DOX; Sigma-Aldrich, St. Louis, MO, USA), rapamycin (RAPA; Sigma-Aldrich, St. Louis, MO, USA), bafilomycin A1 (Selleck Chemicals, Houston, TX, USA), and Z-VAD-FMK (Cayman Chemical Company, Ann Arbor, MI, USA).
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9

Isolation and Characterization of Antiproliferative Compounds from Tree Peony

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Suffruticosol C and resveratrol were isolated from the seeds of the tree peony. The concentration was chosen based on previous studies [27 (link),28 (link),31 (link),32 (link)] and considering that suffruticosol C is a trimer of resveratrol. The secondary antibodies and Erastin (E7781) were provided by Sigma-Aldrich (St. Louis, MO, USA). RSL3 (1219810-16-8) was obtained from Cayman (Ann Arbor, MI, USA), and Bafilomycin A1 (S1413) was obtained from Selleck Chemicals (Houston, TX, USA). PBS and trypsin were obtained from HyClone (Logan, UT, USA). The RPMI 1640 and DMEM media, streptomycin, β-mercaptoethanol, penicillin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). The TB Green qRT-PCR kit (RR820A), PrimeScript™ RT reagent Kit (RR047A) and TRIzol were provided by Takara (Dalian, China). The primary antibodies used are listed as follows: Bcl-2 (12789-1-AP), Bax (50599-2-Ig), LC3II (18725-1-AP), p62 (18420-1-AP), and Actin (20536-1-AP) were purchased from Proteintech (Rosemont, IL, USA); S6 (2217S), p-S6 (4858S), AKT (9272), pT389-S6K (9234S/L), S6K (9202S), and Cleaved Caspase-3 (D175) were purchased from Cell Signaling Technology (Danvers, MA, USA).
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10

Ovarian Tissue Culture with Inhibitors

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Ovaries were separated by microdissection from the mesonephros or ovarian capsule in prechilled PBS (10 mM, pH 7.4) under a stereomicroscope (ZSA302, COIC). The isolated ovaries were cultured in 6‐well culture dishes (NEST Biotechnology) with basic DMEM/F‐12 medium (Gibco, Life Technologies) and Penicillin‐Streptomycin at 37°C in a 5% CO2, 95% air atmosphere with saturated humidity.
Ovaries were cultured in either medium with dimethylsulfoxide (DMSO) or medium supplemented with inhibitor. The concentration of inhibitors used in this study: GSK‐LSD1‐2Hcl (S7574; Selleck): 64 μM; 3MA (S2767; Selleck, USA): 2.5 mM; Z‐VAD‐fmk (S7023; Selleck): 50 μM; Chloroquine diphosphate (C6688; Sigma): 10 μM; Bafilomycin A1 (S1413; Selleck): 60 nM; MG132 (S2619; Selleck): 5 μM; Cycloheximide (HY‐12320; MedChemExpress): 2 nM; and SP2509 (S7680; Selleck): 5 nM.
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