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221 protocols using lcms 2020

1

Synthesis and Characterization of AESIS-1 Peptide

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The novel small molecule peptide AESIS-1 contains 19 amino acids and has an expected molecular weight of 2121.4 Da (Peptron, Inc., Daejeon, Korea). AESIS-1 peptide was generated using the ASP48S (Peptron, Inc.), using the solid phase peptide synthesis (SPSS) method. High-purity peptide was obtained from the major fraction of the synthesized peptide pool using SHIMADZU Prominence HPLC (Shimadzu, Kyoto, Japan). Purified synthetic peptide was prepared by the freeze-drying method. Purity of synthetic peptide (>95%) was assessed by SHIMADZU Prominence HPLC and peptide molecular weight was determined by liquid chromatography–mass spectrometry (LC-MS) using the SHIMADZU LCMS-2020 (Shimadzu). The properties of AESIS-1 peptide are listed in Table 2.
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2

Solubility Characterization of Compounds

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Solubility method: 10mg of each respective compound was dissolved in 2mL of DMAC. The water solubility (pH = 7) samples were prepared by adding 10 μL of the resulting DMAC solution to 2mL of DI H2O and sonicated at 37°C for 2 hours. The acidic solubility (pH = 2) samples were prepared by adding 10 μL of the resulting DMAC solution to 2mL of 0.01 M aq HCl and held at 37°C for 2 hours. The mixtures were then filtered using a 0.45 micron syringe filter. The resultant solutions were injected on a LC-MS with Shimadzu LCMS 2020, (Shimadzu Scientific Instruments, Columbia, MD) using a SIM mode (Dual Ion Source (DUIS) ionization, simultaneous ESI and APCI) method calibrated to the respective retention times and mass units of each compound. Compound peaks were resolved using a Shimadzu C18 3 μm 50 × 4.6mm reversed phase LC column. LC mobile phase: 90% acetonitrile (w. 0.1% TFA) and 10% H2O (w/ 0.1% TFA). Calibration curves using standard solutions (n = 5) of each compound dissolved in DMAC were used to calculate the unknown aq concentrations of each compound, n=3. The cLogP data was calculated using ChemBioDraw® Ultra (ver. 13.0.0.3015).37 , 61 (link) Data shown in Table 4.
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3

HPLC-MS Analysis of Compounds

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For HPLC analysis, a system with a Shimadzu Prominence LC-20 (Shimadzu Corporation, Kioto, Japan) column and a convection fraction collector connected with a single quadrupole mass spectrometer Shimadzu LCMS-2020 (Shimadzu Corporation, Kioto, Japan) with dual ionization source DUIS-ESI-APCI were used. The analytical and preparative column was Phenomenex Luna 3u C18 100A.
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4

Synthesis and Characterization of Organic Compounds

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All reactions were performed in oven-dried round-bottom flasks with magnetic stir bars or overhead mechanical stirrers under an argon atmosphere unless the reaction conditions were supposed to contain water. Organic solvents were purified when necessary by standard methods55 or purchased from Sigma-Aldrich.™ Chemicals were purchased from either Sigma Aldrich™, Oakwood Chemical, Alfa Aesar, Matrix Scientific, or Acros Organic. The progress of the reactions was monitored by TLC on a silica gel plate (25% EtOAc in hexanes or 10% MeOH in DCM). The 1H and 13C NMR data were obtained on Bruker Spectrospin 300 MHz and GE 500 MHz instruments with the chemical shifts in δ (ppm) reported relative to TMS. The HRMS spectral data was obtained on a LCMS-IT-TOF by Shimadzu Scientific. Purity of all final compounds was 98% or higher and was determined by HPLC on a LC-MS with Shimadzu LCMS 2020, (Shimadzu Scientific Instruments, Columbia, MD) using a PDA detector at 254 nm. The column was a Shimadzu C18 3 μm 50 × 4.6mm reversed phase LC column. LC mobile phase: 90% acetonitrile (w. 0.1% TFA) and 10% H2O (w/ 0.1% TFA) with a flow rate of 1 mL min−1, column temperature: 25 °C, injection size: 1.0μL.
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5

Metabolite Analysis of Pyrazoloquinolinones

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Metabolite analysis by LCMS confirmed OCH3 rate > OCD3 rate and that the primary metabolites for the PQs was generated via O-demethylation of the methoxy groups to form hydroxypyrazoloquinolinones. The 60 min samples from the metabolism study above were injected on a LC-MS with Shimadzu LCMS 2020, (Shimadzu Scientific Instruments, Columbia, MD) using a SIM mode (Dual Ion Source (DUIS) ionization, simultaneous ESI and APCI) method calibrated to the respective retention times and mass units of each component and the respective peak intensities were measured. Compound peaks were resolved using a Shimadzu C18 3 μm 50 × 4.6mm reversed phase LC column. LC mobile phase: 90% acetonitrile (w. 0.1% TFA) and 10% H2O (w/ 0.1% TFA). Results shown in Scheme 4.
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6

Characterization of Recombinant R. palustris Ferredoxin:NADP+ Oxidoreductase

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Recombinant R. palustris ferredoxin:NADP+ oxidoreductase was prepared as previously described [16 (link)]. Its concentration was determined spectrophotometrically according to ε466 = 10.8 mM−1 cm−1 [16 (link)]. 2,4,6-Trinitrotoluene (TNT) and 2,4,6-trinitrophenyl-N-methylnitramine (tetryl), synthesized as described [21 (link)], and 3-amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine) and its 7-methyl- and 7-fluoro- derivatives, synthesized according to [22 (link)], were a generous gift from Dr. Jonas Šarlauskas (Institute of Biochemistry, Vilnius). 5-(1-Aziridinyl)-2,4-dinitrobenzamide (CB-1954) synthesized as described in [23 (link)], was a generous gift from Dr. Vanda Miškinienė (Institute of Biochemistry, Vilnius). The above compounds were characterized by their melting points and their 1H-NMR, UV, and IR spectra. The purity of compounds determined using HPLC-MS (LCMS-2020, Shimadzu, Kyoto, Japan) was >98%. NADPH, 3-acetylpyridine adenine dinucleotide phosphate (AcPyP+), horse heart cytochrome c, superoxide dismutase, and other reagents were obtained from Sigma-Aldrich (St. Louis, MO, USA) and used as received.
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7

Secondary Metabolite Detection in Mono- and Co-cultures

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For the detection of secondary metabolites from mono- and cocultures, LC-MS measurements were performed on a Shimadzu UHPLC-MS System (LC-30AD, SPD-M30A, and LCMS-2020). The system is equipped with an electrospray ion source and a Kinetex C18 column (50 × 2.1 mm, particle size 1.7 μm, pore diameter 100 Å, Phenomenex). Column oven was set to 40 °C; scan range of MS was set to m/z 150 to 2,000 with a scan speed of 10,000 atomic mass units/s and event time of 0.25 s under positive and negative mode. Desolvation line temperature was set to 250 °C with an interface temperature of 350 °C and a heat block temperature of 400 °C. The nebulizing-gas flow was set to 1.5 L ⋅ min−1 and dry-gas flow to 15 L ⋅ min−1. If not otherwise stated, the following standard LC method was used: flow rate = 0.7 mL ⋅ min−1; 0 to 0.5 min: 10% (vol/vol) MeCN in water containing 0.1% formic acid; 0.5 to 8.5 min: linear gradient 10 to 100% MeCN in water containing 0.1% formic acid; 8.5 to 11.5 min: 100% MeCN in water containing 0.1% formic acid; and injection volume: 10 μL. LC-MS results were analyzed using LabSolutions Postrun and Browser (version 5.60).
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8

LC-MS Analysis of Phytohormones

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For analysis, phytohormone extracts were injected into the Shimadzu LCMS-2020 (Shimadzu Corporation, Kyoto, Japan) system coupled with the YMC-Triart C18 ExRS column (100 mm × 2.0 mm; internal diameter, 8 nm; particle size, 1.9 μm). Thereafter, 10 µL of the extract was loaded into the system using a mobile phase comprising (A) water with 0.2% formic acid and (B) acetonitrile with 0.2% formic acid. The flow rate of the mobile phase was set at 0.25 ml/min, and gradient elution was applied. For conditioning, 100% solvent was eluted for 1 min, followed by 30% B for 3 min and then 60% B for 17 min. For mass spectrometry analysis, the following conditions were used: nebulizing gas flow rate, 1.5 l/min; drying gas flow rate, 15 l/min; scan mode, negative; mass analysis range, 120-550 m/z; and scan speed, 883 u/s.
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9

Peptide Purification and Characterization

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The peptide’s purity was verified by reverse-phase high-performance liquid chromatography (RP-HPLC), which separates the molecules based on their hydrophobicity. A Jasco chromatograph with UV-2075 Plus detector, PU-2089 Plus quaternary pump, and AS-2055 Plus autosampler was used, with a Water Corp XBridge BEH130 C18 3.5 μm dp, 4.6 × 100 mm column. The peptides were analyzed using a gradient of 0–70% acetonitrile (ACN) for 8 min and detection at 220 nm. The retention times of the crude peptides were determined, and purification was subsequently carried out on Clean-Up®CEC18153 C-18 columns (UCT, Bristol, PA, USA). The peptides were eluted according to the percentages of ACN observed in the analysis with the RP-HPLC. Next, the ACN solvent was removed from samples with a SpeedVac® Concentrator (Thermo Fisher, Waltham, MA, USA), and then the peptides were frozen and lyophilized.
The characterization of the molecular weight of the purified peptides was carried out in a UFLC-ESI Shimadzu LCMS-2020 equipment, using a 0–100% ACN gradient in 20 min. The peptide was injected and dissolved in water.
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10

HPLC-MS Analysis of Compounds

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High-performance liquid chromatography–mass spectrometry (HPLC-MS) analyses were performed using a high-performance liquid chromatography system, equipped with a photo diode array detector (SPD-M20A) and a mass spectrometer (LCMS-2020), equipped with an electrospray ionization (ESI) source (Shimadzu, Kyoto, Japan). The chromatographic separation was conducted using a YMC Pack Pro column (YMC, Kyoto, Japan), 3 × 150 mm at 40 °C and a mobile phase that consisted of 0.1% formic acid water solution (solvent A) and acetonitrile (solvent B). Mass spectrometry data was acquired in both positive and negative ionization mode and analyzed using the LabSolutions LCMS software, version 5.42 SP6.
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